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[galaxyproject/galaxy] a18db4: Warn job runner plugin writers not to emulate cond...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a18db4513ad9e3f7b2d08e70ffc4d810137c2480 https://github.com/galaxyproject/galaxy/commit/a18db4513ad9e3f7b2d08e70ffc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Warn job runner plugin writers not to emulate condor.py. Better to write a CLI plugin I think (https://github.com/galaxyproject/galaxy/pull/6751#issuecomment-425079201) Commit: 872b6f57ed7c588b8ae58891253a1a584cd98952 https://github.com/galaxyproject/galaxy/commit/872b6f57ed7c588b8ae58891253a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #6783 from jmchilton/drm_cli_warn Warn job runner plugin writers not to emulate condor.py. Compare: https://github.com/galaxyproject/galaxy/compare/7787d3ae8e3f...872b6f57ed7c **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.

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[galaxyproject/galaxy] 6cb4c3: Add 6768
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 6cb4c32eb4e613b4d90680450d11804779e5b4a5 https://github.com/galaxyproject/galaxy/commit/6cb4c32eb4e613b4d90680450d11… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6768 Commit: ee47fdb50cef70dd2b940c42594611863e51bde7 https://github.com/galaxyproject/galaxy/commit/ee47fdb50cef70dd2b940c425946… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6753, 6771 Compare: https://github.com/galaxyproject/galaxy/compare/d3db21fa82a8...ee47fdb50cef **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.

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[galaxyproject/galaxy] 384a16: Allow schema to validate
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: 2209c3171de52dbe83683d2644b0ec6befbaa763 https://github.com/galaxyproject/galaxy/commit/2209c3171de52dbe83683d2644b0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor cleanup. Commit: 037ddfeab5decd47d4d2bd8771e975dc1857703a https://github.com/galaxyproject/galaxy/commit/037ddfeab5decd47d4d2bd8771e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Fix active content setting for views with explicitly defined models Commit: 96593cb444063d6cc6819dd77d7b2fb89c250054 https://github.com/galaxyproject/galaxy/commit/96593cb444063d6cc6819dd77d7b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Import cleanup and documentation for dataset-li-edit. Commit: 11b5157825ee318b763f6c48b674b968f114aebb https://github.com/galaxyproject/galaxy/commit/11b5157825ee318b763f6c48b674… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-17 (Mon, 17 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use standard faIconButton for visualize. Commit: 806beaca9b4b51322214e68619407e8a0545a19d https://github.com/galaxyproject/galaxy/commit/806beaca9b4b51322214e6861940… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Test that newest version will be returned if tool id or version don't match Commit: c8552970dd7c2eeb9d765911843ed3e866b84ce3 https://github.com/galaxyproject/galaxy/commit/c8552970dd7c2eeb9d765911843e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort by tool version when picking a tool with an unavailable version Commit: 94082a878dca784eb57c6be1fd552a63f85bcfad https://github.com/galaxyproject/galaxy/commit/94082a878dca784eb57c6be1fd55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Unit test that fails if we don't return the latest version upon version mismatch Commit: 3ea9d086bfe295a210d6f249ef2c39d8a65ef042 https://github.com/galaxyproject/galaxy/commit/3ea9d086bfe295a210d6f249ef2c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Sort rval so that newest tool appears last in rval Commit: f6f526a0a50a98143d4845f8907067b6f42e1dea https://github.com/galaxyproject/galaxy/commit/f6f526a0a50a98143d4845f89070… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Use tool_version instead of version parameter To be consistent with other routes that accept this parameter. Commit: 3017568e77cf950b8b611a16ea7ce9fcc2159e81 https://github.com/galaxyproject/galaxy/commit/3017568e77cf950b8b611a16ea7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Drop unnecessary history in test_show_with_wrong_tool_version_in_tool_id test Commit: 4aa2b8f919f28b798ba9a2401c602990287338b6 https://github.com/galaxyproject/galaxy/commit/4aa2b8f919f28b798ba9a2401c60… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Disentangle this/self/frames in scratchbook's events. Commit: 077f3088ece5c8617b044d53764aebff1768b34f https://github.com/galaxyproject/galaxy/commit/077f3088ece5c8617b044d53764a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Correct visualization link to use router or scratchbook as appropriate. Commit: 3f29d32898efd121f315b2147e917584e9dec28f https://github.com/galaxyproject/galaxy/commit/3f29d32898efd121f315b2147e91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Strip unused function, cleanup. Commit: 0018ab989b117c953dd2b02e1e06cc80af1ddff2 https://github.com/galaxyproject/galaxy/commit/0018ab989b117c953dd2b02e1e06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Add event hook for non-bb-view center panel id setting, use it for dataset visualization. Commit: d17ea03442448472f1e5e5d4e12e73459f1736e7 https://github.com/galaxyproject/galaxy/commit/d17ea03442448472f1e5e5d4e12e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Minor formatting tweaks. Commit: 87ecf1428e841bced376e504d1d468319a7853c9 https://github.com/galaxyproject/galaxy/commit/87ecf1428e841bced376e504d1d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Use pre-fetched dataset id Commit: b5e221929687809adfb30cad8280767f3a8412c5 https://github.com/galaxyproject/galaxy/commit/b5e221929687809adfb30cad8280… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-19 (Wed, 19 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Fix page editor height for flex panels. Commit: f65e616c1afe6d9ec0bb9680fa90ee8e9d311900 https://github.com/galaxyproject/galaxy/commit/f65e616c1afe6d9ec0bb9680fa90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Use mapped-over collectionType when inferring collectionType through format_source Commit: 02c177152bd7dbef02d4ea5d40449745e913b38b https://github.com/galaxyproject/galaxy/commit/02c177152bd7dbef02d4ea5d4044… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #6740 from mvdbeek/backport_tool_version_select_fixes [18.05] Backport tool version select fixes Commit: 3ffbf5b4b6138177ed7581d7845432bec138ee23 https://github.com/galaxyproject/galaxy/commit/3ffbf5b4b6138177ed7581d78454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Append mapped-over collection type to output collection type So if for instance the connected input is a regular input with a list:list input and the output is a paired collection we set the output collection type to list:list:paired. Commit: eb37ad3752f5dbe4806e74f85b4fcee63ab407fa https://github.com/galaxyproject/galaxy/commit/eb37ad3752f5dbe4806e74f85b4f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Only reset the right hand side of a connection on disconnect Commit: 30728899054dde65ddd9fe99dc8424166ee0c5ad https://github.com/galaxyproject/galaxy/commit/30728899054dde65ddd9fe99dc84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 287648f5d9f95ccd1b625037e30de0ab3e62e7f5 https://github.com/galaxyproject/galaxy/commit/287648f5d9f95ccd1b625037e30d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js Log Message: ----------- Merge pull request #6725 from dannon/fix_active_highlight [18.09] Fix active highlight Commit: 9b5045a05c882c652935d9daaf589a10d776190c https://github.com/galaxyproject/galaxy/commit/9b5045a05c882c652935d9daaf58… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M templates/webapps/galaxy/page/editor.mako Log Message: ----------- Merge pull request #6747 from dannon/fix_page_editor_height [18.09] Fix page editor height for flex panels. Commit: 7eac08979b1f474254e9a6a0b2005d365e09c143 https://github.com/galaxyproject/galaxy/commit/7eac08979b1f474254e9a6a0b200… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-20 (Thu, 20 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Undo auto-propagation of group tags. @mvdbeek and I discussed this in the Galaxy project gitter a few weeks ago and decided the propagation is too aggressive and should likely be done manually at the end of a workflow for now - using for instance the set tags collection operation tool. Commit: f3298953d41cb0e2b37812242a88d226a890e8aa https://github.com/galaxyproject/galaxy/commit/f3298953d41cb0e2b37812242a88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't skip build on release/master moving forward. Commit: bd5d12049b238c4475f267fbbf63bd3a124b0a58 https://github.com/galaxyproject/galaxy/commit/bd5d12049b238c4475f267fbbf63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Swap nodeenv to a pinned requirement. Commit: 4d6d984fbd8d66b30c7da3cd5022903f11218b09 https://github.com/galaxyproject/galaxy/commit/4d6d984fbd8d66b30c7da3cd5022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/README.md Log Message: ----------- Update client/README Commit: 3f8c2beff252587cd1347142ab84ad20afd57b03 https://github.com/galaxyproject/galaxy/commit/3f8c2beff252587cd1347142ab84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though) Commit: 0fb115e046b3a492db6b592d8b38459104d696bf https://github.com/galaxyproject/galaxy/commit/0fb115e046b3a492db6b592d8b38… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6750 from jmchilton/1809_tags_walkback [18.09] Undo auto-propagation of group tags. Commit: e10180dea108785a017b7be37b7ff5d85a2eebf1 https://github.com/galaxyproject/galaxy/commit/e10180dea108785a017b7be37b7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- (minor) client-format Commit: 8a4fe72f6710270ca453b75d61e8dbc96feadcc5 https://github.com/galaxyproject/galaxy/commit/8a4fe72f6710270ca453b75d61e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge branch 'collection_type_source_followup' into release_18.09 Commit: 679603b7c9a2b1f8c136dcc29d2eb41174bd6b31 https://github.com/galaxyproject/galaxy/commit/679603b7c9a2b1f8c136dcc29d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok, so that it doesn't interrupt processing other jobs. That was discovered because attempting to delete purged job outputs on failure was raising ObjectNotFound since dataset object store assignment is done later now. So also, catch that ObjectNotFound. Commit: 1a19043789498f1d45725840b0761939d5dad2a5 https://github.com/galaxyproject/galaxy/commit/1a19043789498f1d45725840b076… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add graph DOT datatype Commit: 8d025aa4ed75f63924d9e11f9d0c65ca3aca7be0 https://github.com/galaxyproject/galaxy/commit/8d025aa4ed75f63924d9e11f9d0c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-09-23 (Sun, 23 Sep 2018) Changed paths: M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- add graph_dot datatype to graphvis Commit: ac65832cb5e4fa7a3e57af3722a09c7dfa4ac2ea https://github.com/galaxyproject/galaxy/commit/ac65832cb5e4fa7a3e57af3722a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/graphviz/config/graphviz.xml Log Message: ----------- Merge pull request #6760 from bgruening/graph_dot [18.09] Add graph dot datatype and enable it in visualisations Commit: 611764b81a761c034bfd040b76818187a555807e https://github.com/galaxyproject/galaxy/commit/611764b81a761c034bfd040b7681… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Remove cruft releated to upgrading from 17.05 Galaxies. These interact poorly with recent changes in 18.09 and in nearly all cases should no longer be needed at this point. Commit: ea7359b08b21a9e0febe6cd98a9fd4488c133546 https://github.com/galaxyproject/galaxy/commit/ea7359b08b21a9e0febe6cd98a9f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6761 from jmchilton/remove_upgrade_cruft [18.09] Remove upgrade cruft related to datatypes. Commit: de6dc00236ad2947d3bef479b5d7df5c3bef7ba4 https://github.com/galaxyproject/galaxy/commit/de6dc00236ad2947d3bef479b5d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: a0ad5adf6fc02c6a0864308f8d6f8a612a83f308 https://github.com/galaxyproject/galaxy/commit/a0ad5adf6fc02c6a0864308f8d6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Increase the maximum number of stderr lines that will be scanned for slurm warnings to strip to 3. Commit: a89184aa707a477f14905bd44b368006c7cae427 https://github.com/galaxyproject/galaxy/commit/a89184aa707a477f14905bd44b36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6766 from natefoo/remove-more-slurm-warnings [18.09] Increase the maximum number of stderr lines that will be scanned for slurm warnings Commit: 529ed61c3b48e2d8a830e6a890d93b16a4f42ea4 https://github.com/galaxyproject/galaxy/commit/529ed61c3b48e2d8a830e6a890d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6765 from natefoo/job-stdout-none-fix [18.09] Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: 9f688b2f9141683e02ea9aa759a15ebd46174042 https://github.com/galaxyproject/galaxy/commit/9f688b2f9141683e02ea9aa759a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6755 from natefoo/job-object-store-fixes [18.09] Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok Commit: 300d316ad1bcd0ec1a7b762e859232bbe8c9548c https://github.com/galaxyproject/galaxy/commit/300d316ad1bcd0ec1a7b762e8592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Resilience of success message handling Commit: 46dd1801cbc11cb24bb7fdd0d8a4f8e71fa9ef9e https://github.com/galaxyproject/galaxy/commit/46dd1801cbc11cb24bb7fdd0d8a4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #6768 from martenson/backport_resilience_of_success_message_handling [18.09] backport of: Resilience of success message handling Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Commit: eb1980ec087d7a2c3da6d138155f6c11895a8b26 https://github.com/galaxyproject/galaxy/commit/eb1980ec087d7a2c3da6d138155f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #6753 from dannon/client-build-startup-changes [18.09] Client build startup changes Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: c3d4be2e2cb1ccbdfc68ea14ebf3fb71bdec2e97 https://github.com/galaxyproject/galaxy/commit/c3d4be2e2cb1ccbdfc68ea14ebf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 04d2d2ef4672d3ee5f24d7dffe68a7f24238a7f0 https://github.com/galaxyproject/galaxy/commit/04d2d2ef4672d3ee5f24d7dffe68… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6772 from dannon/release_18.09 [18.09] Merge forward from 18.01, 18.05 Commit: 7787d3ae8e3fb9a69c4a5bab129051e59e104b2a https://github.com/galaxyproject/galaxy/commit/7787d3ae8e3fb9a69c4a5bab1290… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-view-edit-current.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M config/plugins/visualizations/graphviz/config/graphviz.xml M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/common_startup.sh M templates/webapps/galaxy/page/editor.mako M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/cb5b054aa0c9...7787d3ae8e3f **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.

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[galaxyproject/galaxy] 384a16: Allow schema to validate
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: c3d4be2e2cb1ccbdfc68ea14ebf3fb71bdec2e97 https://github.com/galaxyproject/galaxy/commit/c3d4be2e2cb1ccbdfc68ea14ebf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into release_18.09 Commit: 04d2d2ef4672d3ee5f24d7dffe68a7f24238a7f0 https://github.com/galaxyproject/galaxy/commit/04d2d2ef4672d3ee5f24d7dffe68… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #6772 from dannon/release_18.09 [18.09] Merge forward from 18.01, 18.05 Compare: https://github.com/galaxyproject/galaxy/compare/eb1980ec087d...04d2d2ef4672 **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.

1 0

[galaxyproject/galaxy] 384a16: Allow schema to validate
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 384a165aab2d579ee4c2dceba61f21c42c8c2dc4 https://github.com/galaxyproject/galaxy/commit/384a165aab2d579ee4c2dceba61f… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Allow schema to validate Commit: 0b95898ccf68b8497dff9f322b44abc5668dfce6 https://github.com/galaxyproject/galaxy/commit/0b95898ccf68b8497dff9f322b44… Author: E Rasche <hxr(a)hx42.org> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Document pbkdf2 Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 3efda23b4fe84f1a61d83aba07186e46c81990ce https://github.com/galaxyproject/galaxy/commit/3efda23b4fe84f1a61d83aba0718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Restore logging block in galaxy config schema. Commit: 7d7a875af398c440040e78dcc2516aae1c6eb041 https://github.com/galaxyproject/galaxy/commit/7d7a875af398c440040e78dcc251… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-07 (Fri, 07 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Merge pull request #5919 from erasche/fix-config-validate [18.01] Allow schema to validate Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Commit: cf62a1dafd90df9b65f811bed74d1d173542babc https://github.com/galaxyproject/galaxy/commit/cf62a1dafd90df9b65f811bed74d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_workflows.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/5a97e4fcea77...cf62a1dafd90 **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.

1 0

[galaxyproject/galaxy] 7eb0be: Restore log_destination = stdout configuration opt...
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Compare: https://github.com/galaxyproject/galaxy/compare/7d7a875af398...71b561512db9 **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.

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[galaxyproject/galaxy] f32989: Don't skip build on release/master moving forward.
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: f3298953d41cb0e2b37812242a88d226a890e8aa https://github.com/galaxyproject/galaxy/commit/f3298953d41cb0e2b37812242a88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't skip build on release/master moving forward. Commit: bd5d12049b238c4475f267fbbf63bd3a124b0a58 https://github.com/galaxyproject/galaxy/commit/bd5d12049b238c4475f267fbbf63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Swap nodeenv to a pinned requirement. Commit: 4d6d984fbd8d66b30c7da3cd5022903f11218b09 https://github.com/galaxyproject/galaxy/commit/4d6d984fbd8d66b30c7da3cd5022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/README.md Log Message: ----------- Update client/README Commit: 3f8c2beff252587cd1347142ab84ad20afd57b03 https://github.com/galaxyproject/galaxy/commit/3f8c2beff252587cd1347142ab84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though) Commit: eb1980ec087d7a2c3da6d138155f6c11895a8b26 https://github.com/galaxyproject/galaxy/commit/eb1980ec087d7a2c3da6d138155f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #6753 from dannon/client-build-startup-changes [18.09] Client build startup changes Compare: https://github.com/galaxyproject/galaxy/compare/46dd1801cbc1...eb1980ec087d **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.

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[galaxyproject/galaxy] 2d9b80: Use UserRoleAssociation to get private roles
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Compare: https://github.com/galaxyproject/galaxy/compare/02c177152bd7...5a97e4fcea77 **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.

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[galaxyproject/galaxy] 60c416: Fix unit tests that access output label
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60c4162ffafdbdb8b741d01b472d271910025de5 https://github.com/galaxyproject/galaxy/commit/60c4162ffafdbdb8b741d01b472d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Fix unit tests that access output label Commit: cb5b054aa0c995d106ea9dff12fbade43c9233a1 https://github.com/galaxyproject/galaxy/commit/cb5b054aa0c995d106ea9dff12fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'display_label_in_wf' of https://github.com/mvdbeek/galaxy into display_label_in_wf Compare: https://github.com/galaxyproject/galaxy/compare/7bb0c3904c4f...cb5b054aa0c9 **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.

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[galaxyproject/galaxy] 4cdd07: Display output label in workflow editor if present
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cdd0774c5fd5b9a1eaafe034ae1c20c077abf92 https://github.com/galaxyproject/galaxy/commit/4cdd0774c5fd5b9a1eaafe034ae1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M lib/galaxy/workflow/modules.py Log Message: ----------- Display output label in workflow editor if present Commit: ba7c5a7162cffd13ff61201a4d2346e9b1b55afb https://github.com/galaxyproject/galaxy/commit/ba7c5a7162cffd13ff61201a4d23… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Display labels in output actions This displays the output label (if available) in the output section, for instance `Configure Output: 'Table split on column'` instead of `Configure Output: 'out1'`, and it displays available input variables as a list in the Rename dataset section, with the label next to the variable name. Commit: 7bb0c3904c4fe00ae3a8294088717b2de74d7462 https://github.com/galaxyproject/galaxy/commit/7bb0c3904c4fe00ae3a829408871… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Client format re-sync. Compare: https://github.com/galaxyproject/galaxy/compare/66c6c84c4d61...7bb0c3904c4f **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.

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