August 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5f1b7d: Show verison button in workflow editor and trigger...
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f1b7d5a5060c3c45601b499a953113e0b1b3125 https://github.com/galaxyproject/galaxy/commit/5f1b7d5a5060c3c45601b499a953… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Show verison button in workflow editor and trigger on_change Commit: 25e05b62c7b529b0379e3ff50fc75ccb5b8c28b6 https://github.com/galaxyproject/galaxy/commit/25e05b62c7b529b0379e3ff50fc7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Do postchange action only when modifiying tool versions in the workflow editor Commit: 5afe490822325d4aa6c9be726183175743dc88f6 https://github.com/galaxyproject/galaxy/commit/5afe490822325d4aa6c9be726183… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix qunit test Commit: 36ce9113f7ccb6372bc2d1f8e92e95a8aafdd066 https://github.com/galaxyproject/galaxy/commit/36ce9113f7ccb6372bc2d1f8e92e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Keep spacing consistent (thx @nsoranzo) Commit: 526e98e372e61747b1e3cd4b86a04603ca08959b https://github.com/galaxyproject/galaxy/commit/526e98e372e61747b1e3cd4b86a0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Reset outputs when changing tool versions in wf-editor Commit: db2ea853f699bf6b55b67cf7199ab355196910bc https://github.com/galaxyproject/galaxy/commit/db2ea853f699bf6b55b67cf7199a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow Commit: ea1f4f866658e77465d1272b4d7f37bb85ee488b https://github.com/galaxyproject/galaxy/commit/ea1f4f866658e77465d1272b4d7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date Commit: bc95f5e81b46a0bee54f6ffdd5c3a6615258af20 https://github.com/galaxyproject/galaxy/commit/bc95f5e81b46a0bee54f6ffdd5c3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic Commit: 92fedc0ae86127d670f3ff8e829d07ee657f30d7 https://github.com/galaxyproject/galaxy/commit/92fedc0ae86127d670f3ff8e829d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix logic for adding and removing outputs Commit: 1c286b158a8304380f499709b2f14c958b6fe203 https://github.com/galaxyproject/galaxy/commit/1c286b158a8304380f499709b2f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Remove extra newlines Commit: 2e95026317e2e781163cf8bd4449bfd5ddfb894f https://github.com/galaxyproject/galaxy/commit/2e95026317e2e781163cf8bd4449… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove unused old_version variable Commit: 31c423a45a4186c41981f71d41a590177bad033d https://github.com/galaxyproject/galaxy/commit/31c423a45a4186c41981f71d41a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix typo and remove leftover comment (thanks @nsoranzo) Commit: df91881c1f4dba06a9fb6a1720db68d059664041 https://github.com/galaxyproject/galaxy/commit/df91881c1f4dba06a9fb6a1720db… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-13 (Sun, 13 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Remove unused workflow outputs Commit: 73f4141d96ad54c25fdf7a3ffb458f2b1933e14e https://github.com/galaxyproject/galaxy/commit/73f4141d96ad54c25fdf7a3ffb45… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add static JS Commit: aa7be28960a43802bd476be1d7d996c85134c055 https://github.com/galaxyproject/galaxy/commit/aa7be28960a43802bd476be1d7d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/workflows.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/api/test_tools.py M test/base/api.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into switch_versions_in_workflows Commit: 27be24963837354af6cac1f429c1bc06e95626e1 https://github.com/galaxyproject/galaxy/commit/27be24963837354af6cac1f429c1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #4373 from mvdbeek/switch_versions_in_workflows Allow switching tool versions in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/44548f8f2fe2...27be24963837

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[galaxyproject/galaxy] 4dd503: Update conda channel order to sync with Bioconda
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4dd503046f59b13e925a76f88862882747dc6ad7 https://github.com/galaxyproject/galaxy/commit/4dd503046f59b13e925a76f88862… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Update conda channel order to sync with Bioconda Commit: 420e7a4f3408ec064403a4283ba22a134b65ece5 https://github.com/galaxyproject/galaxy/commit/420e7a4f3408ec064403a4283ba2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Remove _ensure_conda_context() function and make conda_context argument mandatory in functions/methods. This should help making sure the correct context (e.g. channels) is used for all Conda operations. Also remove unused is_target_available() function. Commit: cdbac056cb664e4c51f84c41c2519993d0412d74 https://github.com/galaxyproject/galaxy/commit/cdbac056cb664e4c51f84c41c251… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Override channel list on the command line instead of modifying condarc The way we were modifying condarc in the ensure_channels_configured() method was broken because we were appending the missing channels at the end, so the final order may not be the one specified in conda_ensure_channels . Also: - not modifying the user condarc is a much better approach - overriding the channel list on the command line will make debugging easier Commit: 44548f8f2fe258051ad2df45b153642586b85e00 https://github.com/galaxyproject/galaxy/commit/44548f8f2fe258051ad2df45b153… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4409 from nsoranzo/fix_conda_channel_order Update conda channel order to sync with Bioconda Compare: https://github.com/galaxyproject/galaxy/compare/8721da8ca2e1...44548f8f2fe2

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[galaxyproject/galaxy] 68555f: some unicoding
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68555f5571b5b872a39a34f8fa6035bfad67ea43 https://github.com/galaxyproject/galaxy/commit/68555f5571b5b872a39a34f8fa60… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- some unicoding Commit: 8721da8ca2e1f78a018baf4c43d8229327eb477f https://github.com/galaxyproject/galaxy/commit/8721da8ca2e1f78a018baf4c43d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4426 from erasche/local-runner-unicode some unicoding for local runner Compare: https://github.com/galaxyproject/galaxy/compare/9cbabef17e9a...8721da8ca2e1

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[galaxyproject/galaxy] d0b06a: Don't cast tool_version to string if tool_version ...
by GitHub 15 Aug '17

15 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153) Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Compare: https://github.com/galaxyproject/galaxy/compare/4faf496c9898...7f78ee7b18b8

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[galaxyproject/galaxy] 6c6c80: When a page is involved, the ID will be wrong
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591 https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- When a page is involved, the ID will be wrong Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226 https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client Commit: a2229783177b76786f581cc78040b059cbd2aab5 https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4355 from erasche/patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9 https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Commit: 9cbabef17e9afb4953324516d0883976edd51e87 https://github.com/galaxyproject/galaxy/commit/9cbabef17e9afb4953324516d088… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: static/maps/mvc/library/library-foldertoolbar-view.js.map static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/library/library-foldertoolbar-view.js Compare: https://github.com/galaxyproject/galaxy/compare/e594152de2dd...9cbabef17e9a

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[galaxyproject/galaxy] ba3249: Add missing chemical formats to datatypes_conf.xml...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Compare: https://github.com/galaxyproject/galaxy/compare/10efd7fac6e3...4faf496c9898

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[galaxyproject/galaxy] ba3249: Add missing chemical formats to datatypes_conf.xml...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/bfb3ce6e7907...0f5ad34eaf6b

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[galaxyproject/galaxy] e901a0: Bugfix for loading subworkflows from workflow desc...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e901a0c867cfa9af3420536c4725cbc001621cf8 https://github.com/galaxyproject/galaxy/commit/e901a0c867cfa9af3420536c4725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Bugfix for loading subworkflows from workflow descriptions. Sometimes unrelated workflow steps can be flushed in a half complete state and violate integrity constraints when a subworkflow step causes a flush of during the load of a different step. This fixes that by preloading all subworkflows during workflow import. This PR doesn't include a test case but one will be included if the CWL branch is merged at a later date (xref https://github.com/common-workflow-language/common-workflow-language/pull/4…) Commit: e594152de2dd33dbdff2feb8e05f05ad5810ab27 https://github.com/galaxyproject/galaxy/commit/e594152de2dd33dbdff2feb8e05f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4394 from jmchilton/subworkflow_loading_fix Bugfix for loading subworkflows from workflow descriptions. Compare: https://github.com/galaxyproject/galaxy/compare/8e192dbf4ca2...e594152de2dd

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[galaxyproject/galaxy] d39483: Revise summarize history errors to display more da...
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d39483bf0a88aa6c62cb69928abc8195e9082db7 https://github.com/galaxyproject/galaxy/commit/d39483bf0a88aa6c62cb69928abc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/base/interactor.py Log Message: ----------- Revise summarize history errors to display more data and outline collections. Commit: 67f9e34f530d1d505e12fcca9fef2648025d877e https://github.com/galaxyproject/galaxy/commit/67f9e34f530d1d505e12fcca9fef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/api/test_tools.py M test/base/populators.py Log Message: ----------- Implement test lib history context. Commit: b7fe2fa2ecc44bde964be1c44e73e2ea11586bf5 https://github.com/galaxyproject/galaxy/commit/b7fe2fa2ecc44bde964be1c44e73… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M test/base/interactor.py M test/base/populators.py Log Message: ----------- Rework summarizing histories on errors to include all datasets. ``` -------------------- >> begin captured stdout << --------------------- Problem in history with id adb5f5c93f827949 - summary of datasets below. -------------------------------------- | 1 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 1 line | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 1 line | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 3 - multi_data_param on data 1 and data 2 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>1 2 3</td></tr><tr><td>4 5 6</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 4 - multi_data_param on data 1 and data 2 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 2 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>4 5 6</td></tr><tr><td>1 2 3</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- ``` Commit: 8e192dbf4ca2f7c6c0860430a4d8085de7732ab1 https://github.com/galaxyproject/galaxy/commit/8e192dbf4ca2f7c6c0860430a4d8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M test/api/test_tools.py M test/base/interactor.py M test/base/populators.py Log Message: ----------- Merge pull request #4397 from jmchilton/api_test_enhancement Better Error Summaries for API Tests Compare: https://github.com/galaxyproject/galaxy/compare/f849c7e6feaf...8e192dbf4ca2

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[galaxyproject/galaxy] 7a1fbd: Fix bug in upload HTML checker.
by GitHub 14 Aug '17

14 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a1fbd37e9fb262432daed6eefc4e9c54ceff406 https://github.com/galaxyproject/galaxy/commit/7a1fbd37e9fb262432daed6eefc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Fix bug in upload HTML checker. If a chunk was passed into the check_html function - e.g. it was read from a compressed file - it would search through each character in the string for certain HTML content instead of each line in the string. Commit: 59aa11864a795861484133dfc85212bf9150cf4a https://github.com/galaxyproject/galaxy/commit/59aa11864a795861484133dfc852… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/util/checkers.py M tools/data_source/upload.py Log Message: ----------- Add configuration option to disable upload content checking. Commit: 53b0b25456c170990ad3345021aab16f68e6e185 https://github.com/galaxyproject/galaxy/commit/53b0b25456c170990ad3345021aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M test/base/populators.py Log Message: ----------- Better error reporting in test/base/populators.py. Commit: bee6af1e4117e7ff6f7caac0d9c84253ec1c4882 https://github.com/galaxyproject/galaxy/commit/bee6af1e4117e7ff6f7caac0d9c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M test/base/api.py Log Message: ----------- Allow API tests to work with admin users (not just admin keys). Commit: fec1eab82dc6dea2d03711127ed08b3038ad5bf1 https://github.com/galaxyproject/galaxy/commit/fec1eab82dc6dea2d03711127ed0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M test/base/populators.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Add ability to arbitrarily not decompress files on upload via API. Commit: 06ca789f92ad2f4dfaffc36d3fa0bafb3c74920d https://github.com/galaxyproject/galaxy/commit/06ca789f92ad2f4dfaffc36d3fa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-12 (Sat, 12 Aug 2017) Changed paths: A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py Log Message: ----------- Configuration tests for the last few upload enhancements. Commit: f849c7e6feafabf905653bd008fde23dc1413a85 https://github.com/galaxyproject/galaxy/commit/f849c7e6feafabf905653bd008fd… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/checkers.py A test-data/1.sam.gz A test-data/bad.html.gz A test-data/random-file M test/base/api.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml A test/integration/test_upload_configuration_options.py M tools/data_source/upload.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #4417 from jmchilton/upload_enhance Fixes and enhancements for the upload API Compare: https://github.com/galaxyproject/galaxy/compare/fc861cdf38d1...f849c7e6feaf

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