15.10

Enhancements

• Greatly enhance the reports application - including improved styling, new landing page, pagination, and sparklines. Huge thanks to @Airistotal. Pull Request 370, Pull Request 410, Pull Request 609, Pull Request 472, Pull Request 576, Pull Request 678 Pull Request 675, Pull Request 584

• Enhanced upload tool - with support for composite types and improved styling. Pull Request 605, Pull Request 620, Pull Request 577, Pull Request 628

• Improved API and UI for data libraries - including new support for library folder management and search. Pull Request 806, Pull Request 820

• Expose more history panel options for collection datasets. Pull Request 854

• Improve UI encapsulation for panel rendering, iframes and tool forms. Pull Request 706, Pull Request 739, Pull Request 786

• Implement whitelist for tools that generate HTML. Pull Request 510

• Add regex_replace tool dependency install action. Pull Request 457

• Document Galaxy interactive environments (GIEs). (Thanks to @hexylena.) Pull Request 803

• Explicit project procedure language on reversions and WIP. (Thanks to @hexylena.) Pull Request 556

• Readme improvemenets - GitHub issues, security email contact and CI testing (Thanks to @nsoranzo.) Pull Request 574

• Remove history controller methods. Pull Request 578

• Remove older references to get_disk_size and associated methods in histories code. Pull Request 582

• Cleanup of the Tool Shed’s url handling methods. Pull Request 586

• Remove old cloudlaunch in favor of new web application. Pull Request 597

• Enable a Grunt develop mode. Pull Request 601

• Allow tools to explicitly produce nested collections. Pull Request 538

• Update output actions code for some collection operations. Pull Request 544

• Allow discover_datasets tag to use format attribute (instead of ext). Pull Request 764

• Implement min and max attributes for multiple data input parameters. Pull Request 765

• Style fixes a test fixes for all tool shed code. (Thanks to @nsoranzo.) Pull Request 650

• Style fixes for lib/galaxy_utils/. (Thanks to @nsoranzo.) Pull Request 604

• Style fixes for test/. (Thanks to @nsoranzo.) Pull Request 653

• Style fixes for contrib/ and lib/tool_shed/. (Thanks to @nsoranzo.) Pull Request 708

• Style fixes violated when merging from release_15.07. (Thanks to @nsoranzo.) Pull Request 688

• Style fixes for tool shed database migrations. (Thanks to @nsoranzo.) Pull Request 770

• Changed refresh time on reports homepage (Thanks to @Airistotal.) Pull Request 609

• Remove unused fastx_clipper_sequences.txt file. (Thanks to @lparsons.) Pull Request 611

• Move manual_builds.txt to manual_builds.txt.sample. (Thanks to @lparsons.) Pull Request 612

• Expose tool shed version through API. Pull Request 613

• Improvements to history API allowing fetching of histories shared with given user. Pull Request 614

• Allow deserializing dataset permissions via the API. Pull Request 640, Pull Request 496

• Merge nearly-identical methods in shed_util_common module. Pull Request 651

• Expose tool config file path to admins via the API. Pull Request 652

• Add Galaxy developer documentation section to docs. (Thanks to @hexylena.) Pull Request 654

• Password reset improvements. Pull Request 655

• Allow accessing repeat and conditional elements in workflow post job action parameters. Pull Request 662

• Use new path variable syntax available since Routes 1.9. (Thanks to @nsoranzo.) Pull Request 665

• Lazy-load histories into multi-history view. Pull Request 676

• Use standard Galaxy message box styles on tool help texts that use rST admonitions. Pull Request 685

• Set a default value for copy history dialog radio input (to copy all). Pull Request 693

• Remove various code duplication. (Thanks to @hexylena.) Pull Request 694

• Use setup.py for Python all installations during dependency installation. (Thanks to @bgruening.) Pull Request 698

• Reorganize procedures documentation content. (Thanks to @nsoranzo.) Pull Request 702

• Upgrade sqlalchemy to 1.0.8. Pull Request 709

• Enhance GenomeSpace tools to report the GS tool name. Pull Request 711

• Add Oxli datatypes. (Thanks to @dib-lab.) Pull Request 721

• Extend root controller to allow specifying a history id. Pull Request 725

• Fix multi-history copy/new to set the history as current. Pull Request 727

• Fix workflow post job actions when rerunning a job. Pull Request 730

• Trigger iframe event for history. Pull Request 732

• Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. Pull Request 738

• Do not explicitly require pexpect Python dependency. Pull Request 741

• API and UI enhancements for history copying. Pull Request 742

• Remove deprecated objectstore options from sample documentation. Pull Request 748

• Improved jobs API documentation. Pull Request 751

• Improved state tracking of collections in history panel. Pull Request 755, Pull Request 819

• Updates and fixes for dockerized Galaxy testing. Pull Request 759

• When submitting tool error reports, include ‘old’ tool id as part of subject line. Pull Request 761

• Eliminate use of bare exceptions from code. Pull Request 763

• Add encoded IDs to job error reports and also include a link to show_params Pull Request 771

• In log of collecting job metrics, print id of has_metrics object Pull Request 772

• Add docker command wrapper. (Thanks to @scholtalbers.) Pull Request 777

• Unify the docker command, command_inject, and command_wrapper (Thanks to @hexylena.) Pull Request 782

• Test case to prevent regression of #753. Pull Request 784

• Refactor interactive environment launching to use Docker’s -P option. (Thanks to @hexylena.) Pull Request 790

• Print has_metrics class name instead of object memory address. (Thanks to @nsoranzo.) Pull Request 791

• Improved state tracking of datasets in the history panel. Pull Request 793

• Add sentry configuration option and doc to galaxy.ini.sample. Pull Request 799

• Small tweaks to tool loading. Pull Request 813

• Implment request timing middleware via statsd. Pull Request 821

• Various small run_tests.sh fixes/enhancements. Pull Request 825

• Remove test broken after #786. (Thanks to @nsoranzo.) Pull Request 828

• Improved file handling in local runner. Pull Request 830

• Swap debug mode to be off by default in galaxy.ini.sample. Pull Request 840

• Update documentation for the gff_filter_by_attribute tool (Thanks to @bgruening.) Pull Request 842

• Allow reuse of parent /tmp directory in dockerized testing. Pull Request 843

• More small adjustments to test script run_tests.sh. Pull Request 844

• UCSC tool cleanup - remove unused, deprecated code and add citations to existing tools. Pull Request 846

• Add more distribution tool citations. Pull Request 847

• Remove unused echo tool Pull Request 848

• Update interactive environments for this release. (Thanks to @hexylena.) Pull Request 849

• Enhancements for IPython interactive environment allowing it run in certain deployments. (Thanks to @scholtalbers.) Pull Request 462

• Update style tools grunt-contrib-less, grunt-spritesmith. Pull Request 473

• Preserve tags and annotations when copying datasets between histories. Pull Request 482

• Implement grunt task for compiling handlerbars templates. Pull Request 484

• Improve shortcut logic in Python job code. Pull Request 488

• Do not render dataset selector when there are no datasets to select in history. Pull Request 491

• Clean up the formatting on mapping.py Pull Request 492

• Allow interactive environments to have their own static base url. Pull Request 500

• Improve history dataset manager testing to verify set order of tags. Pull Request 493

• Enhance directory handling for tool shed installations. (Thanks to @gregvonkuster.) Pull Request 511

• Improved tag handling for anonymous users. Pull Request 516

• Allow uninstalling multiple toolshed repositories at once. Pull Request 517

• Allow the user to add the dataset for Trackster visualization to and existing visualization. Pull Request 526

• Tool extract_genomic_dna tool to support for 2bit files from local data. (Thanks to @yhoogstrate.) Pull Request 529

• Remove unused serializer _get_history_data. Pull Request 530

• Render nice_size on the client. Pull Request 532

• Swap track_jobs_in_database to be True by default. Pull Request 533

• Update client libs: farbtastic, jqtouch, bib2json Pull Request 536

• Standardize nice_size() import. (Thanks to @nsoranzo.) Pull Request 537

• Remove older, unused history CSS rules. Pull Request 539

• Allow ordering of the history index list using an order query parameter. Pull Request 540

• Improve job config error message when no handler elements are defined. Pull Request 543

• Allow use of History disk_size as a column in queries. Pull Request 550

• Implement API for dealing with converted datasets. Pull Request 553

• Include tool shed API information in Galaxy’s documentation. Pull Request 569

• Stop creating unneeded database/message.mako.py file. Pull Request 575

• Page Saved Histories at 10 histories. Pull Request 581

• Remove older references to get_disk_size and associated methods. Pull Request 582

• Remove osme unused files in /static. Pull Request 583

• Minor cleanup of some Python iterator usages. Pull Request 589

• Minor tool shed code style cleanup. Pull Request 591

• Include valid_tools as part of metadata returned with the repository install information. Pull Request 592

• New API for published histories. Pull Request 594

Fixes

• Fix batch mode input in new tool form UI. (Thanks to @ericenns.) Pull Request 568

• Tool lineage fixes. (Thanks to @nsoranzo.) Pull Request 596

• Fix bug in reload API where id wasn’t recognised. (Thanks to @hexylena.) Pull Request 619

• Correct typo in tool shed action handler code. (Thanks to @hexylena.) Pull Request 561

• Small fixes for UI functional tests. Pull Request 485, Pull Request 487

• Bug fixes related style adjustments. (Thanks in part to @nsoranzo.) Pull Request 478, Pull Request 479, Pull Request 480, Pull Request 481

• Fixes to make Sweepster functional. Pull Request 486

• Add client to ignore so that tox locally doesn’t try to test JavaScript. Pull Request 494

• Fix for server error when installing certain repositories. Pull Request 495

• Fix BBI data provider underflow bug when computing standard deviation. Pull Request 499

• Add numpad support to integer inputs. Pull Request 509

• Fix for rdata datatype. Pull Request 512

• Fix for toolshed escape method, where an error/log message contains non- ASCII characters. Pull Request 514

• Restore line wrongly removed in fa7c5c5 and again in 9805294 . (Thanks to @nsoranzo.) Pull Request 515

• Ensure file exists before attempting chmod in tool shed install code. Pull Request 545

• Filter deleted library datasets when using the library data parameter. Pull Request 546

• Correct examples in workflow invocation documentation. Pull Request 565

• Fix the CSS class for reports brand. Pull Request 585

• Retab .loc.sample files. Pull Request 587

• liftOver.loc was not accessible in local data (Thanks to @yhoogstrate.) Pull Request 588

• Ensure removal of temporary tool shed files. Pull Request 607

• Bug fix in Reports (Thanks to @Airistotal.) Pull Request 626

• Cleaner commit history for #629 and array syntax for pathspec (Thanks to @chambm.) Pull Request 632

• add missing js build Pull Request 648

• Reports - Small bug fixes (Thanks to @Airistotal.) Pull Request 656

• Fix tool image paths Pull Request 660

• remove reports style that affected the whole application Pull Request 661

• Fix centering bug in firefox (Thanks to @Airistotal.) Pull Request 669

• Don’t overwrite $R_LIBS path during installation. (Thanks to @bgruening.) Pull Request 671

• Fix tool shed installation issue (#525). (Thanks to @mvdbeek.) Pull Request 681

• Return copied collection from manager copy method. Pull Request 682

• Fix multi-history fetch flag to allow re-fetching after collection sort. Pull Request 695

• Small fixes for LDAP auth. (Thanks to @nsoranzo.) Pull Request 696

• Fix regression introduced in tool shed code this cycle. (Thanks to @nsoranzo.) Pull Request 701

• Fix workflow editor post job action argument display. Pull Request 703

• Fix to get custom tabular datatypes. (Thanks to @richard-burhans.) Pull Request 705

• Fix for logging in using OpenID when the OpenID isn’t associated. Pull Request 712

• Misc fixes. (Thanks to @nsoranzo.) Pull Request 720

• Fix history option flags. Pull Request 726

• Fix Galaxy.user in client code to be available when not using a require. Pull Request 728

• Remove no-op __init__ methods from lib/galaxy/datatypes/binary.py. (Thanks to @mr-c.) Pull Request 729

• Fix more API tests. (Thanks to @nsoranzo.) Pull Request 731

• Fixes for framework test cases. (Thanks to @nsoranzo.) Pull Request 752, Pull Request 757

• Bugfix in test error reporting handling code. Pull Request 760

• Tool form error messages and rerun fixes. Pull Request 766

• Quote value to fix configparser error in interactive environments. (Thanks to @hexylena.) Pull Request 775

• Fix upload event binding. Pull Request 778

• Fix _JAVA_OPTIONS example in job_conf.xml.sample_advanced. Pull Request 796

• Fix errors when starting ./run_tests.sh -with_framework_test_tools -api. (Thanks to @nsoranzo.) Pull Request 800

• Tweak password reset email template to truly be plain text. Pull Request 812

• Fix returned tuple from creating_job. Pull Request 817

• Fix database initialization when galaxy.ini doesn’t exist. Pull Request 822

• Fix default value for optional select fields. Pull Request 826

• Use dependency handling in lib/galaxy/datatypes/. (Thanks to @nsoranzo.) Pull Request 838

• Expose all API keys to admins under REMOTE_USER. (Thanks to @hexylena.) Pull Request 873

• Various fixes for data libraries. Pull Request 878

• Minor fixes to the history UI. Pull Request 910

• Fix command quoting and remove size from text input for Cut tool. Pull Request 913