- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f5b29b: WIP - show/add/remove workflow tags
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5b29b82d29548a05da911b03d1b3e0dce5dc6e7 https://github.com/galaxyproject/galaxy/commit/f5b29b82d29548a05da911b03d1b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- WIP - show/add/remove workflow tags Commit: 5e667a7d54eba623bbf6cb42865507e063bdb4a5 https://github.com/galaxyproject/galaxy/commit/5e667a7d54eba623bbf6cb428655… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Allow editing tags in workflow overview page Commit: b57b2de7dac8c2fb36e4f3a626d6d33c57da6064 https://github.com/galaxyproject/galaxy/commit/b57b2de7dac8c2fb36e4f3a626d6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Allow exporting and importing workflow tags Commit: e1b5a459dcfd183327d8ea1d3485fb5f509b6d82 https://github.com/galaxyproject/galaxy/commit/e1b5a459dcfd183327d8ea1d3485… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Allow updating workflows from partial information The workflow overview page gets workflow information from the /api/workflows, which returns a reduced amount of information, most notably the steps are not being returned. This commit skips updating the actual workflow steps if the steps are not included in the workflow payload. We can now update name, tags and whether a workflow should be shown in the tool panel. We also return owner and number of steps in the response to importing workflows. Commit: e2d1fabf58f813c2d722849ad9bf5d1d46517665 https://github.com/galaxyproject/galaxy/commit/e2d1fabf58f813c2d722849ad9bf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js Log Message: ----------- Remove unncessary boilerplate from workflow model Commit: 17be825cdf3714d2f335ba20ad2b6f51ad10c622 https://github.com/galaxyproject/galaxy/commit/17be825cdf3714d2f335ba20ad2b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Allow renaming, downloading, dropping workflow files to import Commit: 5dfe36deceb6d4e38a82c0130a011956c29c06df https://github.com/galaxyproject/galaxy/commit/5dfe36deceb6d4e38a82c0130a01… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Only access tags if workflow exists Commit: 060952fa88dd84af04bc1e879e67726596cbc7ff https://github.com/galaxyproject/galaxy/commit/060952fa88dd84af04bc1e879e67… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Allow downloading .ga workflows via the UI Commit: 1a4effa70e9ad8088e19ae334753b7a898d286aa https://github.com/galaxyproject/galaxy/commit/1a4effa70e9ad8088e19ae334753… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove downloading workflows through controller Commit: 1015b510f81723b927866546390d179abef796f9 https://github.com/galaxyproject/galaxy/commit/1015b510f81723b927866546390d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly raise Exception if tool not found Commit: 70c889435892ebfd1fb88edaab187cb84ba1dccf https://github.com/galaxyproject/galaxy/commit/70c889435892ebfd1fb88edaab18… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Copy workflows without reloading page Commit: 1dcfe56bb9f1c81567efe68f5ebe4c2f4c6bfb7f https://github.com/galaxyproject/galaxy/commit/1dcfe56bb9f1c81567efe68f5ebe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge WorkflowTagsEditor with TagsEditor Commit: f1f412ff298a3d859da1f4fe8b7640d722827a1f https://github.com/galaxyproject/galaxy/commit/f1f412ff298a3d859da1f4fe8b76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Make tag_editor local variable Commit: 911c969631a1dcfb7eee2f2499f81d662b617800 https://github.com/galaxyproject/galaxy/commit/911c969631a1dcfb7eee2f2499f8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix logic for determining whether username should be mentioned Commit: e54b1d1c379f56f2b45ef129a9863be77c379ae7 https://github.com/galaxyproject/galaxy/commit/e54b1d1c379f56f2b45ef129a986… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix adjusting dropdown menu Commit: 0aa4e5463d410df448f484c13174b0e8d6ba87f8 https://github.com/galaxyproject/galaxy/commit/0aa4e5463d410df448f484c13174… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Use toastr for informing user about success/failure Commit: 61ac1d77a4679938c98e43f54bea9e52073ae32e https://github.com/galaxyproject/galaxy/commit/61ac1d77a4679938c98e43f54bea… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less Log Message: ----------- Highlight workflow dropzone Commit: 09f66a6394303a70b279a34c8f63458b059febc5 https://github.com/galaxyproject/galaxy/commit/09f66a6394303a70b279a34c8f63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove unused $el_wf_link variable Commit: 1de485d3f70165ca1860fbc388a30f40d1a21888 https://github.com/galaxyproject/galaxy/commit/1de485d3f70165ca1860fbc388a3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- camelCase functions and variables Commit: bbaf59a05a7ff6bb048f93fe1eb192157301d6db https://github.com/galaxyproject/galaxy/commit/bbaf59a05a7ff6bb048f93fe1eb1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Display errors to user Commit: 2968e0e588e35da24caecd0cc4223f694332673b https://github.com/galaxyproject/galaxy/commit/2968e0e588e35da24caecd0cc422… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Show toast at the top-right (which is the default setting) Commit: 268a895d2b787d9c77a5b87d04ec772382615a8b https://github.com/galaxyproject/galaxy/commit/268a895d2b787d9c77a5b87d04ec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js Log Message: ----------- Describe workflow model and collection (thx @martenson) Commit: aa49c0053a278d40dcc0affaf894b0e60b3d3949 https://github.com/galaxyproject/galaxy/commit/aa49c0053a278d40dcc0affaf894… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Move fetching out of WorkflowCollection thx for the hint @martenson. Commit: 9a331363cb51733b446aa44eca71f3439152d4ab https://github.com/galaxyproject/galaxy/commit/9a331363cb51733b446aa44eca71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Improve error reporting to user Commit: ede8c200f944a9cc21d894654fb6ec0027747333 https://github.com/galaxyproject/galaxy/commit/ede8c200f944a9cc21d894654fb6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Add static JS Commit: d0df3886fa7acaa3d5f63360e2af78aab2deaaaa https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- More workflow index page Selenium tests. - Fix rename test for recent change to using alert. - Test basic adding a tag. - Outline of a test for downloading workflows. - Add test for publishing display on index. - Add test for using the search box on the workflow index page. Commit: 47efd8089c5b1dfc67af7cf3887ce5b8b907e057 https://github.com/galaxyproject/galaxy/commit/47efd8089c5b1dfc67af7cf3887c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/tag.js A client/galaxy/scripts/mvc/workflow/workflow-model.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tag.js.map A static/maps/mvc/workflow/workflow-model.js.map M static/maps/mvc/workflow/workflow.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tag.js A static/scripts/mvc/workflow/workflow-model.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4476 from mvdbeek/workflow_view_tags Show tags, import by drag-and-drop and avoid refreshed in workflow page Compare: https://github.com/galaxyproject/galaxy/compare/558e22a49cbd...47efd8089c5b

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[galaxyproject/galaxy] de624b: Sync non-CWL galaxy-lib changes.
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de624b48b14f491841921363e4ef7d1ba72db3f3 https://github.com/galaxyproject/galaxy/commit/de624b48b14f491841921363e4ef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py Log Message: ----------- Sync non-CWL galaxy-lib changes. Covers https://github.com/galaxyproject/galaxy-lib/pull/71 and https://github.com/galaxyproject/galaxy-lib/pull/69. Commit: 558e22a49cbd9a1622a6b7db77ad6f66f17b5229 https://github.com/galaxyproject/galaxy/commit/558e22a49cbd9a1622a6b7db77ad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/help.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #4535 from jmchilton/galaxy-lib Sync non-CWL galaxy-lib changes. Compare: https://github.com/galaxyproject/galaxy/compare/dd9c757a15e9...558e22a49cbd

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[galaxyproject/galaxy] a0bd78: Optimize loading of StoredWorkflow attributes
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0bd78034defb11adf2140f7c6dd90e63bc7da43 https://github.com/galaxyproject/galaxy/commit/a0bd78034defb11adf2140f7c6dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Optimize loading of StoredWorkflow attributes WorkflowsManager.get_stored_workflow is used when exporting or editing workflows. In these cases we iterate over the related workflow objects steps as well as the related tags and annotation objects. Each iteration will emit a new SQL statement. Joinedloading these relations here speeds up the workflow run form and the editor. With sqlite as backend this speeds up exporting a workflow for the workflow editor by about 5X. Commit: 62204de0aeb4a833e43e5a1f81657293853ffb03 https://github.com/galaxyproject/galaxy/commit/62204de0aeb4a833e43e5a1f8165… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/model/item_attrs.py Log Message: ----------- Use pre-existing annotations object if possible This avoids additional requests to the database. Commit: db04f295d34e8ca03b151f462e7ffd1d613a1321 https://github.com/galaxyproject/galaxy/commit/db04f295d34e8ca03b151f462e7f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Do not provide a history in workflow_building_mode Commit: cb1392fd2d707587859bcbbb3e1744fb472ebf22 https://github.com/galaxyproject/galaxy/commit/cb1392fd2d707587859bcbbb3e17… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Use WorkflowManager to get StoredWorkflow in workflow web controller Commit: 83bb7b108e90086ae0f421d63107c3870dea5d73 https://github.com/galaxyproject/galaxy/commit/83bb7b108e90086ae0f421d63107… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid ToolShedRepository attributes where possible Commit: d5eee194252270ebf4be008c6cf0492d5c6c3340 https://github.com/galaxyproject/galaxy/commit/d5eee194252270ebf4be008c6cf0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use workflow_building_modes.ENABLED instead of True Commit: e4f4dc91eebe7d5e4fbf8667bff52079498d88ea https://github.com/galaxyproject/galaxy/commit/e4f4dc91eebe7d5e4fbf8667bff5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Cache edam_data and edam_formats Commit: 17246225d962f4d1494b4b718440f42631fd6210 https://github.com/galaxyproject/galaxy/commit/17246225d962f4d1494b4b718440… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use joinedload for latest_workflow.steps when building workflow editor config Commit: 1a1232e11dd31b96284d2842292d13f9b67ee22e https://github.com/galaxyproject/galaxy/commit/1a1232e11dd31b96284d2842292d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-27 (Sun, 27 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use get_item_annotation_str instead of get_item_annotation_obj Commit: 2faa56eefe7a8b029ed62b9b4402894c2a26248f https://github.com/galaxyproject/galaxy/commit/2faa56eefe7a8b029ed62b9b4402… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Rework if statement to be more explicit Commit: dd9c757a15e929be2ab6d138fb181f0ed543c156 https://github.com/galaxyproject/galaxy/commit/dd9c757a15e929be2ab6d138fb18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/item_attrs.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4500 from mvdbeek/workflow_loading_speedup Workflow loading speedup Compare: https://github.com/galaxyproject/galaxy/compare/9fb78b1010f8...dd9c757a15e9

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[galaxyproject/galaxy] a85d65: Another fix for Selenium worklow tests.
by GitHub 01 Sep '17

01 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a85d65c6a2ce3fd0a166e130f8a89dc198c3e0c7 https://github.com/galaxyproject/galaxy/commit/a85d65c6a2ce3fd0a166e130f8a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/selenium_tests/test_workflow_run.py Log Message: ----------- Another fix for Selenium worklow tests. This time for the workflow upgrade message test, mirrors the fix in #4524 - the content we are searching for in on this page is no longer in the iframe. Commit: 9fb78b1010f8e106d34bf0b44888265b980521fd https://github.com/galaxyproject/galaxy/commit/9fb78b1010f8e106d34bf0b44888… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #4531 from jmchilton/selenium_fixes_17 Another fix for Selenium worklow tests. Compare: https://github.com/galaxyproject/galaxy/compare/7db1a3fb3e6f...9fb78b1010f8

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[galaxyproject/galaxy] 326477: implement influxdb error reporter
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 326477d957bda9c32f63497b5fc911e8c2a9731d https://github.com/galaxyproject/galaxy/commit/326477d957bda9c32f63497b5fc9… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py Log Message: ----------- implement influxdb error reporter Commit: f67fa22dd9bd05d72df859065a3e126af0161d62 https://github.com/galaxyproject/galaxy/commit/f67fa22dd9bd05d72df859065a3e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- also add destination id everywhere Commit: 7db1a3fb3e6f61540f1354a899fce1c55e834775 https://github.com/galaxyproject/galaxy/commit/7db1a3fb3e6f61540f1354a899fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #4533 from erasche/influxdb-error-reporter Implement influxdb error reporter Compare: https://github.com/galaxyproject/galaxy/compare/49f243862207...7db1a3fb3e6f

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[galaxyproject/galaxy] b75f79: Load tools with collection type source attributes ...
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b75f793ea4c58786747da3a9571ba3bd938cd181 https://github.com/galaxyproject/galaxy/commit/b75f793ea4c58786747da3a9571b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Load tools with collection type source attributes into the workflow editor. Should allow using filter failed and merge collection tools within workflows. Commit: ba8a7f0e3a540c99b3d8e7be3ea67008e2e76ff2 https://github.com/galaxyproject/galaxy/commit/ba8a7f0e3a540c99b3d8e7be3ea6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.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/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Pack client. Commit: 01d16358efa5a71f7030c48c302129cca515e6c6 https://github.com/galaxyproject/galaxy/commit/01d16358efa5a71f7030c48c3021… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map Log Message: ----------- Adjust JS styling for workflow-terminal.js. Commit: 49f2438622075f3e9cbe9097ad31b177c97f532a https://github.com/galaxyproject/galaxy/commit/49f2438622075f3e9cbe9097ad31… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.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/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Merge pull request #4514 from jmchilton/collection_operations Load tools with collection type source attributes into the workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/d09ced249d72...49f243862207

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[galaxyproject/galaxy] 43fd81: More logging for selenium tests.
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43fd81df59c1862c745813e3b340e93976ef1e2b https://github.com/galaxyproject/galaxy/commit/43fd81df59c1862c745813e3b340… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py Log Message: ----------- More logging for selenium tests. Dumb the browser log and the driver log out as JSON to the test error directory for that test. Commit: f35fed29356d1f55af803f2f24cd2e54634cc8a6 https://github.com/galaxyproject/galaxy/commit/f35fed29356d1f55af803f2f24cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/galaxy_selenium/sizzle.py A test/selenium_tests/test_sizzle_loading.py Log Message: ----------- Improve setting up Sizzle for Selenium tests. Something releated to AMD broke our way of injecting Sizzle into Galaxy for Selenium tests. This is a much better way that seems to work - just use jQuery ($) as Sizzle if it is available. Avoids an external dependency and another page fetch per test as well as fixing the problem. Add a test case that just tests the sizzle stuff works on its own. It will be a clear indiciation what is broken if there are related regressions in the future. Commit: d09ced249d729b5c0a2098a9d5e81472c91f62b6 https://github.com/galaxyproject/galaxy/commit/d09ced249d729b5c0a2098a9d5e8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/framework.py A test/selenium_tests/test_sizzle_loading.py Log Message: ----------- Merge pull request #4523 from jmchilton/selenium_fixes_15 Selenium test fixes and improvements. Compare: https://github.com/galaxyproject/galaxy/compare/823eb1d4ec84...d09ced249d72

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[galaxyproject/usegalaxy-playbook] c2a31c: Implicit FTPS for Main
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c2a31c974a32b624d67e9508a2d20b0a6bfd7600 https://github.com/galaxyproject/usegalaxy-playbook/commit/c2a31c974a32b624… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M env/main/group_vars/ftpservers/vars.yml Log Message: ----------- Implicit FTPS for Main Commit: e182b92886f820027e54ba7b1ae96793475cda80 https://github.com/galaxyproject/usegalaxy-playbook/commit/e182b92886f82002… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M env/test/group_vars/ftpservers/vars.yml Log Message: ----------- Correction for a harmless ProFTPD config error Commit: d9fae1cdf31102f33b981eeb2d9a6a1f6cfc8d2a https://github.com/galaxyproject/usegalaxy-playbook/commit/d9fae1cdf31102f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 Log Message: ----------- Fix Galaxy log rotation Commit: 0a5fe4b442509159560a15f555f1a5eafe33cd6e https://github.com/galaxyproject/usegalaxy-playbook/commit/0a5fe4b442509159… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d4ea9ac0c217...…

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[galaxyproject/galaxy] 514250: Make a couple workflow invocation tests more robus...
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5142509f131591b978ecadebbaefc1bb6f608f47 https://github.com/galaxyproject/galaxy/commit/5142509f131591b978ecadebbaef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Make a couple workflow invocation tests more robust. Less random sleeping, wait for actual invocation. I think this is likely the cause this transient failure (https://jenkins.galaxyproject.org/job/docker-api/8215/testReport/junit/api.…) picking up the input as the last dataset in the history instead of the output - I bet the workflow just hadn't been invoked yet. Commit: 823eb1d4ec84f17f92e4bbf2a12194b2bc0ea9d0 https://github.com/galaxyproject/galaxy/commit/823eb1d4ec84f17f92e4bbf2a121… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #4530 from jmchilton/api_test_fixes More robust workflow invocation testing. Compare: https://github.com/galaxyproject/galaxy/compare/bd13cadbddbb...823eb1d4ec84

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[galaxyproject/galaxy] e8de89: Display d3 hierarchy files in uploader
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8de89afd56b5e125e1e879855d7168a7d2c79b5 https://github.com/galaxyproject/galaxy/commit/e8de89afd56b5e125e1e879855d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Display d3 hierarchy files in uploader Commit: bd13cadbddbbd991460095ad94d9c974cc2a40c9 https://github.com/galaxyproject/galaxy/commit/bd13cadbddbbd991460095ad94d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #4522 from guerler/d3_hierarchy_in_uploader Display d3 hierarchy datatype in upload interface Compare: https://github.com/galaxyproject/galaxy/compare/2f9cd0ee491c...bd13cadbddbb

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[galaxyproject/galaxy] 5ab286: Prevent transient job state test failures from fai...
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab28634cabc1df2aa14e9db303247e41b9ea311 https://github.com/galaxyproject/galaxy/commit/5ab28634cabc1df2aa14e9db3032… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Prevent transient job state test failures from failing the build. A precondition to the real meat of the test is failing to be met sometimes in production - this failure is indicating a problem with the test and not with Galaxy. I previously tried to address this with https://github.com/galaxyproject/galaxy/pull/3988 but that didn't work. Now if the trainsient ok occurs the test will be skipped. Most of the time it won't skip and the rest of the test will execute and ensure there aren't regressions in behaviors related to cleaning up datasets after job completion. I'm placing the skips a couple different places so hopefully we can get a stack trace at somepoint - knowing where the code is when the job state is changing from running to ok will help puzzle out what is handing for the two minutes the job is running in the test framework. Commit: 2f9cd0ee491cc99af4a64416e21ce95e6e7dbb33 https://github.com/galaxyproject/galaxy/commit/2f9cd0ee491cc99af4a64416e21c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #4510 from jmchilton/job_test_fix Prevent transient job state test failures from failing the build. Compare: https://github.com/galaxyproject/galaxy/compare/f3b8a121b7d9...2f9cd0ee491c

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[galaxyproject/galaxy] eefc26: add the first test: history grid
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eefc268eae2961186a84dc396921326549ea4822 https://github.com/galaxyproject/galaxy/commit/eefc268eae2961186a84dc396921… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A test/selenium_tests/test_published_history_grid.py Log Message: ----------- add the first test: history grid Commit: b664f26aa0d7a3ad151f236ba569efecb09a5526 https://github.com/galaxyproject/galaxy/commit/b664f26aa0d7a3ad151f236ba569… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- add standard search test Commit: 0e1cbc09f8a604c1b45127faf30170ba1b67bb1b https://github.com/galaxyproject/galaxy/commit/0e1cbc09f8a604c1b45127faf301… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- add 'sort by name/owner' tests Commit: 72195e14baa5e5f3131f2364858e71c4e4fb960c https://github.com/galaxyproject/galaxy/commit/72195e14baa5e5f3131f2364858e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- [WIP]: add advanced search tests Commit: 2403916c7b6a29810e74cb3485d3634ef904dde6 https://github.com/galaxyproject/galaxy/commit/2403916c7b6a29810e74cb3485d3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- test clicking tags Commit: 2f547b09737d6711e44de7d9c7600384aa97038e https://github.com/galaxyproject/galaxy/commit/2f547b09737d6711e44de7d9c760… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- small improvements Commit: da1518db48265617cb2e2a00f9b738058c648f4b https://github.com/galaxyproject/galaxy/commit/da1518db48265617cb2e2a00f9b7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- set annotations Commit: 2dda34a00240a9af990a23c14cd73abb87db4268 https://github.com/galaxyproject/galaxy/commit/2dda34a00240a9af990a23c14cd7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: A test/selenium_tests/test_published_histories_grid.py R test/selenium_tests/test_published_history_grid.py Log Message: ----------- rename the file Commit: 773029bd364037943a810506a79cebca85f2a260 https://github.com/galaxyproject/galaxy/commit/773029bd364037943a810506a79c… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- fix flake8 issues Commit: a464fe9db6ab993e282feb1ba9ec4eea78ada376 https://github.com/galaxyproject/galaxy/commit/a464fe9db6ab993e282feb1ba9ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Rework published histories selenium test a bit. - Wait for elements to be clickable before clicking them. - Allow individual tests to be run on their own and out of order. - Use randomly generated emails - the tests still can't really be applied to an external Galaxy test server but this gets us closer. Commit: f3b8a121b7d9d5535381aa8cae7887bd978f9678 https://github.com/galaxyproject/galaxy/commit/f3b8a121b7d9d5535381aa8cae78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: A test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4502 from anatskiy/published_history_test Published History Grid tests Compare: https://github.com/galaxyproject/galaxy/compare/21eac0d445cb...f3b8a121b7d9

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[galaxyproject/galaxy] 2d9ae7: Fix another bad merge issue?
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d9ae75cae83969b3a708c0921ca33841ad08ef5 https://github.com/galaxyproject/galaxy/commit/2d9ae75cae83969b3a708c0921ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix another bad merge issue? Commit: 21eac0d445cbf8523cd48402d0992dc7ff1720c6 https://github.com/galaxyproject/galaxy/commit/21eac0d445cbf8523cd48402d099… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #4515 from jmchilton/another_merge_issue Fix subdirectory listing for extra files Compare: https://github.com/galaxyproject/galaxy/compare/d56fcf6777d9...21eac0d445cb

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[galaxyproject/usegalaxy-playbook] c565b0: Upgrade galaxyproject.proftpd
by GitHub 29 Aug '17

29 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c565b0e7b893ee4a455cc6889e5c9d6578422c0d https://github.com/galaxyproject/usegalaxy-playbook/commit/c565b0e7b893ee4a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M roles/galaxyproject.proftpd/README.md M roles/galaxyproject.proftpd/defaults/main.yml M roles/galaxyproject.proftpd/handlers/main.yml A roles/galaxyproject.proftpd/meta/.galaxy_install_info M roles/galaxyproject.proftpd/tasks/debian.yml M roles/galaxyproject.proftpd/tasks/galaxy_auth.yml M roles/galaxyproject.proftpd/tasks/main.yml M roles/galaxyproject.proftpd/tasks/redhat.yml M roles/galaxyproject.proftpd/tasks/tls.yml M roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 A roles/galaxyproject.proftpd/templates/global.conf.j2 M roles/galaxyproject.proftpd/templates/tls.conf.j2 A roles/galaxyproject.proftpd/templates/virtualhost.conf.j2 M roles/galaxyproject.proftpd/tests/test.yml M roles/galaxyproject.proftpd/vars/main.yml Log Message: ----------- Upgrade galaxyproject.proftpd Commit: d4ea9ac0c2171835d9228955d68a84777040c19b https://github.com/galaxyproject/usegalaxy-playbook/commit/d4ea9ac0c2171835… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/common/stack.yml M env/test/group_vars/dbservers/vault.yml R env/test/group_vars/ftpservers.yml A env/test/group_vars/ftpservers/vars.yml A env/test/group_vars/ftpservers/vault.yml Log Message: ----------- Enable implicit FTPS on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/234608edacbe...…

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[galaxyproject/usegalaxy-playbook] 0e7812: Update Test
by GitHub 29 Aug '17

29 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e78126edb671cf27de4f1f6c098f578870d1e0d https://github.com/galaxyproject/usegalaxy-playbook/commit/0e78126edb671cf2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: ac6645a8edf5a0903ed7b5e65d55a32fee263961 https://github.com/galaxyproject/usegalaxy-playbook/commit/ac6645a8edf5a090… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run unicycler on bridges (Forgot to commit this when it was actually done) Commit: 234608edacbed51473b34a8418b79ec20b4e7a44 https://github.com/galaxyproject/usegalaxy-playbook/commit/234608edacbed514… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/6db4d2f31a05...…

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[galaxyproject/usegalaxy-playbook] 6db4d2: Update Galaxy on non-CVMFS Pulsar servers when upd...
by GitHub 29 Aug '17

29 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6db4d2f31a05891846f26dfa3f67de22d7d3efa0 https://github.com/galaxyproject/usegalaxy-playbook/commit/6db4d2f31a058918… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/common/update.yml Log Message: ----------- Update Galaxy on non-CVMFS Pulsar servers when updating Galaxy

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[galaxyproject/galaxy] 2ede34: Fix bad merge of security patch from 17.05 into de...
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ede34659b688089ed549ea24416f7610be0a698 https://github.com/galaxyproject/galaxy/commit/2ede34659b688089ed549ea24416… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix bad merge of security patch from 17.05 into dev. Commit: d56fcf6777d93c83db5ebbc4af7968cb9889e524 https://github.com/galaxyproject/galaxy/commit/d56fcf6777d93c83db5ebbc4af79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #4508 from jmchilton/dev_merge_fix Fix bad merge of security patch from 17.05 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/15b1a41df839...d56fcf6777d9

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[galaxyproject/galaxy] ce7d8a: Validate workflow step after step argument injecti...
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601 https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Fix drag and drop from history for firefox Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6 https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #4496 from guerler/fix_drag_drop_firefox [17.05] Fix drag and drop from history for Firefox Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 9337c9fdc118f7c4883a6c7b4cada483b09461c7 https://github.com/galaxyproject/galaxy/commit/9337c9fdc118f7c4883a6c7b4cad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge branch 'release_17.05' into merge-release1705 Commit: 8aefa9d49535b7592bd7398541f9cbeaba9146ce https://github.com/galaxyproject/galaxy/commit/8aefa9d49535b7592bd7398541f9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M static/maps/mvc/ui/ui-select-content.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/bundled/login.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- repack client Commit: 15b1a41df83940961d8f516e4023cd410b38964b https://github.com/galaxyproject/galaxy/commit/15b1a41df83940961d8f516e4023… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/datatypes/data.py M lib/galaxy/workflow/modules.py M static/maps/mvc/ui/ui-select-content.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/bundled/login.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge pull request #4506 from martenson/merge-release1705 Merge release_17.05 to dev Compare: https://github.com/galaxyproject/galaxy/compare/f159df391ea4...15b1a41df839

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[galaxyproject/galaxy] e61553: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6155367e61d8b4e66883992db6af88444f346a0 https://github.com/galaxyproject/galaxy/commit/e6155367e61d8b4e66883992db6a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: f159df391ea4eeaac01779426cfad00e38b5f907 https://github.com/galaxyproject/galaxy/commit/f159df391ea4eeaac01779426cfa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- Merge pull request #4501 from erasche/2017-08-security 2017-08 Security Patch Compare: https://github.com/galaxyproject/galaxy/compare/4b9b14979a71...f159df391ea4

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[galaxyproject/galaxy] 2ff429: move to somewhere it can be overridden
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2ff4292cd6171fc128e91ddbb66f5124368c25ee https://github.com/galaxyproject/galaxy/commit/2ff4292cd6171fc128e91ddbb66f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- move to somewhere it can be overridden Commit: 68f9c6905ef56ce9b82e2889a48b4185370e83b4 https://github.com/galaxyproject/galaxy/commit/68f9c6905ef56ce9b82e2889a48b… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less Log Message: ----------- Large click target for tools Commit: cd6cc88ac19b5d7c218e31fb14c74382d2439a1f https://github.com/galaxyproject/galaxy/commit/cd6cc88ac19b5d7c218e31fb14c7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/theme/plain.less M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js Log Message: ----------- Plain theme Commit: 97ee0f1fcdd7d059d5c37e1bb25a8c3389559698 https://github.com/galaxyproject/galaxy/commit/97ee0f1fcdd7d059d5c37e1bb25a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M static/style/blue/base.css Log Message: ----------- rebuild style Commit: 4b9b14979a7137f4aca90e1e1e7869e88ae1bb6e https://github.com/galaxyproject/galaxy/commit/4b9b14979a7137f4aca90e1e1e78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less A client/galaxy/style/less/theme/plain.less M static/maps/mvc/tool/tools.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tools.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4470 from erasche/retheme Nicer tool click targets for base + "plain" theme Compare: https://github.com/galaxyproject/galaxy/compare/426aa310fd21...4b9b14979a71

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[galaxyproject/galaxy] 1d4853: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch

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[galaxyproject/galaxy] 5a1846: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 5a18464d547d7497285ee25067050ee4cd665eda https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch

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[galaxyproject/galaxy] 47ba64: 2017-08 Security Patch
by GitHub 28 Aug '17

28 Aug '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch

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[galaxyproject/galaxy] ce7d8a: Validate workflow step after step argument injecti...
by GitHub 26 Aug '17

26 Aug '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Compare: https://github.com/galaxyproject/galaxy/compare/cf897795fe8b...c70926445fb7

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[galaxyproject/galaxy] 89c811: Move 'Copy History Items' to the bottom of the sec...
by GitHub 25 Aug '17

25 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89c811b790d7ef3508f361195ca4333903e5b955 https://github.com/galaxyproject/galaxy/commit/89c811b790d7ef3508f361195ca4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Move 'Copy History Items' to the bottom of the second column in the old copy histories page. Commit: 426aa310fd21f320767b575dcd209ae63ad88b24 https://github.com/galaxyproject/galaxy/commit/426aa310fd21f320767b575dcd20… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M templates/webapps/galaxy/dataset/copy_view.mako Log Message: ----------- Merge pull request #4486 from dannon/copy_history_minor_improvement Minor copy datasets dialog improvement. Compare: https://github.com/galaxyproject/galaxy/compare/0010f6c0d8ab...426aa310fd21

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