Galaxy datatype framework and datatypes
Project description
Overview
The Galaxy models, datatype framework, and datatype implementations.
History
24.1.1 (2024-07-02)
Bug fixes
Enhancements
Enable all-vs-all collection analysis patterns. by @jmchilton in #17366
Visualizing workflow runs with an invocation graph view by @ahmedhamidawan in #17413
Better display of estimated line numbers and add number of columns for tabular by @bernt-matthias in #17492
Enable storage management by object store by @jmchilton in #17500
Set minimal metadata also for empty bed datasets by @wm75 in #17586
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
Outline use of type_annotation_map to fix mypy issues by @jmchilton in #17902
Add email notifications channel by @davelopez in #17914
Enable warn_unused_ignores mypy option by @nsoranzo in #17991
Refactor galaxy.files plugin loading + config handling. by @jmchilton in #18049
Add stronger type annotations in file sources + refactoring by @davelopez in #18050
Add support for additional media types by @arash77 in #18054
Update Python dependencies by @galaxybot in #18063
Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067
Script for deleting userless histories from database + testing + drop unused model testing code by @jdavcs in #18079
Add Net datatype by @martenson in #18080
Empower users to bring their own storage and file sources by @jmchilton in #18127
Harden User Object Store and File Source Creation by @jmchilton in #18172
Tighten axt sniffer by @martenson in #18204
More structured indexing for user data objects. by @jmchilton in #18291
Other changes
Chore: remove repetitive words by @tianzedavid in #18076
24.0.3 (2024-06-28)
Bug fixes
Downgrade count lines error to warning by @mvdbeek in #18175
Don’t set dataset peek for errored jobs by @mvdbeek in #18231
Transparently open compressed files in DatasetDataProvider by @mvdbeek in #18248
Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249
Set page importable to false when serializing by @mvdbeek in #18263
Do not copy purged outputs to object store by @mvdbeek in #18342
Fix user’s private role can be missing by @davelopez in #18381
Assign default data extension on discovered collection output by @mvdbeek in #18389
Other changes
24.0.2 (2024-05-07)
No recorded changes since last release
24.0.1 (2024-05-02)
Bug fixes
Always serialize element_count and populated when listing contents by @mvdbeek in #17890
Fix deadlock that can occur when changing job state by @mvdbeek in #17896
Fix tool form building if select filters from unavailable dataset metadata by @mvdbeek in #17930
Fix InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands. by @mvdbeek in #17932
Never fail dataset serialization if display_peek fails by @mvdbeek in #17937
Fix output datatype when uncompressing a dataset with incorrect datatype by @nsoranzo in #17944
Use or copy StoredWorkflow when copying step by @mvdbeek in #17988
Raise MessageException when report references invalid workflow output by @mvdbeek in #18009
Fix History Dataset Association creation so that hid is always set by @mvdbeek in #18036
Fix history export with missing dataset hids by @davelopez in #18052
Fix comments lost on import by @ElectronicBlueberry in #18060
Fix history update time after bulk operation by @davelopez in #18068
24.0.0 (2024-04-02)
Bug fixes
Fix for converter tests by @bernt-matthias in #17188
correct dbkey for minerva display app by @hexylena in #17196
Fix invocation serialization if no state was set by @mvdbeek in #17278
Fix quotas ID encoding by @davelopez in #17335
Fix model store exports that include implicit conversions. by @jmchilton in #17346
Fix bug: create new PSAAssociation if not in database by @jdavcs in #17516
Fix ancient bug: incorrect usage of func.coalesce in User model by @jdavcs in #17577
Account for newlines in CIF Datatype sniffer by @patrick-austin in #17582
Anticipate PendingRollbackError in check_database_connection by @mvdbeek in #17598
Add basic model import attribute validation by @mvdbeek in #17628
More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632
Npz sniffing: do not read the whole file by @bernt-matthias in #17672
Assert that at least one file in npz zipfile ends with .npy by @mvdbeek in #17679
Workflow Comment Indexing by @ElectronicBlueberry in #17700
Fix source history update_time being updated when importing a public history by @jmchilton in #17728
Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777
Defer job attributes that are usually not needed by @mvdbeek in #17795
Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803
Minor refactor of query building logic for readability by @jdavcs in #17835
Fix user login when duplicate UserRoleAssociation exists by @mvdbeek in #17854
Enhancements
Make columns types an empty list for empty tabular data by @bernt-matthias in #13918
port invocation API to fastapi by @martenson in #16707
Expose more tool information / navigability in UI. by @jmchilton in #17105
Add support for (fast5.tar).xz binary compressed files by @tuncK in #17106
SA2.0 updates: handling “object is being merged into a Session along the backref cascade path” by @jdavcs in #17122
Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132
Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in #17153
Much simpler default dataset permissions for typical users. by @jmchilton in #17166
Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222
API endpoint that allows “changing” the objectstore for “safe” scenarios. by @jmchilton in #17329
Fix type annotation of code using XML etree by @nsoranzo in #17367
Add explicit cache_ok attribute to JSONType subclass by @mvdbeek in #17376
More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381
Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435
UI for “relocating” a dataset to a new object store (when safe) by @jmchilton in #17437
Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460
Faster FASTA and FASTQ metadata setting by @bernt-matthias in #17462
Feature SBOL datatypes by @guillaume-gricourt in #17482
Display workflow invocation counts. by @jmchilton in #17488
add npy datatype by @astrovsky01 in #17517
Enhance Avivator display app to support regular Tiffs by @davelopez in #17554
Update Python dependencies by @galaxybot in #17580
Add migrations revision identifier for 24.0 by @jdavcs in #17589
23.2.1 (2024-02-21)
Bug fixes
Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in #16553
MINERVA display application: enable cors, add for tabular by @hexylena in #16737
Fix cardinality violation error: subquery returns multiple results by @jdavcs in #17224
Fix Display Application link generation by @mvdbeek in #17227
Set metadata states on dataset association, not dataset by @mvdbeek in #17474
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
Display beginning of non-text files as text instead of triggering a download by @SergeyYakubov in #15447
Tool Shed 2.0 by @jmchilton in #15639
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 #16409
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
Implement datatype upload warnings by @jmchilton in #16564
Support new genome browser chain file format by @claudiofr in #16576
Workflow Comments 💬 by @ElectronicBlueberry in #16612
Bump samtools converters by @bernt-matthias in #16668
Misc. edits/refactorings to session handling by @jdavcs in #16712
Migrate collection elements store to Pinia by @davelopez in #16725
Optimize iteration in DatasetInstance model + SA2.0 fix by @jdavcs in #16776
Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778
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
Allow partial matches in workflow name tag search and search all tags for unquoted query by @ahmedhamidawan in #16860
Fix invocation report to target correct workflow version. by @jmchilton in #17008
optimize object store cache operations by @SergeyYakubov in #17025
Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342
Add magres datatype by @martenson in #17499
Other changes
23.1.4 (2024-01-04)
Bug fixes
Other changes
23.1.3 (2023-12-01)
Bug fixes
23.1.2 (2023-11-29)
Bug fixes
Skip change_datatype things if we’re not actually changing the extension by @mvdbeek in #16931
Fix copying metadata to copied job outputs by @mvdbeek in #17007
Assert that DatasetCollectioElement has an associated object by @mvdbeek in #17071
Fix input dates in notifications: consider timezone offset by @davelopez in #17088
Allow relative URLs in broadcasts action links by @davelopez in #17093
Enhancements
Add support for larch datatypes by @patrick-austin in #17080
23.1.1 (2023-10-23)
Bug fixes
Fix bad auto-merge of dev. by @jmchilton in #15386
Merge conflicting db migration branches into one by @jdavcs in #15771
Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811
Fix anonymous user uploads when vault is configured by @tchaussepiedifb in #15858
Fix nullable deleted column in API Keys table by @davelopez in #15956
Attempt to fix mypy check by @davelopez in #16103
Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207
Update 23.1 release tags for migration scripts by @jdavcs in #16294
Fix tags ownership by @davelopez in #16339
Fix disk usage recalculation for distributed object stores by @mvdbeek in #16380
Fix histories count by @davelopez in #16400
Fix double-encoding notification content by @mvdbeek in #16530
Fixes for conditional subworkflow steps by @mvdbeek in #16632
Copy the collection contents by default when copying a collection by @mvdbeek in #16717
Fix allowlist deserialization in file sources by @mvdbeek in #16729
Fix workflow output display without label by @mvdbeek in #16749
Fix and prevent persisting null file_size by @mvdbeek in #16855
Fix workflow import losing tool_version by @mvdbeek in #16869
Remove more flushes in database operation tools by @mvdbeek in #16875
Fix join condition for nested collection query by @mvdbeek in #16880
Enhancements
Empower Users to Select Storage Destination by @jmchilton in #14073
Add Storage Dashboard visualizations for histories by @davelopez in #14820
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
Update Python dependencies by @galaxybot in #15564
Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in #15633
Add Galaxy Notification System by @davelopez in #15663
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
Update Python dependencies by @galaxybot in #15890
FITS data format by @volodymyrss in #15905
Improve display chunk generation for BAMs by @wm75 in #15972
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
Dataset chunking tests (and small fixes) by @jmchilton in #16069
Add create_foreign_key migration utility by @jdavcs in #16077
Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in #16080
Use automated naming convention to generate indexes and constraints in database by @jdavcs in #16089
Add zipped mongodb and genenotebook datatypes by @abretaud in #16173
Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198
bring grids for (published) pages on par with workflows by @martenson in #16209
Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in #16255
Filter deleted keys from api_keys relationship by @dannon in #16321
Increase CustosAuthnzToken.external_user_id column size by @davelopez in #16818
Other changes
Follow up on object store selection PR. by @jmchilton in #15654
Fix Enums in API docs by @davelopez in #15740
merge release_23.0 into dev by @martenson in #15830
backport of pysam tostring by @martenson in #16822
23.0.6 (2023-10-23)
Bug fixes
23.0.5 (2023-07-29)
Bug fixes
23.0.4 (2023-06-30)
No recorded changes since last release
23.0.3 (2023-06-26)
No recorded changes since last release
23.0.2 (2023-06-13)
No recorded changes since last release
23.0.1 (2023-06-08)
Bug fixes
Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744
Fix RO-crate invocation export with complex collections by @davelopez in #15971
Backport Improve display chunk generation for BAMs by @mvdbeek in #16007
Ensure history export contains all expected datasets by @davelopez in #16013
Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099
Fix extended metadata file size handling by @mvdbeek in #16109
Fix implicit converters with optional parameters by @mvdbeek in #16133
Make ctx_rev optional in InstalledToolShedRepository response model by @dannon in #16139
Fix optional fields being validated as missing in ts api by @jmchilton in #16141
Verify existence of default value attribute for user forms fields by @guerler in #16205
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.
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