October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] fea863: Add a workaround to return a proper error code if ...
by GitHub 11 Oct '15

11 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fea863081ce8a41bbd10c8d26c2409c660e0ad88 https://github.com/galaxyproject/galaxy/commit/fea863081ce8a41bbd10c8d26c24… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add a workaround to return a proper error code if a R packge fails to install. Commit: 858eed632a6e8228ab71c02c2d7b74f3f9ea5dcd https://github.com/galaxyproject/galaxy/commit/858eed632a6e8228ab71c02c2d7b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-11 (Sun, 11 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #892 from bgruening/setupRinstall-fail Add a workaround to return a proper error code Compare: https://github.com/galaxyproject/galaxy/compare/408c82c43d6d...858eed632a6e

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[galaxyproject/galaxy] 45763b: Use common exceptions in tools
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45763bf85e2a868476b2807bac1ddf92be844f76 https://github.com/galaxyproject/galaxy/commit/45763bf85e2a868476b2807bac1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Use common exceptions in tools Commit: 408c82c43d6d05650668067b82aee8e8ece7d678 https://github.com/galaxyproject/galaxy/commit/408c82c43d6d05650668067b82ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-10 (Sat, 10 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #874 from guerler/tool_execution_001 Use common exceptions in tools Compare: https://github.com/galaxyproject/galaxy/compare/fae21e30f56e...408c82c43d6d

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[galaxyproject/usegalaxy-playbook] ad9674: Main: virtualenv and module fixes for Stampede
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ad96740f1a88fec30aea159dc810a06f7398edaf https://github.com/galaxyproject/usegalaxy-playbook/commit/ad96740f1a88fec3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Main: virtualenv and module fixes for Stampede

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[galaxyproject/usegalaxy-playbook] a17ff1: Test mutable configs
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a17ff1ef2c59d335cc15521964e7ea55bbbff59b https://github.com/galaxyproject/usegalaxy-playbook/commit/a17ff1ef2c59d335… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: 89cbe794153c334a723ff0b80f9db8aa07bd3f84 https://github.com/galaxyproject/usegalaxy-playbook/commit/89cbe794153c334a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 6757018a7c6397365f2cc459db853857c6bb5b1a https://github.com/galaxyproject/usegalaxy-playbook/commit/6757018a7c639736… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Test: Ensure Pulsar jobs use Galaxy's venv, not Pulsar's. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3b6a3b14c56f...…

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[galaxyproject/galaxy] 31c89e: UI, Collections: allow expansion to fetch details ...
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31c89ea29c2c504878f336d90dfcf320b873b2ee https://github.com/galaxyproject/galaxy/commit/31c89ea29c2c504878f336d90dfc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- UI, Collections: allow expansion to fetch details for DatasetDCEs (assuming they're HDAs); move rerunnable and creating_job fetch to HDAs Commit: 69cd5a98dcda30771ce78118ebd3a934dfb09c65 https://github.com/galaxyproject/galaxy/commit/69cd5a98dcda30771ce78118ebd3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- Merge pull request #854 from carlfeberhard/release_15.10 [15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… Commit: 4705409d386f6cabe1874ac044617d6ed226a80e https://github.com/galaxyproject/galaxy/commit/4705409d386f6cabe1874ac04461… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a0ad2b75c29eca2c33ccfcdd4aa4a834c06c5265 https://github.com/galaxyproject/galaxy/commit/a0ad2b75c29eca2c33ccfcdd4aa4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #873 from erasche/api-key-backpatch [release_15.10] Expose all API keys to admins under REMOTE_USER Commit: 90506ba1c6b83731cf5e11badabfde1f8d3e34c4 https://github.com/galaxyproject/galaxy/commit/90506ba1c6b83731cf5e11badabf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Fix for no longer being able to access data managers. Have datamanager links point to root with tool_id provided while targeting a new window. Commit: 38b9ca3400eaf482c50c6224438d3341241453c1 https://github.com/galaxyproject/galaxy/commit/38b9ca3400eaf482c50c6224438d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #879 from blankenberg/datamanager-fix [15.10] Fix for no longer being able to access data managers. Commit: fae21e30f56e5a1e92aa80f58daa684eeb87aaa9 https://github.com/galaxyproject/galaxy/commit/fae21e30f56e5a1e92aa80f58daa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_15.10' into dev Conflicts: lib/galaxy/web/framework/middleware/remoteuser.py Compare: https://github.com/galaxyproject/galaxy/compare/f10047c4d31e...fae21e30f56e

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[galaxyproject/galaxy] 90506b: Fix for no longer being able to access data manage...
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 90506ba1c6b83731cf5e11badabfde1f8d3e34c4 https://github.com/galaxyproject/galaxy/commit/90506ba1c6b83731cf5e11badabf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Fix for no longer being able to access data managers. Have datamanager links point to root with tool_id provided while targeting a new window. Commit: 38b9ca3400eaf482c50c6224438d3341241453c1 https://github.com/galaxyproject/galaxy/commit/38b9ca3400eaf482c50c6224438d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #879 from blankenberg/datamanager-fix [15.10] Fix for no longer being able to access data managers. Compare: https://github.com/galaxyproject/galaxy/compare/a0ad2b75c29e...38b9ca3400ea

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[galaxyproject/galaxy] c72618: Slight tweak to sidebar section naming from 'secur...
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c72618680287d9affd56f5c4434ef7a9b9525e8d https://github.com/galaxyproject/galaxy/commit/c72618680287d9affd56f5c4434e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Slight tweak to sidebar section naming from 'security' to 'user management', for users, groups, roles, api keys Commit: f10047c4d31ef44ca6be03894224ecc36d44627e https://github.com/galaxyproject/galaxy/commit/f10047c4d31ef44ca6be03894224… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Merge pull request #877 from dannon/minor_naming_tweak Slight tweak to sidebar section naming from 'security' to 'user manag… Compare: https://github.com/galaxyproject/galaxy/compare/77307e686b31...f10047c4d31e

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[galaxyproject/galaxy] c95955: Remove unused variable
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c95955e79e3c9dedb36b75734a859842a1c1dbed https://github.com/galaxyproject/galaxy/commit/c95955e79e3c9dedb36b75734a85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove unused variable Commit: e62b7e16950efd4aa798683f1b1909e3fdc37308 https://github.com/galaxyproject/galaxy/commit/e62b7e16950efd4aa798683f1b19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Reinsert update state Commit: f6bfe8f7d0a00ea62e81cc1a1571ad40b5db0a2f https://github.com/galaxyproject/galaxy/commit/f6bfe8f7d0a00ea62e81cc1a1571… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove upload dataset handling Commit: 77307e686b31b2e300669f874b580d89be0e7fee https://github.com/galaxyproject/galaxy/commit/77307e686b31b2e300669f874b58… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #876 from guerler/tool_execution_002 Reinsert update state function to fix workflow execution which still relies on it. Compare: https://github.com/galaxyproject/galaxy/compare/60f6dc178580...77307e686b31

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[galaxyproject/galaxy] 7db17b: Refactor the remote user middleware for complexity
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7db17bb9a836d33a8dcb5a67febba0cbe4d3319c https://github.com/galaxyproject/galaxy/commit/7db17bb9a836d33a8dcb5a67febb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Refactor the remote user middleware for complexity Commit: cf7d10b3b55a979e7f6abe69059a660eac253b74 https://github.com/galaxyproject/galaxy/commit/cf7d10b3b55a979e7f6abe69059a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Correct typo Commit: 60f6dc1785802d307a0ac0e6c3bb33ca0b3fc161 https://github.com/galaxyproject/galaxy/commit/60f6dc1785802d307a0ac0e6c3bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #875 from erasche/remoteuser-middleware-cleanup Refactor the remote user middleware for complexity Compare: https://github.com/galaxyproject/galaxy/compare/a937e233acb1...60f6dc178580

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[galaxyproject/galaxy] 470540: Expose all API keys to admins under REMOTE_USER
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 4705409d386f6cabe1874ac044617d6ed226a80e https://github.com/galaxyproject/galaxy/commit/4705409d386f6cabe1874ac04461… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a0ad2b75c29eca2c33ccfcdd4aa4a834c06c5265 https://github.com/galaxyproject/galaxy/commit/a0ad2b75c29eca2c33ccfcdd4aa4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #873 from erasche/api-key-backpatch [release_15.10] Expose all API keys to admins under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/69cd5a98dcda...a0ad2b75c29e

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