Release v22

CHANGELOG.md

@@ -1,4 +1,6 @@
-# 22-pre
+# 23-pre
+
+# 22
 
 - Added:
 	- filter histogram: replaces bit.ly's data_hacks with a built-in AWK program to calculate a histogram. May not be entirely portable @hexylena.

CITATION.cff

@@ -51,5 +51,5 @@ keywords:
   - galaxy
   - galaxyproject
 license: GPL-3.0-or-later
-version: v21
-date-released: '2023-02-07'
+version: v22
+date-released: 2024-03-28

docs/README.filter.md

@@ -43,6 +43,7 @@ filter histogram -  Generate a small histogram of the input values. It must be a
 **NOTES**
 
 Generate a histogram of inputs
+
     $ cat out.txt | ./gxadmin filter histogram
     ( -23.000,  -20.615) n=1
     [ -20.615,  -18.231) n=4

docs/README.galaxy.md

@@ -7,7 +7,7 @@ Command | Description
 [`galaxy cleanup-jwd`](#galaxy-cleanup-jwd) | (NEW) Cleanup job working directories
 [`galaxy decode`](#galaxy-decode) | Decode an encoded ID
 [`galaxy encode`](#galaxy-encode) | Encode an ID
-[`galaxy fav_tools`](#galaxy-fav_tools) | Favourite tools in Galaxy DB
+[`galaxy fav-tools`](#galaxy-fav-tools) | Favourite tools in Galaxy DB
 [`galaxy fix-conda-env`](#galaxy-fix-conda-env) | Fix broken conda environments
 [`galaxy ie-list`](#galaxy-ie-list) | List GIEs
 [`galaxy ie-show`](#galaxy-ie-show) | Report on a GIE [HTCondor Only!]
@@ -125,14 +125,14 @@ Encode an unecoded ID
     6fe4eea8c591a9c4
 
 
-## galaxy fav_tools
+## galaxy fav-tools
 
-([*source*](https://github.com/galaxyproject/gxadmin/search?q=galaxy_fav_tools&type=Code))
-galaxy fav_tools -  Favourite tools in Galaxy DB
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=galaxy_fav-tools&type=Code))
+galaxy fav-tools -  Favourite tools in Galaxy DB
 
 **SYNOPSIS**
 
-    gxadmin galaxy fav_tools
+    gxadmin galaxy fav-tools
 
 **NOTES**
 

docs/README.mutate.md

@@ -7,6 +7,7 @@ Command | Description
 [`mutate assign-unassigned-workflows`](#mutate-assign-unassigned-workflows) | Randomly assigns unassigned workflows to handlers. Workaround for galaxyproject/galaxy#8209
 [`mutate dataset-mark-purged`](#mutate-dataset-mark-purged) | Purge dataset and mark downstream HDAs as purged as well
 [`mutate delete-group-role`](#mutate-delete-group-role) | Remove the group, role, and any user-group + user-role associations
+[`mutate derive-missing-username-from-email`](#mutate-derive-missing-username-from-email) | Set empty username to email address for users created before 2011
 [`mutate drop-extraneous-workflow-step-output-associations`](#mutate-drop-extraneous-workflow-step-output-associations) | #8418, drop extraneous connection
 [`mutate fail-history`](#mutate-fail-history) | Mark all jobs within a history to state error
 [`mutate fail-job`](#mutate-fail-job) | Sets a job state to error
@@ -23,6 +24,8 @@ Command | Description
 [`mutate reassign-job-to-handler`](#mutate-reassign-job-to-handler) | Reassign a job to a different handler
 [`mutate reassign-workflows-to-handler`](#mutate-reassign-workflows-to-handler) | Reassign workflows in 'new' state to a different handler.
 [`mutate restart-jobs`](#mutate-restart-jobs) | Restart some jobs
+[`mutate scale-table-autovacuum`](#mutate-scale-table-autovacuum) | Update autovacuum and autoanalyze scale for large tables.
+[`mutate set-missing-username-to-random-uuid`](#mutate-set-missing-username-to-random-uuid) | Set empty username to random uuid
 [`mutate set-quota-for-oidc-user`](#mutate-set-quota-for-oidc-user) | Set quota for OIDC users.
 
 ## mutate anonymise-db-for-release
@@ -98,6 +101,26 @@ mutate delete-group-role -  Remove the group, role, and any user-group + user-ro
 Wipe out a group+role, and user associations.
 
 
+## mutate derive-missing-username-from-email
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_derive-missing-username-from-email&type=Code))
+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 "[email protected]"
+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()
+
+
 ## mutate drop-extraneous-workflow-step-output-associations
 
 ([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_drop-extraneous-workflow-step-output-associations&type=Code))
@@ -379,6 +402,39 @@ mutate restart-jobs -  Restart some jobs
 Restart jobs
 
 
+## mutate scale-table-autovacuum
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_scale-table-autovacuum&type=Code))
+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]).
+
+
+## mutate set-missing-username-to-random-uuid
+
+([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_set-missing-username-to-random-uuid&type=Code))
+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.
+
+
 ## mutate set-quota-for-oidc-user
 
 ([*source*](https://github.com/galaxyproject/gxadmin/search?q=mutate_set-quota-for-oidc-user&type=Code))