16.04

Enhancements

• Overhaul of Tools and Jobs Pull Request 1688

• Implement an Embedded Pulsar Job Runner Pull Request 2057

• Use the API to install repositories instead of loading the Tool Shed in an iframe. (Beta) Pull Request 1392

• Phinch interactive environment (thanks to @shiltemann.) Pull Request 1647

• Add iobio external display applications for BAM and VCF. Pull Request 1926

• add chemical datatypes (thanks to @bgruening.) Pull Request 1941

• Scratchbook tour Pull Request 1463

• Work toward automating release management. Pull Request 1613

• Basic tool error Sentry reporting. Pull Request 1900

• disable ‘hg push’ to TS repositories Pull Request 2033

• Generic GIE Launcher, GIE Image Chooser, multiple datasets (thanks to @hexylena.) Pull Request 1403

• The entire Python source code is now continuously checked with flake8 for PEP-8 style consistency and common errors. The last 3500 errors were fixed in this release (thanks to @nsoranzo.) Pull Request 1489, Pull Request 1713, Pull Request 1755

• Implement new GIE proxy (thanks to @hexylena.) Pull Request 1807

• Workflow editor overview click navigation Pull Request 1843

• API, history contents: allow filters, limit/offset, and ordering Pull Request 1602

• datalibs: introduce folder management; fix various glitches; refactor Pull Request 1562

• Add makefile target for release process (thanks to @hexylena.) Pull Request 1433

• libraries: provide select all/none options when importing Pull Request 1970

• libraries: add ‘create history &import to it’ feature Pull Request 2017

• Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type (thanks to @markiskander.) Pull Request 1148

• Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1 (thanks to @jj-umn.) Pull Request 1280

• Docker Testing - Newer versions of phantomjs and casperjs, in container wheels. Pull Request 1449

• Add run_toolshed_tests.html to .gitignore . (thanks to @nsoranzo.) Pull Request 1456

• Allow sorting of discover_datasets elements. Pull Request 1512

• Cleanup common ui elements, add test cases Pull Request 1519

• add minor styling to tour popover Pull Request 1539

• Code design and legacy cleanup of datatypes and metadata. Pull Request 1556

• show_params input walking Pull Request 1561

• Add API endpoint for fetching all metadata for a repository. Pull Request 1565

• Fix parameter validation Pull Request 1572

• Remove recovery hack for REALLY old jobs. Pull Request 1574

• Clarify area github tags. Pull Request 1579

• update pinned-requirements.txt (thanks to @matthdsm.) Pull Request 1605

• Improve dbkey handling for discovered datasets. Pull Request 1610

• Various improvements to the heartbeat Pull Request 1614

• Visualization plugins: add routes that more closely match potential static assets. Pull Request 1615

• Disable individual file metadata changes in upload Pull Request 1625

• added resolver dependency display to the tool view page (thanks to @zipho.) Pull Request 1632

• Cherry-picked changes from pull request #1392. Pull Request 1821

• Export toolshed repository information for workflow portability (thanks to @mvdbeek.) Pull Request 1636

• Lint optional handling on conditional test parameters. Pull Request 1639

• Updated hashes for bioblend v0.7.0 (thanks to @matthdsm.) Pull Request 1646

• Add tox startup (run.sh) test and test on OS X and linux (thanks to @mvdbeek.) Pull Request 1649

• Optionally pass dataset lists as a single file within tool wrappers (thanks to @einon.) Pull Request 1658

• add a zip datatype which won’t be extracted (thanks to @lecorguille.) Pull Request 1665

• Tour improvements and bugfixes Pull Request 1671

• Add Marius van den Beek to Galaxy committer group. Pull Request 1699

• Revise tool parameter handling, remove redundancies Pull Request 1711

• Python 2/3 string handling (thanks to @mvdbeek.) Pull Request 1731

• workaround for error message on tool lookup in case original toolshed had been disabled (thanks to @mvdbeek.) Pull Request 1738

• Make api/tools return tool_shed_repository information. (thanks to @mvdbeek.) Pull Request 1752

• Use visit inputs for check_and_update_param_values Pull Request 1764

• Update makefile and add the script I used to apply security patches for 16.01 Pull Request 1793

• Implement dataset empty input validator. Pull Request 1808

• Makefile help target + formatting (thanks to @hexylena.) Pull Request 1824

• Add license and repository information to package.json. Pull Request 1829

• Improved logging during tool executions. Pull Request 1832

• Do not access the history when loading the workflow editor Pull Request 1861

• Tones down the warning message about tool changes (thanks to @bwlang.) Pull Request 1893

• Use shared value serialization for tool model Pull Request 1901

• adding contrib init for reports and modifying status check to have output by process in case multiprocess (thanks to @miloaec.) Pull Request 1911

• Retrieve authentification also for long urls (thanks to @mvdbeek.) Pull Request 1912

• Modify run.sh to add –restart option, for a more consistent use of parameters. (thanks to @remimarenco.) Pull Request 1914

• Rename tool_shed_get to url_get. Pull Request 1918

• Allow testing element counts in tool output collections. Pull Request 1942

• Use database query rather than dataset iteration to compute dataset counts in saved histories grid. Pull Request 1948

• Add “new” state to list of dataset states in saved history list. Pull Request 1949

• Add IUC as a new default bioconda channel (thanks to @bgruening.) Pull Request 1950

• More job related timing logging. Pull Request 1956

• Improvements to workflow scaling performance testing scripts. Pull Request 1958

• Optimization for discovering datasets for dynamic output collection. Pull Request 1959

• Improve tabular datatypes. (thanks to @brenninc and @nsoranzo.) Pull Request 1968, Pull Request 2317

• Optimize adding datasets to large histories. Pull Request 1983

• Much more friendly route mapping. Pull Request 2002

• Revise content selection, add test cases Pull Request 2011

• Don’t setup a default tool_data_table_config_path in the shed. Pull Request 2025

• data_column to json config file (thanks to @bgruening.) Pull Request 2026

• Revise input wrapper, add test cases Pull Request 2027

• enable obfs datatype during upload (thanks to @bgruening.) Pull Request 2028

• Better element_identifier handling in repeat sections (thanks to @mvdbeek.) Pull Request 2029

• Pulsar-As-A-Dependency Pull Request 2052

• Simplify Workflow sharing menu (thanks to @nturaga.) Pull Request 2060

• Add Phinch as an external display application. Pull Request 2069

• For non-shed tool data - read loc from sample if available. Pull Request 2070

• tool lineage for versionless toolshed tool_ids (thanks to @mvdbeek.) Pull Request 2082

• make new beta TS tools installation via API configurable Pull Request 2088

• Patch in visual separation of section parameters (thanks to @hexylena.) Pull Request 2091

• Add sample supervisor config (thanks to @mvdbeek.) Pull Request 2096

• Fix cli runner: use embed_metadata_in_job parameter (thanks to @ThomasWollmann.) Pull Request 2107

• Switch Dockerized commands to use sh instead of bash. Pull Request 2282

• Remove IPython IE, which was replaced by Jupyter IE. (thanks to @bgruening.) Pull Request 1402

• Added py34-lint tox target but forgot to update .travis.yml. Pull Request 1457

• fix old jobparam hack for importing files to library Pull Request 1488

• An attempt to add limit/offset to history contents Pull Request 1490

• Revise label handling in form Pull Request 1496

• History UI: clean up. Pull Request 1522

• Client-build, Webpack: add tasks to grunt for the common webpack tasks, update readme Pull Request 1523

• Remove handlebars and rely solely on underscore templates Pull Request 1537

• disable email notifications from travis Pull Request 1592

• Remove unnecessary variable and assignment of job command (thanks to @einon.) Pull Request 1616

• Implement the ratable mixin Pull Request 1618

• Tour cleanup, remove a few globals. Pull Request 1621

• Refactor workflow loading. Pull Request 1735

• Swapping from svgfig to svgwrite Pull Request 1747

• various libraries refactoring and bugfixes Pull Request 1751

• Refactor the Html Datatype Class into text.py instead of images.py (thanks to @remimarenco.) Pull Request 1760

• Drop python2.6 (deprecated, will not be supported in 16.04) from testing. Pull Request 1785

• Rework history updating Pull Request 1788

• Tests for some of the 16.01 security vulnerabilities Pull Request 1794

• Reduce the use of mutable types in toolshed test framework’s method definitions. Pull Request 1813

• Remove decryption/encryption of tool states Pull Request 1838

• Do not import dumps and loads from galaxy.util.json . (thanks to @nsoranzo.) Pull Request 1840

• Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship. (thanks to @mvdbeek.) Pull Request 1868

• Cosmetic comma fixes :) (thanks to @remimarenco.) Pull Request 1874

• More debugging for transiently failing tool shed test. Pull Request 1939

• Improve logging and retry for another TS test… Pull Request 1961

• Add page layout test cases Pull Request 1991

• Fix inconsistency in update state handling for tool modules Pull Request 1993

• Functional Test Drivers Overhaul Pull Request 2016

• Remove install and test code. Pull Request 2018

• Remove twill functional tests we don’t actively run. Pull Request 2019

• Fix transiently failing tool shed tests. Pull Request 2030

• Libraries: faster, refactored, cleaned Pull Request 2031

• Adjust testing directories so no python root is ever “tool_shed”. Pull Request 2067

• Fix pbs runner file touch. Pull Request 2074

• Move scripts out of lib/tool_shed. Pull Request 2093

• Consolidate duplicated method in tool_shed/model. Pull Request 2099

• Remove redundant ui divs, move masthead into #everything Pull Request 2182

• Remove SLURM memory limit warning from stderr if the job was successful (thanks to @nsoranzo). Pull Request 2309

Fixes

• upgrade mercurial wheel to latest (fixing CVE issues) Pull Request 2045

• Add changeset_revision to tool attributes, avoid self.tool_shed_repository. (thanks to @mvdbeek.) Pull Request 1802

• Do not convert spaces to tabs when importing datasets into a library (thanks to @nsoranzo). Pull Request 1985

• Fix that typo in relation_builder. Pull Request 1453

• URL generation tweaks for utils.js Pull Request 1478

• Fix project linting for new pep8 Pull Request 1483

• Fix Python 3 problem causing Travis failure of dev. Pull Request 1505

• catch Exception and properly log errors Pull Request 1510

• Change python print() format to be backward compatible with older versions. (thanks to @einon.) Pull Request 1520

• Add js for mako based masthead Pull Request 1533

• restrict blue popover to tours Pull Request 1577

• small spelling error (thanks to @matthdsm.) Pull Request 1582

• Fix installation of repository suites outside of tool panel section (thanks to @mvdbeek.) Pull Request 1601

• Fixes <param argument=”–set” /> not working when help=”” is not set (thanks to @yhoogstrate.) Pull Request 1650

• Fix validation for data source tools Pull Request 1654

• Better fix for missing element identifier (thanks to @mvdbeek.) Pull Request 1693

• Update david identifier types (thanks to @pavanvidem.) Pull Request 1696

• Drop Ross from the committers group. Pull Request 1698

• Wrap conditional test parameters Pull Request 1714

• Remove len(stderr), breaks on recent docker versions (thanks to @mvdbeek.) Pull Request 1769

• Strip URL of download_file and download_by_url install actions. (thanks to @nsoranzo.) Pull Request 1775

• Fix tool form rendering of sections Pull Request 1783

• Fix unused import. (thanks to @nsoranzo.) Pull Request 1796

• Fix tool shed tests for commit e4a1d5727805168a9fd15aca1cdd21630ada2bbc (thanks to @nsoranzo). Pull Request 1798

• Checks for api_key before checking for header from SSO. (thanks to @MatthewRalston.) Pull Request 1801

• Ensure tool.changeset_revision is set… Pull Request 1806

• Change many job mapped properties to lazy loads Pull Request 1809

• Whitelist logging tweaks Pull Request 1819

• Fix upload tool routing Pull Request 1827

• Using node 5.7, ‘grunt style’ fails with the error: Pull Request 1841

• Do not create text values for failed inputs Pull Request 1844

• Prevent tours from kicking off within iframes Pull Request 1846

• Fix repeat prefix Pull Request 1848

• also update rrda when repairing or updating a repository (thanks to @mvdbeek.) Pull Request 1850

• Fix regex validator Pull Request 1862

• Tour routing overhaul Pull Request 1870

• Add dedicated client endpoint to the root controller. Pull Request 1879

• Update check_python.py now dropping Python 2.6 (thanks to @peterjc.) Pull Request 1883

• Fix citation-model to fail silently/gracefully Pull Request 1884

• Change to sentry middleware to work with modern raven clients. Pull Request 1895

• svgfig->svgwrite in unpinned requirements Pull Request 1896

• Fix icon sizes Pull Request 1934

• Fix tool downloads in tool form Pull Request 1935

• Fixing error in run.sh script (thanks to @kellrott.) Pull Request 1954

• Fix typo: send–>sent Pull Request 1965

• Fix farbtastic’s use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako . Pull Request 1972

• Remove duplicate help target (thanks to @hexylena.) Pull Request 1980

• Fix booleans in workflow editor Pull Request 1990

• libraries: change default size of fa in iconspans Pull Request 2000

• libraries: move text out of icon spans for library dataset view Pull Request 2008

• Fix unbound error that is possible if using tool bursting. Pull Request 2009

• Fix multiple flag for workflow dataset inputs Pull Request 2021

• fix duplication of select2 entries Pull Request 2022

• Fix fluent query log serialization when datetime types are in use. Pull Request 2039

• Workflow import fix when tools are missing. Pull Request 2048

• Managers: remove UTC zone when parsing dates (thanks also to @nsoranzo). Pull Request 2042, Pull Request 2062, Pull Request 2065

• Change user disk usage pgcalc function up a bit to make a slightly safer dry-run. Pull Request 2063

• Allow tool confs with a tool_path to not be interpreted as shed confs. Pull Request 2066

• Fix deps.command.download_command on Mac OS X. Pull Request 2075

• Show sections in workflow run Pull Request 2087

• Workflow section fix backport (thanks to @hexylena.) Pull Request 2092

• Run external local set_metadata jobs in the job’s working directory Pull Request 2094

• make dependencies browsable again Pull Request 2101

• Convert the DRMAA runner to use Pulsar’s DRMAA session wrapper Pull Request 2102

• Updated to Dependency change in b167a741a444c3988447b0d63a1ba3dc5e4e62f5 (thanks to @Christian-B.) Pull Request 2104

• Fix datatype list in workflow editor Pull Request 2105

• Workaround for the toolshed’s hgweb. Pull Request 2106

• Update debian init script (thanks to @mvdbeek.) Pull Request 2109

• Rev Pulsar to 0.7.0.dev3. Pull Request 2122

• change run_tool_shed.py to see the file in the correct lcoation (thanks to @nturaga.) Pull Request 2131

• Fixes due to #2093 and #2018 (thanks to @nsoranzo.) Pull Request 2133

• markupsafe.escape() in Python2 does not work on str containing non-ASCII characters (thanks to @nsoranzo.) Pull Request 2138

• load options from config, not from options Pull Request 2139

• fix/replace biomart data source Pull Request 2149

• Add tool parameters back to parameters and expose for certain tools Pull Request 2156

• Fix wrapper issue, overload __ne__ Pull Request 2161

• Fix grouping tool and enhance performance when removing lines. Pull Request 2166

• libraries: always fetch new permissions as we are reusing the view Pull Request 2176

• Fix for redirecting a non-user when a tool has require_login=True. Pull Request 2180

• Fix.published history long titles have to be truncated Pull Request 2189

• fix a bug with missing history_id in libraries dataset import Pull Request 2190

• Fix message in legacy panel mako Pull Request 2191

• Prepass on remote user header based on maildomain and normalize config. Pull Request 2195

• Extend to_json for dataset tool parameters Pull Request 2196

• Pages parser fix Pull Request 2197

• Translate data source tool parameters on parameter expansion Pull Request 2201

• Sync job_script module with Pulsar to fix doctest. Pull Request 2203

• Improve error message for data source tools, executed through the tool_runner controller Pull Request 2204

• Add fixed validation check for data_source tools URL parameter Pull Request 2208

• Fix tool action redirect url for non-default tools Pull Request 2211

• Browse library date handling for non-ascii month abbreviations Pull Request 2214

• Avoid reset of cursor position for input fields during manual entry Pull Request 2218

• Add conditional statsd requirement Pull Request 2227

• Fix js value validator Pull Request 2234

• Encode collection reduce in serializable fashion Pull Request 2238

• Update _condarc automatically (thanks to @bgruening.) Pull Request 2255

• Truncate job name in DRMAA runner by default for PBSPro. Pull Request 2265

• Cherrypick of encoding fix Pull Request 2266

• If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue Pull Request 2311

• Unicodify pretty datetimes which can contain non-ASCII chars (thanks to @nsoranzo). Pull Request 2312

• Relax default value acceptance condition Pull Request 2316

• Fixes the proxy naming (thanks to @bgruening.) Pull Request 2333

• Re-fix the bug with multiple preceding ‘/’ characters in the GIE proxy prefix Pull Request 2339

• Do not pollute param_dict with a non JSONifiable dict (thanks to @nsoranzo.) Pull Request 2345