galaxy-data 26.0.1.dev0

Galaxy datatype framework and datatypes

Overview

The Galaxy models, datatype framework, and datatype implementations.

• Code: https://github.com/galaxyproject/galaxy

History

26.0.1.dev0

26.0.0 (2026-04-08)

Bug fixes

• Drop down revision for drop_job_params migration by @mvdbeek in #21122

• Create alembic merge by @mvdbeek in #21447

• Provide more accurate step hints for failing subworkflow steps by @mvdbeek in #21514

• Fix width and height assignment for image metadata using Pillow by @kostrykin in #21554

• Avoid slash duplication in display application urls by @guerler in #21809

• Fix redirect upon impersonation by @guerler in #21810

• Fix dataset collection tag duplication when copying a history by @mvdbeek in #21984

• Fix AttributeError serializing implicit output collections during job prep by @mvdbeek in #22034

• Fix preferred_object_store_id not respected for discovered outputs with extended metadata by @mvdbeek in #22056

• Fix TypeError when column_names metadata is None by @mvdbeek in #22057

• Fail job gracefully when output name exceeds 255 character DB limit by @mvdbeek in #22059

• Fix nested collection query performance by @mvdbeek in #22119

• Fix CardinalityViolation in nested collection ARRAY walk scalar subqueries by @mvdbeek in #22123

• Use skip_locked also when updating collection by @mvdbeek in #22133

• Fix redundant empty collection elements by @mvdbeek in #22154

• Don’t fail on probable delete race by @mvdbeek in #22183

• Back port collection fixes from #22170. by @jmchilton in #22193

• Optimize dataset get_edit API by deferring expensive role queries by @mvdbeek in #22232

• Batch-prefetch HDCA job_state_summary in history contents listing by @mvdbeek in #22256

• Sequence datatypes: only read first character per line for setting metadata by @bernt-matthias in #22276

• Fix slow get_private_role_user_emails_dict query by @mvdbeek in #22307

• Fix timestamp parsing in job import/export by @mvdbeek in #22372

• Ensure x-content-truncated header is string by @mvdbeek in #22386

• Fix dataset preview rendering to preserve newlines by @mvdbeek in #22397

Enhancements

• Refactor display application handling by @guerler in #15076

• Tool Request API by @jmchilton in #20935

• Remove Trackster by @guerler in #20974

• Move database revision tags to separate file by @guerler in #20998

• Update Python dependencies by @galaxybot in #21043

• Remove Job.params by @jdavcs in #21075

• Remove tabular chunked, binary and large file mako by @guerler in #21106

• Add type annotations to job handling code by @nsoranzo in #21171

• Reimplement keycloak/cilogon as PSA providers and remove custos by @nuwang in #21234

• Slight improvement of mztab2 datatype by @nguilhot in #21258

• Move js-client bootstrapping to FastAPI by @guerler in #21264

• Implement GA4GH WES API by @jmchilton in #21335

• Fix: tool execution typing improvements/fixes by @jmchilton in #21374

• Add initial support for the DICOM format by @kostrykin in #21385

• Add AI Agent Framework and ChatGXY 2.0 by @dannon in #21434

• Enable attaching sample sheet to landing requests by @mvdbeek in #21489

• Discriminate decompression tools by @mvdbeek in #21510

• Include subworkflow jobs in invocation metrics by @mvdbeek in #21511

• Implement subworkflow invocation export by @mvdbeek in #21512

• Implement workflow completion monitoring with extensible hooks by @mvdbeek in #21532

• Clean up code with pyupgrade by @nsoranzo in #21540

• Drop support for Python 3.9 by @nsoranzo in #21583

• Apply 2026 black style by @galaxybot in #21618

• Allow connecting sample sheet inputs to compatible collection inputs in editor by @mvdbeek in #21859

• Add new datatypes: .taf and .taf.gz by @Maed0x in #22242

• Add _F/_R auto-pairing filter for forward/reverse datasets by @jmchilton in #22267

Other changes

• Update revision tags for release 25.1 by @arash77 in #21022

• Merge 25.1 into dev and create alembic merge revision by @mvdbeek in #21440

• Add Database Revision for 26.0 by @guerler in #21675

• Fix on_complete column type mismatch by @mvdbeek in #21765

25.1.2 (2026-03-09)

Bug fixes

• Fix private dataset sharing error handling by @davelopez in #21689

• Fix database migration error from 25.0 > 25.1 by @jdavcs in #21737

• Make database heartbeat more robust (backport) by @mvdbeek in #21812

• Fix recording duplicate workflow_request_input_step_parameter rows by @mvdbeek in #21980

Other changes

• Fix worker segfault in gunicorn preload mode on OSX by @mvdbeek in #21837

25.1.1 (2026-02-03)

Bug fixes

• Sample sheet column fix by @mvdbeek in #21446

• Maintain column definitions on map over by @mvdbeek in #21468

• Add missing test file for sig datatype by @SaimMomin12 in #21473

• Do not update a user’s update_time when an admin archives (and purges) a history by @natefoo in #21484

• Add missing ending newline to test.sig test data file by @nsoranzo in #21485

• Usability fixes for sample sheet selection. by @jmchilton in #21503

• Fix exception message to enable debugging of missing dataset issue. by @jmchilton in #21504

• Add missing dependencies to galaxy-files package by @nsoranzo in #21518

• Fix job cache collection copy by @mvdbeek in #21558

• Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by @jmchilton in #21584

• Fix race condition in workflow collection populated state check by @mvdbeek in #21613

• Fix collection job state not preserved during history export/import by @mvdbeek in #21716

Enhancements

• Add Sourmash sig new datatype by @SaimMomin12 in #21469

• Add database operation tool to convert sample sheets to list collections by @mvdbeek in #21625

25.1.0 (2025-12-12)

Bug fixes

• Fix alembic down_revision for trigger replacement migration by @mvdbeek in #20501

• Add a merge migration, revert previous edit by @jdavcs in #20507

• Add missing cleanup table by @jdavcs in #20594

• Fix anndata metadata by @nilchia in #20778

• Fix Ipynb datatype sniffer and add unit tests. by @ksuderman in #20811

• Bump requirement of directory converters by @bernt-matthias in #20834

• Extract: do not use common prefix dir by @bernt-matthias in #20929

• Ensure that conversion_key is defined by @guerler in #20984

• Fix invocation export dataset exclusion by @davelopez in #21091

• Restore job.get_param_values by @mvdbeek in #21130

• Improve _touch_collection_update_time_cte performance by @mvdbeek in #21134

• Assorted workbook upload fixes. by @jmchilton in #21203

• Fix database revision tags by @jdavcs in #21377

• Maintain columns on sample sheet map over by @mvdbeek in #21436

Enhancements

• Support credentials(secrets/variables) in tool requirements by @arash77 in #19084

• Implement Sample Sheets by @jmchilton in #19305

• Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288

• Add short term storage expiration indicator to history items by @davelopez in #20332

• Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424

• Implement dataset source requested transformations. by @jmchilton in #20435

• Remove deprecated tool document cache by @nsoranzo in #20510

• Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547

• Implement Data Landing Requests by @jmchilton in #20592

• Clean up code from pyupgrade by @nsoranzo in #20642

• Update Python dependencies by @galaxybot in #20680

• Attempt to reuse previously materialized datasets by @mvdbeek in #20718

• Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728

• Hierarchical display collection dataset states by @mvdbeek in #20731

• Use a streaming based parser (ijson) when setting metadata for biom1 files. by @ksuderman in #20851

• Improve type annotation for job runners and InteractiveToolManager by @nsoranzo in #20871

• Update Python dependencies by @galaxybot in #20905

• Allow sending and tracking landing request origin by @mvdbeek in #20957

• Track landing request with invocation by @mvdbeek in #20960

• Optimize /api/invocations/steps/{step_id} by @mvdbeek in #21249

• A better way to designate config_watcher by @jdavcs in #21426

Other changes

• Small tweaks and cleanup from sample sheets branch by @jmchilton in #20229

• Merge release_25.0 into dev by @davelopez in #20484

• Merge release_25.0 into dev by @davelopez in #20490

• Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749

• Add tool_id and tool_version column to tool_landing_request table by @mvdbeek in #20795

• Add 25.1 migration tags by @ahmedhamidawan in #21017

• Restore .get_metadata function by @mvdbeek in #21045

• Fix forward merge by @mvdbeek in #21307

• Fix db revision tags by @mvdbeek in #21442

25.0.4 (2025-11-18)

Bug fixes

• Add safetensors datatype by @nilchia in #20754

• Skip sam metadata if we have too many references by @mvdbeek in #20820

• Backport of #20984 by @davelopez in #20994

• Backport fix anndata datatype update by @nilchia in #21111

• Create new datasets when creating skipped database operation tool outputs by @mvdbeek in #21142

• Fix optional param unset in RO-Crate export by @davelopez in #21192

Enhancements

• Add Auspice JSON datatype by @pvanheus in #20466

• Add SpatialData datatype by @nilchia in #21000

• Use job cache also for implicit conversions by @mvdbeek in #21021

• support ZARR v3 for Spatialdata dt by @nilchia in #21265

25.0.3 (2025-09-23)

Bug fixes

• Ensure that workflow invocations are persisted with state by @mvdbeek in #20784

• Fix password reset functionality for lowercase emails by @jdavcs in #20801

• Drop eager argument from invocation related methods by @mvdbeek in #20863

• Use populated_optimized when serializing collection by @mvdbeek in #20872

• Speed up ImplicitCollectionJobs.job_list by @mvdbeek in #20887

• Add LDDA purged property by @mvdbeek in #20895

• Avoid potential race condition in replacement_for_connection by @mvdbeek in #20909

• Fix sessionless tag creation by @mvdbeek in #20925

Enhancements

• Fix DOCX detection and add PPTX support by @arash77 in #20827

• Add HiC datatype by @abretaud in #20874

Other changes

• Undo accidental push by @bernt-matthias in #20854

• Merge 25.0 into dev by @ahmedhamidawan in #20911

25.0.2 (2025-08-13)

Bug fixes

• Remove num_unique_values tiff metadata element by @mvdbeek in #20464

• Propagate cached job output replacement to copies of outputs by @mvdbeek in #20553

• Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650

• Add num_unique_values tiff metadata element, fixed by @kostrykin in #20669

Enhancements

• Improve workflow monitor loop times by @mvdbeek in #20522

• Pairtool updated format and sniffers by @Smeds in #20634

• Add support for M4A audio files by @arash77 in #20667

25.0.1 (2025-06-20)

Bug fixes

• Pin isa-rwval 0.10.11, drop conditional import handling by @natefoo in #20527

25.0.0 (2025-06-18)

Bug fixes

• Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394

• Alternative format_source fix by @mvdbeek in #19395

• Use id entity attribute when setting exampleOfWork property by @nsoranzo in #19396

• Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by @jdavcs in #19620

• Fix Galaxy ignoring job object_store_id for quota check by @bernt-matthias in #19854

• Fix various mypy issues around mapped attributes by @mvdbeek in #19883

• More fixes to FormData drag and drop and typing by @ahmedhamidawan in #19900

• Use lower case extension for setting datatype in data discovery by @bernt-matthias in #19954

• Add new line to vtpascii test file by @guerler in #20051

• Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in #20152

• Update tabular_csv.py to use less memory in tsv->csv conversion by @cat-bro in #20187

• Fix tool-provided metadata for CONVERTER_tar_to_directory by @mr-c in #20260

• Log invalid vault paths by @mvdbeek in #20363

• Update triggers by @jdavcs in #20425

• Fix copying of job metrics for cached jobs by @mvdbeek in #20436

• Dataset Display and Preferred Viz fixes by @dannon in #20439

• Recreate triggers by @jdavcs in #20491

Enhancements

• Workflow Editor Activity Bar by @ElectronicBlueberry in #18729

• Add author and tools details in RO-Crate by @Marie59 in #18820

• Extend image metadata by @kostrykin in #18951

• Implement tool markdown reports. by @jmchilton in #19054

• Let file sources choose a path for uploaded files by @kysrpex in #19154

• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181

• Fix UP031 errors - Part 1 by @nsoranzo in #19194

• Fix UP031 errors - Part 4 by @nsoranzo in #19235

• Fix UP031 errors - Part 5 by @nsoranzo in #19282

• Fix UP031 errors - Part 6 by @nsoranzo in #19314

• Misc fixes 202412 by @nsoranzo in #19341

• Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372

• Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377

• SQLAlchemy 2.0 follow-up by @jdavcs in #19388

• Set safe default extraction filter for tar archives by @nsoranzo in #19406

• Remove transaction helper by @jdavcs in #19407

• Prevent users from reusing a banned email after account is purged by @jdavcs in #19413

• Add IGB display support for CRAM files by @paige-kulzer in #19428

• Add User-Defined Tools by @mvdbeek in #19434

• Type annotation improvements by @nsoranzo in #19485

• Update Python dependencies by @galaxybot in #19567

• Expand workflow metadata for readme. by @jmchilton in #19591

• Format code with black 25.1.0 by @nsoranzo in #19625

• Type annotation improvements by @nsoranzo in #19642

• Generate correct types for Dataset source transformations on backend. by @jmchilton in #19666

• Drop support for Python 3.8 by @nsoranzo in #19685

• Define simple models for job messages. by @jmchilton in #19688

• Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in #19706

• Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in #19726

• Add bigbed to bed converter and tests by @d-callan in #19787

• Update Python dependencies by @galaxybot in #19816

• Populate image metadata without allocating memory for the entire image content by @kostrykin in #19830

• Add mandatory RO-Crate metadata when exporting by @elichad in #19846

• Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852

• Drop old galaxy_session records by @jdavcs in #19872

• Clarify is_active method usage for Python Social Auth in Galaxy by @dannon in #19899

• Drop old job metrics by @jdavcs in #19936

• Allow PathLike parameters in make_fast_zipfile() by @nsoranzo in #19955

• Add type hints around collection copying and job things by @mvdbeek in #19961

• Job cache allow different names when possible by @mvdbeek in #19962

• Improve type annotation of tool parameter wrapping by @nsoranzo in #19991

• Implement dataset collection support in workflow landing requests by @mvdbeek in #20004

• Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008

• Add vitesscejson datatype by @guerler in #20027

• Add VTK Visualization Toolkit Plugin by @guerler in #20028

• Add DOI to workflow metadata by @jdavcs in #20033

• Add sample datasets for visualizations by @guerler in #20046

• Add docx datatype by @bgruening in #20055

• Add flac audio format by @bgruening in #20057

• Improve type annotation of galaxy.util submodules by @nsoranzo in #20104

• Add specific datatypes for Cytoscape and Kepler.gl by @guerler in #20117

• Visualization-First Display functionality by @dannon in #20190

• Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in #20194

• Improve performance of job cache query by @mvdbeek in #20319

• DatasetView and Card Polish by @dannon in #20342

Other changes

• Merge 24.2 into dev by @ahmedhamidawan in #19933

• Fix copying job output from discovered outputs by @mvdbeek in #19999

• Add 25.0 migration tags by @ahmedhamidawan in #20265

• Rename vitessce_json file_ext to vitessce.json by @mvdbeek in #20473

24.2.4 (2025-06-17)

Bug fixes

• Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819

• Try to recover from recurring activation link error by @jdavcs in #19844

• Check if index exists before creating by @jdavcs in #19873

• Let pysam use extra threads available in job by @mvdbeek in #19917

• Handle special charater in raw SQL by @jdavcs in #19925

• Use make_fast_zipfile directly by @mvdbeek in #19947

• Job cache backports by @mvdbeek in #20078

• Conditionally import from galaxy.config in galaxy.model.mapping if TYPE_CHECKING by @natefoo in #20209

• Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by @natefoo in #20239

• Make response header values strings by @mvdbeek in #20475

• Link workflow invocation outputs upon importing invocation by @mvdbeek in #20485

• Make optional edam-ontology in datatypes registry optional by @natefoo in #20492

Enhancements

• Bump up max_peek_size to 50MB by @mvdbeek in #19823

24.2.3 (2025-03-16)

Bug fixes

• Fix private role name performance issue by @jdavcs in #19679

• Fix anndata metadata setting for data with integer indexes by @mvdbeek in #19774

• Fix parameter model constructions with leading underscores, fixes converter linting by @mvdbeek in #19790

Enhancements

• Add rDock prm datatype by @nsoranzo in #19783

24.2.2 (2025-03-08)

Bug fixes

• Fix recording transform action name. by @jmchilton in #19672

Enhancements

• Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

Other changes

• Backport #19620 by @nsoranzo in #19725

24.2.1 (2025-02-28)

Bug fixes

• Set content-type to text/plain if dataset not safe by @mvdbeek in #19563

• Fail request explicitly when sqlite provider used on non-sqlite file by @mvdbeek in #19630

• Fix various bugs around tool data table bundles by @mvdbeek in #19659

24.2.0 (2025-02-11)

Bug fixes

• Drop “Send to cloud” tool and associated cloudauthz code by @jdavcs in #18196

• Raise Message Exception when displaying binary data by @mvdbeek in #18503

• Fixes for errors reported by mypy 1.11.0 by @nsoranzo in #18608

• Fix new flake8-bugbear B039 and mypy type-var errors by @nsoranzo in #18755

• Fix migration data fixes tests by @jdavcs in #18885

• Fix backend role sharing bug by @jdavcs in #18942

• Add merge migration to merge 2 heads by @jdavcs in #19163

• Record implicitly converted dataset as input dataset by @mvdbeek in #19301

• Fix quota usage with user object stores by @davelopez in #19323

• Fix workflows with optional non-default parameter input by @mvdbeek in #19332

• Fix importing shared workflows with deeply nested subworkflows by @mvdbeek in #19335

• Backport fix from #19396 by @nsoranzo in #19399

• Prevent cycling through failing conversion jobs in trackster by @mvdbeek in #19494

• Fix extracting workflows from purged and deleted histories by @mvdbeek in #19525

• Fix error message when subworkflow input connection missing by @mvdbeek in #19526

• Fix admin cancel job message not being displayed to the user by @davelopez in #19537

• Add tool_id index on job table by @mvdbeek in #19543

• Update 24.2 db revision tags by @jdavcs in #19550

• Provide guidance in case of deadlock during db migration by @jdavcs in #19551

• Fix job paused on user defined object store by @davelopez in #19578

• Handle isatools dependency by @jdavcs in #19582

Enhancements

• Experimental galactic wizard by @dannon in #15860

• Improve usability of Directory datatype by @wm75 in #17614

• Update Python dependencies by @galaxybot in #18226

• Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by @jmchilton in #18272

• More data access tests, some refactoring and cleanup by @jdavcs in #18312

• Update Python dependencies by @galaxybot in #18406

• Add pod5 datatype by @TomHarrop in #18419

• Prepare for NumPy 2.0 by @nsoranzo in #18422

• Add unique constraints to the email and username fields in the galaxy_user table by @jdavcs in #18493

• Improvements for K8S deployment (especially ITs) by @almahmoud in #18514

• Refactor LibraryDatasetsManager and fix type annotation issue by @nsoranzo in #18773

• Handle compressed content in dataset preview for all sequence classes by @PlushZ in #18776

• Backend handling of setting user-role, user-group, and group-role associations by @jdavcs in #18777

• Workflow Landing Requests by @jmchilton in #18807

• Update Mypy to 1.11.2 and fix new signature override errors by @nsoranzo in #18811

• Refactor migration testing setup code by @jdavcs in #18886

• Allow setting a few global defaults for file source plugin types. by @jmchilton in #18909

• Type annotations and fixes by @nsoranzo in #18911

• Add filter null collection operation tool by @mvdbeek in #18928

• Fix extra files path type hint by @davelopez in #18958

• Decouple user email from role name by @jdavcs in #18966

• Optimize to_history_dataset_association in create_datasets_from_library_folder by @arash77 in #18970

• Workflow landing improvements by @mvdbeek in #18979

• Allow recovering a normalized version of workflow request state from API by @jmchilton in #18985

• Add some Zarr-based datatypes by @davelopez in #19040

• Run installed Galaxy with no config and a simplified entry point by @natefoo in #19050

• Annotate DatasetAssociationManager as generic type by @nsoranzo in #19063

• Move TRS import into WorkflowContentManager by @mvdbeek in #19070

• Allow deferred datasets to behave as URIs by @davelopez in #19077

• Better cleanup of sharing roles on user purge by @jdavcs in #19096

• Add XML based vtk datatype by @tStehling in #19104

• Access public history in job cache / job search by @mvdbeek in #19108

• Always validate hashes when provided by @nsoranzo in #19110

• Enable specifying dataset hash in test jobs by @mvdbeek in #19113

• Enhance UTF-8 support for filename handling in downloads by @arash77 in #19161

• Backport of Workflow Editor Activity Bar by @dannon in #19212

• Fix default value handling for parameters connected to required parameters by @mvdbeek in #19219

Other changes

• Merge 24.1 by @jdavcs in #18386

• Format dev to fix linting. by @jmchilton in #18860

• Add 24.2 migration tags by @jdavcs in #19169

• Fix type annotations for pysam 0.23.0 by @nsoranzo in #19571

24.1.4 (2024-12-11)

Bug fixes

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

• Improve workflow-related exception reporting by @mvdbeek in #18447

• 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

• Fix shared caches with extended metadata collection. by @jmchilton in #18520

• Also check dataset.deleted when determining if data can be displayed by @mvdbeek in #18547

• Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

• Fix h5ad metadata by @nilchia in #18635

• Don’t set file size to zero by @mvdbeek in #18653

• Make sure we set file size also for purged outputs by @mvdbeek in #18681

• Fix wrong extension on pick data output by @mvdbeek in #18798

• Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802

• Make pylibmagic import optional by @mvdbeek in #18813

• Ignore converted datasets in invalid input states by @mvdbeek in #18850

• Fix discovered outputs with directory metadata and distributed object by @mvdbeek in #18855

• Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

• Fix wrong final state when init_from is used by @mvdbeek in #18871

• Fix history import when parent_hda not serialized by @mvdbeek in #18873

• Limit max number of items in dataproviders by @mvdbeek in #18881

• Allow cors in biom and q2view display applications by @mvdbeek in #18890

• Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

• Optimize/fix sqlite hid update statement by @mvdbeek in #19106

• Prefer auto-decompressed datatype when picking conversion target by @mvdbeek in #19162

• Fix various invocation export issues by @mvdbeek in #19215

• Fix bad merge conflict resolution by @nsoranzo in #19297

Other changes

• Backport pod5 datatype by @TomHarrop in #18507

24.1.3 (2024-10-25)

Bug fixes

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

• Improve workflow-related exception reporting by @mvdbeek in #18447

• 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

• Fix shared caches with extended metadata collection. by @jmchilton in #18520

• Also check dataset.deleted when determining if data can be displayed by @mvdbeek in #18547

• Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

• Fix h5ad metadata by @nilchia in #18635

• Don’t set file size to zero by @mvdbeek in #18653

• Make sure we set file size also for purged outputs by @mvdbeek in #18681

• Fix wrong extension on pick data output by @mvdbeek in #18798

• Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802

• Make pylibmagic import optional by @mvdbeek in #18813

• Ignore converted datasets in invalid input states by @mvdbeek in #18850

• Fix discovered outputs with directory metadata and distributed object by @mvdbeek in #18855

• Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

• Fix wrong final state when init_from is used by @mvdbeek in #18871

• Fix history import when parent_hda not serialized by @mvdbeek in #18873

• Limit max number of items in dataproviders by @mvdbeek in #18881

• Allow cors in biom and q2view display applications by @mvdbeek in #18890

• Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

Other changes

• Backport pod5 datatype by @TomHarrop in #18507

24.1.2 (2024-09-25)

Bug fixes

• 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

• Fix shared caches with extended metadata collection. by @jmchilton in #18520

• Also check dataset.deleted when determining if data can be displayed by @mvdbeek in #18547

• Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

• Fix h5ad metadata by @nilchia in #18635

• Don’t set file size to zero by @mvdbeek in #18653

• Make sure we set file size also for purged outputs by @mvdbeek in #18681

• Fix wrong extension on pick data output by @mvdbeek in #18798

• Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802

• Make pylibmagic import optional by @mvdbeek in #18813

• Ignore converted datasets in invalid input states by @mvdbeek in #18850

• Fix discovered outputs with directory metadata and distributed object by @mvdbeek in #18855

• Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

• Fix wrong final state when init_from is used by @mvdbeek in #18871

• Fix history import when parent_hda not serialized by @mvdbeek in #18873

Other changes

• Backport pod5 datatype by @TomHarrop in #18507

24.1.1 (2024-07-02)

Bug fixes

• Fix syntax for SA2.0 by @jdavcs in #17663

• Fix empty usernames in database + bug in username generation by @jdavcs in #18379

• Fix input_step_parameters missing values that don’t have a label by @ahmedhamidawan in #18405

• Improve workflow-related exception reporting by @mvdbeek in #18447

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 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

• SQLAlchemy 2.0 by @jdavcs in #17778

• Outline use of type_annotation_map to fix mypy issues by @jmchilton in #17902

• Add email notifications channel by @davelopez in #17914

• Model edits and bug fixes by @jdavcs in #17922

• Model typing and SA2.0 follow-up by @jdavcs in #17958

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

• Add galaxy to user agent by @mvdbeek in #18003

• 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

• Update db revision 24.1 release tags by @jdavcs in #18183

• 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

• Fix import broken with forward merge by @mvdbeek in #18152

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

• Fix first_dataset_element type hint by @mvdbeek in #18284

• 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

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

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 tag regex pattern by @jdavcs in #18025

• 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 social_core methods by @jdavcs in #17530

• 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

• Simplify nested collection joins by @mvdbeek in #17817

• Fix very slow user data table query by @mvdbeek in #17830

• Update db revision 24.0 release tags by @jdavcs in #17834

• 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

• SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932

• Python 3.8 as minimum by @mr-c in #16954

• 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

• Add future=True flag to SA engine by @jdavcs in #17174

• Add future=True flag to SA session by @jdavcs in #17179

• Vueifiy History Grids by @guerler in #17219

• Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222

• Migrate models to pydantic 2 by @mvdbeek in #17262

• API endpoint that allows “changing” the objectstore for “safe” scenarios. by @jmchilton in #17329

• Enable warn_unreachable mypy option by @mvdbeek in #17365

• 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

• Update to black 2024 stable style by @nsoranzo in #17391

• 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

• Use AlignedSegment.to_string by @mvdbeek in #16803

• Ruff and flake8 fixes by @nsoranzo in #16884

• prep for updated h5py and typos by @mr-c in #16963

• Fix cardinality violation error: subquery returns multiple results by @jdavcs in #17224

• Fix Display Application link generation by @mvdbeek in #17227

• Display application fixes and tests by @mvdbeek in #17233

• Rollback invalidated transaction by @jdavcs in #17280

• 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

• SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in #16724

• Migrate collection elements store to Pinia by @davelopez in #16725

• Reset autocommit to False by @jdavcs in #16745

• Drop legacy server-side search by @jdavcs in #16755

• 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

• Vueify Visualizations Grid by @guerler in #16892

• Standardize to W3C naming for color. by @dannon in #16949

• Move and re-use persist_extra_files by @mvdbeek in #16955

• 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

• Merge 23.1 into dev by @mvdbeek in #16534

• Merge release_23.1 into dev by @mvdbeek in #16768

• Create db head merge revision. by @dannon in #16838

• merge release_23.1 into dev by @martenson in #16933

• Minor clarification/typo fix in datatypes.data by @dannon in #16993

• Fix .file_name access in merge forward by @mvdbeek in #17097

• Backport model store fixes by @mvdbeek in #17439

• Fix succces typo by @mvdbeek in #17481

23.1.4 (2024-01-04)

Bug fixes

• Fix User.current_galaxy_session by @mvdbeek in #17232

Other changes

• Backport #17188: Fix for converter tests by @mvdbeek in #17231

23.1.3 (2023-12-01)

Bug fixes

• Add missing optional description field, fixes ephemeris data library example by @mvdbeek in #17116

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

• Update tar_to_directory dependency by @mvdbeek in #17009

• 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

• Improve invocation error reporting by @mvdbeek in #16917

• 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

• Enable strict_equality mypy option by @nsoranzo in #15808

• 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

• Reset autocommit to True (temporarily) by @jdavcs in #16283

• Update 23.1 release tags for migration scripts by @jdavcs in #16294

• Fix form builder value handling by @guerler in #16304

• Fix tags ownership by @davelopez in #16339

• Fix disk usage recalculation for distributed object stores by @mvdbeek in #16380

• Job cache fixes for DCEs by @mvdbeek in #16384

• Fix histories count by @davelopez in #16400

• Fix double-encoding notification content by @mvdbeek in #16530

• Optimize getting current user session by @mvdbeek in #16604

• 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

• Towards decoupling datatypes and model by @jdavcs in #15186

• Add Storage Management API by @davelopez in #15295

• OIDC tokens by @SergeyYakubov in #15300

• Expose additional beaker caching backends by @claudiofr in #15349

• Follow up to #15186 by @jdavcs in #15388

• 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

• Unify url handling with filesources by @nuwang in #15497

• Move TS to Alembic by @jdavcs in #15509

• 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

• Drop model mapping unit tests by @jdavcs in #15669

• 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

• Drop database views by @jdavcs in #15876

• 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

• Add alter_column migration utility by @jdavcs in #16009

• 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

• Fix linting of FITS datatype code by @mvdbeek in #16169

• backport of pysam tostring by @martenson in #16822

23.0.6 (2023-10-23)

Bug fixes

• Fix extra files path handling by @mvdbeek in #16541

• Don’t fail invocation message without dependent_workflow_step_id by @mvdbeek in #16628

23.0.5 (2023-07-29)

Bug fixes

• Copy when_expression when copying workflow step by @mvdbeek in #16377

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 folder listing via file browser by @mvdbeek in #15950

• 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

• Various fixes to path prefix handling by @mvdbeek in #16033

• Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099

• Fix mypy error due to alembic 1.11.0 by @nsoranzo in #16104

• 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

• Support ro crate 0.8.0 and 0.7.0 by @mvdbeek in #16193

• 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.