20.05

Enhancements

• New data types for OpenMS (thanks to @bernt-matthias). Pull Request 8109

• Refactor Workflow Run Form Toward Vue (part 1) Pull Request 9138

• Refactor Workflow Run Form Toward Vue (part 2) Pull Request 9147

• Replace Workflow Editor Tool Panel with Vue component Pull Request 9201

• Replace right panel in Workflow Editor with Vue component Pull Request 9249

• Replacing Workflow Editor Node with Vue-component Pull Request 9332

• Render workflow node connections using d3 Pull Request 9471

• Make Toolshed Python 3 compatible & tests Pull Request 9528

• Migrate interactive tools from EU server (thanks to @astrovsky01). Pull Request 9559

• Allow Tool Data Tables to be backed by refgenie Pull Request 9600

• Startup speedups (XML doc cache, delay non-essential tool param parsing & indexing) Pull Request 9610

• Enable admin to resend activation email Pull Request 9154

• Create Python3 virtualenv by default (thanks to @nsoranzo). Pull Request 9344

• iRODS object store rewrite (thanks to @kxk302). Pull Request 9438

• Tool recommendation (thanks to @anuprulez). Pull Request 9440

• Tool recommendations in workflow editor (thanks to @anuprulez). Pull Request 9569

• Added whitelisting option for user registration (thanks to @MiguelJulia). Pull Request 9501

• Editor as visualization (thanks to @OlegZharkov). Pull Request 9531

• Chira visualization for Chimeras (thanks to @OlegZharkov). Pull Request 9562

• Datasource tool for SRA manifest Pull Request 9613, Pull Request 9892

• Skip visualization build, if no changes were registered (thanks to @OlegZharkov). Pull Request 9634

• Add tpr datatype (thanks to @simonbray). Pull Request 9244

• Add datatypes for xcms and camera (thanks to @computational-metabolomics). Pull Request 9470

• index with -c flag for large bam (one region larger than 2**29 - 1) (thanks to @FredericBGA). Pull Request 9570

• Sniffer for multi-member zip archives (thanks to @lecorguille). Pull Request 9595

• Followup to shed tool static fixes Pull Request 9450

• Remove deprecated interpreter attribute from tools <command> (thanks to @nsoranzo). Pull Request 9490

• Resize D3 tree and make it responsive (thanks to @anuprulez). Pull Request 9547

• Fix ITs to work in remote Kubernetes Pull Request 9614

• Fix galaxy_tool_util for composite file input testing in workflows. Pull Request 9312

• Refactor toward testing workflow collection outputs. Pull Request 9340

• Remove Backbone and Globals dependency from Workflow client code Pull Request 9346

• Allow anonymous downloading of public workflows Pull Request 9736

• MS Edge Fixes Pull Request 9289

• Refactor more of jobs admin component toward API. Pull Request 9093

• make more tool parsing errors contain id (thanks to @bernt-matthias). Pull Request 9139

• “Normalize” more custom functions in admin jobs index. Pull Request 9157

• Job Lock VueJS component. Pull Request 9181

• add a new function to get the local ip address (thanks to @gmauro). Pull Request 9353

• Integration test for GxITs against remote proxies. Pull Request 9504

• paramiko: load system host keys (thanks to @eancelet). Pull Request 9553

• Optimize setting external ID for jobs. Pull Request 9691

• Enable manual user activation Pull Request 9143

• Skip migration if uninitialized database exists Pull Request 9491

• Add Okta as OIDC authentication option (thanks to @selten). Pull Request 7497

• Added trigger to dataset table to update history.update_time Pull Request 8187

• Notifications on job completion (thanks to @astrovsky01). Pull Request 8427

• Issue #8445: Clicking on user/email in User menu triggers a page refresh - fix (thanks to @janani-prasad). Pull Request 8644

• Third Party Identity Management (thanks to @juleengraham). Pull Request 9060

• Disable the admin_toolshed controller (except for tests). Pull Request 9072

• Upgrade to Fontawesome 5 Pull Request 9101

• Add a test for a tool with from_working_dir, outputs_to_working_directory and pulsar (thanks to @bgruening). Pull Request 9108

• Client build work (HMR, build upgrades, refactoring asset placement) Pull Request 9123

• Correct typos, update location of api tests Pull Request 9158

• Add more repository installation test cases Pull Request 9160

• Add support for logging out of OIDC Identity Provider (thanks to @machristie). Pull Request 9162

• Vue-ify Upload Dialog w/small fixes Pull Request 9167

• Update galaxy.tool_util.cwl for latest changes in CWL branch. Pull Request 9175

• More progress on Tool shed cleanup Pull Request 9186

• Full Python dependencies update (thanks to @nsoranzo). Pull Request 9188, Pull Request 9402, Pull Request 9529, Pull Request 9697

• Allow mixed store_by objectstore configurations. Pull Request 9197

• implement workflow bookmark selenium test (thanks to @OlegZharkov). Pull Request 9208

• Use a Galaxy root path with a space for integration tests (thanks to @nsoranzo). Pull Request 9223

• implementing a global tools-view component + schema.org support (thanks to @OlegZharkov). Pull Request 9261

• Add icons to dropdowns in dataset and workflow list Pull Request 9273

• extend config file inputs tests (thanks to @bernt-matthias). Pull Request 9279

• Do not strip tab characters from data_column reference and clarify documentation for use_header_names (thanks to @bernt-matthias). Pull Request 9291

• Update CONTRIBUTING.md (thanks to @nsoranzo). Pull Request 9299

• Add more info to debug logging for loading datatypes. Pull Request 9301

• Add do_not_cache decorator, apply to codebase. Pull Request 9311

• Use Bootstrap components to build the Workflow Editor Toolbar Pull Request 9324

• implement selenium test User->Preferences->Manage information (thanks to @OlegZharkov). Pull Request 9355

• Fix success message in user preferences, add help text to toolbox filter page Pull Request 9368

• CSS changes for a modern look and feel (thanks to @bedroesb). Pull Request 9386

• Added conda python update (thanks to @astrovsky01). Pull Request 9390

• Replace editor grid image with css, add editor client unit tests Pull Request 9392

• Vuefy interactive tools (thanks to @OlegZharkov). Pull Request 9409

• Add delta_frac for sim_size to specify relative file size differences (thanks to @bernt-matthias). Pull Request 9425

• Make mutable_config_dir configurable + rename Pull Request 9444

• Remove virtualenv<20 requirement for mulled tests (thanks to @nsoranzo). Pull Request 9447

• Remove mapping related abstraction classes from workflow client, increase node header contrast Pull Request 9474

• Add eslint rule to check for invalid slot specifications Pull Request 9481

• Another undocumented option: job metrics path (thanks to @hexylena). Pull Request 9482

• Document maxpctfull objecto store option (thanks to @hexylena). Pull Request 9498

• Selenium Multi-History View (thanks to @OlegZharkov). Pull Request 9505

• Adjust dataset error reporting page, remove email option, remove long info text Pull Request 9508

• Drop remaining Python 2.7 CircleCI tests (thanks to @nsoranzo). Pull Request 9518

• Implementation selenium test for user change password (thanks to @Realjuan). Pull Request 9521

• Rename and modify current_history_contents method Pull Request 9526

• Improvement to the selenium test to change password from user preferences (thanks to @Realjuan). Pull Request 9545

• Implementation of Selenium test for signout from user preferences (thanks to @Realjuan). Pull Request 9546

• Move OSX startup tests to github CI, drop travis tests Pull Request 9563

• Check if path is set before joining Pull Request 9568

• Sort Tool Search Result by ranking (thanks to @juleengraham). Pull Request 9579

• TS performance fixes Pull Request 9580

• Vuefy Job Destination Parameters (thanks to @OlegZharkov). Pull Request 9583

• Fix kubernetes test failures again Pull Request 9585

• Enabled various object store types to store data objects by uuid. (thanks to @kxk302). Pull Request 9609

• Add IDs to admin links and selenium navigation. Pull Request 9616

• Feature/refactor rule builder (thanks to @assuntad23). Pull Request 9619

• Add selenium test for admin toolshed operations. Pull Request 9628

• Add unit tests for all schema-defined config properties Pull Request 9631

• Officially allow adding new datatypes to the latest tagged release (thanks to @nsoranzo). Pull Request 9632

• Update the main readme with new Python version Pull Request 9635

• Minor IT doc clarification Pull Request 9668

• Enhance toolshed selenium test. Pull Request 9678

• Optimize history_content union and filtering query Pull Request 9680

• Add CSS class to messages in error report pages to make errors more visible (thanks to @hexylena). Pull Request 9690

• Feature/3937 advanced search tooltip (thanks to @assuntad23). Pull Request 9696

• Rename function, params in ConfigSerializer Pull Request 9247

• Make str.join()s more efficient (thanks to @nsoranzo). Pull Request 9258

• Faster and cleaner set creation (thanks to @nsoranzo). Pull Request 9300

• Remove broken script (thanks to @nsoranzo). Pull Request 9302

• Clean up old ‘blue’ style path, update documentation and samples Pull Request 9306

• Consistent “import” of maketrans (thanks to @nsoranzo). Pull Request 9351

• Move schema loading/validating code out of config Pull Request 9371

• Remove more duplication from TS, galaxy config Pull Request 9379

• Unify default values used for delta (sim_size) (thanks to @bernt-matthias). Pull Request 9439

• Vue slot refactoring Pull Request 9443

• Move sanitize_whitelist into mutable_config_dir Pull Request 9455

• Use auto_create functionality of get_private_user_role() (thanks to @nsoranzo). Pull Request 9509

• Combine selenium tests for creating and switching histories Pull Request 9527

• Eslint one-var spec / airbnbstyle Pull Request 9532

• unify usage of Popen (thanks to @bernt-matthias). Pull Request 9544

• Prettier 2.0 Pull Request 9552

• Abstract ObjectStore interface implementation Pull Request 9554

• Misc. refactoring of galaxy+TS config Pull Request 9582

• Use PyGithub for issue creation Pull Request 9637

• clean up code to use helper function instead (thanks to @lawrence14701). Pull Request 9643

• Respect retry-after header, raise on unexpected status codes Pull Request 9659

• restore tool_util.deps.commands (thanks to @bernt-matthias). Pull Request 9707

Fixes

• Update charts entrypoint inclusion of dist artifacts Pull Request 9511

• Python3 compatible SnpEff and SnpSift metadata detection (thanks to @wm75). Pull Request 9282

• Add PAF, GFA1 and odgi datatypes (thanks to @nsoranzo). Pull Request 9592

• Add xg, vg and protobuf datatypes (thanks to @bgruening). Pull Request 9593

• Fix gff3.gz and gff3.bz2 datatypes Pull Request 9731

• Use right extension in bz2_to_uncompressed.xml Pull Request 9734

• Fix disappearing datatypes after restart Pull Request 9835

• fix error in bundled tool: shrimp_color_wrapper (thanks to @bernt-matthias). Pull Request 9665

• extract_genomic_dna.py: import Comment, Header from bx.tabular.io instead of bx.intervals.io (thanks to @cat-bro). Pull Request 9748

• Move some tools that no longer need galaxy on the PATH (thanks to @bernt-matthias). Pull Request 9850

• Fix workflow list filtering dropdown Pull Request 9468

• Fix workfow parameter connections and default values Pull Request 9648

• Fix ChangeOutputDatatype being dropped on node update Pull Request 9676

• Trigger onchange event, fixes tool version changes being lost Pull Request 9695

• Input dataset module format filtering fix; Pull Request 9884

• fix for python3 and GEDA, was getting “Connection closed at byte 0” Pull Request 9507

• Checkbox bugfix Pull Request 9667

• Fix none type exception in provided metadata handling. Pull Request 9173

• Handles floats correctly in ByteSize (thanks to @pcm32). Pull Request 9418

• unicodify message (thanks to @ieguinoa). Pull Request 9494

• Fixes for embedded Pulsar with MQ (with tests) Pull Request 9519

• Fix outputs written to storage despite outputs_to_working_directory Pull Request 9683

• Fix collection mapping in extended metadata mode. Pull Request 9709

• Force container image names to lower case to satisfy Docker (thanks to @nuwang). Pull Request 9733

• Make watcher more resilient to missing files (thanks to @nuwang). Pull Request 9738

• Improved exception handling for kubernetes runner (thanks to @nuwang). Pull Request 9751

• Check dataset is accessible and use payload in job error API (thanks to @nsoranzo). Pull Request 9753

• Fix the cleanup condition when job state is OK and cleanup_job is set as “onsuccess’ (thanks to @gmauro). Pull Request 9761

• Migrate condor runner to jwd for job-files (thanks to @bgruening). Pull Request 9833

• Fix incorrect variable assignment Pull Request 9907

• Fix vue helper in admin router, fixes toolshed installation, avoids console errors Pull Request 9220

• Fix default quota creation message. Pull Request 9479

• Fix data manager table headers Pull Request 9480

• Save integrated tool panel once on toolbox reload Pull Request 9487

• Cannot find migrate directory for tools database (thanks to @phac-nml). Pull Request 9699

• Fix S3 issue discovered during admin training (thanks to @hexylena). Pull Request 7294

• Make failing to load tools from a tool_dir non-fatal. Pull Request 9106

• Fix incorrect reference to app (thanks to @nuwang). Pull Request 9159

• Missing env in AskOmics IT (thanks to @xgaia). Pull Request 9177

• Check return value of quick_load Pull Request 9185

• Fix sending email error on python-3.7 (thanks to @shenweiyan). Pull Request 9204

• Properly quote paths in upload tool (thanks to @bernt-matthias). Pull Request 9222

• Fix reference in workflows API docs (thanks to @nsoranzo). Pull Request 9259

• Fix target_str_to_targets Pull Request 9268

• Do not test config_dir default value Pull Request 9288

• Remove a dead symlink (thanks to @abretaud). Pull Request 9292

• Fixes reports app under py3 Pull Request 9305

• Allow setting container path for docker_volumes (thanks to @AndreasSko). Pull Request 9310

• Skip test_config_option[build_sites_config_file] (thanks to @nsoranzo). Pull Request 9357

• fix special characters in citation field (thanks to @OlegZharkov). Pull Request 9373

• Use ES6 function declaration to handle error response in workflow form Pull Request 9412

• Fix first_startup Travis tests (thanks to @nsoranzo). Pull Request 9423

• Use a Galaxy root path with a space for converters and mulled tests (thanks to @nsoranzo). Pull Request 9429

• Fix test_run_simple() test broken on Python 2 by virtualenv 20.0.5 (thanks to @nsoranzo). Pull Request 9458

• Use browser locale over global default Pull Request 9460

• Fix login handling w/ redirects and user creation disabled. Pull Request 9462

• Add missing pygithub dev-requirement (thanks to @nsoranzo). Pull Request 9463

• Drop manage_dependency_relationships option Pull Request 9465

• fix options_filter_attribute: needs to be str (thanks to @galaxyproject). Pull Request 9466

• History Dropdown Fix Pull Request 9469

• Print error message if no action is selected in pgcleanup script (thanks to @nsoranzo). Pull Request 9489

• Drop custom json encoding for tool test API endpoint (thanks to @nvk747). Pull Request 9496

• Keep status code on message exception and history import/export fixes Pull Request 9500

• Fixed tool locations (thanks to @astrovsky01). Pull Request 9512

• Update the current_history method in navigates_galaxy.py Pull Request 9514

• Free space before running tests Pull Request 9533

• History import/export fixes Pull Request 9535

• Retry reading tool conf on IOError Pull Request 9537

• Fix citation ids and vue unit test in ToolsView (thanks to @OlegZharkov). Pull Request 9538

• Bump tensorflow from 1.12.2 to 1.15.2 in /lib/galaxy/dependencies (thanks to @galaxyproject). Pull Request 9540

• Incremental indexing for tool shed whoosh indexes Pull Request 9541

• fix documentation for data checksum attribute (thanks to @bernt-matthias). Pull Request 9543

• Prevent exception in toolshed if userid is ‘current’ Pull Request 9548

• Fix setting annotation that contains only integers Pull Request 9549

• Fix docs to update conda from conda-forge (thanks to @nsoranzo). Pull Request 9550

• Disable workflow parameter switch for data inputs, augment form handling Pull Request 9551

• Hide LDDA when creating collection in library interface Pull Request 9561

• Fix indexing script Pull Request 9565

• Assign random password in user manager if none specified (thanks to @nuwang, @nsoranzo). Pull Request 9587, Pull Request 9851

• Fix removal of workflow outputs from workflow nodes in editor Pull Request 9606

• Fix ELIXIR AAI (thanks to @lecorguille). Pull Request 9620

• Fix tensorflow bug (thanks to @anuprulez). Pull Request 9622

• Change session timeout redirect URL to login entrypoint. Pull Request 9626

• Changed CSS overflow property from scroll to hidden to make table scrollable (thanks to @assuntad23). Pull Request 9627

• fix links in Galaxy xsd docs (thanks to @bernt-matthias). Pull Request 9633

• Fix TypeError: OSError object is not subscriptable under Python 3 (thanks to @nsoranzo). Pull Request 9640

• Fix vcf_bgzip mimetype, allow cors, tbi from metadata element Pull Request 9653

• Hide “python: not found” error when Python 2 is not installed (thanks to @nsoranzo). Pull Request 9657

• Fix for time.clock() removal in Python 3.8 (thanks to @nsoranzo). Pull Request 9666

• Fixed an issue in object store integration tests (thanks to @kxk302). Pull Request 9677

• Plugin build hash bugfix Pull Request 9679

• Backport auth process lock fix Pull Request 9681

• Update documentation (thanks to @nsoranzo). Pull Request 9693

• Rename galaxy.util.logging to galaxy.util.custom_logging Pull Request 9705

• Make collection import from library import into correct history Pull Request 9715

• Fix workflow steps import feature in workflow editor Pull Request 9724

• Fix custos credential fetching in python3 Pull Request 9726

• oidc-based authnz provider overhaul; breaking changes for keycloak Pull Request 9730

• Sort Workflow list by last updated time instead of created time Pull Request 9740

• Remove dummy tool sequence (thanks to @anuprulez). Pull Request 9752

• Switch to lxml for xml parsing Pull Request 9759

• Set UTF-8 for parsing tool xml (thanks to @AndreasSko). Pull Request 9760

• inputs config file generation depend on profile (thanks to @bernt-matthias). Pull Request 9776

• Pass through IOError/OSError in tool_shed parse_xml Pull Request 9781

• Maintain whitespace when parsing token from xml Pull Request 9815

• Log exception if reading tool file failed unexpectedly Pull Request 9816

• Drop custom in-process lock class Pull Request 9817

• Update NoseHTML to 0.4.6 for Python 3.8 compatibility (thanks to @nsoranzo). Pull Request 9821

• Tolerate exception in container resolution Pull Request 9824

• Invalidate tool cache when tool modified outside of Galaxy Pull Request 9866

• Custos spec fixes Pull Request 9889

• Fixes for flake8 3.8 and bugbear (thanks to @nsoranzo). Pull Request 9896

• Fix webpack import proxy prefix Pull Request 9898

• Fix extra preference values leaking between requests (thanks to @nuwang). Pull Request 9913

• Rewrite check_html() and Text.count_data_lines() to read a chunk of each line (thanks to @nsoranzo). Pull Request 9920

• Make cookie handling more robust Pull Request 9921

• Enable regex validator to validate lists of values. Pull Request 9925

• oidc: fix dict_keys does not support indexing (thanks to @almahmoud). Pull Request 9931

• Move the --debug flag after the conda subcommand (thanks to @nsoranzo). Pull Request 9932