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rdms:access:linux:icommands [2024/09/02 10:18] – changed .json file to reflect 4.3 changes giuliordms:access:linux:icommands [2025/07/03 11:48] (current) – [Common iCommands Usage Examples] Note about ibun and symlinks jelte
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 2. Create the configuration file: 2. Create the configuration file:
  
-Create the file ''~/.irods/irods_environment.json'' using your preferred text editor.  The file must contain plain ASCII characters.  Add the following lines to the file, modifying as instructed below:+Create the file ''~/.irods/irods_environment.json'' using your preferred text editor.  The file must contain plain ASCII characters. [[https://wiki.hpc.rug.nl/rdms/solution/multizone|The Default and Sensitive data (SD) zones]] have different configurations. Add the following lines to the file, modifying as instructed below:
  
-<hidden Click to display configuration file><code>+<hidden Click to display configuration file for Default zone><code>
 { {
     "irods_authentication_scheme": "pam_password",     "irods_authentication_scheme": "pam_password",
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     "irods_user_name": "<emailadress>",     "irods_user_name": "<emailadress>",
     "irods_zone_name": "rug"     "irods_zone_name": "rug"
 +}
 +</code></hidden>\\
 +
 +<hidden Click to display configuration file for Sensitive data zone><code>
 +{
 +    "irods_authentication_scheme": "pam_password",
 +    "irods_client_server_negotiation": "request_server_negotiation",
 +    "irods_client_server_policy": "CS_NEG_REQUIRE",
 +    "irods_default_resource": "rootResc",
 +    "irods_encryption_algorithm": "AES-256-CBC",
 +    "irods_encryption_key_size": 32,
 +    "irods_encryption_num_hash_rounds": 16,
 +    "irods_encryption_salt_size": 8,
 +    "irods_host": "store-sd.data.rug.nl",
 +    "irods_port": 1247,
 +    "irods_ssl_verify_server": "cert",
 +    "irods_user_name": "<emailadress>",
 +    "irods_zone_name": "sdrugZone"
 } }
 </code></hidden>\\ </code></hidden>\\
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 For the explanation of commonly used ''iCommands'', we will split the ''iCommands'' into three different sections: For the explanation of commonly used ''iCommands'', we will split the ''iCommands'' into three different sections:
  
-  - **iCommands for Navigation** will describe the iCommands that are used to navigate the RDMS from the CLI, but also contain information about starting/ending of the connection.+  - **iCommands for Navigation** will describe the ''iCommands'' that are used to navigate the RDMS from the CLI, but also contain information about starting/ending of the connection.
   - **iCommands for (Meta)data Management** will describe how to transfer data in/out of the RDMS, explain how to set permissions for other users, how to work with metadata from the CLI, including a more detailed description on how to query the database for more extensive searches.   - **iCommands for (Meta)data Management** will describe how to transfer data in/out of the RDMS, explain how to set permissions for other users, how to work with metadata from the CLI, including a more detailed description on how to query the database for more extensive searches.
   -  **iCommands for Group Management** will focus on the respective commands that can be used by 'groupadmins' to manage RDMS groups from the CLI. As this section is not relevant for all users, it will be discussed separately.    -  **iCommands for Group Management** will focus on the respective commands that can be used by 'groupadmins' to manage RDMS groups from the CLI. As this section is not relevant for all users, it will be discussed separately. 
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   * The bundling and extraction operations do not display a progress. For large folders/archives, it might take a longer time to finish while your terminal seems to be stuck.   * The bundling and extraction operations do not display a progress. For large folders/archives, it might take a longer time to finish while your terminal seems to be stuck.
   * If you want to overwrite, you can again use the additional ''-f'' flag.   * If you want to overwrite, you can again use the additional ''-f'' flag.
 +  * Notes that extraction via ''ibun -x'' will fail if your archive contains symlinks as they are not supported by ''ibun'' (also see info in the [[rdms:bestpractices|Best Practices]] section). 
  
 **Assigning Data Permission**\\ **Assigning Data Permission**\\
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 </code> </code>
 </hidden>\\ </hidden>\\
 +
 +**How to manage files in the RDMS trash folder**\\
 +Files that have been deleted either via the web interface or using  the command ''irm'' are not permanently removed from the system, but are stored in the ''trash'' folder of the RDMS. Should you wish to empty your ''trash'' folder, you can simply run the ''irmtrash'' command without any further parameter.
 +
 +If you wish to restore files in the ''trash'' folder using ''iCommands'', you can do so by running the following commands:
 +<hidden>
 +<code>
 +#To locate a file in the trash folder, you will need to know the filename:
 +$ ilocate -t <filename>  
 +
 +# where the -t switch indicates to search in trash. Copy the path given by ilocate, then run any of the suggested commands.
 +
 +# To move the file out of the trash folder (and preserve previously attached metadata):
 +$ imv <logical path(s) from ilocate> <path to RDMS destination folder>
 +
 +# To restore a copy of the file present in the trash folder (without previously attached metadata):
 +$ icp <logical path(s) from ilocate> <path to RDMS destination folder>
 +
 +# To download a copy of the file to a folder on your local system (without previously attached metadata):
 +$ iget <logical path(s) from ilocate> <path to local destination folder>
 +
 +</code>
 +</hidden>\\
 +
 +You can also use the **RDMS web interface to restore a file** from the ''trash''. If you would prefer to use the web interface for this operation, please refer to the section of the wiki [[https://wiki.hpc.rug.nl/rdms/webapp/databrowser#how_to_restore_deleted_files|How to restore deleted files]].
 +
 **Working with Metadata**\\ **Working with Metadata**\\
 The ''iCommands'' can be also used to add metadata to a file/folder, list already existing metadata, modify existing metadata, and also query (search) for objects that contain certain metadata.  The ''iCommands'' can be also used to add metadata to a file/folder, list already existing metadata, modify existing metadata, and also query (search) for objects that contain certain metadata.