| Command | Description |
|---|---|
mutate anonymise-db-for-release |
This will attempt to make a database completely safe to release publicly. |
mutate approve-user |
Approve a user in the database |
mutate assign-unassigned-workflows |
Randomly assigns unassigned workflows to handlers. Workaround for galaxyproject/galaxy#8209 |
mutate dataset-mark-purged |
Purge dataset and mark downstream HDAs as purged as well |
mutate delete-group-role |
Remove the group, role, and any user-group + user-role associations |
mutate derive-missing-username-from-email |
Set empty username to email address for users created before 2011 |
mutate drop-extraneous-workflow-step-output-associations |
#8418, drop extraneous connection |
mutate fail-history |
Mark all jobs within a history to state error |
mutate fail-job |
Sets a job state to error |
mutate fail-misbehaving-gxits |
Fails misbehaving GxITs. |
mutate fail-terminal-datasets |
Causes the output datasets of jobs which were manually failed, to be marked as failed |
mutate fail-wfi |
Sets a workflow invocation state to failed |
mutate force-publish-history |
Removes the access restriction on every dataset in a specified history |
mutate generate-unset-api-keys |
Generate API keys for users which do not have one set. |
mutate oidc-by-emails |
Reassign OIDC account between users. |
mutate oidc-role-find-affected |
Find users affected by galaxyproject/galaxy#8244 |
mutate oidc-role-fix |
Fix permissions for users logged in via OIDC. Workaround for galaxyproject/galaxy#8244 |
mutate purge-old-job-metrics |
Purge job metrics older than 1 year. |
mutate reassign-active-workflows-to-handler |
Reassign workflows with state 'scheduled' or 'new' to a different handler. |
mutate reassign-job-to-handler |
Reassign a job to a different handler |
mutate reassign-workflows-to-handler |
Reassign workflows in 'new' state to a different handler. |
mutate restart-jobs |
Restart some jobs |
mutate scale-table-autovacuum |
Update autovacuum and autoanalyze scale for large tables. |
mutate set-missing-username-to-random-uuid |
Set empty username to random uuid |
mutate set-quota-for-oidc-user |
Set quota for OIDC users. |
(source) mutate anonymise-db-for-release - This will attempt to make a database completely safe to release publicly.
SYNOPSIS
gxadmin mutate anonymise-db-for-release [--commit|--very-unsafe]
NOTES
THIS WILL DESTROY YOUR DATABASE.
--commit will do it and wrap it in a transaction --very-unsafe will just run it without the transaction
(source) mutate approve-user - Approve a user in the database
SYNOPSIS
gxadmin mutate approve-user <username|email|user_id>
NOTES
There is no --commit flag on this because it is relatively safe
(source) mutate assign-unassigned-workflows - Randomly assigns unassigned workflows to handlers. Workaround for galaxyproject/galaxy#8209
SYNOPSIS
gxadmin mutate assign-unassigned-workflows <handler_prefix> <handler_count> [--commit]
NOTES
Workaround for galaxyproject/galaxy#8209
Handler names should have number as postfix, so "some_string_##". In this case handler_prefix is "some_string_" and count is however many handlers you want to schedule workflows across.
(source) mutate dataset-mark-purged - Purge dataset and mark downstream HDAs as purged as well
SYNOPSIS
gxadmin mutate dataset-mark-purged <dataset_uuid> [--commit]
(source) mutate delete-group-role - Remove the group, role, and any user-group + user-role associations
SYNOPSIS
gxadmin mutate delete-group-role <group_name> [--commit]
NOTES
Wipe out a group+role, and user associations.
(source) mutate derive-missing-username-from-email - Set empty username to email address for users created before 2011
SYNOPSIS
gxadmin mutate derive-missing-username-from-email [--commit]
NOTES
Galaxy did not require setting a username for users registered prior to 2011. This will set the username to the lowercased substring of the email addres before the first @. The username for a user with the email address "Jane.DoE@example.com" will be set to "jane.doe" if the the user did not have a username and no other user has been registered with that username. It is recommended that usernames that could not be changed due to conflicts are fixed using mutate set-missing-username-to-random-uuid()
(source) mutate drop-extraneous-workflow-step-output-associations - #8418, drop extraneous connection
SYNOPSIS
gxadmin mutate drop-extraneous-workflow-step-output-associations [--commit]
NOTES
Per galaxyproject/galaxy#8418, this drops the workflow step output associations that are not necessary.
This only needs to be run once, on servers which have run Galaxy<=19.05 to remove duplicate entries in the following tables:
- workflow_invocation_step_output_dataset_association
- workflow_invocation_step_output_dataset_collection_association
(source) mutate fail-history - Mark all jobs within a history to state error
SYNOPSIS
gxadmin mutate fail-history <history_id> [--commit]
NOTES
Set all jobs within a history to error
(source) mutate fail-job - Sets a job state to error
SYNOPSIS
gxadmin mutate fail-job <job_id> [--commit]
NOTES
Sets a job's state to "error"
(source) mutate fail-misbehaving-gxits - Fails misbehaving GxITs.
SYNOPSIS
gxadmin mutate fail-misbehaving-gxits [--commit]
NOTES
Set quota for OIDC users.
(source) mutate fail-terminal-datasets - Causes the output datasets of jobs which were manually failed, to be marked as failed
SYNOPSIS
gxadmin mutate fail-terminal-datasets [--commit]
NOTES
Whenever an admin marks a job as failed manually (e.g. by updating the state in the database), the output datasets are not accordingly updated by default. And this causes users to mistakenly think their jobs are still running when they have long since failed.
This command provides a way to select those jobs in error states (deleted, deleted_new, error, error_manually_dropped, new_manually_dropped), find their associated output datasets, and fail them with a blurb mentionining that they should contact the admin in case of any question
Running without any arguments will execute the command within a transaction and then roll it back, allowing you to see counts of rows and giving you an idea if it is doing the right thing.
WARNINGS
!> This does NOT currently work on collections
EXAMPLES
The process is to first query how many datasets will be failed, if this looks correct you're ready to go.
$ gxadmin mutate fail-terminal-datasets
BEGIN
SELECT 1
jobs_per_month_to_be_failed | count
-----------------------------+-------
2019-02-01 00:00:00 | 1
(1 row)
UPDATE 1
UPDATE 1
ROLLBACK
Then to run with the --commit flag to commit the changes
$ gxadmin mutate fail-terminal-datasets --commit
BEGIN
SELECT 1
jobs_per_month_to_be_failed | count
-----------------------------+-------
2019-02-01 00:00:00 | 1
(1 row)
UPDATE 1
UPDATE 1
COMMIT
(source) mutate fail-wfi - Sets a workflow invocation state to failed
SYNOPSIS
gxadmin mutate fail-wfi <wf-invocation-d> [--commit]
NOTES
Sets a workflow invocation's state to "failed"
(source) mutate force-publish-history - Removes the access restriction on every dataset in a specified history
SYNOPSIS
gxadmin mutate force-publish-history <history_id> [--commit]
NOTES
Workaround for Galaxy bug galaxyproject/galaxy#13001
(source) mutate generate-unset-api-keys - Generate API keys for users which do not have one set.
SYNOPSIS
gxadmin mutate generate-unset-api-keys [--commit]
NOTES
For some use cases (IEs), it is preferrable that everyone has an API key set for them, if they don't choose to set one themselves. So we set a base64'd key to be a bit extra secure just in case. These work just fine like hex keys.
(source) mutate oidc-by-emails - Reassign OIDC account between users.
SYNOPSIS
gxadmin mutate oidc-by-emails <email_from> <email_to> [--commit]
NOTES
Workaround for users creating a new account by clicking the OIDC button, with case mismatching between existing accounts. Please note that this function is case-sensitive. Fixes galaxyproject/galaxy#9981.
(source) mutate oidc-role-find-affected - Find users affected by galaxyproject/galaxy#8244
SYNOPSIS
gxadmin mutate oidc-role-find-affected
NOTES
Workaround for galaxyproject/galaxy#8244
This finds all of the OIDC authenticated users which do not have any roles associated to them. (Should be sufficient?)
(source) mutate oidc-role-fix - Fix permissions for users logged in via OIDC. Workaround for galaxyproject/galaxy#8244
SYNOPSIS
gxadmin mutate oidc-role-fix <username|email|user_id>
NOTES
Workaround for galaxyproject/galaxy#8244
(source) mutate purge-old-job-metrics - Purge job metrics older than 1 year.
SYNOPSIS
gxadmin mutate purge-old-job-metrics [--commit]
(source) mutate reassign-active-workflows-to-handler - Reassign workflows with state 'scheduled' or 'new' to a different handler.
SYNOPSIS
gxadmin mutate reassign-active-workflows-to-handler <handler_from> <handler_to> [--commit]
NOTES
Another workaround for galaxyproject/galaxy#8209
Need to use the full handler names e.g. handler_main_0
(source) mutate reassign-job-to-handler - Reassign a job to a different handler
SYNOPSIS
gxadmin mutate reassign-job-to-handler <job_id> <handler_id> [--commit]
(source) mutate reassign-workflows-to-handler - Reassign workflows in 'new' state to a different handler.
SYNOPSIS
gxadmin mutate reassign-workflows-to-handler <handler_from> <handler_to> [--commit]
NOTES
Another workaround for galaxyproject/galaxy#8209
Need to use the full handler names e.g. handler_main_0
(source) mutate restart-jobs - Restart some jobs
SYNOPSIS
gxadmin mutate restart-jobs [--commit] <-|job_id [job_id [...]]>
NOTES
Restart jobs
(source) mutate scale-table-autovacuum - Update autovacuum and autoanalyze scale for large tables.
SYNOPSIS
gxadmin mutate scale-table-autovacuum [--shift=16] [--commit]
NOTES
Set autovacuum_vacuum_scale_factor and autovacuum_analyze_scale_factor dynamically based on size for large tables. See https://www.enterprisedb.com/blog/postgresql-vacuum-and-analyze-best-practice-tips
Table row counts are shifted right by --shift, any shifted value over 1 will have its autovacuum scale adjusted to 0.2/log(rows >> [shift]) and autoanalyze scale adjusted to 0.1/log(rows >> [shift]).
(source) mutate set-missing-username-to-random-uuid - Set empty username to random uuid
SYNOPSIS
gxadmin mutate set-missing-username-to-random-uuid [--commit]
NOTES
Galaxy did not require setting a username for users registered prior to 2011. This will set the username column to a random uuid.
(source) mutate set-quota-for-oidc-user - Set quota for OIDC users.
SYNOPSIS
gxadmin mutate set-quota-for-oidc-user <provider_name> <quota_name> [--commit]
NOTES
Set quota for OIDC users.