Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd082663866c06afb35a179327b1df6efd9c77c7 https://github.com/galaxyproject/galaxy/commit/fd082663866c06afb35a179327b1d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Parse name to label on module initialization Commit: 8a4c0eb7e3ea096ed56471a010003e6717f31957 https://github.com/galaxyproject/galaxy/commit/8a4c0eb7e3ea096ed56471a010003... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use shared initialization procedure for subworkflows Commit: fc1e0702542af846c28e2910d77cbd07f0913769 https://github.com/galaxyproject/galaxy/commit/fc1e0702542af846c28e2910d77cb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Hide name input fields for data input modules Commit: b91680a5b2dfc83b8ee974fdc9ed6f2ab405829c https://github.com/galaxyproject/galaxy/commit/b91680a5b2dfc83b8ee974fdc9ed6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use shared label/annotation input parameter building process Commit: e13958ffcd14f2eb62b29f446a535487dd344904 https://github.com/galaxyproject/galaxy/commit/e13958ffcd14f2eb62b29f446a535... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) 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: ----------- Remove tool module related annotation input parameter Commit: 92bd559c11e62ef1ab704b967621966a31f71e39 https://github.com/galaxyproject/galaxy/commit/92bd559c11e62ef1ab704b9676219... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move label/annotation input parameters at top for all modules Commit: 0f742a6d8380af15ac87a9e654e1119a177bd426 https://github.com/galaxyproject/galaxy/commit/0f742a6d8380af15ac87a9e654e11... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move workflow related tool form to workflow directory Commit: 3a7e6b0b744b9331ec175d8104a17519687fa464 https://github.com/galaxyproject/galaxy/commit/3a7e6b0b744b9331ec175d8104a17... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: A client/galaxy/scripts/mvc/workflow/workflow-forms.js R client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Enable labels for all modules, used shared building process Commit: ff7ab0853d6ea901253ba6175aa343fd9ef3a108 https://github.com/galaxyproject/galaxy/commit/ff7ab0853d6ea901253ba6175aa34... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix comments, show default wrapper first in code file Commit: b03904b52c6064e77a378347d9213ec0b270ebb9 https://github.com/galaxyproject/galaxy/commit/b03904b52c6064e77a378347d9213... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) 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/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/workflow/workflow-view.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/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow input specific error handling, fix input parameter configuration Commit: c9b765794bb14adbaee13a44290e9df242778ffe https://github.com/galaxyproject/galaxy/commit/c9b765794bb14adbaee13a44290e9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix form handler Commit: a967c088f78e39819d4cc0bd349166501e00d74e https://github.com/galaxyproject/galaxy/commit/a967c088f78e39819d4cc0bd34916... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid parsing default names of inputs to labels Commit: f652e9c778af3835de929cfa7823cf1f0a0aed8a https://github.com/galaxyproject/galaxy/commit/f652e9c778af3835de929cfa7823c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove hidden input parameters, attempt to identify label directly from previous state Commit: a3de5b042e8edae2f7beee6554ae78e18f5f115b https://github.com/galaxyproject/galaxy/commit/a3de5b042e8edae2f7beee6554ae7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Move backward compatibility handling of former names out of modules to the workflow manager Commit: 81f799c01f38bab0c584e9b39872d2a1dd7f0348 https://github.com/galaxyproject/galaxy/commit/81f799c01f38bab0c584e9b39872d... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Revise comment Commit: afe2a6116a450fa69ae87705c14a4e43a7ef5830 https://github.com/galaxyproject/galaxy/commit/afe2a6116a450fa69ae87705c14a4... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use label to connect workflow steps Commit: ae751adac8ae46d7f0eb2831666258143724bc0f https://github.com/galaxyproject/galaxy/commit/ae751adac8ae46d7f0eb283166625... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Adjust unit test to use labels instead of name through state Commit: 488c42aa4c3e3e903e0234804d3cd90277d9a930 https://github.com/galaxyproject/galaxy/commit/488c42aa4c3e3e903e0234804d3cd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use constants to filter default naming of input modules Commit: dde9ba83acfbedd50a59ccb211cf9d352c86de97 https://github.com/galaxyproject/galaxy/commit/dde9ba83acfbedd50a59ccb211cf9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.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/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: 528b00667d4a053b3b8db4790323b0f655b18f9b https://github.com/galaxyproject/galaxy/commit/528b00667d4a053b3b8db4790323b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix comment Commit: 619bfeffd503681ab7d6072426f621fde7485fd5 https://github.com/galaxyproject/galaxy/commit/619bfeffd503681ab7d6072426f62... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to use fixed default name for unlabeled subworkflow inputs Commit: 007b6599c21a4927d58629210f103829e947011f https://github.com/galaxyproject/galaxy/commit/007b6599c21a4927d58629210f103... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix name handling in build module Commit: 198d36f77bb444572f03a34aec7c695d0adc52e1 https://github.com/galaxyproject/galaxy/commit/198d36f77bb444572f03a34aec7c6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) 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/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-composite.js Log Message: ----------- Fix step title in composite tool form Commit: 05687b8a19785c89772db499d6ede5a097ba47ce https://github.com/galaxyproject/galaxy/commit/05687b8a19785c89772db499d6ede... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Strip debug output Commit: 820c46cf63602b788ed282f4277a19129d4b3dd8 https://github.com/galaxyproject/galaxy/commit/820c46cf63602b788ed282f4277a1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: 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: ----------- Repack scripts Commit: 2f53b1d6d12457e0eaba5ca5da8b95321c69ff54 https://github.com/galaxyproject/galaxy/commit/2f53b1d6d12457e0eaba5ca5da8b9... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py M scripts/bootstrap_history.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: b9ba754ce6eb2d4b23c54aa557cb6c0a512c4082 https://github.com/galaxyproject/galaxy/commit/b9ba754ce6eb2d4b23c54aa557cb6... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix repacked files Commit: c80380dc57305be36e615ec13d1d17aecd285114 https://github.com/galaxyproject/galaxy/commit/c80380dc57305be36e615ec13d1d1... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/grid/grid-view.js M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/bootstrap_history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: d3840c5c4140807297b22ad1e9b7da97eb1a6570 https://github.com/galaxyproject/galaxy/commit/d3840c5c4140807297b22ad1e9b7d... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) 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 R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.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 R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.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/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #3644 from guerler/unify_label_name_000 Introduce labels for all modules, remove name handling field for data inputs Compare: https://github.com/galaxyproject/galaxy/compare/0b4e52c8e93a...d3840c5c4140