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

[galaxyproject/galaxy] 993f5f: Fix DynamicOptions.get_options() when loc file is ...
by GitHub 11 May '18

11 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 993f5f52db08e1851ee9c7e6dd64f3c5e50ee957 https://github.com/galaxyproject/galaxy/commit/993f5f52db08e1851ee9c7e6dd64… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix DynamicOptions.get_options() when loc file is missing Fix https://github.com/galaxyproject/galaxy/issues/2987 Commit: 88202fbc575888285a0ea847fa94baef2595551e https://github.com/galaxyproject/galaxy/commit/88202fbc575888285a0ea847fa94… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Allow speficying columns by name for attribute_value_splitter filter Commit: e25b086dc13e023b139e8844347051f8c1eb1ce3 https://github.com/galaxyproject/galaxy/commit/e25b086dc13e023b139e88443470… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #6103 from nsoranzo/release_17.09_fix_2987 [17.09] Fix DynamicOptions.get_options() when loc file is missing Commit: 3137d84ad7d7901dd4c65f56b7a8cefba5c467c7 https://github.com/galaxyproject/galaxy/commit/3137d84ad7d7901dd4c65f56b7a8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: f1eaaea24e67d96c7c45913beac8622cfa0afdc8 https://github.com/galaxyproject/galaxy/commit/f1eaaea24e67d96c7c45913beac8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/e26691244fc2...f1eaaea24e67 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 993f5f: Fix DynamicOptions.get_options() when loc file is ...
by GitHub 11 May '18

11 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 993f5f52db08e1851ee9c7e6dd64f3c5e50ee957 https://github.com/galaxyproject/galaxy/commit/993f5f52db08e1851ee9c7e6dd64… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix DynamicOptions.get_options() when loc file is missing Fix https://github.com/galaxyproject/galaxy/issues/2987 Commit: 88202fbc575888285a0ea847fa94baef2595551e https://github.com/galaxyproject/galaxy/commit/88202fbc575888285a0ea847fa94… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Allow speficying columns by name for attribute_value_splitter filter Commit: e25b086dc13e023b139e8844347051f8c1eb1ce3 https://github.com/galaxyproject/galaxy/commit/e25b086dc13e023b139e88443470… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #6103 from nsoranzo/release_17.09_fix_2987 [17.09] Fix DynamicOptions.get_options() when loc file is missing Commit: 3137d84ad7d7901dd4c65f56b7a8cefba5c467c7 https://github.com/galaxyproject/galaxy/commit/3137d84ad7d7901dd4c65f56b7a8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/890b446974b0...3137d84ad7d7 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eb29ad: Downgrade python-genomespaceclient to 0.2
by GitHub 11 May '18

11 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb29adc2efd8bad0f15dc6a51b2a3cd33216b8f9 https://github.com/galaxyproject/galaxy/commit/eb29adc2efd8bad0f15dc6a51b2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Downgrade python-genomespaceclient to 0.2 Commit: eae69c26f89aa6b809a3186131f59b32d590bb9e https://github.com/galaxyproject/galaxy/commit/eae69c26f89aa6b809a3186131f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M run_tests.sh Log Message: ----------- [18.05] Fix parsing last argument when running functional tests. Causes Planemo to double test tools. Commit: 9bc73824a5419072b65158a09c0f6c30a9c5b3f0 https://github.com/galaxyproject/galaxy/commit/9bc73824a5419072b65158a09c0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- [18.05] Fix matches_any() checks for dynamic compressed types. See huge conversation on #6093. Commit: ba1f369e2f1c124ffacd60b329364d79d63ed513 https://github.com/galaxyproject/galaxy/commit/ba1f369e2f1c124ffacd60b32936… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Encode dataset ids when loading trackster visualizations Commit: b7f26be45fd0fa13876cfdfdd37c460b9947474b https://github.com/galaxyproject/galaxy/commit/b7f26be45fd0fa13876cfdfdd37c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #6095 from jmchilton/fix_double_test [18.05] Fix parsing last argument when running functional tests. Commit: b6a22584aaed8df8ea3ffc1d1db96c65fe887878 https://github.com/galaxyproject/galaxy/commit/b6a22584aaed8df8ea3ffc1d1db9… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6112 from guerler/fix_hda_access [18.05] Encode dataset ids when loading trackster visualizations Commit: 148d56a9c9d12df6d3d8fbe48a713f75cca6a468 https://github.com/galaxyproject/galaxy/commit/148d56a9c9d12df6d3d8fbe48a71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Many more matches_any tests, better categorization of them with comments. Some of these suggested by @nsoranzo. Commit: 8ca8ead4e592beb73ab92fa1324ee2060beb9188 https://github.com/galaxyproject/galaxy/commit/8ca8ead4e592beb73ab92fa1324e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge pull request #6111 from jmchilton/dynamic_compressed_types_fix_4 [18.05] Fix matches_any() checks for dynamic compressed types. Commit: efc97a440096372d01427942cb19ac82a0d23dd3 https://github.com/galaxyproject/galaxy/commit/efc97a440096372d01427942cb19… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6054 from natefoo/genomespaceclient-downgrade [18.05] Downgrade python-genomespaceclient to 0.2 Commit: 4dedc900b56573a5bc0443daca096afa66da072b https://github.com/galaxyproject/galaxy/commit/4dedc900b56573a5bc0443daca09… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Showed up in esntry as referencing fname before assignment Commit: 890b446974b03daa098130392ee538a1320daa16 https://github.com/galaxyproject/galaxy/commit/890b446974b03daa098130392ee5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #6119 from erasche/error-temp-lib-dl [18.01] Showed up in sentry as referencing fname before assignment Commit: e26691244fc28d15f7ddd8e8913508fba3786b1c https://github.com/galaxyproject/galaxy/commit/e26691244fc28d15f7ddd8e89135… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Commit: 02e8cb65a0b4aabc6ad6f29fca2d99dd2cbe08d0 https://github.com/galaxyproject/galaxy/commit/02e8cb65a0b4aabc6ad6f29fca2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M run_tests.sh A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f69760d66a46...02e8cb65a0b4 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4dedc9: Showed up in esntry as referencing fname before as...
by GitHub 11 May '18

11 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4dedc900b56573a5bc0443daca096afa66da072b https://github.com/galaxyproject/galaxy/commit/4dedc900b56573a5bc0443daca09… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Showed up in esntry as referencing fname before assignment Commit: 890b446974b03daa098130392ee538a1320daa16 https://github.com/galaxyproject/galaxy/commit/890b446974b03daa098130392ee5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #6119 from erasche/error-temp-lib-dl [18.01] Showed up in sentry as referencing fname before assignment Commit: e26691244fc28d15f7ddd8e8913508fba3786b1c https://github.com/galaxyproject/galaxy/commit/e26691244fc28d15f7ddd8e89135… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/efc97a440096...e26691244fc2 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0

[galaxyproject/galaxy] 4dedc9: Showed up in esntry as referencing fname before as...
by GitHub 11 May '18

11 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 4dedc900b56573a5bc0443daca096afa66da072b https://github.com/galaxyproject/galaxy/commit/4dedc900b56573a5bc0443daca09… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Showed up in esntry as referencing fname before assignment Commit: 890b446974b03daa098130392ee538a1320daa16 https://github.com/galaxyproject/galaxy/commit/890b446974b03daa098130392ee5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #6119 from erasche/error-temp-lib-dl [18.01] Showed up in sentry as referencing fname before assignment Compare: https://github.com/galaxyproject/galaxy/compare/250973eb46fc...890b446974b0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 993f5f: Fix DynamicOptions.get_options() when loc file is ...
by GitHub 11 May '18

11 May '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 993f5f52db08e1851ee9c7e6dd64f3c5e50ee957 https://github.com/galaxyproject/galaxy/commit/993f5f52db08e1851ee9c7e6dd64… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Fix DynamicOptions.get_options() when loc file is missing Fix https://github.com/galaxyproject/galaxy/issues/2987 Commit: 88202fbc575888285a0ea847fa94baef2595551e https://github.com/galaxyproject/galaxy/commit/88202fbc575888285a0ea847fa94… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Allow speficying columns by name for attribute_value_splitter filter Commit: e25b086dc13e023b139e8844347051f8c1eb1ce3 https://github.com/galaxyproject/galaxy/commit/e25b086dc13e023b139e88443470… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Merge pull request #6103 from nsoranzo/release_17.09_fix_2987 [17.09] Fix DynamicOptions.get_options() when loc file is missing Compare: https://github.com/galaxyproject/galaxy/compare/d5ec01d5da1d...e25b086dc13e **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7f5206: Add preliminary sharing vue component, redirect ro...
by GitHub 11 May '18

11 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f5206a3b1b880161ca6e3bd38626aabb6c2d528 https://github.com/galaxyproject/galaxy/commit/7f5206a3b1b880161ca6e3bd3862… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/yarn.lock M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add preliminary sharing vue component, redirect routes Commit: 5c6704b8e14c1c0da07b537d01e3274c9746b205 https://github.com/galaxyproject/galaxy/commit/5c6704b8e14c1c0da07b537d01e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Augment user information storage api, separate username from email handling Commit: 718e9bc9d09f915b00910b52a3efe58dc087b242 https://github.com/galaxyproject/galaxy/commit/718e9bc9d09f915b00910b52a3ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: A client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add sharing vue component Commit: 91590243b70e7c7727ff9d83b9589e527b36d9bf https://github.com/galaxyproject/galaxy/commit/91590243b70e7c7727ff9d83b958… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add error flag Commit: d16c71bbb03ea0a05baf884009b313ff5c0b1cc5 https://github.com/galaxyproject/galaxy/commit/d16c71bbb03ea0a05baf884009b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Expand sharing vue component Commit: 2abab4f53698eca07ea2508c41a868cf33ddb310 https://github.com/galaxyproject/galaxy/commit/2abab4f53698eca07ea2508c41a8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Replace mako style url generation Commit: f065ebe903cec29aeca89eb7c9ffe1bf44f13f7e https://github.com/galaxyproject/galaxy/commit/f065ebe903cec29aeca89eb7c9ff… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add remaining sections to vue component Commit: 2b72bbb19f31c8fa633bbeeab8743ba37f0ca9fa https://github.com/galaxyproject/galaxy/commit/2b72bbb19f31c8fa633bbeeab874… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add button labels, fix bugs Commit: 5e9f5aa46c440cf733d4174298f00380c06f0edc https://github.com/galaxyproject/galaxy/commit/5e9f5aa46c440cf733d4174298f0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-29 (Sun, 29 Apr 2018) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Add api support for sharing status handling to histories Commit: 44ed208e47f89ad14230d6e72c82d31e48442e92 https://github.com/galaxyproject/galaxy/commit/44ed208e47f89ad14230d6e72c82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Load initial settings through api Commit: 7edef1b0dd79593f170bde2ddd912381a5563df9 https://github.com/galaxyproject/galaxy/commit/7edef1b0dd79593f170bde2ddd91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add and initialize properties Commit: ca77dedf7c46ac124dc2a066d836ca058166ca93 https://github.com/galaxyproject/galaxy/commit/ca77dedf7c46ac124dc2a066d836… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Retrieve class name from api model Commit: 4830587b02eeeaf06d2a9c2e5b005ddbae07ff03 https://github.com/galaxyproject/galaxy/commit/4830587b02eeeaf06d2a9c2e5b00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-30 (Mon, 30 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Use plural name as property Commit: 51389473e0f5b56d8e5ffe85f2f5dad8e5e534cd https://github.com/galaxyproject/galaxy/commit/51389473e0f5b56d8e5ffe85f2f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/histories.py Log Message: ----------- Fix serializer Commit: 4020ecdb33f55b440ebf12e768f98312dbdf57b8 https://github.com/galaxyproject/galaxy/commit/4020ecdb33f55b440ebf12e768f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Add individual users to view, populate table Commit: a5917387b2705ff88a72d5691e804cf1f5a1215f https://github.com/galaxyproject/galaxy/commit/a5917387b2705ff88a72d5691e80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Fix link to published list Commit: c31b553b7737986756a6ce205eb36bd779f1f0a3 https://github.com/galaxyproject/galaxy/commit/c31b553b7737986756a6ce205eb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-01 (Tue, 01 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix sharing status api endpoint, connect ui Commit: 6e2f4108c50c11d94cdb8a15afad7a3f66e99176 https://github.com/galaxyproject/galaxy/commit/6e2f4108c50c11d94cdb8a15afad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Fix error message handling, properly reflect server response in ui Commit: 606b6e475a432020c8199bde5fab873d457a2e39 https://github.com/galaxyproject/galaxy/commit/606b6e475a432020c8199bde5fab… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Add preliminary support for users having access to the history Commit: 08ffa6ec97df79bbd53e4aa409183a3941682939 https://github.com/galaxyproject/galaxy/commit/08ffa6ec97df79bbd53e4aa40918… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Adjust username handling, fix form submission actions Commit: c281c1a6171383241d6584bbf929beb54c0e6c7b https://github.com/galaxyproject/galaxy/commit/c281c1a6171383241d6584bbf929… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Remove legacy sharing controller endpoint Commit: 93d9a9dc5682f574cce33b5b945892ae039a65e7 https://github.com/galaxyproject/galaxy/commit/93d9a9dc5682f574cce33b5b9458… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue Log Message: ----------- Fix username check flag Commit: b09c6803c36305e8f8634429523970831162091c https://github.com/galaxyproject/galaxy/commit/b09c6803c36305e8f86344295239… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/utils/async-save-text.js Log Message: ----------- Use existing slug editing feature in component Commit: 7a17244acd365be9a10d97961b3c07b9a6382cd7 https://github.com/galaxyproject/galaxy/commit/7a17244acd365be9a10d97961b3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: R templates/sharing_base.mako Log Message: ----------- Remove sharing base mako Commit: 17772d19c5e4f168cba4e9fcb0e83a31e15c7858 https://github.com/galaxyproject/galaxy/commit/17772d19c5e4f168cba4e9fcb0e8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js Log Message: ----------- Link sharing base from history panel Commit: 3507636a4a3d2acc41fb96d464247854a78ea4f2 https://github.com/galaxyproject/galaxy/commit/3507636a4a3d2acc41fb96d46424… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Move sharing status api endpoint to mixin Commit: 258516c055b9ee5288ccb8e2ca3c24578298d87a https://github.com/galaxyproject/galaxy/commit/258516c055b9ee5288ccb8e2ca3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Get sharable object by class name Commit: 6f25fdebc65aba8b7c258749a235a18d78251576 https://github.com/galaxyproject/galaxy/commit/6f25fdebc65aba8b7c258749a235… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/managers/base.py Log Message: ----------- Generalize class name identifer, toolshed corner case Commit: 17a80e3753ab30e09df17951a6a3bc4cd1c9cdaf https://github.com/galaxyproject/galaxy/commit/17a80e3753ab30e09df17951a6a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Use default class name for sharable mixin Commit: c283fd5939ae83140f18df1e2623938421f5e58a https://github.com/galaxyproject/galaxy/commit/c283fd5939ae83140f18df1e2623… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/histories.py M lib/galaxy/managers/sharable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Refactor endpoint, add visualization sharing Commit: ac0db77d2c1b8336862eeb7ab9f9482bf49ca9e5 https://github.com/galaxyproject/galaxy/commit/ac0db77d2c1b8336862eeb7ab9f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Add page sharing routes to client Commit: 9360a1ae0d4410d293d5d404ef88db0e0da8f97d https://github.com/galaxyproject/galaxy/commit/9360a1ae0d4410d293d5d404ef88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/pages.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py Log Message: ----------- Reroute pages sharing view Commit: 7a7c6a76f086cc416df4f652f750ddf140f5b1c0 https://github.com/galaxyproject/galaxy/commit/7a7c6a76f086cc416df4f652f750… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Remove user sharing in detailed history serialization Remove unused function Commit: 7ce1cc445f427a18cf354360a4284c157e39e5b0 https://github.com/galaxyproject/galaxy/commit/7ce1cc445f427a18cf354360a428… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/managers/sharable.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Remove redundant properties Use consistent naming Fix typo Fix Commit: 45ea97eea24adf8fa4043297124399effc50ff33 https://github.com/galaxyproject/galaxy/commit/45ea97eea24adf8fa40432971243… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Move username handling from sharable base controller to workflow controller Commit: 5d2881db01dbe927eb0c003b36b0e890a3a2da73 https://github.com/galaxyproject/galaxy/commit/5d2881db01dbe927eb0c003b36b0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Fix link to sharing view Commit: 22c640608a06abc0f87ab868ef2909b4f59d2c7e https://github.com/galaxyproject/galaxy/commit/22c640608a06abc0f87ab868ef29… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Fix routing from share controller Commit: 1516cfb8b5ad8179395f700e66d1cbc7beb887fd https://github.com/galaxyproject/galaxy/commit/1516cfb8b5ad8179395f700e66d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix history sharing routes, import missing module Commit: 41c3dbfdb3b109aea742e4e27e778415708c586e https://github.com/galaxyproject/galaxy/commit/41c3dbfdb3b109aea742e4e27e77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/managers/sharable.py Log Message: ----------- Add title to serializer Commit: 2a21e273ae06303188cddfdc593cb46184d47234 https://github.com/galaxyproject/galaxy/commit/2a21e273ae06303188cddfdc593c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix lint Commit: a277a4071df754b800a8e9dc14336aea750ff72e https://github.com/galaxyproject/galaxy/commit/a277a4071df754b800a8e9dc1433… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/utils/async-save-text.js Log Message: ----------- Client-format Commit: f69760d66a46a3679bbc9049b7b42032677c656a https://github.com/galaxyproject/galaxy/commit/f69760d66a46a3679bbc9049b7b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-11 (Fri, 11 May 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/Sharing.vue M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/utils/async-save-text.js M lib/galaxy/managers/base.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/sharable.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/visualizations.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M templates/ind_share_base.mako R templates/sharing_base.mako Log Message: ----------- Merge branch 'sharing' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b68def3ebe7f...f69760d66a46 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eb29ad: Downgrade python-genomespaceclient to 0.2
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: eb29adc2efd8bad0f15dc6a51b2a3cd33216b8f9 https://github.com/galaxyproject/galaxy/commit/eb29adc2efd8bad0f15dc6a51b2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Downgrade python-genomespaceclient to 0.2 Commit: efc97a440096372d01427942cb19ac82a0d23dd3 https://github.com/galaxyproject/galaxy/commit/efc97a440096372d01427942cb19… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6054 from natefoo/genomespaceclient-downgrade [18.05] Downgrade python-genomespaceclient to 0.2 Compare: https://github.com/galaxyproject/galaxy/compare/8ca8ead4e592...efc97a440096 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 276a55: Make interactor._{get, post, put, ...} less repetitve
by GitHub 10 May '18

10 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 276a559cf44534361e48a1abddd465fce9217ab2 https://github.com/galaxyproject/galaxy/commit/276a559cf44534361e48a1abddd4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_libraries.py M test/api/test_tools.py Log Message: ----------- Make interactor._{get,post,put,...} less repetitve Also inject api key into params, so that we can use `json.dumps` for the payload instead of writing json strings in python. Commit: 346d2dca3e5b44ba6a37952b632bd1910fd5f468 https://github.com/galaxyproject/galaxy/commit/346d2dca3e5b44ba6a37952b632b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Merge `data` into params I don't think we're parsing GET request payloads. This effectively restore the get behavior prior to the previous commit. Commit: 835c59d109cbca3b58e396bed6ba856caaaf95cf https://github.com/galaxyproject/galaxy/commit/835c59d109cbca3b58e396bed6ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- No request body for DELETE/GET, no params for POST Commit: 0a599089fa3733a22e2f3ed7c7882046255b9a9f https://github.com/galaxyproject/galaxy/commit/0a599089fa3733a22e2f3ed7c788… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M test/api/test_libraries.py M test/api/test_tools.py Log Message: ----------- Don't dump json parameters Commit: 85bf5129b2fdabf1070b475df41190b60a9004f8 https://github.com/galaxyproject/galaxy/commit/85bf5129b2fdabf1070b475df411… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- Replace mutable default argument Commit: b68def3ebe7f4f7d8b8650b9d963d0ed8e56966a https://github.com/galaxyproject/galaxy/commit/b68def3ebe7f4f7d8b8650b9d963… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_libraries.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6070 from mvdbeek/improve_test_api_interactor Make `interactor._{get,post,put,...}` less repetitive Compare: https://github.com/galaxyproject/galaxy/compare/cb8f8322c85e...b68def3ebe7f **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9bc738: [18.05] Fix matches_any() checks for dynamic compr...
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 9bc73824a5419072b65158a09c0f6c30a9c5b3f0 https://github.com/galaxyproject/galaxy/commit/9bc73824a5419072b65158a09c0f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- [18.05] Fix matches_any() checks for dynamic compressed types. See huge conversation on #6093. Commit: 148d56a9c9d12df6d3d8fbe48a713f75cca6a468 https://github.com/galaxyproject/galaxy/commit/148d56a9c9d12df6d3d8fbe48a71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Many more matches_any tests, better categorization of them with comments. Some of these suggested by @nsoranzo. Commit: 8ca8ead4e592beb73ab92fa1324ee2060beb9188 https://github.com/galaxyproject/galaxy/commit/8ca8ead4e592beb73ab92fa1324e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A test/unit/datatypes/test_datatypes_registry.py Log Message: ----------- Merge pull request #6111 from jmchilton/dynamic_compressed_types_fix_4 [18.05] Fix matches_any() checks for dynamic compressed types. Compare: https://github.com/galaxyproject/galaxy/compare/b6a22584aaed...8ca8ead4e592 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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