- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 18977d: Don't load hidden tools into the tool panel at all...
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18977d4132556a0c2bd0348db510cf765d434e6a https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load hidden tools into the tool panel at all. Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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: 04a572e509e875414b07e73c295f1c4bb37c1e0c https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4726 from natefoo/panel-hidden-fix [17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 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 #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf9971… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 3d87afbb4174be1068aa701ca4d36d3b3f89591c https://github.com/galaxyproject/galaxy/commit/3d87afbb4174be1068aa701ca4d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/068c61a310e6...3d87afbb4174

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[galaxyproject/galaxy] 2eed47: Update conda channel order to sync with Bioconda
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 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 #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf9971… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-02 (Mon, 02 Oct 2017) Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/04a572e509e8...280dc48c386f

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[galaxyproject/galaxy] 2eed47: Update conda channel order to sync with Bioconda
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42 https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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: a5b7dce09fb690f09d25f1b806d3339bdf2171c9 https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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. Conflicts: lib/galaxy/tools/deps/conda_util.py Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7 https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-10-02 (Mon, 02 Oct 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: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071 https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 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 #4731 from nsoranzo/release_17.05_backport_4409 [17.05] Backport #4409 Compare: https://github.com/galaxyproject/galaxy/compare/cfabe37d6954...81ece2551cea

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[galaxyproject/galaxy] 18977d: Don't load hidden tools into the tool panel at all...
by GitHub 02 Oct '17

02 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 18977d4132556a0c2bd0348db510cf765d434e6a https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Don't load hidden tools into the tool panel at all. Commit: 04a572e509e875414b07e73c295f1c4bb37c1e0c https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-02 (Mon, 02 Oct 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4726 from natefoo/panel-hidden-fix [17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel Compare: https://github.com/galaxyproject/galaxy/compare/38b19d4c47d2...04a572e509e8

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[galaxyproject/galaxy] 10b9ac: Stricter checks for SDF sniffing
by GitHub 01 Oct '17

01 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10b9ac8c7de9e7f2c04d6a25777209abb350a0cc https://github.com/galaxyproject/galaxy/commit/10b9ac8c7de9e7f2c04d6a257772… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/datatypes/molecules.py Log Message: ----------- Stricter checks for SDF sniffing I had a bunch of protein FASTA files being sniffed as 'sdf'. Also fix https://github.com/galaxyproject/galaxy/issues/4558 . Commit: e3307c5be96d479dc7731fbfefefbb1bc6854fa5 https://github.com/galaxyproject/galaxy/commit/e3307c5be96d479dc7731fbfefef… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- More precise SDF sniffer First check 4th line: if this is conforming, scan up to 10000 lines. Add 2 test files downloaded from: https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d… Commit: 068c61a310e65055a5a7b6747696f71d0fdb0e7f https://github.com/galaxyproject/galaxy/commit/068c61a310e65055a5a7b6747696… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M lib/galaxy/datatypes/molecules.py A lib/galaxy/datatypes/test/chebi_57262.v3k.mol A lib/galaxy/datatypes/test/github88.v3k.sdf Log Message: ----------- Merge pull request #4729 from nsoranzo/fix_molecule_datatypes Stricter checks for SDF sniffing Compare: https://github.com/galaxyproject/galaxy/compare/73bb4ba8c2e5...068c61a310e6

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[galaxyproject/infrastructure-playbook] 3755a8: Make mjolnir0 a jenkins builder.
by GitHub 01 Oct '17

01 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3755a8de3d7ee468278dbc9240591083117cb819 https://github.com/galaxyproject/infrastructure-playbook/commit/3755a8de3d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-30 (Sat, 30 Sep 2017) Changed paths: M common_roles M galaxyenv/files/jenkins/jenkins_server_user_ssh_config M galaxyenv/group_vars/jenkinsslaves.yml M galaxyenv/group_vars/starforgebuilders.yml M galaxyenv/inventory Log Message: ----------- Make mjolnir0 a jenkins builder. Commit: 46d7c1bd9c5fc74d5042071080b1cf36095f1804 https://github.com/galaxyproject/infrastructure-playbook/commit/46d7c1bd9c5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-01 (Sun, 01 Oct 2017) Changed paths: M galaxyenv/templates/nginx/galaxydomains.j2 Log Message: ----------- Fix gdc2010/gcc2011 redirects from galaxy.psu.edu. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/fd16374d80…

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[galaxyproject/infrastructure-playbook] fd1637: Add n7 and n8 as jenkins workers
by GitHub 01 Oct '17

01 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fd16374d80ff59a936cf8409e41f9f9bfb3c24ad https://github.com/galaxyproject/infrastructure-playbook/commit/fd16374d80f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-30 (Sat, 30 Sep 2017) Changed paths: M galaxyenv/inventory Log Message: ----------- Add n7 and n8 as jenkins workers

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[galaxyproject/galaxy] 8420d8: Move history default permissions to history contro...
by GitHub 29 Sep '17

29 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8420d89a55f0e4dafb2711631b6c556a08e3cabc https://github.com/galaxyproject/galaxy/commit/8420d89a55f0e4dafb2711631b6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M templates/webapps/galaxy/history/permissions.mako Log Message: ----------- Move history default permissions to history controller Commit: 49ebf1261da97858b89c307cb7227c847fcc3125 https://github.com/galaxyproject/galaxy/commit/49ebf1261da97858b89c307cb722… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add client routes, link from history panel to controller endpoint for history permissions Commit: 1c3e5f2106e2315824dec04e20179117bb634f58 https://github.com/galaxyproject/galaxy/commit/1c3e5f2106e2315824dec04e2017… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Build preliminary form structure Commit: 5f61ec3d4fc1dd55f89b1e730074684a20f05103 https://github.com/galaxyproject/galaxy/commit/5f61ec3d4fc1dd55f89b1e730074… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add save to history permissions endpoint Commit: 5d3fc7af61614085ceeed3f561875bcddbba8cc0 https://github.com/galaxyproject/galaxy/commit/5d3fc7af61614085ceeed3f56187… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: R templates/webapps/galaxy/history/permissions.mako Log Message: ----------- Remove history permissions mako Commit: 361c0dc2ece875ed46b4edc7095e0b1f20802cd6 https://github.com/galaxyproject/galaxy/commit/361c0dc2ece875ed46b4edc7095e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/history.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Allow history dataset permissions modifications in saved histories grid Commit: b08a81c4059df2bc11773d1fe3328f55631e784d https://github.com/galaxyproject/galaxy/commit/b08a81c4059df2bc11773d1fe332… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Preserve previous drop down order Commit: 7f57010a431aa416dd5574bcdfd6ec9cee9afa1b https://github.com/galaxyproject/galaxy/commit/7f57010a431aa416dd5574bcdfd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Fix spacing Commit: d61db29f29f99598577467a90690ce3deef09844 https://github.com/galaxyproject/galaxy/commit/d61db29f29f99598577467a90690… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Disable multi operation for dataset permissions view Commit: f88ce0b3825c277c181c19c2ff562812a826dd4a https://github.com/galaxyproject/galaxy/commit/f88ce0b3825c277c181c19c2ff56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/onload.js M client/toolshed/scripts/mvc/groups/group-model.js M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/webapp.py M static/maps/galaxy.interactive_environments.js.map M static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/onload.js.map M static/scripts/bundled/admin.bundled.js 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/galaxy.interactive_environments.js M static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/scripts/onload.js M static/toolshed/maps/mvc/groups/group-detail-view.js.map M static/toolshed/maps/mvc/groups/group-list-view.js.map M static/toolshed/maps/mvc/groups/group-listrow-view.js.map M static/toolshed/maps/mvc/groups/group-model.js.map M static/toolshed/scripts/mvc/groups/group-detail-view.js M static/toolshed/scripts/mvc/groups/group-list-view.js M static/toolshed/scripts/mvc/groups/group-listrow-view.js M static/toolshed/scripts/mvc/groups/group-model.js Log Message: ----------- Merge branch 'dev' into replace_history_permission_form Commit: a5c83b3ce95c46a58c05d4f9a6d50d9687048c9c https://github.com/galaxyproject/galaxy/commit/a5c83b3ce95c46a58c05d4f9a6d5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use same push url format as in other push requests Commit: dd4d077a8197649d9f35974e873c67aebf5fdda4 https://github.com/galaxyproject/galaxy/commit/dd4d077a8197649d9f35974e873c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix error message Commit: f97392c1db4ebd0b0d1436f6271fc6727526be33 https://github.com/galaxyproject/galaxy/commit/f97392c1db4ebd0b0d1436f6271f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/onload.js M doc/source/admin/reports.md M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt A lib/galaxy/managers/jobs.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/onload.js M test/api/test_jobs.py Log Message: ----------- Merge branch 'dev' into replace_history_permission_form Commit: 73bb4ba8c2e5e21dce0aa90dcb96394083840e70 https://github.com/galaxyproject/galaxy/commit/73bb4ba8c2e5e21dce0aa90dcb96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R templates/webapps/galaxy/history/permissions.mako Log Message: ----------- Merge pull request #4711 from guerler/replace_history_permission_form Removes the history permissions form mako Compare: https://github.com/galaxyproject/galaxy/compare/e5597639e2f9...73bb4ba8c2e5

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[galaxyproject/galaxy] 4d3c78: Fix typo in function name
by GitHub 29 Sep '17

29 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d3c78d0997aa1c6992cad8bd18133aefae2d4d3 https://github.com/galaxyproject/galaxy/commit/4d3c78d0997aa1c6992cad8bd181… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/tools/loader.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Fix typo in function name Follow-up on https://github.com/galaxyproject/galaxy/pull/4635 Commit: cc983c318b75e861a4b79127201925b289826f09 https://github.com/galaxyproject/galaxy/commit/cc983c318b75e861a4b791272019… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py Log Message: ----------- Typo fixes and small cleanups Commit: e5597639e2f97e09efa63d53dc70d6aa5f83cba9 https://github.com/galaxyproject/galaxy/commit/e5597639e2f97e09efa63d53dc70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py Log Message: ----------- Merge pull request #4725 from nsoranzo/typo_fixes Typo fixes and small cleanups Compare: https://github.com/galaxyproject/galaxy/compare/4b7bd98b3061...e5597639e2f9

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[galaxyproject/galaxy] 92b484: Extend job search for HDCA input
by GitHub 29 Sep '17

29 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 92b48412c5cbb50c31b26e97912c073b7c0f29e2 https://github.com/galaxyproject/galaxy/commit/92b48412c5cbb50c31b26e97912c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Extend job search for HDCA input Commit: 1d37c7d458f156e391d969bf7630044a476b9856 https://github.com/galaxyproject/galaxy/commit/1d37c7d458f156e391d969bf7630… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Check JobParameter match Matching the JobParameters will prevent returning jobs where a job uses the same input datasets, but where the inputs are used in a different order (and hence the result may differ) Commit: 2b7a1631280e19468021931ca827b94567bca457 https://github.com/galaxyproject/galaxy/commit/2b7a1631280e19468021931ca827… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Add job_search tests for other collection types Commit: 7089de8142199e1b5dadaeef215ae015042f018b https://github.com/galaxyproject/galaxy/commit/7089de8142199e1b5dadaeef215a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Reduce job_search test copypaste Commit: 04754c4c4d8c4c287a54e13bc0263f1fdaeaf00c https://github.com/galaxyproject/galaxy/commit/04754c4c4d8c4c287a54e13bc026… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Allow job_search to find job even if current HDCA was copied from another HDCA and make sure that jobs with same inputs matched to different job parameter inputs are not considered as a match Commit: 64cf60b502daea924fbb7b1106c0040976cdbdc1 https://github.com/galaxyproject/galaxy/commit/64cf60b502daea924fbb7b1106c0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Test deleting input datasets and recovering jobs from search This revealed a wrong query filter (comparing JobToInputDatasetAssociation.dataset_id == HistoryDatasetAssociation.id, instead of JobToInputDatasetAssociation.dataset_id == HistoryDatasetAssociation.dataset_id). Commit: df91074a3f587e6bd3270e67c4d00ffc321518af https://github.com/galaxyproject/galaxy/commit/df91074a3f587e6bd3270e67c4d0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Test deleting HDCAs and finding equivalent jobs Commit: 9e3ceaa7f3410127c7ee8c2c1c3854f4208d5afc https://github.com/galaxyproject/galaxy/commit/9e3ceaa7f3410127c7ee8c2c1c38… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Don't return jobs with deleted HDAs/HDCAs from job_search Commit: 07daa4d248ba5f42facb86a0e38370c54fb9e7b6 https://github.com/galaxyproject/galaxy/commit/07daa4d248ba5f42facb86a0e383… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: A lib/galaxy/jobs/search.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Move job_search out of API for re-use Commit: 054cdd146a84460db07f4725a5251036bb42278f https://github.com/galaxyproject/galaxy/commit/054cdd146a84460db07f4725a525… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/jobs/search.py Log Message: ----------- When querying jobs for data input parameters drop all other parameters Commit: 19818cb380889e584741caf4a78462e0502f30c1 https://github.com/galaxyproject/galaxy/commit/19818cb380889e584741caf4a784… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Fix loading of model.JobToInputDatasetCollectionAssociation If we don't load this relationship we do not properly record a job's input_dataset_collections in `DefaultToolAction._record_inputs`. Commit: 87439012602cd500346a1fe442292b2e7cbaaeab https://github.com/galaxyproject/galaxy/commit/87439012602cd500346a1fe44229… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/jobs/search.py Log Message: ----------- Filter jobs on input data using JobToInput*Association. This has the advantage that for complex parameters we don't need to decompose parameter names like `queries_0|input2` in order to compare JobParameters. Commit: 5fc360a0829ae6819dc96ad0228940cda59d4fa7 https://github.com/galaxyproject/galaxy/commit/5fc360a0829ae6819dc96ad02289… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: R lib/galaxy/jobs/search.py A lib/galaxy/managers/jobs.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Move JobSearch to galaxy.managers.jobs Commit: 0e287d38ca1b779c306eb8e0a4c9d3c8bc140882 https://github.com/galaxyproject/galaxy/commit/0e287d38ca1b779c306eb8e0a4c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Return empty list if type is unknown Commit: 480ee7980251848d09e837faef1cd9873b2e2e33 https://github.com/galaxyproject/galaxy/commit/480ee7980251848d09e837faef1c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Skip recording JobToInputDatasetCollection relations if the item to record is not a HistoryDatasetCollectionAssociation. This fixes ``` Error executing tool: Attempting to flush an item of type <class \'galaxy.model.DatasetCollectionElement\'> as a member of collection "JobToInputDatasetCollectionAssociation.dataset_collection". Expected an object of type <class \'galaxy.model.HistoryDatasetCollectionAssociation\'> or a polymorphic subclass of this type.' ``` It isn't ideal, but before 19818cb we didn't record Collection-like elements at all. Commit: 8f5125194630def8530c0e3e30f1b9a4439bd0fb https://github.com/galaxyproject/galaxy/commit/8f5125194630def8530c0e3e30f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/managers/jobs.py Log Message: ----------- Linting fixes and drop unnecessary internal parenthesis (thanks @nsoranzo!). Commit: 7d260d0b50a5858af533fe136105ce357b4ef490 https://github.com/galaxyproject/galaxy/commit/7d260d0b50a5858af533fe136105… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/jobs.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Tighten job search result We now expand incoming tool parameters, so that we have a dictionary of all tool parameters (i.e specified/posted parameters and defaults). We start the search by quering the database for jobs using the same tool id for the same owner with the same input datasets, taking into account copied dataset(-collection)s. We then replace all dataset ids (HDA/LDA or HDCA) in the parameter dict with the input data used for the jobs queried in the first step. This allows us to check every parameter for a match with the job. Commit: 4b7bd98b306155562d9e35610bd8189b4c4e1172 https://github.com/galaxyproject/galaxy/commit/4b7bd98b306155562d9e35610bd8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt A lib/galaxy/managers/jobs.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #4665 from mvdbeek/extend_job_search Extend job search for hdcas Compare: https://github.com/galaxyproject/galaxy/compare/95a5e8d6c867...4b7bd98b3061

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