Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56c78eed802d1be39715965a67db6844308f9955 https://github.com/galaxyproject/galaxy/commit/56c78eed802d1be39715965a67db6... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Handle cases with missing parameter values Commit: 065d9332fe3b09f00d2a515fc5714b3e98abbfe5 https://github.com/galaxyproject/galaxy/commit/065d9332fe3b09f00d2a515fc5714... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/base.less M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/library/library-dataset-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/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css Log Message: ----------- Start to revise handling of missing tools Commit: 41922b0618c945a4eab8136e27a40d6a62f94c21 https://github.com/galaxyproject/galaxy/commit/41922b0618c945a4eab8136e27a40... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Raise exception if step type is invalid for now Commit: 5140b8bdc3f12fb17f5b0513eeb96610bac16f89 https://github.com/galaxyproject/galaxy/commit/5140b8bdc3f12fb17f5b0513eeb96... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) 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: ----------- Remove private function for node element view Commit: ffd44b86f5a06aab38bba46a9952ce150fa4c99e https://github.com/galaxyproject/galaxy/commit/ffd44b86f5a06aab38bba46a9952c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Properly parse step error for missing tools Commit: adadf39b66d410ecf5b8d707b18abe36d5d457e8 https://github.com/galaxyproject/galaxy/commit/adadf39b66d410ecf5b8d707b18ab... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/managers/workflows.py M lib/galaxy/web/base/controller.py M lib/galaxy/workflow/modules.py Log Message: ----------- Add missing tool exception to shared exceptions, unify handling Commit: 7fe719cd414ca3aa194db3e74244e70cb2946bbf https://github.com/galaxyproject/galaxy/commit/7fe719cd414ca3aa194db3e74244e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid storing missing tool errors, resolves naming conflicts Commit: 3535326a46f9e7d53642b13bf404e50d5105ab66 https://github.com/galaxyproject/galaxy/commit/3535326a46f9e7d53642b13bf404e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Rename error identifier to indicate generic step related error Commit: 56bb347765231e4dcc1d7fa865d1a54a53921da5 https://github.com/galaxyproject/galaxy/commit/56bb347765231e4dcc1d7fa865d1a... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- This is not an upgrade message but an error which should be evaluated through step.get_errors Commit: 4b07c13e272ea5e452f7e4d8f76084b9d8a2ecd6 https://github.com/galaxyproject/galaxy/commit/4b07c13e272ea5e452f7e4d8f7608... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/web/base/controller.py Log Message: ----------- Add comment Commit: 109abf0f178ecb9801ffa0c4afd87463e74b4015 https://github.com/galaxyproject/galaxy/commit/109abf0f178ecb9801ffa0c4afd87... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix error message for updating workflow when tool is missing Commit: 20e380ea26b538dcf9c44882634b8f8e06d5167a https://github.com/galaxyproject/galaxy/commit/20e380ea26b538dcf9c44882634b8... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Allow saving workflow without connections Commit: 2abac81f858cb8013f1e7f134901f884aa3acc1a https://github.com/galaxyproject/galaxy/commit/2abac81f858cb8013f1e7f134901f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Prevent saving, connections not resolved for now Commit: dd40b1f64a08b2f9ce3d088eab6cad6374150974 https://github.com/galaxyproject/galaxy/commit/dd40b1f64a08b2f9ce3d088eab6ca... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Repack scripts Commit: 0d6a7b66ff3babf7e6a2627a2631ea873ffed3b1 https://github.com/galaxyproject/galaxy/commit/0d6a7b66ff3babf7e6a2627a2631e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to directly prevent saving workflow with missing nodes Commit: 2263caa44dc40e4ed30e1a67e21b35232576a631 https://github.com/galaxyproject/galaxy/commit/2263caa44dc40e4ed30e1a67e21b3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Validate cycles and step size before building model for workflow execution Commit: cdf31059a5202191e99e6fd10ac21ba088581c3c https://github.com/galaxyproject/galaxy/commit/cdf31059a5202191e99e6fd10ac21... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/workflow/steps.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Always provide an order index, even for cyclic workflows use step index Commit: 3accc1e53ff09a295b54f5b17e68fef443a67f85 https://github.com/galaxyproject/galaxy/commit/3accc1e53ff09a295b54f5b17e68f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) 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: ----------- Only allow text editing if text field is available in regular step editor Commit: 1c9dd0dbe978f09d5fa0845065a7ecfaf953a03c https://github.com/galaxyproject/galaxy/commit/1c9dd0dbe978f09d5fa0845065a7e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Avoid saving step parameters in temporary config object instead of regular state Commit: 6905f5bd413fd3612904ff0674140d4b9f5add92 https://github.com/galaxyproject/galaxy/commit/6905f5bd413fd3612904ff0674140... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js Log Message: ----------- Attempt to unify runtime state handling Commit: 7ebb6a36c9fad2d23c188c2fd173727bbe001d29 https://github.com/galaxyproject/galaxy/commit/7ebb6a36c9fad2d23c188c2fd1737... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add abstract recover state function Commit: 0811c93fd839e4a31b37e4d1788526f163e41708 https://github.com/galaxyproject/galaxy/commit/0811c93fd839e4a31b37e4d178852... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Align caller order, test unified runtime state handler Commit: 0d30b177a20745c3dc1e7f264eb36b47dd453f1b https://github.com/galaxyproject/galaxy/commit/0d30b177a20745c3dc1e7f264eb36... 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test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_sockets.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_external_files.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tools/data_source/fetch.py Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: a82565e5385ccacfeef5aa6dd4d61886e5826ab0 https://github.com/galaxyproject/galaxy/commit/a82565e5385ccacfeef5aa6dd4d61... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove custom update_state caller Commit: 6fa53a4f062652d73d13d9562d43123fa83e4143 https://github.com/galaxyproject/galaxy/commit/6fa53a4f062652d73d13d9562d431... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py Log Message: ----------- Replace update with recover state Commit: e9b49f25919e7228d2d862bf9ba73b134a8600eb https://github.com/galaxyproject/galaxy/commit/e9b49f25919e7228d2d862bf9ba73... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-02 (Fri, 02 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove debug test Commit: 9156d49514082d5ae466a7a639424f4bcea61871 https://github.com/galaxyproject/galaxy/commit/9156d49514082d5ae466a7a639424... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M config/job_conf.xml.sample_advanced M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py M run_tests.sh A scripts/dump_tour.py M scripts/functional_tests.py M templates/show_params.mako M templates/webapps/galaxy/workflow/list.mako M test/api/test_api_batch.py M test/api/test_histories.py M test/base/driver_util.py M test/base/twilltestcase.py R test/casperjs/anon-history-tests.js R test/casperjs/api-batch-tests.js R test/casperjs/api-history-tests.js R test/casperjs/api-tool-tests.js R test/casperjs/api-user-tests.js R test/casperjs/hda-state-tests.js R test/casperjs/history-options-tests.js R test/casperjs/history-panel-tests.js R test/casperjs/history-share-tests.js R test/casperjs/login-tests.js R test/casperjs/registration-tests.js R test/casperjs/upload-tests.js A test/functional/tools/for_tours/filtering.py A test/functional/tools/for_tours/filtering.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/galaxy_selenium/__init__.py A test/galaxy_selenium/cli.py A test/galaxy_selenium/data.py A test/galaxy_selenium/driver_factory.py A test/galaxy_selenium/has_driver.py A test/galaxy_selenium/navigates_galaxy.py A test/galaxy_selenium/navigation-data.yml A test/galaxy_selenium/sizzle.py A test/selenium_tests/__init__.py A test/selenium_tests/framework.py A test/selenium_tests/test_anon_history.py A test/selenium_tests/test_history_dataset_state.py A test/selenium_tests/test_history_options.py A test/selenium_tests/test_history_panel.py A test/selenium_tests/test_history_sharing.py A test/selenium_tests/test_login.py A test/selenium_tests/test_registration.py A test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_uploads.py A test/selenium_tests/test_workflow_editor.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: cfb3b40d6ae9e27162b7de71c0167af93199d7ea https://github.com/galaxyproject/galaxy/commit/cfb3b40d6ae9e27162b7de71c0167... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py R templates/webapps/galaxy/workflow/editor_tool_form.mako Log Message: ----------- Remove workflow editor tool form mako Commit: f532fb2e8581c09dcd64daf87acd158938b35b27 https://github.com/galaxyproject/galaxy/commit/f532fb2e8581c09dcd64daf87acd1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix decode runtime state signature Commit: 9c069a21f68a0ab7a4138ffc6277c4ad2f5aec63 https://github.com/galaxyproject/galaxy/commit/9c069a21f68a0ab7a4138ffc6277c... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M lib/galaxy/exceptions/__init__.py M lib/galaxy/managers/workflows.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Fix lint, unit tests Commit: d2665d88bf9cb60db773793f9f206b6ad4af1edc https://github.com/galaxyproject/galaxy/commit/d2665d88bf9cb60db773793f9f206... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix workflow qunit tests Commit: 61df5ac6f5269da4309b8b17767354b1704baa04 https://github.com/galaxyproject/galaxy/commit/61df5ac6f5269da4309b8b1776735... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Remove redundant and unused update state from test cases, replace with recover state Commit: 6be315ae8f1781eb6fdd9d7ae3ce3a5dc9763acb https://github.com/galaxyproject/galaxy/commit/6be315ae8f1781eb6fdd9d7ae3ce3... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to unify state handling for simple workflow modules Commit: 7a7b833c99d9b4ebc9efc9c8397896ddb16555aa https://github.com/galaxyproject/galaxy/commit/7a7b833c99d9b4ebc9efc9c839789... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-06 (Tue, 06 Dec 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M scripts/bootstrap_history.py M static/welcome.html.sample M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 0e40c7563be74918b8f349725b3ff7a2bea9fa32 https://github.com/galaxyproject/galaxy/commit/0e40c7563be74918b8f349725b3ff... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant state fields array, use default state instead Commit: dda00721676593275f61d74dc4946dd09961adac https://github.com/galaxyproject/galaxy/commit/dda00721676593275f61d74dc4946... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to unify get runtime input dicts and move it export caller since its only used there Commit: eb4c32f14b82b4018e673abfe5798abc8a808c32 https://github.com/galaxyproject/galaxy/commit/eb4c32f14b82b4018e673abfe5798... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to unify recover and get state mechanisms Commit: 9379fc0dbed55f0cfdc92483ca17f39bd1c8256a https://github.com/galaxyproject/galaxy/commit/9379fc0dbed55f0cfdc92483ca17f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use shared from dict and workflow callers Commit: bae00397d80028c15327cf7ca2fed056927d4882 https://github.com/galaxyproject/galaxy/commit/bae00397d80028c15327cf7ca2fed... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove redundant comment Commit: b393f007273274e0ce12efd204d2f59fa28bc34f https://github.com/galaxyproject/galaxy/commit/b393f007273274e0ce12efd204d2f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Strip simple workflow form boilerplate class Commit: 7c479aa8b9f627273b84cb15cb288115d3b3df25 https://github.com/galaxyproject/galaxy/commit/7c479aa8b9f627273b84cb15cb288... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Do not require any module inputs by default, remove unused subworkflow callers Commit: 15c1ecd26b7f1a10dd2f09b96303d5762773f8c3 https://github.com/galaxyproject/galaxy/commit/15c1ecd26b7f1a10dd2f09b96303d... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-07 (Wed, 07 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix lint, spacing Commit: 648d717298de9f5d12e612b1f769bd84e362aa88 https://github.com/galaxyproject/galaxy/commit/648d717298de9f5d12e612b1f769b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Improve state building resilience, fix test cases Commit: db3bb117dac67b8b47bda2fc08f5f26af50bc33f https://github.com/galaxyproject/galaxy/commit/db3bb117dac67b8b47bda2fc08f5f... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Resolve subworkflow data input names through connected data step states Commit: bd91f5aab9d9688af0c78d9b47859415a5c45244 https://github.com/galaxyproject/galaxy/commit/bd91f5aab9d9688af0c78d9b47859... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export with default labels Commit: c02c9e8dd590b0079267305ad8240144e06a2a24 https://github.com/galaxyproject/galaxy/commit/c02c9e8dd590b0079267305ad8240... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M test/api/test_workflow_extraction.py Log Message: ----------- Fix test cases, introduce temporary handling Commit: f745ee3558e0ca67d6d92ba1f19215a45fb7033b https://github.com/galaxyproject/galaxy/commit/f745ee3558e0ca67d6d92ba1f1921... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Remove tool errors from export assertion test, use unified state for all modules Commit: 751f997491a183a28ee2c15ad637b219c04b25b6 https://github.com/galaxyproject/galaxy/commit/751f997491a183a28ee2c15ad637b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix input parameter module types Commit: 38633fad618916d71b6439ef2484c9af9d3f399f https://github.com/galaxyproject/galaxy/commit/38633fad618916d71b6439ef2484c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Basestring->string_types Commit: 34f5506080bc1c76df3e0267fa4aeeb32137f356 https://github.com/galaxyproject/galaxy/commit/34f5506080bc1c76df3e0267fa4ae... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-12-09 (Fri, 09 Dec 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #16 from dannon/py3_basestring Basestring->string_types Commit: f9abb47ebdb54fe0e01607fd076d52c229ff2ca9 https://github.com/galaxyproject/galaxy/commit/f9abb47ebdb54fe0e01607fd076d5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-11 (Sun, 11 Dec 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Use shared safe loads to load module states Commit: 9fc6162b749a4c0dd8c59da4ce0e199e64cfa0aa https://github.com/galaxyproject/galaxy/commit/9fc6162b749a4c0dd8c59da4ce0e1... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-12 (Mon, 12 Dec 2016) 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: ----------- Parse dictionary, avoid unnecessary string conversion Commit: 026b43b92abe6b0c38de329526ebbeaf862b5674 https://github.com/galaxyproject/galaxy/commit/026b43b92abe6b0c38de329526ebb... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-13 (Tue, 13 Dec 2016) 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: ----------- Use regular form build to build input module form Commit: c5f7416c7cde507f32e3ac2d6cd83fce94fcd05b https://github.com/galaxyproject/galaxy/commit/c5f7416c7cde507f32e3ac2d6cd83... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) 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: ----------- Switch to regular form builder for non-tool modules, initial commit Commit: 8cc4e5910398d6dd3adfddabfe7822461b9ab4a5 https://github.com/galaxyproject/galaxy/commit/8cc4e5910398d6dd3adfddabfe782... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py R templates/webapps/galaxy/workflow/editor_generic_form.mako Log Message: ----------- Regular remove regular module form mako Commit: d41b1425e6695c70da052b4927b6990df9bcdd4b https://github.com/galaxyproject/galaxy/commit/d41b1425e6695c70da052b4927b69... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) 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: ----------- Add basic selector for input dataset collection editor form input Commit: f9253351bfb90c51e0ba8ea4bd22e6da25d15d9b https://github.com/galaxyproject/galaxy/commit/f9253351bfb90c51e0ba8ea4bd22e... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-14 (Wed, 14 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Add value details to collection type selector Commit: ca14167cdf7fec0c3372e4a494282ecb58be0173 https://github.com/galaxyproject/galaxy/commit/ca14167cdf7fec0c3372e4a494282... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move non-tool module handling to api, disable workflow parameter info panel for now Commit: 4476a2bfbf89e5abfe24ea9e63da7a3c6c404d09 https://github.com/galaxyproject/galaxy/commit/4476a2bfbf89e5abfe24ea9e63da7... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.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/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Indicate removal of form html building Commit: f2f1f0b3eff1196ec3b94a812972b607586d21b6 https://github.com/galaxyproject/galaxy/commit/f2f1f0b3eff1196ec3b94a812972b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Rename tool form build caller Commit: 7a8486f31f299f5b34014af1dbfc4648500ac3a1 https://github.com/galaxyproject/galaxy/commit/7a8486f31f299f5b34014af1dbfc4... 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test/integration/resubmission_rules/__init__.py A test/integration/resubmission_rules/rules.py A test/integration/resubmission_runners.py A test/integration/test_job_resubmission.py M test/integration/test_resolvers.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_mapper.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gff_filter_by_feature_count.xml Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 5c49af7d0dddbb1e7cdb456535a57854e9460558 https://github.com/galaxyproject/galaxy/commit/5c49af7d0dddbb1e7cdb456535a57... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/workflow/workflow-node.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-parameters.js Log Message: ----------- Parse datalist handler for regular text input fields to front end Commit: da6406202e8848316cc19fbf095922b31c18eebd https://github.com/galaxyproject/galaxy/commit/da6406202e8848316cc19fbf09592... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Show workflow attributes instead of mock node content, remove special handling from show module form caller Commit: a8caede3f836fe1bc74b97dc2c5e50fd1ca95ea6 https://github.com/galaxyproject/galaxy/commit/a8caede3f836fe1bc74b97dc2c5e5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-26 (Mon, 26 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-view.js.map M static/maps/mvc/workflow/workflow-manager.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-view.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Add form message if no inputs are available Commit: 2b8cc0771f77c4e431212acd490c5445e246a63e https://github.com/galaxyproject/galaxy/commit/2b8cc0771f77c4e431212acd490c5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py 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: ----------- Attempt to use build module for module initialization Commit: 9df94f77c122cbc7c77230f83c996c1c9892f603 https://github.com/galaxyproject/galaxy/commit/9df94f77c122cbc7c77230f83c996... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) 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 load state identification, disable spinner for now Commit: 83af3ce467a67712b1c692ab9fd16ba1acc6f50f https://github.com/galaxyproject/galaxy/commit/83af3ce467a67712b1c692ab9fd16... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to remove new module caller, use to_dict caller instead Commit: ebbeecd7b3d80073ba44ef0d6d2c28ffaf1f274e https://github.com/galaxyproject/galaxy/commit/ebbeecd7b3d80073ba44ef0d6d2c2... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/json.py M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Adjust unit tests Commit: 17d2a90c1275750387cedc421bc7b27cb9b0db6a https://github.com/galaxyproject/galaxy/commit/17d2a90c1275750387cedc421bc7b... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M test/qunit/tests/workflow_editor_tests.js Log Message: ----------- Fix qunit tests Commit: c4c870991a39b6e2b195d20c62188a7c2ba6e2f6 https://github.com/galaxyproject/galaxy/commit/c4c870991a39b6e2b195d20c62188... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Fix blank lines Commit: d6a1f995c818c24bfd2d800af4dd498238061e34 https://github.com/galaxyproject/galaxy/commit/d6a1f995c818c24bfd2d800af4dd4... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use safe loads to recover states Commit: 084b9432a643d48e32a202f9396e5edfb9962e54 https://github.com/galaxyproject/galaxy/commit/084b9432a643d48e32a202f9396e5... Author: guerler <aysam.guerler@gmail.com> Date: 2016-12-29 (Thu, 29 Dec 2016) 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 M test/api/test_workflows.py Log Message: ----------- Fix export test case Commit: 1487e144ec198dca788a3737692459857aa37678 https://github.com/galaxyproject/galaxy/commit/1487e144ec198dca788a373769245... 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Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-02 (Mon, 02 Jan 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 workflow parameter panel in workflow editor Commit: d21c77c67b703a7c004ae14cac40c75dc31981de https://github.com/galaxyproject/galaxy/commit/d21c77c67b703a7c004ae14cac40c... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/jobs/actions/post.py M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Parse job actions as dictionary Commit: c86ef0bbb54c19195cff8a46a752a07b246c040f https://github.com/galaxyproject/galaxy/commit/c86ef0bbb54c19195cff8a46a752a... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove temporary fix for imported workflow with conflicting versions and different conditionals Commit: ad92ee376dcb9497697898ea42210b130f77df11 https://github.com/galaxyproject/galaxy/commit/ad92ee376dcb9497697898ea42210... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Handle export for backward compatibility Commit: 422b34aa3dd7d4589bcab723f083842e232ea212 https://github.com/galaxyproject/galaxy/commit/422b34aa3dd7d4589bcab723f0838... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Use trans as provided on module initialization to encode runtime state Commit: 2cbb26ac41d20d8813196222028e28f30ca0d6c0 https://github.com/galaxyproject/galaxy/commit/2cbb26ac41d20d8813196222028e2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove unused import Commit: 24ad65e0ac533f279d3935949c324f61dd4647fc https://github.com/galaxyproject/galaxy/commit/24ad65e0ac533f279d3935949c324... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix api test cases Commit: 10ac745c3ab78249f5c894c8ec1ce73af2d9fe0b https://github.com/galaxyproject/galaxy/commit/10ac745c3ab78249f5c894c8ec1ce... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M lib/tool_shed/util/workflow_util.py Log Message: ----------- Fix toolshed workflow utilities Commit: c8e1c8f53507a219a2f3475f271a202695237942 https://github.com/galaxyproject/galaxy/commit/c8e1c8f53507a219a2f3475f271a2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-04 (Wed, 04 Jan 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: ----------- Remove out commented code block, debug statement Commit: 5d1f8e1fe755c61a133018928d9187db4a26fc7e https://github.com/galaxyproject/galaxy/commit/5d1f8e1fe755c61a133018928d918... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Do not rely on the stored has_error flag when building run requests Commit: 48ba525eb56f349bf00c0554b3e911b42ab4fc43 https://github.com/galaxyproject/galaxy/commit/48ba525eb56f349bf00c0554b3e91... 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test/api/workflows_format_2/__init__.py R test/api/workflows_format_2/converter.py R test/api/workflows_format_2/interface.py R test/api/workflows_format_2/main.py A test/base/data/test_workflow_1.ga A test/base/data/test_workflow_2.ga A test/base/data/test_workflow_batch.ga A test/base/data/test_workflow_map_reduce_pause.ga A test/base/data/test_workflow_matching_lists.ga A test/base/data/test_workflow_missing_tool.ga A test/base/data/test_workflow_pause.ga A test/base/data/test_workflow_topoambigouity.ga A test/base/data/test_workflow_topoambigouity_auto_laidout.ga A test/base/data/test_workflow_validation_1.ga A test/base/data/test_workflow_with_runtime_input.ga A test/base/populators.py A test/base/workflows_format_2/README.txt A test/base/workflows_format_2/__init__.py A test/base/workflows_format_2/converter.py A test/base/workflows_format_2/interface.py A test/base/workflows_format_2/main.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/for_workflows/mapper2.xml A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation-data.yml A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/manual/workflows_scaling.py A test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/framework.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py A test/selenium_tests/test_workflow_management.py A test/selenium_tests/test_workflow_run.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/tools_support.py M test/unit/workflows/workflow_support.py R tools/filters/gff/sort_gtf.py M tox.ini Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 5f3ccc91e31b04e493fa6ff1ddfbe561904374f7 https://github.com/galaxyproject/galaxy/commit/5f3ccc91e31b04e493fa6ff1ddfbe... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Parse keywords in manager since not all modules require the optional exact_tools flag Commit: dc9c6032f25e9ec97f84e8b4e6e15d6a2e9d6f70 https://github.com/galaxyproject/galaxy/commit/dc9c6032f25e9ec97f84e8b4e6e15... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix tool version matching Commit: 82aea503e11e1f5d010f4797d404f02275deb18f https://github.com/galaxyproject/galaxy/commit/82aea503e11e1f5d010f4797d404f... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Make important log message an info instead of a debug. Commit: 0f28f8549bc7dd375d4f5ffbf6d4e0f5b9fb122e https://github.com/galaxyproject/galaxy/commit/0f28f8549bc7dd375d4f5ffbf6d4e... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Document using options within a text parameter. Commit: fb8a9628647eca0b4a35bc23f74f8b946bbbf716 https://github.com/galaxyproject/galaxy/commit/fb8a9628647eca0b4a35bc23f74f8... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/workflow/modules.py A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #17 from jmchilton/fix_workflow_issues_datalist Two small tweaks. Commit: 84d9e171bc9be48d237cc16e5d877de23e67a4d3 https://github.com/galaxyproject/galaxy/commit/84d9e171bc9be48d237cc16e5d877... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-14 (Sat, 14 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/base.less M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/actions/post.py 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/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-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/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.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-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_workflows.py A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge branch 'fix_workflow_issues' of https://github.com/guerler/galaxy into fix_workflow_issues Commit: 0482416c7af9d62edecbb5cde4c88563385dd1bd https://github.com/galaxyproject/galaxy/commit/0482416c7af9d62edecbb5cde4c88... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-17 (Tue, 17 Jan 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/meta.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/util/galaxyops/__init__.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/form/form-view.js.map 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/form/form-view.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 0b0419533a2b1247a426bdf51bbf23636fcfe43a https://github.com/galaxyproject/galaxy/commit/0b0419533a2b1247a426bdf51bbf2... Author: guerler <aysam.guerler@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M README.rst M client/galaxy/scripts/viz/trackster/tracks.js M config/galaxy.ini.sample A config/local_conda_mapping.yml.sample M doc/schema_template.md M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/dependencies.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/errors.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/object_wrapper.py A lib/galaxy/util/oset.py M lib/galaxy/util/properties.py M lib/galaxy/version.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/util/shed_util_common.py M run.sh A scripts/manage_tool_dependencies.py M static/maps/viz/trackster/tracks.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/viz/trackster/tracks.js M test/docker/base/run_test_wrapper.sh M test/functional/tools/column_param.xml A test/functional/tools/explicit_conversion.xml M test/functional/tools/implicit_conversion.xml A test/functional/tools/legacy_r.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_resolvers.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_management.py M test/unit/tools/test_tool_deps.py M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/plotting/bar_chart.xml M tools/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 3c4413d31d991cf06b3217265e5f573c5fc26fc1 https://github.com/galaxyproject/galaxy/commit/3c4413d31d991cf06b3217265e5f5... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/base.less M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/actions/post.py 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/tools/parameters/basic.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/json.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/steps.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/library/library-dataset-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/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view-node.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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/editor_generic_form.mako R templates/webapps/galaxy/workflow/editor_tool_form.mako M test/api/test_workflows.py A test/functional/tools/param_text_option.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/tests/workflow_editor_tests.js M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #3181 from guerler/fix_workflow_issues Normalizes the handling of steps and missing tools for the workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/2ff068f133b0...3c4413d31d99