Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 06cc5f58288fbd6e3762a91fdd8e76b715f7c4e6 https://github.com/galaxyproject/galaxy/commit/06cc5f58288fbd6e3762a91fdd8e7... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. Commit: b6e9f4a6eefb53d2f3b8b415b80e1a674bd7cc8d https://github.com/galaxyproject/galaxy/commit/b6e9f4a6eefb53d2f3b8b415b80e1... Author: John Chilton <jmchilton@gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix workflow extraction of dataset/collections name. It works fine if multiple names are chosen, but if only one input is selected and named it doesn't work. This is a temporary workaround until that page is replaced by API calls with superior typing. Fixes #3247 reported by @peterjc. Commit: 41f5ff48ed848f4fe111f78c8f364e32abdfe405 https://github.com/galaxyproject/galaxy/commit/41f5ff48ed848f4fe111f78c8f364... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. Commit: 63e70f4f2f47f5b952bb7817e93b0e61c8614dd7 https://github.com/galaxyproject/galaxy/commit/63e70f4f2f47f5b952bb7817e93b0... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2017-01-09 (Mon, 09 Jan 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #3376 from jmchilton/fix_3247 [16.10] Fix workflow extraction of dataset/collections name. Commit: 79752b5b4a0e80a6cd4b02aed8cfd93d8d61208a https://github.com/galaxyproject/galaxy/commit/79752b5b4a0e80a6cd4b02aed8cfd... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Do not allow recursive replacements in PJA. May result in infinite loops in workflow scheduling threads. Commit: 24b250ab3369489b91361c22bdf51b1729861e85 https://github.com/galaxyproject/galaxy/commit/24b250ab3369489b91361c22bdf51... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-10 (Tue, 10 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #3397 from jmchilton/backport_3395 [16.10] Backport #3395 Commit: 2d991bba073a9e1f40b18f6c927e4adf6ca1ddb9 https://github.com/galaxyproject/galaxy/commit/2d991bba073a9e1f40b18f6c927e4... Author: yhoogstrate <y.hoogstrate@gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Escapes some variables Commit: 535dd7a5f54617b12684eaa179066b4877965dd2 https://github.com/galaxyproject/galaxy/commit/535dd7a5f54617b12684eaa179066... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako Log Message: ----------- Merge pull request #3404 from dannon/backport_viz_escape [16.10] Backport of visualization hda.name escapes Commit: d49e014a63641db37814ab0b31b7aa4d1eded786 https://github.com/galaxyproject/galaxy/commit/d49e014a63641db37814ab0b31b7a... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- The /user/logout endpoint is now used for both remote and internal users to handle logout logic, and should be accessible here. Commit: b0ac7daecdda4001f6bcd7d70a15bb30375216e5 https://github.com/galaxyproject/galaxy/commit/b0ac7daecdda4001f6bcd7d70a15b... Author: Martin Cech <cech.marten@gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #3405 from dannon/remoteuser_logout_fix [16.10] Remoteuser Logout Fix. Commit: be530a849428393ec2b16f5b0786cbe4fba148cd https://github.com/galaxyproject/galaxy/commit/be530a849428393ec2b16f5b0786c... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.10' into dev Commit: 34458725b826fb9cd8da2d245c094abd5041345c https://github.com/galaxyproject/galaxy/commit/34458725b826fb9cd8da2d245c094... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/workflow.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3406 from dannon/dev Merges 16.10 into dev Compare: https://github.com/galaxyproject/galaxy/compare/8041525223b2...34458725b826