Management Commands

This section briefly lists the management commands available for SODAR administrators with shell access, in addition to the built-in commands in Django and used third party components. For more details on their usage, use the -h or --help argument.

SODAR Core Commands

These commands originate in SODAR Core. More information can be found in the SODAR Core documentation.

addremotesite: Add remote site for remote project synchronization.
batchupdateroles: Batch update project roles and send invites.
checkusers: Check the status of LDAP users. Returns info on users whose accounts are disabled or removed on an LDAP server.
cleanappsettings: Clean up unused application settings.
deletecache: Delete SODAR Cache entries.
geticons: Download and install the latest versions of iconify icon sets. Must be followed by collectstatic to take effect.
removeroles: Remove all roles from a user. Useful when e.g. a user has left the organization. Replaces user’s owner roles with another given user. Can also be used to deactivate the user account after role removal.
synccache: Synchronize the SODAR Cache.
syncgroups: Synchronize user groups.
syncmodifyapi: Create project metadata, project collections, user access and access tickets in iRODS. Generally should only be used in development or in exceptional situations where the iRODS iCAT database needs to be recreated.
syncremote: Synchronize project and user data from a remote site if remote project sync is enabled.

SODAR Commands

These commands originate from the SODAR applications and are specific to operations regarding sample sheets, landing zones, iRODS data and ontologies.

busyzones: Return list of currently busy landing zones.
checksampleaccess: Check for expected user access in all project sample data collections in iRODS and report discrepancies. Useful for validating expected access rights in case of e.g. manual admin user cleanup operations.
importobo: Import OBO format ontology. See Ontology Access Application.
importomimm: Import OMIM catalog as an ontology. See Ontology Access Application.
inactivezones: Return list of landing zones last modified over two weeks ago.
irodsorphans: Find orphans in iRODS project collections.
normalizesheets: Clean up and normalize previously imported sample sheets for non-standard data or other issues. Also updates render tables and creates a backup ISA-Tab version of the normalized sheets.
resetzone: Reset landing zone state. Usable for cases where a zone has entered a frozen state due to e.g. server or network issues. Sets user iRODS access to the zone corresponding to settings after zone initialization and sets the zone status to ACTIVE, allowing for further user activity. Reset will not be performed if active Celery jobs for validation or moving of the same zone exist. Provide the landing zone UUID with the -z or --zone argument.
syncnames: Synchronize alternative names for sample sheet material search.
syncstudytables: Build study render tables in cache for all study tables. These will be automatically built when accessing sample sheets if existing cache is not up-to-date, but this can be used to e.g. regenerate the cache if something has been changed in study table rendering. Given the argument -c or --check, study table rendering can be tested without storing any changes in the cache.
verifyzone: Manually trigger verification of files moved from a landing zone, in case e.g. the automated verify after zone moving failed due to server issues. Provide the landing zone UUID with the -z or --zone argument. Run in synchronous mode with -s or --sync (only recommended for testing or development).