https://snicdocs.nsc.liu.se/w/api.php?action=feedcontributions&user=Dejan+Vitlacil+%28C3SE%29&feedformat=atomSNIC Documentation - User contributions [en]2024-03-29T10:51:14ZUser contributionsMediaWiki 1.31.10https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7797Swestore-iRODS2021-04-13T08:25:46Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the [https://docs.irods.org/master/icommands/user/#irsync irsync] command to synchronise a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an [[i:]] prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on your local filesystem, run the command:<br />
$ irsync -vrK i:/snic.se/projects/myproject/data /tmp/data<br />
We encourage you to use -K option, where:<br />
'''-K''' verify checksum - calculate and verify the checksum on the data<br />
<br />
Synchronise the data from local filesystem into iRODS using the command:<br />
<br />
$ irsync -vrK /tmp/data i:/snic.se/projects/myproject/new_data<br />
<br />
Note 2: We encourage you also to re-run irsync command one additional time after data transfer. Files will not be transfered but checksums will be recomputed and compared. Be aware that this operation is CPU intensive and it will take time.<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7796Swestore-iRODS2021-04-13T08:08:33Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the [https://docs.irods.org/master/icommands/user/#irsync irsync] command to synchronise a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an [[i:]] prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on your local filesystem, run the command:<br />
$ irsync -vrK i:/snic.se/projects/myproject/data /tmp/data<br />
We encourage you to use -K option, where<br />
'''-K''' verify checksum - calculate and verify the checksum on the data<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7795Swestore-iRODS2021-04-13T08:08:09Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the [https://docs.irods.org/master/icommands/user/#irsync irsync] command to synchronise a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an [[i:]] prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on your local filesystem, run the command:<br />
$ irsync -vrK i:/snic.se/projects/myproject/data /tmp/data<br />
<br />
Note: We encourage you to use -K option, where<br />
-K verify checksum - calculate and verify the checksum on the data<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7794Swestore-iRODS2021-04-13T08:06:56Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the [https://docs.irods.org/master/icommands/user/#irsync irsync] command to synchronise a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an [[i:]] prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on your local filesystem, run the command:<br />
$ irsync -vrK i:/snic.se/projects/myproject/data /tmp/data<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7793Swestore-iRODS2021-04-13T08:06:38Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the [https://docs.irods.org/master/icommands/user/#irsync irsync] command to synchronise a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an [[i: ]] prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on your local filesystem, run the command:<br />
$ irsync -vrK i:/snic.se/projects/myproject/data /tmp/data<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7792Swestore-iRODS2021-04-13T08:05:28Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the [https://docs.irods.org/master/icommands/user/#irsync irsync] command to synchronise a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an i: prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on your local filesystem, run the command:<br />
$ irsync -vrK i:/snic.se/projects/myproject/data /tmp/data<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7791Swestore-iRODS2021-04-13T08:01:55Z<p>Dejan Vitlacil (C3SE): /* Transfer your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the irsync (https://docs.irods.org/master/icommands/user/#irsync) command to synchronize a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an i: prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on Klemming, run the command:<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7790Swestore-iRODS2021-04-13T08:01:38Z<p>Dejan Vitlacil (C3SE): /* Publish your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Transfer your data = <br />
<br />
A good way to transfer data from and to Swestore iRODS is to use the irsync command to synchronize a local directory with iRODS (similar to the Unix rsync command). It can be used to make an exact copy of a directory hierarchy on a local disk within iRODS, or retrieve an exact copy of a directory hierarchy already stored in iRODS. It may also be used to create an exact copy of a file or directory within iRODS.<br />
<br />
NOTE: iRODS paths are identified with an i: prefix in the irsync command.<br />
<br />
For example, if you have created a directory within iRODS called “/snic.se/projects/myproject/data”, and you wish to retrieve an exact copy of that “data” directory on Klemming, run the command:<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7778IRODS iCommands installation on Ubuntu 20.042021-03-16T20:11:14Z<p>Dejan Vitlacil (C3SE): /* Install the public key and add the repository */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IRODS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
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Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
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Selecting previously unselected package irods-externals-boost1.67.0-0.<br />
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Selecting previously unselected package irods-externals-libarchive3.3.2-1.<br />
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Selecting previously unselected package irods-externals-nanodbc2.13.0-0.<br />
Preparing to unpack .../08-irods-externals-nanodbc2.13.0-0_1.0~bionic_amd64.deb ...<br />
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Selecting previously unselected package irods-externals-zeromq4-14.1.6-0.<br />
Preparing to unpack .../09-irods-externals-zeromq4-14.1.6-0_1.0~bionic_amd64.deb ...<br />
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Selecting previously unselected package irods-runtime.<br />
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Unpacking irods-runtime (4.2.8) ...<br />
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Preparing to unpack .../11-irods-icommands_4.2.8_amd64.deb ...<br />
Unpacking irods-icommands (4.2.8) ...<br />
Setting up irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$<br />
<br />
== Configure the iRODS environment ==<br />
<br />
dejan@dejan:~$ <br />
dejan@dejan:~$ cat /home/dejan/.irods/irods_environment.json<br />
{<br />
"irods_host": "irods-login.swestore.se", <br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/s_dejvi",<br />
"irods_cwd": "/snic.se/home/s_dejvi",<br />
"irods_user_name": "s_dejvi",<br />
"irods_zone_name": "snic.se", <br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_salt_size": 8,<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme" : "PAM"<br />
}<br />
dejan@dejan:~$<br />
<br />
== Authenticate and test iRODS iCommands client ==<br />
dejan@dejan:~$ iinit<br />
Enter your current PAM password:<br />
dejan@dejan:~$ ils<br />
/snic.se/home/s_dejvi:<br />
.DS_Store<br />
._.DS_Store<br />
SISO.Certificate.pdf<br />
project_role_descriptions.docx<br />
worst-day-fosdem-2014.pdf<br />
C- /snic.se/home/s_dejvi/0 TiddlyWiki<br />
C- /snic.se/home/s_dejvi/0 reading<br />
C- /snic.se/home/s_dejvi/EOSC<br />
C- /snic.se/home/s_dejvi/EUDAT<br />
C- /snic.se/home/s_dejvi/FAIR<br />
C- /snic.se/home/s_dejvi/FitSM<br />
.....<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7777IRODS iCommands installation on Ubuntu 20.042021-03-16T20:00:32Z<p>Dejan Vitlacil (C3SE): /* Configure the iRODS environment */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
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Linking and byte-compiling packages for runtime python2.7...<br />
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Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
Preparing to unpack .../00-python-psutil_5.5.1-1ubuntu4_amd64.deb ...<br />
Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
Preparing to unpack .../01-irods-externals-avro1.9.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-boost1.67.0-0.<br />
Preparing to unpack .../02-irods-externals-boost1.67.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-catch22.3.0-0.<br />
Preparing to unpack .../03-irods-externals-catch22.3.0-0_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../05-irods-externals-fmt6.1.2-1_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../06-irods-externals-json3.7.3-0_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../08-irods-externals-nanodbc2.13.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-zeromq4-14.1.6-0.<br />
Preparing to unpack .../09-irods-externals-zeromq4-14.1.6-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-runtime.<br />
Preparing to unpack .../10-irods-runtime_4.2.8_amd64.deb ...<br />
Unpacking irods-runtime (4.2.8) ...<br />
Selecting previously unselected package irods-icommands.<br />
Preparing to unpack .../11-irods-icommands_4.2.8_amd64.deb ...<br />
Unpacking irods-icommands (4.2.8) ...<br />
Setting up irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$<br />
<br />
== Configure the iRODS environment ==<br />
<br />
dejan@dejan:~$ <br />
dejan@dejan:~$ cat /home/dejan/.irods/irods_environment.json<br />
{<br />
"irods_host": "irods-login.swestore.se", <br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/s_dejvi",<br />
"irods_cwd": "/snic.se/home/s_dejvi",<br />
"irods_user_name": "s_dejvi",<br />
"irods_zone_name": "snic.se", <br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_salt_size": 8,<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme" : "PAM"<br />
}<br />
dejan@dejan:~$<br />
<br />
== Authenticate and test iRODS iCommands client ==<br />
dejan@dejan:~$ iinit<br />
Enter your current PAM password:<br />
dejan@dejan:~$ ils<br />
/snic.se/home/s_dejvi:<br />
.DS_Store<br />
._.DS_Store<br />
SISO.Certificate.pdf<br />
project_role_descriptions.docx<br />
worst-day-fosdem-2014.pdf<br />
C- /snic.se/home/s_dejvi/0 TiddlyWiki<br />
C- /snic.se/home/s_dejvi/0 reading<br />
C- /snic.se/home/s_dejvi/EOSC<br />
C- /snic.se/home/s_dejvi/EUDAT<br />
C- /snic.se/home/s_dejvi/FAIR<br />
C- /snic.se/home/s_dejvi/FitSM<br />
.....<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7776IRODS iCommands installation on Ubuntu 20.042021-03-16T20:00:12Z<p>Dejan Vitlacil (C3SE): /* Configure the iRODS environment */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
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Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
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--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
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<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
Preparing to unpack .../00-python-psutil_5.5.1-1ubuntu4_amd64.deb ...<br />
Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
Preparing to unpack .../01-irods-externals-avro1.9.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-boost1.67.0-0.<br />
Preparing to unpack .../02-irods-externals-boost1.67.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-catch22.3.0-0.<br />
Preparing to unpack .../03-irods-externals-catch22.3.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-clang-runtime6.0-0.<br />
Preparing to unpack .../04-irods-externals-clang-runtime6.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-fmt6.1.2-1.<br />
Preparing to unpack .../05-irods-externals-fmt6.1.2-1_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-json3.7.3-0.<br />
Preparing to unpack .../06-irods-externals-json3.7.3-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-libarchive3.3.2-1.<br />
Preparing to unpack .../07-irods-externals-libarchive3.3.2-1_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-nanodbc2.13.0-0.<br />
Preparing to unpack .../08-irods-externals-nanodbc2.13.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-zeromq4-14.1.6-0.<br />
Preparing to unpack .../09-irods-externals-zeromq4-14.1.6-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-runtime.<br />
Preparing to unpack .../10-irods-runtime_4.2.8_amd64.deb ...<br />
Unpacking irods-runtime (4.2.8) ...<br />
Selecting previously unselected package irods-icommands.<br />
Preparing to unpack .../11-irods-icommands_4.2.8_amd64.deb ...<br />
Unpacking irods-icommands (4.2.8) ...<br />
Setting up irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$<br />
<br />
== Configure the iRODS environment ==<br />
<br />
dejan@dejan:~$ <br />
dejan@dejan:~$ cat /home/dejan/.irods/irods_environment.json<br />
{<br />
"irods_host": "irods-login.swestore.se", <br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/s_dejvi",<br />
"irods_cwd": "/snic.se/home/s_dejvi",<br />
"irods_user_name": "s_dejvi",<br />
"irods_zone_name": "snic.se", <br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_salt_size": 8,<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme" : "PAM"<br />
}<br />
dejan@dejan:~$ <br />
<br />
== Authenticate and test iRODS iCommands client ==<br />
dejan@dejan:~$ iinit<br />
Enter your current PAM password:<br />
dejan@dejan:~$ ils<br />
/snic.se/home/s_dejvi:<br />
.DS_Store<br />
._.DS_Store<br />
SISO.Certificate.pdf<br />
project_role_descriptions.docx<br />
worst-day-fosdem-2014.pdf<br />
C- /snic.se/home/s_dejvi/0 TiddlyWiki<br />
C- /snic.se/home/s_dejvi/0 reading<br />
C- /snic.se/home/s_dejvi/EOSC<br />
C- /snic.se/home/s_dejvi/EUDAT<br />
C- /snic.se/home/s_dejvi/FAIR<br />
C- /snic.se/home/s_dejvi/FitSM<br />
.....<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7775IRODS iCommands installation on Ubuntu 20.042021-03-16T20:00:02Z<p>Dejan Vitlacil (C3SE): /* Configure the iRODS environment */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
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Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
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(Reading database ... 72007 files and directories currently installed.)<br />
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Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
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Unpacking python-certifi (2019.11.28-1) ...<br />
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Selecting previously unselected package python-urllib3.<br />
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Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
Preparing to unpack .../00-python-psutil_5.5.1-1ubuntu4_amd64.deb ...<br />
Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
Preparing to unpack .../01-irods-externals-avro1.9.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-boost1.67.0-0.<br />
Preparing to unpack .../02-irods-externals-boost1.67.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-catch22.3.0-0.<br />
Preparing to unpack .../03-irods-externals-catch22.3.0-0_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../05-irods-externals-fmt6.1.2-1_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../06-irods-externals-json3.7.3-0_1.0~bionic_amd64.deb ...<br />
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Selecting previously unselected package irods-externals-libarchive3.3.2-1.<br />
Preparing to unpack .../07-irods-externals-libarchive3.3.2-1_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-nanodbc2.13.0-0.<br />
Preparing to unpack .../08-irods-externals-nanodbc2.13.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-zeromq4-14.1.6-0.<br />
Preparing to unpack .../09-irods-externals-zeromq4-14.1.6-0_1.0~bionic_amd64.deb ...<br />
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Selecting previously unselected package irods-runtime.<br />
Preparing to unpack .../10-irods-runtime_4.2.8_amd64.deb ...<br />
Unpacking irods-runtime (4.2.8) ...<br />
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Preparing to unpack .../11-irods-icommands_4.2.8_amd64.deb ...<br />
Unpacking irods-icommands (4.2.8) ...<br />
Setting up irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$<br />
<br />
== Configure the iRODS environment ==<br />
<br />
dejan@dejan:~$ <br />
dejan@dejan:~$ cat /home/dejan/.irods/irods_environment.json<br />
{<br />
"irods_host": "irods-login.swestore.se", <br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/s_dejvi",<br />
"irods_cwd": "/snic.se/home/s_dejvi",<br />
"irods_user_name": "s_dejvi",<br />
"irods_zone_name": "snic.se", <br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_salt_size": 8,<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme" : "PAM"<br />
}<br />
dejan@dejan:~$ <br />
<br />
== Authenticate and test iRODS iCommands client ==<br />
dejan@dejan:~$ iinit<br />
Enter your current PAM password:<br />
dejan@dejan:~$ ils<br />
/snic.se/home/s_dejvi:<br />
.DS_Store<br />
._.DS_Store<br />
SISO.Certificate.pdf<br />
project_role_descriptions.docx<br />
worst-day-fosdem-2014.pdf<br />
C- /snic.se/home/s_dejvi/0 TiddlyWiki<br />
C- /snic.se/home/s_dejvi/0 reading<br />
C- /snic.se/home/s_dejvi/EOSC<br />
C- /snic.se/home/s_dejvi/EUDAT<br />
C- /snic.se/home/s_dejvi/FAIR<br />
C- /snic.se/home/s_dejvi/FitSM<br />
.....<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7774IRODS iCommands installation on Ubuntu 20.042021-03-16T19:59:05Z<p>Dejan Vitlacil (C3SE): /* Install iRODS iCommands */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
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Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
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Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
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Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
Preparing to unpack .../00-python-psutil_5.5.1-1ubuntu4_amd64.deb ...<br />
Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
Preparing to unpack .../01-irods-externals-avro1.9.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-boost1.67.0-0.<br />
Preparing to unpack .../02-irods-externals-boost1.67.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
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Preparing to unpack .../03-irods-externals-catch22.3.0-0_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../05-irods-externals-fmt6.1.2-1_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../08-irods-externals-nanodbc2.13.0-0_1.0~bionic_amd64.deb ...<br />
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Preparing to unpack .../09-irods-externals-zeromq4-14.1.6-0_1.0~bionic_amd64.deb ...<br />
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Selecting previously unselected package irods-runtime.<br />
Preparing to unpack .../10-irods-runtime_4.2.8_amd64.deb ...<br />
Unpacking irods-runtime (4.2.8) ...<br />
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Preparing to unpack .../11-irods-icommands_4.2.8_amd64.deb ...<br />
Unpacking irods-icommands (4.2.8) ...<br />
Setting up irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$<br />
<br />
== Configure the iRODS environment ==<br />
<br />
dejan@dejan:~$ vi /home/dejan/.irods/irods_environment.json<br />
dejan@dejan:~$ <br />
dejan@dejan:~$ <br />
dejan@dejan:~$ cat /home/dejan/.irods/irods_environment.json<br />
{<br />
"irods_host": "irods-login.swestore.se", <br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/s_dejvi",<br />
"irods_cwd": "/snic.se/home/s_dejvi",<br />
"irods_user_name": "s_dejvi",<br />
"irods_zone_name": "snic.se", <br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_salt_size": 8,<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme" : "PAM"<br />
}<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ iinit<br />
Enter your current PAM password:<br />
dejan@dejan:~$ ils<br />
/snic.se/home/s_dejvi:<br />
.DS_Store<br />
._.DS_Store<br />
SISO.Certificate.pdf<br />
project_role_descriptions.docx<br />
worst-day-fosdem-2014.pdf<br />
C- /snic.se/home/s_dejvi/0 TiddlyWiki<br />
C- /snic.se/home/s_dejvi/0 reading<br />
C- /snic.se/home/s_dejvi/EOSC<br />
C- /snic.se/home/s_dejvi/EUDAT<br />
C- /snic.se/home/s_dejvi/FAIR<br />
C- /snic.se/home/s_dejvi/FitSM<br />
.....<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7773IRODS iCommands installation on Ubuntu 20.042021-03-16T19:56:05Z<p>Dejan Vitlacil (C3SE): /* Install iRODS iCommands */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
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2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
Preparing to unpack .../00-python-psutil_5.5.1-1ubuntu4_amd64.deb ...<br />
Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
Preparing to unpack .../01-irods-externals-avro1.9.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-boost1.67.0-0.<br />
Preparing to unpack .../02-irods-externals-boost1.67.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-catch22.3.0-0.<br />
Preparing to unpack .../03-irods-externals-catch22.3.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-clang-runtime6.0-0.<br />
Preparing to unpack .../04-irods-externals-clang-runtime6.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-fmt6.1.2-1.<br />
Preparing to unpack .../05-irods-externals-fmt6.1.2-1_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-json3.7.3-0.<br />
Preparing to unpack .../06-irods-externals-json3.7.3-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-libarchive3.3.2-1.<br />
Preparing to unpack .../07-irods-externals-libarchive3.3.2-1_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-nanodbc2.13.0-0.<br />
Preparing to unpack .../08-irods-externals-nanodbc2.13.0-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-externals-zeromq4-14.1.6-0.<br />
Preparing to unpack .../09-irods-externals-zeromq4-14.1.6-0_1.0~bionic_amd64.deb ...<br />
Unpacking irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Selecting previously unselected package irods-runtime.<br />
Preparing to unpack .../10-irods-runtime_4.2.8_amd64.deb ...<br />
Unpacking irods-runtime (4.2.8) ...<br />
Selecting previously unselected package irods-icommands.<br />
Preparing to unpack .../11-irods-icommands_4.2.8_amd64.deb ...<br />
Unpacking irods-icommands (4.2.8) ...<br />
Setting up irods-externals-json3.7.3-0 (1.0~bionic) ...<br />
Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7772IRODS iCommands installation on Ubuntu 20.042021-03-16T19:54:59Z<p>Dejan Vitlacil (C3SE): /* Install iRODS iCommands */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==<br />
<br />
dejan@dejan:~$ sudo apt install -y irods-icommands<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
The following additional packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-runtime python-psutil<br />
Suggested packages:<br />
python-psutil-doc<br />
The following NEW packages will be installed:<br />
irods-externals-avro1.9.0-0 irods-externals-boost1.67.0-0 irods-externals-catch22.3.0-0 irods-externals-clang-runtime6.0-0 irods-externals-fmt6.1.2-1<br />
irods-externals-json3.7.3-0 irods-externals-libarchive3.3.2-1 irods-externals-nanodbc2.13.0-0 irods-externals-zeromq4-14.1.6-0 irods-icommands irods-runtime<br />
python-psutil<br />
0 upgraded, 12 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 31.0 MB of archives.<br />
After this operation, 228 MB of additional disk space will be used.<br />
Get:1 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-psutil amd64 5.5.1-1ubuntu4 [141 kB]<br />
Get:2 https://packages.irods.org/apt bionic/main amd64 irods-externals-avro1.9.0-0 amd64 1.0~bionic [1,886 kB]<br />
Get:3 https://packages.irods.org/apt bionic/main amd64 irods-externals-boost1.67.0-0 amd64 1.0~bionic [17.0 MB]<br />
Get:4 https://packages.irods.org/apt bionic/main amd64 irods-externals-catch22.3.0-0 amd64 1.0~bionic [91.3 kB]<br />
Get:5 https://packages.irods.org/apt bionic/main amd64 irods-externals-clang-runtime6.0-0 amd64 1.0~bionic [378 kB]<br />
Get:6 https://packages.irods.org/apt bionic/main amd64 irods-externals-fmt6.1.2-1 amd64 1.0~bionic [199 kB]<br />
Get:7 https://packages.irods.org/apt bionic/main amd64 irods-externals-json3.7.3-0 amd64 1.0~bionic [136 kB]<br />
Get:8 https://packages.irods.org/apt bionic/main amd64 irods-externals-libarchive3.3.2-1 amd64 1.0~bionic [1,798 kB]<br />
Get:9 https://packages.irods.org/apt bionic/main amd64 irods-externals-nanodbc2.13.0-0 amd64 1.0~bionic [184 kB]<br />
Get:10 https://packages.irods.org/apt bionic/main amd64 irods-externals-zeromq4-14.1.6-0 amd64 1.0~bionic [566 kB]<br />
Get:11 https://packages.irods.org/apt bionic/main amd64 irods-runtime amd64 4.2.8 [7,337 kB]<br />
Get:12 https://packages.irods.org/apt bionic/main amd64 irods-icommands amd64 4.2.8 [1,305 kB]<br />
Fetched 31.0 MB in 3s (9,108 kB/s) <br />
Selecting previously unselected package python-psutil.<br />
(Reading database ... 72415 files and directories currently installed.)<br />
Preparing to unpack .../00-python-psutil_5.5.1-1ubuntu4_amd64.deb ...<br />
Unpacking python-psutil (5.5.1-1ubuntu4) ...<br />
Selecting previously unselected package irods-externals-avro1.9.0-0.<br />
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Unpacking irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
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Setting up irods-externals-avro1.9.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-zeromq4-14.1.6-0 (1.0~bionic) ...<br />
Setting up irods-externals-libarchive3.3.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-clang-runtime6.0-0 (1.0~bionic) ...<br />
Setting up python-psutil (5.5.1-1ubuntu4) ...<br />
Setting up irods-externals-catch22.3.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-fmt6.1.2-1 (1.0~bionic) ...<br />
Setting up irods-externals-nanodbc2.13.0-0 (1.0~bionic) ...<br />
Setting up irods-externals-boost1.67.0-0 (1.0~bionic) ...<br />
Setting up irods-runtime (4.2.8) ...<br />
Setting up irods-icommands (4.2.8) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7771IRODS iCommands installation on Ubuntu 20.042021-03-16T19:53:31Z<p>Dejan Vitlacil (C3SE): /* Install python-urlib3, python-requests and libssl1.0.0 */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB] <br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.) <br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
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Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
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Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7770IRODS iCommands installation on Ubuntu 20.042021-03-16T19:51:02Z<p>Dejan Vitlacil (C3SE): /* Install python-urlib3, python-requests and libssl1.0.0 */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB]<br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.)<br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$<br />
<br />
== Install iRODS iCommands ==</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7769IRODS iCommands installation on Ubuntu 20.042021-03-16T19:50:10Z<p>Dejan Vitlacil (C3SE): </p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$<br />
<br />
<br />
<br />
== Install python-urlib3, python-requests and libssl1.0.0 ==<br />
<br />
* Short version:<br />
wget -c \<br />
http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
sudo apt install \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
rm -rf \<br />
./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
* Long version: <br />
dejan@dejan:~$ wget -c \<br />
> http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/p/python-urllib3/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb<br />
Resolving security.ubuntu.com (security.ubuntu.com)... 91.189.88.142, 91.189.88.152, 91.189.91.38, ...<br />
Connecting to security.ubuntu.com (security.ubuntu.com)|91.189.88.142|:80... connected.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 86024 (84K) [application/x-debian-package]<br />
Saving to: ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’<br />
<br />
python-urllib3_1.22-1ubuntu0.18.04.2_al 100%[===============================================================================>] 84.01K --.-KB/s in 0.06s <br />
<br />
2021-03-16 18:13:02 (1.39 MB/s) - ‘python-urllib3_1.22-1ubuntu0.18.04.2_all.deb’ saved [86024/86024]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/r/requests/python-requests_2.18.4-2ubuntu0.1_all.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 58496 (57K) [application/x-debian-package]<br />
Saving to: ‘python-requests_2.18.4-2ubuntu0.1_all.deb’<br />
<br />
python-requests_2.18.4-2ubuntu0.1_all.d 100%[===============================================================================>] 57.12K --.-KB/s in 0.01s <br />
<br />
2021-03-16 18:13:02 (3.94 MB/s) - ‘python-requests_2.18.4-2ubuntu0.1_all.deb’ saved [58496/58496]<br />
<br />
--2021-03-16 18:13:02-- http://security.ubuntu.com/ubuntu/pool/main/o/openssl1.0/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reusing existing connection to security.ubuntu.com:80.<br />
HTTP request sent, awaiting response... 200 OK<br />
Length: 1088600 (1.0M) [application/x-debian-package]<br />
Saving to: ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’<br />
<br />
libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb 100%[===============================================================================>] 1.04M --.-KB/s in 0.09s <br />
<br />
2021-03-16 18:13:02 (11.1 MB/s) - ‘libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb’ saved [1088600/1088600]<br />
<br />
FINISHED --2021-03-16 18:13:02--<br />
Total wall clock time: 0.4s<br />
Downloaded: 3 files, 1.2M in 0.2s (7.08 MB/s)<br />
dejan@dejan:~$ <br />
<br />
dejan@dejan:~$ sudo apt install \<br />
> ./python-urllib3_1.22-1ubuntu0.18.04.2_all.deb \<br />
> ./python-requests_2.18.4-2ubuntu0.1_all.deb \<br />
> ./libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb<br />
Reading package lists... Done<br />
Building dependency tree <br />
Reading state information... Done<br />
Note, selecting 'python-urllib3' instead of './python-urllib3_1.22-1ubuntu0.18.04.2_all.deb'<br />
Note, selecting 'python-requests' instead of './python-requests_2.18.4-2ubuntu0.1_all.deb'<br />
Note, selecting 'libssl1.0.0' instead of './libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb'<br />
The following additional packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib python-certifi python-cffi-backend python-chardet python-cryptography python-enum34 python-idna<br />
python-ipaddress python-is-python2 python-openssl python-pkg-resources python-six python2 python2-minimal python2.7 python2.7-minimal<br />
Suggested packages:<br />
python-cryptography-doc python-cryptography-vectors python-enum34-doc python-openssl-doc python-openssl-dbg python-setuptools python-socks python-ntlm<br />
python2-doc python-tk python2.7-doc binutils binfmt-support<br />
The following NEW packages will be installed:<br />
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libssl1.0.0 python-certifi python-cffi-backend python-chardet python-cryptography python-enum34<br />
python-idna python-ipaddress python-is-python2 python-openssl python-pkg-resources python-requests python-six python-urllib3 python2 python2-minimal<br />
python2.7 python2.7-minimal<br />
0 upgraded, 21 newly installed, 0 to remove and 23 not upgraded.<br />
Need to get 4,644 kB/5,877 kB of archives.<br />
After this operation, 25.0 MB of additional disk space will be used.<br />
Do you want to continue? [Y/n] y<br />
Get:1 /home/dejan/libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb libssl1.0.0 amd64 1.0.2n-1ubuntu5.6 [1,089 kB]<br />
Get:2 /home/dejan/python-urllib3_1.22-1ubuntu0.18.04.2_all.deb python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]<br />
Get:3 /home/dejan/python-requests_2.18.4-2ubuntu0.1_all.deb python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]<br />
Get:4 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-minimal amd64 2.7.18-1~20.04.1 [335 kB]<br />
Get:5 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7-minimal amd64 2.7.18-1~20.04.1 [1,285 kB]<br />
Get:6 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2-minimal amd64 2.7.17-2ubuntu4 [27.5 kB]<br />
Get:7 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 libpython2.7-stdlib amd64 2.7.18-1~20.04.1 [1,887 kB]<br />
Get:8 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python2.7 amd64 2.7.18-1~20.04.1 [248 kB]<br />
Get:9 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 libpython2-stdlib amd64 2.7.17-2ubuntu4 [7,072 B]<br />
Get:10 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python2 amd64 2.7.17-2ubuntu4 [26.5 kB]<br />
Get:11 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-certifi all 2019.11.28-1 [149 kB]<br />
Get:12 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-cffi-backend amd64 1.14.0-1build1 [69.6 kB]<br />
Get:13 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-pkg-resources all 44.0.0-2 [129 kB]<br />
Get:14 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-chardet all 3.0.4-4build1 [80.5 kB]<br />
Get:15 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-enum34 all 1.1.6-2ubuntu1 [34.9 kB]<br />
Get:16 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-ipaddress all 1.0.17-1build1 [18.4 kB]<br />
Get:17 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-six all 1.14.0-2 [12.0 kB]<br />
Get:18 http://se.archive.ubuntu.com/ubuntu focal-updates/universe amd64 python-cryptography amd64 2.8-3ubuntu0.1 [254 kB]<br />
Get:19 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-idna all 2.8-1 [34.5 kB]<br />
Get:20 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-is-python2 all 2.7.17-4 [2,496 B]<br />
Get:21 http://se.archive.ubuntu.com/ubuntu focal/universe amd64 python-openssl all 19.0.0-1build1 [43.1 kB]<br />
Fetched 4,644 kB in 0s (19.2 MB/s) <br />
Preconfiguring packages ...<br />
Selecting previously unselected package libpython2.7-minimal:amd64.<br />
(Reading database ... 71260 files and directories currently installed.)<br />
Preparing to unpack .../0-libpython2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7-minimal.<br />
Preparing to unpack .../1-python2.7-minimal_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2-minimal.<br />
Preparing to unpack .../2-python2-minimal_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libpython2.7-stdlib:amd64.<br />
Preparing to unpack .../3-libpython2.7-stdlib_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package python2.7.<br />
Preparing to unpack .../4-python2.7_2.7.18-1~20.04.1_amd64.deb ...<br />
Unpacking python2.7 (2.7.18-1~20.04.1) ...<br />
Selecting previously unselected package libpython2-stdlib:amd64.<br />
Preparing to unpack .../5-libpython2-stdlib_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up libpython2.7-minimal:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7-minimal (2.7.18-1~20.04.1) ...<br />
Linking and byte-compiling packages for runtime python2.7...<br />
Setting up python2-minimal (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package python2.<br />
(Reading database ... 72007 files and directories currently installed.)<br />
Preparing to unpack .../00-python2_2.7.17-2ubuntu4_amd64.deb ...<br />
Unpacking python2 (2.7.17-2ubuntu4) ...<br />
Selecting previously unselected package libssl1.0.0:amd64.<br />
Preparing to unpack .../01-libssl1.0.0_1.0.2n-1ubuntu5.6_amd64.deb ...<br />
Unpacking libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Selecting previously unselected package python-certifi.<br />
Preparing to unpack .../02-python-certifi_2019.11.28-1_all.deb ...<br />
Unpacking python-certifi (2019.11.28-1) ...<br />
Selecting previously unselected package python-cffi-backend.<br />
Preparing to unpack .../03-python-cffi-backend_1.14.0-1build1_amd64.deb ...<br />
Unpacking python-cffi-backend (1.14.0-1build1) ...<br />
Selecting previously unselected package python-pkg-resources.<br />
Preparing to unpack .../04-python-pkg-resources_44.0.0-2_all.deb ...<br />
Unpacking python-pkg-resources (44.0.0-2) ...<br />
Selecting previously unselected package python-chardet.<br />
Preparing to unpack .../05-python-chardet_3.0.4-4build1_all.deb ...<br />
Unpacking python-chardet (3.0.4-4build1) ...<br />
Selecting previously unselected package python-enum34.<br />
Preparing to unpack .../06-python-enum34_1.1.6-2ubuntu1_all.deb ...<br />
Unpacking python-enum34 (1.1.6-2ubuntu1) ...<br />
Selecting previously unselected package python-ipaddress.<br />
Preparing to unpack .../07-python-ipaddress_1.0.17-1build1_all.deb ...<br />
Unpacking python-ipaddress (1.0.17-1build1) ...<br />
Selecting previously unselected package python-six.<br />
Preparing to unpack .../08-python-six_1.14.0-2_all.deb ...<br />
Unpacking python-six (1.14.0-2) ...<br />
Selecting previously unselected package python-cryptography.<br />
Preparing to unpack .../09-python-cryptography_2.8-3ubuntu0.1_amd64.deb ...<br />
Unpacking python-cryptography (2.8-3ubuntu0.1) ...<br />
Selecting previously unselected package python-idna.<br />
Preparing to unpack .../10-python-idna_2.8-1_all.deb ...<br />
Unpacking python-idna (2.8-1) ...<br />
Selecting previously unselected package python-is-python2.<br />
Preparing to unpack .../11-python-is-python2_2.7.17-4_all.deb ...<br />
Unpacking python-is-python2 (2.7.17-4) ...<br />
Selecting previously unselected package python-openssl.<br />
Preparing to unpack .../12-python-openssl_19.0.0-1build1_all.deb ...<br />
Unpacking python-openssl (19.0.0-1build1) ...<br />
Selecting previously unselected package python-urllib3.<br />
Preparing to unpack .../13-python-urllib3_1.22-1ubuntu0.18.04.2_all.deb ...<br />
Unpacking python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Selecting previously unselected package python-requests.<br />
Preparing to unpack .../14-python-requests_2.18.4-2ubuntu0.1_all.deb ...<br />
Unpacking python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up libssl1.0.0:amd64 (1.0.2n-1ubuntu5.6) ...<br />
Setting up libpython2.7-stdlib:amd64 (2.7.18-1~20.04.1) ...<br />
Setting up python2.7 (2.7.18-1~20.04.1) ...<br />
Setting up libpython2-stdlib:amd64 (2.7.17-2ubuntu4) ...<br />
Setting up python2 (2.7.17-2ubuntu4) ...<br />
Setting up python-certifi (2019.11.28-1) ...<br />
Setting up python-six (1.14.0-2) ...<br />
Setting up python-idna (2.8-1) ...<br />
Setting up python-ipaddress (1.0.17-1build1) ...<br />
Setting up python-is-python2 (2.7.17-4) ...<br />
Setting up python-cffi-backend (1.14.0-1build1) ...<br />
Setting up python-enum34 (1.1.6-2ubuntu1) ...<br />
Setting up python-urllib3 (1.22-1ubuntu0.18.04.2) ...<br />
Setting up python-pkg-resources (44.0.0-2) ...<br />
Setting up python-cryptography (2.8-3ubuntu0.1) ...<br />
Setting up python-chardet (3.0.4-4build1) ...<br />
Setting up python-requests (2.18.4-2ubuntu0.1) ...<br />
Setting up python-openssl (19.0.0-1build1) ...<br />
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...<br />
Processing triggers for man-db (2.9.1-1) ...<br />
Processing triggers for mime-support (3.64ubuntu1) ...<br />
dejan@dejan:~$ <br />
<br />
<br />
<br />
<br />
== Install iRODS iCommands ==</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7768IRODS iCommands installation on Ubuntu 20.042021-03-16T19:46:10Z<p>Dejan Vitlacil (C3SE): /* List available packages */</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7767IRODS iCommands installation on Ubuntu 20.042021-03-16T19:44:15Z<p>Dejan Vitlacil (C3SE): </p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available) <br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Ubuntu_20.04&diff=7766IRODS iCommands installation on Ubuntu 20.042021-03-16T19:43:44Z<p>Dejan Vitlacil (C3SE): Created page with "== Install the public key and add the repository == Prepare IROS APT repository (#Using bionic repos because focal is not available) dejan@dejan:~$ LSB_RELEASE="bionic" dej..."</p>
<hr />
<div>== Install the public key and add the repository ==<br />
<br />
Prepare IROS APT repository (#Using bionic repos because focal is not available)<br />
<br />
dejan@dejan:~$ LSB_RELEASE="bionic" <br />
dejan@dejan:~$ wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
OK<br />
dejan@dejan:~$ echo "deb [arch=amd64] https://packages.irods.org/apt/ ${LSB_RELEASE} main" \<br />
> | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
deb [arch=amd64] https://packages.irods.org/apt/ bionic main<br />
dejan@dejan:~$ sudo apt-get update<br />
Hit:1 http://se.archive.ubuntu.com/ubuntu focal InRelease<br />
Hit:2 http://se.archive.ubuntu.com/ubuntu focal-updates InRelease<br />
Hit:3 http://se.archive.ubuntu.com/ubuntu focal-backports InRelease<br />
Hit:4 http://se.archive.ubuntu.com/ubuntu focal-security InRelease <br />
Hit:5 https://packages.irods.org/apt bionic InRelease <br />
Reading package lists... Done<br />
dejan@dejan:~$<br />
<br />
== List available packages ==<br />
<br />
dejan@dejan:~$ apt-cache search irods<br />
python3-irodsclient - Client API for iRods<br />
irods-auth-plugin-krb - The integrated Rule-Oriented Data System<br />
irods-database-plugin-mysql - The integrated Rule-Oriented Data System<br />
irods-database-plugin-oracle - The integrated Rule-Oriented Data System<br />
irods-database-plugin-postgres - The integrated Rule-Oriented Data System<br />
irods-dev - The integrated Rule-Oriented Data System<br />
irods-externals-autoconf5ad3567c-0 - iRODS Build Dependency<br />
irods-externals-avro1.8.2-0 - iRODS Build Dependency<br />
irods-externals-avro1.9.0-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-0 - iRODS Build Dependency<br />
irods-externals-aws-sdk-cpp1.4.89-1 - iRODS Build Dependency<br />
irods-externals-boost1.67.0-0 - iRODS Build Dependency<br />
irods-externals-catch22.3.0-0 - iRODS Build Dependency<br />
irods-externals-clang6.0-0 - iRODS Build Dependency<br />
irods-externals-clang-runtime6.0-0 - iRODS Build Dependency<br />
irods-externals-cmake3.11.4-0 - iRODS Build Dependency<br />
irods-externals-cppzmq4.2.3-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-0 - iRODS Build Dependency<br />
irods-externals-cpr1.3.0-1 - iRODS Build Dependency<br />
irods-externals-elasticlient0.1.0-1 - iRODS Build Dependency<br />
irods-externals-fmt6.1.2-1 - iRODS Build Dependency<br />
irods-externals-imagemagick7.0.8-0 - iRODS Build Dependency<br />
irods-externals-jansson2.7-0 - iRODS Build Dependency<br />
irods-externals-json3.1.2-0 - iRODS Build Dependency<br />
irods-externals-json3.7.3-0 - iRODS Build Dependency<br />
irods-externals-libarchive3.3.2-1 - iRODS Build Dependency<br />
irods-externals-libs3a30e55e8-1 - iRODS Build Dependency<br />
irods-externals-libs34e684077-0 - iRODS Build Dependency<br />
irods-externals-libs359b62371-0 - iRODS Build Dependency<br />
irods-externals-mungefs1.0.3-0 - iRODS Build Dependency<br />
irods-externals-nanodbc2.13.0-0 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-1 - iRODS Build Dependency<br />
irods-externals-qpid-with-proton0.34-2 - iRODS Build Dependency<br />
irods-externals-redis4.0.10-0 - iRODS Build Dependency<br />
irods-externals-spdlog0.17.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-0 - iRODS Build Dependency<br />
irods-externals-spdlog1.5.0-1 - iRODS Build Dependency<br />
irods-externals-zeromq4-14.1.6-0 - iRODS Build Dependency<br />
irods-icommands - The integrated Rule-Oriented Data System<br />
irods-microservice-plugins-curl - The integrated Rule-Oriented Data System<br />
irods-resource-plugin-s3 - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-audit-amqp - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-document-type - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-elasticsearch - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-hard-links - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-indexing - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-logical-quotas - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-metadata-guard - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-python - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-unified-storage-tiering - The integrated Rule-Oriented Data System<br />
irods-rule-engine-plugin-update-collection-mtime - The integrated Rule-Oriented Data System<br />
irods-runtime - The integrated Rule-Oriented Data System<br />
irods-server - The integrated Rule-Oriented Data System<br />
dejan@dejan:~$</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7765Swestore-iRODS2021-03-16T19:28:36Z<p>Dejan Vitlacil (C3SE): /* From the command line */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 20.04]] from repository<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7764Swestore-iRODS2021-03-15T10:41:42Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7763Swestore-iRODS2021-03-15T10:40:46Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
NOTE: different port 8888<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7757Swestore-iRODS2021-03-02T14:25:20Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), you can follow two different approaches. The first one is to use Metalnx graphical interface; the second is to use command line interface.<br />
<br />
'''In both cases we are giving [[read]] permissions to [[anonymous]] user!''' <br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7756Swestore-iRODS2021-03-02T14:20:46Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. When under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7755Swestore-iRODS2021-03-02T14:20:21Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to folder to share and select "Permissions" from dropdown box at the end of the path<br />
<br />
N.B. when under heavy load, web interface can be slow. Please have patience, we are looking into this.<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7754Swestore-iRODS2021-03-02T14:13:54Z<p>Dejan Vitlacil (C3SE): </p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Publish your data =<br />
<br />
For publishing your data via Swestore iRODS, please get in touch with Swestore support at [https://supr.snic.se/support/ Swestore Support].<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7753Swestore-iRODS2021-03-02T14:10:14Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make some of your project folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx, web application graphical interface, to change permissions on the folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7752Swestore-iRODS2021-03-02T10:40:11Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
* '''Use command line interface to change permission on folder''' <br />
<br />
[vitlacil@t04n27 ~]$ ichmod -r read anonymous /snic.se/projects/operations/sharefolder<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7751Swestore-iRODS2021-03-02T10:35:39Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:List of shared files.png |350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7749Swestore-iRODS2021-03-02T10:30:36Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7748Swestore-iRODS2021-03-02T10:30:13Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
[[File:Folder sharing.png |350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
[[File:Permissions listing.png |350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
[[File:Folder Permissions.png |350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7747Swestore-iRODS2021-03-02T10:29:42Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
[[File:Folder sharing.png |thumb|350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
[[File:Folder Permissions.png |thumb|350px]]<br />
<br />
4. Now your folder permissions should list read permission to anonymous user<br />
[[File:Permissions listing.png |thumb|350px]]<br />
<br />
4. Now your files are visible and downloadable via http://snic-irods-webdav.pdc.kth.se:8888/snic.se/projects/operations/sharefolder<br />
[[File:Folder Permissions.png |thumb|350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7745Swestore-iRODS2021-03-02T10:26:16Z<p>Dejan Vitlacil (C3SE): /* From a web browser */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to share data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
[[File:Folder Permissions.png |left |thumb|350px]]<br />
<br />
4. Now your files are visible and downloadable via<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7744Swestore-iRODS2021-03-02T10:25:26Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
3. Now you can add '''read''' permission to '''anonymous''' user. Consider also if you are going to apply it to subcollections and files<br />
[[File:Folder Permissions.png |left |thumb|350px]]<br />
<br />
4. Now your files are visible and downloadable via<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7742Swestore-iRODS2021-03-02T10:19:14Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
<br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7741Swestore-iRODS2021-03-02T10:17:13Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
N.B. when under load interface can be slow (we are looking into that)<br />
<br />
See picture:<br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7740Swestore-iRODS2021-03-02T10:16:49Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* '''Use Metalnx interface to change permission on folder''' <br />
1. Go to Metalnx login page and authenticate -> https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
2. Navigate to your folder to share and select "Permissions" from dropdown box at the end of the path. <br />
N.B. when under load interface can be slow (we are looking into that)<br />
See picture:<br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7739Swestore-iRODS2021-03-02T10:11:28Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* Use Metalnx interface to change permission on folder <br />
<br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7738Swestore-iRODS2021-03-02T10:11:07Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
* Use Metalnx interface to change permission on folder <br />
[[File:Folder sharing.png |left |thumb|350px]]<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7737Swestore-iRODS2021-03-02T10:08:49Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
'''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7735Swestore-iRODS2021-03-02T08:38:06Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
1. '''Let's assume you want to share your "sharefolder" with your external collaborators'''<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7734Swestore-iRODS2021-03-02T08:37:34Z<p>Dejan Vitlacil (C3SE): /* Share your data */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data =<br />
<br />
If you want to make your folders world readable (i.e. make them available for download for external collaborators who don't have Swestore account), follow these steps:<br />
<br />
1. Let's assume you want to share your "sharefolder" with your external collaborators<br />
[vitlacil@t04n27 ~]$ ils /snic.se/projects/operations/sharefolder/<br />
/snic.se/projects/operations/sharefolder:<br />
FitSM-0_Overview_and_vocabulary.pdf<br />
FitSM-1_Requirements.pdf<br />
FitSM_Advanced_Training_SOC_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5.pdf<br />
FitSM_Advanced_Training_SPD_V2.5_0.pptx<br />
FitSM_Expert_Training_V1.4.pdf<br />
FitSM_Foundation_Training_V2.10.pdf<br />
FitSM_Foundation_Training_V2.10.pptx<br />
FitSM_Foundation_Training_V2.11.pdf<br />
FitSM_Guide_Identifying_Services_v1.0.pdf<br />
FitSM_Sample_Corporate_SLA_v1.0.docx<br />
FitSM_Sample_Service_Portfolio_Catalogue_v2.0_final.xlsx<br />
FitSM_Template_SLA_1.0.docx<br />
FitSM_Teplate_Basic_Service_Report_1.0.docx<br />
C- /snic.se/projects/operations/sharefolder/README<br />
C- /snic.se/projects/operations/sharefolder/test<br />
[vitlacil@t04n27 ~]$<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7733Swestore-iRODS2021-03-02T08:15:02Z<p>Dejan Vitlacil (C3SE): /* Using Swestore iRODS at PDC */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Share your data = <br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7714Swestore-iRODS2021-01-21T15:48:35Z<p>Dejan Vitlacil (C3SE): /* From the command line */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository (the same procedure is valid for Ubuntu 18.04).<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=Swestore-iRODS&diff=7713Swestore-iRODS2021-01-21T15:33:16Z<p>Dejan Vitlacil (C3SE): /* From the command line */</p>
<hr />
<div>= Swestore iRODS =<br />
Swestore iRODS is distributed across two SNIC centres NSC and PDC. Data is stored in two copies with each copy at a different SNIC centre. This enables the system to cope with a multitude of issues ranging from a simple crash of a storage element to losing an entire site while still providing access to the stored data.<br />
<br />
= Using Swestore iRODS =<br />
<br />
== Basic information ==<br />
<br />
For basic information on how to apply for storage or how to become a member of an existing project, please check the main [[Swestore]] page.<br />
<br />
== Download and upload data== <br />
<br />
=== From the command line ===<br />
There are several command line tools capable of using the protocols provided by Swestore iRODS. For interactive usage on SNIC clusters we recommend using the iCommands which should be installed on all SNIC resources. There are too many commands to document fully here.<br />
<br />
* Please check full and updated documentation at iRODS official [https://docs.irods.org/master/icommands/user/ Documentation].<br />
* For the command line client, iRODS iCommands, please check iRODS [https://irods.org/download/ Download] page.<br />
** Please check "Binary Distributions" and instructions for configuring your package manager to include irods APT, YUM or ZYPPER repository at [https://packages.irods.org Repository of iRODS packages ].<br />
*** You can check here an example of [[iRODS iCommands installation on CentOS 7]] from repository.<br />
*** You can check here an example of [[iRODS iCommands installation on Ubuntu 16.04]] from repository.<br />
*** You can check here an example of [[IRODS iCommands installation on Windows]] from repository.<br />
<br />
* Configuration of the icommands requires a file called irods_environment.json to be placed in a subdirectory .irods/ of your home directory (e.g. ~/.irods/irods_environment.json).<br />
You must edit this with a text editor (not MS word, but notepad for Windows, textEdit for Mac or any Unix editor) and put your SNIC username in the place for <YOUR_SNIC_USER_NAME>.:<br />
<br />
{<br />
"irods_host": "irods-login.swestore.se",<br />
"irods_port": 2432,<br />
"irods_default_resource": "pdc-gpfs",<br />
"irods_home": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_cwd": "/snic.se/home/<YOUR_SNIC_USER_NAME>",<br />
"irods_user_name": "<YOUR_SNIC_USER_NAME>",<br />
"irods_zone_name": "snic.se",<br />
"irods_client_server_negotiation": "request_server_negotiation",<br />
"irods_client_server_policy": "CS_NEG_REFUSE",<br />
"irods_encryption_key_size": 32,<br />
"irods_encryption_salt_size": 8,<br />
"irods_encryption_num_hash_rounds": 16,<br />
"irods_encryption_algorithm": "AES-256-CBC",<br />
"irods_default_hash_scheme": "SHA256",<br />
"irods_match_hash_policy": "compatible",<br />
"irods_authentication_scheme": "PAM" <br />
}<br />
<br />
First issue<br />
iinit<br />
which will ask for your iRODS password. You can specify a longer time limit<br />
for the session using the <code>--ttl</code> option, <code>iinit -h --ttl</code><br />
will print help using this. The default generally will suffice.<br />
<br />
Use<br />
ils<br />
just to check if you can access your home directory. Please use the project<br />
directory to store files, which will be a subdirectory under<br />
<code>//snic.se/projects/<SNIC_PROJECT_NAME></code>.<br />
<br />
To transfer data you can use<br />
<code>irsync</code> like:<br />
irsync -v -r -K local_directory i:irods_directory<br />
where<br />
-v for verbose.<br />
-r for recursive copy of the whole directory tree.<br />
-K to compute and check checksums. This involves higher CPU usage<br />
but gives confidence for the integrity of the data stored.<br />
i.e.:<br />
irsync -r -K mydir i:/snic.se/projects/projectdir<br />
If, for whatever reason the transfer had been interrupted the second<br />
invocation of the command with the same arguments should pick up and<br />
continue from that point.<br />
<br />
The <code>ihelp</code> command will print a short description of the iRODS<br />
commands.<br />
<br />
=== From GUI client ===<br />
Graphical User Interface (GUI) clients are known to work on some operating systems.<br />
<br />
==== Access using WebDAV (map a network drive) ====<br />
[https://en.wikipedia.org/wiki/WebDAV WebDAV] endpoint for Windows 10, Linux and OS X is https://snic-irods-webdav.pdc.kth.se:8443/snic.se/<br />
<br />
===== Mac OS X =====<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Mac OS X<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| This is OS standard WebDAV connection · "Connect to server" function in Finder :<br />
To access Swestore iRODS via WebDAV you'll need to authenticate with your username and password.<br />
1.Click the 'Finder' icon <br />
[[File:MacOSX Finder.png |none|250px]]<br />
2.In 'Finder', locate the menu bar at the top and then navigate to Go > Connect to Server.<br />
[[File:ConnectToServer.png |none|250px]]<br />
3.In the 'Connect to Server' dialog box, enter the URL to Swestore iRODS WebDAV endpoint, in the 'Server Address' field.<br />
<br />
4.Click Connect.<br />
<br />
Once the connection is made, you are prompted for your WebDAV username/password.<br />
<br />
Once you’ve connected, the WebDAV directory is mounted in your 'Finder' and on your desktop.<br />
<br />
You can now start adding, editing, deleting files in this directory from the comfort of your computer.<br />
<br />
[[File:Mounted webdav GUI.png |none|350px]]<br />
<br />
|-<br />
<br />
| This is an example how to mount with iRODS resource via "mount_webdav" command in your terminal<br />
If you prefer to access your Swestore iRODS files via command line, you can mount the WebDAV-enabled server directory via '''mount_webdav''' command<br />
[[File:MacOSX Terminal WebDAV mount.png |none|350px]]<br />
<br />
|}<br />
<br />
===== Windows =====<br />
<br />
{| class="wikitable" <br />
!Accessing Swestore-iRODS via WebDAV on Windows<br />
|- style="text-align:center;"<br />
<br />
| WebDAV is a method for remotely managing files over the internet. With WebDAV, you can access files stored in Swestore iRODS project by using the same interface as you do with your local files. <br />
Once you connect via WebDAV, and you authenticate, you can view and manage the folders and files stored in your project area. You can perform same actions – drag and drop, rename, delete – that you would on files and folders stored on your own computer.<br />
<br />
|-<br />
| How to map the Swestore iRODS to a Windows computer<br />
1. You should have received an email telling you about your Swestore iRODS username <br />
<br />
2. We’ll use "'''s_user'''" for example<br />
<br />
3. We'll assume that you have set your password at SNIC SUPR for the Swestore iRODS account<br />
<br />
4. Open “File Explorer”<br />
<br />
5. Right-click “Network”<br />
<br />
[[File:Screenshot 2020-12-08 at 09.55.18.png |250px]]<br />
<br />
6. Click “Map network drive”<br />
<br />
7. Click the hyperlinked "Connect to a Web site that you can use to store your documents and pictures."<br />
<br />
8. Click "Next" two times (while choosing "Choose a custom network location")<br />
<br />
9. On "Specify the location of your website" enter https://snic-irods-webdav.pdc.kth.se:8443<br />
<br />
[[File:Screenshot 2020-12-08 at 10.03.52.png |250px]]<br />
<br />
10. Enter username and password, e.g. s_user and password<br />
<br />
[[File:Screenshot 2020-12-08 at 10.04.36.png |250px]]<br />
<br />
11. You can choose to name your new network drive with something meaningful<br />
<br />
11. You should now see the folder mapped to File Explorer!<br />
<br />
[[File:Screenshot 2020-12-08 at 10.08.15.png |250px]]<br />
<br />
<br />
|}<br />
<br />
=== From a web browser ===<br />
<br />
{| class="wikitable"<br />
!colspan="6"|Davrods is an Apache WebDAV interface to iRODS<br />
|-<br />
|rowspan="3"|[https://github.com/UtrechtUniversity/davrods Davrods]<br />
|Projects<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/projects/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|rowspan="3"|This interface is intended as '''simple directory index''' interface. It's purpose is to list, view, download, publish, share data. It is NOT intended to upload data. <br />
[[File:Swestore-iRODS simple webdav dir listing.png |center |thumb|350px]]<br />
|-<br />
|Home<br />
|https://snic-irods-webdav.pdc.kth.se:8443/snic.se/home/<br />
| To browse private data you'll need to authenticate with your username and password.<br />
|-<br />
|Public<br />
|http://snic-irods-webdav.pdc.kth.se:8888/snic.se/home/public/<br />
| This web interface is used to publish data with "world" and no authentication is required. <pre style="color: red">NOTE: different port 8888 </pre><br />
<br />
|-<br />
| [https://github.com/irods-contrib/metalnx-web Metalnx]<br />
| Login<br />
| https://snic-irods-web.pdc.kth.se/emc-metalnx-web/login/<br />
|To access SNIC iRODS Zone you'll need to authenticate with your username and password.<br />
| Metalnx is a web application designed to work alongside iRODS. It is a graphical user interface and serves as a client that authenticates to an existing iRODS Zone.<br />
[[File:Screenshot 2020-03-04 at 14.09.10.png |center |thumb|350px]]<br />
<br />
|}<br />
<br />
= Using Swestore iRODS at PDC = <br />
<br />
* [https://www.pdc.kth.se/support/documents/data_management/swestore.html PDC Support pages for Swestore (iRODS)]<br />
* [https://www.pdc.kth.se/support/documents/data_management/file_transfer_swestore.html PDC Support pages about Swestore (iRODS) client on PDC transfer node]<br />
<br />
= Using Swestore iRODS at NSC =<br />
<br />
[https://snicdocs.nsc.liu.se/wiki/Swestore-iRODS-at-NSC Here you can read more about the NSC specific aspects]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Windows&diff=7712IRODS iCommands installation on Windows2021-01-21T15:23:48Z<p>Dejan Vitlacil (C3SE): </p>
<hr />
<div>In order to use iRODS iCommands on Windows, you'll need to follow these steps:<br />
<br />
1. '''Windows Subsystem for Linux Installation Guide for Windows 10'''<br />
<br />
https://docs.microsoft.com/en-us/windows/wsl/install-win10<br />
<br />
2. '''Once you have WSL installed you should install your Linux distribution of choice'''<br />
<br />
- we recommend Ubuntu 18.04 LTS due to binary distributions availability<br />
https://docs.microsoft.com/en-us/windows/wsl/install-win10#step-6---install-your-linux-distribution-of-choice<br />
<br />
- setup your user and password on linux "machine"<br />
<br />
3. '''iRODS Packages in APT repositories''' <br />
<br />
Login and install the public key and add the repository:<br />
<br />
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
sudo apt-get update<br />
<br />
4. '''iCommand installation and configuration'''<br />
<br />
sudo apt install irods-icommands<br />
follow configuration instructions as described here https://docs.snic.se/wiki/Swestore-iRODS#From_the_command_line<br />
<br />
5. '''Mounting Network Drives into Windows Subsystem Linux (optional)'''<br />
info : https://docs.microsoft.com/sv-se/archive/blogs/wsl/wsl-file-system-support<br />
<br />
Microsoft uses a new type of file system called DrvFs behind the scenes to allow the Linux subsystem to talk to native Windows directories. So you end up mounting a network drive just like you would mount any other media normally.<br />
<br />
Let's say you've got a server on your network usually accessible as \\MyNetworkDrive. To mount it into your WSL, you can do the following:<br />
<br />
sudo mkdir /mnt/mynetworkdrive<br />
sudo mount -t drvfs '\\MyNetworkDrive' /mnt/mynetworkdrive<br />
<br />
Note: Use single quotes to avoid awkwardness around the backslashes in the network drive name.<br />
<br />
If you have mapped the network drive to a drive letter S: on your Windows system already: <br />
<br />
sudo mkdir /mnt/mynetworkdrive<br />
sudo mount -t drvfs S: /mnt/mynetworkdrive<br />
<br />
If you ever want to unmount it:<br />
<br />
sudo umount /mnt/mynetworkdrive<br />
<br />
---<br />
<br />
Go back to [[Swestore-iRODS]]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Windows&diff=7711IRODS iCommands installation on Windows2021-01-21T15:23:32Z<p>Dejan Vitlacil (C3SE): </p>
<hr />
<div>In order to use iRODS iCommands on Windows, you'll need to follow these steps:<br />
<br />
1. '''Windows Subsystem for Linux Installation Guide for Windows 10'''<br />
<br />
https://docs.microsoft.com/en-us/windows/wsl/install-win10<br />
<br />
2. '''Once you have WSL installed you should install your Linux distribution of choice'''<br />
<br />
- we recommend Ubuntu 18.04 LTS due to binary distributions availability<br />
https://docs.microsoft.com/en-us/windows/wsl/install-win10#step-6---install-your-linux-distribution-of-choice<br />
<br />
- setup your user and password on linux "machine"<br />
<br />
3. '''iRODS Packages in APT repositories''' <br />
<br />
Login and install the public key and add the repository:<br />
<br />
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
sudo apt-get update<br />
<br />
4. '''iCommand installation and configuration'''<br />
<br />
sudo apt install irods-icommands<br />
follow configuration instructions as described here https://docs.snic.se/wiki/Swestore-iRODS#From_the_command_line<br />
<br />
5. '''Mounting Network Drives into Windows Subsystem Linux (optional)'''<br />
info : https://docs.microsoft.com/sv-se/archive/blogs/wsl/wsl-file-system-support<br />
<br />
Microsoft uses a new type of file system called DrvFs behind the scenes to allow the Linux subsystem to talk to native Windows directories. So you end up mounting a network drive just like you would mount any other media normally.<br />
<br />
Let's say you've got a server on your network usually accessible as \\MyNetworkDrive. To mount it into your WSL, you can do the following:<br />
<br />
sudo mkdir /mnt/mynetworkdrive<br />
sudo mount -t drvfs '\\MyNetworkDrive' /mnt/mynetworkdrive<br />
<br />
Note: Use single quotes to avoid awkwardness around the backslashes in the network drive name.<br />
<br />
If you have mapped the network drive to a drive letter S: on your Windows system already: <br />
<br />
sudo mkdir /mnt/mynetworkdrive<br />
sudo mount -t drvfs S: /mnt/mynetworkdrive<br />
<br />
If you ever want to unmount it:<br />
<br />
sudo umount /mnt/mynetworkdrive<br />
<br />
Go back to [[Swestore-iRODS]]</div>Dejan Vitlacil (C3SE)https://snicdocs.nsc.liu.se/w/index.php?title=IRODS_iCommands_installation_on_Windows&diff=7710IRODS iCommands installation on Windows2021-01-21T15:22:57Z<p>Dejan Vitlacil (C3SE): </p>
<hr />
<div>In order to use iRODS iCommands on Windows, you'll need to follow these steps:<br />
<br />
1. '''Windows Subsystem for Linux Installation Guide for Windows 10'''<br />
<br />
https://docs.microsoft.com/en-us/windows/wsl/install-win10<br />
<br />
2. '''Once you have WSL installed you should install your Linux distribution of choice'''<br />
<br />
- we recommend Ubuntu 18.04 LTS due to binary distributions availability<br />
https://docs.microsoft.com/en-us/windows/wsl/install-win10#step-6---install-your-linux-distribution-of-choice<br />
<br />
- setup your user and password on linux "machine"<br />
<br />
3. '''iRODS Packages in APT repositories''' <br />
<br />
Login and install the public key and add the repository:<br />
<br />
wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -<br />
echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list<br />
sudo apt-get update<br />
<br />
4. '''iCommand installation and configuration'''<br />
<br />
sudo apt install irods-icommands<br />
follow configuration instructions as described here https://docs.snic.se/wiki/Swestore-iRODS#From_the_command_line<br />
<br />
5. '''Mounting Network Drives into Windows Subsystem Linux (optional)'''<br />
info : https://docs.microsoft.com/sv-se/archive/blogs/wsl/wsl-file-system-support<br />
<br />
Microsoft uses a new type of file system called DrvFs behind the scenes to allow the Linux subsystem to talk to native Windows directories. So you end up mounting a network drive just like you would mount any other media normally.<br />
<br />
Let's say you've got a server on your network usually accessible as \\MyNetworkDrive. To mount it into your WSL, you can do the following:<br />
<br />
sudo mkdir /mnt/mynetworkdrive<br />
sudo mount -t drvfs '\\MyNetworkDrive' /mnt/mynetworkdrive<br />
<br />
Note: Use single quotes to avoid awkwardness around the backslashes in the network drive name.<br />
<br />
If you have mapped the network drive to a drive letter S: on your Windows system already: <br />
<br />
sudo mkdir /mnt/mynetworkdrive<br />
sudo mount -t drvfs S: /mnt/mynetworkdrive<br />
<br />
If you ever want to unmount it:<br />
<br />
sudo umount /mnt/mynetworkdrive</div>Dejan Vitlacil (C3SE)