Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63a715f27c5ee31de6bdd0cd4222b309b3f2ce23 https://github.com/galaxyproject/galaxy/commit/63a715f27c5ee31de6bdd0cd4222b... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Fix Tool Shed test broken with PR #706. Commit: ed92a12e78dad1d7290fde30b23768b613e68232 https://github.com/galaxyproject/galaxy/commit/ed92a12e78dad1d7290fde30b2376... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Specify the tool_id of the missing tool when raising MissingToolException. Commit: 760899f9c0ce717df4e6c789e36693973d048c7d https://github.com/galaxyproject/galaxy/commit/760899f9c0ce717df4e6c789e3669... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 65519718b37a0a08c802c131b92ca0335a0b7eda https://github.com/galaxyproject/galaxy/commit/65519718b37a0a08c802c131b92ca... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/yaml_to_workflow.py Log Message: ----------- Fix "KeyError: name" error when running "./run_tests.sh -api". Example traceback for test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections : galaxy.web.framework.decorators: ERROR: Uncaught exception in exposed API method: Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 182, in create return self.__api_import_new_workflow( trans, payload, **kwd ) File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 374, in __api_import_new_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 1111, in _workflow_from_dict publish=publish File "/opt/galaxy/lib/galaxy/managers/workflows.py", line 165, in build_workflow_from_dict missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) KeyError: 'name' Commit: cd456e186dc1ba6f51e3cafb0c54d6b1f1651817 https://github.com/galaxyproject/galaxy/commit/cd456e186dc1ba6f51e3cafb0c54d... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M scripts/check_galaxy.py Log Message: ----------- Print to stderr when calling sys.exit(1) Commit: c01cf85d450a83c4f235ba488b84d2c7a60c4209 https://github.com/galaxyproject/galaxy/commit/c01cf85d450a83c4f235ba488b84d... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Use __file__ when adding paths to sys.path instead of os.getcwd() . Also insert additional paths in position 1 unless strictly necessary. Commit: fef28884fc6f46efb01816c9466667840947f372 https://github.com/galaxyproject/galaxy/commit/fef28884fc6f46efb01816c946666... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M scripts/check_galaxy.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #720 from nsoranzo/misc_fixes Misc fixes Compare: https://github.com/galaxyproject/galaxy/compare/36809cd6f37f...fef28884fc6f