March 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 790a35: Properly handle multiple hidden datasets when popu...
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 790a35ea2e605c3b15e3e59df07f3febc9688f8d https://github.com/galaxyproject/galaxy/commit/790a35ea2e605c3b15e3e59df07f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Properly handle multiple hidden datasets when populating data select options Commit: a0b4ab63d288d04ddd7b4372090c1e956653f4e6 https://github.com/galaxyproject/galaxy/commit/a0b4ab63d288d04ddd7b4372090c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #3842 from guerler/fix_hidden_datasets Properly handle multiple hidden datasets when populating data select options Compare: https://github.com/galaxyproject/galaxy/compare/ab11adfa501a...a0b4ab63d288

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[galaxyproject/galaxy] 371d27: Disable tool shed test function that fails frequen...
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 371d277c5514d0e7d033c8724f8d5cc58878f6bc https://github.com/galaxyproject/galaxy/commit/371d277c5514d0e7d033c8724f8d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Disable tool shed test function that fails frequently on Jenkins. Commit: ab11adfa501ababc2d1f20e731727b8df787b803 https://github.com/galaxyproject/galaxy/commit/ab11adfa501ababc2d1f20e73172… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M test/shed_functional/functional/test_1090_repository_dependency_handling.py Log Message: ----------- Merge pull request #3819 from jmchilton/disable_pesky_ts_test Disable tool shed test function that fails frequently on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/66ca698f5aa4...ab11adfa501a

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[galaxyproject/usegalaxy-playbook] 920016: Add a conda env for set_meta on handlers
by GitHub 29 Mar '17

29 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9200160c4815cb2dea25df3e6448993e4cecc167 https://github.com/galaxyproject/usegalaxy-playbook/commit/9200160c4815cb2d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-29 (Wed, 29 Mar 2017) Changed paths: M templates/supervisor/galaxy_handler.j2 Log Message: ----------- Add a conda env for set_meta on handlers

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[galaxyproject/usegalaxy-playbook] ed7a52: add IE files generated by run
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed7a52e63097edab6710737b6950348b69286033 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed7a52e63097edab… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample M production/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js M production/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako M production/files/interactive_environments/plugins/common/templates/ie.mako A production/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample A production/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml A production/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js A production/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako A production/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample M production/files/interactive_environments/plugins/jupyter/config/jupyter.xml M production/files/interactive_environments/plugins/jupyter/static/js/jupyter.js M production/files/interactive_environments/plugins/jupyter/templates/jupyter.mako A production/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample A production/files/interactive_environments/plugins/neo/config/neo.ini.sample A production/files/interactive_environments/plugins/neo/config/neo.xml A production/files/interactive_environments/plugins/neo/static/js/neo.js A production/files/interactive_environments/plugins/neo/templates/neo.mako M production/files/interactive_environments/plugins/phinch/config/phinch.ini.sample M production/files/interactive_environments/plugins/phinch/static/js/phinch.js M production/files/interactive_environments/plugins/phinch/templates/phinch.mako A production/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample M production/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample M production/files/interactive_environments/plugins/rstudio/config/rstudio.xml M production/files/interactive_environments/plugins/rstudio/static/js/rstudio.js M production/files/interactive_environments/plugins/rstudio/templates/rstudio.mako M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/Dockerfile M production/files/interactive_environments/proxy/lib/main.js M production/files/interactive_environments/proxy/lib/mapper.js M production/files/interactive_environments/proxy/lib/proxy.js M production/files/interactive_environments/proxy/package.json Log Message: ----------- add IE files generated by run

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[galaxyproject/galaxy] d8af12: Update __init__.py
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d8af125af4d3798c32b31793c10f9b9426d7dfe2 https://github.com/galaxyproject/galaxy/commit/d8af125af4d3798c32b31793c10f… Author: Hans-Rudolf Hotz <hrhotz(a)users.noreply.github.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update __init__.py Commit: 3068c9f053554c448a30388d46b91a6979e39cb7 https://github.com/galaxyproject/galaxy/commit/3068c9f053554c448a30388d46b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix CONVERTER_gff_to_fli_0 for striping Galaxy from Python environment. Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822. Commit: 70b22dffc28830b4f9fc3c9a89845d6ccf32e559 https://github.com/galaxyproject/galaxy/commit/70b22dffc28830b4f9fc3c9a8984… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3824 from jmchilton/more_tool_env_fixes [17.01] More CONVERTER fixes for restricting tools' Python environment. Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Commit: 66ca698f5aa4e897a792fe47f81526ed703bc154 https://github.com/galaxyproject/galaxy/commit/66ca698f5aa4e897a792fe47f815… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3829 from galaxyproject/release_17.01 Merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/07be669ed0d3...66ca698f5aa4

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[galaxyproject/galaxy] 21e573: Fix for EtherCalc IE image specification.
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 21e5731355ebcbba2bb4280844091576c7700abf https://github.com/galaxyproject/galaxy/commit/21e5731355ebcbba2bb428084409… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample Log Message: ----------- Fix for EtherCalc IE image specification. Will allow EtherCalc to work in 17.05. Commit: 07be669ed0d392fde70a79aa442bae028cfe3fcd https://github.com/galaxyproject/galaxy/commit/07be669ed0d392fde70a79aa442b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample M config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample Log Message: ----------- Merge pull request #3825 from blankenberg/ethercalc Fix for EtherCalc IE image specification. Compare: https://github.com/galaxyproject/galaxy/compare/c24ed4f8fa2f...07be669ed0d3

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[galaxyproject/galaxy] 1fbdb3: Have IGV bigWig display application make use of bu...
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 https://github.com/galaxyproject/galaxy/commit/1fbdb35d6edb84a3700ea1392dcf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. Commit: a2b5c41de00505179c7ce5a5f28ac0d9f0f1dee7 https://github.com/galaxyproject/galaxy/commit/a2b5c41de00505179c7ce5a5f28a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M display_applications/igv/bigwig.xml Log Message: ----------- Merge pull request #3828 from blankenberg/17.01_bigwig_igv [17.01] Have IGV bigWig display application make use of build_sites/ site_typ… Compare: https://github.com/galaxyproject/galaxy/compare/70b22dffc288...a2b5c41de005

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[galaxyproject/galaxy] f17435: fix link to galaxy logo
by GitHub 28 Mar '17

28 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f174358b9542610ffa4c00588096a4e80583ae0a https://github.com/galaxyproject/galaxy/commit/f174358b9542610ffa4c00588096… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/releases/_header.rst Log Message: ----------- fix link to galaxy logo Commit: 85093dc13ad06eb8d4896f01d934846cd57c1473 https://github.com/galaxyproject/galaxy/commit/85093dc13ad06eb8d4896f01d934… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/admin/useful_scripts.rst Log Message: ----------- reword topic Commit: e02e2cb09e245ab5cbbe48d532e4f3ffe9a1612a https://github.com/galaxyproject/galaxy/commit/e02e2cb09e245ab5cbbe48d532e4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M doc/source/index.rst Log Message: ----------- improve doc-build-urself docs Commit: b4feb85f11280935b0ce13ea5d3693122f4319e8 https://github.com/galaxyproject/galaxy/commit/b4feb85f11280935b0ce13ea5d36… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/ts_api_doc.rst Log Message: ----------- improve accessibility of API docs for both Galaxy and TS Commit: bdcf4807ce5f2d3c1f12cd23120f4f5ec55f0067 https://github.com/galaxyproject/galaxy/commit/bdcf4807ce5f2d3c1f12cd23120f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md Log Message: ----------- add basic Reports documentation Commit: c24ed4f8fa2f277757eccb8e5cdb7d324a3a3521 https://github.com/galaxyproject/galaxy/commit/c24ed4f8fa2f277757eccb8e5cdb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A doc/source/admin/reports.md M doc/source/admin/useful_scripts.rst A doc/source/api/api.rst A doc/source/api/ts_api.rst M doc/source/api_doc.rst M doc/source/conf.py M doc/source/index.rst R doc/source/lib/galaxy.webapps.galaxy.api.rst R doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/releases/_header.rst M doc/source/ts_api_doc.rst Log Message: ----------- Merge pull request #3812 from martenson/admin-docs-imp api & reports documentation improvements Compare: https://github.com/galaxyproject/galaxy/compare/cfd8ec776e69...c24ed4f8fa2f

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[galaxyproject/galaxy] b18736: Updating Cytoscape viewer in Viz/Charts, replacing...
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b18736d82447637d7257f3fd406e1c40a02afed0 https://github.com/galaxyproject/galaxy/commit/b18736d82447637d7257f3fd406e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: 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 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 config/plugins/visualizations/charts/static/repository/registry.json R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Updating Cytoscape viewer in Viz/Charts, replacing the previous 'basic' folder name to 'viewer' and updating the wrapper.js file Commit: 69b9b575172086376657433ff0a066bf732d4e4d https://github.com/galaxyproject/galaxy/commit/69b9b575172086376657433ff0a0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding basic options like layout name and curve style for cytoscape graphs Commit: 504f4ac670b3135b9df885d9d884d176dc494768 https://github.com/galaxyproject/galaxy/commit/504f4ac670b3135b9df885d9d884… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding min and max zoom settings for graphs Commit: b437be2c566c431267d814b7718380969b8bd3b7 https://github.com/galaxyproject/galaxy/commit/b437be2c566c431267d814b77183… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding SIF to JSON converter for Cytoscape viewer Commit: 2275d098eeeaeb115fa69b0d1fa7856f7bfa4d18 https://github.com/galaxyproject/galaxy/commit/2275d098eeeaeb115fa69b0d1fa7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-10 (Fri, 10 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph resize property for window resize Commit: 56338972b9767b9e0be474d99b8f4ea915e6dd96 https://github.com/galaxyproject/galaxy/commit/56338972b9767b9e0be474d99b8f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/utilities/sifjson.js Log Message: ----------- Extending the sif to json converter to allow single nodes to be plotted Commit: c6bd499d001b667f20bd4caf99612a3d56b200c1 https://github.com/galaxyproject/galaxy/commit/c6bd499d001b667f20bd4caf9961… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding node text and colors for graphs Commit: 2a6391550b2256c18f2671b2260f58746b507db7 https://github.com/galaxyproject/galaxy/commit/2a6391550b2256c18f2671b2260f… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-15 (Wed, 15 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding directed/undirected attribute for graphs Commit: 9f42821f57c3126826ebc773407ac02084a965ea https://github.com/galaxyproject/galaxy/commit/9f42821f57c3126826ebc773407a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-16 (Thu, 16 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Breadth First Search for cytoscape graphs. Tapping any node plays BFS Commit: a2affcc618ae5ec8d0f36e55a0f7ef15de53ef68 https://github.com/galaxyproject/galaxy/commit/a2affcc618ae5ec8d0f36e55a0f7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Depth First Search for cytoscape graphs Commit: c658ef3c7efd56986c096dc71a73c06260351ccc https://github.com/galaxyproject/galaxy/commit/c658ef3c7efd56986c096dc71a73… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-19 (Sun, 19 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding Kruskal algorithm for graphs and color choosing scheme for highlighted edges Commit: 0d95b4e2079aa0d442a2e030fe7606c7627bd1e6 https://github.com/galaxyproject/galaxy/commit/0d95b4e2079aa0d442a2e030fe76… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding graph traversal types Commit: cbc7dd17fcf3bfe9eecdd8a0577a6d63e565f509 https://github.com/galaxyproject/galaxy/commit/cbc7dd17fcf3bfe9eecdd8a0577a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-20 (Mon, 20 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing unused if else Commit: 50417de1b4971db4fe42b1c797024081c66deef5 https://github.com/galaxyproject/galaxy/commit/50417de1b4971db4fe42b1c79702… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding A* search algorithm for finding shortest distance between root and destination Commit: 50a51575f1d4f0a7ccc8c476ab0ad7de2ffca3c8 https://github.com/galaxyproject/galaxy/commit/50a51575f1d4f0a7ccc8c476ab0a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/py3_sources.txt M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M 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static/style/blue/base.css R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/grid_base.mako M templates/webapps/galaxy/admin/index.mako A templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/tool_shed/repository/common.mako M test/TESTING.md M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/run_test_wrapper.sh M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml M test/integration/test_resolvers.py M test/qunit/package.json A test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_uploads.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M tools/data_source/upload.py Log Message: ----------- Merging with dev Commit: 086dfd71ca4b82a7aeb2421cb2a08e76975639b3 https://github.com/galaxyproject/galaxy/commit/086dfd71ca4b82a7aeb2421cb2a0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-26 (Sun, 26 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Removing tabs and updating time out for path animation Commit: 04941d0aea0be51fd169cb332070f6a420b71d0c https://github.com/galaxyproject/galaxy/commit/04941d0aea0be51fd169cb332070… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_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/utilities/utils.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png M config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Fixing review comments- removing sliders for colors and zoom and adding color pickers, updating values for min and max zoom and replacing logo of the plugin Commit: f1206a8e352b9ef4288aa08bd18ac6b3387c790e https://github.com/galaxyproject/galaxy/commit/f1206a8e352b9ef4288aa08bd18a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map M config/plugins/visualizations/charts/static/repository/build/registry.js.map Log Message: ----------- Updating library files Commit: 90c534570876c0f76a02458433960d9923a96ec3 https://github.com/galaxyproject/galaxy/commit/90c534570876c0f76a0245843396… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M 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config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js Log Message: ----------- Adding styles for selected nodes and updating default colors for nodes, edges and higlighted elements Commit: 0809c19c36cf5f73f60928bd11c6a091c96e06b2 https://github.com/galaxyproject/galaxy/commit/0809c19c36cf5f73f60928bd11c6… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/__init__.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-view-edit.js.map M static/maps/mvc/tool/tools.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/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/scripts/mvc/tool/tools.js M static/style/blue/base.css M test/api/test_history_contents.py M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merging with dev Commit: cfd8ec776e692fe2706c1bd7cc40dcf1a8c56832 https://github.com/galaxyproject/galaxy/commit/cfd8ec776e692fe2706c1bd7cc40… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-03-28 (Tue, 28 Mar 2017) Changed paths: 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 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 config/plugins/visualizations/charts/static/repository/registry.json A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js M config/plugins/visualizations/charts/static/repository/utilities/utils.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #3817 from bgruening/cytoscape Cytoscape as the Galaxy charts plugin Compare: https://github.com/galaxyproject/galaxy/compare/db09acb02637...cfd8ec776e69

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[galaxyproject/galaxy] d270a2: Allow non-ready jobs in collection builder.
by GitHub 27 Mar '17

27 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d270a21908a8b1d203ac653d96177ae921cb5a5d https://github.com/galaxyproject/galaxy/commit/d270a21908a8b1d203ac653d9617… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/history/history-view-edit.js M static/maps/mvc/collection/list-collection-creator.js.map 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/collection/list-collection-creator.js M static/scripts/mvc/history/history-view-edit.js M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/test_collection_builders.py Log Message: ----------- Allow non-ready jobs in collection builder. This includes two parallel changes to the Selenium tests. - It adds a decorator to allow retrying certain atomic actions that may occur during jQuery transitions automatically. - It refactors things to allow waiting on HIDs to become visible instead of just green. Commit: 3d13a2bb4f75f2224f24511aa96c9f97d8ff3e44 https://github.com/galaxyproject/galaxy/commit/3d13a2bb4f75f2224f24511aa96c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix transiently failing Selenium test of tool form re-running. Reworks addition of staleness checkers introduced in #3780. Commit: c9d06aeb41d9e15c07dddf4fff67630f2ee2237d https://github.com/galaxyproject/galaxy/commit/c9d06aeb41d9e15c07dddf4fff67… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M test/api/test_history_contents.py Log Message: ----------- Allow collection creation API to hide original datasets during creation. Commit: 5fa546749bcc7b5a8c2579c46a1360217d4883c8 https://github.com/galaxyproject/galaxy/commit/5fa546749bcc7b5a8c2579c46a13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/style/less/ui/paired-collection-creator.less M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.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/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/style/blue/base.css Log Message: ----------- Allow collection builders to hide original datasets. Commit: 82ca6931c02b1a4b13fe9dc4e86c7ace6029f5d5 https://github.com/galaxyproject/galaxy/commit/82ca6931c02b1a4b13fe9dc4e86c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-24 (Fri, 24 Mar 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py Log Message: ----------- More test cases for collection builders. - Add test case for building paired lists. - Add tests for new hide original datasets functionality for lists and paired lists. Commit: 810a96caef678462369604afd2a52b5c25c9268c https://github.com/galaxyproject/galaxy/commit/810a96caef678462369604afd2a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/datasets.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/watcher.py M static/maps/mvc/tool/tools.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/tool/tools.js M test/api/test_jobs.py M test/base/api_asserts.py M test/base/driver_util.py M test/base/populators.py M test/functional/tools/create_10.xml A test/functional/tools/create_2.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py Log Message: ----------- Merge branch 'dev' into collection_builder_enhancements Commit: db09acb0263751560714c74d9f7c9ea6fed649ae https://github.com/galaxyproject/galaxy/commit/db09acb0263751560714c74d9f7c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-03-27 (Mon, 27 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/style/less/ui/paired-collection-creator.less M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M static/maps/mvc/collection/base-creator.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/history/history-contents.js.map 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/collection/base-creator.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-view-edit.js M static/style/blue/base.css M test/api/test_history_contents.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/sizzle.py M test/qunit/test-data/paired-collection-creator.data.js M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #3806 from jmchilton/collection_builder_enhancements Small enhancements for collection builders Compare: https://github.com/galaxyproject/galaxy/compare/967d0b6c0aef...db09acb02637

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