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

[galaxyproject/infrastructure-playbook] fd1637: Add n7 and n8 as jenkins workers
by GitHub 30 Sep '17

30 Sep '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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[galaxyproject/galaxy] d49c49: Pull a minor cosmetic fix out of the urlFor refact...
by GitHub 29 Sep '17

29 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d49c49d0eebc4390a0dda7d5e830ae464284b7b9 https://github.com/galaxyproject/galaxy/commit/d49c49d0eebc4390a0dda7d5e830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/onload.js 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 Log Message: ----------- Pull a minor cosmetic fix out of the urlFor refactoring. Might as well be consistent in the release. Commit: 38b19d4c47d227c7eeccb33fa8bfa64f0b0ec297 https://github.com/galaxyproject/galaxy/commit/38b19d4c47d227c7eeccb33fa8bf… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/onload.js 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 Log Message: ----------- Merge pull request #4715 from dannon/proxy_prefix_model_fixes [17.09] Pull a minor tweak out of the JS-side urlFor refactoring Commit: 95a5e8d6c8673ef9304422f64e8327e0799f458d https://github.com/galaxyproject/galaxy/commit/95a5e8d6c8673ef9304422f64e83… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M client/galaxy/scripts/onload.js 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 Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/3004e1149246...95a5e8d6c867

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[galaxyproject/galaxy] d2fd08: Update reports.md with a link to the community hub
by GitHub 29 Sep '17

29 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d2fd0877020a7bdfccd2d2778f0df99b1b18f279 https://github.com/galaxyproject/galaxy/commit/d2fd0877020a7bdfccd2d2778f0d… Author: scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M doc/source/admin/reports.md Log Message: ----------- Update reports.md with a link to the community hub Commit: 911dc61a4d98108bd85ef23470f6f33eb17cade9 https://github.com/galaxyproject/galaxy/commit/911dc61a4d98108bd85ef23470f6… Author: scholtalbers <j.scholtalbers(a)gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M doc/source/admin/reports.md Log Message: ----------- add section anchor to url Commit: 3004e1149246432be865c09495a40954fe5d2a1e https://github.com/galaxyproject/galaxy/commit/3004e1149246432be865c09495a4… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M doc/source/admin/reports.md Log Message: ----------- Merge pull request #4723 from scholtalbers/patch-1 Update reports.md with a link to the community hub Compare: https://github.com/galaxyproject/galaxy/compare/297cb2da4b62...3004e1149246

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[galaxyproject/galaxy] d49c49: Pull a minor cosmetic fix out of the urlFor refact...
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: d49c49d0eebc4390a0dda7d5e830ae464284b7b9 https://github.com/galaxyproject/galaxy/commit/d49c49d0eebc4390a0dda7d5e830… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/onload.js 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 Log Message: ----------- Pull a minor cosmetic fix out of the urlFor refactoring. Might as well be consistent in the release. Commit: 38b19d4c47d227c7eeccb33fa8bfa64f0b0ec297 https://github.com/galaxyproject/galaxy/commit/38b19d4c47d227c7eeccb33fa8bf… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/onload.js 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 Log Message: ----------- Merge pull request #4715 from dannon/proxy_prefix_model_fixes [17.09] Pull a minor tweak out of the JS-side urlFor refactoring Compare: https://github.com/galaxyproject/galaxy/compare/7167c0434b71...38b19d4c47d2

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[galaxyproject/infrastructure-playbook]
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/blog Home: https://github.com/galaxyproject/infrastructure-playbook

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[galaxyproject/infrastructure-playbook] a19ba5: Updated Wiki to Hub page mapping file to reflect t...
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a19ba56e73a9374ae3a8bef6a2661903f0d8f49b https://github.com/galaxyproject/infrastructure-playbook/commit/a19ba56e73a… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Updated Wiki to Hub page mapping file to reflect that the Communinty Log entries are now in blog. Commit: cdcb6dd6f8b0045311dbbf4b6d4bfaaf3415c1cd https://github.com/galaxyproject/infrastructure-playbook/commit/cdcb6dd6f8b… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Restored and modified "this file is maintained by Ansible" comment. Commit: dcf13819c8719182d4dd9af163e2b2d3c8539909 https://github.com/galaxyproject/infrastructure-playbook/commit/dcf13819c87… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M jetstream_common/templates/supervisor/pulsar.j2 Log Message: ----------- Merge branch 'master' into blog Commit: 49bcf5343c6e2835d813c1cd7df47ac91e6af0c6 https://github.com/galaxyproject/infrastructure-playbook/commit/49bcf5343c6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Merge pull request #19 from galaxyproject/blog Updated Wiki to Hub page mapping file to reflect that the Community … Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/10bb73a321…

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[galaxyproject/galaxy] 2d33cc: Add client routes for pages edit attribute form
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d33cc28664f1b5a592576fd149264ccf0a023b7 https://github.com/galaxyproject/galaxy/commit/2d33cc28664f1b5a592576fd1492… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.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 for pages edit attribute form Commit: 8001299333ec7f71efc6233562a5b2f641686c64 https://github.com/galaxyproject/galaxy/commit/8001299333ec7f71efc6233562a5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/controllers/page.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: ----------- Fix url to pages edit controller endpoint Commit: 56cab82eb23f2022af128f1ba6828f8f0bd41206 https://github.com/galaxyproject/galaxy/commit/56cab82eb23f2022af128f1ba682… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Remove debug statement Commit: c038d09f0de31f8ad6d4e2b21b6ede74a9c61cf4 https://github.com/galaxyproject/galaxy/commit/c038d09f0de31f8ad6d4e2b21b6e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Add support to build form and save new attributes Commit: 408a2d212f163656dfe9a42151f64b6b07fbd37a https://github.com/galaxyproject/galaxy/commit/408a2d212f163656dfe9a42151f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Move message exception handler to base controller Commit: 8d4fbc02010f38bbb433b22faa39aeb65ec7d8d6 https://github.com/galaxyproject/galaxy/commit/8d4fbc02010f38bbb433b22faa39… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Use shared message exception handler Commit: a4544284af192a3ade610bbcededa20d4b3f76a0 https://github.com/galaxyproject/galaxy/commit/a4544284af192a3ade610bbceded… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Revise create page endpoint Commit: e42dc9c8ca5a932315e2e37e66e2ad9919a74539 https://github.com/galaxyproject/galaxy/commit/e42dc9c8ca5a932315e2e37e66e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.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: ----------- Add client side route to analysis app Commit: 8f76f7a0b24217af9808e36c7f69354441ae4ff8 https://github.com/galaxyproject/galaxy/commit/8f76f7a0b24217af9808e36c7f69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Redirect grid operation to client route Commit: ea164310a23781c95ae493af376c25a821ecc782 https://github.com/galaxyproject/galaxy/commit/ea164310a23781c95ae493af376c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py R templates/webapps/galaxy/page/create.mako Log Message: ----------- Remove page create mako Commit: 2bfb088ddb52250f88e774299d1f770fbded4926 https://github.com/galaxyproject/galaxy/commit/2bfb088ddb52250f88e774299d1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix input help text, user is required to enter unique identifier Commit: cdf384a8f55c3315c26f09d83b530f7ac6448457 https://github.com/galaxyproject/galaxy/commit/cdf384a8f55c3315c26f09d83b53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Add direct link to view page, analogous to other objects in grids Commit: 08940ad9af56717ec62026db094d90e4599c02e0 https://github.com/galaxyproject/galaxy/commit/08940ad9af56717ec62026db094d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Fix create form title Commit: 90dd81913522db8bc6962845574775e2b5599146 https://github.com/galaxyproject/galaxy/commit/90dd81913522db8bc69628455747… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/forms.py Log Message: ----------- Add blank line to forms controller Commit: a985cf5784f1e04f08ea4e8d86126ee15c3b8274 https://github.com/galaxyproject/galaxy/commit/a985cf5784f1e04f08ea4e8d8612… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-26 (Tue, 26 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CITATION M cron/build_chrom_db.py M cron/parse_builds.py M cron/parse_builds_3_sites.py M lib/galaxy/containers/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/external_services/actions.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/runners/util/kill.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/citations.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/properties.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/async.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webhooks/__init__.py M lib/tool_shed/capsule/capsule_manager.py M scripts/api/data_manager_example_execute.py M scripts/api/display.py M scripts/api/search.py R scripts/binary_compatibility.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/dump_tour.py M scripts/edam_mapping.py M scripts/fetch_eggs.py M scripts/grt/export.py M scripts/grt/upload.py M scripts/manage_tool_dependencies.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py M scripts/paster.py M scripts/rst2html.py M scripts/summarize_timings.py M scripts/tool_shed/api/export.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/deprecate_repositories_without_metadata.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M templates/display_base.mako M templates/display_common.mako M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_datatypes.py M test/api/test_histories.py M test/api/test_history_contents.py M test/api/test_pages.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_visualizations.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/populators.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py M test/functional/twilltestcase.py M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/manual/workflows_scaling.py M test/selenium_tests/framework.py M test/selenium_tests/test_anon_history.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_custom_builds.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_options.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_sizzle_loading.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/selenium_tests/test_workflow_run.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py A test/unit/__init__.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_HistoryManager.py M test/unit/shed_unit/test_installed_repository_manager.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge branch 'dev' into replace_page_edit_form Commit: 4a916413c2c9fb19e8ad350771ed4de53200630a https://github.com/galaxyproject/galaxy/commit/4a916413c2c9fb19e8ad350771ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Touch up identifier error message and help Revise help info for identifier Fix Commit: 075c0a76843170db53a80d98f5618d96a52556a5 https://github.com/galaxyproject/galaxy/commit/075c0a76843170db53a80d98f561… 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 static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused id parsing Commit: a8f59a46a92e29cc054933450da7dc23dda28945 https://github.com/galaxyproject/galaxy/commit/a8f59a46a92e29cc054933450da7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/onload.js M client/toolshed/scripts/mvc/groups/group-model.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako 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/onload.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/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_page_edit_form Commit: 297cb2da4b62067c1582301aa6ebd6b05237edf9 https://github.com/galaxyproject/galaxy/commit/297cb2da4b62067c1582301aa6eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.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/page/create.mako Log Message: ----------- Merge branch 'replace_page_edit_form' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f4941e54224d...297cb2da4b62

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