- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 952f3f: Open select2 dropdown on click
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 952f3f9b7a04a6e7d3185da76d84dea0fa9bca8d https://github.com/galaxyproject/galaxy/commit/952f3f9b7a04a6e7d3185da76d84… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-default.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-default.js M static/style/blue/base.css Log Message: ----------- Open select2 dropdown on click Commit: bca004eff8607e347d440ce5fc5d086d7acb45f9 https://github.com/galaxyproject/galaxy/commit/bca004eff8607e347d440ce5fc5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-11 (Fri, 11 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-select-default.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-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1298 from guerler/fix_select2_open_000 Open select2 drop down on caret click Compare: https://github.com/galaxyproject/galaxy/compare/f8d95abf0616...bca004eff860

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[galaxyproject/galaxy] 833459: Fixes for dataset 'cleanup'/association linking wh...
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 8334593de11e915389b1da58c3b5db26121c7bef https://github.com/galaxyproject/galaxy/commit/8334593de11e915389b1da58c3b5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 7923360dcec48b2e98d7c2a5bcae5f47187d6bf6 https://github.com/galaxyproject/galaxy/commit/7923360dcec48b2e98d7c2a5bcae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Commit: 41a56ead749bd25c6bc46107201b0e62bb65af9a https://github.com/galaxyproject/galaxy/commit/41a56ead749bd25c6bc46107201b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix list collection creator being cutoff by restoring height: 100% Commit: 94b049926d844a8aa54017b6d7a9983b94203316 https://github.com/galaxyproject/galaxy/commit/94b049926d844a8aa54017b6d7a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M static/maps/mvc/collection/list-collection-creator.js.map M static/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Merge pull request #1258 from carlfeberhard/release_15.10 [15.10] Fix list collection creator being cutoff by restoring height: 100% Commit: 2be17071f35bb5db2298883aff107134a53701d1 https://github.com/galaxyproject/galaxy/commit/2be17071f35bb5db2298883aff10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #1228 from blankenberg/wf_extrac_15.10 [15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 0d98cf8ab76a374362302547b5699fa024d5ce21 https://github.com/galaxyproject/galaxy/commit/0d98cf8ab76a374362302547b569… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Log a warning for missing tool whitelist file only if explicitly defined. Also fix the log message. Commit: a9034b5df3f3c80144727ebc161caa38b64ba7a1 https://github.com/galaxyproject/galaxy/commit/a9034b5df3f3c80144727ebc161c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection. Commit: b6e7b9a33b5dec7fdad2ad2f863bbf88980626ec https://github.com/galaxyproject/galaxy/commit/b6e7b9a33b5dec7fdad2ad2f863b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Adjustments to sanitize_whitelist reloading. Commit: 2835aead8f949e3ac8b5c2ece0dc00c872950bde https://github.com/galaxyproject/galaxy/commit/2835aead8f949e3ac8b5c2ece0dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #2 from dannon/release_15.10_config Adjustments to sanitize_whitelist reloading. Commit: f13e9298de2eba4bee36ecb8336477a63345294b https://github.com/galaxyproject/galaxy/commit/f13e9298de2eba4bee36ecb83364… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1278 from nsoranzo/release_15.10_config [15.10] Log a warning for missing tool whitelist file only if explicitly defined. Commit: fba354cb87754450ac41e58252dd405ac073557d https://github.com/galaxyproject/galaxy/commit/fba354cb87754450ac41e58252dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Merge pull request #1282 from natefoo/kombu-el-cap [15.10] Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection Commit: 6a47d2d3a7f27b659e5de5fb1b37c7c1f9d04302 https://github.com/galaxyproject/galaxy/commit/6a47d2d3a7f27b659e5de5fb1b37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1239 from jmchilton/collection_outputs_hidden [15.10] "Fix" collection outputs to hide the HDAs in the history. Compare: https://github.com/galaxyproject/galaxy/compare/7d4eac1535fc...6a47d2d3a7f2

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[galaxyproject/galaxy] a22c09: Fix typos.
by GitHub 11 Dec '15

11 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a22c09b11f5a16b4c429cf88ebd74faa433da97c https://github.com/galaxyproject/galaxy/commit/a22c09b11f5a16b4c429cf88ebd7… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py Log Message: ----------- Fix typos. Commit: f974b0f740d4ed8c44ebafde74908cdea1748a1a https://github.com/galaxyproject/galaxy/commit/f974b0f740d4ed8c44ebafde7490… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py Log Message: ----------- Extend the logging of tool dependency status changes. Also merge handle_tool_dependency_installation_error() in set_tool_dependency_attributes() and consolidate its use. Commit: f8d95abf061608e2dc544e56fc5b83ad3d54d1bd https://github.com/galaxyproject/galaxy/commit/f8d95abf061608e2dc544e56fc5b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/tool_dependency_util.py M test/docker/base/Dockerfile M test/tool_shed/functional/test_1460_data_managers.py Log Message: ----------- Merge pull request #1263 from nsoranzo/dev_tool_shed_fixes Extend the logging of tool dependency status changes. Compare: https://github.com/galaxyproject/galaxy/compare/b455157bd6f3...f8d95abf0616

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[galaxyproject/galaxy] 792336: "Fix" collection outputs to hide the HDAs in the h...
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 7923360dcec48b2e98d7c2a5bcae5f47187d6bf6 https://github.com/galaxyproject/galaxy/commit/7923360dcec48b2e98d7c2a5bcae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- "Fix" collection outputs to hide the HDAs in the history. Long term this is just not a solution, but it is the strategy we use for mapped over output HDAs also. Rebased and fixed based on comments from @nsoranzo indicating the previous attempt did absolutely nothing to fix the problem. xref https://github.com/galaxyproject/tools-iuc/pull/412/files Commit: 6a47d2d3a7f27b659e5de5fb1b37c7c1f9d04302 https://github.com/galaxyproject/galaxy/commit/6a47d2d3a7f27b659e5de5fb1b37… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #1239 from jmchilton/collection_outputs_hidden [15.10] "Fix" collection outputs to hide the HDAs in the history. Compare: https://github.com/galaxyproject/galaxy/compare/fba354cb8775...6a47d2d3a7f2

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[galaxyproject/galaxy] bb2370: White space in BIOM1 datatype.
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb23701fa80c74a6621b1826b050d9e42c12455f https://github.com/galaxyproject/galaxy/commit/bb23701fa80c74a6621b1826b050… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- White space in BIOM1 datatype. Commit: 64506bbd43e21b299a8b42ee3cfd2ef8e40c06d2 https://github.com/galaxyproject/galaxy/commit/64506bbd43e21b299a8b42ee3cfd… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Prevent unneccessary extra read in BIOM1 sniffer. Commit: b5c77a8e8c0255f61ca62a7ff2311d443e224bec https://github.com/galaxyproject/galaxy/commit/b5c77a8e8c0255f61ca62a7ff231… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Add metadata for BIOM1 datatype. I am not yet sure that we should store table_rows and table_columns, as these could grow quite large, but could be useful in tools. Commit: f41540f6137a2f63a6dcb27327e33bf73752f954 https://github.com/galaxyproject/galaxy/commit/f41540f6137a2f63a6dcb27327e3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Most of these should probably not be user visible. Commit: b20fb71e33c1779e42dd67bb68aa9b31b69ffca2 https://github.com/galaxyproject/galaxy/commit/b20fb71e33c1779e42dd67bb68aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix extraneous white space. Commit: 2c6c5236323dbea196cfd2e8fe3915f0c7e4c6df https://github.com/galaxyproject/galaxy/commit/2c6c5236323dbea196cfd2e8fe39… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Only store ids for row and column in BIOM1 datatype. Commit: 3acfa9c786e1fa5567cf313b294b68ab4c508c1b https://github.com/galaxyproject/galaxy/commit/3acfa9c786e1fa5567cf313b294b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Add blank lines around internal function. Commit: b455157bd6f3f23ce2de81d5145b6268e4da77f3 https://github.com/galaxyproject/galaxy/commit/b455157bd6f3f23ce2de81d5145b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1198 from blankenberg/dt-biom BIOM1 Datatype enhancements Compare: https://github.com/galaxyproject/galaxy/compare/7a3aa044fbf9...b455157bd6f3

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[galaxyproject/galaxy] a0c7d8: Ease the grunt uglify process
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0c7d87db35133c2a81d54766f0e718d7fe5f766 https://github.com/galaxyproject/galaxy/commit/a0c7d87db35133c2a81d54766f0e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M doc/source/dev/faq.rst Log Message: ----------- Ease the grunt uglify process Commit: 7cf98d32d811fbf9c8b64f72334c4f4c1e502882 https://github.com/galaxyproject/galaxy/commit/7cf98d32d811fbf9c8b64f72334c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- Align opinions with @jmchilton Commit: 1295f985106a9440135e139368a708ef8dcc0538 https://github.com/galaxyproject/galaxy/commit/1295f985106a9440135e139368a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M Makefile Log Message: ----------- Rename docker image Commit: 0fec39d3bd323b203d6221f087ccac8014c3fefc https://github.com/galaxyproject/galaxy/commit/0fec39d3bd323b203d6221f087cc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M client/Dockerfile Log Message: ----------- Less insane build recipe if it's included in the repo Commit: 7a3aa044fbf968c120832402091cb3b1d70afd7b https://github.com/galaxyproject/galaxy/commit/7a3aa044fbf968c120832402091c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: A Makefile A client/.docker-build.sh A client/Dockerfile M doc/source/dev/faq.rst Log Message: ----------- Merge pull request #1238 from erasche/client-builder Ease the grunt uglify process Compare: https://github.com/galaxyproject/galaxy/compare/25f420fc8f47...7a3aa044fbf9

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[galaxyproject/galaxy] 1ebc0e: UI, Quotameter: correctly update the quotameter fo...
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1ebc0ea9e719bf7557f0e190a7dd4883629257f5 https://github.com/galaxyproject/galaxy/commit/1ebc0ea9e719bf7557f0e190a7dd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- UI, Quotameter: correctly update the quotameter for anon users Commit: 25f420fc8f47865e2cee2da15dc283e2cf130b91 https://github.com/galaxyproject/galaxy/commit/25f420fc8f47865e2cee2da15dc2… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1289 from carlfeberhard/fix.anon-user-quotameter UI, Quotameter: correctly update the quotameter for anon users Compare: https://github.com/galaxyproject/galaxy/compare/bce8140bd9f9...25f420fc8f47

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[galaxyproject/galaxy] a9034b: Update Kombu and AMQP eggs to fix problems with El...
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: a9034b5df3f3c80144727ebc161caa38b64ba7a1 https://github.com/galaxyproject/galaxy/commit/a9034b5df3f3c80144727ebc161c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection. Commit: fba354cb87754450ac41e58252dd405ac073557d https://github.com/galaxyproject/galaxy/commit/fba354cb87754450ac41e58252dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M eggs.ini Log Message: ----------- Merge pull request #1282 from natefoo/kombu-el-cap [15.10] Update Kombu and AMQP eggs to fix problems with El Capitan's System Integrity Protection Compare: https://github.com/galaxyproject/galaxy/compare/f13e9298de2e...fba354cb8775

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[galaxyproject/galaxy] 0d98cf: Log a warning for missing tool whitelist file only...
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 0d98cf8ab76a374362302547b5699fa024d5ce21 https://github.com/galaxyproject/galaxy/commit/0d98cf8ab76a374362302547b569… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Log a warning for missing tool whitelist file only if explicitly defined. Also fix the log message. Commit: b6e7b9a33b5dec7fdad2ad2f863bbf88980626ec https://github.com/galaxyproject/galaxy/commit/b6e7b9a33b5dec7fdad2ad2f863b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Adjustments to sanitize_whitelist reloading. Commit: 2835aead8f949e3ac8b5c2ece0dc00c872950bde https://github.com/galaxyproject/galaxy/commit/2835aead8f949e3ac8b5c2ece0dc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #2 from dannon/release_15.10_config Adjustments to sanitize_whitelist reloading. Commit: f13e9298de2eba4bee36ecb8336477a63345294b https://github.com/galaxyproject/galaxy/commit/f13e9298de2eba4bee36ecb83364… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1278 from nsoranzo/release_15.10_config [15.10] Log a warning for missing tool whitelist file only if explicitly defined. Compare: https://github.com/galaxyproject/galaxy/compare/2be17071f35b...f13e9298de2e

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[galaxyproject/galaxy] 133e5f: Various small API testing fixes/improvements.
by GitHub 10 Dec '15

10 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 133e5f2e24eed9650a0862ced42092d35f8a6566 https://github.com/galaxyproject/galaxy/commit/133e5f2e24eed9650a0862ced420… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py Log Message: ----------- Various small API testing fixes/improvements. Commit: 09a68adb1e2a837f4ae01ca9ec25b4d6d0fab446 https://github.com/galaxyproject/galaxy/commit/09a68adb1e2a837f4ae01ca9ec25… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Add another API test verifying validation of workflow substitions. A little different because it targets a different tool, validation, and is inside a repeat. Commit: 928ff581efa3ace63a57e97db80e7a9c21c09841 https://github.com/galaxyproject/galaxy/commit/928ff581efa3ace63a57e97db80e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/base/interactor.py Log Message: ----------- Fix typo spotted by @nsoranzo. Commit: bce8140bd9f9c3e069c83f765ae892d0fd1656b7 https://github.com/galaxyproject/galaxy/commit/bce8140bd9f9c3e069c83f765ae8… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M test/api/test_tools.py M test/api/test_workflows.py M test/base/interactor.py Log Message: ----------- Merge pull request #1285 from jmchilton/test_improvemnts_1 Small API Test Improvements Compare: https://github.com/galaxyproject/galaxy/compare/183c3c11b60a...bce8140bd9f9

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[galaxyproject/galaxy] d72dd3: Client, polyfills: check for sessionStorage using ...
by GitHub 09 Dec '15

09 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d72dd3735c0dfd652fb45a117fe1942f10ff726d https://github.com/galaxyproject/galaxy/commit/d72dd3735c0dfd652fb45a117fe1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/polyfills.js M static/maps/mvc/base-mvc.js.map M static/maps/polyfills.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/mvc/base-mvc.js M static/scripts/polyfills.js Log Message: ----------- Client, polyfills: check for sessionStorage using a more cross-browser (apparently) way Commit: 183c3c11b60aa5a36747dbe7b0ac069dc3bac6fc https://github.com/galaxyproject/galaxy/commit/183c3c11b60aa5a36747dbe7b0ac… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/polyfills.js M static/maps/mvc/base-mvc.js.map M static/maps/polyfills.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/mvc/base-mvc.js M static/scripts/polyfills.js Log Message: ----------- Merge pull request #1279 from carlfeberhard/fix.casper Client, polyfills: check for sessionStorage using a more cross-browse… Compare: https://github.com/galaxyproject/galaxy/compare/c39544807565...183c3c11b60a

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[galaxyproject/usegalaxy-playbook] 113af6: Slide rotation update.
by GitHub 09 Dec '15

09 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 113af63cfc376e983470b6b0881a6919380fd9e8 https://github.com/galaxyproject/usegalaxy-playbook/commit/113af63cfc376e98… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-12-09 (Wed, 09 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 templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Slide rotation update.

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[galaxyproject/galaxy] f0fc8d: update used galaxy/testing-base to 15.10.3
by GitHub 09 Dec '15

09 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f0fc8d6d4cc59afaacccb8a7ae036b15f5b7f681 https://github.com/galaxyproject/galaxy/commit/f0fc8d6d4cc59afaacccb8a7ae03… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- update used galaxy/testing-base to 15.10.3 Commit: c39544807565d4e345963d1d280deb28b85d281a https://github.com/galaxyproject/galaxy/commit/c39544807565d4e345963d1d280d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1277 from martenson/update-docker-image-v update used galaxy/testing-base to 15.10.3 Compare: https://github.com/galaxyproject/galaxy/compare/d41ea8d315be...c39544807565

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[galaxyproject/galaxy] c3e4ae: set client_encoding for TS dockerized test db
by GitHub 09 Dec '15

09 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c3e4ae11b06d0e10f1fd5a3c2df0433b90f527b7 https://github.com/galaxyproject/galaxy/commit/c3e4ae11b06d0e10f1fd5a3c2df0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- set client_encoding for TS dockerized test db Commit: d41ea8d315be735ab506d2643cf2dcb67e030c9c https://github.com/galaxyproject/galaxy/commit/d41ea8d315be735ab506d2643cf2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #1276 from martenson/fix-ts-dbconnection-tag set client_encoding for TS dockerized test db Compare: https://github.com/galaxyproject/galaxy/compare/bd1349eb9b62...d41ea8d315be

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[galaxyproject/galaxy] 379315: Fix tool shed tests for recent workflow changes.
by GitHub 09 Dec '15

09 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 37931505d4c967d70e495467fd615f9540202e4b https://github.com/galaxyproject/galaxy/commit/37931505d4c967d70e495467fd61… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix tool shed tests for recent workflow changes. Thanks for bug report by @nsoranzo on https://github.com/galaxyproject/galaxy/pull/1263. Commit: bd1349eb9b62dfac0b1affbd1a4ea8e1fe109c2c https://github.com/galaxyproject/galaxy/commit/bd1349eb9b62dfac0b1affbd1a4e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Merge pull request #1274 from jmchilton/workflow_fix_3 Fix tool shed tests for recent workflow changes. Compare: https://github.com/galaxyproject/galaxy/compare/7dbbac31b358...bd1349eb9b62

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[galaxyproject/galaxy] a033d7: Remove: history_options and options.mako (history ...
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a033d798de1c36484a1a16d135860a3b5fb5af33 https://github.com/galaxyproject/galaxy/commit/a033d798de1c36484a1a16d13586… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py R templates/webapps/galaxy/history/options.mako Log Message: ----------- Remove: history_options and options.mako (history options as a page) Commit: 7dbbac31b3581d43445a8030e2cba990c90e1b2e https://github.com/galaxyproject/galaxy/commit/7dbbac31b3581d43445a8030e2cb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py R templates/webapps/galaxy/history/options.mako Log Message: ----------- Merge pull request #1271 from carlfeberhard/jettison.history-options Remove: history_options and options.mako (history options as a page) Compare: https://github.com/galaxyproject/galaxy/compare/864472870f7e...7dbbac31b358

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[galaxyproject/galaxy] b273e3: Improve logging during package installation
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b273e3b0c51c13f7e46ccc2977925d9247033289 https://github.com/galaxyproject/galaxy/commit/b273e3b0c51c13f7e46ccc297792… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py Log Message: ----------- Improve logging during package installation Commit: 864472870f7e1af14a5807effe1fc5685f16e92f https://github.com/galaxyproject/galaxy/commit/864472870f7e1af14a5807effe1f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py Log Message: ----------- Merge pull request #1267 from erasche/install-logging Log command executed during package installation Compare: https://github.com/galaxyproject/galaxy/compare/6d16549a46a3...864472870f7e

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[galaxyproject/usegalaxy-playbook] ce0739: update Test better
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ce0739f2eb1b5594e05c0a63a5f1d356ec703453 https://github.com/galaxyproject/usegalaxy-playbook/commit/ce0739f2eb1b5594… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test better

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[galaxyproject/galaxy] 7f4c3f: Managers, users: properly return a boolean from ha...
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f4c3fcfc88914cb91e325fe95f08c90c034ef3e https://github.com/galaxyproject/galaxy/commit/7f4c3fcfc88914cb91e325fe95f0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/managers/users.py Log Message: ----------- Managers, users: properly return a boolean from has_requests Commit: 38a9aa6a5c3b006867e16877999545e1e0e7ddea https://github.com/galaxyproject/galaxy/commit/38a9aa6a5c3b006867e168779995… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/managers/users.py M test/unit/managers/test_UserManager.py Log Message: ----------- Managers, users: update serialized key 'requests' to 'has_requests', update test Commit: 6d16549a46a330d50eccfa73684e0090a397b3c6 https://github.com/galaxyproject/galaxy/commit/6d16549a46a330d50eccfa73684e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/managers/users.py M test/unit/managers/test_UserManager.py Log Message: ----------- Merge pull request #1262 from carlfeberhard/fix.js-app-mako Managers, users: properly return a boolean from has_requests Compare: https://github.com/galaxyproject/galaxy/compare/fe1c9dd2931f...6d16549a46a3

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[galaxyproject/usegalaxy-playbook] bf85b3: update Test
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bf85b35f106bdd19c282ff68193561fc79449290 https://github.com/galaxyproject/usegalaxy-playbook/commit/bf85b35f106bdd19… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test

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[galaxyproject/galaxy] b11002: Don't iterate over unused key.
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b11002bef32d83b058e3495f96695c8dc12cb91b https://github.com/galaxyproject/galaxy/commit/b11002bef32d83b058e3495f9669… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Don't iterate over unused key. Thanks to @bgruening. Commit: 2aa7f04364e10e46c655de636925883a43698694 https://github.com/galaxyproject/galaxy/commit/2aa7f04364e10e46c655de636925… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M test/api/workflows_format_2/converter.py Log Message: ----------- Replace __rip_value with dict.pop. Thanks @bgruening. Commit: 98249058e85d8133748519ac59ebed96a28a77ac https://github.com/galaxyproject/galaxy/commit/98249058e85d8133748519ac59eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Cleanup error message. Thanks @bgruening. Commit: f17a6c996a060f68bc8a250effa23f60b96b44a7 https://github.com/galaxyproject/galaxy/commit/f17a6c996a060f68bc8a250effa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/web/base/controller.py Log Message: ----------- Synchronize decoding ids across base controller and manager base. To ensure we have the same kind of exception thrown in both cases. Commit: f6d26c9ee6f148fd033d1b070c2dbe8c69b08fa8 https://github.com/galaxyproject/galaxy/commit/f6d26c9ee6f148fd033d1b070c2d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Small refactor making workflow views and modules tad more generic. - Reduce duplication between initializing generic modules and tool modules. - Switch tool_id to content_id as variable names throughout the client. - Rename get_tool_id to get_content_id on workflow modules. - Add some minimal documentation to the workflow module about get_content_id. Downstream in the subworkflow commit I switch the over-the-wire communication to use content_id instead of tool_id also and use content_ids to refer to workflow ids in subworkflow moduls. Commit: 73bfbf016347f764a0747ad7c6d138c74b6f519d https://github.com/galaxyproject/galaxy/commit/73bfbf016347f764a0747ad7c6d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Refactor some workflow API code into workflows manager. This allows for reuse outside of the API controller, such as loading subworkflows downstream. Commit: f92220a74f216d937dc5b147472261d154779512 https://github.com/galaxyproject/galaxy/commit/f92220a74f216d937dc5b1474722… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow workflow outputs on non-tool steps. Commit: d18c75ceb875632f9e68a74ebeb88389262d6fa8 https://github.com/galaxyproject/galaxy/commit/d18c75ceb875632f9e68a74ebeb8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Bring gneric and tool module styles into alignment in workflow editor. Commit: d7ac52f6bb61fe360198f91310a3e22076183d7b https://github.com/galaxyproject/galaxy/commit/d7ac52f6bb61fe360198f91310a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add icons to existing workflow steps in workflow editor. Tools have an icon there. Commit: e3161b4671e9fb19a47c7f341e3fb46617111a9e https://github.com/galaxyproject/galaxy/commit/e3161b4671e9fb19a47c7f341e3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-06 (Sun, 06 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Add support for workflow step labels in editor. - If a step has a label, display it in the step editor side panel title. - Allow clicking the title to change the label. - Display the label (if set) as the workflow node box title. - Add icon to workflow node since the title might not be related to type anymore. - Enforce unique labels accross the workflow in the editor. - Qunit test cases for some of this behavior and other recent changes. Commit: ef0b6cc459a40227db2e63ee709e9dd5d8fd37c6 https://github.com/galaxyproject/galaxy/commit/ef0b6cc459a40227db2e63ee709e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- show notifications as Toasts and not like JS alerts (bleh) Commit: 4a9dad9f14b94df14b52f41466c9e66dbbfb0556 https://github.com/galaxyproject/galaxy/commit/4a9dad9f14b94df14b52f41466c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-07 (Mon, 07 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #12 from martenson/labels_toastr show notifications as Toasts and not like JS alerts (bleh) Commit: 3f8950628c3e31d9e2abe0b4f4a360c035133b8e https://github.com/galaxyproject/galaxy/commit/3f8950628c3e31d9e2abe0b4f4a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Workflow label UI refinement. - Escape workflow labels in mako. - Handle unlabelling steps properly (restore original node name to node and editor form titles). Commit: fe1c9dd2931fb8efccb98fb1646c3e1063b0ab52 https://github.com/galaxyproject/galaxy/commit/fe1c9dd2931fb8efccb98fb1646c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/base.py M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor_generic_form.mako M test/api/workflows_format_2/converter.py M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #1251 from jmchilton/workflow_labels_2 Workflow Editor UI for Step Labels Compare: https://github.com/galaxyproject/galaxy/compare/0e5d42f3d67e...fe1c9dd2931f

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[galaxyproject/galaxy] 5ff098: UI, Citations: fix require of bibtex parser
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ff09896f7d4ee5208f2f39ca16a7846690af229 https://github.com/galaxyproject/galaxy/commit/5ff09896f7d4ee5208f2f39ca16a… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-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/citation/citation-model.js Log Message: ----------- UI, Citations: fix require of bibtex parser Commit: 6ba86d89bc9d2b6b45dddb13d8dc79a4e2c395a0 https://github.com/galaxyproject/galaxy/commit/6ba86d89bc9d2b6b45dddb13d8dc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-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/citation/citation-model.js Log Message: ----------- UI, Citations: don't create new BibtexParser, remove debugging Commit: 0e5d42f3d67e5f75dea4abe78909539df3716f1e https://github.com/galaxyproject/galaxy/commit/0e5d42f3d67e5f75dea4abe78909… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-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/citation/citation-model.js Log Message: ----------- Merge pull request #1261 from carlfeberhard/fix.citations UI, Citations: fix require of bibtex parser Compare: https://github.com/galaxyproject/galaxy/compare/bcf8ddfbd0a9...0e5d42f3d67e

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[galaxyproject/galaxy] 833459: Fixes for dataset 'cleanup'/association linking wh...
by GitHub 08 Dec '15

08 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 8334593de11e915389b1da58c3b5db26121c7bef https://github.com/galaxyproject/galaxy/commit/8334593de11e915389b1da58c3b5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Commit: 2be17071f35bb5db2298883aff107134a53701d1 https://github.com/galaxyproject/galaxy/commit/2be17071f35bb5db2298883aff10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- Merge pull request #1228 from blankenberg/wf_extrac_15.10 [15.10] Fixes for dataset 'cleanup'/association linking when extracting workflows from a history. Compare: https://github.com/galaxyproject/galaxy/compare/94b049926d84...2be17071f35b

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