- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fc90ae: Fix virtualenv activation for some scripts
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Commit: 64af1bd9e96265cbd6b21faadbad5adea4a2d613 https://github.com/galaxyproject/galaxy/commit/64af1bd9e96265cbd6b21faadbad… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c5ff555ec4ef...64af1bd9e962

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[galaxyproject/galaxy] 6c6c80: When a page is involved, the ID will be wrong
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 6c6c804ab63866c6239299f4221fa436dd4a9591 https://github.com/galaxyproject/galaxy/commit/6c6c804ab63866c6239299f4221f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- When a page is involved, the ID will be wrong Commit: 33a0c7fac3a0624d26efd8d08dabbca5f7e8c226 https://github.com/galaxyproject/galaxy/commit/33a0c7fac3a0624d26efd8d08dab… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Make client Commit: a2229783177b76786f581cc78040b059cbd2aab5 https://github.com/galaxyproject/galaxy/commit/a2229783177b76786f581cc78040… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4355 from erasche/patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ecfb90ef9f8037575db2e62ae49d8bbb7e4e427b https://github.com/galaxyproject/galaxy/commit/ecfb90ef9f8037575db2e62ae49d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 163e4ebbe1fbfc5f1f97b5aabc804621fdd426c9 https://github.com/galaxyproject/galaxy/commit/163e4ebbe1fbfc5f1f97b5aabc80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js R static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map R static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4356 from galaxyproject/revert-4355-patch-wrong-folder-id Revert "[release_17.05] Patch bug preventing creation of dataset library folders" Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Commit: ba3249acf07ca1a44a813e2c68a9d6074d2b7c4c https://github.com/galaxyproject/galaxy/commit/ba3249acf07ca1a44a813e2c68a9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Add missing chemical formats to datatypes_conf.xml.sample Commit: 61d172f18d8f7740585b038dd786e81178ca1831 https://github.com/galaxyproject/galaxy/commit/61d172f18d8f7740585b038dd786… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M setup.cfg M tox.ini Log Message: ----------- Update pin for flake8-docstrings Similar to commit 2586df45637d794c63252838573b2d1e6d692243 . Commit: a249dc01a5d0afa42474a6e4075ed2a3ad80400f https://github.com/galaxyproject/galaxy/commit/a249dc01a5d0afa42474a6e4075e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-11 (Fri, 11 Aug 2017) Changed paths: M .travis.yml Log Message: ----------- Use container-based infrastructure (sudo: false) in TravisCI Commit: d0b06a3b1da09ff3394e9ea036d788676817b58f https://github.com/galaxyproject/galaxy/commit/d0b06a3b1da09ff3394e9ea036d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Don't cast tool_version to string if tool_version is None-type If a version is not specifically requested a wrong version (`None` cast to `'None'`) of a tool will be loaded in the workflow editor instead of the latest version. That should address @martenson's remark in https://github.com/galaxyproject/galaxy/pull/4373#issuecomment-321896674 (and maybe also https://github.com/galaxyproject/galaxy/issues/557#issuecomment-213498153) Commit: 6ad6fd9252bf5ec44beb00cb434876e170dc9548 https://github.com/galaxyproject/galaxy/commit/6ad6fd9252bf5ec44beb00cb4348… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Rebuild tool_version_cache on DetachedInstanceError Commit: 0f5ad34eaf6b65a2d258f308aa6fea8b4f39a52a https://github.com/galaxyproject/galaxy/commit/0f5ad34eaf6b65a2d258f308aa6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M .travis.yml M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py M setup.cfg M tox.ini Log Message: ----------- Merge pull request #4413 from nsoranzo/release_17.01_really_add_datatypes [17.01] Add missing chemical formats to datatypes_conf.xml.sample Commit: 4faf496c9898786e8f504bd36b28dc70df4e3e26 https://github.com/galaxyproject/galaxy/commit/4faf496c9898786e8f504bd36b28… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-14 (Mon, 14 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/molecules.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: tox.ini Commit: 7f78ee7b18b83961b305cac19aa8949a4452710d https://github.com/galaxyproject/galaxy/commit/7f78ee7b18b83961b305cac19aa8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4420 from mvdbeek/fix_wrong_tool_version_cast [17.05] Don't cast tool_version to string if tool_version is None-type Commit: 1e1c549e695cf6541c4dcac5d554c852165e7b6a https://github.com/galaxyproject/galaxy/commit/1e1c549e695cf6541c4dcac5d554… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: a1b8a54ef8009ccf9ac64a699ed848cd56bba283 https://github.com/galaxyproject/galaxy/commit/a1b8a54ef8009ccf9ac64a699ed8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 349c9c8f10f6f5eeac45c1a14e3b4a6c23cc373e https://github.com/galaxyproject/galaxy/commit/349c9c8f10f6f5eeac45c1a14e3b… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: a76547281f59b80acd27ddfa098c97e65a72d81a https://github.com/galaxyproject/galaxy/commit/a76547281f59b80acd27ddfa098c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 748539a3a671552eea60e114a6c6e4dd7b48c7de https://github.com/galaxyproject/galaxy/commit/748539a3a671552eea60e114a6c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4450 from mvdbeek/fix_file_lock_error [17.01] Fix file lock error handling Commit: 685b9de09bca5a2973de336b93865273c9fa975c https://github.com/galaxyproject/galaxy/commit/685b9de09bca5a2973de336b9386… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Commit: ce7d8a2fc1bcc1f9241028b3d437c653edccda0c https://github.com/galaxyproject/galaxy/commit/ce7d8a2fc1bcc1f9241028b3d437… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Validate workflow step after step argument injection Commit: 3ef39b390c8d2f66ff890a29b712f785b6376601 https://github.com/galaxyproject/galaxy/commit/3ef39b390c8d2f66ff890a29b712… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map 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/ui/ui-select-content.js Log Message: ----------- Fix drag and drop from history for firefox Commit: cf897795fe8b544bc4cb5899585b1be2ee0063e6 https://github.com/galaxyproject/galaxy/commit/cf897795fe8b544bc4cb5899585b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map 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/ui/ui-select-content.js Log Message: ----------- Merge pull request #4496 from guerler/fix_drag_drop_firefox [17.05] Fix drag and drop from history for Firefox Commit: c70926445fb7518e1f2ebf755477ca3327dea6a3 https://github.com/galaxyproject/galaxy/commit/c70926445fb7518e1f2ebf755477… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #4483 from guerler/fix_workflow_validation [17.05] Validate workflow step after step argument injection Commit: 47ba644de78dd82cfaed205128bd34056aa99078 https://github.com/galaxyproject/galaxy/commit/47ba644de78dd82cfaed205128bd… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 5a18464d547d7497285ee25067050ee4cd665eda https://github.com/galaxyproject/galaxy/commit/5a18464d547d7497285ee2506705… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch Commit: 1d485390b0af80441c4e577f8fb7ddde265f9618 https://github.com/galaxyproject/galaxy/commit/1d485390b0af80441c4e577f8fb7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/web/framework/base.py Log Message: ----------- 2017-08 Security Patch 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 Commit: 140c570517df5c9c0728c6d5be442d82b2f78ae9 https://github.com/galaxyproject/galaxy/commit/140c570517df5c9c0728c6d5be44… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: 759780b72c03efd6563c0c53efc9edff9505979c https://github.com/galaxyproject/galaxy/commit/759780b72c03efd6563c0c53efc9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 41fe55129a3af95d7ef84ecb387b954b14509843 https://github.com/galaxyproject/galaxy/commit/41fe55129a3af95d7ef84ecb387b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-06 (Wed, 06 Sep 2017) Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Conflicts: lib/galaxy/datatypes/data.py Commit: b17fbfb968b8921729798c909220e522abfb29fd https://github.com/galaxyproject/galaxy/commit/b17fbfb968b8921729798c909220… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix startup of galaxy when wehbooks dir is empty Reported by @alpapan on gitter. Commit: c86bf78c6a966b52d3c9e21ffae71bbf134ecdb4 https://github.com/galaxyproject/galaxy/commit/c86bf78c6a966b52d3c9e21ffae7… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Merge pull request #4570 from mvdbeek/webhook_loading_fix [17.05] Bug: Fix startup of galaxy when wehbooks dir is empty Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698 https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview Commit: a9facdc7568f68af06ba7474611feeeabf60466b https://github.com/galaxyproject/galaxy/commit/a9facdc7568f68af06ba7474611f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 83b363d5207625b916523b7d08b4fff26e8379ed https://github.com/galaxyproject/galaxy/commit/83b363d5207625b916523b7d08b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.js.map 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M config/datatypes_conf.xml.sample M create_db.sh M extract_dataset_parts.sh M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/deps/installable.py M lib/galaxy/web/framework/base.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/workflow/modules.py M manage_db.sh M manage_tools.sh M static/maps/mvc/base/controlled-fetch-collection.js.map A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/ui/ui-select-content.js.map 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/base/controlled-fetch-collection.js A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Merge branch 'release_17.05' Compare: https://github.com/galaxyproject/galaxy/compare/4a7045c8d210...0a39bfcbf7dc

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[galaxyproject/galaxy] fc90ae: Fix virtualenv activation for some scripts
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: fc90aec7fe4a3267868fdf3cc2c2123f935f15a2 https://github.com/galaxyproject/galaxy/commit/fc90aec7fe4a3267868fdf3cc2c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 97e8e36185312ff6e1afea15fec7e83aadafd25b https://github.com/galaxyproject/galaxy/commit/97e8e36185312ff6e1afea15fec7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4624 from nsoranzo/release_17.05_fix_scripts [17.05] Backport of #4616 Compare: https://github.com/galaxyproject/galaxy/compare/83b363d52076...97e8e3618531

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[galaxyproject/galaxy] d8dfbe: unify library dataset permission frontend for all...
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8dfbe56c427e73f359595609c932105114950eb https://github.com/galaxyproject/galaxy/commit/d8dfbe56c427e73f359595609c93… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- unify library dataset permission frontend for all users also refactor Commit: 028aac0a3dabe31a5392feaf35a93900ac7eb8b7 https://github.com/galaxyproject/galaxy/commit/028aac0a3dabe31a5392feaf35a9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- respect expose_user_email when offering roles to datalib permissions Commit: a1cd3bd1e41d4da17d116c1a8cde1eedb6143ab9 https://github.com/galaxyproject/galaxy/commit/a1cd3bd1e41d4da17d116c1a8cde… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M static/maps/mvc/library/library-dataset-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 Log Message: ----------- rebuild client Commit: 1b2221cd5600823285737fae5d7819c3f2670cfb https://github.com/galaxyproject/galaxy/commit/1b2221cd5600823285737fae5d78… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- fix indent Commit: 9084edd8200cc7c7387d62ae969921daf3feec86 https://github.com/galaxyproject/galaxy/commit/9084edd8200cc7c7387d62ae9699… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/scripts/mvc/library/library-dataset-view.js Log Message: ----------- fix typo thanks @dannon Commit: c5ff555ec4ef32e0d12020c4ea4e0f52f214e31e https://github.com/galaxyproject/galaxy/commit/c5ff555ec4ef32e0d12020c4ea4e… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M static/maps/mvc/library/library-dataset-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 Log Message: ----------- Merge pull request #4611 from martenson/respect-email-exposure respect expose_user_email configuration in datalibraries permissions list Compare: https://github.com/galaxyproject/galaxy/compare/c677621481ab...c5ff555ec4ef

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[galaxyproject/galaxy] d6ae91: Fix group creation label in admin panel
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d6ae9127ebb7c654ea93f98b1de18ccb92705713 https://github.com/galaxyproject/galaxy/commit/d6ae9127ebb7c654ea93f98b1de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix group creation label in admin panel Commit: d247d698a29e3e24816068624061411be97d6ad1 https://github.com/galaxyproject/galaxy/commit/d247d698a29e3e24816068624061… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix auto create checkbox name Commit: c677621481abf7823f2d77a506c8aa6908070022 https://github.com/galaxyproject/galaxy/commit/c677621481abf7823f2d77a506c8… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Merge pull request #4619 from guerler/fix_group_label Fix group creation label in admin panel and checkbox name Compare: https://github.com/galaxyproject/galaxy/compare/90eed104f0d8...c677621481ab

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[galaxyproject/galaxy] e1be66: Fix virtualenv activation for some scripts
by GitHub 15 Sep '17

15 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1be66312b536a419383746b8e702b6148edeeec https://github.com/galaxyproject/galaxy/commit/e1be66312b536a419383746b8e70… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Fix virtualenv activation for some scripts In particular add virtualenv activation to extract_dataset_parts.sh to fix the following error when running tools which use `<parallelism>`: ``` Fatal error: /tmp/tmpOoQ01k/job_working_directory/000/12/task_0: Traceback (most recent call last): File "./scripts/extract_dataset_part.py", line 17, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/galaxyproject_galaxy_release_17.05/lib/galaxy/model/__init__.py", line 20, in <module> from six import string_types ModuleNotFoundError: No module named 'six' ``` Commit: 90eed104f0d80fed13ac6b5cfc13f96d28d01771 https://github.com/galaxyproject/galaxy/commit/90eed104f0d80fed13ac6b5cfc13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-15 (Fri, 15 Sep 2017) Changed paths: M create_db.sh M extract_dataset_parts.sh M manage_db.sh M manage_tools.sh Log Message: ----------- Merge pull request #4616 from nsoranzo/fix_scripts Fix virtualenv activation for some scripts Compare: https://github.com/galaxyproject/galaxy/compare/8b9e91310fd9...90eed104f0d8

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[galaxyproject/galaxy] b17fbf: Fix startup of galaxy when wehbooks dir is empty
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b17fbfb968b8921729798c909220e522abfb29fd https://github.com/galaxyproject/galaxy/commit/b17fbfb968b8921729798c909220… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix startup of galaxy when wehbooks dir is empty Reported by @alpapan on gitter. Commit: c86bf78c6a966b52d3c9e21ffae71bbf134ecdb4 https://github.com/galaxyproject/galaxy/commit/c86bf78c6a966b52d3c9e21ffae7… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Merge pull request #4570 from mvdbeek/webhook_loading_fix [17.05] Bug: Fix startup of galaxy when wehbooks dir is empty Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698 https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview Commit: a9facdc7568f68af06ba7474611feeeabf60466b https://github.com/galaxyproject/galaxy/commit/a9facdc7568f68af06ba7474611f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 83b363d5207625b916523b7d08b4fff26e8379ed https://github.com/galaxyproject/galaxy/commit/83b363d5207625b916523b7d08b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.js.map 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 8b9e91310fd98c9e21bc3511df940b0cba5720b7 https://github.com/galaxyproject/galaxy/commit/8b9e91310fd98c9e21bc3511df94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/95969267c226...8b9e91310fd9

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[galaxyproject/galaxy] 7fdce2: Allow fetchMore to actually specify a 0 offset whe...
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698 https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview Commit: a9facdc7568f68af06ba7474611feeeabf60466b https://github.com/galaxyproject/galaxy/commit/a9facdc7568f68af06ba7474611f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: 83b363d5207625b916523b7d08b4fff26e8379ed https://github.com/galaxyproject/galaxy/commit/83b363d5207625b916523b7d08b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.js.map 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/c86bf78c6a96...83b363d52076

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[galaxyproject/galaxy] 7fdce2: Allow fetchMore to actually specify a 0 offset whe...
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698 https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview Commit: a9facdc7568f68af06ba7474611feeeabf60466b https://github.com/galaxyproject/galaxy/commit/a9facdc7568f68af06ba7474611f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/759780b72c03...a9facdc7568f

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[galaxyproject/galaxy] 7fdce2: Allow fetchMore to actually specify a 0 offset whe...
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 7fdce2efd951f79e8ad5a4e2cf9fe8d04340454d https://github.com/galaxyproject/galaxy/commit/7fdce2efd951f79e8ad5a4e2cf9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 14ceb6d91b57563f1203ccd82312b96fdafa8698 https://github.com/galaxyproject/galaxy/commit/14ceb6d91b57563f1203ccd82312… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/package.json M static/maps/mvc/base/controlled-fetch-collection.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4615 from dannon/release_16.10_backport2 [16.10] Allow fetchMore to actually specify a 0 offset when intentional, fixes multiview Compare: https://github.com/galaxyproject/galaxy/compare/140c570517df...14ceb6d91b57

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[galaxyproject/galaxy] 4f93f8: Allow fetchMore to actually specify a 0 offset whe...
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f93f88f0a2df07c5a8c3fa7c62fd4bda40fb3c1 https://github.com/galaxyproject/galaxy/commit/4f93f88f0a2df07c5a8c3fa7c62f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M static/maps/mvc/base/controlled-fetch-collection.js.map 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/base/controlled-fetch-collection.js Log Message: ----------- Allow fetchMore to actually specify a 0 offset when intentional. This should fix the mysterious missing history in multiview bug. Commit: 1502e0067552b72b87853834d3f857a409ead379 https://github.com/galaxyproject/galaxy/commit/1502e0067552b72b87853834d3f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/base/controlled-fetch-collection.js Log Message: ----------- Some cruft fixing and configuring of Galaxy.debug output instead of commented out console.logs -- should help immensely for troubleshooting Commit: 62e73a37d3736063113f2118b3e997449e54c75e https://github.com/galaxyproject/galaxy/commit/62e73a37d3736063113f2118b3e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 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-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py M lib/galaxy_ext/metadata/set_metadata.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-librarylist-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-librarylist-view.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fix_missing_histories Commit: 95969267c226193152e62b537824e6567144c1db https://github.com/galaxyproject/galaxy/commit/95969267c226193152e62b537824… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/base/controlled-fetch-collection.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js 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/base/controlled-fetch-collection.js Log Message: ----------- Merge pull request #4610 from dannon/fix_missing_histories Multiview missing histories fix Compare: https://github.com/galaxyproject/galaxy/compare/cdb95d604573...95969267c226

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[galaxyproject/galaxy] 38add8: remove unused cruft
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38add849710c4e7bb8d350dfae2d7b86b7c8b50b https://github.com/galaxyproject/galaxy/commit/38add849710c4e7bb8d350dfae2d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- remove unused cruft Commit: 2daf4317f1f22a683ae29f44e566ad9c2bf4883e https://github.com/galaxyproject/galaxy/commit/2daf4317f1f22a683ae29f44e566… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- show the first page of search results insted of the current selected (would hide short resutls) Commit: bf8940071372d0244314795723a24118b3c622bf https://github.com/galaxyproject/galaxy/commit/bf8940071372d0244314795723a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- remove unused requirements thanks @anuprulez Commit: cdca22b33e84053df4c6aa6eae7b2d9f5157d9a7 https://github.com/galaxyproject/galaxy/commit/cdca22b33e84053df4c6aa6eae7b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: 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 Log Message: ----------- rebuild client Commit: cdb95d6045739175e440e68e643e0f4cebadfe50 https://github.com/galaxyproject/galaxy/commit/cdb95d6045739175e440e68e643e… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-14 (Thu, 14 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/toolshed/scripts/mvc/groups/group-list-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/scripts/mvc/library/library-librarylist-view.js Log Message: ----------- Merge pull request #4594 from martenson/fix-search-pagination Fix datalib search pagination Compare: https://github.com/galaxyproject/galaxy/compare/a9bfb04caa41...cdb95d604573

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[galaxyproject/galaxy] e76960: remove cruft
by GitHub 14 Sep '17

14 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7696027e489c0438fda83293b0efb04a494e465 https://github.com/galaxyproject/galaxy/commit/e7696027e489c0438fda83293b0e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 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-library-view.js 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-library-view.js.map M static/scripts/bundled/analysis.bundled.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-library-view.js Log Message: ----------- remove cruft Commit: 1f69ae5d5bc58a31963a91df2e74807c5746d76b https://github.com/galaxyproject/galaxy/commit/1f69ae5d5bc58a31963a91df2e74… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- refactor few functionas and rename variables Commit: d63601eacf2ae5de703a24efb470255ee8baf535 https://github.com/galaxyproject/galaxy/commit/d63601eacf2ae5de703a24efb470… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 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: ----------- fix the bug with accessing length instead of the variable itself Commit: ba3ffd82d3a56d9ae66e462d0fe82979e5e70a66 https://github.com/galaxyproject/galaxy/commit/ba3ffd82d3a56d9ae66e462d0fe8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: 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 Log Message: ----------- rebuild client Commit: a9bfb04caa41129ffb524b1caf880f1ce90544b5 https://github.com/galaxyproject/galaxy/commit/a9bfb04caa41129ffb524b1caf88… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-14 (Thu, 14 Sep 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 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/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 Log Message: ----------- Merge pull request #4595 from martenson/datalib-various-fixes Datalibs various fixes Compare: https://github.com/galaxyproject/galaxy/compare/a6acf116cd50...a9bfb04caa41

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[galaxyproject/galaxy] 191d11: Python 3 fixes for set_metadata.py
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 191d11c4a096df44e3e469328197358d6200dd20 https://github.com/galaxyproject/galaxy/commit/191d11c4a096df44e3e469328197… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Python 3 fixes for set_metadata.py Commit: b442113e76fde691577bf14bfd0717fcca166539 https://github.com/galaxyproject/galaxy/commit/b442113e76fde691577bf14bfd07… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Don't use + on iterators. Commit: a6acf116cd50aec61fbf9d670145e30f2273a5fc https://github.com/galaxyproject/galaxy/commit/a6acf116cd50aec61fbf9d670145… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #4607 from natefoo/py3-set-meta Python 3 fixes for set_metadata.py Compare: https://github.com/galaxyproject/galaxy/compare/52436aa4f93d...a6acf116cd50

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[galaxyproject/galaxy] b3b713: Write out registry once per job
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3b71343c101ce7ca39ced3308bd2540dcccc59c https://github.com/galaxyproject/galaxy/commit/b3b71343c101ce7ca39ced3308bd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Write out registry once per job Commit: 51f2ecf857dbbdd0e2fd3c78d7f515a87b0ff7e5 https://github.com/galaxyproject/galaxy/commit/51f2ecf857dbbdd0e2fd3c78d7f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Use a string template to write registry xml Commit: 49884cdfa3d9cc06192d204c3cc0d727449987d5 https://github.com/galaxyproject/galaxy/commit/49884cdfa3d9cc06192d204c3cc0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py Log Message: ----------- Remove references to integrated_datatypes_config Commit: 194b249e1d53a480a38910d51e24e267d3164a46 https://github.com/galaxyproject/galaxy/commit/194b249e1d53a480a38910d51e24… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix import order Commit: 52436aa4f93d13a5d2345deaed7a8f0a343a0074 https://github.com/galaxyproject/galaxy/commit/52436aa4f93d13a5d2345deaed7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/evaluation.py Log Message: ----------- Merge pull request #4600 from mvdbeek/datatypes_registroy_in_working_directory Write datatypes registry xml to working directory Compare: https://github.com/galaxyproject/galaxy/compare/11d4380d2b40...52436aa4f93d

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[galaxyproject/usegalaxy-playbook] e7ade3: Changelog for Test Unicycler
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e7ade35498d92021d72e35afb194ec93078471bd https://github.com/galaxyproject/usegalaxy-playbook/commit/e7ade35498d92021… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M CHANGELOG.md Log Message: ----------- Changelog for Test Unicycler

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[galaxyproject/galaxy] c5a081: Retry job submissions in ShellJobRunner
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5a08186b7ff8090b5ec7191ed149c3e13c9aa90 https://github.com/galaxyproject/galaxy/commit/c5a08186b7ff8090b5ec7191ed14… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Retry job submissions in ShellJobRunner If I submit a large amount of jobs in a very short time I sometimes see ``` galaxy.jobs.runners.cli ERROR 2017-09-11 05:03:02,404 (17633) submission failed (stderr): qsub: submit error (Invalid credential) ``` in my logs for a minor subset of jobs (2 out of 120 in the last instance that this happened). In this case waiting a little while and trying again solves the problem. By default we will try submitting the job 3 times, and sleep 10 seconds before trying again. Commit: ecd8b90e44decbef60db4359bf4837ef5b12ed1f https://github.com/galaxyproject/galaxy/commit/ecd8b90e44decbef60db4359bf48… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Decrease log-level for resubmission msg and specifiy log level directly in if/else clause. Thx @erasche. Commit: 11d4380d2b40b4e18806f6b2d1e07f4a6eec1f8b https://github.com/galaxyproject/galaxy/commit/11d4380d2b40b4e18806f6b2d1e0… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Merge pull request #4599 from mvdbeek/make_qsub_submissions_more_robust Retry job submissions in ShellJobRunner Compare: https://github.com/galaxyproject/galaxy/compare/e33b35def345...11d4380d2b40

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[galaxyproject/galaxy] 60dd73: Remove unreachable statements
by GitHub 13 Sep '17

13 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60dd7306d04c47aa4a9b2efed149cb3c4d259a10 https://github.com/galaxyproject/galaxy/commit/60dd7306d04c47aa4a9b2efed149… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Remove unreachable statements Commit: 61e05670c26cb75b9a76e3660e049a6f9383a644 https://github.com/galaxyproject/galaxy/commit/61e05670c26cb75b9a76e3660e04… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py Log Message: ----------- now unused imports Commit: e33b35def3453d6158bf6ed4109c3ec2dbffbc37 https://github.com/galaxyproject/galaxy/commit/e33b35def3453d6158bf6ed4109c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-13 (Wed, 13 Sep 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/model/metadata.py M lib/galaxy/objectstore/azure_blob.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/grids/repository_grids.py Log Message: ----------- Merge pull request #4603 from erasche/dead-code Remove unreachable statements Compare: https://github.com/galaxyproject/galaxy/compare/26c7abb130ba...e33b35def345

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[galaxyproject/galaxy] 8adbf0: Add show/hide deleted/hidden links when history is...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8adbf03f565b1d60fb42ca986d184387e19e94af https://github.com/galaxyproject/galaxy/commit/8adbf03f565b1d60fb42ca986d18… Author: chambm <matt.chambers42(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Add show/hide deleted/hidden links when history is filtered by find box; addresses #4103 Commit: 97264e3de8d9ea8cd0b4cec9bbe91b1b3d81636d https://github.com/galaxyproject/galaxy/commit/97264e3de8d9ea8cd0b4cec9bbe9… Author: chambm <matt.chambers42(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Try to start personal CI build Commit: 1aadd7866f6b94460a5703a8aa35949f7632adcf https://github.com/galaxyproject/galaxy/commit/1aadd7866f6b94460a5703a8aa35… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M static/maps/mvc/history/history-view-edit.js.map 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/history/history-view-edit.js Log Message: ----------- Make client. Commit: fd1926767996a161cd2fc8bd184e6835fd688765 https://github.com/galaxyproject/galaxy/commit/fd1926767996a161cd2fc8bd184e… Author: Matt Chambers <matt.chambers42(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M static/maps/mvc/history/history-view-edit.js.map 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/history/history-view-edit.js Log Message: ----------- Merge pull request #2 from dannon/chambmdev Make client Commit: 26c7abb130bade73b64284956f0077f35067095f https://github.com/galaxyproject/galaxy/commit/26c7abb130bade73b64284956f00… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/history/history-view-edit.js.map 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/history/history-view-edit.js Log Message: ----------- Merge remote-tracking branch 'chambm/dev' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9468bef057f6...26c7abb130ba

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[galaxyproject/galaxy] 79a378: Small improvements to workflow editor Selenium tes...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 79a37830bb75ccd4d8c18236f7938a50a83f87c2 https://github.com/galaxyproject/galaxy/commit/79a37830bb75ccd4d8c18236f793… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Small improvements to workflow editor Selenium tests. I saw a failed test earlier that would have been fixed by a switch to wait_for_and_click in workflow_editor_click_options. This makes that switch and moves some of these workflow editor helper functions into navigates_galaxy.py for reuse by other test cases and by library users. Commit: 9468bef057f6372f75ceaee832457386c79e39cc https://github.com/galaxyproject/galaxy/commit/9468bef057f6372f75ceaee83245… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #4592 from jmchilton/workflow_click_fix Small improvements to workflow editor Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/2e160935d9ce...9468bef057f6

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[galaxyproject/galaxy] 822678: Support for applying window title on display() of ...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 82267855ed3bc6d3f8911acf6e7e388023f6693d https://github.com/galaxyproject/galaxy/commit/82267855ed3bc6d3f8911acf6e7e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/layout/page.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js 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/layout/page.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Support for applying window title on display() of views. Commit: 9a66adb4fe7a3be6e07baaec6cef8f553d6b486d https://github.com/galaxyproject/galaxy/commit/9a66adb4fe7a3be6e07baaec6cef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Standard (for now) paren spacing. Commit: 84de84294c95110f0ee3059ad8a5e9924daf6a9d https://github.com/galaxyproject/galaxy/commit/84de84294c95110f0ee3059ad8a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js 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/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js Log Message: ----------- History List, Tours, and User Preferences titles Commit: 6b2277e37dd0520de26442701407badcf792cfab https://github.com/galaxyproject/galaxy/commit/6b2277e37dd0520de26442701407… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Automatically append 'Galaxy | ' to title instead of requiring it for all view titles. Commit: 2cb8a28f7be2ff8b7076ef04a6d575d276e3bca6 https://github.com/galaxyproject/galaxy/commit/2cb8a28f7be2ff8b7076ef04a6d5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M static/maps/layout/page.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js 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/layout/page.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Rebuild. Commit: 9a0506c5c0832c93dcd7844ea9de92b619c00773 https://github.com/galaxyproject/galaxy/commit/9a0506c5c0832c93dcd7844ea9de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Include Galaxy brand in titles. Commit: 91eb849500faec57bebb35228a5a2e2638be70aa https://github.com/galaxyproject/galaxy/commit/91eb849500faec57bebb35228a5a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Use 'Galaxy / Brand' consistent styling instead of 'Galaxy | Brand' Commit: 935f25aa32b3a22a53de02d5bfe4b5f7de819a0b https://github.com/galaxyproject/galaxy/commit/935f25aa32b3a22a53de02d5bfe4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M static/maps/mvc/grid/grid-shared.js.map 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/grid/grid-shared.js Log Message: ----------- Titles for abstract grids w/ plural set. Commit: f83188e7f3c19a5686a623d9bb30f683cd04ff27 https://github.com/galaxyproject/galaxy/commit/f83188e7f3c19a5686a623d9bb30… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map 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/grid/grid-view.js Log Message: ----------- Normal grid title propagation. Commit: 928ad294936c4f6ca4ebc007963578527886af02 https://github.com/galaxyproject/galaxy/commit/928ad294936c4f6ca4ebc0079635… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-09 (Sat, 09 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Localize displayed titles. Commit: 6b14dda216d103da518a906f4eda018eb58bafbe https://github.com/galaxyproject/galaxy/commit/6b14dda216d103da518a906f4eda… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js 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/layout/page.js M static/scripts/mvc/grid/grid-view.js Log Message: ----------- Grids do a late initialization and the title isn't available until this happens (after display()), so provide a way to allow views to set title late if necessary. Commit: 59d0e297f7217faed3d7c6d30e88678f1eaef600 https://github.com/galaxyproject/galaxy/commit/59d0e297f7217faed3d7c6d30e88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- When title isn't set, revert to the default -- otherwise display()'d contents without titles show up with the previous and incorrect titles. Commit: 2c40efb6c236220ccaffd7893fafa1b8969f1ad2 https://github.com/galaxyproject/galaxy/commit/2c40efb6c236220ccaffd7893faf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/utils/utils.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js 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/layout/page.js M static/scripts/mvc/grid/grid-view.js M static/scripts/utils/utils.js Log Message: ----------- Minor refactor, use a single Utils.setWindowTitle() method. Commit: a5dbf29e13e1d558ac1c6798e7952963b0599e6e https://github.com/galaxyproject/galaxy/commit/a5dbf29e13e1d558ac1c6798e795… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Use standard naming for Utils import. Commit: ecb4e06799fb61c4577e1a52276359149670cdf7 https://github.com/galaxyproject/galaxy/commit/ecb4e06799fb61c4577e1a522763… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/utils/utils.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- We apparently always use '|' in the title, even though masthead uses '/'. It does look better. Commit: ae1c68c7dbb9214def95e97a2f6714c68e23927b https://github.com/galaxyproject/galaxy/commit/ae1c68c7dbb9214def95e97a2f67… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Set title on base admin page. Commit: ff5b430319196a61e2a593b04a4bc60859062e3c https://github.com/galaxyproject/galaxy/commit/ff5b430319196a61e2a593b04a4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Workflow editor title fix (not new-style, to keep it simple and use the approach consistent with the .mako layout used. Commit: c71d3035ab7bbcdfb682a39e4e9e3cb49417289d https://github.com/galaxyproject/galaxy/commit/c71d3035ab7bbcdfb682a39e4e9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_panel.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_published_histories_grid.py A test/selenium_tests/test_saved_histories.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into titles_in_views Commit: 2e160935d9ceb3ca8441e3b51107594b9539573d https://github.com/galaxyproject/galaxy/commit/2e160935d9ceb3ca8441e3b51107… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/utils/utils.js M static/maps/layout/page.js.map M static/maps/mvc/grid/grid-shared.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/history-list.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js 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/layout/page.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/tours.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #4578 from dannon/titles_in_views Delegate displaying of page titles to Layout.display() Compare: https://github.com/galaxyproject/galaxy/compare/36a3a6b3d9c0...2e160935d9ce

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[galaxyproject/galaxy] 87b798: FAST5 archive support
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87b798d40a5acb78ddf428d82639f2d5a7f40098 https://github.com/galaxyproject/galaxy/commit/87b798d40a5acb78ddf428d82639… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- FAST5 archive support Commit: 9e6cb13e314d451cba7e0eaf841f05410ac19750 https://github.com/galaxyproject/galaxy/commit/9e6cb13e314d451cba7e0eaf841f… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-06 (Wed, 06 Sep 2017) Changed paths: A .ci/autopep8.sh M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/docker-compose.yml M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A SECURITY_POLICY.md M client/bower.json A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/mvc/citation/citation-view.js A client/galaxy/scripts/mvc/collection/base-creator.js M 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client/galaxy/scripts/onload.js M client/galaxy/scripts/reports_webapp/run_stats.js M client/galaxy/scripts/ui/scroll-panel.js M client/galaxy/scripts/utils/graph.js M client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/galaxy_bootstrap/overrides.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/galaxy_variables.less M client/galaxy/style/less/history.less R client/galaxy/style/less/iphone.less A client/galaxy/style/less/theme/plain.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/ui/paired-collection-creator.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js A client/package-lock.json M client/package.json M client/toolshed/scripts/mvc/groups/group-list-view.js M client/webpack.config.js A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/dependency_resolvers_conf.xml.sample A config/error_report.yml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A config/lmod_modules_mapping.yml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/jupyter/static/js/jupyter.js M config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/neo/config/neo.xml M config/plugins/interactive_environments/neo/static/js/neo.js M config/plugins/interactive_environments/neo/templates/neo.mako M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M config/plugins/visualizations/charts/static/client/components/screenshot.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js M 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config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako A config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/static/script.js A config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/tool_list/config/tool_list.yml A config/plugins/webhooks/demo/tool_list/helper/__init__.py A 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tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wc_gnu.xml M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg.xml M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into fast5 Commit: 2fc60430a187cc4a95e2d935b89b65f52acd86b8 https://github.com/galaxyproject/galaxy/commit/2fc60430a187cc4a95e2d935b89b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix formatting to make tox happy Commit: f07c6a98431f1a4c2a2d81f99d3b54a23f0a901e https://github.com/galaxyproject/galaxy/commit/f07c6a98431f1a4c2a2d81f99d3b… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- optimized sniffing, subclassed different tarball types Commit: 297d2353ce594b3325d029fb72c3ffd825c07f57 https://github.com/galaxyproject/galaxy/commit/297d2353ce594b3325d029fb72c3… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz Log Message: ----------- add datatype tests Commit: 49258a7df8bb0f8c489c06dc2a77c27b2244b5f9 https://github.com/galaxyproject/galaxy/commit/49258a7df8bb0f8c489c06dc2a77… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fixed sniff order and misc linting errors Commit: 08b5a47c396d38d288d54806edb87e9e717b799d https://github.com/galaxyproject/galaxy/commit/08b5a47c396d38d288d54806edb8… Author: jvolkening <jdv(a)base2bio.com> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/utils/uploadbox.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/utils/uploadbox.js.map 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/history/options-menu.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/utils/uploadbox.js A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_published_histories_grid.py M tools/data_source/upload.py M tools/filters/join.py M tools/filters/joiner.xml Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into fast5 Commit: 36a3a6b3d9c0b00c26ae861649983a441f725ae8 https://github.com/galaxyproject/galaxy/commit/36a3a6b3d9c0b00c26ae86164998… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/test.fast5.tar A lib/galaxy/datatypes/test/test.fast5.tar.bz2 A lib/galaxy/datatypes/test/test.fast5.tar.gz Log Message: ----------- Merge pull request #4569 from jvolkening/fast5 fast5_archive datatype Compare: https://github.com/galaxyproject/galaxy/compare/c0e2db2d98ea...36a3a6b3d9c0

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[galaxyproject/galaxy] 7e2727: Remove bam to bai converter
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e2727bc0a74868198e7e457f99df3d1e39f1ddb https://github.com/galaxyproject/galaxy/commit/7e2727bc0a74868198e7e457f99d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Remove bam to bai converter This converter served no real purpose (you can download bam index files by clicking on the floppy icon, and we never had a bai datatype). Commit: c0e2db2d98ead7f9d532ad0f5106d644019d5265 https://github.com/galaxyproject/galaxy/commit/c0e2db2d98ead7f9d532ad0f5106… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #4598 from mvdbeek/remove_bai_converter Remove bam to bai converter Compare: https://github.com/galaxyproject/galaxy/compare/e1cdb740cb43...c0e2db2d98ea

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[galaxyproject/galaxy] 5da62c: Cancel workflow invocations when histories are del...
by GitHub 12 Sep '17

12 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5da62ca264826bca0318a08f10d9d5e0ab6a3cc8 https://github.com/galaxyproject/galaxy/commit/5da62ca264826bca0318a08f10d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Cancel workflow invocations when histories are deleted. With test case, rebased with spelling fixes thanks to @nsoranzo. xref #3555 (third point) Commit: 7efe561867b7c5a3a16e873c215889c58d225277 https://github.com/galaxyproject/galaxy/commit/7efe561867b7c5a3a16e873c2158… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Rework invocation state tracking in API tests. At the insistence of @nsoranzo, be more explicit about waiting for workflow test in API tests. While I was in there I also setup new abstractions for waiting on state and updated various workflow cancelling tests to use test_history context for better error reporting. Commit: e1cdb740cb431104439dbbd63c2f1c0472d2c16b https://github.com/galaxyproject/galaxy/commit/e1cdb740cb431104439dbbd63c2f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-09-12 (Tue, 12 Sep 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #4580 from jmchilton/deleted_history Cancel workflow invocations when histories are deleted. Compare: https://github.com/galaxyproject/galaxy/compare/74a486084bcb...e1cdb740cb43

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[galaxyproject/galaxy] 0a54a3: remove unneeded property, fix import from history ...
by GitHub 11 Sep '17

11 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0a54a313b77b7c47cf57d5f7365cd37231b879ea https://github.com/galaxyproject/galaxy/commit/0a54a313b77b7c47cf57d5f7365c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-foldertoolbar-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/style/blue/base.css M static/style/blue/library.css Log Message: ----------- remove unneeded property, fix import from history targets some refactoring Commit: 5b87754ab77dbba1aab632345517e404bc421295 https://github.com/galaxyproject/galaxy/commit/5b87754ab77dbba1aab632345517… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-09-08 (Fri, 08 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- refactor traversing to use latest() instead Commit: 74a486084bcb5d0aef50bebe499b9b39b8a68a74 https://github.com/galaxyproject/galaxy/commit/74a486084bcb5d0aef50bebe499b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-11 (Mon, 11 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-foldertoolbar-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-folderlist-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #4579 from martenson/fix-reload-error datalibs: fix two bugs, refactor Compare: https://github.com/galaxyproject/galaxy/compare/a190903bd031...74a486084bcb

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