Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e32e93d6d8e048cbc77cb94f7c97b5ae0cfc6d6 https://github.com/galaxyproject/galaxy/commit/8e32e93d6d8e048cbc77cb94f7c97... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py M test/base/workflows_format_2/converter.py Log Message: ----------- Implement more collection workflow post job actions. Implement hide, delete, add tag, and remove tag for output collections and mapped over collections. Fixes https://github.com/galaxyproject/galaxy/issues/1680. Commit: 5aed347c3025ad061c572c6a2bbdf53a7626d3cc https://github.com/galaxyproject/galaxy/commit/5aed347c3025ad061c572c6a2bbdf... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/actions/post.py 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 #5418 from jmchilton/collection_pja [18.01] Implement more intuitive collection PJA Commit: 935b8c948cf4e47d1ea08fbe51332b7c6f15caa0 https://github.com/galaxyproject/galaxy/commit/935b8c948cf4e47d1ea08fbe51332... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Add --skip_flakey_fails flag to CI script for API tests xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551 and following comments. Commit: 1bd8c4fd26b6dbb2824922cbc7f24ab9e8929bfe https://github.com/galaxyproject/galaxy/commit/1bd8c4fd26b6dbb2824922cbc7f24... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/jenkins/api/run_tests.sh Log Message: ----------- Merge pull request #5455 from jmchilton/backport_flakey [18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests Commit: 7bbc46658a77d74a2447095b61b28e6e4ca32e06 https://github.com/galaxyproject/galaxy/commit/7bbc46658a77d74a2447095b61b28... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix setting job failure exception This can happen when the job's tool is unavailble and outputs_to_working_directory is activated. Fixes https://github.com/galaxyproject/galaxy/issues/5424. Commit: f99299f8332a75a6075f49176770078be9cda571 https://github.com/galaxyproject/galaxy/commit/f99299f8332a75a6075f491767700... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py Log Message: ----------- Pre-compute more collection state during mapping. Still dealing with fallout from 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping. Commit: 51e030f4f3b608710adbba9ed4647db3d20196cb https://github.com/galaxyproject/galaxy/commit/51e030f4f3b608710adbba9ed4647... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Bring in @mvdbeek's test cases from #5431. Commit: b2e8d891b7ca7e24aaf86b6e559356e7d62f3373 https://github.com/galaxyproject/galaxy/commit/b2e8d891b7ca7e24aaf86b6e55935... Author: John Chilton <jmchilton@gmail.com> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable Fix setting job failure exception Commit: 207f5faba0ab70747c70de2d8d66a16ee2b00ecb https://github.com/galaxyproject/galaxy/commit/207f5faba0ab70747c70de2d8d66a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/execute.py M test/api/test_tools.py Log Message: ----------- Merge pull request #5449 from jmchilton/collection_mapping_fixes [18.01] Collection mapping fixes for regression in 18.01. Commit: 3864a1763ffa101384314090066c671bca5ba23d https://github.com/galaxyproject/galaxy/commit/3864a1763ffa101384314090066c6... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-02-05 (Mon, 05 Feb 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/tools/execute.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 dev Compare: https://github.com/galaxyproject/galaxy/compare/f8d21f098af2...3864a1763ffa