- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 98a189: Fix warning message formatting in sharing controller
by Nicola Soranzo 11 Mar '19

11 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 98a189ceff8e0fd329acfbb4fdec585d85317e95 https://github.com/galaxyproject/galaxy/commit/98a189ceff8e0fd329acfbb4fdec… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Fix warning message formatting in sharing controller Reported by @erasche in https://github.com/galaxyproject/galaxy/issues/7503#issuecomment-471496500, broken in https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Commit: 7b316215f4d4653c11d5a421002255ed6f43d944 https://github.com/galaxyproject/galaxy/commit/7b316215f4d4653c11d5a4210022… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #7504 from mvdbeek/logging_fix [18.09] Fix warning message formatting in sharing controller Compare: https://github.com/galaxyproject/galaxy/compare/8e125b769879...7b316215f4d4

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[galaxyproject/galaxy] 1d0e4b: New, portable metadata generation.
by John Chilton 11 Mar '19

11 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1d0e4bcb2cd4eb47ef0a5c1d6027f25547292b06 https://github.com/galaxyproject/galaxy/commit/1d0e4bcb2cd4eb47ef0a5c1d6027… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M test/unit/tools/test_metadata.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- New, portable metadata generation. Variant of external metadata generation that doesn't use command-line arguments or absolute paths and simply takes operates on the current, job working directory and knows what to do. - Uses relative paths allowing the directory to be staged elsewhere via Pulsar, Condor, or Docker for instance. - Avoids DB objects for hard-coded paths making everything more robust. - Avoids huge command-lines which for huge collection reduction jobs might hit system limits for command-line length. - Uses JSON dicts to communicate parameters - meaning we can avoid awkward argument parsing as this evolves (see old max_metadata_value_size handling in set_metadata.py for instance). - Uses output names instead of database IDs to key files - so file naming is consistent and human readable. Commit: 17cb35bc25b2b7a9338d23d65d3cbaa8870c93bb https://github.com/galaxyproject/galaxy/commit/17cb35bc25b2b7a9338d23d65d3c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/tools/provided_metadata.py A lib/galaxy_ext/metadata/_provided_metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Use ToolProvidedMetadata abstraction in set_metadata. There is are somethings that happen in set_metadata.py that assume the old style galaxy.json. This sets the stage for proper external metadata collection of newer style galaxy.json files. Commit: 395380fc66c76dbbc49ef8f99792c17c23e5e3ba https://github.com/galaxyproject/galaxy/commit/395380fc66c76dbbc49ef8f99792… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/tools/provided_metadata.py Log Message: ----------- Fix: Handle galaxy.json entries without dataset_id in galaxy.json. Commit: e7676868162497df4cdf35f86bc4afa31c2f8267 https://github.com/galaxyproject/galaxy/commit/e7676868162497df4cdf35f86bc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy/metadata/__init__.py Log Message: ----------- Better I/O in metadata package. Commit: f0912eb4040185df5a11cff1c7e1865a6b18f33f https://github.com/galaxyproject/galaxy/commit/f0912eb4040185df5a11cff1c7e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix set_metadata executing from wrong directory when using tool. Commit: 1ca256aaba84fb101f144c67447363435ec44622 https://github.com/galaxyproject/galaxy/commit/1ca256aaba84fb101f144c674473… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-11 (Mon, 11 Mar 2019) Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/__init__.py M lib/galaxy/metadata/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/provided_metadata.py A lib/galaxy_ext/metadata/_provided_metadata.py M lib/galaxy_ext/metadata/set_metadata.py M test/unit/tools/test_metadata.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #7470 from jmchilton/portable_metadata Implement portable metadata generation. Compare: https://github.com/galaxyproject/galaxy/compare/417292b5013b...1ca256aaba84

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[galaxyproject/galaxy] 1a636c: Fix HiddenParameter use
by Nicola Soranzo 10 Mar '19

10 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a636c376fe7fbdaa0ead866989ddfbf0ed7e943 https://github.com/galaxyproject/galaxy/commit/1a636c376fe7fbdaa0ead866989d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix HiddenParameter use Broken in https://github.com/galaxyproject/galaxy/commit/dd8d74f364770a1272555a3753f5… Fixes https://github.com/galaxyproject/galaxy/issues/7454 Commit: 76be1263cac3ed5f7954e451693352d7276e69a7 https://github.com/galaxyproject/galaxy/commit/76be1263cac3ed5f7954e4516933… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test that workflows with hidden params can be run Commit: b5bbdfd89fc64796a2049ffd2f3f4d568afbd7f3 https://github.com/galaxyproject/galaxy/commit/b5bbdfd89fc64796a2049ffd2f3f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-04 (Mon, 04 Mar 2019) Changed paths: M run_tests.sh Log Message: ----------- Also use correct image Commit: 9c711e7efabafbd13c0f35f6ec348a32c3a115dd https://github.com/galaxyproject/galaxy/commit/9c711e7efabafbd13c0f35f6ec34… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/workflow/modules.py M run_tests.sh M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #7458 from mvdbeek/fix_broken_hidden_parameter [19.01] Fix hidden parameter use in workflows Commit: c1a9095ad4fa37c5ca729b6f900d4aaca09496cc https://github.com/galaxyproject/galaxy/commit/c1a9095ad4fa37c5ca729b6f900d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 Commit: 0ab05b3ce69e69f9ea865a9aae596ac5e36ebc71 https://github.com/galaxyproject/galaxy/commit/0ab05b3ce69e69f9ea865a9aae59… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins Commit: 8e125b76987914ae48616cc1d8594b8e94a414cb https://github.com/galaxyproject/galaxy/commit/8e125b76987914ae48616cc1d859… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: aef53f6cde6feaea9443ea341304f966b7847a7e https://github.com/galaxyproject/galaxy/commit/aef53f6cde6feaea9443ea341304… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: 417292b5013b3b6b4d57a15b3567d08288733f9f https://github.com/galaxyproject/galaxy/commit/417292b5013b3b6b4d57a15b3567… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py A test/functional/tools/hidden_param.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d4dadca145d9...417292b5013b

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[galaxyproject/galaxy] c1a909: Restrict loading of JSON files on the server via t...
by Nicola Soranzo 10 Mar '19

10 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: c1a9095ad4fa37c5ca729b6f900d4aaca09496cc https://github.com/galaxyproject/galaxy/commit/c1a9095ad4fa37c5ca729b6f900d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 Commit: 0ab05b3ce69e69f9ea865a9aae596ac5e36ebc71 https://github.com/galaxyproject/galaxy/commit/0ab05b3ce69e69f9ea865a9aae59… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins Commit: 8e125b76987914ae48616cc1d8594b8e94a414cb https://github.com/galaxyproject/galaxy/commit/8e125b76987914ae48616cc1d859… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: aef53f6cde6feaea9443ea341304f966b7847a7e https://github.com/galaxyproject/galaxy/commit/aef53f6cde6feaea9443ea341304… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/9c711e7efaba...aef53f6cde6f

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[galaxyproject/galaxy] c1a909: Restrict loading of JSON files on the server via t...
by Nicola Soranzo 10 Mar '19

10 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: c1a9095ad4fa37c5ca729b6f900d4aaca09496cc https://github.com/galaxyproject/galaxy/commit/c1a9095ad4fa37c5ca729b6f900d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 Commit: 0ab05b3ce69e69f9ea865a9aae596ac5e36ebc71 https://github.com/galaxyproject/galaxy/commit/0ab05b3ce69e69f9ea865a9aae59… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins Commit: 8e125b76987914ae48616cc1d8594b8e94a414cb https://github.com/galaxyproject/galaxy/commit/8e125b76987914ae48616cc1d859… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/996d7c9a60f0...8e125b769879

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[galaxyproject/galaxy] c1a909: Restrict loading of JSON files on the server via t...
by Dannon 10 Mar '19

10 Mar '19

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c1a9095ad4fa37c5ca729b6f900d4aaca09496cc https://github.com/galaxyproject/galaxy/commit/c1a9095ad4fa37c5ca729b6f900d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restrict loading of JSON files on the server via the workflow API to Galaxy admins Fix https://github.com/galaxyproject/security/issues/29 Commit: 0ab05b3ce69e69f9ea865a9aae596ac5e36ebc71 https://github.com/galaxyproject/galaxy/commit/0ab05b3ce69e69f9ea865a9aae59… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-10 (Sun, 10 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7499 from nsoranzo/release_18.05_fix_security_29 [18.05] Restrict loading of JSON files on the server via the workflow API to Galaxy admins Compare: https://github.com/galaxyproject/galaxy/compare/1529758ecb78...0ab05b3ce69e

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[galaxyproject/infrastructure-playbook] c6ed3c: Set the Mailman site owner address
by Nate Coraor 08 Mar '19

08 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c6ed3cefd38266a9391b664073915e561ebd0950 https://github.com/galaxyproject/infrastructure-playbook/commit/c6ed3cefd38… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M env/mailman/TODO.txt M env/mailman/group_vars/listservers/vars.yml Log Message: ----------- Set the Mailman site owner address

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[galaxyproject/galaxy] a28945: Update of tours overview according to #5860
by Dannon 08 Mar '19

08 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a289451b3ee2ca0050a75b522c2a87b893e14c32 https://github.com/galaxyproject/galaxy/commit/a289451b3ee2ca0050a75b522c2a… Author: Peter Selten <peter(a)ubuntu-base.localdomain> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Update of tours overview according to #5860 Commit: 4f160520eed0534b7e5877a0d93ad812d89830e7 https://github.com/galaxyproject/galaxy/commit/4f160520eed0534b7e5877a0d93a… Author: Peter Selten <peter(a)pselten.info> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Update of tours overview, all tags of a tour need to be disabled not to display the tour now Commit: cd25179f7c69f0d525573e5e704fbb53be121db2 https://github.com/galaxyproject/galaxy/commit/cd25179f7c69f0d525573e5e704f… Author: selten <selten(a)users.noreply.github.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Remove unused variable Commit: 10bef1ed229ab21565775c868431487883262b9a https://github.com/galaxyproject/galaxy/commit/10bef1ed229ab21565775c868431… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Client formatting/cleanup. Commit: d4dadca145d96c12af36446edf261a3bfd650c27 https://github.com/galaxyproject/galaxy/commit/d4dadca145d96c12af36446edf26… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Merge pull request #7478 from selten/tours-update Update of tours overview according to #5860 Compare: https://github.com/galaxyproject/galaxy/compare/27fa6abb63d9...d4dadca145d9

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[galaxyproject/infrastructure-playbook] 678020: Change Mailman superusers
by Nate Coraor 08 Mar '19

08 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6780203db8727ada47e9b8f0efd87949c53e6ff9 https://github.com/galaxyproject/infrastructure-playbook/commit/6780203db87… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vault.yml Log Message: ----------- Change Mailman superusers

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[galaxyproject/galaxy] 676cdf: Log exception in set_metadata.py.
by Martin Cech 08 Mar '19

08 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 676cdf7678704742629558e4c313b3447c393b83 https://github.com/galaxyproject/galaxy/commit/676cdf7678704742629558e4c313… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Log exception in set_metadata.py. We can finally do this as a result of #7095 I believe! Commit: 27fa6abb63d968014754c691c5ade991f1d44bc2 https://github.com/galaxyproject/galaxy/commit/27fa6abb63d968014754c691c5ad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7483 from jmchilton/set_meta_logging Log exception in set_metadata.py. Compare: https://github.com/galaxyproject/galaxy/compare/05d1cdcd6db1...27fa6abb63d9

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