- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] dd5996: CORS header for InterMine on Test
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd5996384aba954e30f1c9a05d711b4813a6897c https://github.com/galaxyproject/usegalaxy-playbook/commit/dd5996384aba954e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- CORS header for InterMine on Test **NOTE:** This service has 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/usegalaxy-playbook] f96ac0: CORS header for InterMine on Test
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/swarmscale-2.0 Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f96ac07e3c4319a8c1aa6d2a5036a4d080172488 https://github.com/galaxyproject/usegalaxy-playbook/commit/f96ac07e3c4319a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- CORS header for InterMine on Test **NOTE:** This service has 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] c2ab74: Add download option to workflow editor menu
by GitHub 14 Aug '18

14 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2ab74985148781f9a7eae16dec2fde89a0c154d https://github.com/galaxyproject/galaxy/commit/c2ab74985148781f9a7eae16dec2… Author: Anup Kumar <anup.rulez(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add download option to workflow editor menu Commit: 164a7d7f04be50e2ecd8edc64646a8e947680f4a https://github.com/galaxyproject/galaxy/commit/164a7d7f04be50e2ecd8edc64646… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-14 (Tue, 14 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6596 from bgruening/export_wf_galaxy_wf_editor Add download option to workflow editor menu Compare: https://github.com/galaxyproject/galaxy/compare/3d0763f71c79...164a7d7f04be **NOTE:** This service has 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] 00e8d4: Quote Filter1 input and output
by GitHub 13 Aug '18

13 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 00e8d4ee76c65652e6a0b208f44d957c79db40b1 https://github.com/galaxyproject/galaxy/commit/00e8d4ee76c65652e6a0b208f44d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- Quote Filter1 input and output Commit: 819ee07af36d10734b32474fa832ce9e09e1b376 https://github.com/galaxyproject/galaxy/commit/819ee07af36d10734b32474fa832… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Respect unavilable peek when serializing HDA Also call display_peek() just once. That fixes the following exception that occurs when running the Filter1 tool through the API: ``` galaxy.datatypes.tabular ERROR 2018-08-12 22:53:42,939 make_html_peek_rows failed on HDA 64 Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 186, in make_html_peek_rows dataset.set_peek() File "/Users/mvandenb/src/galaxy/lib/galaxy/model/__init__.py", line 2264, in set_peek return self.datatype.set_peek(self) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/tabular.py", line 57, in set_peek super(TabularData, self).set_peek(dataset, line_count=line_count, WIDTH=WIDTH, skipchars=skipchars, line_wrap=False) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 813, in set_peek dataset.peek = get_file_peek(dataset.file_name, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap) File "/Users/mvandenb/src/galaxy/lib/galaxy/datatypes/data.py", line 1029, in get_file_peek with compression_utils.get_fileobj(file_name, "U") as temp: File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 29, in get_fileobj return get_fileobj_raw(filename, mode, compressed_formats)[1] File "/Users/mvandenb/src/galaxy/lib/galaxy/util/compression_utils.py", line 58, in get_fileobj_raw return compressed_format, io.open(filename, mode, encoding='utf-8') FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpan_4qaow/tmpfzus9jhv/tmplqjtbp5c/database/files/000/dataset_40.dat' ``` This is because we serialize the HDA just after the job has been created, meaning the file may not exist yet. Commit: f4343d876f13e55e92ca228582b4430dcd01e4aa https://github.com/galaxyproject/galaxy/commit/f4343d876f13e55e92ca228582b4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Clarify set_peek setting when finishing job Commit: 3d0763f71c795549e6c133f2734cf7ae5337c296 https://github.com/galaxyproject/galaxy/commit/3d0763f71c795549e6c133f2734c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M tools/stats/filtering.xml Log Message: ----------- Merge pull request #6594 from mvdbeek/respect_unavailable_display_peek Respect unavailable display peek Compare: https://github.com/galaxyproject/galaxy/compare/e853762fdbb2...3d0763f71c79 **NOTE:** This service has 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] 07d415: Show workflow parameters in worklfow editor below ...
by GitHub 13 Aug '18

13 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07d41517460eedf514071cd1b66c7d958ad23037 https://github.com/galaxyproject/galaxy/commit/07d41517460eedf514071cd1b66c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Show workflow parameters in worklfow editor below title header Commit: 4550a7152c1be518effac678b807da9748b997eb https://github.com/galaxyproject/galaxy/commit/4550a7152c1be518effac678b807… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Workflow parameter positioning tweaks, keeps display to the right and minimally large. Commit: e853762fdbb20c7d9396223f17b2cd728d29dd68 https://github.com/galaxyproject/galaxy/commit/e853762fdbb20c7d9396223f17b2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-13 (Mon, 13 Aug 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6592 from guerler/fix_workflow_parameters Resolve overlap of workflow parameter container with gear-icon in editor header Compare: https://github.com/galaxyproject/galaxy/compare/0b1d804cf675...e853762fdbb2 **NOTE:** This service has 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] e3435e: Remove backbone thumbnail element
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3435eb23d62815f5a08aca7dbaf68991b05ab60 https://github.com/galaxyproject/galaxy/commit/e3435eb23d62815f5a08aca7dbaf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Remove backbone thumbnail element Commit: 03702d0a61733682cd80ee3d4849cd094c00d0d1 https://github.com/galaxyproject/galaxy/commit/03702d0a61733682cd80ee3d4849… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Remove unused thumbnail styles Commit: 0b1d804cf675fb47f4132363f32b27680becbdf8 https://github.com/galaxyproject/galaxy/commit/0b1d804cf675fb47f4132363f32b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M client/galaxy/scripts/components/PluginList.vue R client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/qunit/tests/ui_tests.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6587 from guerler/remove_bb_thumbnail Remove backbone version of thumbnail element Compare: https://github.com/galaxyproject/galaxy/compare/0ea1430136c5...0b1d804cf675 **NOTE:** This service has 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] 1d0f51: Fix upload file selector value resetting
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Fix upload file selector value resetting Fix Commit: f992980d458edeebc0501ac036c2ee5c6fba7989 https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M client/galaxy/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6573 from guerler/fix_upload_naming [18.05] Fix upload file selector value resetting Commit: ec60327f983ced46fa2a8489c359100960b72d5b https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Client rebuild to include uploadbox value fix in release branch. Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183 https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #6574 from dannon/release_18.05 [18.05] Client rebuild to include uploadbox value fix in release branch. Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Commit: 0ea1430136c51c5558f17e4a051e8d1a58009fd3 https://github.com/galaxyproject/galaxy/commit/0ea1430136c51c5558f17e4a051e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9910ea47d9b3...0ea1430136c5 **NOTE:** This service has 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] 2f8708: Use object store to check for existence of extra_f...
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2f87087ba2a88d71d539f888401d79167997a4ea https://github.com/galaxyproject/galaxy/commit/2f87087ba2a88d71d539f888401d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Use object store to check for existence of extra_files_path This should fix https://github.com/galaxyproject/galaxy/issues/6585 Commit: 1ddaf4a64d6307fd477653d3bba7353a30e88eb2 https://github.com/galaxyproject/galaxy/commit/1ddaf4a64d6307fd477653d3bba7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #6588 from mvdbeek/extra_path_nested_object_store_issue [18.05] Use object store to check for existence of extra_files_path Compare: https://github.com/galaxyproject/galaxy/compare/d7398672a1a3...1ddaf4a64d63 **NOTE:** This service has 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] 4d1ce0: Cancel jobs when exiting test_history decorator.
by GitHub 10 Aug '18

10 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d1ce0f431d337a45964eee3aa3813be1f4e41c6 https://github.com/galaxyproject/galaxy/commit/4d1ce0f431d337a45964eee3aa38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Cancel jobs when exiting test_history decorator. Should reduce the probability of a test interferring with other tests. Commit: 136255c0ad7a2aca6584f4c1fa3d10ea5e4a632e https://github.com/galaxyproject/galaxy/commit/136255c0ad7a2aca6584f4c1fa3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M run_tests.sh M test/base/populators.py Log Message: ----------- Allow test_history context to annotate whether new histories are needed by test. Usually tests should have new histories but we should still capture this information so we can target tests are particular histories for debugging interactively and so we could potentially reduce the number of new histories created when testing remote Galaxies (there have been complaints about this in the past). Commit: 36e1d6cfce946b46f5904af3cc924cb0f21970ee https://github.com/galaxyproject/galaxy/commit/36e1d6cfce946b46f5904af3cc92… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-09 (Thu, 09 Aug 2018) Changed paths: M test/api/test_tools.py M test/base/populators.py Log Message: ----------- More use of test_history contextmanager in test_tools. Commit: 9910ea47d9b353fe61fc510469a0599210009a25 https://github.com/galaxyproject/galaxy/commit/9910ea47d9b353fe61fc510469a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M run_tests.sh M test/api/test_tools.py M test/base/populators.py M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #6586 from jmchilton/toward_test_history_cleaning Smarter Test Histories (Part I) Compare: https://github.com/galaxyproject/galaxy/compare/5d85c32da243...9910ea47d9b3 **NOTE:** This service has 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] 38e581: Redirect unindentifed routes in admin panel
by GitHub 08 Aug '18

08 Aug '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38e5816b06d0804324dfe2a9c642859d990cfdb9 https://github.com/galaxyproject/galaxy/commit/38e5816b06d0804324dfe2a9c642… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-07-28 (Sat, 28 Jul 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Redirect unindentifed routes in admin panel Fix Commit: af755a098061f8db55db5ecc398c3410f180f9e1 https://github.com/galaxyproject/galaxy/commit/af755a098061f8db55db5ecc398c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-08-02 (Thu, 02 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Minor import cleanup, formatting. Commit: 4072d68e0d6d182a4249df143ab4fcba3e8f35cf https://github.com/galaxyproject/galaxy/commit/4072d68e0d6d182a4249df143ab4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Redirect without using backbone Commit: 5d85c32da24396a4853d09cf5fccb12481f1ccee https://github.com/galaxyproject/galaxy/commit/5d85c32da24396a4853d09cf5fcc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge pull request #6551 from guerler/fix_admin_routes Redirect unidentified routes in admin panel Compare: https://github.com/galaxyproject/galaxy/compare/75e50d3fdd98...5d85c32da243 **NOTE:** This service has 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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