March 2019 - galaxy-commits - lists.galaxyproject.org

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[galaxyproject/galaxy] 64b461: Update Platform LSF to Spectrum LSF
by Nicola Soranzo 08 Mar '19

08 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 64b461eac80d9e8ee8fc62a48db541f7ead1754f https://github.com/galaxyproject/galaxy/commit/64b461eac80d9e8ee8fc62a48db5… Author: Peter Selten <peter(a)pselten.info> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update Platform LSF to Spectrum LSF Commit: 844839f028273d213573378d8d7b90b8e6901585 https://github.com/galaxyproject/galaxy/commit/844839f028273d213573378d8d7b… Author: Peter Selten <peter(a)pselten.info> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update CLIJobRunner to ShellJobRunner according to #7433 Commit: 05d1cdcd6db18813ffbc1a5e19b47e40a32edda0 https://github.com/galaxyproject/galaxy/commit/05d1cdcd6db18813ffbc1a5e19b4… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #7486 from selten/doc-LSF-upgrade Update Platform LSF to Spectrum LSF Compare: https://github.com/galaxyproject/galaxy/compare/c714b6e66500...05d1cdcd6db1

1 0

[galaxyproject/infrastructure-playbook] d84727: Use X-Forwarded-Hosts to fix FILTER_VHOST
by Nate Coraor 08 Mar '19

08 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d847272935ace7d566fa2b0e805de32b0c3ce29a https://github.com/galaxyproject/infrastructure-playbook/commit/d847272935a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml Log Message: ----------- Use X-Forwarded-Hosts to fix FILTER_VHOST Commit: d43fefe0c51923a4711c638b5a9e0b66f5bc3c0c https://github.com/galaxyproject/infrastructure-playbook/commit/d43fefe0c51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-03-08 (Fri, 08 Mar 2019) Changed paths: M env/galaxy/inventory M env/galaxy/playbook.yml M env/galaxy/templates/nginx/lists.j2 M env/mailman/TODO.txt M env/mailman/group_vars/listservers/vars.yml M env/mailman/listservers.yml M env/mailman/templates/nginx/mailman_ssl.j2 M roles/postfix/templates/main.cf.j2 Log Message: ----------- Mailman 3 is live Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a950a46bf8…

1 0

[galaxyproject/galaxy] 19816f: Add a validator that ensures one metadata is betwe...
by Martin Cech 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19816f2c25777805bbb3bb7406f36a1fe4fbdb52 https://github.com/galaxyproject/galaxy/commit/19816f2c25777805bbb3bb7406f3… Author: Fabien Mareuil <fmareuil(a)pasteur.fr> Date: 2019-01-31 (Thu, 31 Jan 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Add a validator that ensures one metadata is between min and max values Commit: 1ef8e0afe1e743ad514e176490e709b63ce10620 https://github.com/galaxyproject/galaxy/commit/1ef8e0afe1e743ad514e176490e7… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-02-01 (Fri, 01 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Update validation.py pylint correction Commit: f6bc62dbd26a4633f153ee13ea34f9b50f0548de https://github.com/galaxyproject/galaxy/commit/f6bc62dbd26a4633f153ee13ea34… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-02-05 (Tue, 05 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Update validation.py tool_data_table_conf is not required Commit: 531f4f8d9fd0977f3958afb919f8abba40fe9f8a https://github.com/galaxyproject/galaxy/commit/531f4f8d9fd0977f3958afb919f8… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-02-07 (Thu, 07 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Update validation.py Bug fix: raise an error if metadata is missing Commit: 05481d57a13fd5e791ae314a1af21bf1aab002a4 https://github.com/galaxyproject/galaxy/commit/05481d57a13fd5e791ae314a1af2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Add tool test for metadata_in_range Reduce copy and paste by inheriting from InRangeValidator and add new validator to xsd schema. Commit: f0066ca19414ee625eb4a11a5b4901ce0994a4d7 https://github.com/galaxyproject/galaxy/commit/f0066ca19414ee625eb4a11a5b49… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Merge pull request #1 from mvdbeek/fmareuil-dev Add tool test for metadata_in_range Commit: 8212f5d57d1227ee9bbfd85f12c141705abcb961 https://github.com/galaxyproject/galaxy/commit/8212f5d57d1227ee9bbfd85f12c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-05 (Tue, 05 Mar 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Fix test tool label and tool xsd Commit: b8c5ee37680f166246d247bbf06e1800e4d8310b https://github.com/galaxyproject/galaxy/commit/b8c5ee37680f166246d247bbf06e… Author: fmareuil <fmareuil(a)pasteur.fr> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Merge pull request #2 from mvdbeek/fmareuil-dev Fix test tool label and tool xsd Commit: c714b6e665003cc693f6dcc844032fd1c58d851e https://github.com/galaxyproject/galaxy/commit/c714b6e665003cc693f6dcc84403… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_metadata_in_range.xml Log Message: ----------- Merge pull request #7288 from fmareuil/dev Add a validator that ensures one metadata is between min and max values Compare: https://github.com/galaxyproject/galaxy/compare/192a091d1655...c714b6e66500

1 0

[galaxyproject/galaxy] 4bcd46: Show an exception message if authentication has fa...
by John Chilton 07 Mar '19

07 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4bcd46acf55897c2b56b470b1dddcd59f756093f https://github.com/galaxyproject/galaxy/commit/4bcd46acf55897c2b56b470b1ddd… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Show an exception message if authentication has failed. Commit: 56b36cb4b51432796ac32d3819795a66b1bd8af4 https://github.com/galaxyproject/galaxy/commit/56b36cb4b51432796ac32d381979… Author: vahid <jalili.vahid(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/authnz/managers.py Log Message: ----------- Correctly report the unrecognized provider name. Commit: 192a091d16552fae610eef9df8f821afb04a6594 https://github.com/galaxyproject/galaxy/commit/192a091d16552fae610eef9df8f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-07 (Thu, 07 Mar 2019) Changed paths: M lib/galaxy/authnz/managers.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #7442 from VJalili/upgrade_psa Inform users if an exception has happened authenticating via OIDC Compare: https://github.com/galaxyproject/galaxy/compare/a10813a4f8c8...192a091d1655

1 0