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

[galaxyproject/galaxy] eed703: Fix share with another user in 18.05
by GitHub 19 Jun '18

19 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: eed703eef8b3884f70019070210633f0e033b39b https://github.com/galaxyproject/galaxy/commit/eed703eef8b3884f700190702106… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix share with another user in 18.05 Commit: 48fafa8096fd179e9c74c56bac7be9b042cbade8 https://github.com/galaxyproject/galaxy/commit/48fafa8096fd179e9c74c56bac7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Merge pull request #6358 from dannon/1805sharingfix [18.01] Fix 'share with another user' Compare: https://github.com/galaxyproject/galaxy/compare/470299a2ce6e...48fafa8096fd **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] 2b8b4e: grt - wrap every write in try-except
by GitHub 18 Jun '18

18 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2b8b4e198d4f4f498284017d1c9696cbec5f7cf0 https://github.com/galaxyproject/galaxy/commit/2b8b4e198d4f4f498284017d1c96… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- grt - wrap every write in try-except and just fail the row if the data is crap (like {NULL, SOH, STX, ETX} and friends) Commit: f21c8caf83f6b511de6bd5b78e1aa75326823c47 https://github.com/galaxyproject/galaxy/commit/f21c8caf83f6b511de6bd5b78e1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- unname the exception Commit: bde05ac88b66af597e9243d68b7ae8bb364e7653 https://github.com/galaxyproject/galaxy/commit/bde05ac88b66af597e9243d68b7a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6354 from martenson/superdefensive-grt [18.05] grt - wrap every write in try-except Compare: https://github.com/galaxyproject/galaxy/compare/e8beea0d60c1...bde05ac88b66 **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] 5a20ea: Add api/jobs/{job_id}/resume endpint
by GitHub 18 Jun '18

18 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a20ea2b41b16071830212eb77fb3f5c6671da3d https://github.com/galaxyproject/galaxy/commit/5a20ea2b41b16071830212eb77fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add api/jobs/{job_id}/resume endpint Commit: 90c091b5ab50347f3d43c62b8df8cb5c3365650e https://github.com/galaxyproject/galaxy/commit/90c091b5ab50347f3d43c62b8df8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M test/api/test_jobs.py Log Message: ----------- Add a test that exercises the new job resume API endpoint Commit: 1c7387c53a0bb1e80a989c5b11ae22c0aef57780 https://github.com/galaxyproject/galaxy/commit/1c7387c53a0bb1e80a989c5b11ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #6072 from mvdbeek/add_resume_job_api Add resume job api Compare: https://github.com/galaxyproject/galaxy/compare/e9efb47b5982...1c7387c53a0b **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] 676886: Fix non-strict tabular relabel operation
by GitHub 18 Jun '18

18 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 676886195d1fbe17cdff16af8acad6f5c2115ee1 https://github.com/galaxyproject/galaxy/commit/676886195d1fbe17cdff16af8aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix non-strict tabular relabel operation Commit: 3b3deb314f4a78684bea9707d2f0d856e306f006 https://github.com/galaxyproject/galaxy/commit/3b3deb314f4a78684bea9707d2f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Use strict mode when testing strict mode ... Commit: 470299a2ce6ef1e5d894a0247bd43f24fd463d41 https://github.com/galaxyproject/galaxy/commit/470299a2ce6ef1e5d894a0247bd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Merge pull request #6234 from mvdbeek/fix_relabel_non_strict [18.01] Fix non-strict tabular relabel operation Compare: https://github.com/galaxyproject/galaxy/compare/3707fb4eb128...470299a2ce6e **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] b9233b: Add specific datatype for CuffDiff SQLite database...
by GitHub 18 Jun '18

18 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b9233b282bc72f17b4db55264b768c1db52ac0fc https://github.com/galaxyproject/galaxy/commit/b9233b282bc72f17b4db55264b76… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add specific datatype for CuffDiff SQLite database. Commit: 887bf8c07c7fbfad935d2955ee1bfd1589d6f43a https://github.com/galaxyproject/galaxy/commit/887bf8c07c7fbfad935d2955ee1b… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Properly store metadata for cuffdiff.sqlite datatype. Commit: e9efb47b59823eb97caaf1d8ec2911e08536534e https://github.com/galaxyproject/galaxy/commit/e9efb47b59823eb97caaf1d8ec29… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6302 from davebx/cuffdiff_datatype Add specific datatype for CuffDiff SQLite database. Compare: https://github.com/galaxyproject/galaxy/compare/6e02c9aff765...e9efb47b5982 **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] 3a17db: Backbone model url fixes (urlRoot isn't necessary ...
by GitHub 17 Jun '18

17 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3a17db8f205f57902b35b2245c8367802beb5faa https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things Convert history-contents urlroot to instance var remove outdated comment Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7 https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Rebuild client w/ maps. Commit: c2307f3f1aae8f46fd1023accdf0a6c1c435eba3 https://github.com/galaxyproject/galaxy/commit/c2307f3f1aae8f46fd1023accdf0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added missing level fatal_oom to xsd Commit: 8d75a67386f72814c17ad1abef5d0154b247a521 https://github.com/galaxyproject/galaxy/commit/8d75a67386f72814c17ad1abef5d… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- also added missing documentation Commit: fc47618f6798d48f3ab903a8ea6231067bf0fed2 https://github.com/galaxyproject/galaxy/commit/fc47618f6798d48f3ab903a8ea62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: A scripts/plugin_staging.py Log Message: ----------- Initial python-based plugin staging. to be used from common startup. Commit: e110489cc55f25b7d5ec7b9e5cbc5d914215b806 https://github.com/galaxyproject/galaxy/commit/e110489cc55f25b7d5ec7b9e5cbc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently) Commit: 9ac0161891a92db7a359e13a74e831ec17a79317 https://github.com/galaxyproject/galaxy/commit/9ac0161891a92db7a359e13a74e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update description for installing pbs-python Commit: 370ea25d2c58b7e55f6bc062062e9a962a08ea7d https://github.com/galaxyproject/galaxy/commit/370ea25d2c58b7e55f6bc062062e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Minor refactoring, comments. Commit: 8364ebebcd81b6f8bf6c1122e5271a5c5eb23868 https://github.com/galaxyproject/galaxy/commit/8364ebebcd81b6f8bf6c1122e527… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink Commit: 4cdd210bb27cd1c271e69c8dfd46585f0c232ef9 https://github.com/galaxyproject/galaxy/commit/4cdd210bb27cd1c271e69c8dfd46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Use os.pardir instead of ../. Thanks @nsoranzo Commit: 37ad1a8bdce963b4152331685e3755a60777e633 https://github.com/galaxyproject/galaxy/commit/37ad1a8bdce963b4152331685e37… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #6345 from mvdbeek/update_pbs_python_doc [18.01] Update description for installing pbs-python Commit: cddee94e4bb043381433030e34f3f9129382830f https://github.com/galaxyproject/galaxy/commit/cddee94e4bb043381433030e34f3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Small fixes Commit: 12a05c782099da0eb846069fe96355fb50212fef https://github.com/galaxyproject/galaxy/commit/12a05c782099da0eb846069fe963… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/common_startup.sh M scripts/get_uwsgi_args.py A scripts/plugin_staging.py Log Message: ----------- Merge pull request #6344 from dannon/python_static_staging [18.05] Visualization static staging Commit: a2ff5efbce3023b12a774600b331867d7320898a https://github.com/galaxyproject/galaxy/commit/a2ff5efbce3023b12a774600b331… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-16 (Sat, 16 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6341 from bernt-matthias/release_18.05_fix_xsd [18.05] Added missing level fatal_oom to xsd Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #6336 from dannon/backport_url_fix_flattened [18.01] Backport backbone url fixes (flattened) Commit: e8beea0d60c1a4b88b67cc3f176e11ae76215f67 https://github.com/galaxyproject/galaxy/commit/e8beea0d60c1a4b88b67cc3f176e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 6e02c9aff7650f6dad05ff18683ac19b10648ee4 https://github.com/galaxyproject/galaxy/commit/6e02c9aff7650f6dad05ff18683a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M doc/source/admin/cluster.md M lib/galaxy/tools/xsd/galaxy.xsd M scripts/common_startup.sh M scripts/get_uwsgi_args.py A scripts/plugin_staging.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/02974b79c7a9...6e02c9aff765 **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] 3a17db: Backbone model url fixes (urlRoot isn't necessary ...
by GitHub 17 Jun '18

17 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 3a17db8f205f57902b35b2245c8367802beb5faa https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things Convert history-contents urlroot to instance var remove outdated comment Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7 https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Rebuild client w/ maps. Commit: 9ac0161891a92db7a359e13a74e831ec17a79317 https://github.com/galaxyproject/galaxy/commit/9ac0161891a92db7a359e13a74e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update description for installing pbs-python Commit: 37ad1a8bdce963b4152331685e3755a60777e633 https://github.com/galaxyproject/galaxy/commit/37ad1a8bdce963b4152331685e37… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #6345 from mvdbeek/update_pbs_python_doc [18.01] Update description for installing pbs-python Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #6336 from dannon/backport_url_fix_flattened [18.01] Backport backbone url fixes (flattened) Commit: e8beea0d60c1a4b88b67cc3f176e11ae76215f67 https://github.com/galaxyproject/galaxy/commit/e8beea0d60c1a4b88b67cc3f176e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/a2ff5efbce30...e8beea0d60c1 **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] 3a17db: Backbone model url fixes (urlRoot isn't necessary ...
by GitHub 17 Jun '18

17 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 3a17db8f205f57902b35b2245c8367802beb5faa https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things Convert history-contents urlroot to instance var remove outdated comment Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7 https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Rebuild client w/ maps. Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #6336 from dannon/backport_url_fix_flattened [18.01] Backport backbone url fixes (flattened) Compare: https://github.com/galaxyproject/galaxy/compare/37ad1a8bdce9...3707fb4eb128 **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] 7c8ac3: Add a condition to FilterFailedDatasetsTool to rem...
by GitHub 17 Jun '18

17 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c8ac3ed7209d6076dad937ef0e390d7b95c0fa8 https://github.com/galaxyproject/galaxy/commit/7c8ac3ed7209d6076dad937ef0e3… Author: Mataivic <victor.mataigne(a)wanadoo.fr> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add a condition to FilterFailedDatasetsTool to remove empty files Hello, Here is an extra-condition for the tool ``FilterFailedDatasetsTool`` to allow it to remove empty datasets as well as failed datasets in a collection. I tested it on my data and it seems to work fine. Since it's my first time looking at galaxy's source code, I don't know if there is a proper way to do that ... And I didn't make the improvement for paired datasets because I don't have proper data to test it. But I assume it would be something like ``if forward_o.is_ok and reverse_o.is_ok and forward_o.has_data() and reverse_o.has_data():`` ? Commit: b27281aaedbf0dc26c8d577d20168e8592bdfc9c https://github.com/galaxyproject/galaxy/commit/b27281aaedbf0dc26c8d577d2016… Author: Mataivic <victor.mataigne(a)wanadoo.fr> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- improved filtering of empty files in a collection (1) - Supplemental parameter : 'remove_empty' which allow the user to choose if he/she wants to keep or not empty files in the collection. - Coming next : the modified wrapper. (Edited directly on GitHub). Commit: f4ec64a0057c81a62baf3874e3ac726f89fa86ac https://github.com/galaxyproject/galaxy/commit/f4ec64a0057c81a62baf3874e3ac… Author: Mataivic <victor.mataigne(a)wanadoo.fr> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- modified wrapper filter_failed_collection - Supplemental 'select' parameter : 'remove_empty' Commit: 7c87dfdffda17b2cc6878e3a7dba9da9a70da45b https://github.com/galaxyproject/galaxy/commit/7c87dfdffda17b2cc6878e3a7dba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Simplify and modularize FilterFailedDatasetsTool class Commit: 8a4d18fba160aed43e15d2852093d6f8ded96dc9 https://github.com/galaxyproject/galaxy/commit/8a4d18fba160aed43e15d2852093… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_empty_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add filter empty collection tool I think having a separate tool for this task makes sense and makes the distinction between empty and fialed datasets clearer. Commit: babe2e5cc58502d9d0ba33fbd1ec0caf7a1c2b56 https://github.com/galaxyproject/galaxy/commit/babe2e5cc58502d9d0ba33fbd1ec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Change get_new_elements to _get_new_elements And use same order for arguments in signature and caller. Commit: 46d8b318baac455ac3ff4c5782cfd9f6718e55bc https://github.com/galaxyproject/galaxy/commit/46d8b318baac455ac3ff4c5782cf… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Correct help text of filter_failed_collection and filter_empty_collection tools Commit: 0507818bbe3c712b506045458702122293780741 https://github.com/galaxyproject/galaxy/commit/0507818bbe3c712b506045458702… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Add tests for filtering list:pair and list:list:pair collections Commit: 5992629619a39408f9e8a3082de96f1d73592f7c https://github.com/galaxyproject/galaxy/commit/5992629619a39408f9e8a3082de9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Map over list or list:paired collection in filter collection tools Commit: 72dd53f55e7ae8ad3a18278da88cc800d7f6572e https://github.com/galaxyproject/galaxy/commit/72dd53f55e7ae8ad3a18278da88c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update comments to the fact that we're processing list or list:paired collections Commit: 02974b79c7a9d9cbe45b8ad08d7a532c11fcbe0b https://github.com/galaxyproject/galaxy/commit/02974b79c7a9d9cbe45b8ad08d7a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml M test/api/test_tools.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5640 from Mataivic/patch-1 Add a FilterEmptyDatasetsTool and allow filtering tools to apply to arbitrary collection structures Compare: https://github.com/galaxyproject/galaxy/compare/db11a2549d33...02974b79c7a9 **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] c2307f: added missing level fatal_oom to xsd
by GitHub 16 Jun '18

16 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c2307f3f1aae8f46fd1023accdf0a6c1c435eba3 https://github.com/galaxyproject/galaxy/commit/c2307f3f1aae8f46fd1023accdf0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added missing level fatal_oom to xsd Commit: 8d75a67386f72814c17ad1abef5d0154b247a521 https://github.com/galaxyproject/galaxy/commit/8d75a67386f72814c17ad1abef5d… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- also added missing documentation Commit: cddee94e4bb043381433030e34f3f9129382830f https://github.com/galaxyproject/galaxy/commit/cddee94e4bb043381433030e34f3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Small fixes Commit: a2ff5efbce3023b12a774600b331867d7320898a https://github.com/galaxyproject/galaxy/commit/a2ff5efbce3023b12a774600b331… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-16 (Sat, 16 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6341 from bernt-matthias/release_18.05_fix_xsd [18.05] Added missing level fatal_oom to xsd Compare: https://github.com/galaxyproject/galaxy/compare/12a05c782099...a2ff5efbce30 **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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