Release v21

Author: hexylena

CHANGELOG.md

@@ -1,4 +1,6 @@
-# 21-pre
+# 22-pre
+
+# 21
 
 - Added:
 	- query queue-detail-drm, from @cat-bro and @slugger70, a better version of queue-details potentially.

docs/README.galaxy.md

@@ -259,3 +259,9 @@ galaxy migrate-tool-install-to-sqlite -  Converts normal potsgres toolshed repos
 ## galaxy prune-gxit-routes
 
 ([*source*](https://github.com/galaxyproject/gxadmin/search?q=galaxy_prune-gxit-routes&type=Code))
+galaxy prune-gxit-routes -  Prunes dead routes
+
+**SYNOPSIS**
+
+    gxadmin galaxy prune-gxit-routes <interactivetools_map>
+

docs/README.mutate.md

@@ -77,6 +77,12 @@ handlers you want to schedule workflows across.
 ## mutate dataset-mark-purged
 
 ([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_dataset-mark-purged&type=Code))
+mutate dataset-mark-purged -  Purge dataset and mark downstream HDAs as purged as well
+
+**SYNOPSIS**
+
+    gxadmin mutate dataset-mark-purged <dataset_uuid> [--commit]
+
 
 ## mutate delete-group-role
 
@@ -140,3 +146,249 @@ mutate fail-job -  Sets a job state to error
 
 Sets a job's state to "error"
 
+
+## mutate fail-misbehaving-gxits
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_fail-misbehaving-gxits&type=Code))
+mutate fail-misbehaving-gxits -  Fails misbehaving GxITs.
+
+**SYNOPSIS**
+
+    gxadmin mutate fail-misbehaving-gxits [--commit]
+
+**NOTES**
+
+Set quota for OIDC users.
+
+
+## mutate fail-terminal-datasets
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_fail-terminal-datasets&type=Code))
+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
+
+
+## mutate fail-wfi
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_fail-wfi&type=Code))
+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"
+
+
+## mutate force-publish-history
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_force-publish-history&type=Code))
+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 https://github.com/galaxyproject/galaxy/issues/13001
+
+
+## mutate generate-unset-api-keys
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_generate-unset-api-keys&type=Code))
+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.
+
+
+## mutate oidc-by-emails
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_oidc-by-emails&type=Code))
+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 https://github.com/galaxyproject/galaxy/issues/9981.
+
+
+## mutate oidc-role-find-affected
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_oidc-role-find-affected&type=Code))
+mutate oidc-role-find-affected -  Find users affected by galaxyproject/galaxy#8244
+
+**SYNOPSIS**
+
+    gxadmin mutate oidc-role-find-affected
+
+**NOTES**
+
+Workaround for https://github.com/galaxyproject/galaxy/issues/8244
+
+This finds all of the OIDC authenticated users which do not have any
+roles associated to them. (Should be sufficient?)
+
+
+## mutate oidc-role-fix
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_oidc-role-fix&type=Code))
+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 https://github.com/galaxyproject/galaxy/issues/8244
+
+
+## mutate purge-old-job-metrics
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_purge-old-job-metrics&type=Code))
+mutate purge-old-job-metrics -  Purge job metrics older than 1 year.
+
+**SYNOPSIS**
+
+    gxadmin mutate purge-old-job-metrics [--commit]
+
+
+## mutate reassign-active-workflows-to-handler
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_reassign-active-workflows-to-handler&type=Code))
+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 https://github.com/galaxyproject/galaxy/issues/8209
+
+Need to use the full handler names e.g. handler_main_0
+
+
+## mutate reassign-job-to-handler
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_reassign-job-to-handler&type=Code))
+mutate reassign-job-to-handler -  Reassign a job to a different handler
+
+**SYNOPSIS**
+
+    gxadmin mutate reassign-job-to-handler <job_id> <handler_id> [--commit]
+
+
+## mutate reassign-workflows-to-handler
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_reassign-workflows-to-handler&type=Code))
+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 https://github.com/galaxyproject/galaxy/issues/8209
+
+Need to use the full handler names e.g. handler_main_0
+
+
+## mutate restart-jobs
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_restart-jobs&type=Code))
+mutate restart-jobs -  Restart some jobs
+
+**SYNOPSIS**
+
+    gxadmin mutate restart-jobs [--commit] <-|job_id [job_id [...]]>
+
+**NOTES**
+
+Restart jobs
+
+
+## mutate set-quota-for-oidc-user
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_set-quota-for-oidc-user&type=Code))
+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.
+