March 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6b782a: Changed GenomeSpace token handling to use manual O...
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73 https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Changed GenomeSpace token handling to use manual OpenID association only Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- replace syntax that is too new Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67 https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M static/maps/mvc/ui/ui-select-genomespace.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.map M static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css Log Message: ----------- build client Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08 https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-genomespace.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.map M static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5631 from martenson/genomespace [17.09] Changed GenomeSpace token handling to use manual OpenID association only Commit: 10f8c3bc82b3a87dfa4125aa6eca9eb9071d3609 https://github.com/galaxyproject/galaxy/commit/10f8c3bc82b3a87dfa4125aa6eca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 dropped all static content from merge except of styles Commit: e5d0c1c0eeffe9406f58f08b112fad332655e229 https://github.com/galaxyproject/galaxy/commit/e5d0c1c0eeffe9406f58f08b112f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'merge-in-18.01' into dev Commit: cf369e84e3a8f1989bfb82284a6703994fdbe971 https://github.com/galaxyproject/galaxy/commit/cf369e84e3a8f1989bfb82284a67… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- re-add erroneously removed line Commit: 300fffe73ee07d42a59c22b869eb3666b47dc720 https://github.com/galaxyproject/galaxy/commit/300fffe73ee07d42a59c22b869eb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5660 from martenson/merge-genomespace Merge forward genomespace changes Compare: https://github.com/galaxyproject/galaxy/compare/fffca430d216...300fffe73ee0

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[galaxyproject/galaxy] 6b782a: Changed GenomeSpace token handling to use manual O...
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73 https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Changed GenomeSpace token handling to use manual OpenID association only Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- replace syntax that is too new Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67 https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M static/maps/mvc/ui/ui-select-genomespace.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.map M static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css Log Message: ----------- build client Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08 https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-genomespace.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.map M static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5631 from martenson/genomespace [17.09] Changed GenomeSpace token handling to use manual OpenID association only Commit: 10f8c3bc82b3a87dfa4125aa6eca9eb9071d3609 https://github.com/galaxyproject/galaxy/commit/10f8c3bc82b3a87dfa4125aa6eca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge branch 'release_17.09' into release_18.01 dropped all static content from merge except of styles Commit: b655a499f82a73f82f89bc8f962d4f0f0097cabc https://github.com/galaxyproject/galaxy/commit/b655a499f82a73f82f89bc8f962d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- re-add erroneously removed line Commit: b601bcc429b47617e684158a62166575c244fd61 https://github.com/galaxyproject/galaxy/commit/b601bcc429b47617e684158a6216… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5659 from martenson/merge-in-17.09 [18.01] Merge with 17.09 Compare: https://github.com/galaxyproject/galaxy/compare/9e6f3f57a0b2...b601bcc429b4

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[galaxyproject/galaxy] 4adaad: Fix sanitazion of MathML and SVG
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4adaad4f0ee5444c6ef099f90681845c81901b82 https://github.com/galaxyproject/galaxy/commit/4adaad4f0ee5444c6ef099f90681… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Fix sanitazion of MathML and SVG Broken in commit 66944ba7de178cc45ffa7a4aa9253ec4512cb6fd . Commit: bacc1bf90b68a182492d484e5ded9003b5b03819 https://github.com/galaxyproject/galaxy/commit/bacc1bf90b68a182492d484e5ded… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/util/sanitize_html.py Log Message: ----------- Remove unused code Commit: 271feecefa37aa69726ec3e47f4d73f12bb847e6 https://github.com/galaxyproject/galaxy/commit/271feecefa37aa69726ec3e47f4d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Use HTMLParser instead of Python2-only sgmllib Commit: 326a564eb95f34c359cea14c2078f35c0ba55259 https://github.com/galaxyproject/galaxy/commit/326a564eb95f34c359cea14c2078… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py Log Message: ----------- Stop shipping old BeautifulSoup library Commit: 6906d15d928ef9da375227c14be4ff905941e30c https://github.com/galaxyproject/galaxy/commit/6906d15d928ef9da375227c14be4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Use bleach library for HTML sanitizing Commit: 71c1c52d22e7fdbef2dc7d7b4b7993cc7f2de69d https://github.com/galaxyproject/galaxy/commit/71c1c52d22e7fdbef2dc7d7b4b79… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/util/sanitize_html.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Update code from upstream feedparser. Simplify __init__() Commit: cd8a44ff195729c7e772ad461d9fab4797bbe252 https://github.com/galaxyproject/galaxy/commit/cd8a44ff195729c7e772ad461d9f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/util/sanitize_html.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Merge _BaseHTMLProcessor class in _PageContentProcessor Derive from HTMLParser instead of SGMLParser. Commit: fffca430d21655ede9f0369fe078f3a1972910b1 https://github.com/galaxyproject/galaxy/commit/fffca430d21655ede9f0369fe078… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/util/workflow_util.py R scripts/microbes/BeautifulSoup.py M scripts/microbes/harvest_bacteria.py Log Message: ----------- Merge pull request #5642 from nsoranzo/evict_sgmllib Python3: evict sgmllib and BeautifulSoup Compare: https://github.com/galaxyproject/galaxy/compare/6675959069b0...fffca430d216

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[galaxyproject/galaxy] cb43b6: Bring in the latest galaxy-lib updates.
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb43b6b5316d76a1043409e95607a4a3b4aa7aa1 https://github.com/galaxyproject/galaxy/commit/cb43b6b5316d76a1043409e95607… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Bring in the latest galaxy-lib updates. These fixes include: - Python 3 fix for assertion testing code (https://github.com/galaxyproject/galaxy-lib/pull/101) - Mulled enhancement to escape quotes in test code for mulled images - https://github.com/galaxyproject/galaxy-lib/pull/100. - Mulled enhancement to make CONDA_IMAGE configurable - https://github.com/galaxyproject/galaxy-lib/pull/99. - Fix galaxy.util.path for import on Windows (https://github.com/galaxyproject/galaxy-lib/pull/98) Commit: 6675959069b0b5cb776f3194cd24c2b9a97f59c4 https://github.com/galaxyproject/galaxy/commit/6675959069b0b5cb776f3194cd24… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #5653 from jmchilton/galaxy-lib-update-20180307 Bring in the latest galaxy-lib updates. Compare: https://github.com/galaxyproject/galaxy/compare/3afb4abad3a3...6675959069b0

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[galaxyproject/galaxy] 58ed03: Create fewer objects when instantiating tools.
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58ed0308faa7fa94f1b36dc2e62b866ac6f49bdd https://github.com/galaxyproject/galaxy/commit/58ed0308faa7fa94f1b36dc2e62b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/__init__.py Log Message: ----------- Create fewer objects when instantiating tools. Commit: 5e6c1c9f517ad7d6353db777e82c8e48f4769f06 https://github.com/galaxyproject/galaxy/commit/5e6c1c9f517ad7d6353db777e82c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M config/plugins/webhooks/demo/tour_generator/__init__.py M lib/galaxy/app.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py Log Message: ----------- New abstraction to obtain tool test data paths. Can be shared between tests and TDTs. A step toward not requiring one to load the tool to test the tool (important for external testing of tools). Commit: 210d5cbd7a52ecc3bbbef24c1bee4362fbcb9770 https://github.com/galaxyproject/galaxy/commit/210d5cbd7a52ecc3bbbef24c1bee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M test/base/driver_util.py M test/base/testcase.py Log Message: ----------- Eliminate shed tools dict no longer used. Commit: 58ac3b6eff5f2158d5690d684a143716c4471ba4 https://github.com/galaxyproject/galaxy/commit/58ac3b6eff5f2158d5690d684a14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: R test/base/tool_shed_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Eliminate tool shed test helper no longer used. Commit: 7e372c5dd217fdb4c19f4da6a49d86d65d205f76 https://github.com/galaxyproject/galaxy/commit/7e372c5dd217fdb4c19f4da6a49d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py M test/base/interactor.py M test/base/testcase.py Log Message: ----------- Refactor more tool test verification code into galaxy-lib. Should enable greater reuse from outside the test framework (e.g. standalone scripts and Planemo). Commit: 70e76cae9f1f354540a3b97020323be1caba9817 https://github.com/galaxyproject/galaxy/commit/70e76cae9f1f354540a3b9702032… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M test/base/interactor.py M test/base/testcase.py Log Message: ----------- Refactor polling code from testcase into more standalone interactor. Working toward making interactor stand-alone and independent of the test framework. Commit: 289937506bc97b7c8783975316e0a236a6ebf76b https://github.com/galaxyproject/galaxy/commit/289937506bc97b7c8783975316e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/__init__.py A lib/galaxy/tools/verify/interactor.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py Log Message: ----------- Refactor much more tool testing code into galaxy-lib. Commit: 508047f00ece58c98ba0f9bb093d2ae7506ade77 https://github.com/galaxyproject/galaxy/commit/508047f00ece58c98ba0f9bb093d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/interactor.py M test/functional/test_toolbox.py Log Message: ----------- Refactor ToolTestBuilder to not require an in-memory Tool object. This gets us a lot closer to being able to construct a ToolTestBuilder from simple dictionaries generated from the API for instance or from any tool really. Commit: c3af6c8feae90bc2d4b6328559fb79e3d7d35a5c https://github.com/galaxyproject/galaxy/commit/c3af6c8feae90bc2d4b6328559fb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_tools.py M test/base/driver_util.py M test/base/testcase.py M test/functional/test_toolbox.py Log Message: ----------- Serialize tool test descriptions through the API. Use this is in tool testing. Prevents needing to load / have tools in memory to run tool tests - should allow external tool testing. Commit: b1779e1a46564d976a7c024084c48c94df2db8e5 https://github.com/galaxyproject/galaxy/commit/b1779e1a46564d976a7c024084c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M test/base/driver_util.py M test/functional/test_toolbox.py Log Message: ----------- Refactor tool test outline construction to allow more reuse. Commit: cd002615ee8a1f251eac9c0a5ae3cc12c45d2bde https://github.com/galaxyproject/galaxy/commit/cd002615ee8a1f251eac9c0a5ae3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/test_data.py Log Message: ----------- Setup a default GALAXY_TEST_FILE_DIR in case unset in the Galaxy itself. Previously this was set in the test framework but that doesn't help running Galaxies. Commit: 6f908a76c5db474725c2e45b51ad6ee9c27487cc https://github.com/galaxyproject/galaxy/commit/6f908a76c5db474725c2e45b51ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M test/integration/test_data_manager_table_reload.py A test/integration/uses_shed.py Log Message: ----------- Refactor data manager test to allow more integration tests with tool shed. Commit: 662f29fda271454a9976fbf4fdad273300a89bfa https://github.com/galaxyproject/galaxy/commit/662f29fda271454a9976fbf4fdad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: A test/integration/test_shed_tool_tests.py Log Message: ----------- Integration test case for running tool tests against shed installed tools. Commit: db6dafac07b92a06cac1da728f8fffb979d81d87 https://github.com/galaxyproject/galaxy/commit/db6dafac07b92a06cac1da728f8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Revise repository directory calculation in tool class. Based on conversations with @mvdbeek on https://github.com/galaxyproject/galaxy/pull/5545/files. Commit: e7f7759cc22aac8ace05eaeab5b706634322a80b https://github.com/galaxyproject/galaxy/commit/e7f7759cc22aac8ace05eaeab5b7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/config_schema.yml Log Message: ----------- Better default configuration of Galaxy test data directory. Commit: dc080b926ec3c0ecb967224ffa3b505e0128f783 https://github.com/galaxyproject/galaxy/commit/dc080b926ec3c0ecb967224ffa3b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/script.py Log Message: ----------- Add structured output json example to galaxy.tools.verify.script. Capture more information about the test. Commit: 52b6bf2486b08aa8bbe621961baed42bd27c1ddd https://github.com/galaxyproject/galaxy/commit/52b6bf2486b08aa8bbe621961bae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools.py Log Message: ----------- Stronger security around test data path resolution, now with tests. Commit: bb7de2c0db60d6a69d84401279830fa87e8d9000 https://github.com/galaxyproject/galaxy/commit/bb7de2c0db60d6a69d8440127983… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py M lib/galaxy/tools/verify/interactor.py M test/unit/tools/test_parsing.py Log Message: ----------- Improved tool test API. Cleanup up internal representations used to bridge the tool parser and the tool testing modules to produce more sensible dictified representations when exported via the API. This is mostly replacing tuples (which get converted to JSON lists) to dicts but there are some other small cleanups. Commit: 28ba0279d90dfae7603cdb06bed69235bf4f6f06 https://github.com/galaxyproject/galaxy/commit/28ba0279d90dfae7603cdb06bed6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Bug fix for exclude mercurial repo from test data search. Thanks to :eagle::eyes:. Commit: 227bf4ad045fcecc1aaab77a9b04f0ad0daa1e19 https://github.com/galaxyproject/galaxy/commit/227bf4ad045fcecc1aaab77a9b04… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/tools/verify/interactor.py M test/base/driver_util.py Log Message: ----------- Cleanup external tool testing based on @nsoranzo's comments. Commit: f741ab142adc2411397fb6ef28710b850e02db78 https://github.com/galaxyproject/galaxy/commit/f741ab142adc2411397fb6ef2871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Switch default tool test dbkey to '?'. This makes a lot more sense, since the target Galaxy may not be configured with this dbkey. Thanks to @mvdbeek for the catch (https://github.com/galaxyproject/galaxy/pull/5628#pullrequestreview-1014615…) Restore the legacy behavior with "export GALAXY_TEST_DEFAULT_DBKEY=hg17". Commit: 3afb4abad3a387997c0cb1c9398f8644219b0298 https://github.com/galaxyproject/galaxy/commit/3afb4abad3a387997c0cb1c9398f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M config/galaxy.yml.sample M config/plugins/webhooks/demo/tour_generator/__init__.py M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/test.py A lib/galaxy/tools/verify/interactor.py A lib/galaxy/tools/verify/script.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M test/api/test_tools.py M test/base/api.py M test/base/driver_util.py M test/base/interactor.py M test/base/testcase.py R test/base/tool_shed_util.py M test/functional/test_data_managers.py M test/functional/test_toolbox.py M test/functional/twilltestcase.py M test/integration/test_data_manager_table_reload.py A test/integration/test_shed_tool_tests.py A test/integration/uses_shed.py M test/shed_functional/base/twilltestcase.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #5628 from jmchilton/external_tool_tests_better_api Externally Executable Tool Tests 2 (with better API) Compare: https://github.com/galaxyproject/galaxy/compare/7ceb24601822...3afb4abad3a3

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[galaxyproject/galaxy] 90b700: Do not sniff BamInputSorted
by GitHub 07 Mar '18

07 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90b700be42da9f7f6fa69bae6f8d71776badd351 https://github.com/galaxyproject/galaxy/commit/90b700be42da9f7f6fa69bae6f8d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Do not sniff BamInputSorted Only aligners should produce this datatype. If an alignment is not explicitly coordinate or queryname sorted it should be BamNative. Also addresses https://github.com/galaxyproject/galaxy/pull/5628#issuecomment-370874329, though I think the sniff order should be dependent on the order with which datatypes are loaded. Commit: 9e6f3f57a0b27ad3b64cd4e3ea2cb51f10a3b8e7 https://github.com/galaxyproject/galaxy/commit/9e6f3f57a0b27ad3b64cd4e3ea2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5644 from mvdbeek/disable_sniffer_qname_input_sorted [18.01] Do not sniff BamInputSorted Commit: 7ceb24601822b884d9024e19bae8a9bb927e4360 https://github.com/galaxyproject/galaxy/commit/7ceb24601822b884d9024e19bae8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a69fb6e331d9...7ceb24601822

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[galaxyproject/galaxy] 90b700: Do not sniff BamInputSorted
by GitHub 07 Mar '18

07 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 90b700be42da9f7f6fa69bae6f8d71776badd351 https://github.com/galaxyproject/galaxy/commit/90b700be42da9f7f6fa69bae6f8d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Do not sniff BamInputSorted Only aligners should produce this datatype. If an alignment is not explicitly coordinate or queryname sorted it should be BamNative. Also addresses https://github.com/galaxyproject/galaxy/pull/5628#issuecomment-370874329, though I think the sniff order should be dependent on the order with which datatypes are loaded. Commit: 9e6f3f57a0b27ad3b64cd4e3ea2cb51f10a3b8e7 https://github.com/galaxyproject/galaxy/commit/9e6f3f57a0b27ad3b64cd4e3ea2c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5644 from mvdbeek/disable_sniffer_qname_input_sorted [18.01] Do not sniff BamInputSorted Compare: https://github.com/galaxyproject/galaxy/compare/4850ca5c839c...9e6f3f57a0b2

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[galaxyproject/galaxy] 166fe7: Conda fixes for 18.01 - stdout redirection.
by GitHub 06 Mar '18

06 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 166fe7eada87d242be506a8d1369df019acd20b1 https://github.com/galaxyproject/galaxy/commit/166fe7eada87d242be506a8d1369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda fixes for 18.01 - stdout redirection. Broken in #5397 I think. Commit: 4850ca5c839cb80bff202c86b7d9a4d04c318dcb https://github.com/galaxyproject/galaxy/commit/4850ca5c839cb80bff202c86b7d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5620 from jmchilton/conda_fixes_1801 [18.01] Conda fix for commands using stdout redirection. Commit: a69fb6e331d99b16567c819849e10073b5d92ff2 https://github.com/galaxyproject/galaxy/commit/a69fb6e331d99b16567c819849e1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-06 (Tue, 06 Mar 2018) Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1118e6f1be87...a69fb6e331d9

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[galaxyproject/galaxy] 166fe7: Conda fixes for 18.01 - stdout redirection.
by GitHub 06 Mar '18

06 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 166fe7eada87d242be506a8d1369df019acd20b1 https://github.com/galaxyproject/galaxy/commit/166fe7eada87d242be506a8d1369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda fixes for 18.01 - stdout redirection. Broken in #5397 I think. Commit: 4850ca5c839cb80bff202c86b7d9a4d04c318dcb https://github.com/galaxyproject/galaxy/commit/4850ca5c839cb80bff202c86b7d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5620 from jmchilton/conda_fixes_1801 [18.01] Conda fix for commands using stdout redirection. Compare: https://github.com/galaxyproject/galaxy/compare/ff9bc843fab9...4850ca5c839c

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[galaxyproject/galaxy] 6b782a: Changed GenomeSpace token handling to use manual O...
by GitHub 06 Mar '18

06 Mar '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 6b782ad16d010d6da7808ac7deaecef3ec301b73 https://github.com/galaxyproject/galaxy/commit/6b782ad16d010d6da7808ac7deae… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Changed GenomeSpace token handling to use manual OpenID association only Commit: 10cf046ea8604a367b734b7d1b58e623705ed11c https://github.com/galaxyproject/galaxy/commit/10cf046ea8604a367b734b7d1b58… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js Log Message: ----------- replace syntax that is too new Commit: 69bbcda0b3577edcb7042cdf26f4373ea1ed5f67 https://github.com/galaxyproject/galaxy/commit/69bbcda0b3577edcb7042cdf26f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M static/maps/mvc/ui/ui-select-genomespace.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.map M static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css Log Message: ----------- build client Commit: f8d44c2b69516f9464aad4acfc2bbf68ce3ede08 https://github.com/galaxyproject/galaxy/commit/f8d44c2b69516f9464aad4acfc2b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-genomespace.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.map M static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #5631 from martenson/genomespace [17.09] Changed GenomeSpace token handling to use manual OpenID association only Compare: https://github.com/galaxyproject/galaxy/compare/28724ab795ac...f8d44c2b6951

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