- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 8e32e9: Implement more collection workflow post job action...
by GitHub 05 Feb '18

05 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e32e93d6d8e048cbc77cb94f7c97b5ae0cfc6d6 https://github.com/galaxyproject/galaxy/commit/8e32e93d6d8e048cbc77cb94f7c9… Author: John Chilton <jmchilton(a)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/5aed347c3025ad061c572c6a2bbd… Author: Marius van den Beek <m.vandenbeek(a)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/935b8c948cf4e47d1ea08fbe5133… Author: Nicola Soranzo <nicola.soranzo(a)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/1bd8c4fd26b6dbb2824922cbc7f2… Author: Martin Cech <marten(a)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/7bbc46658a77d74a2447095b61b2… Author: mvdbeek <m.vandenbeek(a)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/f99299f8332a75a6075f49176770… Author: John Chilton <jmchilton(a)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/51e030f4f3b608710adbba9ed464… Author: John Chilton <jmchilton(a)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/b2e8d891b7ca7e24aaf86b6e5593… Author: John Chilton <jmchilton(a)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/207f5faba0ab70747c70de2d8d66… Author: Dannon Baker <dannon.baker(a)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/3864a1763ffa101384314090066c… Author: Nicola Soranzo <nicola.soranzo(a)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

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[galaxyproject/galaxy] f99299: Pre-compute more collection state during mapping.
by GitHub 04 Feb '18

04 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: f99299f8332a75a6075f49176770078be9cda571 https://github.com/galaxyproject/galaxy/commit/f99299f8332a75a6075f49176770… Author: John Chilton <jmchilton(a)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/51e030f4f3b608710adbba9ed464… Author: John Chilton <jmchilton(a)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: 207f5faba0ab70747c70de2d8d66a16ee2b00ecb https://github.com/galaxyproject/galaxy/commit/207f5faba0ab70747c70de2d8d66… Author: Dannon Baker <dannon.baker(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/b2e8d891b7ca...207f5faba0ab

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[galaxyproject/galaxy] 6b2150: Restore WebHelpers functions used in visualization...
by GitHub 04 Feb '18

04 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6b2150b1feaca405d2e718bace5cb743b8a60376 https://github.com/galaxyproject/galaxy/commit/6b2150b1feaca405d2e718bace5c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py Log Message: ----------- Restore WebHelpers functions used in visualization makos Broken in commit fbd33a57e0033a1547c3bf6f9812dd574cdb36d2 . Reported by @guerler. Commit: f8d21f098af23db441ad4b81e1a25f2f8bd148b3 https://github.com/galaxyproject/galaxy/commit/f8d21f098af23db441ad4b81e1a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/__init__.py A lib/galaxy/web/framework/helpers/tags.py Log Message: ----------- Merge pull request #5451 from nsoranzo/webhelpers_removal_followup Restore WebHelpers functions used in visualization makos Compare: https://github.com/galaxyproject/galaxy/compare/0b60de76b93e...f8d21f098af2

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[galaxyproject/galaxy] 2be7eb: Add py34-first_startup and py34-unit tox environme...
by GitHub 04 Feb '18

04 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2be7eb8cfa0640dbec5954de006bab3c10f700f2 https://github.com/galaxyproject/galaxy/commit/2be7eb8cfa0640dbec5954de006b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .travis.yml M tox.ini Log Message: ----------- Add py34-first_startup and py34-unit tox environments Also: - rename `first_startup` to `py27-first_startup` - rename other tox environments to use hyphens only to delimit factors - use the more specific ``` setenv = GALAXY_VIRTUAL_ENV={envdir} ``` instead of passing `--no-create-venv` to run unit tests inside the tox virtualenv (xref. commit 744835bbfe8bb07041600326af2f2f5d203365f5). Previously, `.venv` would be used if present. Commit: 6346b9e30949cd72a57eb683abd9bbaf431dd732 https://github.com/galaxyproject/galaxy/commit/6346b9e30949cd72a57eb683abd9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .gitignore Log Message: ----------- Ignore the future default Python3 virtualenv Commit: f2c6e083a15eab453ea7c94565464575b0356ae1 https://github.com/galaxyproject/galaxy/commit/f2c6e083a15eab453ea7c9456546… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- twill and pygithub3 are not Python3-compatible Commit: 0a44e77a89f6533c7ceaad99ffb9942517989ea4 https://github.com/galaxyproject/galaxy/commit/0a44e77a89f6533c7ceaad99ffb9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M lib/tool_shed/util/repository_util.py Log Message: ----------- Fix missing space Commit: 0b60de76b93edbfeae5560a3a531d27e31e027f6 https://github.com/galaxyproject/galaxy/commit/0b60de76b93edbfeae5560a3a531… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .gitignore M .travis.yml M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/tool_shed/util/repository_util.py M tox.ini Log Message: ----------- Merge pull request #5453 from nsoranzo/python3 Preparations for testing under Python3 Compare: https://github.com/galaxyproject/galaxy/compare/245394acb694...0b60de76b93e

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[galaxyproject/galaxy] 7bbc46: Fix setting job failure exception
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7bbc46658a77d74a2447095b61b28e6e4ca32e06 https://github.com/galaxyproject/galaxy/commit/7bbc46658a77d74a2447095b61b2… Author: mvdbeek <m.vandenbeek(a)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: b2e8d891b7ca7e24aaf86b6e559356e7d62f3373 https://github.com/galaxyproject/galaxy/commit/b2e8d891b7ca7e24aaf86b6e5593… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/1bd8c4fd26b6...b2e8d891b7ca

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[galaxyproject/galaxy] 935b8c: Add --skip_flakey_fails flag to CI script for API ...
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 935b8c948cf4e47d1ea08fbe51332b7c6f15caa0 https://github.com/galaxyproject/galaxy/commit/935b8c948cf4e47d1ea08fbe5133… Author: Nicola Soranzo <nicola.soranzo(a)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/1bd8c4fd26b6dbb2824922cbc7f2… Author: Martin Cech <marten(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/5aed347c3025...1bd8c4fd26b6

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[galaxyproject/galaxy] 8e32e9: Implement more collection workflow post job action...
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8e32e93d6d8e048cbc77cb94f7c97b5ae0cfc6d6 https://github.com/galaxyproject/galaxy/commit/8e32e93d6d8e048cbc77cb94f7c9… Author: John Chilton <jmchilton(a)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/5aed347c3025ad061c572c6a2bbd… Author: Marius van den Beek <m.vandenbeek(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/fbfbdd51bb3e...5aed347c3025

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[galaxyproject/infrastructure-playbook] cbf3e0: Bug fixes for slurm partition balancing
by GitHub 03 Feb '18

03 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: cbf3e016a8ccf8d9f90b0f157ff517c105cf5d72 https://github.com/galaxyproject/infrastructure-playbook/commit/cbf3e016a8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-03 (Sat, 03 Feb 2018) Changed paths: M taccenv/files/slurm/spartbalance Log Message: ----------- Bug fixes for slurm partition balancing

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[galaxyproject/galaxy] 6d8edc: Admin doc corrections
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d8edce33157e81112889ae7f241903747da3c92 https://github.com/galaxyproject/galaxy/commit/6d8edce33157e81112889ae7f241… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Admin doc corrections Commit: f24043e8a74e3cb2070b06652d9a72be46e6a278 https://github.com/galaxyproject/galaxy/commit/f24043e8a74e3cb2070b06652d9a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 [18.01] Admin doc corrections Commit: 7490fd452046b4a4578f6401501439773cbf2f28 https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f64015014… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- More robust nametag discovery and propagation. - Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool. - Nametags weren't being propagated to the outputs of collection operations. Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6 https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cleanup collection operation tagging implementation thanks to @mvdbeek comments. Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386 https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle optional inputs when collecting preserved tags. https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450 Commit: 60561c20307cf0585e553d0fa5cd612716ab7975 https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- Merge pull request #5403 from jmchilton/collection_operation_tags [18.01] More robust nametag discovery and propagation. Commit: a392b5750aa776fbc8ba27736d78901ddf0db29d https://github.com/galaxyproject/galaxy/commit/a392b5750aa776fbc8ba27736d78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3 https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf… Author: John Chilton <jmchilton(a)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 Log Message: ----------- Apply rename PJA to collection outputs including $ replacements. Update PJA collection test to test HDCA is renamed also. Commit: f6f9f9a8914845c995d665dc5396ac5e43187324 https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396… Author: John Chilton <jmchilton(a)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 Log Message: ----------- Extend mapped collection output rename PJAs to include # replacements. Also make sure output collections in non-mapping scenarios are also properly renamed as well. Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615 https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix bug in PJAs for collection mapping. Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157) Commit: 6c013d0cb3eebffdb69c865a4cbe4019bd8ab95e https://github.com/galaxyproject/galaxy/commit/6c013d0cb3eebffdb69c865a4cbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5444 from dannon/multidelete_fix [18.01] Ensure jobStateSummariesCollection exists; Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4 https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0ce… Author: Marius van den Beek <m.vandenbeek(a)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 Log Message: ----------- Merge pull request #5416 from jmchilton/rename_collections_pja [18.01] Fix rename post job actions to be more intuitive when mapping over collections. Commit: 245394acb694020c0f9f78185749fbccf45ec587 https://github.com/galaxyproject/galaxy/commit/245394acb694020c0f9f78185749… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/988cab4db7ef...245394acb694

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[galaxyproject/galaxy] 2b8df1: Apply rename PJA to collection outputs including $...
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2b8df110d0fad7c874c35c3176bf18d65cbcdbe3 https://github.com/galaxyproject/galaxy/commit/2b8df110d0fad7c874c35c3176bf… Author: John Chilton <jmchilton(a)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 Log Message: ----------- Apply rename PJA to collection outputs including $ replacements. Update PJA collection test to test HDCA is renamed also. Commit: f6f9f9a8914845c995d665dc5396ac5e43187324 https://github.com/galaxyproject/galaxy/commit/f6f9f9a8914845c995d665dc5396… Author: John Chilton <jmchilton(a)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 Log Message: ----------- Extend mapped collection output rename PJAs to include # replacements. Also make sure output collections in non-mapping scenarios are also properly renamed as well. Commit: 0529153ac090de0601f38af2fbf4f9a4fcccb615 https://github.com/galaxyproject/galaxy/commit/0529153ac090de0601f38af2fbf4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix bug in PJAs for collection mapping. Reported by @mvdbeek here (https://github.com/galaxyproject/galaxy/pull/5416#issuecomment-362194157) Commit: fbfbdd51bb3e06754efc1ae9e0cec4c1c1db9ce4 https://github.com/galaxyproject/galaxy/commit/fbfbdd51bb3e06754efc1ae9e0ce… Author: Marius van den Beek <m.vandenbeek(a)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 Log Message: ----------- Merge pull request #5416 from jmchilton/rename_collections_pja [18.01] Fix rename post job actions to be more intuitive when mapping over collections. Compare: https://github.com/galaxyproject/galaxy/compare/6c013d0cb3ee...fbfbdd51bb3e

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[galaxyproject/galaxy] a392b5: Ensure jobStateSummariesCollection exists; events ...
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: a392b5750aa776fbc8ba27736d78901ddf0db29d https://github.com/galaxyproject/galaxy/commit/a392b5750aa776fbc8ba27736d78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Ensure jobStateSummariesCollection exists; events can fire during deletion actions causing this event to fail Commit: 6c013d0cb3eebffdb69c865a4cbe4019bd8ab95e https://github.com/galaxyproject/galaxy/commit/6c013d0cb3eebffdb69c865a4cbe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #5444 from dannon/multidelete_fix [18.01] Ensure jobStateSummariesCollection exists; Compare: https://github.com/galaxyproject/galaxy/compare/60561c20307c...6c013d0cb3ee

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[galaxyproject/galaxy] bc50c1: Drop py26 XML parsing variant
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc50c14490e4f81144e5bc59f76e6abe2d93a8fa https://github.com/galaxyproject/galaxy/commit/bc50c14490e4f81144e5bc59f76e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- Drop py26 XML parsing variant Commit: 49872e7612070df9aee607897fb4cf5cb9cb2242 https://github.com/galaxyproject/galaxy/commit/49872e7612070df9aee607897fb4… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/util/logging/__init__.py M lib/galaxy/web/stack/message.py Log Message: ----------- Use six.create_bound_method() instead of types.MethodType() On Python2 the MethodType constructor requires the object's class to be passed. Commit: f43a3268b11841f65d3de195611bc6b0a940544c https://github.com/galaxyproject/galaxy/commit/f43a3268b11841f65d3de195611b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M templates/webapps/galaxy/dataset/security_common.mako Log Message: ----------- Use builtin set Commit: 39104af3b42e6d253391a9b73f6912cf4423e783 https://github.com/galaxyproject/galaxy/commit/39104af3b42e6d253391a9b73f69… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/web/framework/base.py Log Message: ----------- Define file_types instead of types.FileType and pull up TarFile Commit: 046f3265dd50ec6ff53470a96a4dfdb0193d7c17 https://github.com/galaxyproject/galaxy/commit/046f3265dd50ec6ff53470a96a4d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Fix loading custom JSONType Commit: 0be36ef4fce3b50bec37d199af2a404f3372ed65 https://github.com/galaxyproject/galaxy/commit/0be36ef4fce3b50bec37d199af2a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Use string.ascii_letters instead of string.letters for Py2/3 compat Update <sanitizer> documentation. Commit: 553d165087335528892232b17706b398bb3bf941 https://github.com/galaxyproject/galaxy/commit/553d165087335528892232b17706… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M templates/galaxy_client_app.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Python3 exception syntax fixes in templates/ Commit: 52586fcca2ef6ef6926fcd25b6c6f1b9ed598a6e https://github.com/galaxyproject/galaxy/commit/52586fcca2ef6ef6926fcd25b6c6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/phylip.py Log Message: ----------- Fix relative import to be Python3-compatible Commit: 386526d928be1de57268163db1814640baa13459 https://github.com/galaxyproject/galaxy/commit/386526d928be1de57268163db181… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: 988cab4db7ef83714cf6f0c57f73f4255e3f075d https://github.com/galaxyproject/galaxy/commit/988cab4db7ef83714cf6f0c57f73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/merge_collection.xml M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/logging/__init__.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/stack/message.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/tool_shed/util/xml_util.py M templates/galaxy_client_app.mako M templates/webapps/galaxy/dataset/security_common.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/tool_shed/repository/tool_form.mako Log Message: ----------- Merge pull request #5422 from nsoranzo/python3 Mixed Python3 fixes Compare: https://github.com/galaxyproject/galaxy/compare/5a31ac84ce12...988cab4db7ef

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[galaxyproject/galaxy] c7b6af: Add a script for dumping library file paths for ba...
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7b6afbcd25fdeef9d7a59df95e3ace3136e0fa9 https://github.com/galaxyproject/galaxy/commit/c7b6afbcd25fdeef9d7a59df95e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: A scripts/dump_library_paths.py Log Message: ----------- Add a script for dumping library file paths for backup Commit: 5a31ac84ce129d03aea5fcbd73edaa4d67c465e5 https://github.com/galaxyproject/galaxy/commit/5a31ac84ce129d03aea5fcbd73ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: A scripts/dump_library_paths.py Log Message: ----------- Merge pull request #5436 from natefoo/dump-library-paths A script for dumping library file paths for backup Compare: https://github.com/galaxyproject/galaxy/compare/b1df43a1f83a...5a31ac84ce12

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[galaxyproject/galaxy] 7490fd: More robust nametag discovery and propagation.
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7490fd452046b4a4578f6401501439773cbf2f28 https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f64015014… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- More robust nametag discovery and propagation. - Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool. - Nametags weren't being propagated to the outputs of collection operations. Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6 https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cleanup collection operation tagging implementation thanks to @mvdbeek comments. Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386 https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle optional inputs when collecting preserved tags. https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450 Commit: 60561c20307cf0585e553d0fa5cd612716ab7975 https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- Merge pull request #5403 from jmchilton/collection_operation_tags [18.01] More robust nametag discovery and propagation. Compare: https://github.com/galaxyproject/galaxy/compare/f24043e8a74e...60561c20307c

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[galaxyproject/usegalaxy-playbook] 0a1fad: Update TTS
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0a1fada824cfa1e26991b9a6adeac5db27590915 https://github.com/galaxyproject/usegalaxy-playbook/commit/0a1fada824cfa1e2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS

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[galaxyproject/galaxy] 6d8edc: Admin doc corrections
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6d8edce33157e81112889ae7f241903747da3c92 https://github.com/galaxyproject/galaxy/commit/6d8edce33157e81112889ae7f241… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Admin doc corrections Commit: f24043e8a74e3cb2070b06652d9a72be46e6a278 https://github.com/galaxyproject/galaxy/commit/f24043e8a74e3cb2070b06652d9a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 [18.01] Admin doc corrections Compare: https://github.com/galaxyproject/galaxy/compare/ffaabe0a63f4...f24043e8a74e

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[galaxyproject/galaxy] a1662e: remove lib/galaxy/dependencies/conda-environment.t...
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1662e37059e6956cdca3cb3eb235fd7b890b5c4 https://github.com/galaxyproject/galaxy/commit/a1662e37059e6956cdca3cb3eb23… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: R lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- remove lib/galaxy/dependencies/conda-environment.txt the file is no longer valid and has been replaced by conda-file.sh I believe Commit: b1df43a1f83a2b3026e23758843017d428e56a64 https://github.com/galaxyproject/galaxy/commit/b1df43a1f83a2b3026e237588430… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: R lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #5440 from martenson/remove-condaenv-txt remove lib/galaxy/dependencies/conda-environment.txt Compare: https://github.com/galaxyproject/galaxy/compare/b4cdce925bf4...b1df43a1f83a

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[galaxyproject/infrastructure-playbook] 8b1d72: Automatically balance normal/multi partitions on r...
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8b1d7203ee90d92a15d8f6b6fba2e26f6b8a546e https://github.com/galaxyproject/infrastructure-playbook/commit/8b1d7203ee9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: A taccenv/files/slurm/spartbalance A taccenv/group_vars/slurmservers.yml Log Message: ----------- Automatically balance normal/multi partitions on roundup to try to avoid waiting normal jobs.

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[galaxyproject/galaxy] 6bdd75: WIP framework dependencies doc update
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6bdd755aafbb008422db46231949ad3c6e4e608f https://github.com/galaxyproject/galaxy/commit/6bdd755aafbb008422db46231949… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- WIP framework dependencies doc update Commit: fd96864bd6fca8f4ff149ca0ba270ebb164254ac https://github.com/galaxyproject/galaxy/commit/fd96864bd6fca8f4ff149ca0ba27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Finish updates to framework dependencies doc Commit: 6333e83a6517830599d17e42707f0bead367d135 https://github.com/galaxyproject/galaxy/commit/6333e83a6517830599d17e42707f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Doc corrections from @nsoranzo Commit: 6070bf07e18b0d3ebc210f3c4c44a1ed14b1dd27 https://github.com/galaxyproject/galaxy/commit/6070bf07e18b0d3ebc210f3c4c44… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css Log Message: ----------- simplify Webhooks' structure Commit: ada76931d8231a83ff15667ccec652b06bd793d4 https://github.com/galaxyproject/galaxy/commit/ada76931d8231a83ff15667ccec6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M lib/galaxy/webhooks/__init__.py Log Message: ----------- add weighted random webhook pick Commit: 90d59ac9234d7a756eb3040cccb35c6e181826ec https://github.com/galaxyproject/galaxy/commit/90d59ac9234d7a756eb3040cccb3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M test/api/test_webhooks.py M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- fix webhooks tests Commit: 57c1fc78043220ec16081255c2b15e854cac976c https://github.com/galaxyproject/galaxy/commit/57c1fc78043220ec16081255c2b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js Log Message: ----------- Client formatting of webhooks changes. Commit: 0ac7b7830dd06ef474002a57c677ca429913d766 https://github.com/galaxyproject/galaxy/commit/0ac7b7830dd06ef474002a57c677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix import order in webhooks/__init__.py Commit: 3b7daece0460286288a8678c5020dd6530d5457f https://github.com/galaxyproject/galaxy/commit/3b7daece0460286288a8678c5020… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/webhooks.js Log Message: ----------- Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported. Commit: 22b0b2f2e90249feacacd0f8cfb60a9335bb40e9 https://github.com/galaxyproject/galaxy/commit/22b0b2f2e90249feacacd0f8cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/qunit/tests/page_tests.js Log Message: ----------- Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes. Commit: fa0ba22f97cbf69c30828205ea94358094b654e0 https://github.com/galaxyproject/galaxy/commit/fa0ba22f97cbf69c30828205ea94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix webhook filtering, make it a bit more defensive. Minor other tweaks. Commit: 9b4465efd37fe7c27276971a2348283e41cc9027 https://github.com/galaxyproject/galaxy/commit/9b4465efd37fe7c27276971a2348… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- fix webhook's property name Commit: 29c766167a64f302341101b0a7301fcd29634698 https://github.com/galaxyproject/galaxy/commit/29c766167a64f302341101b0a730… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- update webhooks docs Commit: a37b638491bc1d04be266bf9a14852fcfb62c342 https://github.com/galaxyproject/galaxy/commit/a37b638491bc1d04be266bf9a148… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #5390 from natefoo/framework-dependencies-doc-update [18.01] Update framework dependencies documentation Commit: ffaabe0a63f47c57cd9785de84cf9e77e398b95c https://github.com/galaxyproject/galaxy/commit/ffaabe0a63f47c57cd9785de84cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge pull request #5342 from dannon/integration.webhooks_improvements [18.01] Webhooks improvements Commit: b4cdce925bf485ecdb24868bacdcffe2f4e7a717 https://github.com/galaxyproject/galaxy/commit/b4cdce925bf485ecdb24868bacdc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/webhooks.rst A lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M scripts/common_startup.sh M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge branch 'release_18.01' into dev I removed the conflicted file that was modified in dev after removal in 18.01 Compare: https://github.com/galaxyproject/galaxy/compare/a76614486be3...b4cdce925bf4

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[galaxyproject/usegalaxy-playbook] db03a5: More mutable configs
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: db03a5e84cfde3cc40a7682fe273477ffd28e558 https://github.com/galaxyproject/usegalaxy-playbook/commit/db03a5e84cfde3cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- More mutable configs

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[galaxyproject/usegalaxy-playbook] 67ad45: Set slow log threshold correctly
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 67ad4503c6c4bc15c0a5a775203a9b08fd9eaeb1 https://github.com/galaxyproject/usegalaxy-playbook/commit/67ad4503c6c4bc15… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Set slow log threshold correctly Commit: 76c3ef26730370ec44b808964e9d85cae6b15c87 https://github.com/galaxyproject/usegalaxy-playbook/commit/76c3ef26730370ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b68ea53bac01...…

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[galaxyproject/usegalaxy-playbook] 173e0b: Attempt to log queries on Test slower than 1s
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 173e0b72b56cd125481012d86fb7efe9ac79ac58 https://github.com/galaxyproject/usegalaxy-playbook/commit/173e0b72b56cd125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Attempt to log queries on Test slower than 1s Commit: 02e5f3474715cf2887e187ab832159de558fdd40 https://github.com/galaxyproject/usegalaxy-playbook/commit/02e5f3474715cf28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run IUC Trinity on Bridges. Commit: b68ea53bac010a37a4091a8ee3076bdeec27d71c https://github.com/galaxyproject/usegalaxy-playbook/commit/b68ea53bac010a37… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M CHANGELOG.md M env/common/files/pulsar/config/bridges_dependency_resolvers_conf.xml Log Message: ----------- More Bridges fixes for Trinity. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2f5e366ffe6f...…

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[galaxyproject/infrastructure-playbook] e29926: Updates for the zfs admin module
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e2992640880d0df95df4256a16219e4059bbb90a https://github.com/galaxyproject/infrastructure-playbook/commit/e2992640880… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M common_roles M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml Log Message: ----------- Updates for the zfs admin module

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[galaxyproject/galaxy] 6070bf: simplify Webhooks' structure
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6070bf07e18b0d3ebc210f3c4c44a1ed14b1dd27 https://github.com/galaxyproject/galaxy/commit/6070bf07e18b0d3ebc210f3c4c44… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css Log Message: ----------- simplify Webhooks' structure Commit: ada76931d8231a83ff15667ccec652b06bd793d4 https://github.com/galaxyproject/galaxy/commit/ada76931d8231a83ff15667ccec6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M lib/galaxy/webhooks/__init__.py Log Message: ----------- add weighted random webhook pick Commit: 90d59ac9234d7a756eb3040cccb35c6e181826ec https://github.com/galaxyproject/galaxy/commit/90d59ac9234d7a756eb3040cccb3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M test/api/test_webhooks.py M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- fix webhooks tests Commit: 57c1fc78043220ec16081255c2b15e854cac976c https://github.com/galaxyproject/galaxy/commit/57c1fc78043220ec16081255c2b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js Log Message: ----------- Client formatting of webhooks changes. Commit: 0ac7b7830dd06ef474002a57c677ca429913d766 https://github.com/galaxyproject/galaxy/commit/0ac7b7830dd06ef474002a57c677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix import order in webhooks/__init__.py Commit: 3b7daece0460286288a8678c5020dd6530d5457f https://github.com/galaxyproject/galaxy/commit/3b7daece0460286288a8678c5020… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/webhooks.js Log Message: ----------- Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported. Commit: 22b0b2f2e90249feacacd0f8cfb60a9335bb40e9 https://github.com/galaxyproject/galaxy/commit/22b0b2f2e90249feacacd0f8cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/qunit/tests/page_tests.js Log Message: ----------- Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes. Commit: fa0ba22f97cbf69c30828205ea94358094b654e0 https://github.com/galaxyproject/galaxy/commit/fa0ba22f97cbf69c30828205ea94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix webhook filtering, make it a bit more defensive. Minor other tweaks. Commit: 9b4465efd37fe7c27276971a2348283e41cc9027 https://github.com/galaxyproject/galaxy/commit/9b4465efd37fe7c27276971a2348… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- fix webhook's property name Commit: 29c766167a64f302341101b0a7301fcd29634698 https://github.com/galaxyproject/galaxy/commit/29c766167a64f302341101b0a730… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- update webhooks docs Commit: ffaabe0a63f47c57cd9785de84cf9e77e398b95c https://github.com/galaxyproject/galaxy/commit/ffaabe0a63f47c57cd9785de84cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge pull request #5342 from dannon/integration.webhooks_improvements [18.01] Webhooks improvements Compare: https://github.com/galaxyproject/galaxy/compare/a37b638491bc...ffaabe0a63f4

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[galaxyproject/galaxy] 6bdd75: WIP framework dependencies doc update
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6bdd755aafbb008422db46231949ad3c6e4e608f https://github.com/galaxyproject/galaxy/commit/6bdd755aafbb008422db46231949… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- WIP framework dependencies doc update Commit: fd96864bd6fca8f4ff149ca0ba270ebb164254ac https://github.com/galaxyproject/galaxy/commit/fd96864bd6fca8f4ff149ca0ba27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Finish updates to framework dependencies doc Commit: 6333e83a6517830599d17e42707f0bead367d135 https://github.com/galaxyproject/galaxy/commit/6333e83a6517830599d17e42707f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Doc corrections from @nsoranzo Commit: a37b638491bc1d04be266bf9a14852fcfb62c342 https://github.com/galaxyproject/galaxy/commit/a37b638491bc1d04be266bf9a148… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #5390 from natefoo/framework-dependencies-doc-update [18.01] Update framework dependencies documentation Compare: https://github.com/galaxyproject/galaxy/compare/6b0542f7c287...a37b638491bc

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