- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 02c779: [16.01] Backport uwsgi fix from #2836.
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4345d8e7d7a3f27a46b6a06ce54637b74951915a https://github.com/galaxyproject/galaxy/commit/4345d8e7d7a3f27a46b6a06ce546… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/config.py Compare: https://github.com/galaxyproject/galaxy/compare/5a39d47b0add...4345d8e7d7a3

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[galaxyproject/galaxy] 02c779: [16.01] Backport uwsgi fix from #2836.
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Commit: dad5563cac852971776d6670c8401b0cb6a2ce6a https://github.com/galaxyproject/galaxy/commit/dad5563cac852971776d6670c840… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/2528a89bd087...dad5563cac85

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[galaxyproject/galaxy] 02c779: [16.01] Backport uwsgi fix from #2836.
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 02c77929852d99ed837e0599140d2b3f40d89767 https://github.com/galaxyproject/galaxy/commit/02c77929852d99ed837e0599140d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- [16.01] Backport uwsgi fix from #2836. Now that newer releases require a library that the mere presence of breaks an older version of Galaxy, I think this will be encountered more during development. It is breaking Planemo's ability to switch between different versions of Galaxy. https://github.com/galaxyproject/galaxy/pull/2836 Commit: 2207e7f8aa20702fd3074fec63977520d3213299 https://github.com/galaxyproject/galaxy/commit/2207e7f8aa20702fd3074fec6397… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #4565 from jmchilton/backport_uwsgi_fix [16.01] Backport uwsgi fix from #2836. Compare: https://github.com/galaxyproject/galaxy/compare/4c07734f5745...2207e7f8aa20

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[galaxyproject/galaxy] b12d29: improve docs and access checks
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b12d29d14b64ce9aa267f1e1a9dd7a452ecf6270 https://github.com/galaxyproject/galaxy/commit/b12d29d14b64ce9aa267f1e1a9dd… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- improve docs and access checks thanks @nsoranzo Commit: f78eca89126f8f35062541d201af4a85c602808e https://github.com/galaxyproject/galaxy/commit/f78eca89126f8f35062541d201af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/library_datasets.py Log Message: ----------- remove unused import Commit: 37802abee2b545a2524ef10b8ebaa628a03681fa https://github.com/galaxyproject/galaxy/commit/37802abee2b545a2524ef10b8eba… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #4560 from martenson/improving-datalibraries improve docs and access checks in datalibs manager/api Compare: https://github.com/galaxyproject/galaxy/compare/486f436e76b0...37802abee2b5

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[galaxyproject/galaxy] 46c85f: Allow working with pbzip2 compressed files
by GitHub 06 Sep '17

06 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46c85ffa986ec2211bbda7be4f90ab579d3fff69 https://github.com/galaxyproject/galaxy/commit/46c85ffa986ec2211bbda7be4f90… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/commit_util.py M tools/data_source/upload.py Log Message: ----------- Allow working with pbzip2 compressed files This adds supprt for uploading and uncompressing pbzip2 compressed files by exchanging the bz2 module with bz2file (recommended as workaround in https://docs.python.org/2/library/bz2.html) The problem was reported by @alpapan in #4538 and this commit should fix #4538. Depends on https://github.com/galaxyproject/starforge/pull/147 for the bz2file wheel. Commit: 4de0ec59f396868c5b56fb139929672c5ac8c3cd https://github.com/galaxyproject/galaxy/commit/4de0ec59f396868c5b56fb139929… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add bz2file to list of requirements Commit: cccf79ac5f1d4ef8dcd6d66585b5cc7966847bca https://github.com/galaxyproject/galaxy/commit/cccf79ac5f1d4ef8dcd6d66585b5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/commit_util.py M tools/data_source/upload.py Log Message: ----------- Make bz2file dependency conditional on python being below version 3.3 Commit: 8c4716e71d600711021041fc31bc8b02972c24c4 https://github.com/galaxyproject/galaxy/commit/8c4716e71d600711021041fc31bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Use environment markers to select bz2file when python is < 3.3 Commit: 486f436e76b0d3c67514a0d676a85002e5b82f1e https://github.com/galaxyproject/galaxy/commit/486f436e76b0d3c67514a0d676a8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/tool_shed/util/commit_util.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #4559 from mvdbeek/use_bzip2file Allow working with pbzip2 compressed files Compare: https://github.com/galaxyproject/galaxy/compare/3aacbdffd63c...486f436e76b0

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[galaxyproject/galaxy] 4071fb: allow linking, posix and spaces conversions
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4071fb65c3a8ee83dad2d45fa33c76a787ed3842 https://github.com/galaxyproject/galaxy/commit/4071fb65c3a8ee83dad2d45fa33c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- allow linking, posix and spaces conversions closes #2977 Commit: 63392a61071b89d699f26f06d036d7b42a235ff7 https://github.com/galaxyproject/galaxy/commit/63392a61071b89d699f26f06d036… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix copypasta Commit: 3aacbdffd63c4e6a0570b3144082edffdcad175a https://github.com/galaxyproject/galaxy/commit/3aacbdffd63c4e6a0570b3144082… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4547 from martenson/library-import-conversions allow linking, posix and spaces conversions in datalib imports Compare: https://github.com/galaxyproject/galaxy/compare/7db47e7e3c01...3aacbdffd63c

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[galaxyproject/usegalaxy-playbook] 13310f: Workaround for SLASH2 incompatibilities with OpenJ...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 13310f470d7ff256da5d75b766233ad6d7372527 https://github.com/galaxyproject/usegalaxy-playbook/commit/13310f470d7ff256… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: A CHANGELOG.md M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Workaround for SLASH2 incompatibilities with OpenJDK < 9. Commit: 49b8d60e5ce91a82343a69b49e1fb406a3d41276 https://github.com/galaxyproject/usegalaxy-playbook/commit/49b8d60e5ce91a82… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M env/main/group_vars/ftpservers/vars.yml M env/test/group_vars/ftpservers/vars.yml Log Message: ----------- Workaround for the issue described in proftpd/proftpd#568 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0a5fe4b44250...…

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[galaxyproject/galaxy] c67158: Prevent unbound variable error history controller.
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c6715819006256e429bf4e589dd456835b8d349c https://github.com/galaxyproject/galaxy/commit/c6715819006256e429bf4e589dd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Prevent unbound variable error history controller. Fixes #4423 I suppose - thanks @erasche. Commit: 7db47e7e3c012d34fd27cfb7aadfca17469b2480 https://github.com/galaxyproject/galaxy/commit/7db47e7e3c012d34fd27cfb7aadf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #4557 from jmchilton/shared_histories_unbound Prevent unbound variable error history controller. Compare: https://github.com/galaxyproject/galaxy/compare/b734581495f4...7db47e7e3c01

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[galaxyproject/galaxy] 254192: Revert "Remove Selenium test that is broken becaus...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2541928855159504caf049dd58ffca9570b8bde1 https://github.com/galaxyproject/galaxy/commit/2541928855159504caf049dd58ff… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Revert "Remove Selenium test that is broken because Galaxy is broken." This reverts commit a91c03d4403ad57336ce5cc235b22cf4be5ebd6d. Commit: b734581495f4bf39da16013ce8ae5536d0cc4437 https://github.com/galaxyproject/galaxy/commit/b734581495f4bf39da16013ce8ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #4561 from mvdbeek/reintroduce_missing_tool_test Revert "Remove Selenium test that is broken because Galaxy is broken." Compare: https://github.com/galaxyproject/galaxy/compare/3962ba94d756...b734581495f4

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[galaxyproject/galaxy] 4d3452: Update the default testing Selenium Chrome Docker ...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4d3452c09e67be62812a13ea7ad803f62ce76fbb https://github.com/galaxyproject/galaxy/commit/4d3452c09e67be62812a13ea7ad8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M .ci/jenkins/selenium/docker-compose.yml Log Message: ----------- Update the default testing Selenium Chrome Docker target. Some recent changes was incompatible with some bug in the older version (possibly this bug https://bugs.chromium.org/p/chromedriver/issues/detail?id=1552) the result is a huge number of failures in Jenkins as some persistent session error occurs. For example the older (https://jenkins.galaxyproject.org/job/selenium/209/testReport/) but with me hacking the Jenkins job to make this change only two tests fail (https://jenkins.galaxyproject.org/job/selenium/210/testReport/) Commit: ebcb4aa623dce9f92b904bf1f2ad58f59f07dbaf https://github.com/galaxyproject/galaxy/commit/ebcb4aa623dce9f92b904bf1f2ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Possible fix for a transient failure in the published histories grid tests. See failure here (https://jenkins.galaxyproject.org/job/selenium/210/testReport/selenium_test…) Uses technique to retry atomic assertions that may not be immediately true but will settle as the DOM is updated in response to changes to be true (added in https://github.com/galaxyproject/galaxy/commit/d0df3886fa7acaa3d5f63360e2af…) Commit: a91c03d4403ad57336ce5cc235b22cf4be5ebd6d https://github.com/galaxyproject/galaxy/commit/a91c03d4403ad57336ce5cc235b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Remove Selenium test that is broken because Galaxy is broken. See (https://github.com/galaxyproject/galaxy/issues/4548) for more information on the underlying issue. Commit: 3962ba94d756defce37b49375d77e221890904d7 https://github.com/galaxyproject/galaxy/commit/3962ba94d756defce37b49375d77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M .ci/jenkins/selenium/docker-compose.yml M test/selenium_tests/test_published_histories_grid.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #4549 from jmchilton/selenium_fixes_18 Assorted Selenium test fixes Compare: https://github.com/galaxyproject/galaxy/compare/235bdca1eb94...3962ba94d756

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