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

[galaxyproject/usegalaxy-playbook] b48412: Fix the manual hackery employed by
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b4841230c39de5e87136d371a9a7366b8055689d https://github.com/galaxyproject/usegalaxy-playbook/commit/b4841230c39de5e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M templates/supervisor/toolshed.conf.j2 Log Message: ----------- Fix the manual hackery employed by 0db21fc8feab6ff45a5346e307f8d178c7fdeef2 by using uwsgi's -H/--home/--virtualenv/--venv/--pyhome

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[galaxyproject/infrastructure-playbook] 633d58: Give radegast the "lite" env and minor related imp...
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 633d582b88ebc48ce23884a30a8ad47d97b0ef03 https://github.com/galaxyproject/infrastructure-playbook/commit/633d582b88e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M galaxyenv/inventory R roles/nfs/defaults/main.yml M roles/nfs/tasks/main.yml A roles/nfs/vars/debian_8.yml A roles/nfs/vars/default.yml Log Message: ----------- Give radegast the "lite" env and minor related improvements to the nfs role

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[galaxyproject/galaxy] 58911e: Remove worklfow casperjs API test.
by GitHub 15 Dec '15

15 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58911edbfb5aa6e858addd9452e90d6ed389b0d2 https://github.com/galaxyproject/galaxy/commit/58911edbfb5aa6e858addd9452e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Remove worklfow casperjs API test. It has good and more updated coverage in the Python API testing framework. Commit: 86632afdd3b7f2dbfed47671779818835a075496 https://github.com/galaxyproject/galaxy/commit/86632afdd3b7f2dbfed476717798… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: R test/casperjs/api-workflow-tests.js M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #1316 from jmchilton/remove_casper_api_tests Remove worklfow casperjs API test. Compare: https://github.com/galaxyproject/galaxy/compare/b2a3684f03e4...86632afdd3b7

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[galaxyproject/galaxy] 7f7010: Remove left over packed scripts.
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7f7010dbd96b4b9ce494ba320b853e6441162f5e https://github.com/galaxyproject/galaxy/commit/7f7010dbd96b4b9ce494ba320b85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove left over packed scripts. The source files have been deleted. Commit: b2a3684f03e42d3743d02f4d4f039d429bf5e235 https://github.com/galaxyproject/galaxy/commit/b2a3684f03e42d3743d02f4d4f03… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: R static/scripts/mvc/collection/paired-collection-creator.js R static/scripts/mvc/history/history-panel.js R static/scripts/mvc/upload/upload-row.js R static/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #1323 from jmchilton/fix_deleted_static Remove left over packed scripts. Compare: https://github.com/galaxyproject/galaxy/compare/cc67557df848...b2a3684f03e4

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[galaxyproject/galaxy] 8e2db2: Fix workflow output step entries
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8e2db2944cbd546fa0f6f6cb46bf78d470ab31c8 https://github.com/galaxyproject/galaxy/commit/8e2db2944cbd546fa0f6f6cb46bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow output step entries Commit: cc67557df8483899e7058f2047607d0e5339c4eb https://github.com/galaxyproject/galaxy/commit/cc67557df8483899e7058f204760… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1322 from guerler/fix_workflow_outputs Fix workflow output step entries Compare: https://github.com/galaxyproject/galaxy/compare/19cb62660a37...cc67557df848

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[galaxyproject/galaxy] ce5793: Show a more user-friendly error when the webserver...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce57930342c2a4f7eb672f95dc0b19c93c2322f8 https://github.com/galaxyproject/galaxy/commit/ce57930342c2a4f7eb672f95dc0b… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Show a more user-friendly error when the webserver port is blocked Commit: a42328f0002955295cfb70bc6e16fcf83e42ad82 https://github.com/galaxyproject/galaxy/commit/a42328f0002955295cfb70bc6e16… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Removing unnecessary line Commit: c14bb93a60dba72db34996cadcf20ee0e19a7f19 https://github.com/galaxyproject/galaxy/commit/c14bb93a60dba72db34996cadcf2… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py Log Message: ----------- Tidying code for linter Commit: 541231bb1723b2aac3fede7f45ca0455ca954894 https://github.com/galaxyproject/galaxy/commit/541231bb1723b2aac3fede7f45ca… Author: shane <shane(a)shanedowling.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Config-based port checker has been removed and adding in an exception checker for paste response Commit: 19cb62660a3779a6333696ec645f7fcee3db5bc5 https://github.com/galaxyproject/galaxy/commit/19cb62660a3779a6333696ec645f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Merge pull request #1320 from shano/dev Show a more user-friendly error when the webserver port is blocked Compare: https://github.com/galaxyproject/galaxy/compare/4c3dfc7cd471...19cb62660a37

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[galaxyproject/galaxy] 2acdbe: UI, Citations: fix citation-model's import of bibt...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2acdbe54f76312cb748693e018d2d505cf95c3a2 https://github.com/galaxyproject/galaxy/commit/2acdbe54f76312cb748693e018d2… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-14 (Mon, 14 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 M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- UI, Citations: fix citation-model's import of bibtex to use *either* commonjs or global Commit: 4c3dfc7cd471181edc406724ca8f039e6b2a83d1 https://github.com/galaxyproject/galaxy/commit/4c3dfc7cd471181edc406724ca8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 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 M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #1321 from carlfeberhard/fix.citations UI, Citations: fix citation-model's import of bibtex to use *either* … Compare: https://github.com/galaxyproject/galaxy/compare/5bf926bf3ec1...4c3dfc7cd471

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[galaxyproject/infrastructure-playbook] c767b4: Modified authorized users
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c767b40a2d3641c5736e8dd7fd706dbeb2b6d987 https://github.com/galaxyproject/infrastructure-playbook/commit/c767b40a2d3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Modified authorized users

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[galaxyproject/galaxy] 886f6d: Improved validation of tools during workflow execu...
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 886f6d2d707a9b4e2a80b0aaa89157e1137415ad https://github.com/galaxyproject/galaxy/commit/886f6d2d707a9b4e2a80b0aaa891… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- Improved validation of tools during workflow execution. Do a more complete validation of everything after workflow parameters have been replaced and inputs connected up. Attempt 2 at the idea in https://github.com/galaxyproject/galaxy/pull/1284. Commit: cdd9ca16f0a38ffab5fe54d559fc4bb4e4a7a37d https://github.com/galaxyproject/galaxy/commit/cdd9ca16f0a38ffab5fe54d559fc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py Log Message: ----------- Don't silently swallow job creation problems when running workflows. Commit: ce787adff93dafb950341243f3951221cadfc813 https://github.com/galaxyproject/galaxy/commit/ce787adff93dafb950341243f395… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix bug related to collection reductions state. Commit: 5bf926bf3ec19933c0ef82e51c919c0595bfc741 https://github.com/galaxyproject/galaxy/commit/5bf926bf3ec19933c0ef82e51c91… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #1302 from jmchilton/workflow_validation_1 Improved validation of tools during workflow execution. Compare: https://github.com/galaxyproject/galaxy/compare/e838b0330096...5bf926bf3ec1

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[galaxyproject/galaxy] 458766: Add run workflow tool form
by GitHub 14 Dec '15

14 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 458766b00f05a2d46c834d461e59201796ff0358 https://github.com/galaxyproject/galaxy/commit/458766b00f05a2d46c834d461e59… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js M client/galaxy/scripts/mvc/tools.js R client/galaxy/scripts/mvc/tools/tools-form-base.js R client/galaxy/scripts/mvc/tools/tools-form-workflow.js R client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/tools/tools-jobs.js R client/galaxy/scripts/mvc/tools/tools-template.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map M static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map R static/maps/mvc/tools/tools-form-workflow.js.map R static/maps/mvc/tools/tools-form.js.map R static/maps/mvc/tools/tools-jobs.js.map R static/maps/mvc/tools/tools-template.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js M static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js R static/scripts/mvc/tools/tools-form-workflow.js R static/scripts/mvc/tools/tools-form.js R static/scripts/mvc/tools/tools-jobs.js R static/scripts/mvc/tools/tools-template.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add run workflow tool form Move styles to css Improve handling of numeric workflow parameters Commit: 9f7dff740f0133d6ba66abe067fb2edeb7a6b705 https://github.com/galaxyproject/galaxy/commit/9f7dff740f0133d6ba66abe067fb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Revise is_workflow setting Commit: 0770d8d988b20e36c2178d906bd05c6471018edf https://github.com/galaxyproject/galaxy/commit/0770d8d988b20e36c2178d906bd0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Revise workflow mode flag handling Fix comment Commit: 28715a5bca299933c69859559d5b88b381b6c998 https://github.com/galaxyproject/galaxy/commit/28715a5bca299933c69859559d5b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/__init__.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css Log Message: ----------- Add runtime modification switch Commit: 2f31a3cbcd087f26caa9b8754920a6dddb924b30 https://github.com/galaxyproject/galaxy/commit/2f31a3cbcd087f26caa9b8754920… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Cleanup collapsible handling Commit: 3017c61f380c8caa722ff04d11e2e3d37ca56b1c https://github.com/galaxyproject/galaxy/commit/3017c61f380c8caa722ff04d11e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix step order Commit: 98e738d6f0cb2faae1c304a889baaa66b10df953 https://github.com/galaxyproject/galaxy/commit/98e738d6f0cb2faae1c304a889ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Show pja info inside form portlet Improve readability Commit: aa90e346dd4e10850482e38c7331864bef50f007 https://github.com/galaxyproject/galaxy/commit/aa90e346dd4e10850482e38c7331… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise form base Fix style Commit: a8a4480d5c7e92e0f121eefd66357f5504c4cb26 https://github.com/galaxyproject/galaxy/commit/a8a4480d5c7e92e0f121eefd6635… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix dataset matching Commit: ac79cf191c0a0588cdaf45b5075a2494bf097f57 https://github.com/galaxyproject/galaxy/commit/ac79cf191c0a0588cdaf45b5075a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-input.js.map M static/scripts/mvc/form/form-input.js M static/style/blue/base.css Log Message: ----------- Fix style naming Commit: 4dc134d43bfa415cf3d1b77475dc0d4a3efb05b1 https://github.com/galaxyproject/galaxy/commit/4dc134d43bfa415cf3d1b77475dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-05 (Sat, 05 Dec 2015) Changed paths: M .gitignore M README.rst M client/GruntFile.js A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R 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static/scripts/mvc/form/form-section.js Log Message: ----------- Add fallback for missing section and repeat title Commit: 2b63427e965837eb29df54e5918cf8f84004f534 https://github.com/galaxyproject/galaxy/commit/2b63427e965837eb29df54e5918c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-08 (Tue, 08 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dynamic_options.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Handle late validated dataset references Commit: 636e9900ba5e82c37a26fee84f56872c9413bd1b https://github.com/galaxyproject/galaxy/commit/636e9900ba5e82c37a26fee84f56… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Improve handling of unspecified workflow editor values Commit: 9a4c8343701c676ccf996cbbaa864f12135bac5b https://github.com/galaxyproject/galaxy/commit/9a4c8343701c676ccf996cbbaa86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-drilldown.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-drilldown.js M static/style/blue/base.css Log Message: ----------- Use fa icons for drill down expansion Commit: c61a5529b4c788580d2c3615c7dab2386a9b8e4e https://github.com/galaxyproject/galaxy/commit/c61a5529b4c788580d2c3615c7da… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: A .ci/check_controller.sh A 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Changed paths: M config/galaxy.ini.sample M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Add config setting, disable by default Commit: 42edfca679f204aa7e69a6c3df6dc14c8118e22c https://github.com/galaxyproject/galaxy/commit/42edfca679f204aa7e69a6c3df6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/__init__.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Repack, refix section validation Commit: 10fff14ce5ba6952f21da10c81a31ceda397a666 https://github.com/galaxyproject/galaxy/commit/10fff14ce5ba6952f21da10c81a3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix missing wf parameter issue in classic form Commit: 57bc4660cf4e21ebe8b73035095e021e4f298680 https://github.com/galaxyproject/galaxy/commit/57bc4660cf4e21ebe8b73035095e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix workflow parameter validation Commit: 3108ba5c01ded7b0209685f57ab231c2cfe92938 https://github.com/galaxyproject/galaxy/commit/3108ba5c01ded7b0209685f57ab2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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-misc.js Log Message: ----------- Ensure that text fields only display text Commit: a440813e37941d050ac503a0898dcf00c5f1b4fe https://github.com/galaxyproject/galaxy/commit/a440813e37941d050ac503a0898d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add workflow_mode flag to validation Commit: e838b03300964615bc2144ceeb9ba785cf5f7a7d https://github.com/galaxyproject/galaxy/commit/e838b03300964615bc2144ceeb9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-14 (Mon, 14 Dec 2015) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/tool/tool-form-base.js A client/galaxy/scripts/mvc/tool/tool-form-composite.js A client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/tool/tool-template.js R client/galaxy/scripts/mvc/tool/tools-form-base.js R client/galaxy/scripts/mvc/tool/tools-form-workflow.js R client/galaxy/scripts/mvc/tool/tools-form.js R client/galaxy/scripts/mvc/tool/tools-jobs.js R client/galaxy/scripts/mvc/tool/tools-template.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/library/ui-table-form.js M config/plugins/visualizations/charts/static/views/editor.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/webapps/galaxy/api/workflows.py A static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map A static/maps/mvc/tool/tool-form-base.js.map A static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/tool/tool-form.js.map A static/maps/mvc/tool/tool-template.js.map R static/maps/mvc/tool/tools-form-base.js.map R static/maps/mvc/tool/tools-form-workflow.js.map R static/maps/mvc/tool/tools-form.js.map R static/maps/mvc/tool/tools-jobs.js.map R static/maps/mvc/tool/tools-template.js.map M static/maps/mvc/tool/tools.js.map R static/maps/mvc/tools.js.map R static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-drilldown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-slider.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js A static/scripts/mvc/tool/tool-form-base.js A static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/tool/tool-form.js A static/scripts/mvc/tool/tool-template.js R static/scripts/mvc/tool/tools-form-base.js R static/scripts/mvc/tool/tools-form-workflow.js R static/scripts/mvc/tool/tools-form.js R static/scripts/mvc/tool/tools-jobs.js R static/scripts/mvc/tool/tools-template.js M static/scripts/mvc/tool/tools.js R static/scripts/mvc/tools.js R static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-misc.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-slider.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/utils.js M static/style/blue/base.css M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1249 from guerler/run_workflow_form_004 Run workflow form Compare: https://github.com/galaxyproject/galaxy/compare/0fce226b96f9...e838b0330096

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