Package Health Score

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popularity
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maintenance
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Active

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Popularity

Small

GitHub Stars: 1.42K
Forks: 1.01K
Contributors: 270

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Based on project statistics from the GitHub repository for the PyPI package galaxy-app, we found that it has been starred 1,415 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Dec 11, 2024
Direct Vulnerabilities: 0
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L
Indirect Vulnerabilities: 0
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License Risk: 0
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All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

AFL-3.0

Security Policy

Yes

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Maintenance

Healthy

Commit Frequency

Open Issues: 2.11K
Open PR: 249
Last Release: 7 days ago
Last Commit: 27 days ago

Further analysis of the maintenance status of galaxy-app based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that galaxy-app demonstrates a positive version release cadence with at least one new version released in the past 3 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 270
Funding: No

A good and healthy external contribution signal for galaxy-app project, which invites more than one hundred open source maintainers to collaborate on the repository.

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Package

Python Versions Compatibility: >=3.8

Age: 4 years
Latest Release: 7 days ago
Dependencies: 33 Direct
Versions: 24
Maintainers: 0
Wheels: OS Independent

Readme

Overview

The Galaxy application logic (backend).

Code:

History

24.1.4 (2024-12-11)

Bug fixes

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428
Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434
Fix dropped when_expression on step upgrade by @mvdbeek in #18446
Improve workflow-related exception reporting by @mvdbeek in #18447
Fix subwofklow tags serialization type by @arash77 in #18456
by @laperlej in #18459
Add input extra files to get_input_fnames by @mvdbeek in #18462
Return generic message for password reset email by @ahmedhamidawan in #18479
Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
Don't call job_runner.stop_job on jobs in new state by @mvdbeek in #18495
Prevent job submission if input collection element is deleted by @mvdbeek in #18517
Strip unicode null from tool stdio by @mvdbeek in #18527
Fix map over calculation for runtime inputs by @mvdbeek in #18535
Fix for not-null in 'column_list' object by @hujambo-dunia in #18553
Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
Set minimum weasyprint version by @mvdbeek in #18606
Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
Make sure we set file size also for purged outputs by @mvdbeek in #18681
File source and object store instance api fixes by @mvdbeek in #18685
Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
Fill in missing help for cross product tools. by @jmchilton in #18698
Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
Fix directory get or create logic by @mvdbeek in #18752
Fix job summary for optional unset job data inputs by @mvdbeek in #18754
Allow to change only the description of a quota by @bernt-matthias in #18775
Fix wrong extension on pick data output by @mvdbeek in #18798
Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
Fix named cursor is not valid anymore by @mvdbeek in #18825
Tighten TRS url check by @mvdbeek in #18841
Fix Workflow index bookmark filter by @itisAliRH in #18842
Skip metric collection if job working directory doesn't exist by @mvdbeek in #18845
Extend on disk checks to running, queued and error states by @mvdbeek in #18846
Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
Fix data_column ref to nested collection by @mvdbeek in #18875
Fix loading very old workflows with data inputs by @mvdbeek in #18876
Access tool data table filters in workflow building mode by @mvdbeek in #18900
Fix username used in invocation report by @mvdbeek in #18932
Disable locking when opening h5 files, add missing with by @mvdbeek in #18976
Fix job search statement building by @mvdbeek in #19010
Put cached jobs back into queue on handler restart by @mvdbeek in #19012
Fix various invocation export issues by @mvdbeek in #19215
Create harmonized collections from correct tool outputs by @wm75 in #19222

Enhancements

Include workflow invocation id in exception logs by @mvdbeek in #18594
Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
Collect job metrics also when job failed by @mvdbeek in #18809
prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

24.1.3 (2024-10-25)

Bug fixes

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428
Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434
Fix dropped when_expression on step upgrade by @mvdbeek in #18446
Improve workflow-related exception reporting by @mvdbeek in #18447
Fix subwofklow tags serialization type by @arash77 in #18456
by @laperlej in #18459
Add input extra files to get_input_fnames by @mvdbeek in #18462
Return generic message for password reset email by @ahmedhamidawan in #18479
Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
Prevent job submission if input collection element is deleted by @mvdbeek in #18517
Strip unicode null from tool stdio by @mvdbeek in #18527
Fix map over calculation for runtime inputs by @mvdbeek in #18535
Fix for not-null in 'column_list' object by @hujambo-dunia in #18553
Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
Set minimum weasyprint version by @mvdbeek in #18606
Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
Make sure we set file size also for purged outputs by @mvdbeek in #18681
File source and object store instance api fixes by @mvdbeek in #18685
Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
Fill in missing help for cross product tools. by @jmchilton in #18698
Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
Fix directory get or create logic by @mvdbeek in #18752
Fix job summary for optional unset job data inputs by @mvdbeek in #18754
Allow to change only the description of a quota by @bernt-matthias in #18775
Fix wrong extension on pick data output by @mvdbeek in #18798
Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
Fix named cursor is not valid anymore by @mvdbeek in #18825
Tighten TRS url check by @mvdbeek in #18841
Fix Workflow index bookmark filter by @itisAliRH in #18842
Skip metric collection if job working directory doesn't exist by @mvdbeek in #18845
Extend on disk checks to running, queued and error states by @mvdbeek in #18846
Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
Fix data_column ref to nested collection by @mvdbeek in #18875
Fix loading very old workflows with data inputs by @mvdbeek in #18876
Access tool data table filters in workflow building mode by @mvdbeek in #18900
Fix username used in invocation report by @mvdbeek in #18932
Disable locking when opening h5 files, add missing with by @mvdbeek in #18976
Fix job search statement building by @mvdbeek in #19010
Put cached jobs back into queue on handler restart by @mvdbeek in #19012

Enhancements

Include workflow invocation id in exception logs by @mvdbeek in #18594
Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
Collect job metrics also when job failed by @mvdbeek in #18809
prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

24.1.2 (2024-09-25)

Bug fixes

Return generic message for password reset email by @ahmedhamidawan in #18479
Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
Prevent job submission if input collection element is deleted by @mvdbeek in #18517
Strip unicode null from tool stdio by @mvdbeek in #18527
Fix map over calculation for runtime inputs by @mvdbeek in #18535
Fix for not-null in 'column_list' object by @hujambo-dunia in #18553
Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
Set minimum weasyprint version by @mvdbeek in #18606
Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
Make sure we set file size also for purged outputs by @mvdbeek in #18681
File source and object store instance api fixes by @mvdbeek in #18685
Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
Fill in missing help for cross product tools. by @jmchilton in #18698
Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
Fix directory get or create logic by @mvdbeek in #18752
Fix job summary for optional unset job data inputs by @mvdbeek in #18754
Allow to change only the description of a quota by @bernt-matthias in #18775
Fix wrong extension on pick data output by @mvdbeek in #18798
Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
Fix named cursor is not valid anymore by @mvdbeek in #18825
Tighten TRS url check by @mvdbeek in #18841
Fix Workflow index bookmark filter by @itisAliRH in #18842
Skip metric collection if job working directory doesn't exist by @mvdbeek in #18845
Extend on disk checks to running, queued and error states by @mvdbeek in #18846
Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
Fix data_column ref to nested collection by @mvdbeek in #18875
Fix loading very old workflows with data inputs by @mvdbeek in #18876

Enhancements

Include workflow invocation id in exception logs by @mvdbeek in #18594
Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
Collect job metrics also when job failed by @mvdbeek in #18809
prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

24.1.1 (2024-07-02)

Bug fixes

Unpin social-auth-core dependency by @nsoranzo in #17607
Dynamic tool fixes by @dcore94 in #18085
Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106
Revert some requests import changes by @nsoranzo in #18199
Small bug fixes for user data plugins by @jmchilton in #18246
Fix handler: access to result row items changed in SA2.0 by @jdavcs in #18274
Fix various packages' issues by @nsoranzo in #18301
Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in #18305
Fix empty usernames in database + bug in username generation by @jdavcs in #18379
Add TypedDict for JobsSummary by @mvdbeek in #18418
Pin pydantic to >=2.7.4 by @nsoranzo in #18423
Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434
Fix dropped when_expression on step upgrade by @mvdbeek in #18446
Improve workflow-related exception reporting by @mvdbeek in #18447
Fix subwofklow tags serialization type by @arash77 in #18456
Disable password reset for deleted users [GCC2024_COFEST] by @laperlej in #18459
Add input extra files to get_input_fnames by @mvdbeek in #18462

Enhancements

Only include tool stdout/stderr in HDA info by @natefoo in #16730
Adding object store plugin for Rucio by @SergeyYakubov in #17156
Enable all-vs-all collection analysis patterns. by @jmchilton in #17366
Add onedata objectstore by @bwalkowi in #17540
Type annotation improvements by @nsoranzo in #17601
Type annotation and CWL-related improvements by @nsoranzo in #17630
Update Python dependencies by @galaxybot in #17653
Code cleanups from ruff and pyupgrade by @nsoranzo in #17654
Update Python dependencies by @galaxybot in #17764
SQLAlchemy 2.0 by @jdavcs in #17778
Update Python dependencies by @galaxybot in #17819
Update Python dependencies by @galaxybot in #17870
Add email notifications channel by @davelopez in #17914
Model edits and bug fixes by @jdavcs in #17922
Update Python dependencies by @galaxybot in #17923
Model typing and SA2.0 follow-up by @jdavcs in #17958
Error reporting unit tests by @jmchilton in #17968
Make urgent notifications mandatory by @davelopez in #17975
Update Python dependencies by @galaxybot in #17982
Enable warn_unused_ignores mypy option by @nsoranzo in #17991
Add galaxy to user agent by @mvdbeek in #18003
Add Zenodo integration by @davelopez in #18022
Update Python dependencies by @galaxybot in #18035
Add stronger type annotations in file sources + refactoring by @davelopez in #18050
Add pagination support to Files Source plugins by @davelopez in #18059
Update Python dependencies by @galaxybot in #18063
Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067
Ensure history update_time is set when exporting by @davelopez in #18086
Overhaul Azure storage infrastructure. by @jmchilton in #18087
Update Python dependencies by @galaxybot in #18095
Update Python dependencies by @galaxybot in #18125
Revises handling of warnings in the workflow run form by @guerler in #18126
Empower users to bring their own storage and file sources by @jmchilton in #18127
Update s3fs dependency. by @jmchilton in #18135
More unit testing for object store stuff. by @jmchilton in #18136
Harden User Object Store and File Source Creation by @jmchilton in #18172
Fix boto3-stubs typecheck dependency by @nsoranzo in #18173
More structured indexing for user data objects. by @jmchilton in #18291
Onedada object store and files source stability fixes by @bwalkowi in #18372
Allow running and editing workflows for specific versions by @ahmedhamidawan in #18378

Other changes

Chore: remove repetitive words by @tianzedavid in #18076
Fix #18316 (anonymous file sources) by @jmchilton in #18352
Merge 24.0 into 24.1 by @jdavcs in #18353
Merge 24.0 into 24.1 by @jdavcs in #18365

24.0.3 (2024-06-28)

Bug fixes

Raise exception if collection elements missing during download by @jdavcs in #18094
Allow purge query param, deprecate purge body param by @mvdbeek in #18105
Backport OIDC schema fix by @mvdbeek in #18111
Don't log exception if cancelled slurm job doesn't have stderr file by @mvdbeek in #18121
Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123
Fix data default values not getting added to history by @mvdbeek in #18132
Drop redundant error message by @mvdbeek in #18156
Emit warning when user-cancelled job already complete by @mvdbeek in #18178
Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190
Add string cast for dbkey / genome_build by @mvdbeek in #18207
Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214
Don't set dataset peek for errored jobs by @mvdbeek in #18231
Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249
Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250
Don't attempt to download purged datasets by @mvdbeek in #18278
Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283
Don't serialize display application links for deleted datasets by @mvdbeek in #18307
Downgrade doi fetch error to debug by @mvdbeek in #18330
Fix authentication error for anonymous users querying jobs by @davelopez in #18333
Fix seek in slurm memory check by @mvdbeek in #18338
Do not copy purged outputs to object store by @mvdbeek in #18342
Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348
Allow DCE as outer input to to_cwl by @mvdbeek in #18349
Fix anonymous user job retrieval logic by @davelopez in #18358
Fix update group API payload model by @davelopez in #18374
Fix user's private role can be missing by @davelopez in #18381
Fix null inputs in database operation tools by @mvdbeek in #18385
Assign default data extension on discovered collection output by @mvdbeek in #18389
Fix get_accessible_job if called without session by @mvdbeek in #18400
Fix invocation step_job_summary for new collections by @mvdbeek in #18402
Really allow in-range validator for txt by @bernt-matthias in #18411
Fix collection map over status for dragged collections by @mvdbeek in #18416
Serialize purged flag for datasets in collections by @davelopez in #18420

Other changes

Minor linting cleanup by @mvdbeek in #18421
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

24.0.2 (2024-05-07)

Bug fixes

Adds logging of messageExceptions in the fastapi exception handler. by @dannon in #18041
Improve error message for Extract dataset tool by @mvdbeek in #18078

24.0.1 (2024-05-02)

Bug fixes

Fix tool version switch in editor by @mvdbeek in #17858
Fix workflow run form failing on certain histories by @mvdbeek in #17869
Always serialize element_count and populated when listing contents by @mvdbeek in #17890
Fix saving workflows with freehand_comments only by @mvdbeek in #17901
Always discard session after __handle_waiting_jobs is done by @mvdbeek in #17913
Fix workflow run form for workflows with null rename PJA by @mvdbeek in #17929
Revert unnecessary error change by @mvdbeek in #17948
Fix missing implicit conversion for mapped over jobs by @mvdbeek in #17952
Fix get_content_as_text for compressed text datatypes by @mvdbeek in #17976
Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in #17981
Fix LengthValidator if no value passed by @mvdbeek in #17983
Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in #17985
Don't attempt to commit in dry_run mode by @mvdbeek in #17987
Don't fail if reporting invalid parameter values by @mvdbeek in #18002
Include exception info when something goes wrong while refreshing tokens by @mvdbeek in #18008
Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in #18011
Don't commit without having set a hid by @mvdbeek in #18014
Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in #18023
Fix tag regex pattern by @jdavcs in #18025
Fix History Dataset Association creation so that hid is always set by @mvdbeek in #18036
Change wrong quota_source value from KeyError to ValueError by @mvdbeek in #18040
Check database connection to issue a rollback if no connection by @jdavcs in #18070

Enhancements

Fix remote files sources error handling by @davelopez in #18027

Other changes

Drop left-over debug statement by @mvdbeek in #17939

24.0.0 (2024-04-02)

Bug fixes

Reload built-in converters on toolbox reload by @bernt-matthias in #17209
Optional Reply-to SMTP header in tool error reports by @neoformit in #17243
Package tests fixes by @nsoranzo in #17301
Follow-up on #17274 and #17262 by @nsoranzo in #17302
Rollback invalidated transaction: catch them earlier by @jdavcs in #17312
Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340
Fix data_source and data_source_async bugs by @wm75 in #17422
More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632
Don't index tasks without task_uuid by @mvdbeek in #17646
Separate ConnectedValue from RuntimeValue by @mvdbeek in #17678
Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in #17716
Fix usage of DISTINCT by @jdavcs in #17759
Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777
Use hg clone --stream to clone repos by @mvdbeek in #17786
Defer job attributes that are usually not needed by @mvdbeek in #17795
Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803
Fix archived histories mixing with active in histories list by @davelopez in #17856
Normalize extensions when loading tool by @mvdbeek in #17868
Ignore user data table errors for now by @mvdbeek in #17880

Enhancements

Add harmonize collections tool (or whatever other name) by @lldelisle in #16662
Add support for Python 3.12 by @tuncK in #16796
SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932
Python 3.8 as minimum by @mr-c in #16954
Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977
Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979
Extend regex groups in stdio regex matches by @bernt-matthias in #17016
Vueify Admin User Grid by @guerler in #17030
Remove web framework dependency from tools by @davelopez in #17058
Add select parameter with options from remote resources by @mvdbeek in #17087
Expose more tool information / navigability in UI. by @jmchilton in #17105
Vueify Admin Roles Grid by @guerler in #17118
SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by @jdavcs in #17122
Update Python dependencies by @galaxybot in #17123
Vueify Admin Groups Grid by @guerler in #17126
Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132
Vueify Admin Forms and Quota grids by @guerler in #17141
Update Python dependencies by @galaxybot in #17157
Update Python dependencies by @galaxybot in #17201
Vendorize fastapi-utls.cbv by @jdavcs in #17205
Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216
Vueifiy History Grids by @guerler in #17219
Update Python dependencies by @galaxybot in #17230
Update Python dependencies by @galaxybot in #17235
Allow job files to consume TUS uploads by @jmchilton in #17242
Update Python dependencies by @galaxybot in #17247
Migrate models to pydantic 2 by @mvdbeek in #17262
Consider Null inputs by @bernt-matthias in #17271
Add OIDC backend configuration schema and validation by @uwwint in #17274
Adds delete, purge and undelete batch operations to History Grid by @guerler in #17282
Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294
Improve ModelManager type hints by @mvdbeek in #17299
API endpoint that allows "changing" the objectstore for "safe" scenarios. by @jmchilton in #17329
Update Python dependencies by @galaxybot in #17333
Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357
Remove unused statements in job search function by @mvdbeek in #17361
Enable warn_unreachable mypy option by @mvdbeek in #17365
Fix type annotation of code using XML etree by @nsoranzo in #17367
More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381
Cancel all active jobs when the user is deleted by @davelopez in #17390
Update to black 2024 stable style by @nsoranzo in #17391
Purge groups and roles from DB (for real) by @davelopez in #17411
Update Python dependencies by @galaxybot in #17420
Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435
Adds published histories to grid list by @guerler in #17449
Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460
data_column parameter: use column_names metadata if present by @bernt-matthias in #17478
Update Python dependencies by @galaxybot in #17486
Consolidate resource grids into tab views by @guerler in #17487
Update k8s docker python to 3.12 by @nuwang in #17494
add encode ID API endpoint by @mira-miracoli in #17510
Fixing data_source tools and incrementing tool profile by @wm75 in #17515
Update Python dependencies by @galaxybot in #17541
Add image_diff comparison method for test output verification using images by @kostrykin in #17556
Filter out subworkflow invocations by @mvdbeek in #17558
Update Python dependencies by @galaxybot in #17580
Restore histories API behavior for keys query parameter by @davelopez in #17779
Fix datasets API custom keys encoding by @davelopez in #17793
Improved error messages for runtime sharing problems. by @jmchilton in #17794
Allow admin to sharpen language about selected object stores. by @jmchilton in #17806

Other changes

consistently compare profile versions by @bernt-matthias in #16492

23.2.1 (2024-02-21)

Bug fixes

pin fs.dropboxfs to >=1 by @bernt-matthias in #16451
Remove unnecessary check: item cannot be None by @jdavcs in #16550
Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561
Fix dependency update GitHub workflow by @nsoranzo in #16639
Ensure Job belongs to current SA session by @jdavcs in #16647
Account for shared usage between TS and galaxy apps by @jdavcs in #16746
move the email and username redacting from the role loop by @martenson in #16805
Fix shed unit test by @mvdbeek in #16811
chore: fix typos by @afuetterer in #16851
Fix bug in SQLAlchemy statement by @jdavcs in #16881
Ruff and flake8 fixes by @nsoranzo in #16884
Update help in relabel_from_file.xml by @lldelisle in #16891
Fix subtle bug in listify function + simplify list munging by @jdavcs in #16904
prep for updated h5py and typos by @mr-c in #16963
Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in #17018
Expose file_name property in DatasetFilenameWrapper by @jdavcs in #17107
Fix to_cwl for nested collections by @mvdbeek in #17276
Rollback invalidated transaction by @jdavcs in #17280
Install newer celery on python 3.8+ by @mvdbeek in #17309
Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in #17315
Discard sqlalchemy session after task completion by @mvdbeek in #17317
Scope session for job runner monitor loop by @mvdbeek in #17319
Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in #17384
Update python-multipart to 0.0.7 by @nsoranzo in #17429
Build param dict before creating entrypoint by @mvdbeek in #17440
Fix bug: true >> True by @jdavcs in #17446
Set metadata states on dataset association, not dataset by @mvdbeek in #17474
Remove two print statements by @bernt-matthias in #17480
Provide working routes.url_for every ASGI request by @mvdbeek in #17497

Enhancements

Implement default locations for data and collection parameters. by @jmchilton in #14955
Enable job resubmissions in k8s runner by @pcm32 in #15238
Add parameter name to validation errors by @bernt-matthias in #15440
Tool Shed 2.0 by @jmchilton in #15639
Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825
Limit number of celery task executions per second per user by @claudiofr in #16232
Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in #16252
Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264
Update Python dependencies by @galaxybot in #16305
Add carbon emissions admin configuration options by @Renni771 in #16307
Migrate a part of the users API to Fast API by @heisner-tillman in #16341
Update Python dependencies by @galaxybot in #16360
Add Invenio RDM repository integration by @davelopez in #16381
Update Python dependencies by @galaxybot in #16389
Update Python dependencies by @galaxybot in #16409
Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420
Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431
SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in #16434
Update Python dependencies by @galaxybot in #16436
Update Python dependencies by @galaxybot in #16485
Rename MetadataEqualsValidator by @bernt-matthias in #16489
Add support for CILogon deployments in different regions than the US by @uwwint in #16490
Refactor/OIDC custos by @uwwint in #16497
Update Python dependencies by @galaxybot in #16521
Move database access code out of galaxy.util by @jdavcs in #16526
Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536
Update Python dependencies by @galaxybot in #16577
Vueify Tool Form Data Selector by @guerler in #16578
Workflow Comments 💬 by @ElectronicBlueberry in #16612
Switch out conditional requirement parser by @mvdbeek in #16636
Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642
Bump samtools converters by @bernt-matthias in #16668
Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in #16672
Implement instance URLs in Galaxy markdown. by @jmchilton in #16675
Change Sentry error reporting plug-in by @kysrpex in #16686
Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690
Enhance task monitor composable by @davelopez in #16695
Misc. edits/refactorings to session handling by @jdavcs in #16712
SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in #16724
Update Python dependencies by @galaxybot in #16735
Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in #16758
Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762
Update Python dependencies by @galaxybot in #16770
Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778
Add EGI Check-in as OIDC authentication option by @enolfc in #16782
Replace file_name property with get_file_name function by @SergeyYakubov in #16783
Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in #16795
Galaxy help forum integration by @ElectronicBlueberry in #16798
Update Python dependencies by @galaxybot in #16807
Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in #16833
Remove remaining legacy backbone form input elements by @guerler in #16834
SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in #16852
Update Python dependencies by @galaxybot in #16853
Drop unused HistoryContentManager code and related tests by @jdavcs in #16882
Vueify Visualizations Grid by @guerler in #16892
Update Python dependencies by @galaxybot in #16896
Enable some flake8-logging-format rules in ruff by @nsoranzo in #16915
Remove "Create Workflow" form and allow workflow creation in editor by @ahmedhamidawan in #16938
Update Python dependencies by @galaxybot in #16939
Add helper to get dataset or collection via src and id by @mr-c in #16953
Allow non-optional integer/float params without value attribute by @nsoranzo in #16966
Update Python dependencies by @galaxybot in #16978
Fix invocation report to target correct workflow version. by @jmchilton in #17008
Update Python dependencies by @galaxybot in #17011
Upgrade job manager's index_query method to SA2.0 by @jdavcs in #17020
optimize object store cache operations by @SergeyYakubov in #17025
Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in #17038
Update Python dependencies by @galaxybot in #17050
Migrate groups API to fastAPI by @arash77 in #17051
Migrate ItemTags API to FastAPI by @arash77 in #17064
Update Python dependencies by @galaxybot in #17084
Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342

Other changes

Merge 23.1 into dev by @mvdbeek in #16534
Revert "[23.1] Enable job resubmissions in k8s runner" by @nuwang in #17323
Fix succces typo by @mvdbeek in #17481

23.1.4 (2024-01-04)

Bug fixes

Fix workflow index total matches counting by @davelopez in #17176
Fix url_for in tool error reports by @davelopez in #17210

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

Fix unbound runner variable when there is an error in the job config by @mvdbeek in #16906
Fix discarded dataset ordering in Storage Dashboard by @davelopez in #16929
Include owner's annotation when exporting workflow by @dannon in #16930
Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in #16937
Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961
Prevent workflow submission with missing input values by @mvdbeek in #17048
Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in #17067
Remove rollback from __check_jobs_at_startup by @mvdbeek in #17085

Enhancements

Improve invocation error reporting by @mvdbeek in #16917

23.1.1 (2023-10-23)

Bug fixes

read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in #15596
Fix some drs handling issues by @nuwang in #15777
Fix filesource file url support by @nuwang in #15794
Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811
Change confusing pulsar logs message by @kysrpex in #16038
Fix and test startup with Python 3.11 on macOS by @nsoranzo in #16082
Fix : Ignore error messages for admin created accounts by @jvanbraekel in #16132
Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207
Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by @jdavcs in #16208
Fix ordering of data libraries from API by @martenson in #16300
qualify querying for an api-key by @martenson in #16320
Fix tags ownership by @davelopez in #16339
Job cache fixes for DCEs by @mvdbeek in #16384
Fix histories count by @davelopez in #16400
Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in #16421
Fix up unit tests for local use by @mvdbeek in #16483
Run through tmp_dir_creation_statement only once by @mvdbeek in #16529
Fix double-encoding notification content by @mvdbeek in #16530
Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537
Fix multiple remote test data by @davelopez in #16542
Ignore errors with user-set job resources by @mvdbeek in #16579
Fix replacement parameters for subworkflows. by @jmchilton in #16592
make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in #16594
Bump minimum tpv version to 2.3.2 by @mvdbeek in #16597
Backport tool mem fixes by @mvdbeek in #16601
Reload toolbox after forking when using --preload by @mvdbeek in #16620
Account for expires/expires_in when refreshing token by @mvdbeek in #16621
Fixes for conditional subworkflow steps by @mvdbeek in #16632
Fix nested conditional workflow steps by @mvdbeek in #16641
Ensure Job belongs to current SA session by @mvdbeek in #16655
Fix expression evaluation for nested state by @mvdbeek in #16656
Make sort_collection tool require terminal datasets by @mvdbeek in #16661
Push to object store even if set_meta fails by @mvdbeek in #16667
Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in #16678
Fix regex validation for global inline flags by @mvdbeek in #16683
Fix closed transaction error on galaxy startup/check jobs by @jdavcs in #16687
Add missing join condition in job search by @mvdbeek in #16710
Fix job search query by @mvdbeek in #16714
Copy the collection contents by default when copying a collection by @mvdbeek in #16717
Fix collection id encoding by @davelopez in #16718
Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728
move the email and username redacting from the role loop by @martenson in #16820
Fix parameter display in job info page for tools with sections by @mvdbeek in #16821
Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in #16829
Fix up local tool version handling by @mvdbeek in #16836
Fix and prevent persisting null file_size by @mvdbeek in #16855
Allow referring to steps by label only in markdown editor by @mvdbeek in #16861
Fix safe update version handling in run form by @mvdbeek in #16865
Remove more flushes in database operation tools by @mvdbeek in #16875
Fix tag ownership check by @mvdbeek in #16877

Enhancements

Empower Users to Select Storage Destination by @jmchilton in #14073
External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019
Add slack error reporting plugin by @hexylena in #15025
Various Tool Shed Cleanup by @jmchilton in #15247
Add Storage Management API by @davelopez in #15295
OIDC tokens by @SergeyYakubov in #15300
Expose additional beaker caching backends by @claudiofr in #15349
Add support for visualizing HDF5 datasets. by @jarrah42 in #15394
Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421
Update Python dependencies by @galaxybot in #15435
Fix for new style conda packages by @bernt-matthias in #15446
Move database access code out of tool_util by @jdavcs in #15467
Protection against problematic boolean parameters. by @jmchilton in #15493
Use connection instead of session for ItemGrabber by @jdavcs in #15496
Unify url handling with filesources by @nuwang in #15497
Move TS to Alembic by @jdavcs in #15509
Explore tool remote test data by @davelopez in #15510
Handle "email_from" config option consistently, as per schema description by @jdavcs in #15557
Update Python dependencies by @galaxybot in #15564
Drop workflow exports to myexperiment.org by @dannon in #15576
Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628
Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643
Add Galaxy Notification System by @davelopez in #15663
Unpin Beaker requirement by @nsoranzo in #15665
Add transactional state to JobHandlerStopQueue by @jdavcs in #15671
Verify that activation and reset emails are properly generated by @guerler in #15681
Add transactional state to workflow scheduling manager by @jdavcs in #15683
Remove DELETED_NEW job state from code base by @jdavcs in #15690
Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786
Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844
Drop use_legacy_history from config by @dannon in #15861
Drop database views by @jdavcs in #15876
Update Python dependencies by @galaxybot in #15890
Allow pending inputs in some collection operation tools by @mvdbeek in #15892
Updated doc and tests for attribute value filter by @tuncK in #15929
Update Python dependencies by @galaxybot in #15942
Record input datasets and collections at full parameter path by @mvdbeek in #15978
Export tool citations configurable message by @minh-biocommons in #15998
Add History Archival feature by @davelopez in #16003
Code cleanups from ruff and pyupgrade by @nsoranzo in #16035
Add missing fields to HistorySummary schema model by @davelopez in #16041
Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058
Add Repository owner field to ToolSearch by @ahmedhamidawan in #16061
Add count support for listing filters by @davelopez in #16075
Update Python dependencies by @galaxybot in #16086
Improved Cache Monitoring for Object Stores by @jmchilton in #16110
Integrate accessibility testing into Selenium testing by @jmchilton in #16122
Update Python dependencies by @galaxybot in #16123
Improve histories and datasets immutability checks by @davelopez in #16143
Update Python dependencies by @galaxybot in #16153
Migrate display applications API to Fast API by @heisner-tillman in #16156
adjust grid sharing indicators by @martenson in #16163
Update Python dependencies by @galaxybot in #16182
Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198
Remove various fallback behaviors by @mvdbeek in #16199
bring grids for (published) pages on par with workflows by @martenson in #16209
Update Python dependencies by @galaxybot in #16227
Update Python dependencies by @galaxybot in #16267
Fix tool remote test data by @davelopez in #16311
Hide conditionally skipped output by @mvdbeek in #16356
Fix Storage Dashboard missing archived histories by @davelopez in #16473
Bump bx-python to 0.10.0 by @mvdbeek in #16484
Drop expunge_all() call in WebTransactionRequest by @mvdbeek in #16606

Other changes

Follow up on object store selection PR. by @jmchilton in #15654
merge release_23.0 into dev by @martenson in #15830
Move axe-selenium-python to dev dependencies by @nsoranzo in #16162
Bump msal version by @mvdbeek in #16285
Fix error_reports linting by @mvdbeek in #16465

23.0.6 (2023-10-23)

Bug fixes

Fix upload paramfile handling (for real user setups) by @bernt-matthias in #16504
Fix extra files path handling by @mvdbeek in #16541
Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569
Fix conditional step evaluation with datasets in repeats by @mvdbeek in #16584
Don't read request body into memory by @mvdbeek in #16585
Fixes for extra files handling and cached object stores by @mvdbeek in #16595
Lazy load tool data tables in celery worker by @mvdbeek in #16640
Force __DUPLICATE_FILE_TO_COLLECTION__ 'size' param to integer by @simonbray in #16659

Enhancements

Update pulsar client library to 0.15.5 by @mvdbeek in #16701

23.0.5 (2023-07-29)

Bug fixes

Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by @bernt-matthias in #16403
Fix test discovery in vscode by @mvdbeek in #16413
Fixes for (gitlab) error reporting by @bernt-matthias in #16424

23.0.4 (2023-06-30)

Bug fixes

Fix default when statement evaluation by @mvdbeek in #16332
Redact private role name and description when purging user by @mvdbeek in #16349

23.0.3 (2023-06-26)

Bug fixes

Bump galaxy-release-util version to 0.1.2 by @mvdbeek in #16241

Enhancements

When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

Other changes

Forward port of slugify username received from oidc by @nuwang in #16271

23.0.2 (2023-06-13)

Bug fixes

Fix Text File Busy errors at the source by @mvdbeek in #16212

Enhancements

Point release deps fixes and docs by @mvdbeek in #16214
Use galaxy-release-util to upload python packages by @mvdbeek in #16240

23.0.1 (2023-06-08)

Bug fixes

Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744
Fix mixed outputs_to_working_directory pulsar destinations by @mvdbeek in #15927
Update Gravity to 1.0.3 by @natefoo in #15939
Various fixes to path prefix handling by @mvdbeek in #16033
Fix case sensitive filtering by name in histories by @davelopez in #16036
Fix gcsfs test discovery by @mvdbeek in #16039
Replace httpbin service with pytest-httpserver by @mvdbeek in #16042
Update pulsar to 0.15.2 by @mvdbeek in #16050
Anonymous User tool link bug fix by @ahmedhamidawan in #16065
Fix BCO export by updating gxformat2 by @mvdbeek in #16081
Fix job failure handling when condor indicates job failure by @mvdbeek in #16096
Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099
Extract HDA for code_file validate_input hook by @mvdbeek in #16120
Fix sort error when re-running job with DCE collection input by @mvdbeek in #16126
Fix related-hid in bulk contents API by @mvdbeek in #16128
Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in #16137
Tool warnings can either be None or a Dictionary but not a String by @guerler in #16183
Pin minimum tpv version by @mvdbeek in #16201

Other changes

Startup fix when tool removed between reboot by @mvdbeek in #16175

20.9.0 (2020-10-15)

First release from the 20.09 branch of Galaxy.

20.5.0 (2020-07-04)

First release from the 20.05 branch of Galaxy.

FAQs

What is galaxy-app?

Galaxy application (backend). Visit Snyk Advisor to see a full health score report for galaxy-app, including popularity, security, maintenance & community analysis.

Is galaxy-app popular?

The python package galaxy-app receives a total of 411 weekly downloads. As such, galaxy-app popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is galaxy-app well maintained?

We found that galaxy-app demonstrated a healthy version release cadence and project activity. It has a community of 270 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is galaxy-app safe to use?

The python package galaxy-app was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 18 December-2024, at 23:04 (UTC).

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Overview

History

24.1.4 (2024-12-11)

Bug fixes

Enhancements

24.1.3 (2024-10-25)

Bug fixes

Enhancements

24.1.2 (2024-09-25)

Bug fixes

Enhancements

24.1.1 (2024-07-02)

Bug fixes

Enhancements

Other changes

24.0.3 (2024-06-28)

Bug fixes

Other changes

24.0.2 (2024-05-07)

Bug fixes

24.0.1 (2024-05-02)

Bug fixes

Enhancements

Other changes

24.0.0 (2024-04-02)

Bug fixes

Enhancements

Other changes

23.2.1 (2024-02-21)

Bug fixes

Enhancements

Other changes

23.1.4 (2024-01-04)

Bug fixes

23.1.3 (2023-12-01)

23.1.2 (2023-11-29)

Bug fixes

Enhancements

23.1.1 (2023-10-23)

Bug fixes

Enhancements

Other changes

23.0.6 (2023-10-23)

Bug fixes

Enhancements

23.0.5 (2023-07-29)

Bug fixes

23.0.4 (2023-06-30)

Bug fixes

23.0.3 (2023-06-26)

Bug fixes

Enhancements

Other changes

23.0.2 (2023-06-13)

Bug fixes

Enhancements

23.0.1 (2023-06-08)

Bug fixes

Other changes

20.9.0 (2020-10-15)

20.5.0 (2020-07-04)

galaxy-app dependencies

FAQs

What is galaxy-app?

Is galaxy-app popular?

Is galaxy-app well maintained?

Is galaxy-app safe to use?

Build a secure application checklist

Select a recommended open source package

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