Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168 https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Allow invalid optional param values for old tools For tools with profile < 18.09 we return None for provided, but illegal default values. This can happen when referencing columns of an optional dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842. This used to pass prior to 18.05 because we would always return the value if there were no legal values. This was changed in https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302fd... where we would only allow this in workflow building mode. Commit: 9794d835e507c31d82aa82c79e86998154419980 https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e869... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Fix to_dict with io_details=True for tools with collection outputs. Fixes #6537 and includes a test case. Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1a... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Fix empty handling rule. Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8 https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017b... Author: Dannon <dannon.baker@gmail.com> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values [18.05] Allow invalid optional param values for tools profile versions < 18.09 Commit: 0a9010156e30a20d730324807c3e238510f44b77 https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e2... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-07-26 (Thu, 26 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6538 from jmchilton/tool_output_io [18.01] Fix to_dict with io_details=True for tools with collection outputs. Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f9... Author: Dannon <dannon.baker@gmail.com> Date: 2018-07-30 (Mon, 30 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/unit/test_rule_utils.py Log Message: ----------- Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend [18.05] Fix "filter empty" rule in Python rule handling framework. Commit: 9630699c21875199fec75bc3f607d5b81a224348 https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-07-31 (Tue, 31 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev) Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd6718796093... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Introduce test for auto-labelling subworkflow workflow outputs Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75 https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use subworkflow index when setting auto-label Previously this would reference the parent workflow index, while the get_data module would use the subworkflow index. This means defining workflows worked fine, but executing would fail when trying to find the output to replace. Using the subworkflow index here seems like the correct thing to do. Fixes https://github.com/galaxyproject/galaxy/issues/6560 Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe42... Author: guerler <aysam.guerler@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix worklfow run link for extracted workflows Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #6532 from dannon/fix-dataset-copy-tags [18.05] Fix dataset copy tags Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94 https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e21... Author: Dannon <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery [18.01] Use subworkflow index when setting auto-label Commit: d7959568f85b45f378f6972d971075f7169cffc4 https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d97107... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5 https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613fc... Author: Dannon <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6571 from guerler/fix_link [18.05] Fix workflow run link for extracted workflows Commit: d1423b6e18cbf054799027d6c6700b1b1186d6a9 https://github.com/galaxyproject/galaxy/commit/d1423b6e18cbf054799027d6c6700... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-08-06 (Mon, 06 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py M test/unit/test_rule_utils.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/561e0099bc22...d1423b6e18cb **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.