January 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 56c78e: Handle cases with missing parameter values
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56c78eed802d1be39715965a67db6844308f9955 https://github.com/galaxyproject/galaxy/commit/56c78eed802d1be39715965a67db… Author: guerler <aysam.guerler(a)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/065d9332fe3b09f00d2a515fc571… Author: guerler <aysam.guerler(a)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/41922b0618c945a4eab8136e27a4… Author: guerler <aysam.guerler(a)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/5140b8bdc3f12fb17f5b0513eeb9… Author: guerler <aysam.guerler(a)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/ffd44b86f5a06aab38bba46a9952… Author: guerler <aysam.guerler(a)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/adadf39b66d410ecf5b8d707b18a… Author: guerler <aysam.guerler(a)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/7fe719cd414ca3aa194db3e74244… Author: guerler <aysam.guerler(a)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/3535326a46f9e7d53642b13bf404… Author: guerler <aysam.guerler(a)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/56bb347765231e4dcc1d7fa865d1… Author: guerler <aysam.guerler(a)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/4b07c13e272ea5e452f7e4d8f760… Author: guerler <aysam.guerler(a)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/109abf0f178ecb9801ffa0c4afd8… Author: guerler <aysam.guerler(a)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/20e380ea26b538dcf9c44882634b… Author: guerler <aysam.guerler(a)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/2abac81f858cb8013f1e7f134901… Author: guerler <aysam.guerler(a)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/dd40b1f64a08b2f9ce3d088eab6c… Author: guerler <aysam.guerler(a)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/0d6a7b66ff3babf7e6a2627a2631… Author: guerler <aysam.guerler(a)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/2263caa44dc40e4ed30e1a67e21b… Author: guerler <aysam.guerler(a)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/cdf31059a5202191e99e6fd10ac2… Author: guerler <aysam.guerler(a)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/3accc1e53ff09a295b54f5b17e68… Author: guerler <aysam.guerler(a)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/1c9dd0dbe978f09d5fa0845065a7… Author: guerler <aysam.guerler(a)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/6905f5bd413fd3612904ff067414… Author: guerler <aysam.guerler(a)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/7ebb6a36c9fad2d23c188c2fd173… Author: guerler <aysam.guerler(a)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/0811c93fd839e4a31b37e4d17885… Author: guerler <aysam.guerler(a)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/0d30b177a20745c3dc1e7f264eb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-01 (Thu, 01 Dec 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-misc.js A client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/visualizations/charts/static/repository/build/registry.js M config/plugins/visualizations/charts/static/repository/build/registry.js.map M doc/source/project/organization.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/config.py M 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lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/parameters/input_translation.py M lib/galaxy/tools/parameters/sanitize.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/dbkeys.py M lib/galaxy/version.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/external_services.py M 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scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/drmaa_external_runner.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-workflow.js.map M static/maps/mvc/tool/tools.js.map M static/maps/mvc/ui/ui-misc.js.map A static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tools.js M static/scripts/mvc/ui/ui-misc.js A static/scripts/mvc/user/user-preferences.js M static/style/blue/base.css M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako R templates/user/change_password.mako R templates/user/communication_settings.mako R templates/user/edit_address.mako R templates/user/new_address.mako R templates/user/permissions.mako M templates/user/register.mako R templates/user/toolbox_filters.mako R templates/user/username.mako R templates/webapps/galaxy/user/api_keys.mako M templates/webapps/galaxy/user/list_users.mako R templates/webapps/galaxy/user/manage_info.mako M templates/webapps/galaxy/workflow/editor.mako A templates/webapps/tool_shed/user/api_keys.mako A templates/webapps/tool_shed/user/change_password.mako A templates/webapps/tool_shed/user/index.mako A templates/webapps/tool_shed/user/username.mako A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/api/test_configuration.py M test/api/test_datasets.py M test/api/test_history_contents_provenance.py M test/api/test_users.py M test/base/api.py M test/base/interactor.py M test/base/twilltestcase.py R test/casperjs/api-configuration-tests.js M test/functional/test_library_templates.py A test/functional/tools/sam_to_bam.xml M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_runner_local.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M 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/a82565e5385ccacfeef5aa6dd4d6… Author: guerler <aysam.guerler(a)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/6fa53a4f062652d73d13d9562d43… Author: guerler <aysam.guerler(a)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 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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/cfb3b40d6ae9e27162b7de71c016… Author: guerler <aysam.guerler(a)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/f532fb2e8581c09dcd64daf87acd… Author: guerler <aysam.guerler(a)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/9c069a21f68a0ab7a4138ffc6277… Author: guerler <aysam.guerler(a)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/d2665d88bf9cb60db773793f9f20… Author: guerler <aysam.guerler(a)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/61df5ac6f5269da4309b8b177673… Author: guerler <aysam.guerler(a)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/6be315ae8f1781eb6fdd9d7ae3ce… Author: guerler <aysam.guerler(a)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 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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/bae00397d80028c15327cf7ca2fe… Author: guerler <aysam.guerler(a)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/b393f007273274e0ce12efd204d2… Author: guerler <aysam.guerler(a)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/7c479aa8b9f627273b84cb15cb28… Author: guerler <aysam.guerler(a)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/15c1ecd26b7f1a10dd2f09b96303… Author: guerler <aysam.guerler(a)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/648d717298de9f5d12e612b1f769… Author: guerler <aysam.guerler(a)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/db3bb117dac67b8b47bda2fc08f5… Author: guerler <aysam.guerler(a)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/bd91f5aab9d9688af0c78d9b4785… Author: guerler <aysam.guerler(a)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/c02c9e8dd590b0079267305ad824… Author: guerler <aysam.guerler(a)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/f745ee3558e0ca67d6d92ba1f192… Author: guerler <aysam.guerler(a)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/751f997491a183a28ee2c15ad637… Author: guerler <aysam.guerler(a)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/38633fad618916d71b6439ef2484… Author: Dannon Baker <dannon.baker(a)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/34f5506080bc1c76df3e0267fa4a… Author: Aysam Guerler <aysam.guerler(a)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/f9abb47ebdb54fe0e01607fd076d… Author: guerler <aysam.guerler(a)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/9fc6162b749a4c0dd8c59da4ce0e… Author: guerler <aysam.guerler(a)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/026b43b92abe6b0c38de329526eb… Author: guerler <aysam.guerler(a)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/c5f7416c7cde507f32e3ac2d6cd8… Author: guerler <aysam.guerler(a)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/8cc4e5910398d6dd3adfddabfe78… Author: guerler <aysam.guerler(a)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/d41b1425e6695c70da052b4927b6… Author: guerler <aysam.guerler(a)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/f9253351bfb90c51e0ba8ea4bd22… Author: guerler <aysam.guerler(a)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/ca14167cdf7fec0c3372e4a49428… Author: guerler <aysam.guerler(a)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/4476a2bfbf89e5abfe24ea9e63da… Author: guerler <aysam.guerler(a)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: 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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/5c49af7d0dddbb1e7cdb456535a5… Author: guerler <aysam.guerler(a)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/da6406202e8848316cc19fbf0959… Author: guerler <aysam.guerler(a)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 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83af3ce467a67712b1c692ab9fd16ba1acc6f50f https://github.com/galaxyproject/galaxy/commit/83af3ce467a67712b1c692ab9fd1… Author: guerler <aysam.guerler(a)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/ebbeecd7b3d80073ba44ef0d6d2c… Author: guerler <aysam.guerler(a)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/17d2a90c1275750387cedc421bc7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-28 (Wed, 28 Dec 2016) Changed paths: M 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scripts/functional_tests.py R scripts/run_selenium_tests.sh M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M templates/show_params.mako M test/base/driver_util.py R test/functional/workflow.py M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_job_resubmission.py M test/selenium_tests/test_history_dataset_state.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_stock_tours.py A test/selenium_tests/test_tool_form.py Log Message: ----------- Merge branch 'dev' into fix_workflow_issues Commit: 9133618c041ba89e26d3661fb836e882c5b27e94 https://github.com/galaxyproject/galaxy/commit/9133618c041ba89e26d3661fb836… Author: guerler <aysam.guerler(a)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/d21c77c67b703a7c004ae14cac40… Author: guerler <aysam.guerler(a)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/c86ef0bbb54c19195cff8a46a752… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-02 (Mon, 02 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log 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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/24ad65e0ac533f279d3935949c32… Author: guerler <aysam.guerler(a)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/10ac745c3ab78249f5c894c8ec1c… Author: guerler <aysam.guerler(a)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/c8e1c8f53507a219a2f3475f271a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M 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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/5f3ccc91e31b04e493fa6ff1ddfb… Author: guerler <aysam.guerler(a)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/dc9c6032f25e9ec97f84e8b4e6e1… Author: guerler <aysam.guerler(a)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/82aea503e11e1f5d010f4797d404… Author: John Chilton <jmchilton(a)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/0f28f8549bc7dd375d4f5ffbf6d4… Author: John Chilton <jmchilton(a)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/fb8a9628647eca0b4a35bc23f74f… Author: Aysam Guerler <aysam.guerler(a)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/84d9e171bc9be48d237cc16e5d87… Author: guerler <aysam.guerler(a)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/0482416c7af9d62edecbb5cde4c8… Author: guerler <aysam.guerler(a)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/0b0419533a2b1247a426bdf51bbf… Author: guerler <aysam.guerler(a)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/3c4413d31d991cf06b3217265e5f… Author: John Chilton <jmchilton(a)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

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[galaxyproject/galaxy] 84b574: Change link to appropriate test tool
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84b5748b5396281cea8f606505d0b00dcb910a57 https://github.com/galaxyproject/galaxy/commit/84b5748b5396281cea8f606505d0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Change link to appropriate test tool Commit: ff10ba6f83d41dd58cd02cf78c26b436c8999434 https://github.com/galaxyproject/galaxy/commit/ff10ba6f83d41dd58cd02cf78c26… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Add missing "remove_value" filter type and meta_ref filter attribute Fix links to tools. Commit: 03a807e374f8340c79e3e49ac52c686b3fc4b537 https://github.com/galaxyproject/galaxy/commit/03a807e374f8340c79e3e49ac52c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: 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/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Lint some tools Commit: 2ff068f133b0cce1d7d1822758ef272eb2b027c9 https://github.com/galaxyproject/galaxy/commit/2ff068f133b0cce1d7d1822758ef… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd 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/stats/aggregate_binned_scores_in_intervals.xml Log Message: ----------- Merge pull request #3468 from nsoranzo/lint_tools Lint some tools Compare: https://github.com/galaxyproject/galaxy/compare/10eba9a9990e...2ff068f133b0

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[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: ffa4af0a8e79acb673e90e543d67b7be0be3b631 https://github.com/galaxyproject/galaxy/commit/ffa4af0a8e79acb673e90e543d67… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3466 from jmchilton/version-17.01 [17.01] Update version to 17.01.rc1 Commit: c85b28c6d2c3e39801ea9138d84bfa2a0ded536c https://github.com/galaxyproject/galaxy/commit/c85b28c6d2c3e39801ea9138d84b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Commit: df8be3add7fc87fc5ad6e4e38217332a57d3915a https://github.com/galaxyproject/galaxy/commit/df8be3add7fc87fc5ad6e4e38217… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Fix cached dependency manager. Broken with baf9b82847fc526af56ed8efa7aba4d31d62f400. Also fix test case that made me think it was okay in the first place. Commit: 28b7b1faff9420c0010c117b573917741b1974ef https://github.com/galaxyproject/galaxy/commit/28b7b1faff9420c0010c117b5739… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Upgrade six to 1.10.0. This is required by the setuptools release released today. So if anything uses setuptools (e.g. it seems we get twill from PyPI instead of wheels.galaxyproject.org) it will fail because we have downgraded six it seems. Commit: 0bf7efb89a189e14e3b9d85ef2355a3821a498ce https://github.com/galaxyproject/galaxy/commit/0bf7efb89a189e14e3b9d85ef235… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3471 from jmchilton/17_01_six_upgrade [17.01] Upgrade six to 1.10.0. Commit: dc49b1c220bb96b1675ab50bdbccf7eca8d739bc https://github.com/galaxyproject/galaxy/commit/dc49b1c220bb96b1675ab50bdbcc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3470 from jmchilton/cached_dependency_manager_fixes [17.01] Fix cached dependency manager. Commit: 10eba9a9990ec093fddb7adebcf0daf8893b374c https://github.com/galaxyproject/galaxy/commit/10eba9a9990ec093fddb7adebcf0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0d05b3d089d1...10eba9a9990e

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[galaxyproject/galaxy] df8be3: Fix cached dependency manager.
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: df8be3add7fc87fc5ad6e4e38217332a57d3915a https://github.com/galaxyproject/galaxy/commit/df8be3add7fc87fc5ad6e4e38217… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Fix cached dependency manager. Broken with baf9b82847fc526af56ed8efa7aba4d31d62f400. Also fix test case that made me think it was okay in the first place. Commit: dc49b1c220bb96b1675ab50bdbccf7eca8d739bc https://github.com/galaxyproject/galaxy/commit/dc49b1c220bb96b1675ab50bdbcc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3470 from jmchilton/cached_dependency_manager_fixes [17.01] Fix cached dependency manager. Compare: https://github.com/galaxyproject/galaxy/compare/0bf7efb89a18...dc49b1c220bb

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[galaxyproject/galaxy] 28b7b1: Upgrade six to 1.10.0.
by GitHub 24 Jan '17

24 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 28b7b1faff9420c0010c117b573917741b1974ef https://github.com/galaxyproject/galaxy/commit/28b7b1faff9420c0010c117b5739… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Upgrade six to 1.10.0. This is required by the setuptools release released today. So if anything uses setuptools (e.g. it seems we get twill from PyPI instead of wheels.galaxyproject.org) it will fail because we have downgraded six it seems. Commit: 0bf7efb89a189e14e3b9d85ef2355a3821a498ce https://github.com/galaxyproject/galaxy/commit/0bf7efb89a189e14e3b9d85ef235… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-24 (Tue, 24 Jan 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #3471 from jmchilton/17_01_six_upgrade [17.01] Upgrade six to 1.10.0. Compare: https://github.com/galaxyproject/galaxy/compare/c85b28c6d2c3...0bf7efb89a18

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[galaxyproject/usegalaxy-playbook] 84be4a: enable toolbox monitor, remove gff filters from te...
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 84be4aee0d3a9d88fb2fb6c2a92865bf67474ca3 https://github.com/galaxyproject/usegalaxy-playbook/commit/84be4aee0d3a9d88… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-05 (Mon, 05 Dec 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/tool_conf.xml M files/galaxy/usegalaxy.org/config/tool_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml Log Message: ----------- enable toolbox monitor, remove gff filters from test, update mutable Commit: 6bba141db14d14d8f802b7b034fcb1120cda3065 https://github.com/galaxyproject/usegalaxy-playbook/commit/6bba141db14d14d8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: A files/galaxy/common/static/welcome_img/GAMe2017RegisterNow.png A files/galaxy/common/static/welcome_img/ImmPortGalaxy.png A files/galaxy/common/static/welcome_img/PAG2017.png M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/config/tool_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M production/galaxy_version.yml M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 M stage/galaxy_version.yml M templates/galaxy/common/static/welcome.html.j2 M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/37566d989afa...…

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[galaxyproject/galaxy] ea96b5: update badges
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea96b5cdf0a7c191380e03209f646e3ad43e7ac3 https://github.com/galaxyproject/galaxy/commit/ea96b5cdf0a7c191380e03209f64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- update badges Commit: 1dc7df578a3cf9d7179002b8a2338669931bce47 https://github.com/galaxyproject/galaxy/commit/1dc7df578a3cf9d7179002b8a233… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- fix badge style, flat is default Commit: 04458cef52a519872fd496f86b4289e6b5f9ec4e https://github.com/galaxyproject/galaxy/commit/04458cef52a519872fd496f86b42… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- change badge docs color Commit: 0d05b3d089d1d80cf171b998a5f3cd282f030f5b https://github.com/galaxyproject/galaxy/commit/0d05b3d089d1d80cf171b998a5f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M README.rst Log Message: ----------- Merge pull request #3465 from martenson/gitter-button update readme badges Compare: https://github.com/galaxyproject/galaxy/compare/1ef900ab48ac...0d05b3d089d1

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[galaxyproject/galaxy] 3f93b1: fix condor containers
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 3f93b19ff34bf51d81b353eb5e11e1748fa35df4 https://github.com/galaxyproject/galaxy/commit/3f93b19ff34bf51d81b353eb5e11… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- fix condor containers Commit: 915b653b91af25bf126125be875bd6ab2d9f320c https://github.com/galaxyproject/galaxy/commit/915b653b91af25bf126125be875b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #3463 from jmchilton/16.07_container_fix [16.07] fix condor containers Commit: 1c0c378debdee4aeb9699f11ad2b3314323888b6 https://github.com/galaxyproject/galaxy/commit/1c0c378debdee4aeb9699f11ad2b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: c85b28c6d2c3e39801ea9138d84bfa2a0ded536c https://github.com/galaxyproject/galaxy/commit/c85b28c6d2c3e39801ea9138d84b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Compare: https://github.com/galaxyproject/galaxy/compare/ffa4af0a8e79...c85b28c6d2c3

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[galaxyproject/galaxy] ab8721: Update version to 17.01.rc1
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ab87216d59178dee482adf4d065cc507d590f1f8 https://github.com/galaxyproject/galaxy/commit/ab87216d59178dee482adf4d065c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.rc1 Commit: ffa4af0a8e79acb673e90e543d67b7be0be3b631 https://github.com/galaxyproject/galaxy/commit/ffa4af0a8e79acb673e90e543d67… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3466 from jmchilton/version-17.01 [17.01] Update version to 17.01.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/d19f22e3fabf...ffa4af0a8e79

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[galaxyproject/galaxy] ab8721: Update version to 17.01.rc1
by GitHub 23 Jan '17

23 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab87216d59178dee482adf4d065cc507d590f1f8 https://github.com/galaxyproject/galaxy/commit/ab87216d59178dee482adf4d065c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.rc1 Commit: 68a033655f12cfa4c63073b60340a5d1e26d272e https://github.com/galaxyproject/galaxy/commit/68a033655f12cfa4c63073b60340… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.05.dev Commit: d4f567201e9f084a851d07a393b2814793f51684 https://github.com/galaxyproject/galaxy/commit/d4f567201e9f084a851d07a393b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Log Message: ----------- Merge branch 'version-17.01' into version-17.05.dev Commit: 1ef900ab48acd9904ae16fa5f287c5167e217260 https://github.com/galaxyproject/galaxy/commit/1ef900ab48acd9904ae16fa5f287… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3467 from jmchilton/version-17.05.dev Version 17.05.dev Compare: https://github.com/galaxyproject/galaxy/compare/d19f22e3fabf...1ef900ab48ac

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