- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e8a128: [17.09] Deployer doc fixes.
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: e8a1280f78e1fa19e2173f922f2221ea28279964 https://github.com/galaxyproject/galaxy/commit/e8a1280f78e1fa19e2173f922f22… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- [17.09] Deployer doc fixes. Commit: 42c572f34469ec39a55588504a97f1466c59f332 https://github.com/galaxyproject/galaxy/commit/42c572f34469ec39a55588504a97… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5147 from jmchilton/1709_docs_fixes [17.09] Small deployer doc fixes. Compare: https://github.com/galaxyproject/galaxy/compare/e9f05cb1b11d...42c572f34469

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[galaxyproject/galaxy] 82f444: Resolve broken link in for all workflows
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82f44479fcc92fae0507c50aad19b2f2776ccadc https://github.com/galaxyproject/galaxy/commit/82f44479fcc92fae0507c50aad19… Author: Milad Miladi <mmiladi(a)users.noreply.github.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Resolve broken link in for all workflows The docker galaxy flavors built on dev branch have a broken link in tool panel, href in "All workflows" section. This should fix it. Commit: eab3c32cfad9b3acebeceb56e3d948320558d0b9 https://github.com/galaxyproject/galaxy/commit/eab3c32cfad9b3acebeceb56e3d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M client/galaxy/scripts/apps/panels/tool-panel.js Log Message: ----------- Merge branch 'toolpanel-fixlink' into dev Commit: db317b6341e9267371a048131fb95a9387c31842 https://github.com/galaxyproject/galaxy/commit/db317b6341e9267371a048131fb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js Log Message: ----------- Client build w/ merge of mmiladi:toolpanel-fixlink Compare: https://github.com/galaxyproject/galaxy/compare/044dcfbb216a...db317b6341e9

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[galaxyproject/galaxy] 3dcf95: Test resubmit for completely dynamic JobDestinatio...
by GitHub 08 Dec '17

08 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dcf9549f6bb4a3d0a5420185c2e7dedb78cc4d5 https://github.com/galaxyproject/galaxy/commit/3dcf9549f6bb4a3d0a5420185c2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py Log Message: ----------- Test resubmit for completely dynamic JobDestination structures. Commit: 044dcfbb216ad1b2fb46933c6b21597828e42a91 https://github.com/galaxyproject/galaxy/commit/044dcfbb216ad1b2fb46933c6b21… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py M test/integration/test_job_resubmission.py Log Message: ----------- Merge pull request #5139 from jmchilton/resubmit_dynamic Test resubmit for dynamic JobDestination structures. Compare: https://github.com/galaxyproject/galaxy/compare/fe0fdeb4ce35...044dcfbb216a

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[galaxyproject/galaxy] 3dfbbc: Provide Galaxy.config var to indicate whether onlo...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3dfbbc7e081cae0c8b95b727e3791915afcc47ec https://github.com/galaxyproject/galaxy/commit/3dfbbc7e081cae0c8b95b727e379… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Provide Galaxy.config var to indicate whether onload webhooks should kick off; use it. Fixes shed/reports use of them. Commit: 6f80bed294e99abbc5f880ea7ee0b781e60f7e2a https://github.com/galaxyproject/galaxy/commit/6f80bed294e99abbc5f880ea7ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Minor onload.js cleanup. Commit: 7f1b77ff16c2678327130f3d7282cd900130def8 https://github.com/galaxyproject/galaxy/commit/7f1b77ff16c2678327130f3d7282… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js Log Message: ----------- Move tours kicker out of onload.js; just use the import. Commit: 8858b5511cdaf282eb5a1e75eda42ce7dde25b42 https://github.com/galaxyproject/galaxy/commit/8858b5511cdaf282eb5a1e75eda4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/onload.js Log Message: ----------- Standardize import naming a little. Commit: d87e5755c73c59c3dfc4291b76da059fe8a81675 https://github.com/galaxyproject/galaxy/commit/d87e5755c73c59c3dfc4291b76da… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Tours import/export cleanup. tour_opts is internal only. Commit: 3f5aabbf150bd126b8bfa209214874a42399c666 https://github.com/galaxyproject/galaxy/commit/3f5aabbf150bd126b8bfa2092148… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Tour launching refactoring. Commit: a2cf121e34dc4cdb556ffb47337199d1e8a15f1b https://github.com/galaxyproject/galaxy/commit/a2cf121e34dc4cdb556ffb473371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Reduce tour launch duplication, refine module interface. Commit: d68dd305d86ae5767b00a0dbd7b2736101500e0a https://github.com/galaxyproject/galaxy/commit/d68dd305d86ae5767b00a0dbd7b2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Run client-format. Commit: 03062992cfe037ea6d190c8587de39e66070fc55 https://github.com/galaxyproject/galaxy/commit/03062992cfe037ea6d190c8587de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M config/plugins/webhooks/demo/tour_generator/static/script.js Log Message: ----------- Actually add /config to the commit... Commit: afae7c5dbd05bd4e69f4278902b8a0d1e3fde900 https://github.com/galaxyproject/galaxy/commit/afae7c5dbd05bd4e69f4278902b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Slight reorg in tours.js; internal stuff first, exports at the end. Commit: 2a7daaaefb605e7567cdafb71d49903e3db3389d https://github.com/galaxyproject/galaxy/commit/2a7daaaefb605e7567cdafb71d49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Rebuild client. Commit: fe0fdeb4ce35dc1de9fa2ce26ffffab6276552e0 https://github.com/galaxyproject/galaxy/commit/fe0fdeb4ce35dc1de9fa2ce26fff… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tour_generator/static/script.js M lib/galaxy/webapps/galaxy/controllers/root.py M static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/masthead.bundled.js M static/scripts/bundled/viz.bundled.js M static/scripts/bundled/workflow.bundled.js M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #5116 from dannon/onload_webhook_segmentation Onload webhook toggles. Compare: https://github.com/galaxyproject/galaxy/compare/30196f5941df...fe0fdeb4ce35

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[galaxyproject/galaxy] 688128: Minor tweak; use dot notation in history-list.js
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 688128feed6147e359969f19775630d11a5281c1 https://github.com/galaxyproject/galaxy/commit/688128feed6147e359969f197756… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Minor tweak; use dot notation in history-list.js Commit: 12da37bb9ab1fbf35b13a36ba808d23f054a738c https://github.com/galaxyproject/galaxy/commit/12da37bb9ab1fbf35b13a36ba808… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Grid-view cleanup. Commit: 35d854b8c13d951692e9f0bc9564031d1dc790e0 https://github.com/galaxyproject/galaxy/commit/35d854b8c13d951692e9f0bc9564… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Fixes in grid-template. A couple redefined vars, one used out of scope, and some general cleanup. Commit: f296d1f3334098481f56ac82ea861554cb48ab38 https://github.com/galaxyproject/galaxy/commit/f296d1f3334098481f56ac82ea86… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Minor formatting. Commit: 53bcd063bce83257546a46918d73074491693324 https://github.com/galaxyproject/galaxy/commit/53bcd063bce83257546a46918d73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Started refactoring more dramatically, but I think we probably want to do a bigger rewrite of this stuff with Vue grid components, Vuex, etc., so this simple subclassing should fix the problems we're seeing for now. Commit: cb6bbe3a0fbf5fb12507ddc391366b24177724c0 https://github.com/galaxyproject/galaxy/commit/cb6bbe3a0fbf5fb12507ddc39136… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js Log Message: ----------- Client format. Commit: 556c17d154e2efe496484b917f25acacaaba7c87 https://github.com/galaxyproject/galaxy/commit/556c17d154e2efe496484b917f25… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Convert a bunch of iterables to use 'of' syntax instead of 'in'. Commit: eca993539a2e00895e32316e939e09fdfb79b84d https://github.com/galaxyproject/galaxy/commit/eca993539a2e00895e32316e939e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js A doc/source/admin/cluster.md M doc/source/admin/index.rst A doc/source/admin/jobs.md A doc/source/admin/production.md A doc/source/admin/scaling.md A doc/source/admin/special_topics/apache.md A doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/job_metrics.md A doc/source/admin/special_topics/nginx.md M doc/source/conf.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/parameters/basic.py A lib/galaxy/tools/repositories.py A lib/galaxy/util/renamed_temporary_file.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/workflow/run.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js M test/api/test_workflows.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/tools/test_tool_validation.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix-history-copy Commit: a92da1c109c3e5cbc530d17cd148a5877098a676 https://github.com/galaxyproject/galaxy/commit/a92da1c109c3e5cbc530d17cd148… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- use encoded ids for popup anchor identifiers instead of sequence; this is more robust Commit: e08a3d0ffd01a7d58ad7445ef19050e6fbbefae3 https://github.com/galaxyproject/galaxy/commit/e08a3d0ffd01a7d58ad7445ef190… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Make client Commit: 30196f5941df704f6bb0a2a215315db08ffc92bf https://github.com/galaxyproject/galaxy/commit/30196f5941df704f6bb0a2a21531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js Log Message: ----------- Merge pull request #5144 from dannon/fix-history-copy Fix history copy Compare: https://github.com/galaxyproject/galaxy/compare/ef13e2857851...30196f5941df

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Commit: ef13e28578513f94014a705127585a42aba1c470 https://github.com/galaxyproject/galaxy/commit/ef13e28578513f94014a70512758… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/228623a133fd...ef13e2857851

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Compare: https://github.com/galaxyproject/galaxy/compare/a0eae9510c9e...e9f05cb1b11d

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 228623a133fd05f0a310fe0ab063b48fa748c3b5 https://github.com/galaxyproject/galaxy/commit/228623a133fd05f0a310fe0ab063… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6055de286d6c...228623a133fd

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/cd1454c40a43...a0eae9510c9e

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Compare: https://github.com/galaxyproject/galaxy/compare/a0eae9510c9e...e9f05cb1b11d

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