Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07a92fd3ef084a6d7cbe27199d281e534e35cec1 https://github.com/galaxyproject/galaxy/commit/07a92fd3ef084a6d7cbe27199d281... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool_model usage from client Commit: 171655930aa44227d6b88709aac638dea77a6cd0 https://github.com/galaxyproject/galaxy/commit/171655930aa44227d6b88709aac63... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Move populate state to parameter handling module Commit: 3e3eb4d1397effc8b46c913bb80f3c02773ac506 https://github.com/galaxyproject/galaxy/commit/3e3eb4d1397effc8b46c913bb80f3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Unify build_module handler Commit: 62d42f711e26e0ab176041ce9a552d1af1290f1a https://github.com/galaxyproject/galaxy/commit/62d42f711e26e0ab176041ce9a552... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-09 (Thu, 09 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Parse payload directly to from_dict handler, handle tool specific attributes in corresponding module wrapper Commit: d27e0570cb0b372288114498fa1ad26a1f5df188 https://github.com/galaxyproject/galaxy/commit/d27e0570cb0b372288114498fa1ad... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Remove name handling field from workflow module forms Commit: 1858e43d46355be344c0fab9e61a2e5a57dc8947 https://github.com/galaxyproject/galaxy/commit/1858e43d46355be344c0fab9e61a2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Unify handling/parsing of label and fixed module name to build title in workflow run form Commit: d484355832a1c6518d38326ef4fbb526423c0e34 https://github.com/galaxyproject/galaxy/commit/d484355832a1c6518d38326ef4fbb... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Provide attributes to front-end, build title on client side Commit: b9f1e29eaf32cda146fea2b102157489a639ea51 https://github.com/galaxyproject/galaxy/commit/b9f1e29eaf32cda146fea2b102157... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant label handling from subworkflows Commit: 7ac954f757d2485ae7543db15f400dca0b94fdf3 https://github.com/galaxyproject/galaxy/commit/7ac954f757d2485ae7543db15f400... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py Log Message: ----------- Strip name handler Commit: 11f9e1863f9616d58fc00a22526f71b2bca7b880 https://github.com/galaxyproject/galaxy/commit/11f9e1863f9616d58fc00a22526f7... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix label and annotation handling for subworkflows Commit: c6c210a4fa47d0fc47306d30b9dbf40589f68cd8 https://github.com/galaxyproject/galaxy/commit/c6c210a4fa47d0fc47306d30b9dbf... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Remove uncommented code block from request builder Commit: eb95131ab3a03a3675c3e6d6db23caca524b3da6 https://github.com/galaxyproject/galaxy/commit/eb95131ab3a03a3675c3e6d6db23c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-10 (Fri, 10 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export label instead of name for description export Commit: d298c1c0da5871105898166ca72dd224f7897fc6 https://github.com/galaxyproject/galaxy/commit/d298c1c0da5871105898166ca72dd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix lint issues Commit: 047c833db79fef8daa25ddf022f85d2ef9386d63 https://github.com/galaxyproject/galaxy/commit/047c833db79fef8daa25ddf022f85... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-11 (Sat, 11 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Align subworkflow handling, fix run request through input name Commit: dfa1ddacb93acf341b71148114450c993379adc1 https://github.com/galaxyproject/galaxy/commit/dfa1ddacb93acf341b71148114450... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore legacy name handling for backward compatibility Commit: 93f190dd0518005f195960333895b645556860cd https://github.com/galaxyproject/galaxy/commit/93f190dd0518005f195960333895b... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Restore previous export behavior Commit: c4491b2d834cdbb61cf009d57c1d3f1086bcfbdb https://github.com/galaxyproject/galaxy/commit/c4491b2d834cdbb61cf009d57c1d3... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix quotes Commit: 79c24066b444b7bd7a85f0ec2ccdd4b131c4da9e https://github.com/galaxyproject/galaxy/commit/79c24066b444b7bd7a85f0ec2ccdd... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M CONTRIBUTING.md M client/galaxy/scripts/mvc/tool/tool-form-base.js M config/datatypes_conf.xml.sample M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml M contrib/nagios/check_galaxy M contrib/nagios/check_galaxy.py 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 lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/steps.py M scripts/slideshow/slideshow_template.html 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 M test/api/test_tools.py M test/api/test_workflow_extraction.py M test/base/populators.py A test/functional/tools/output_format_deprecated_when.xml M test/functional/tools/samples_tool_conf.xml M test/selenium_tests/framework.py M test/selenium_tests/test_stock_tours.py M test/selenium_tests/test_uploads.py Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 1cb8a5da38006cace8c48966a5326b2d3747c574 https://github.com/galaxyproject/galaxy/commit/1cb8a5da38006cace8c48966a5326... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix import order Commit: 6330f6051790b7d86bdd5674697163efc3c2a0f0 https://github.com/galaxyproject/galaxy/commit/6330f6051790b7d86bdd567469716... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: dcda376c9ca68742eb58efe6f3438d4d6c5f834f https://github.com/galaxyproject/galaxy/commit/dcda376c9ca68742eb58efe6f3438... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-14 (Tue, 14 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Restore subworkflow behavior, no need for modifications anymore Commit: 5cd05161413b73c5eb6ea7393b78cafd213409b9 https://github.com/galaxyproject/galaxy/commit/5cd05161413b73c5eb6ea7393b78c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/mapping.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-quotameter.js M static/scripts/mvc/workflow/workflow-view.js M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge branch 'dev' into unify_name_label Commit: 678a8627984852ea4282f6a25bf8c5176783c7c3 https://github.com/galaxyproject/galaxy/commit/678a8627984852ea4282f6a25bf8c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Fix Commit: 7ad46c22694ac7b58acdaefca59ca82cca328f25 https://github.com/galaxyproject/galaxy/commit/7ad46c22694ac7b58acdaefca59ca... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-15 (Wed, 15 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix subworkflow caller Commit: c75671484058bc5c0cec8f07dda081cff7c0eb57 https://github.com/galaxyproject/galaxy/commit/c75671484058bc5c0cec8f07dda08... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly initialize subworkflow parameter Commit: 841cbfd9c7bf1efe2c10bbbff59da22ce67e800c https://github.com/galaxyproject/galaxy/commit/841cbfd9c7bf1efe2c10bbbff59da... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix content id parsing, through error if subworkflow could not be found Commit: 4610da47863c9ca9c5eb092bfd031f32c6984b96 https://github.com/galaxyproject/galaxy/commit/4610da47863c9ca9c5eb092bfd031... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix style Commit: f548af88076b11d33e3a24b50102108a076df1b4 https://github.com/galaxyproject/galaxy/commit/f548af88076b11d33e3a24b501021... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-16 (Thu, 16 Feb 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Add test case for state populating Commit: 8557c32034c9723dc110719b26082312dde1a998 https://github.com/galaxyproject/galaxy/commit/8557c32034c9723dc110719b26082... Author: guerler <aysam.guerler@gmail.com> Date: 2017-02-20 (Mon, 20 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/mvc/tool/tool-form-composite.js Log Message: ----------- Fix sanitization Commit: cdb15f63925e9879744ae38e5e140e5eb9cc6c19 https://github.com/galaxyproject/galaxy/commit/cdb15f63925e9879744ae38e5e140... Author: John Chilton <jmchilton@gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: 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/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/util/workflow_util.py 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/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/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/workflow/workflow-view.js Log Message: ----------- Merge pull request #3593 from guerler/unify_name_label Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler Compare: https://github.com/galaxyproject/galaxy/compare/430ac221baea...cdb15f63925e