Package: galaxy-app
OverviewTheGalaxyapplication logic (backend).Code:https://github.com/galaxyproject/galaxyHistory23.2.1 (2024-02-21)Bug fixespin fs.dropboxfs to >=1 by@bernt-matthiasin#16451Remove unnecessary check: item cannot be None by@jdavcsin#16550Fix: serializetool_shed_urlsdirectly from the API by@davelopezin#16561Fix dependency update GitHub workflow by@nsoranzoin#16639Ensure Job belongs to current SA session by@jdavcsin#16647Account for shared usage between TS and galaxy apps by@jdavcsin#16746move the email and username redacting from the role loop by@martensonin#16805Fix shed unit test by@mvdbeekin#16811chore: fix typos by@afuettererin#16851Fix bug in SQLAlchemy statement by@jdavcsin#16881Ruff and flake8 fixes by@nsoranzoin#16884Update help in relabel_from_file.xml by@lldelislein#16891Fix subtle bug in listify function + simplify list munging by@jdavcsin#16904prep for updated h5py and typos by@mr-cin#16963Enhancement to Tool Form page, Repeating form fields implement parameter instructions by@hujambo-duniain#17018Expose file_name property in DatasetFilenameWrapper by@jdavcsin#17107Fixto_cwlfor nested collections by@mvdbeekin#17276Rollback invalidated transaction by@jdavcsin#17280Install newer celery on python 3.8+ by@mvdbeekin#17309Backport Rollback invalidated transaction: catch them earlier by@mvdbeekin#17315Discard sqlalchemy session after task completion by@mvdbeekin#17317Scope session for job  runner monitor loop by@mvdbeekin#17319Fix History contentsgenome_buildfilter postgresql bug by@ahmedhamidawanin#17384Update python-multipart to 0.0.7 by@nsoranzoin#17429Build param dict before creating entrypoint by@mvdbeekin#17440Fix bug: true >> True by@jdavcsin#17446Set metadata states on dataset association, not dataset by@mvdbeekin#17474Remove two print statements by@bernt-matthiasin#17480Provide working routes.url_for every ASGI request by@mvdbeekin#17497EnhancementsImplement default locations for data and collection parameters. by@jmchiltonin#14955Enable job resubmissions in k8s runner by@pcm32in#15238Add parameter name to validation errors by@bernt-matthiasin#15440Tool Shed 2.0 by@jmchiltonin#15639Add ability to assert metadata properties on input dataset parameters by@bernt-matthiasin#15825Limit 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#16305Add carbon emissions admin configuration options by@Renni771in#16307Migrate a part of the users API to Fast API by@heisner-tillmanin#16341Update Python dependencies by@galaxybotin#16360Add Invenio RDM repository integration by@davelopezin#16381Update Python dependencies by@galaxybotin#16389Update Python dependencies by@galaxybotin#16409Refactor FilesDialog + Remote Files API schema improvements by@davelopezin#16420Towards 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#16436Update Python dependencies by@galaxybotin#16485Rename MetadataEqualsValidator by@bernt-matthiasin#16489Add support for CILogon deployments in different regions than the US by@uwwintin#16490Refactor/OIDC custos by@uwwintin#16497Update Python dependencies by@galaxybotin#16521Move database access code out ofgalaxy.utilby@jdavcsin#16526Tweak tool memory use and optimize shared memory when using preload by@mvdbeekin#16536Update Python dependencies by@galaxybotin#16577Vueify Tool Form Data Selector by@guerlerin#16578Workflow Comments 💬 by@ElectronicBlueberryin#16612Switch out conditional requirement parser by@mvdbeekin#16636Add scroll pagination and username filter toHistoryPublishedListby@ahmedhamidawanin#16642Bump samtools converters by@bernt-matthiasin#16668Galaxy Markdown - add workflow image and license to Galaxy markdown. by@jmchiltonin#16672Implement instance URLs in Galaxy markdown. by@jmchiltonin#16675Change Sentry error reporting plug-in by@kysrpexin#16686Use fs.onedatarestfs for Onedata files source plugin implementation by@lopiolain#16690Enhance task monitor composable by@davelopezin#16695Misc. edits/refactorings to session handling  by@jdavcsin#16712SQLAlchemy 2.0 upgrades (part 2) by@jdavcsin#16724Update Python dependencies by@galaxybotin#16735Convert ISO to UTC for Date/Time in workflow reports by@assuntad23in#16758Replace ELIXIR AAI button with Life Science login by@sebastian-schaafin#16762Update Python dependencies by@galaxybotin#16770Migrate a part of the jobs API to Fast API by@heisner-tillmanin#16778Add EGI Check-in as OIDC authentication option by@enolfcin#16782Replace 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#16795Galaxy help forum integration by@ElectronicBlueberryin#16798Update Python dependencies by@galaxybotin#16807Another batch of SA2.0 edits in TS2.0 (part 3) by@jdavcsin#16833Remove remaining legacy backbone form input elements by@guerlerin#16834SQLAlchemy 2.0 upgrades (part 4) by@jdavcsin#16852Update Python dependencies by@galaxybotin#16853Drop unused HistoryContentManager code and related tests by@jdavcsin#16882Vueify Visualizations Grid by@guerlerin#16892Update Python dependencies by@galaxybotin#16896Enable some flake8-logging-format rules in ruff by@nsoranzoin#16915Remove “Create Workflow” form and allow workflow creation in editor by@ahmedhamidawanin#16938Update Python dependencies by@galaxybotin#16939Add helper to get dataset or collection viasrcandidby@mr-cin#16953Allow non-optional integer/float params without value attribute by@nsoranzoin#16966Update Python dependencies by@galaxybotin#16978Fix invocation report to target correct workflow version. by@jmchiltonin#17008Update Python dependencies by@galaxybotin#17011Upgrade job manager’s index_query method to SA2.0 by@jdavcsin#17020optimize object store cache operations by@SergeyYakubovin#17025Require name for workflows on save, set default to Unnamed Workflow by@ahmedhamidawanin#17038Update Python dependencies by@galaxybotin#17050Migrate groups API to fastAPI by@arash77in#17051Migrate ItemTags API to FastAPI by@arash77in#17064Update Python dependencies by@galaxybotin#17084Use python-isal for fast zip deflate compression in rocrate export by@mvdbeekin#17342Other changesMerge 23.1 into dev by@mvdbeekin#16534Revert “[23.1] Enable job resubmissions in k8s runner” by@nuwangin#17323Fix succces typo by@mvdbeekin#1748123.1.4 (2024-01-04)Bug fixesFix workflow index total matches counting by@davelopezin#17176Fixurl_forin tool error reports by@davelopezin#1721023.1.3 (2023-12-01)No recorded changes since last release23.1.2 (2023-11-29)Bug fixesFix unboundrunnervariable when there is an error in the job config by@mvdbeekin#16906Fix discarded dataset ordering in Storage Dashboard by@davelopezin#16929Include owner’s annotation when exporting workflow by@dannonin#16930Skip state filtering in__MERGE_COLLECTION__tool  by@mvdbeekin#16937Prevent Singular external auth users from disconnecting identity by@ahmedhamidawanin#16961Prevent workflow submission with missing input values by@mvdbeekin#17048Fix extra files collection if usingstore_by="id"andoutputs_to_working_directoryby@mvdbeekin#17067Remove rollback from__check_jobs_at_startupby@mvdbeekin#17085EnhancementsImprove invocation error reporting by@mvdbeekin#1691723.1.1 (2023-10-23)Bug fixesread job_conf directly fromconfig_dirinstead of computing it again fromconfig_fileby@bernt-matthiasin#15596Fix some drs handling issues by@nuwangin#15777Fix filesource file url support by@nuwangin#15794Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by@jdavcsin#15811Change confusing pulsar logs message by@kysrpexin#16038Fix and test startup with Python 3.11 on macOS by@nsoranzoin#16082Fix : Ignore error messages for admin created accounts by@jvanbraekelin#16132Ensure session is request-scoped for legacy endpoints by@jdavcsin#16207Fix “database is locked” error (occurring in the context of workflow testing under SQLite) by@jdavcsin#16208Fix ordering of data libraries from API by@martensonin#16300qualify querying for an api-key by@martensonin#16320Fix tags ownership by@davelopezin#16339Job cache fixes for DCEs by@mvdbeekin#16384Fix histories count by@davelopezin#16400Fix select statement syntax for SQLAlchemy 2.0 by@jdavcsin#16421Fix up unit tests for local use by@mvdbeekin#16483Run through tmp_dir_creation_statement only once by@mvdbeekin#16529Fix double-encoding notification content by@mvdbeekin#16530Limit tool document cache to tool configs with explicit cache path by@mvdbeekin#16537Fixmultipleremote test data by@davelopezin#16542Ignore errors with user-set job resources by@mvdbeekin#16579Fix replacement parameters for subworkflows. by@jmchiltonin#16592make sure that TMP, TEMP, and TMPDIR are set by@bernt-matthiasin#16594Bump minimum tpv version to 2.3.2 by@mvdbeekin#16597Backport tool mem fixes by@mvdbeekin#16601Reload toolbox after forking when using–preloadby@mvdbeekin#16620Account for expires/expires_in when refreshing token by@mvdbeekin#16621Fixes for conditional subworkflow steps by@mvdbeekin#16632Fix nested conditional workflow steps by@mvdbeekin#16641Ensure Job belongs to current SA session by@mvdbeekin#16655Fix expression evaluation for nested state by@mvdbeekin#16656Make sort_collection tool require terminal datasets by@mvdbeekin#16661Push to object store even ifset_metafails by@mvdbeekin#16667Fix metadata setting in extended metadata + outputs_to_working_directory mode by@mvdbeekin#16678Fix regex validation for global inline flags by@mvdbeekin#16683Fix closed transaction error on galaxy startup/check jobs by@jdavcsin#16687Add missing join condition in job search by@mvdbeekin#16710Fix job search query by@mvdbeekin#16714Copy the collection contents by default when copying a collection by@mvdbeekin#16717Fix collection id encoding by@davelopezin#16718Workaround for XML nodes of job resource parameters losing their children by@kysrpexin#16728move the email and username redacting from the role loop by@martensonin#16820Fix parameter display in job info page for tools with sections by@mvdbeekin#16821Fix workflow preview display if tool state does not contain all parameter values by@mvdbeekin#16829Fix up local tool version handling by@mvdbeekin#16836Fix and prevent persisting null file_size by@mvdbeekin#16855Allow referring to steps by label only in markdown editor by@mvdbeekin#16861Fix safe update version handling in run form by@mvdbeekin#16865Remove more flushes in database operation tools by@mvdbeekin#16875Fix tag ownership check by@mvdbeekin#16877EnhancementsEmpower Users to Select Storage Destination by@jmchiltonin#14073External Login Flow: Redirect users if account already exists by@ahmedhamidawanin#15019Add slack error reporting plugin by@hexylenain#15025Various Tool Shed Cleanup by@jmchiltonin#15247Add Storage Management API by@davelopezin#15295OIDC tokens by@SergeyYakubovin#15300Expose additional beaker caching backends  by@claudiofrin#15349Add support for visualizing HDF5 datasets. by@jarrah42in#15394Towards SQLAlchemy 2.0: drop session autocommit setting by@jdavcsin#15421Update Python dependencies by@galaxybotin#15435Fix for new style conda packages by@bernt-matthiasin#15446Move database access code out of tool_util by@jdavcsin#15467Protection against problematic boolean parameters. by@jmchiltonin#15493Use connection instead of session for ItemGrabber by@jdavcsin#15496Unify url handling with filesources by@nuwangin#15497Move TS to Alembic by@jdavcsin#15509Explore tool remote test data by@davelopezin#15510Handle “email_from” config option consistently, as per schema description by@jdavcsin#15557Update Python dependencies by@galaxybotin#15564Drop workflow exports to myexperiment.org by@dannonin#15576Update database_heartbeat for SA 2.0 compatibility by@jdavcsin#15611Add suggested Training material to Tool Form by@ElectronicBlueberryin#15628Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by@jdavcsin#15643Add Galaxy Notification System by@davelopezin#15663Unpin Beaker requirement by@nsoranzoin#15665Add transactional state to JobHandlerStopQueue by@jdavcsin#15671Verify that activation and reset emails are properly generated by@guerlerin#15681Add 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#15739Add API test and refactor code for related:hid history filter by@ahmedhamidawanin#15786Migrate to MyST-Parser for Markdown docs by@nsoranzoin#15844Drop use_legacy_history from config  by@dannonin#15861Drop database views by@jdavcsin#15876Update Python dependencies by@galaxybotin#15890Allow pending inputs in some collection operation tools by@mvdbeekin#15892Updated doc and tests for attribute value filter by@tuncKin#15929Update Python dependencies by@galaxybotin#15942Record input datasets and collections at full parameter path by@mvdbeekin#15978Export tool citations configurable message by@minh-biocommonsin#15998Add History Archival feature by@davelopezin#16003Code cleanups from ruff and pyupgrade by@nsoranzoin#16035Add missing fields to HistorySummary schema model by@davelopezin#16041Vendorisepackaging.versions.LegacyVersionby@nsoranzoin#16058Add Repository owner field to ToolSearch by@ahmedhamidawanin#16061Add count support for listing filters by@davelopezin#16075Update Python dependencies by@galaxybotin#16086Improved Cache Monitoring for Object Stores by@jmchiltonin#16110Integrate accessibility testing into Selenium testing by@jmchiltonin#16122Update Python dependencies by@galaxybotin#16123Improve histories and datasets immutability checks by@davelopezin#16143Update Python dependencies by@galaxybotin#16153Migrate display applications API to Fast API by@heisner-tillmanin#16156adjust grid sharing indicators by@martensonin#16163Update Python dependencies by@galaxybotin#16182Drop workarounds for old ro-crate-py and docutils versions by@mvdbeekin#16198Remove various fallback behaviors by@mvdbeekin#16199bring grids for (published) pages on par with workflows by@martensonin#16209Update Python dependencies by@galaxybotin#16227Update Python dependencies by@galaxybotin#16267Fix tool remote test data by@davelopezin#16311Hide conditionally skipped output by@mvdbeekin#16356Fix Storage Dashboard missing archived histories by@davelopezin#16473Bump bx-python to 0.10.0 by@mvdbeekin#16484Drop expunge_all() call in WebTransactionRequest by@mvdbeekin#16606Other changesFollow up on object store selection PR. by@jmchiltonin#15654merge release_23.0 into dev by@martensonin#15830Move axe-selenium-python to dev dependencies by@nsoranzoin#16162Bump msal version by@mvdbeekin#16285Fix error_reports linting by@mvdbeekin#1646523.0.6 (2023-10-23)Bug fixesFix upload paramfile handling (for real user setups) by@bernt-matthiasin#16504Fix extra files path handling by@mvdbeekin#16541Make sure job_wrapper uses a consistent metadata strategy by@mvdbeekin#16569Fix conditional step evaluation with datasets in repeats by@mvdbeekin#16584Don’t read request body into memory by@mvdbeekin#16585Fixes for extra files handling and cached object stores  by@mvdbeekin#16595Lazy load tool data tables in celery worker by@mvdbeekin#16640Force__DUPLICATE_FILE_TO_COLLECTION__‘size’ param to integer by@simonbrayin#16659EnhancementsUpdate pulsar client library to 0.15.5 by@mvdbeekin#1670123.0.5 (2023-07-29)Bug fixesSkip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by@bernt-matthiasin#16403Fix test discovery in vscode by@mvdbeekin#16413Fixes for (gitlab) error reporting by@bernt-matthiasin#1642423.0.4 (2023-06-30)Bug fixesFix default when statement evaluation by@mvdbeekin#16332Redact private role name and description when purging user by@mvdbeekin#1634923.0.3 (2023-06-26)Bug fixesBump galaxy-release-util version to 0.1.2 by@mvdbeekin#16241EnhancementsWhen importing tool data bundles, use the first loc file for the matching table by@natefooin#16247Other changesForward port of slugify username received from oidc by@nuwangin#1627123.0.2 (2023-06-13)Bug fixesFixText File Busyerrors at the source by@mvdbeekin#16212EnhancementsPoint release deps fixes and docs by@mvdbeekin#16214Use galaxy-release-util to upload python packages by@mvdbeekin#1624023.0.1 (2023-06-08)Bug fixesDisplay DCE in job parameter component, allow rerunning with DCE input by@mvdbeekin#15744Fix mixed outputs_to_working_directory pulsar destinations by@mvdbeekin#15927Update Gravity to 1.0.3 by@natefooin#15939Various fixes to path prefix handling by@mvdbeekin#16033Fix case sensitive filtering by name in histories by@davelopezin#16036Fix gcsfs test discovery by@mvdbeekin#16039Replace httpbin service with pytest-httpserver by@mvdbeekin#16042Update pulsar to 0.15.2 by@mvdbeekin#16050Anonymous User tool link bug fix by@ahmedhamidawanin#16065Fix BCO export by updating gxformat2 by@mvdbeekin#16081Fix job failure handling when condor indicates job failure by@mvdbeekin#16096Fix dataype_change not updating HDCA update_time by@mvdbeekin#16099Extract HDA for code_file validate_input hook by@mvdbeekin#16120Fix sort error when re-running job with DCE collection input by@mvdbeekin#16126Fix related-hid in bulk contents API by@mvdbeekin#16128Fix rank calculation for jobs waiting to be run by anonymous users by@jdavcsin#16137Tool warnings can either be None or a Dictionary but not a String by@guerlerin#16183Pin minimum tpv version by@mvdbeekin#16201Other changesStartup fix when tool removed between reboot by@mvdbeekin#1617520.9.0 (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.