Package: galaxy-data
OverviewTheGalaxymodels, datatype framework, and datatype implementations.Code:https://github.com/galaxyproject/galaxyHistory23.2.1 (2024-02-21)Bug fixesRename to_dict to populate in FormDefintion to fix bug by@jdavcsin#16553MINERVA display application: enable cors, add for tabular by@hexylenain#16737Use AlignedSegment.to_string by@mvdbeekin#16803Ruff and flake8 fixes by@nsoranzoin#16884prep for updated h5py and typos by@mr-cin#16963Fix cardinality violation error: subquery returns multiple results by@jdavcsin#17224Fix Display Application link generation by@mvdbeekin#17227Display application fixes and tests by@mvdbeekin#17233Rollback invalidated transaction by@jdavcsin#17280Set metadata states on dataset association, not dataset by@mvdbeekin#17474Provide working routes.url_for every ASGI request by@mvdbeekin#17497EnhancementsImplement default locations for data and collection parameters. by@jmchiltonin#14955Display beginning of non-text files as text instead of triggering a download by@SergeyYakubovin#15447Tool Shed 2.0 by@jmchiltonin#15639Limit number of celery task executions per second per user by@claudiofrin#16232Delete non-terminal jobs and subworkflow invocations when cancelling invocation by@mvdbeekin#16252Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by@jdavcsin#16264Update Python dependencies by@galaxybotin#16409Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by@jdavcsin#16431SQLAlchemy 2.0 upgrades to ORM usage in /lib by@jdavcsin#16434Update Python dependencies by@galaxybotin#16436Implement datatype upload warnings by@jmchiltonin#16564Support new genome browser chain file format by@claudiofrin#16576Workflow Comments 💬 by@ElectronicBlueberryin#16612Bump samtools converters by@bernt-matthiasin#16668Misc. edits/refactorings to session handling  by@jdavcsin#16712SQLAlchemy 2.0 upgrades (part 2) by@jdavcsin#16724Migratecollection elementsstore to Pinia by@davelopezin#16725Reset autocommit to False by@jdavcsin#16745Drop legacy server-side search by@jdavcsin#16755Optimize iteration in DatasetInstance model + SA2.0 fix by@jdavcsin#16776Migrate a part of the jobs API to Fast API by@heisner-tillmanin#16778Replace file_name property with get_file_name function by@SergeyYakubovin#16783Updated 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@sveinuguin#16795Allow partial matches in workflow name tag search and search all tags for unquoted query by@ahmedhamidawanin#16860Vueify Visualizations Grid by@guerlerin#16892Standardize to W3C naming for color. by@dannonin#16949Move and re-use persist_extra_files by@mvdbeekin#16955Fix invocation report to target correct workflow version. by@jmchiltonin#17008optimize object store cache operations by@SergeyYakubovin#17025Use python-isal for fast zip deflate compression in rocrate export by@mvdbeekin#17342Add magres datatype by@martensonin#17499Other changesMerge 23.1 into dev by@mvdbeekin#16534Merge release_23.1 into dev by@mvdbeekin#16768Create db head merge revision. by@dannonin#16838merge release_23.1 into dev by@martensonin#16933Minor clarification/typo fix in datatypes.data by@dannonin#16993Fix.file_nameaccess in merge forward by@mvdbeekin#17097Backport model store fixes by@mvdbeekin#17439Fix succces typo by@mvdbeekin#1748123.1.4 (2024-01-04)Bug fixesFix User.current_galaxy_session by@mvdbeekin#17232Other changesBackport #17188: Fix for converter tests by@mvdbeekin#1723123.1.3 (2023-12-01)Bug fixesAdd missing optional description field, fixes ephemeris data library example by@mvdbeekin#1711623.1.2 (2023-11-29)Bug fixesSkip change_datatype things if we’re not actually changing the extension by@mvdbeekin#16931Fix copying metadata to copied job outputs by@mvdbeekin#17007Update tar_to_directory dependency by@mvdbeekin#17009Assert thatDatasetCollectioElementhas an associated object by@mvdbeekin#17071Fix input dates in notifications: consider timezone offset by@davelopezin#17088Allow relative URLs in broadcasts action links by@davelopezin#17093EnhancementsImprove invocation error reporting by@mvdbeekin#16917Add support for larch datatypes by@patrick-austinin#1708023.1.1 (2023-10-23)Bug fixesFix bad auto-merge of dev. by@jmchiltonin#15386Merge conflicting db migration branches into one by@jdavcsin#15771Enablestrict_equalitymypy option by@nsoranzoin#15808Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by@jdavcsin#15811Fix anonymous user uploads when vault is configured by@tchaussepiedifbin#15858Fix nullable deleted column in API Keys table by@davelopezin#15956Attempt to fix mypy check by@davelopezin#16103Ensure session is request-scoped for legacy endpoints by@jdavcsin#16207Reset autocommit to True (temporarily) by@jdavcsin#16283Update 23.1 release tags for migration scripts by@jdavcsin#16294Fix form builder value handling by@guerlerin#16304Fix tags ownership by@davelopezin#16339Fix disk usage recalculation for distributed object stores by@mvdbeekin#16380Job cache fixes for DCEs by@mvdbeekin#16384Fix histories count by@davelopezin#16400Fix double-encoding notification content by@mvdbeekin#16530Optimize getting current user session by@mvdbeekin#16604Fixes for conditional subworkflow steps by@mvdbeekin#16632Copy the collection contents by default when copying a collection by@mvdbeekin#16717Fix allowlist deserialization in file sources by@mvdbeekin#16729Fix workflow output display without label by@mvdbeekin#16749Fix and prevent persisting null file_size by@mvdbeekin#16855Fix workflow import losing tool_version by@mvdbeekin#16869Remove more flushes in database operation tools by@mvdbeekin#16875Fix join condition for nested collection query by@mvdbeekin#16880EnhancementsEmpower Users to Select Storage Destination by@jmchiltonin#14073Add Storage Dashboard visualizations for histories by@davelopezin#14820Towards decoupling datatypes and model by@jdavcsin#15186Add Storage Management API by@davelopezin#15295OIDC tokens by@SergeyYakubovin#15300Expose additional beaker caching backends  by@claudiofrin#15349Follow up to #15186 by@jdavcsin#15388Add support for visualizing HDF5 datasets. by@jarrah42in#15394Towards SQLAlchemy 2.0: drop session autocommit setting by@jdavcsin#15421Update Python dependencies by@galaxybotin#15435Unify url handling with filesources by@nuwangin#15497Move TS to Alembic by@jdavcsin#15509Update Python dependencies by@galaxybotin#15564Update database_heartbeat for SA 2.0 compatibility by@jdavcsin#15611Update supports_skip_locked, supports_returning for SA 2.0 compatibility by@jdavcsin#15633Add Galaxy Notification System by@davelopezin#15663Drop model mapping unit tests by@jdavcsin#15669Add transactional state to workflow scheduling manager by@jdavcsin#15683Remove DELETED_NEW job state from code base by@jdavcsin#15690Fix/Enhance recalculate disk usage API endpoint by@davelopezin#15739Drop database views by@jdavcsin#15876Update Python dependencies by@galaxybotin#15890FITS data format by@volodymyrssin#15905Improve display chunk generation for BAMs by@wm75in#15972Add History Archival feature by@davelopezin#16003Add alter_column migration utility by@jdavcsin#16009Code cleanups from ruff and pyupgrade by@nsoranzoin#16035Add missing fields to HistorySummary schema model by@davelopezin#16041Dataset chunking tests (and small fixes) by@jmchiltonin#16069Add create_foreign_key migration utility by@jdavcsin#16077Refactor models enums to eliminate schema dependency on model layer. by@jmchiltonin#16080Use automated naming convention to generate indexes and constraints in database by@jdavcsin#16089Add zipped mongodb and genenotebook datatypes by@abretaudin#16173Drop workarounds for old ro-crate-py and docutils versions by@mvdbeekin#16198bring grids for (published) pages on par with workflows by@martensonin#16209Add Visium datatype for squidpy and spatialomics tools by@astrovsky01in#16255Filter deleted keys from api_keys relationship by@dannonin#16321IncreaseCustosAuthnzToken.external_user_idcolumn size by@davelopezin#16818Other changesFollow up on object store selection PR. by@jmchiltonin#15654Fix Enums in API docs by@davelopezin#15740merge release_23.0 into dev by@martensonin#15830Fix linting of FITS datatype code by@mvdbeekin#16169backport of pysam tostring by@martensonin#1682223.0.6 (2023-10-23)Bug fixesFix extra files path handling by@mvdbeekin#16541Don’t fail invocation message without dependent_workflow_step_id by@mvdbeekin#1662823.0.5 (2023-07-29)Bug fixesCopy when_expression when copying workflow step by@mvdbeekin#1637723.0.4 (2023-06-30)No recorded changes since last release23.0.3 (2023-06-26)No recorded changes since last release23.0.2 (2023-06-13)No recorded changes since last release23.0.1 (2023-06-08)Bug fixesDisplay DCE in job parameter component, allow rerunning with DCE input by@mvdbeekin#15744Fix folder listing via file browser by@mvdbeekin#15950Fix RO-crate invocation export with complex collections by@davelopezin#15971Backport Improve display chunk generation for BAMs by@mvdbeekin#16007Ensure history export contains all expected datasets by@davelopezin#16013Various fixes to path prefix handling by@mvdbeekin#16033Fix dataype_change not updating HDCA update_time by@mvdbeekin#16099Fix mypy error due to alembic 1.11.0 by@nsoranzoin#16104Fix extended metadata file size handling by@mvdbeekin#16109Fix implicit converters with optional parameters by@mvdbeekin#16133Makectx_revoptional in InstalledToolShedRepository response model by@dannonin#16139Fix optional fields being validated as missing in ts api by@jmchiltonin#16141Support ro crate 0.8.0 and 0.7.0 by@mvdbeekin#16193Verify existence of default value attribute for user forms fields by@guerlerin#1620520.9.0 (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.