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

[galaxyproject/galaxy] 1931bd: lazy load metadata to speed up history loading
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1931bd59077f97946a1af6daa93bc920fceee58e https://github.com/galaxyproject/galaxy/commit/1931bd59077f97946a1af6daa93b… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- lazy load metadata to speed up history loading Commit: 7d4f0d82de328ffb763737c067fc9332b61534e9 https://github.com/galaxyproject/galaxy/commit/7d4f0d82de328ffb763737c067fc… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- fix indentation Commit: 52078baf99ed2aadae4b30f6b71ae00aecba521a https://github.com/galaxyproject/galaxy/commit/52078baf99ed2aadae4b30f6b71a… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- don't load or overwrite a value with a not-yet-loaded value (i.e. None) Commit: 27e43e8907a5fb529cdf36175a6ffe04de762379 https://github.com/galaxyproject/galaxy/commit/27e43e8907a5fb529cdf36175a6f… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/datatypes/metadata.py Log Message: ----------- Load deferred column before pickling dataset instance Commit: 0fce226b96f98bf3393935602e0b5e9a8762bc4e https://github.com/galaxyproject/galaxy/commit/0fce226b96f98bf3393935602e0b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/datatypes/metadata.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py Log Message: ----------- Merge pull request #1179 from abretaud/defer_metadata Lazy load HDA/LDDA metadata to speed up history loading Compare: https://github.com/galaxyproject/galaxy/compare/dd429b640ffe...0fce226b96f9

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[galaxyproject/galaxy] f14b38: UI, list of pairs collection creator: prevent vice...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f14b38124bc08c228bfce30f27d1815d7dd27c0b https://github.com/galaxyproject/galaxy/commit/f14b38124bc08c228bfce30f27d1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: prevent vice-versa pair duplication by removing paired dataset from both temp lists during auto pairing Commit: c1ce8ef0ce074271c9ba7a9a1718258482cca69f https://github.com/galaxyproject/galaxy/commit/c1ce8ef0ce074271c9ba7a9a1718… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.js Log Message: ----------- UI, list of pairs collection creator: improve auto-pair error message to be more beginner friendly(?) Commit: dd429b640ffeb656a1fd61b49e88db890e7743cf https://github.com/galaxyproject/galaxy/commit/dd429b640ffeb656a1fd61b49e88… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/maps/mvc/collection/list-of-pairs-collection-creator.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/collection/list-of-pairs-collection-creator.js Log Message: ----------- Merge pull request #1310 from carlfeberhard/fix.lop-creator UI, list of pairs creator: properly remove datasets from the filtered lists when pairing Compare: https://github.com/galaxyproject/galaxy/compare/812343d8ccc1...dd429b640ffe

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[galaxyproject/galaxy] 195928: Include link to toolshed repository, and make sure...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1959288637bf8c4f11da70df5cd5558c1bc1099a https://github.com/galaxyproject/galaxy/commit/1959288637bf8c4f11da70df5cd5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Include link to toolshed repository, and make sure upgrade message is not overwritten by tool_version changes. Commit: c143748e62e976fa3a43a721ed49bdbdc78ea980 https://github.com/galaxyproject/galaxy/commit/c143748e62e976fa3a43a721ed49… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Better formatting of workflow warning message. Commit: cd61cdc51b387d6cfb7905307c669e17111ab96d https://github.com/galaxyproject/galaxy/commit/cd61cdc51b387d6cfb7905307c66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add back tool id to pass unit tests. Commit: b633c949c875788d5bba9ae0126882b3439d7f7e https://github.com/galaxyproject/galaxy/commit/b633c949c875788d5bba9ae01268… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Mention tool id as hover text on version changes. Commit: 812343d8ccc10a77bab58287178cceb64ad9cb39 https://github.com/galaxyproject/galaxy/commit/812343d8ccc10a77bab58287178c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1286 from mvdbeek/cross_toolshed_tool_fetching Include link to old and new toolshed repository, and make sure upgrade message is… Compare: https://github.com/galaxyproject/galaxy/compare/a7e60eae2c27...812343d8ccc1

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[galaxyproject/galaxy] 6c9a82: Fix for Section upgrade messages.
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 6c9a82e142c5bf70ae4612f094b8d0c89e3fd2f3 https://github.com/galaxyproject/galaxy/commit/6c9a82e142c5bf70ae4612f094b8… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for Section upgrade messages. Commit: 2c0ad432f8485cb40719adfa8ecbbf1a342afd03 https://github.com/galaxyproject/galaxy/commit/2c0ad432f8485cb40719adfa8ecb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use test param label instead of param label in conditional upgrade missing message. Commit: 989f961fb6351d1f63374b4fc40429c1e897b1e2 https://github.com/galaxyproject/galaxy/commit/989f961fb6351d1f63374b4fc404… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1218 from blankenberg/rerunfix_15.10 [15.10] Fix for Section and conditional upgrade messages. Compare: https://github.com/galaxyproject/galaxy/compare/66146ad5d0e1...989f961fb635

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[galaxyproject/galaxy] ce6cd0: Enforce metrics related to moving toward modern cl...
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce6cd03f6c7f020a8127025c49224f1bb920bc18 https://github.com/galaxyproject/galaxy/commit/ce6cd03f6c7f020a8127025c4922… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M tox.ini Log Message: ----------- Enforce metrics related to moving toward modern client infrastructure. Having a CI enforced blacklist and then a whitelist of files failing to meet style guidelines (as well as expanding list of rules enforced) may have helped create incentive to rework Galaxy toward a more compliant and uniform Python styling. We briefly discussed the possibility of doing this with other team code base objectives on a conference call - in particular to help the transition toward replacing all of the web controllers with API controllers and eliminating the use of Python mako files for rendering web content and replacing it with client side templates. To do this I have created two rough metrics - the number of lines of web controller code in the Galaxy app and the number of mako files in the templates directory. The hope is that people feel ... compelled to lower these numbers. While these metrics are admittedly rough, they do also encourage de-duplication of mako templates and transition of API code into managers (in addition to elimination of functions) both of these secondary incentives are also good things and should be project objectives. Commit: a7e60eae2c2721e7d4377112b7aaceb8424fd3da https://github.com/galaxyproject/galaxy/commit/a7e60eae2c2721e7d4377112b7aa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M tox.ini Log Message: ----------- Merge pull request #1292 from jmchilton/client_incentives Enforce metrics related to moving toward modern client infrastructure. Compare: https://github.com/galaxyproject/galaxy/compare/eb4b8e716d26...a7e60eae2c27

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[galaxyproject/galaxy] 760c2b: Properly show and label hidden datasets on rerurn
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 760c2b56bee664f2f874e2cc26d2129858da1bb1 https://github.com/galaxyproject/galaxy/commit/760c2b56bee664f2f874e2cc26d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly show and label hidden datasets on rerurn Commit: 66146ad5d0e17e35b6eee50699b0261422835000 https://github.com/galaxyproject/galaxy/commit/66146ad5d0e17e35b6eee50699b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1305 from guerler/fix_workflow_rerun_001 [15.10] Properly show and label hidden datasets on workflow reruns Compare: https://github.com/galaxyproject/galaxy/compare/6a47d2d3a7f2...66146ad5d0e1

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[galaxyproject/galaxy] 1aafc4: Dead sendmail_path vars, this is unused in favor o...
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aafc489356d4ad62a00b82f1b0679d66f037be4 https://github.com/galaxyproject/galaxy/commit/1aafc489356d4ad62a00b82f1b06… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Dead sendmail_path vars, this is unused in favor of smtp (as of a long time ago) Commit: c0b349306f17ed924a5673fab465d105d2cfdaf2 https://github.com/galaxyproject/galaxy/commit/c0b349306f17ed924a5673fab465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Add smtp_ssl option to toolshed mailing capabilities, update .sample to include the smtp auth/ssl. Commit: eb4b8e716d26897e58c78c08e9a2d62a770604f5 https://github.com/galaxyproject/galaxy/commit/eb4b8e716d26897e58c78c08e9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Merge pull request #1299 from dannon/mail_fixes Minor mail config cleanup Compare: https://github.com/galaxyproject/galaxy/compare/6580d5129386...eb4b8e716d26

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[galaxyproject/galaxy] 48064c: * Clarify comment in XML
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48064cc20352d3e38f985769ba5b2eeb66f051a8 https://github.com/galaxyproject/galaxy/commit/48064cc20352d3e38f985769ba5b… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- * Clarify comment in XML Commit: e40fbe5374f906139f8be7a3ceb001f049a6b244 https://github.com/galaxyproject/galaxy/commit/e40fbe5374f906139f8be7a3ceb0… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst Log Message: ----------- * Add comment about base_path in sample config * Add documentation on dependency resolvers Commit: 584d886b5ee68257921dff24c4dbe0a2dbb0c00c https://github.com/galaxyproject/galaxy/commit/584d886b5ee68257921dff24c4db… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py Log Message: ----------- * Mention modulepath attribute in dependency resolver docs * Use modulepath in both environment modules resolvers * Export MODULEPATH in generated shell command * Add logging for operation of dependency resolvers Commit: 035f1b5d663841fa61d32ba79e1b43553dab4fab https://github.com/galaxyproject/galaxy/commit/035f1b5d663841fa61d32ba79e1b… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- * Incorporate documentation fixes from nsoranzo * Replace {} and .format with %s and % to preserve Python 2.6 compatibility * Add a modulepath= paranter to the fake resolver (Bunch object) used to test the modules dependency resolver Commit: 2b90ca9b0e23715bd7a03614fa989bcf540f73e9 https://github.com/galaxyproject/galaxy/commit/2b90ca9b0e23715bd7a03614fa98… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- * Replaced incorrect %b with %s Commit: 73b6fb23db300501c9124c61c90d73d2c28dc7a4 https://github.com/galaxyproject/galaxy/commit/73b6fb23db300501c9124c61c90d… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M doc/source/admin/dependency_resolvers.rst Log Message: ----------- * Replaced all references to "version number" with "version string" Commit: 6580d5129386ab5b8634583c5378dfc340ed2800 https://github.com/galaxyproject/galaxy/commit/6580d5129386ab5b8634583c5378… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M config/dependency_resolvers_conf.xml.sample A doc/source/admin/dependency_resolvers.rst M doc/source/admin/index.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/modules.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #1296 from pvanheus/env-modules-resolve Documentation for dependency resolvers Compare: https://github.com/galaxyproject/galaxy/compare/bca004eff860...6580d5129386

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[galaxyproject/usegalaxy-playbook] 5ccdca: Update Test
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ccdca872d0821f0cac607105e852ec16de18468 https://github.com/galaxyproject/usegalaxy-playbook/commit/5ccdca872d0821f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.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 M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version A stage/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample A stage/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.xml A stage/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js A stage/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M stage/files/interactive_environments/plugins/common/templates/ie.mako M stage/files/interactive_environments/plugins/ipython/config/ipython.ini.sample M stage/files/interactive_environments/plugins/ipython/static/js/ipython.js M stage/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 5757ee61c1a6cf4c6972451191da20555be33162 https://github.com/galaxyproject/usegalaxy-playbook/commit/5757ee61c1a6cf4c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: A files/galaxy/common/static/welcome_img/Barcelona_2015.png A files/galaxy/common/static/welcome_img/MPI-HLR-Galaxy.png M stage/group_vars/all.yml M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Conflicts: stage/group_vars/all.yml Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0db21fc8feab...…

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[galaxyproject/usegalaxy-playbook] 0db21f: Update Test Tool Shed to latest dev and use wheels...
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0db21fc8feab6ff45a5346e307f8d178c7fdeef2 https://github.com/galaxyproject/usegalaxy-playbook/commit/0db21fc8feab6ff4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M stage/group_vars/toolshedservers.yml M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Update Test Tool Shed to latest dev and use wheels. WARNING: paste and repoze were fixed *manually* (by manually copying their __init__.pys after installing), see galaxyproject/galaxy#1301.

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