- 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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[galaxyproject/galaxy] 932a3a: Make chronos dependency conditional.
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 932a3aa3be3327938b619b6c7f97d837264a12a6 https://github.com/galaxyproject/galaxy/commit/932a3aa3be3327938b619b6c7f97… Author: John Chilton <jmchilton(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 Log Message: ----------- Make chronos dependency conditional. Fixes #4085. Commit: 235bdca1eb942605eadedf719190de54559fde3a https://github.com/galaxyproject/galaxy/commit/235bdca1eb942605eadedf719190… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> 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 Log Message: ----------- Merge pull request #4556 from jmchilton/conditional_chronos Make chronos dependency conditional. Compare: https://github.com/galaxyproject/galaxy/compare/65b86e3eb015...235bdca1eb94

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[galaxyproject/galaxy] bff6b5: Allow exporting workflows when tool is uninstalled
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bff6b58a1ba356f904af7ec17735a88be4b348de https://github.com/galaxyproject/galaxy/commit/bff6b58a1ba356f904af7ec17735… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow exporting workflows when tool is uninstalled Commit: 65b86e3eb0152f872a4d30b3be6741972f2fe7f7 https://github.com/galaxyproject/galaxy/commit/65b86e3eb0152f872a4d30b3be67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4553 from mvdbeek/allow_exporting_workflow_with_uninstalled_tools Allow exporting workflows when tool is uninstalled Compare: https://github.com/galaxyproject/galaxy/compare/338b0c994cf8...65b86e3eb015

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[galaxyproject/galaxy] 6deff3: import of history works even if we use symlink in ...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6deff3f9e518a1c7b51cea584ced1e4755ba9254 https://github.com/galaxyproject/galaxy/commit/6deff3f9e518a1c7b51cea584ced… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- import of history works even if we use symlink in database directory Commit: d76e304d9bec3d09867c2c264af3f73eabcd17dc https://github.com/galaxyproject/galaxy/commit/d76e304d9bec3d09867c2c264af3… Author: Frederic Sapet <frederic.sapet(a)biogemma.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- remove the redundant call to os.path.abspath(), which is called internally by os.path.realpath() Commit: 338b0c994cf8f249ac2f4cd7dce2ced811e3a58a https://github.com/galaxyproject/galaxy/commit/338b0c994cf8f249ac2f4cd7dce2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #4511 from FredericBGA/import_history_and_symlink import of history works even if we use symlink in database directory Compare: https://github.com/galaxyproject/galaxy/compare/a13bd06f48eb...338b0c994cf8

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[galaxyproject/galaxy] 96cf1b: Lower threshold for auto-matching dataset pairs in...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 96cf1b94f14b7c92c767943fa4595e638eb322e3 https://github.com/galaxyproject/galaxy/commit/96cf1b94f14b7c92c767943fa459… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Lower threshold for auto-matching dataset pairs in the collection builder. Thanks to @mvdbeek for originally testing this and verifying it works. Fixes #4349. Commit: a13bd06f48eb1eda43c034e3fe0a3d9363d8cda4 https://github.com/galaxyproject/galaxy/commit/a13bd06f48eb1eda43c034e3fe0a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #4555 from jmchilton/lower_matching_threshold Lower threshold for auto-matching dataset pairs in the collection builder Compare: https://github.com/galaxyproject/galaxy/compare/1e3bd2d4e831...a13bd06f48eb

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[galaxyproject/galaxy] 946d64: LMOD Dependency resolver - Initial commit (lib lmo...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 946d64b8f7dc08b92ebb03f34a91cab8aa7ecfbb https://github.com/galaxyproject/galaxy/commit/946d64b8f7dc08b92ebb03f34a91… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- LMOD Dependency resolver - Initial commit (lib lmod.py) Initial commit of a prototype dependency resolver based on the LMOD environment modules system. Commit: 4d143479d5998531cc4803af11579e12d160c87b https://github.com/galaxyproject/galaxy/commit/4d143479d5998531cc4803af1157… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- Update of the dependency_resolvers_conf.xml.sample file Addition of the LMOD Dependency resolver to the appropriate sample configuration file (dependency_resolvers_conf.xml.sample). Comment lines have also been added to describe the possible attributes of the resolver as well as their default values. Commit: e84284c477182b3c03e785b79f93dd88d63e6ebd https://github.com/galaxyproject/galaxy/commit/e84284c477182b3c03e785b79f93… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- LMOD Dependency resolver - Default mapping file If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules. Commit: fed3206a87e4ae4ede380c90cfa3409220847cf7 https://github.com/galaxyproject/galaxy/commit/fed3206a87e4ae4ede380c90cfa3… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Fix errors reported by the initial Travis tests Fix incorrect numbers of blank lines. Fix deprecated syntax. Commit: 09887529765ba88adb70e739d1b9d8896cb86229 https://github.com/galaxyproject/galaxy/commit/09887529765ba88adb70e739d1b9… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Syntax fix in the shell_commands method The built command now reflect more directly the command that is really executed by the the LMOD "module" bash function when a user execute "module load package_name/package_version". Commit: 574e697a4d66a53f298f37f4987d31db96ff8e14 https://github.com/galaxyproject/galaxy/commit/574e697a4d66a53f298f37f4987d… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- Dependency_resolvers_conf.xml - More explanations Some more explanations about the versionless mode have been added. Commit: db5efdaa7cbc197eaf6a777d4d390de24b212e88 https://github.com/galaxyproject/galaxy/commit/db5efdaa7cbc197eaf6a777d4d39… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Clearer comment lines in the has_module method A comment of the has_module method of the AvailModuleChecker class has been modified to be clearer and more explicit. Commit: eda36ffb99a1abec8f878c0b7ae194938781c8d6 https://github.com/galaxyproject/galaxy/commit/eda36ffb99a1abec8f878c0b7ae1… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- LMOD Dependency resolver - Unit tests added The unit/tools/tests_tool_deps.py script has been updated to includ unit tests for the LMOD dependency resolver. Commit: bbec357bbd744b9e0d760e8d0903adfa43d1b7e2 https://github.com/galaxyproject/galaxy/commit/bbec357bbd744b9e0d760e8d0903… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix the import order error raised by Travis The order of the import statements in the test_tool_deps script was incorrect (as stated by travis). That should no longer be the case. Commit: 9822f5f2a91fae7e3420a06c58f2621a2cf084ac https://github.com/galaxyproject/galaxy/commit/9822f5f2a91fae7e3420a06c58f2… Author: Aurélien Bernard <aurelien.bernard.bioinfo63(a)gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix attempt for the modulepath issue in unit tests On a computer where LMOD is not installed, the MODULEPATH variable is not defined and the modulepath attributes of the LMOD dependency resolver must be used. Commit: 1e3bd2d4e831331b8e3b314bac287288fa4533fc https://github.com/galaxyproject/galaxy/commit/1e3bd2d4e831331b8e3b314bac28… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample A lib/galaxy/tools/deps/resolvers/lmod.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #4489 from arbernard/LMOD_Dependency_resolver New Dependency resolver for the LMOD environment modules system Compare: https://github.com/galaxyproject/galaxy/compare/6e6845b4987a...1e3bd2d4e831

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[galaxyproject/galaxy] cfefee: Refactor history import/export tests to allow coll...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfefeebdd713552c9e0776b932fca59fe65961a3 https://github.com/galaxyproject/galaxy/commit/cfefeebdd713552c9e0776b932fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/api/test_histories.py Log Message: ----------- Refactor history import/export tests to allow collection testing (not yet implemented). xref #4345, #4532 Commit: 6e6845b4987ab2de5608e216b1f537ad9b1f0fd5 https://github.com/galaxyproject/galaxy/commit/6e6845b4987ab2de5608e216b1f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M test/api/test_histories.py Log Message: ----------- Merge pull request #4534 from jmchilton/collection_import_export_test_case Refactor history import/export tests to allow collection testing. Compare: https://github.com/galaxyproject/galaxy/compare/af9173d7cfa8...6e6845b4987a

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[galaxyproject/galaxy] 686cb4: Alternative fix for workflow editor hang with miss...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 686cb48c716912212effc3d584d194ead54f216e https://github.com/galaxyproject/galaxy/commit/686cb48c716912212effc3d584d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Alternative fix for workflow editor hang with missing tools Commit: 33defd130772a0c7a3b63594aad27307e108ead9 https://github.com/galaxyproject/galaxy/commit/33defd130772a0c7a3b63594aad2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Revert "Properly raise Exception if tool not found" This reverts commit 1015b510f81723b927866546390d179abef796f9. Commit: 09c96dace2f6eb84ae33c856183fcf25175b65bf https://github.com/galaxyproject/galaxy/commit/09c96dace2f6eb84ae33c856183f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix extra-space (thx @nsoranzo) Commit: 40c9ca5ee9e3ab6eee8396218a8467a311225d37 https://github.com/galaxyproject/galaxy/commit/40c9ca5ee9e3ab6eee8396218a84… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Log warning for missing tools when building workflow modules Commit: af9173d7cfa85156babca323e1a93d98f53acffd https://github.com/galaxyproject/galaxy/commit/af9173d7cfa85156babca323e1a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4552 from mvdbeek/fix_missing_tools_wf_editor_alternative Fix missing tools wf editor alternative Compare: https://github.com/galaxyproject/galaxy/compare/9b4cd096e1e9...af9173d7cfa8

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[galaxyproject/galaxy] cd1c38: Break up populator methods for greater composibili...
by GitHub 05 Sep '17

05 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd1c38c527e54b8f7b0817eda5ac9aa0c68dc349 https://github.com/galaxyproject/galaxy/commit/cd1c38c527e54b8f7b0817eda5ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/base/populators.py Log Message: ----------- Break up populator methods for greater composibility and reuse. All of these changes are needed for various downstream enhancements I'm working on for things like CWL support and extra file testing - but I think they should all be okay refactorings on their own. Commit: 5a7a15d161bececf0a3cd93714e15768b329d95f https://github.com/galaxyproject/galaxy/commit/5a7a15d161bececf0a3cd93714e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Test and clarifications for composite uploads. - Add an API test for datatype-defined composite uploads - including exercising newline conversion and the space_to_tab parameter. - Add a test decorator skip_without_datatype to mirror skip_without_tool for this test, improve both decorators. - The ftype parameter in the composite test tools does nothing - drop it and drop it from the XSD spec. - Slightly improve the documentation for these composite_data elements in the XSD. Commit: 9b4cd096e1e9cbbd86aafb384e5b7773abf585ab https://github.com/galaxyproject/galaxy/commit/9b4cd096e1e9cbbd86aafb384e5b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py M test/base/interactor.py M test/base/populators.py M test/functional/tools/composite.xml M test/functional/tools/composite_output.xml M test/functional/tools/composite_output_tests.xml M test/functional/tools/metadata.xml M tools/sr_assembly/velvetg.xml Log Message: ----------- Merge pull request #4505 from jmchilton/composite_upload_refine Tests and clarifications for composite uploads. Compare: https://github.com/galaxyproject/galaxy/compare/003344ac2f0e...9b4cd096e1e9

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[galaxyproject/galaxy] 9556c4: Check user roles only once if user has no roles
by GitHub 04 Sep '17

04 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9556c467e3a4c9947939f8444873530b53b39c20 https://github.com/galaxyproject/galaxy/commit/9556c467e3a4c9947939f8444873… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Check user roles only once if user has no roles The previous implementation in #4541 would check user roles multiple times if a user has no roles. Noticed by @nsoranzo, many thanks! Commit: 003344ac2f0e6ebd13d78aa8222b958f93bfcf93 https://github.com/galaxyproject/galaxy/commit/003344ac2f0e6ebd13d78aa8222b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4546 from mvdbeek/tool_form_followup Check user roles only once if user has no roles Compare: https://github.com/galaxyproject/galaxy/compare/3d9809a50d94...003344ac2f0e

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[galaxyproject/galaxy] 042386: wip on improving libraries
by GitHub 04 Sep '17

04 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 042386ff8733874fe7004c900fabb16b7798d031 https://github.com/galaxyproject/galaxy/commit/042386ff8733874fe7004c900fab… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- wip on improving libraries Commit: 61eb0114034703d5ec225c42e3b781b96b02b7f6 https://github.com/galaxyproject/galaxy/commit/61eb0114034703d5ec225c42e3b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- refactor decode_id method to use base manager Commit: dc834a52c1dfa2bcca61e3cdb74ed9606c752340 https://github.com/galaxyproject/galaxy/commit/dc834a52c1dfa2bcca61e3cdb74e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/managers/libraries.py Log Message: ----------- fix copypasta error Commit: e17ab411e338043dce2391672322ebc3468d049e https://github.com/galaxyproject/galaxy/commit/e17ab411e338043dce2391672322… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: A lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- refactor show method to use new manager Commit: cd09d1327a075f83e0c83323da26377ec0336d03 https://github.com/galaxyproject/galaxy/commit/cd09d1327a075f83e0c83323da26… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- refactor the rest of the module to use new manager Commit: 50ebc19afd6788125285cbf051f85aec6ac34d00 https://github.com/galaxyproject/galaxy/commit/50ebc19afd6788125285cbf051f8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- rename lda_datasets to library_datasets Commit: d883fc162e4d0a6606b9e4408337e5c564fd1840 https://github.com/galaxyproject/galaxy/commit/d883fc162e4d0a6606b9e4408337… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- add ommitted conflict resolution Commit: ac5be429e70a8533aae3583fed9cd29cb17fc13f https://github.com/galaxyproject/galaxy/commit/ac5be429e70a8533aae3583fed9c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- repack Commit: 6613df5b7a826e8147b2a46c8e87391b230f4315 https://github.com/galaxyproject/galaxy/commit/6613df5b7a826e8147b2a46c8e87… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add methods for vlidating and updating ld's attributes Commit: a394faf3be18eceae72ca68dae67596123c89ff6 https://github.com/galaxyproject/galaxy/commit/a394faf3be18eceae72ca68dae67… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- fix refactoring error Commit: c060bbb5fa54c7062a8daf8df7192d793e354e6e https://github.com/galaxyproject/galaxy/commit/c060bbb5fa54c7062a8daf8df719… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/managers/library_datasets.py Log Message: ----------- fix wrongly called exceptions Commit: b096155637e922ab87bab9b86c606e08ef82fea1 https://github.com/galaxyproject/galaxy/commit/b096155637e922ab87bab9b86c60… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/managers/library_datasets.py M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- add functionality to the UI for updating library dataset Commit: 3ac0c7ced7224e63bc55cde9fad3679b390d9628 https://github.com/galaxyproject/galaxy/commit/3ac0c7ced7224e63bc55cde9fad3… 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: ----------- improve UX of importing from history to folder fixes #4151 Commit: 48bb43b8b04b1bdcfb636277c9a595c6a8cbbbb6 https://github.com/galaxyproject/galaxy/commit/48bb43b8b04b1bdcfb636277c9a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/managers/library_datasets.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- fix travis issues - whitespace, imports Commit: f79eba25b532e42e38fec5f6df25229ea6085a03 https://github.com/galaxyproject/galaxy/commit/f79eba25b532e42e38fec5f6df25… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/managers/library_datasets.py M test/api/test_libraries.py Log Message: ----------- fix small regressions and add tests for the new API Commit: 65185f5e435a733c0f6b4639ac91f607b12eb844 https://github.com/galaxyproject/galaxy/commit/65185f5e435a733c0f6b4639ac91… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- lint imports Commit: 3d9809a50d942e51c8afc7dd4cbae8e775b33147 https://github.com/galaxyproject/galaxy/commit/3d9809a50d942e51c8afc7dd4cba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-04 (Mon, 04 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M lib/galaxy/managers/libraries.py A lib/galaxy/managers/library_datasets.py M lib/galaxy/managers/workflows.py R lib/galaxy/webapps/galaxy/api/lda_datasets.py A lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M test/api/test_libraries.py Log Message: ----------- Merge pull request #4512 from martenson/improving-datalibraries A round of data libraries improvements. Compare: https://github.com/galaxyproject/galaxy/compare/8f1303217eea...3d9809a50d94

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[galaxyproject/galaxy] a904df: Only parse once
by GitHub 04 Sep '17

04 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a904df604ef6962628916635d42068ece1368d01 https://github.com/galaxyproject/galaxy/commit/a904df604ef6962628916635d420… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Only parse once Commit: cbe6970a4cf5c5a3b7bb55c97d7190fef4019388 https://github.com/galaxyproject/galaxy/commit/cbe6970a4cf5c5a3b7bb55c97d71… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- per @nsoranzo, only log error message when it is there Commit: e130b55b04c8bc7c30b85ac7e2688890b890c71c https://github.com/galaxyproject/galaxy/commit/e130b55b04c8bc7c30b85ac7e268… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/tool_shed/util/xml_util.py Log Message: ----------- log error if does not exist Commit: 0159162c9e7b3463b2f667fec820d3ae83bfd3dc https://github.com/galaxyproject/galaxy/commit/0159162c9e7b3463b2f667fec820… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py Log Message: ----------- Merge branch 'parse-once' of github.com:erasche/galaxy into parse-once Commit: 8f1303217eea29e4973cbbbd13c4b3f8b47f8d5c https://github.com/galaxyproject/galaxy/commit/8f1303217eea29e4973cbbbd13c4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/util/xml_util.py Log Message: ----------- Merge pull request #4495 from erasche/parse-once 41% reduction in freiburg galaxy startup time Compare: https://github.com/galaxyproject/galaxy/compare/f6fa7c39f104...8f1303217eea

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[galaxyproject/galaxy] 634f7d: Add a small howto on profiling galaxy code
by GitHub 04 Sep '17

04 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 634f7dcd3917eef17994a29c1f63f91c4b22a4b9 https://github.com/galaxyproject/galaxy/commit/634f7dcd3917eef17994a29c1f63… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: A doc/source/dev/finding_and_improving_slow_code.rst Log Message: ----------- Add a small howto on profiling galaxy code Commit: 2e5bbad353ca76f25bff9588fea2958cd6d5596a https://github.com/galaxyproject/galaxy/commit/2e5bbad353ca76f25bff9588fea2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M doc/source/dev/finding_and_improving_slow_code.rst Log Message: ----------- Clarify the last section Commit: f6fa7c39f104d390f4a7df62d0b227ab1823c838 https://github.com/galaxyproject/galaxy/commit/f6fa7c39f104d390f4a7df62d0b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: A doc/source/dev/finding_and_improving_slow_code.rst Log Message: ----------- Merge pull request #4542 from mvdbeek/build_module_speedup Add a small howto on profiling galaxy code Compare: https://github.com/galaxyproject/galaxy/compare/b2ceef5b6c25...f6fa7c39f104

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[galaxyproject/galaxy] 259e12: Continue separation of FunctionalTestCase from Twi...
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 259e12d760c721badf9a6f65da90a9bb5bcb0983 https://github.com/galaxyproject/galaxy/commit/259e12d760c721badf9a6f65da90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/api.py A test/base/testcase.py M test/base/twilltestcase.py M test/functional/test_toolbox.py M test/selenium_tests/framework.py Log Message: ----------- Continue separation of FunctionalTestCase from TwillTestCase. Move non-twill stuff out into its own module including FunctionalTestCase. Commit: 6e17ff57ea62320e8764b390e50135d95aaa242d https://github.com/galaxyproject/galaxy/commit/6e17ff57ea62320e8764b390e501… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: R test/functional/test_library_templates.py Log Message: ----------- Remove test/functional/test_library_templates.py. Hasn't been run in forever and it seems like we are deprecating these features. Commit: 6d7c8b3136e24ff3e752efecb14f57574cd53174 https://github.com/galaxyproject/galaxy/commit/6d7c8b3136e24ff3e752efecb14f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/tool_shed_util.py Log Message: ----------- Cleanup sys.path hacking in test/base/tool_shed_util.py. Commit: 7343463daca00ef60836e99faecdf90f85c9fd2a https://github.com/galaxyproject/galaxy/commit/7343463daca00ef60836e99faecd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/driver_util.py R test/base/test_db_util.py R test/functional/database_contexts.py M test/shed_functional/base/test_db_util.py Log Message: ----------- Rework hack to inject database contexts into Tool Shed tests. Rather than depend on something in ``functional`` test module from ``base.driver_util``, just set these global hacks up in ``driver_util`` itself. This eliminates a dependency of ``functional`` on ``base`` - ideally ``base`` would not depend on any other test modules. Commit: aba726a89f69fe1dbd4b4147e725c7ce0a7a3a33 https://github.com/galaxyproject/galaxy/commit/aba726a89f69fe1dbd4b4147e725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: R test/base/twilltestcase.py M test/functional/test_toolbox.py A test/functional/twilltestcase.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Move twilltestcase from ``base`` to ``functional`` module. This way nothing in ``base`` has any dependencies on Twill anymore. Commit: 5358db58231482312850351d3d1dded25797dec8 https://github.com/galaxyproject/galaxy/commit/5358db58231482312850351d3d1d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-01 (Fri, 01 Sep 2017) Changed paths: M test/base/tool_shed_util.py Log Message: ----------- fix lint order Commit: b2ceef5b6c258b0d6bc90240549299dbcc3d6ee4 https://github.com/galaxyproject/galaxy/commit/b2ceef5b6c258b0d6bc902405492… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M test/base/api.py M test/base/driver_util.py R test/base/test_db_util.py A test/base/testcase.py M test/base/tool_shed_util.py R test/base/twilltestcase.py R test/functional/database_contexts.py R test/functional/test_library_templates.py M test/functional/test_toolbox.py A test/functional/twilltestcase.py M test/selenium_tests/framework.py M test/shed_functional/base/test_db_util.py M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #4536 from jmchilton/test_refactoring Refactor test modules toward cleaner dependencies Compare: https://github.com/galaxyproject/galaxy/compare/ae7e1f97f0b7...b2ceef5b6c25

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[galaxyproject/galaxy] 471707: Build converters_by_datatype only once per registr...
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 471707bd7dfa048a412aad9cdcc1d0b4aea70bc7 https://github.com/galaxyproject/galaxy/commit/471707bd7dfa048a412aad9cdcc1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Build converters_by_datatype only once per registry lifetime Commit: d1a2007275f128fea051ead55fb47d2c2686abf5 https://github.com/galaxyproject/galaxy/commit/d1a2007275f128fea051ead55fb4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/work/context.py Log Message: ----------- Cache user roles during WorkRequestContext lifetime This speeds up building the tool module by a factor of 5. Commit: 2d8b242e697a08775879fc873578b5f244d4d5cb https://github.com/galaxyproject/galaxy/commit/2d8b242e697a08775879fc873578… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix caching of `get_converters_by_datatype` result Commit: ae7e1f97f0b71f90968abd09dd2f88387d0dc2e4 https://github.com/galaxyproject/galaxy/commit/ae7e1f97f0b71f90968abd09dd2f… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/work/context.py Log Message: ----------- Merge pull request #4541 from mvdbeek/build_module_speedup Speedup toolform building Compare: https://github.com/galaxyproject/galaxy/compare/ea9f5f7eb253...ae7e1f97f0b7

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[galaxyproject/galaxy] 354ce1: Fix workflow run Selenium test and make it more ro...
by GitHub 03 Sep '17

03 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 354ce19677bae15d5cf976386ca988586a0c3eff https://github.com/galaxyproject/galaxy/commit/354ce19677bae15d5cf976386ca9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Fix workflow run Selenium test and make it more robust. This test went from transiently broken to always broken during this release cycle. This PR makes two changes to try to fix both of those conditions. It correct the frame and button Selector for the new workflow run UX for the newer error and this allows explicitly refreshing the browser when waiting for datasets to appear to deal with the transient problems. Commit: edd3b07c3dcace5263dafafef72b8564c8b7ce06 https://github.com/galaxyproject/galaxy/commit/edd3b07c3dcace5263dafafef72b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/galaxy_selenium/driver_factory.py Log Message: ----------- Fix "all" vs. "ALL" in Selenium logging configuration. The previous value broke all the tests on Jenkins. Commit: ea9f5f7eb2536765a175f7e411f8d64cb8c34cad https://github.com/galaxyproject/galaxy/commit/ea9f5f7eb2536765a175f7e411f8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-09-03 (Sun, 03 Sep 2017) Changed paths: M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #4524 from jmchilton/selenium_fixes_16 Fix workflow run Selenium test and make it more robust. Compare: https://github.com/galaxyproject/galaxy/compare/47efd8089c5b...ea9f5f7eb253

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