Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c376a2d94823f3777930c4312b6f2f70a4021e4c https://github.com/galaxyproject/galaxy/commit/c376a2d94823f3777930c4312b6f2... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-15 (Tue, 15 Dec 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/base.py Log Message: ----------- Core, CORS: allow (non-preflighted) CORS requests by echoing back the origin header if the requesting client is allowed Commit: 8a5ed3a092b5c86c5d5a6641410a6ca800e05f26 https://github.com/galaxyproject/galaxy/commit/8a5ed3a092b5c86c5d5a6641410a6... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A .ci/flake8_py3_wrapper.sh A .ci/py3_sources.txt M Makefile M client/README.md M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/copy-dialog.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/ui/popup-menu.js M client/galaxy/scripts/mvc/ui/ui-modal.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-data.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/utils/ajax-queue.js A config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/Detector.js A config/plugins/visualizations/csg/static/OrbitControls.js A config/plugins/visualizations/csg/static/PLYLoader.js A config/plugins/visualizations/csg/static/VTKLoader.js A config/plugins/visualizations/csg/static/dat.gui.min.js A config/plugins/visualizations/csg/static/three.min.js A config/plugins/visualizations/csg/templates/csg.mako M lib/galaxy/app.py R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/metrics/collectl/processes.py M lib/galaxy/jobs/metrics/instrumenters/meminfo.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py R lib/galaxy/tools/parameters/output.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/interface.py A lib/galaxy/tools/parser/output_actions.py A lib/galaxy/tools/parser/output_collection_def.py A lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/util/__init__.py M lib/galaxy/util/aliaspickler.py M lib/galaxy/util/backports/importlib/__init__.py M lib/galaxy/util/biostar.py A lib/galaxy/util/checkers.py R lib/galaxy/util/debugging.py A lib/galaxy/util/dictifiable.py M lib/galaxy/util/dictobj.py M lib/galaxy/util/expressions.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py R lib/galaxy/util/lrucache.py A lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/pastescript/serve.py M lib/galaxy/util/sanitize_html.py M lib/galaxy/util/validation.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/formbuilder.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/mvc/history/copy-dialog.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/ui/popup-menu.js.map M static/maps/mvc/ui/ui-modal.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-data.js.map M static/maps/mvc/workflow/workflow-view-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/utils/ajax-queue.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/layout/menu.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view-data.js M static/scripts/mvc/workflow/workflow-view-node.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/utils/ajax-queue.js M templates/display_base.mako M templates/grid_base.mako R templates/webapps/galaxy/history/copy.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/grid.mako A templates/webapps/galaxy/history/grid_js.mako A templates/webapps/galaxy/history/shared_grid.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/display_in_frame.mako M templates/webapps/galaxy/workflow/editor.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/api/workflows_format_2/converter.py M test/casperjs/api-anon-history-permission-tests.js M test/casperjs/api-anon-history-tests.js M test/qunit/tests/workflow_editor_tests.js M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.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/upload.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'origin/dev' into CORS Commit: d717f26581cf83e57fdca476455db4effd5f32d7 https://github.com/galaxyproject/galaxy/commit/d717f26581cf83e57fdca476455db... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/style/less/base.less M client/galaxy/style/less/frame.less R client/galaxy/style/less/masthead.less M client/galaxy/style/less/ui.less M config/dependency_resolvers_conf.xml.sample M config/galaxy.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample A config/plugins/interactive_environments/jupyter/config/jupyter.xml A config/plugins/interactive_environments/jupyter/static/js/jupyter.js A config/plugins/interactive_environments/jupyter/templates/jupyter.mako M config/plugins/visualizations/charts/templates/charts.mako M config/tool_conf.xml.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/binary.py A lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/objectstore/pulsar.py M lib/galaxy/tools/__init__.py A lib/galaxy/tools/cwl/__init__.py A lib/galaxy/tools/cwl/cwltool_deps.py A lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/representation.py A lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/commands.py A lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/resolvers/__init__.py A lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py A lib/galaxy/tools/deps/views.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/history_query.py A lib/galaxy/tools/parameters/wrapped_json.py A lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py A lib/galaxy/tools/toolbox/cache.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/panel.py A lib/galaxy/tools/toolbox/parser.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/directory_hash.py M lib/galaxy/util/expressions.py M lib/galaxy/util/heartbeat.py M lib/galaxy/util/json.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/odict.py M lib/galaxy/util/topsort.py M lib/galaxy/util/xml_macros.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/tool_util.py M run.sh M run_tests.sh M scripts/common_startup.sh M static/maps/layout/masthead.js.map M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/ui/ui-frames.js.map M static/maps/mvc/ui/ui-modal.js.map M static/maps/mvc/ui/ui-popover.js.map M static/maps/mvc/upload/default/default-view.js.map M static/maps/mvc/upload/upload-ftp.js.map M static/maps/mvc/upload/upload-settings.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/onload.js.map M static/maps/utils/uploadbox.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/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-modal.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-settings.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/onload.js M static/scripts/utils/uploadbox.js M static/style/blue/base.css M static/style/blue/masthead.css M templates/admin/reload_tool.mako M templates/webapps/galaxy/galaxy.masthead.mako A test/api/test_workflow_missing_tool.ga M test/api/test_workflows.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml M test/qunit/test-app.js A test/qunit/tests/masthead_tests.html A test/qunit/tests/masthead_tests.js A test/qunit/tests/modal_tests.html A test/qunit/tests/modal_tests.js A test/qunit/tests/popover_tests.html A test/qunit/tests/popover_tests.js M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/test_routes.py A test/unit/tools/test_conda_resolution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into CORS Commit: 0ea67c6d76df009b6ea3f113bac3336550655db0 https://github.com/galaxyproject/galaxy/commit/0ea67c6d76df009b6ea3f113bac33... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/ui/ui-frames.js M static/maps/layout/menu.js.map M static/maps/mvc/ui/ui-frames.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/ui/ui-frames.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into CORS Commit: 80cce3f42827d95d9b6b9894f0af942c9bfa942d https://github.com/galaxyproject/galaxy/commit/80cce3f42827d95d9b6b9894f0af9... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-05 (Tue, 05 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/base.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- CORS: remove basestring, remove log, null-proofing, allow unicode regexp, add testing Commit: 575a5a440297cb20431cb6bd7e922ab868b57a33 https://github.com/galaxyproject/galaxy/commit/575a5a440297cb20431cb6bd7e922... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-07 (Thu, 07 Jan 2016) Changed paths: M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/webapp.py A test/unit/test_config.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- CORS: move check/setter to webapp.GalaxyWebTransaction from base.WebApplication, bail on lack of config key, rework tests, add test files Commit: 0d399f6919cc24fc0e3e288fa21784ea544edb29 https://github.com/galaxyproject/galaxy/commit/0d399f6919cc24fc0e3e288fa2178... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: R test/unit/test_config.py M test/unit/web/framework/test_webapp.py Log Message: ----------- CORS: cache and restore tempfile.tempdir when using test Configuration instances as it persists across tests and fails any tempfile related tests that follow, move test_config tests into test_webapp (cohesive subject v. ortho file struct) Commit: 1a5bc43a80da4917df0d225b715b9b789e70c522 https://github.com/galaxyproject/galaxy/commit/1a5bc43a80da4917df0d225b715b9... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M test/unit/web/framework/test_webapp.py Log Message: ----------- CORS: try fixing tests again, this time by avoiding use of Configuration altogether Commit: 274af50792aaaf367520c22d7c13e22e70000d4d https://github.com/galaxyproject/galaxy/commit/274af50792aaaf367520c22d7c13e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/framework/webapp.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge pull request #1331 from carlfeberhard/CORS Core, CORS: allow (non-preflighted) CORS requests by echoing back the… Compare: https://github.com/galaxyproject/galaxy/compare/84105b56d987...274af50792aa