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

[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Commit: ef13e28578513f94014a705127585a42aba1c470 https://github.com/galaxyproject/galaxy/commit/ef13e28578513f94014a70512758… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/228623a133fd...ef13e2857851

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Compare: https://github.com/galaxyproject/galaxy/compare/a0eae9510c9e...e9f05cb1b11d

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Commit: 228623a133fd05f0a310fe0ab063b48fa748c3b5 https://github.com/galaxyproject/galaxy/commit/228623a133fd05f0a310fe0ab063… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6055de286d6c...228623a133fd

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/cd1454c40a43...a0eae9510c9e

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[galaxyproject/galaxy] 562ea1: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 562ea1d5e2f5662c7cce0ca954541c3c5833b839 https://github.com/galaxyproject/galaxy/commit/562ea1d5e2f5662c7cce0ca95454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Do not write shed_tool_data_table_config in place This should prevent errors such as: ``` galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml Traceback (most recent call last): File "lib/galaxy/util/__init__.py", line 217, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse self._root = parser.close() File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close self._raiseerror(v) File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror raise err ParseError: no element found: line 1, column 0 ``` reported in https://github.com/galaxyproject/galaxy/issues/5031. Commit: eb3d2eac203ccc6673a961b842117176535a8b24 https://github.com/galaxyproject/galaxy/commit/eb3d2eac203ccc6673a961b84211… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-11-30 (Thu, 30 Nov 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py Log Message: ----------- Fix installation of data manager revision updates Without this updates of data managers fails with ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__ iterable = self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision persist=True) File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__ metadata_dict=metadata_dict, user=None) File "tool_shed/metadata/metadata_generator.py", line 63, in __init__ self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)} ``` Commit: e9f05cb1b11db20a729ac73520f886ee619c6b90 https://github.com/galaxyproject/galaxy/commit/e9f05cb1b11db20a729ac73520f8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/tools/data/__init__.py A lib/galaxy/util/renamed_temporary_file.py Log Message: ----------- Merge pull request #5099 from mvdbeek/toolshed_install_stability [17.09] Toolshed install stability improvements Compare: https://github.com/galaxyproject/galaxy/compare/a0eae9510c9e...e9f05cb1b11d

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Commit: a0eae9510c9e22f9d0526624765b342b7f11827a https://github.com/galaxyproject/galaxy/commit/a0eae9510c9e22f9d0526624765b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/cd1454c40a43...a0eae9510c9e

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[galaxyproject/galaxy] fd223e: Fix connecting non-input modules to subworkflow in...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: fd223e3033f07f718d79a24d8b7efb1c97e234f4 https://github.com/galaxyproject/galaxy/commit/fd223e3033f07f718d79a24d8b7e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix connecting non-input modules to subworkflow inputs. It has been broken since introduced in 16.01, it just happens that the test tools I normally use have the same complete hack of an output type. Commit: 86ab6fd227b6c02622b68d3cf20e1e39e449d533 https://github.com/galaxyproject/galaxy/commit/86ab6fd227b6c02622b68d3cf20e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5140 from jmchilton/subworkflow_fixes [17.05] Fix connecting non-input modules to subworkflow inputs. Compare: https://github.com/galaxyproject/galaxy/compare/eab30c96522a...86ab6fd227b6

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[galaxyproject/galaxy] 934542: Fix duplicate import of _l in workflows
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 934542dd1113cefb19840f68b465f8604a0fd4c9 https://github.com/galaxyproject/galaxy/commit/934542dd1113cefb19840f68b465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix duplicate import of _l in workflows Commit: 8a3c3c15a43f64b615bceba9cf4449f5f230b9a2 https://github.com/galaxyproject/galaxy/commit/8a3c3c15a43f64b615bceba9cf44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js Log Message: ----------- Client format. Commit: 440aba01b4cc87d472f9871999378233181a3f22 https://github.com/galaxyproject/galaxy/commit/440aba01b4cc87d472f987199937… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js Log Message: ----------- Client build. Commit: 6055de286d6c8d36a5c29f960390c5ac65c1c3b5 https://github.com/galaxyproject/galaxy/commit/6055de286d6c8d36a5c29f960390… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/shed-list-view.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-frames.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-genomespace.js M static/scripts/mvc/upload/collection/collection-row.js M static/scripts/mvc/upload/collection/collection-view.js M static/scripts/mvc/upload/composite/composite-row.js M static/scripts/mvc/upload/composite/composite-view.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/default/default-view.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/user/user-custom-builds.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5156 from dannon/fix_localization_and_build Fix localization and build client. Compare: https://github.com/galaxyproject/galaxy/compare/c8d45dd4b37c...6055de286d6c

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[galaxyproject/galaxy] b7be41: Re-allow workflow outputs that aren't produced dur...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7be4162bd2f5ea43b318dc7ea3f552b6475d9a2 https://github.com/galaxyproject/galaxy/commit/b7be4162bd2f5ea43b318dc7ea3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Re-allow workflow outputs that aren't produced during workflow scheduling. These are sort of an error in the workflow definition but we don't have a means to competently display this information to the user via the UI so I think we need to just allow this to happen. I've attached a test case that exhibits this behavior and passes under 17.09 but fails under the current dev branch without these fixes. This was broken in https://github.com/galaxyproject/galaxy/commit/d5f98f49045bca351e982f17cac9… when we started to actually persist pointers to workflow invocation outputs (as part of https://github.com/galaxyproject/galaxy/pull/5013) Commit: 4925660ab4aa2974c6ac8e94180180bac7db9781 https://github.com/galaxyproject/galaxy/commit/4925660ab4aa2974c6ac8e941801… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Revert extra assertions that are causing unrelated issues to surface. The unrelated issues are serious problems though and I've created an issue to track them https://github.com/galaxyproject/galaxy/issues/5146. Commit: c8d45dd4b37c707d8ebe1d104c8a3e72d016bb9d https://github.com/galaxyproject/galaxy/commit/c8d45dd4b37c707d8ebe1d104c8a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5143 from jmchilton/fix_missing_outputs Re-allow workflow outputs that aren't produced during workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/c8937c8929a5...c8d45dd4b37c

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[galaxyproject/galaxy] b1d6c0: Fixes for handling delayed steps within subworkflo...
by GitHub 07 Dec '17

07 Dec '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1d6c017d03a1202c7fbc17f4e3ec3872d8f57b4 https://github.com/galaxyproject/galaxy/commit/b1d6c017d03a1202c7fbc17f4e3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-06 (Wed, 06 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Fixes for handling delayed steps within subworkflows. With new test case to verify this fix is needed. The previous test case that was verifying collection mapping and rescheduling of subworkflows turned out to really be testing the connections with respect to the outer workflow since only the last step of the subworkflow required rescheduling iterations. This newer test case verifies the connections within the subworkflow also - in addition to re-testing the connections and mapping in the outer workflow. Commit: c8937c8929a5d582a8d8ed033e07cd38432342d3 https://github.com/galaxyproject/galaxy/commit/c8937c8929a5d582a8d8ed033e07… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-12-07 (Thu, 07 Dec 2017) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5145 from jmchilton/subworkflow_delayed_handling Fixes for handling delayed steps within subworkflows. Compare: https://github.com/galaxyproject/galaxy/compare/d042f446a4c2...c8937c8929a5

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