v22

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.
  • mutate scale-table-autovacuum: Dynamically update autovacuum and autoanalyze scale for large tables. @natefoo
  • query tools-usage-per-month from @lldelisle
  • mutate derive-missing-username-from-email and mutate set-missing-username-to-random-uuid from @mvdbeek
  • query monthly-jobs-by-new-multiday-users @afgane
  • query users-engaged-multiday @afgane
  • query monthly-jobs-by-new-users @afgane
• Updated:
  • query monthly-cpu-stats to add --nb_users --filter_email by @lldelisle
  • query monthly-users-active to add YYYY-MM parameter @afgane
  • query monthly-users-registered to add YYYY-MM parameter @afgane
  • query monthly-jobs to add YYYY-MM and --by_state parameters @afgane
  • query total-jobs to add date and --total parameters @afgane
• Fixed:
  • Replaced hardcoded metric_name with the variable in query_tool-metrics function @sanjaysrikakulam
  • improved man pages a tad
  • fixed query monthly-cpu-stats when year was specified

v21

21

• Added:
  • query queue-detail-drm, from @cat-bro and @Slugger70, a better version of queue-details potentially.
  • mutate reassign-active-workflows-to-handler, from @mira-miracoli, as workaround for galaxyproject/galaxy#8209
  • --help-man can now be used in addition to --help on specific query/function commands. It assumes that pandoc is installed, and will render the help instead as a manual page.
  • query large-old-histories, finds old large and probably easily removable histories, @hexylena
  • query potentially-duplicated-datasets, finds duplicate datasets @hexylena
  • query potentially-duplicated-reclaimable-space, finds the potential reclaimable space, @hexylena
  • CGI mode, use sudo fcgiwrap -s unix:/run/cgi.sock -f -p pwd/gxadmin to activate, wrap in nginx, @hexylena
• Updated:
  • Add summary and limit options to tool-metrics query, by @natefoo.
  • Updated the Wonderful Argument Parser with a fancier version, @hexylena
• Fixed:
  • Wonderful Argument Parser arg values could not contain spaces, @natefoo
• Removed:
  • uwsgi series of commands are now completely deprecated, as Galaxy no longer supports uwsgi. If you need these commands, please install an older version of gxadmin.

v20

20

• Fixed:
  • Broken things in preview anonymisation script
  • Unified uwsgi-status command (thanks @gmauro)
  • Unified galaxy user/email/id filtering and made it stricter in what it accepts (#60).
  • Updated "query user-disk-usage" to add a "--use-precalc" flag which uses the value calculated by Galaxy.
  • Enabled GXADMIN_PYTHON from the environment, by @gmauro.
  • Updated "galaxy cleanup" to avoid to set update_time on updated objects, by @gmauro.
  • fixed broken latest-users query
  • fixed broken errored-jobs query, by @gmauro.
  • several fixes in galaxy ie-show command, @gmauro.
  • Generalized the "uwsgi lastlog" function to proper handle journalctl's output, by @gmauro.
  • Updated "query upload-gb-in-past-hour" to include also datasets created by the DATA_FETCH tool, by @gmauro.
• Added:
  • query dump-users, for @shiltemann
  • "did you mean" when a command isn't found.
  • query job-metrics, by @anuprulez and @simonbray.
  • uwsgi active-user count
  • exports PGAPPNAME setting the application name for postgres connections. This becomes visible in pg_stat_activity.
  • mutate set_quota_for_oidc_user, by @gmauro.
  • iquery support for queue-detail query
  • query tool-usage-over-time which can be used to make charts of specific tools over time.
  • improved use of FZF for both the search and 'typo' functions, when it is available.
  • query pulsar-gb-transferred: sums up data in/out (minus collections) of pulsar.
  • mutate fail-misbehaving-gxits: Works aroud a gxit issue.
  • galaxy prune-gxit-routes: Prunes dead routes
  • mutate force-publish-history: Workaround for Galaxy bug #13001
  • report group-info, by @pavanvidem
  • query tool-use-by-group, by @gavindi
  • query job-state-stats, by @gavindi
  • query disk-usage-library, by @gregvonkuster
  • query monthly-workflow-invocations, by @gmauro.
  • query monthly-job-runtimes, by @gregvonkuster
  • query job-state, by @natefoo
  • query largest-dataset-users, by @hexylena
  • query dataset-usage-and-imports, by @hexylena
  • mutate dataset-mark-purged, by @hexylena
• Updated:
  • Add option to include error counts in tool-popularity query, thanks @natefoo
  • Add option to exclude unsuccessful jobs from tool-metrics query, thanks @natefoo

v19

• Fixed:
  • Fixed broken slurping from previous release (Thanks @slugger70 for catching it.)
  • Made changelog updates mandatory so I don't have to ask people for it. Finally.
• Added:
  • encode/decode ID
  • Benchmarking via ASV (preview)
  • anonymise-db-for-release (preview)
  • Add '--by_group' flag to several monthly queries (Thanks @slugger70)
  • query monthly-cpu-stats (Thanks @gmauro)
  • workflow trace archive commands
  • query queue has a new optional parameter for splitting queues by various attributes (Thanks @natefoo)
  • query pg-rows-per-table to find out which tables have data.
  • mutate fail-wfi
  • mutate oidc-by-emails, mutate users affected by galaxyproject/galaxy#9981
  • mutate now supports echo/explain prefixes.
  • very-unsafe flag to most mutate methods, avoiding the transaction.
  • added the wonderful argument parsing for parsing function signatures into arguments automatically, making contribution easier.

v18

gxadmin, now with more features than ever! A large internal refactoring to clean up some of the function discovery and unify it a bit.

Subcommands

Adding a subcommand can now be done with one file + one other change, e.g:

• adding the subcommand
• registering the function

Which should simplify things for other contributors in the future.

Testing

More testing is in process, see the test/ directory. The eventual goal is to have a reference database against which we can run gxadmin.

Changelog

Fixed

• All previous '--nice' flags are rewritten to '--human' (Thanks @lldelisle)
• Update 'user-disk-usage' to support iquery (Thanks @lldelisle)
• Update 'largest-histories' to support iquery (Thanks @lldelisle)
• uwsgi-memory now looks at workflow schedulers
• Exposed bash autocompletion and documented it

Added

• query workers, only works on Galaxy 20.01 or newer and retrieves the hostname and PID of Galaxy worker processes
• '--details' option to query errored-jobs to include the job_stderr column
• query monthly-cpu-stats (Thanks @gmauro!)
• total number of jobs with exit states for galaxxy instance (Thanks @bruggerk)
• query workflow-invocation-totals
• server subcommand exposing previously hidden functions gxadmin meta gxadmin-as-a-service: run gxadmin query as a JSON responding webservice! Now with 100% more microservices.
• query wfi
• query wfq
• query wfsteps
• query wfij
• query wfj

Removed

• filter hexdecodelines, this is now replaced by a built-in postgres function

Changed

• Refactored internal function search to unify local, query, mutate, with the rest.

v17

Release v17

v16

This will be the last release where a compiled gxadmin is in the codebase. Future releases will include it only in the github release.

v15

Release v15