Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57f023529aef13723cb1555dc3ad5ea59aef009c https://github.com/galaxyproject/galaxy/commit/57f023529aef13723cb1555dc3ad5... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Remove tool form mako Fix new-line Commit: f5a6e25ebd9d96a709781291cf04bc9e461216c6 https://github.com/galaxyproject/galaxy/commit/f5a6e25ebd9d96a709781291cf04b... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/tool_runner.py Log Message: ----------- Reinsert data_source tool execution into tool runner controller (requires separate PR) Commit: c1faf48d819ded4317995fe5f5ca436f847a4d09 https://github.com/galaxyproject/galaxy/commit/c1faf48d819ded4317995fe5f5ca4... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add large message style and use for initial tool loading notifications Commit: 7777ea8f91928a9dd2c581eed53ba7e2ed1f3255 https://github.com/galaxyproject/galaxy/commit/7777ea8f91928a9dd2c581eed53ba... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Extend large ui-messages to cover states (info, warning, danger, success) Commit: 6d00f38f0a08281d5597872616154af0b3d306c2 https://github.com/galaxyproject/galaxy/commit/6d00f38f0a08281d5597872616154... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py A lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/folders.py M lib/galaxy/managers/libraries.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py A lib/galaxy/tools/imp_exp/exp_history_to_archive.xml M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/run.py M lib/pulsar/client/amqp_exchange.py M scripts/common_startup.sh M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/tools/tools-jobs.js A test-data/1.RData M test/api/helpers.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 Conflicts: client/galaxy/scripts/mvc/tools/tools-form.js static/maps/mvc/tools/tools-form.js.map static/scripts/mvc/tools/tools-form.js Commit: 082c8952e03d11a44bd0cd354a3560f2471305e0 https://github.com/galaxyproject/galaxy/commit/082c8952e03d11a44bd0cd354a356... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Undo initial errors Commit: 728c5450906c8b2ba395f06fa4dbe7e7cc5a7aa6 https://github.com/galaxyproject/galaxy/commit/728c5450906c8b2ba395f06fa4dbe... Author: guerler <aysam.guerler@gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/tools.js M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/tools.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/tools.js Log Message: ----------- Hide regular tool form for upload tool Commit: 6ee9a08cf2d3624985ceed2cf4f4bfd46ca24563 https://github.com/galaxyproject/galaxy/commit/6ee9a08cf2d3624985ceed2cf4f4b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/app/app-view.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form.js M static/scripts/mvc/ui/ui-misc.js R templates/webapps/galaxy/tool_form.mako M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #786 from guerler/tool_form_003 Remove tool form mako, reduce tool runner, fix job resubmission options Compare: https://github.com/galaxyproject/galaxy/compare/b1a8aebad680...6ee9a08cf2d3