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

[galaxyproject/galaxy] 93453e: Avoid html response when reloading tool through th...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93453e490f2490899d818473d79eeddf9f6d0808 https://github.com/galaxyproject/galaxy/commit/93453e490f2490899d818473d79e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M templates/admin/reload_tool.mako Log Message: ----------- Avoid html response when reloading tool through the api Commit: b466ff6cd8dc86c03f0d6322e26b94605087bb39 https://github.com/galaxyproject/galaxy/commit/b466ff6cd8dc86c03f0d6322e26b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Fix root location for tool reloader Commit: 1aa459f19d45221957ff0be6a5f708bf6bd41a41 https://github.com/galaxyproject/galaxy/commit/1aa459f19d45221957ff0be6a5f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Use shared modal viewer Commit: cd52f20961fcdee3453b5c5ce28b84f25b50f3f3 https://github.com/galaxyproject/galaxy/commit/cd52f20961fcdee3453b5c5ce28b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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 Log Message: ----------- Align code style to existing code in tool form base Commit: 727bfbd258c548917d2025708368f73b57199648 https://github.com/galaxyproject/galaxy/commit/727bfbd258c548917d2025708368… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Fix error message style, raise message exception if tool has not been found Commit: 8e59ec1e2be863dc00cb86d1689e7169cd43b6e5 https://github.com/galaxyproject/galaxy/commit/8e59ec1e2be863dc00cb86d1689e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Remove unused tooltips for submenu options, fix response Commit: 10943712b829ac48760fc5ecd25405d768cc9dd4 https://github.com/galaxyproject/galaxy/commit/10943712b829ac48760fc5ecd254… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Revise dropdown item label Commit: 9590d4551439c7b9ae13f704508bfef376ff1fc4 https://github.com/galaxyproject/galaxy/commit/9590d4551439c7b9ae13f704508b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js 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/tool-form-base.js Log Message: ----------- Improve success message upon tool xml reloading Commit: 73b8fc45aa088b17970c5309108442d968c70a7b https://github.com/galaxyproject/galaxy/commit/73b8fc45aa088b17970c53091084… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Check once for admin operations when building dropdown list in tool form Commit: 4fc0b84910adef446daa20a68cd69b0721a4d362 https://github.com/galaxyproject/galaxy/commit/4fc0b84910adef446daa20a68cd6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/toolbox/base.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js M templates/admin/reload_tool.mako Log Message: ----------- Merge remote-tracking branch 'guerler/fix_tool_reload_003' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9f9d0cb4082b...4fc0b84910ad

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[galaxyproject/galaxy] 4483f0: Fix ScIdx datatype sniffer
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4483f014107d92340573c7113745821e4863c148 https://github.com/galaxyproject/galaxy/commit/4483f014107d92340573c7113745… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx datatype sniffer Check for EOF before line stripping, otherwise empty or whitespace lines will be considered EOF. Found when uploading a GFF file which was erroneously sniffed as scidx. Commit: 5db0b7681bb60e0671c0d80d06e3d980ef3aab6e https://github.com/galaxyproject/galaxy/commit/5db0b7681bb60e0671c0d80d06e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #3602 from nsoranzo/release_17.01_fix_scidx_sniffer Fix ScIdx datatype sniffer Commit: 9f9d0cb4082b66e385bd43e31995cbaa5a2a0e09 https://github.com/galaxyproject/galaxy/commit/9f9d0cb4082b66e385bd43e31995… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b4b75b276c9d...9f9d0cb4082b

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[galaxyproject/galaxy] 4483f0: Fix ScIdx datatype sniffer
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 4483f014107d92340573c7113745821e4863c148 https://github.com/galaxyproject/galaxy/commit/4483f014107d92340573c7113745… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx datatype sniffer Check for EOF before line stripping, otherwise empty or whitespace lines will be considered EOF. Found when uploading a GFF file which was erroneously sniffed as scidx. Commit: 5db0b7681bb60e0671c0d80d06e3d980ef3aab6e https://github.com/galaxyproject/galaxy/commit/5db0b7681bb60e0671c0d80d06e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #3602 from nsoranzo/release_17.01_fix_scidx_sniffer Fix ScIdx datatype sniffer Compare: https://github.com/galaxyproject/galaxy/compare/4a22bb902b12...5db0b7681bb6

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[galaxyproject/galaxy] 7e98cd: Update tool XSD for (hopefully deprecated) change_...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e98cde0a9cf62f60b907ed14ee407f6183dee72 https://github.com/galaxyproject/galaxy/commit/7e98cde0a9cf62f60b907ed14ee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Update tool XSD for (hopefully deprecated) change_format syntax. Fixes #3552. Commit: b4b75b276c9d41181e89322754c64abba57cd753 https://github.com/galaxyproject/galaxy/commit/b4b75b276c9d41181e89322754c6… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3579 from jmchilton/deprecated_change_format_when Update tool XSD for (hopefully deprecated) change_format syntax. Compare: https://github.com/galaxyproject/galaxy/compare/e06f56a61521...b4b75b276c9d

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[galaxyproject/galaxy] 69552b: Fix root location for tool reloader
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 69552ba63b90604a0d0f0315cad5f42e3344eac5 https://github.com/galaxyproject/galaxy/commit/69552ba63b90604a0d0f0315cad5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Fix root location for tool reloader Commit: 4a22bb902b121f91c370b30c64590dd46997a412 https://github.com/galaxyproject/galaxy/commit/4a22bb902b121f91c370b30c6459… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Merge pull request #3595 from guerler/fix_tool_reload_002 [17.01] Fix root location for tool reloader Commit: e06f56a61521563f1bd17c5ad09df94264d45772 https://github.com/galaxyproject/galaxy/commit/e06f56a61521563f1bd17c5ad09d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: static/maps/mvc/tool/tool-form-base.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-base.js Compare: https://github.com/galaxyproject/galaxy/compare/75a17bc31166...e06f56a61521

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[galaxyproject/galaxy] a79ae2: Align architecture slides with training-material r...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a79ae2a8c297c1c0f6c0e61271a2ca05ae0aa0f0 https://github.com/galaxyproject/galaxy/commit/a79ae2a8c297c1c0f6c0e61271a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M CONTRIBUTING.md M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M scripts/slideshow/slideshow_template.html Log Message: ----------- Align architecture slides with training-material remarkjs template. - Copy over the training material style CSS template and add to it only what is needed. - Cleanup style and layout handling in architecture slides markdown. - Update generated images for white background. - Small updates in content to architecture for recent changes (and CONTRIBUTING.md linked to from slides). Commit: d066ae2223ef006a7621ddaa30ecd24ffa2942dd https://github.com/galaxyproject/galaxy/commit/d066ae2223ef006a7621ddaa30ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M doc/source/slideshow/architecture/galaxy_architecture.md Log Message: ----------- Link fixes thanks to @nsoranzo. Commit: 75a17bc311662fae24b679a7b41146552f796992 https://github.com/galaxyproject/galaxy/commit/75a17bc311662fae24b679a7b411… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M CONTRIBUTING.md M doc/source/slideshow/architecture/galaxy_architecture.md M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg M doc/source/slideshow/architecture/images/objectstore.plantuml.svg M doc/source/slideshow/architecture/images/plantuml_options.txt M doc/source/slideshow/architecture/images/server_client.plantuml.svg M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg M doc/source/slideshow/architecture/images/webapp.plantuml.svg M doc/source/slideshow/architecture/style.css M scripts/slideshow/slideshow_template.html Log Message: ----------- Merge pull request #3594 from jmchilton/architecture_touchup Align architecture slides with training-material remarkjs template. Compare: https://github.com/galaxyproject/galaxy/compare/d382537008da...75a17bc31166

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[galaxyproject/galaxy] dc0e9f: Avoid step duplication when ordering steps on the ...
by GitHub 13 Feb '17

13 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc0e9fd79eaff575a731409ed7f1771c6cd82b93 https://github.com/galaxyproject/galaxy/commit/dc0e9fd79eaff575a731409ed7f1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Avoid step duplication when ordering steps on the fly Commit: d382537008da588b68a86925a42f0828a9e376d8 https://github.com/galaxyproject/galaxy/commit/d382537008da588b68a86925a42f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-13 (Mon, 13 Feb 2017) Changed paths: M lib/galaxy/workflow/steps.py Log Message: ----------- Merge pull request #3590 from guerler/fix_order_steps Avoid step duplication when ordering steps on the fly Compare: https://github.com/galaxyproject/galaxy/compare/9ceaa0d41583...d382537008da

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[galaxyproject/galaxy] 2e7873: Disable transiently failing tour test.
by GitHub 12 Feb '17

12 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e787394cc0b9ea1a73ba87235faa4f38c1e495e https://github.com/galaxyproject/galaxy/commit/2e787394cc0b9ea1a73ba87235fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M test/selenium_tests/test_stock_tours.py Log Message: ----------- Disable transiently failing tour test. See code comment for more information - I am tracking the issue here https://github.com/galaxyproject/galaxy/issues/3598. I think it is important to resolve that test and fix the usability problems with current tours but I'd like to get the Selenium tests stable and testing against new PRs first. Commit: 9ceaa0d41583b66efb1c228755ca4368c0bdb6af https://github.com/galaxyproject/galaxy/commit/9ceaa0d41583b66efb1c228755ca… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-12 (Sun, 12 Feb 2017) Changed paths: M test/selenium_tests/test_stock_tours.py Log Message: ----------- Merge pull request #3599 from jmchilton/disable_galaxy_ui_test Disable transiently failing tour test. Compare: https://github.com/galaxyproject/galaxy/compare/d9b36176a818...9ceaa0d41583

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[galaxyproject/galaxy] 69552b: Fix root location for tool reloader
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 69552ba63b90604a0d0f0315cad5f42e3344eac5 https://github.com/galaxyproject/galaxy/commit/69552ba63b90604a0d0f0315cad5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Fix root location for tool reloader Commit: 4a22bb902b121f91c370b30c64590dd46997a412 https://github.com/galaxyproject/galaxy/commit/4a22bb902b121f91c370b30c6459… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool-form-base.js Log Message: ----------- Merge pull request #3595 from guerler/fix_tool_reload_002 [17.01] Fix root location for tool reloader Compare: https://github.com/galaxyproject/galaxy/compare/087c75e76ff4...4a22bb902b12

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[galaxyproject/galaxy] 0815e6: Add d3_hierarchy subclass
by GitHub 10 Feb '17

10 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0815e6b8813b0ef980cc95ddf08244c44e8fb2e0 https://github.com/galaxyproject/galaxy/commit/0815e6b8813b0ef980cc95ddf082… Author: Jim Johnson <jj(a)umn.edu> Date: 2017-02-08 (Wed, 08 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add d3_hierarchy subclass This is to support Unipept API tool and visualization: https://github.com/unipept/unipept-visualizations The unipept visualization would only apply to the d3_hierarchy of json datasets. Commit: d9b36176a8181168f5c4553ead4f9e6545d7e856 https://github.com/galaxyproject/galaxy/commit/d9b36176a8181168f5c4553ead4f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #3580 from jj-umn/patch-5 Add d3_hierarchy subclass Compare: https://github.com/galaxyproject/galaxy/compare/66a24c8830f5...d9b36176a818

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