January 2022 Galaxy Release (v 22.01)

Highlights

Galaxy starts as FastAPI application by default

Starting Galaxy via run.sh will use the new gravity process manager. The new configuration uses gunicorn and FastAPI to drive Galaxy’s web process and starts job handler and Celery processes automatically. For more details and instructions please consult the Migrating to Gunicorn documentation. (Pull Request 13224).

User Preferences can be encrypted in Galaxy Vault

Galaxy can now be configured to store secrets in an external vault, which is useful for secure handling and centralization of secrets management. In particular, information fields in the “Manage information” section of the user profile, such as dropbox keys, can be configured to be encrypted at rest in a vault (Hashicorp, Custos or database) instead of being stored as plain text in the user preferences table. For detailed information on configuration, refer to the vault section of the admin documentation. (Pull Request 12940).

Resumable uploads via tus.io, improved upload provenance

Galaxy now supports chunked and resumable uploads via the tus protocol. This is more performant and easier to setup than the current nginx-based solutions. For detailed configuration instructions, see the documentation. Galaxy now displays all manipulations that were performed during an upload, such as newline conversions, converting spaces to tabs or dataset grooming. (Pull Request 12656, Pull Request 12861, Pull Request 13313, Pull Request 12912).

Also check out the 22.01 user release notes

Get Galaxy

The code lives at GitHub and you should have Git to obtain it.

To get a new Galaxy repository run:

$ git clone -b release_22.01 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:

$ git fetch origin && git checkout release_22.01 && git pull --ff-only origin release_22.01

See the community hub for additional details on source code locations.

Deprecation Notices

PostgreSQL 9.x is now EOL and is no longer supported. Please upgrade to PostgreSQL 10 or higher. Python 3.6 is officially EOL and Galaxy no longer tests or maintains compatibility. This release will be the last Galaxy release that can run under Paste or uWSGI. Please consult the Migrating to Gunicorn documentation for . instructions on how to upgrade.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample:galaxy

• mapping.galaxy.mapping.enable_tool_source_display

• mapping.galaxy.mapping.galaxy_url_prefix

• mapping.galaxy.mapping.load_tool_shed_datatypes

• mapping.galaxy.mapping.max_discovered_files

• mapping.galaxy.mapping.maximum_upload_file_size

• mapping.galaxy.mapping.tool_evaluation_strategy

• mapping.galaxy.mapping.tus_upload_store

• mapping.galaxy.mapping.vault_config_file

Changed

The following configuration options have been changed

config/galaxy.yml.sample:galaxy

• mapping.reports.mapping.file_path.default has changed from

  database/files
  

  to

  database/objects
  

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

• mapping.galaxy.mapping.check_migrate_tools

• mapping.galaxy.mapping.enable_openid

• mapping.galaxy.mapping.force_beta_workflow_scheduled_for_collections

• mapping.galaxy.mapping.force_beta_workflow_scheduled_min_steps

• mapping.galaxy.mapping.openid_consumer_cache_path

Release Notes

Enhancements

• Swap to Webpack5 Pull Request 11710

• Remote / Late evaluation of tools Pull Request 12459

• File sources for gdrive, gcs, onedata, basespace (thanks to @nuwang). Pull Request 12500

• Add support for caching the Singularity cached images directory Pull Request 12524

• Various extensions and improvements for asserts (thanks to @bernt-matthias). Pull Request 12528

• New interactive tool - iSEE (thanks to @neoformit). Pull Request 12650

• Resumable file uploads with tus.io Pull Request 12656

• Make directory path editable in remote files (thanks to @OlegZharkov). Pull Request 12759

• Display tool source in tool form Pull Request 12811

• Modify history contents/near endpoint to support new history scroller Pull Request 12892

• Vault abstraction for Galaxy (thanks to @nuwang). Pull Request 12940

• Sort icon on List Collection Creator (thanks to @assuntad23). Pull Request 12945

• Provide more context for lint context (thanks to @bernt-matthias). Pull Request 12978

• Add mulled-hash command to galaxy-tool-util (thanks to @simonbray). Pull Request 13061

• Add parquet to csv datatype converter Pull Request 13078

• XML macros: add named yields, tokenized macros, tokens for attributes, and fix replacement of toplevel yield (thanks to @bernt-matthias). Pull Request 13152

• Enable setting SQLALCHEMY_WARN_20 Pull Request 13171

• Add new datatype GRIB (thanks to @annefou). Pull Request 13175

• Use Gravity to run Galaxy Pull Request 13224

• Add datatype iml_dataset subclassing html (thanks to @knutwa-ext). Pull Request 12099

• Mark sniffer for fastqillumina as not implemented (thanks to @bernt-matthias). Pull Request 12685

• Create sniffer for GRO file type (thanks to @simonbray). Pull Request 12885

• Agp datatype Pull Request 12891

• Type updates from @mr-c - part 2 (thanks to @common-workflow-lab). Pull Request 12899

• 3rd round of type updates to support CWL import (thanks to @common-workflow-lab). Pull Request 12913

• Tighten type ignores (thanks to @common-workflow-lab). Pull Request 12965

• Remove is_multi_byte (thanks to @bernt-matthias). Pull Request 12996

• Add ludwig model datatype (thanks to @qiagu). Pull Request 13073

• Add ampvis2 datatype (thanks to @bernt-matthias). Pull Request 13083

• Add Neper and Gmsh datatypes (thanks to @jj-umn). Pull Request 13087

• Add description of inpcrd and prmtop (thanks to @thepineapplepirate). Pull Request 13126

• Add compression converter (thanks to @gallardoalba). Pull Request 13223

• Change display_in_upload to true for PHAR datatype (thanks to @simonbray). Pull Request 13238

• Add gz as datatype (thanks to @astrovsky01). Pull Request 13271

• Limit required element validation to safe elements Pull Request 13299

• Add phyloseq datatype (thanks to @bernt-matthias). Pull Request 13462

• Allow any format in export tool (thanks to @astrovsky01). Pull Request 13151

• Add bioconductor as valid xref for tools (thanks to @bgruening). Pull Request 13268

• Test cases to verify only admins can import workflows from paths. Pull Request 12513

• Remove deprecated workflow run path through the API. Pull Request 12516

• Type updates (thanks to @common-workflow-lab). Pull Request 12868

• Allow workflows to automatically filter inputs by tag (thanks to @astrovsky01). Pull Request 12930

• Enable macros for workflow scheduler config (thanks to @bernt-matthias). Pull Request 13167

• Remove history service worker Pull Request 12510

• Implement fastAPI prefix handling, run selenium tests against prefix Pull Request 13103

• Hide form fields and button upon successful submission of bug report Pull Request 13237

• Fix toolbox cache Pull Request 13333

• Limit maximum number of discovered files per job Pull Request 13170

• Fixes for HTML sanitization (thanks to @abretaud). Pull Request 13059

• Make admin user list sortable by last login (thanks to @cat-bro). Pull Request 13209

• Support “show all running” in admin job interface Pull Request 13215

• Add config variable for setting tus upload directory Pull Request 13313

• Document gunicorn and nginx Pull Request 13436

• Update interactive tool docs for Gunicorn / dropping uWSGI Pull Request 13470

• Add Migrating from uWSGI to Gunicorn and FastAPI document Pull Request 13480

• Support --preload and worker_id for server processes Pull Request 13514

• Separated data PVC (thanks to @almahmoud). Pull Request 12345

• Revised download() so parallel get() is utilized. Small refactor. (thanks to @kxk302). Pull Request 12522

• More linting for requirements (thanks to @bernt-matthias). Pull Request 12527

• Preserve important dataset metadata when importing/exporting histories. Pull Request 12537

• Modify description of the “database” label Pull Request 12540

• Add Oleg Zharkov to committers group Pull Request 12544

• Add David López to committers group Pull Request 12545

• Update container_resolvers_conf.xml.sample (thanks to @gmauro). Pull Request 12560

• Add test for dataset HTML sanitization interface Pull Request 12573

• FastAPI: migrate history contents routes (thanks to @davelopez). Pull Request 12578

• Update localization directive to trim whitepsace around text content. Pull Request 12580

• Added more caching for github actions which use tox and venv (thanks to @nuwang). Pull Request 12632

• More typing for API tests (especially test_workflows). Pull Request 12636

• Better model store abstractions. Pull Request 12638

• More Python unit test typing fixes. Pull Request 12647

• Annotate more tests as requiring Github to be online. Pull Request 12649

• Change logged-in-as to use username (thanks to @hexylena). Pull Request 12652

• Add buttons to expand and collapse history dataset display in pages Pull Request 12660

• Formalize dependency of galaxy-data package on galaxy.files module. Pull Request 12665

• Check types of modules without type annotations in the their signatures on new modules. Pull Request 12691

• Rev Python tooling to latest mypy release. Pull Request 12695

• Assorted random typing fixes. Pull Request 12696

• Add Tag validation in API requests (thanks to @davelopez). Pull Request 12697

• Framework support for integration tests requiring celery. Pull Request 12700

• Allow passing Pydantic models as arguments to Celery tasks. Pull Request 12701

• Discourage the use of true/falsevalue for boolean test parameters (thanks to @bernt-matthias). Pull Request 12706

• Extend debugging test instructions for GHA Pull Request 12707

• Split integration tests more evenly Pull Request 12711

• Tool linter: simple test for test params absent from inputs (thanks to @bernt-matthias). Pull Request 12723

• Add test for invoking a workflow on a new autocreated history (thanks to @nsoranzo). Pull Request 12773

• More Python type fixes from deferred data branch. Pull Request 12778

• Type fixes for HDAs and LDDAs manager. Pull Request 12780

• FastAPI: migrate Dataset Collections API (thanks to @davelopez). Pull Request 12781

• Type fixes for various visualization backend Python files. Pull Request 12783

• Add various include/exclude patterns for github workflows Pull Request 12787

• Force strict channel priority when building images with mulled (thanks to @rhpvorderman). Pull Request 12788

• More type fixes for various pieces of managers code. Pull Request 12801

• Beta history menu reorg, display fixes. Pull Request 12802

• More type fixes for managers code. Pull Request 12812

• Fixes and test for PDF generation. Pull Request 12813

• Upgrade FastAPI to v0.70.0 (thanks to @davelopez). Pull Request 12836

• Stronger typing of upload code. Pull Request 12845

• Sync Selenium GitHub workflows (thanks to @nsoranzo). Pull Request 12849

• Update all Python dependencies (thanks to @nsoranzo). Pull Request 12858

• Drop legacy uploadpost Pull Request 12861

• Vuefy color input form element (thanks to @OlegZharkov). Pull Request 12867

• Show error codes when running mypy (thanks to @nsoranzo). Pull Request 12894

• Update cwltool pin to 3.1.20211107152837 (thanks to @nsoranzo). Pull Request 12895

• Increase directory check specificity, of particular use with AnVIL (thanks to @luke-c-sargent). Pull Request 12902

• Create codeql-analysis.yml (thanks to @common-workflow-lab). Pull Request 12908

• Improved Upload Provenance and Correctness Pull Request 12912

• Update Python dependencies (thanks to @galaxybot). Pull Request 12916

• Lint for option without text or value (thanks to @bernt-matthias). Pull Request 12921

• FastAPI: migrate datasets API (thanks to @davelopez). Pull Request 12924

• Vuefy Number and Slider Form inputs (thanks to @OlegZharkov). Pull Request 12937

• Allow labeling of subworkflow outputs in parent workflow Pull Request 12939

• Linting: check for test expecting failure with outputs (thanks to @bernt-matthias). Pull Request 12960

• Add CWL conformance API tests (thanks to @nsoranzo). Pull Request 12966

• Allow unit testing tool init to specify paths. (thanks to @common-workflow-lab). Pull Request 12969

• Lint for inputs with redundant name (thanks to @bernt-matthias). Pull Request 12974

• Support running celery when cwd is not galaxy_root by setting $GALAXY_ROOT_DIR Pull Request 12977

• Split run_tool_raw() out of BaseDatasetPopulator.run_tool() (thanks to @nsoranzo). Pull Request 12994

• Move galaxy_tasks decorator to galaxy.celery Pull Request 13000

• Show display applications together with visualizations in center panel Pull Request 13018

• Update Python dependencies (thanks to @galaxybot). Pull Request 13029

• Explicit singularity cache (thanks to @rhpvorderman). Pull Request 13032

• Add “diff-format” Makefile target (thanks to @common-workflow-lab). Pull Request 13034

• Drop support for Python 3.6, add Python 3.10 (thanks to @nsoranzo). Pull Request 13035

• Allow param_value filter to refer to parameters with multiple values (thanks to @bernt-matthias). Pull Request 13039

• Add support for CWL CommandLineTool and ExpressionTool to DynamicToolManager.create_tool() (thanks to @nsoranzo). Pull Request 13041

• Update Python dependencies (thanks to @galaxybot). Pull Request 13051

• Allow admin access to datasets API (thanks to @davelopez). Pull Request 13060

• Drop non-actionable warnings from LibraryPermissionsWarning Pull Request 13063

• Beta History: homogeneous collection indication (thanks to @davelopez). Pull Request 13068

• Add documentation for test/param/metadata in xsd (thanks to @bernt-matthias). Pull Request 13082

• Update Python dependencies (thanks to @galaxybot). Pull Request 13086

• Add tox environment and GitHub workflow for reports startup test (thanks to @nsoranzo). Pull Request 13088

• Allow duplicated static options (thanks to @bernt-matthias). Pull Request 13094

• Beta History: additional small fixes at collection level (thanks to @davelopez). Pull Request 13097

• Add Back button in file source navigation and ftp helper text (thanks to @itisAliRH). Pull Request 13104

• Add job reports for node types and execution times (thanks to @gregvonkuster). Pull Request 13121

• Initial typing for model discover module. Pull Request 13123

• Remove Oleg from committers list Pull Request 13128

• Remove Dave C. from committers list Pull Request 13129

• Update Python dependencies (thanks to @galaxybot). Pull Request 13135

• Fix MetadataValidator (thanks to @bernt-matthias). Pull Request 13139

• Update DatasetError.vue Pull Request 13148

• Assorted Data Libraries fixes (thanks to @davelopez). Pull Request 13159

• Provide even more context to the lint context (thanks to @bernt-matthias). Pull Request 13186

• Skip non-Selenium tests if only lib/galaxy_test/selenium is touched Pull Request 13227

• Add documentation for output action attributes (thanks to @bernt-matthias). Pull Request 13236

• Add openPBS cli support, rebuild CLI test images Pull Request 13251

• Add missing collection types to xsd doc (thanks to @bernt-matthias). Pull Request 13267

• Update dependencies Pull Request 13273

• Only create HDAH entries for undeleted HDAs (thanks to @bernt-matthias). Pull Request 13309

• Add version.json for exposing extra api information about docker container (thanks to @nuwang). Pull Request 13433

• Document gunicorn and apache Pull Request 13439

• Update jobs and cluster documentation Pull Request 13440

• Update performance tracking for Gunicorn Pull Request 13441

• Drop interactive environment build instructions from docs Pull Request 13442

• Create config package, move app-related functionality to app Pull Request 13461

• Fix pgcleanup.py for datasets stored by UUID Pull Request 13474

• Pin gravity to 0.10.0 Pull Request 13483

• Include gravity in sample config Pull Request 13531

• FastAPI: Histories API migration (thanks to @davelopez). Pull Request 12386

• Vue component dangling bracket style fix (prettier upgrade) Pull Request 12428

• Remove unused relationships from model Pull Request 12468

• Remove workflow API hooks for tool shed. Pull Request 12512

• Vueify Form Recursion Pull Request 12518

• FastAPI: Add request wrapper for SessionRequestContext (thanks to @davelopez). Pull Request 12531

• Update SQLAlchemy to 1.4.25 Pull Request 12538

• Establish unittest utils for galaxy-{data,objectstore} packages. Pull Request 12546

• Move API services to their own package (thanks to @davelopez). Pull Request 12548

• Establish galaxy-app unit tests. Pull Request 12549

• Establish galaxy-job-execution unit test directory. Pull Request 12550

• Establish galaxy-job-metrics unit test directory. Pull Request 12551

• Fix up small issues around packaging of galaxy-tool-util code. Pull Request 12552

• Move more webapps unit tests in test/unit/webapps. Pull Request 12554

• Share a tool_util unittest method via packing to fix up unit test dependencies. Pull Request 12555

• Better path handling in app unit tests for packaging. Pull Request 12556

• Selenium abstractions for dataset information. Pull Request 12569

• TS model: declarative mapping + prep for SQLAlchemy 2.0 Pull Request 12666

• Remove unused script and history_delete controller endpoint Pull Request 12668

• Remove ui-table backbone component Pull Request 12671

• Libraries (legacy) backbone entrypoint and component removal Pull Request 12674

• Ignore type in unused function Pull Request 12694

• Misc. fixes for SQLAlchemy 2.0 Pull Request 12698

• Upgrade to lagom 1.4.1 (thanks to @meadsteve). Pull Request 12703

• Remove galaxy.util.getfullargspec (thanks to @bernt-matthias). Pull Request 12755

• Convert install_model to declarative mapping Pull Request 12756

• Mapping tests: restructure, refactor, decouple session and engine, improve Pull Request 12765

• New pyupgrade cleanups (thanks to @nsoranzo). Pull Request 12774

• Refactor workflow bookmark (thanks to @OlegZharkov). Pull Request 12810

• Replace boolean input parameter with Vue component in forms Pull Request 12820

• Replace hidden field input element with Vue Pull Request 12841

• Refactor datasets API (thanks to @davelopez). Pull Request 12847

• Vuefy library folder details modal (thanks to @OlegZharkov). Pull Request 12886

• Remove chart utilities and artifacts from code base Pull Request 12890

• Vuefy DirectoryUri form input field (thanks to @OlegZharkov). Pull Request 12898

• Simplify Augustus datatype sniffer (thanks to @nsoranzo). Pull Request 12905

• Modify logic in history_contents/near to accommodate scroller Pull Request 12914

• FastAPI: Add response wrapper for SessionRequestContext (thanks to @davelopez). Pull Request 12929

• Eliminate a lot of while: True loops in datatype code Pull Request 12942

• Small tweaks to facilitate deferred dataset implementation. Pull Request 12944

• Modifications to next hid_counter generation Pull Request 12948

• Don’t bind model’s MetaData to engine Pull Request 12949

• Vuefy library dataset (thanks to @OlegZharkov). Pull Request 12950

• Assorted mapping cleanup Pull Request 12951

• Move wait_for_invocation_and_jobs() method to BaseWorkflowPopulator (thanks to @nsoranzo). Pull Request 12954

• Avoid setting response headers through trans in datatypes (thanks to @davelopez). Pull Request 12956

• Use lazy="joined" instead of lazy=False Pull Request 12962

• Minor type fixes Pull Request 12963

• Add type hints to JobHandlerQueue Pull Request 12976

• Fix flaky legacy API tests (hopefully) (thanks to @davelopez). Pull Request 12980

• Create select() construct explicitly Pull Request 12983

• Remove unused dataset conversion code Pull Request 12991

• Remove unnecessary list creations (thanks to @nsoranzo). Pull Request 13002

• Don’t use triple-quoted strings as comments (thanks to @nsoranzo). Pull Request 13007

• Misc fixes - round 4 (thanks to @nsoranzo). Pull Request 13026

• Refactor uploadbox / partially remove jQuery Pull Request 13047

• Initial refactoring to separate History rendering and provider components Pull Request 13049

• Log missing version file as warning. Pull Request 13062

• Importing math.inf no longer needs try/except Pull Request 13065

• Avoid imports of history provider internals Pull Request 13098

• Drop tool migration scripts and related code Pull Request 13099

• Remove duplicated pydantic models (thanks to @davelopez). Pull Request 13125

• Remove migrate tools-related code Pull Request 13163

• Replace backref with back_populates Pull Request 13165

• Prevent a future regression Pull Request 13218

• Remove jquery.complexify from everywhere (thanks to @itisAliRH). Pull Request 13228

• Replace custom tour ids in forms with regular DOM identifiers Pull Request 13252

• Drop pkg_resources Pull Request 13454

Fixes

• Large peptide IDs (thanks to @reid-wagner). Pull Request 13261

• Try to unit test more of DictParser in Viz component. Pull Request 13385

• Fix jqplot_bar import, adjust plugin hash saving Pull Request 13493

• Allow trailing semicolon in last column of gff3 (thanks to @bernt-matthias). Pull Request 12673

• Fix gff-version header sniffing (thanks to @nsoranzo). Pull Request 12676

• Fix gff and scidx parsing (thanks to @bernt-matthias). Pull Request 12687

• Version bump galaxy tool util and converter dependency fix Pull Request 12844

• Downgrade bowtie requirement for CONVERTER_fasta_to_bowtie_color_index (thanks to @nsoranzo). Pull Request 12851

• Fix constructive_solid_geometry.py for non_utf8_error (thanks to @jj-umn). Pull Request 13057

• Show yaml files in preview Pull Request 13176

• Enable display of BAM data without sequence info (thanks to @wm75). Pull Request 13219

• Fix containerized NCBI Datasets Genomes data source tool Pull Request 12915

• Update interactivetool_pyiron.xml (thanks to @gmauro). Pull Request 12990

• Add dynamic step to FormNumber range slider (thanks to @davelopez). Pull Request 13233

• FormNumber: notify value change on slider change (thanks to @davelopez). Pull Request 13260

• Always display digest in name for refgenie assets. Pull Request 13403

• Fix UnboundLocalError in sort collection tool (thanks to @davelopez). Pull Request 13429

• Misc fixes - round 2 (thanks to @nsoranzo). Pull Request 12982

• Fix workflow connections for outputs that are not displayed in uploads Pull Request 13174

• Sync tool identifier string with tool version in workflow editor Pull Request 13185

• Allow mapping of collection outputs to parameter inputs Pull Request 13189

• Fix tool id update when updating tool shed tools in editor Pull Request 13196

• Ensure tool_id/content_id is updated when refactoring workflows (thanks to @simonbray). Pull Request 13231

• Fix construction of SelectToolParameter default value Pull Request 13293

• Return actual tool id instead of specified tool id in workflow step Pull Request 13536

• RxJS major version upgrade, client unit testing enhancements. Pull Request 12686

• Polyfill overhaul, fixes. Pull Request 12889

• Fix publicPath and asset handling when using webpack-dev-server for HMR Pull Request 13155

• Bump markdown-it from 12.2.0 to 12.3.2 in /client Pull Request 13205

• Bump engine.io from 4.1.1 to 4.1.2 in /client Pull Request 13206

• Bump follow-redirects from 1.14.4 to 1.14.7 in /client Pull Request 13207

• Bump log4js from 6.3.0 to 6.4.0 in /client Pull Request 13225

• Bump nanoid from 3.1.29 to 3.2.0 in /client Pull Request 13226

• Guard against instance of GenomeIndexToolData Pull Request 12523

• Fix job runner shutdown Pull Request 12744

• Fix parsing of yml job conf file in galaxy.dependencies (thanks to @cat-bro). Pull Request 12893

• Rev pulsar-galaxy-lib. Pull Request 12896

• Don’t pass all Galaxy environment variables to jobs (thanks to @nsoranzo). Pull Request 13011

• Unit test fixes (thanks to @nsoranzo). Pull Request 13033

• Fix re-run with rerun_remap_job_id hiding collection Pull Request 13157

• Fix univa job runner setup without nativeSpecification (thanks to @Smithsonian). Pull Request 13301

• Make __link_file_check more robust Pull Request 13316

• Don’t record version command as part of command line Pull Request 13317

• Fix resuming job when job has optional data parameters Pull Request 13325

• Allow UNIVA destinations without runtime and memory max given in the nativespec (thanks to @bernt-matthias). Pull Request 13343

• Fix header content-length, add test for send_file Pull Request 13120

• Add option for disabling tool shed datatypes Pull Request 13250

• Drop OpenID post authentication protocols Pull Request 13281

• Restore Metadata size limit Pull Request 13315

• Drop uWSGI from scaling documentation Pull Request 13381

• Reimplement collection order test, add wrong order, add expect_test_failure attribute (thanks to @bernt-matthias). Pull Request 10304

• Fix test_sharing_valid_by_id selenium test (thanks to @OlegZharkov). Pull Request 12547

• Update and correct sample object store config file Pull Request 12571

• Fix user_library_import_symlink_allowlist option (thanks to @scholtalbers). Pull Request 12608

• Fix selenium populators to respect the json parameter. Pull Request 12626

• Fix how beta history panel decides when downloads are available. Pull Request 12642

• Typing fixes for various unit tests. Pull Request 12644

• Fix database display for beta history panel. Pull Request 12646

• Fix deprecation warnings from the threading module (thanks to @nsoranzo). Pull Request 12659

• Join thread that hosts asyncio loop for embedded uvicorn Pull Request 12710

• Removing unusable Name field from Collections upload (thanks to @assuntad23). Pull Request 12736

• Removing last character of pair name for Paired List Collections if it’s a . or _ (thanks to @assuntad23). Pull Request 12739

• Avoid double ‘/’ when generating fully qualified API URLs in API tests (thanks to @davelopez). Pull Request 12791

• Create new history for anonymous API users via history/current_histor… Pull Request 12829

• Avoid console error when cloning newly created nodes Pull Request 12831

• GxITs: don’t always add trailing slash to entry point url (thanks to @abretaud). Pull Request 12833

• fix typo in bookmarking (thanks to @OlegZharkov). Pull Request 12838

• Fix bookmarking workflow twice (thanks to @OlegZharkov). Pull Request 12840

• Temporary downgrade FastAPI to v0.68.2 (thanks to @davelopez). Pull Request 12856

• Fix startup with edam (thanks to @abretaud). Pull Request 12860

• Fixes for packages (thanks to @nsoranzo). Pull Request 12883

• Fix parse_input_sources() method to return a list (thanks to @nsoranzo). Pull Request 12888

• Consider a history not new once there are any items in it Pull Request 12897

• Bump tensorflow from 2.5.1 to 2.5.2 in /lib/galaxy/dependencies Pull Request 12900

• Sync package deps with pyproject.toml (thanks to @nsoranzo). Pull Request 12904

• Fix menu overflow in right panel Pull Request 12906

• Tweak docs for container_resolver_* options Pull Request 12910

• Fix installation of tools with biotools id Pull Request 12919

• Fix linter for select inputs (thanks to @bernt-matthias). Pull Request 12920

• Fix OpenAPI docs not rendering (thanks to @davelopez). Pull Request 12923

• Fix default value of runners in job_conf_dict (thanks to @nsoranzo). Pull Request 12926

• Provide 2 types of scoped_session in DI (initially “type of session parameter should be scoped_session”) Pull Request 12931

• Move the titleonly option to input element component Pull Request 12932

• fix value_in_data_table validator for multiple selects (thanks to @bernt-matthias). Pull Request 12936

• Update link to “Python for Biologists” page. (thanks to @neoformit). Pull Request 12946

• Try cimg/node:14 to fix circleci js builds Pull Request 12947

• Misc fixes (thanks to @nsoranzo). Pull Request 12972

• BugFix: Update social-auth-core library version to fix OIDC problem (thanks to @IslamHeggy). Pull Request 12973

• Fix Rerun in the new form (thanks to @OlegZharkov). Pull Request 12984

• Show error message when history id is invalid (thanks to @OlegZharkov). Pull Request 12985

• Reconstruct separate scoped session for ToolShedRepositoryCache Pull Request 12989

• Misc fixes - round 3 (thanks to @nsoranzo). Pull Request 12993

• Bump python-ldap from 3.2.0 to 3.4.0 in /lib/galaxy/dependencies Pull Request 13003

• Fix known marcos typo Pull Request 13009

• Refactor Sentry middleware/client changes for Tool Shed Pull Request 13010

• Drop stream_template_mako function, replace with fill_template_mako Pull Request 13017

• Copy HDCA member items to new history when copying history Pull Request 13021

• Make dataset display route sessionless as well as anonymous Pull Request 13024

• Trigger visualization update on chart initialization Pull Request 13025

• Fix running test/integration/test_remote_files.py directly. Pull Request 13038

• Misc fixes - round 5 (thanks to @nsoranzo). Pull Request 13044

• Fix dynamic optional + multiple select parameters: allow to select no option (thanks to @bernt-matthias). Pull Request 13048

• Add tools to IMPLICITLY_REQUIRED_TOOL_FILES in tools/__init__.py (thanks to @cat-bro). Pull Request 13050

• Only check profile version in Galaxy Pull Request 13055

• Fix private history publishing (thanks to @davelopez). Pull Request 13056

• Improve dataset search help (thanks to @wm75). Pull Request 13058

• Change default file_path variable for galaxy reports (thanks to @quacksawbones). Pull Request 13067

• Drop old sqlalchemy patterns that break reports app Pull Request 13069

• Add iRODS resource name in calls to irods (thanks to @kxk302). Pull Request 13072

• Fix Cloud object store (thanks to @bioflowy). Pull Request 13074

• Use yield_per option to limit amount of ORM objects loaded into memory Pull Request 13076

• Fix issue with uploading cached file to irods (thanks to @kxk302). Pull Request 13080

• Fix tag attribute parsing on input element (thanks to @astrovsky01). Pull Request 13081

• Fix dataset details button when using prefix Pull Request 13092

• Fix center panel reload when clicking help button Pull Request 13093

• Limit possible size of info field, read only 100 MB of stdio Pull Request 13096

• Disable cleanup thread for cloud object store in set metadata (thanks to @bioflowy). Pull Request 13102

• Prevent select all in FilesDialog when no entries and select empty resource (thanks to @itisAliRH). Pull Request 13107

• Fix selenium test via dropping redundant test case Pull Request 13112

• Delay iframe creation for news until clicked Pull Request 13116

• Webhooks robustification for news and gtn Pull Request 13118

• Fix routing for tool execution from gtn webhook Pull Request 13130

• Fix history import for datasets with tags Pull Request 13134

• Add more required dependencies for installed Galaxy Pull Request 13143

• Path resolution fixes for installed Galaxy Pull Request 13147

• Limit lifetime of repository cache Pull Request 13154

• converting forward and reverse filters to reactive Vue array (thanks to @assuntad23). Pull Request 13166

• Fix stdio parsing (thanks to @bernt-matthias). Pull Request 13178

• Catch exceptions when job.user is None (thanks to @rhpvorderman). Pull Request 13179

• Fix redirect to login page when login is required to perform operations Pull Request 13188

• Fix workflow invocation name overflow (thanks to @davelopez). Pull Request 13193

• Fix metadata source access in tool shed Pull Request 13202

• Fix error getting toolshed repo metadata when no repo found (thanks to @simonbray). Pull Request 13203

• Bugfix for allowing +’s in tool urls Pull Request 13204

• Fix test_deserialize_* unit tests (thanks to @nsoranzo). Pull Request 13208

• Fix hide collections in batch (thanks to @davelopez). Pull Request 13214

• Handle unique tag name constraints Pull Request 13216

• Ensure that jQuery updates drop target locations during dragging Pull Request 13217

• Fix adding new files via tarball upload Pull Request 13230

• Initialize error attribute in input model for workflows Pull Request 13246

• Fix imported sub-workflows cannot be edited (thanks to @davelopez). Pull Request 13254

• Fix expect_test_failure for expect_num_outputs (thanks to @bernt-matthias). Pull Request 13265

• Fix gravity requirement for Poetry (thanks to @nsoranzo). Pull Request 13278

• Fix dataset details and drag and drop Pull Request 13290

• Fix stopping ITs on slurm Pull Request 13304

• Ensure Notification API is available prior to trying to use it Pull Request 13322

• Fix toolbox handling of spaces in old tools Pull Request 13347

• Fix macro parsing (thanks to @bernt-matthias). Pull Request 13373

• Clarify that history exports are not kept forever Pull Request 13389

• Fix history search help popover not closing on click outside (thanks to @davelopez). Pull Request 13390

• Ensure $GRAVITY_STATE_DIR is present in venv activate script any time run.sh/common_startup.sh is called normally Pull Request 13392

• Use a2wsgi to serve WSGI app Pull Request 13396

• Dataset annotations are optional and should not be required Pull Request 13420

• Fix repository uploads with remove_repo_files_not_in_tar Pull Request 13425

• Wrap reports app in static, fix tool shed entry point Pull Request 13430

• enabling Reset button for Rule Builder tab (thanks to @assuntad23). Pull Request 13443

• Initial fix for quay.io repo query issue Pull Request 13468

• Add profile version to ethercalc Pull Request 13469

• Backport and fix webapps tests Pull Request 13478

• Use timeout instead of interval when polling, optionally terminate polling Pull Request 13485

• Pin corresponding playbook repo to sync with Galaxy release (thanks to @nuwang). Pull Request 13497

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The Galaxy Team