Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eca2c3bcee2c9f05dee062c60607251a589a93fd https://github.com/galaxyproject/galaxy/commit/eca2c3bcee2c9f05dee062c606072... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Failing test case to exhibit #1514. Commit: f1394d250db103eda0bc88044eaa92f54f56476c https://github.com/galaxyproject/galaxy/commit/f1394d250db103eda0bc88044eaa9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Fix #1514. Prior to PR #1302 workflows wouldn't validate call validate at all on inputs. 1302 was perhaps an over correction that causes validate to be called on datasets that aren't yet READY but require metadata. This rolls that back somewhat, other parameters will still validate - but validation asserting the existence of metadata won't get called in workflows. This is still not ideal but after 1302 and this - we are still in a better, more secure place than beforehand. One might argue that since we need to introduce a new validation point (right before a job is scheduled and set to QUEUED) - that we would be better off rolling back #1302 entirely. I've considered that, but I still think it is better to fail fast on the other problems, also I would rather call the validation code too many times than not enough and it would be very late in the release cycle for such a change. Commit: 3f51101527fee096761a4c22ee8841e64b98f7a6 https://github.com/galaxyproject/galaxy/commit/3f51101527fee096761a4c22ee884... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Attempt to fix #1531. I was unable to reproduce #1531 in testing, but if the problem is something to do with stale state the following sledge hammer should fix it. Runt the new test case with: ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_delete_intermediate_datasets_pja_1 Commit: cd95635197eddaeee55be88f96543dc3a97e9343 https://github.com/galaxyproject/galaxy/commit/cd95635197eddaeee55be88f96543... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1538. Displaying subcollection mapping in tool forms was broken with #1308 - this fixes that I believe. Commit: bbff72e0ce9876b495971d20223780f1244d1f03 https://github.com/galaxyproject/galaxy/commit/bbff72e0ce9876b495971d2022378... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-20 (Wed, 20 Jan 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: ----------- Fix upgrade messages Commit: 035a67d0b5a1deeb54592937150a9ae82fab997e https://github.com/galaxyproject/galaxy/commit/035a67d0b5a1deeb54592937150a9... Author: guerler <aysam.guerler@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.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-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Keep track of hidden datasets Commit: 1b43e8d68ffd44780f552e2472010d02dbc274b6 https://github.com/galaxyproject/galaxy/commit/1b43e8d68ffd44780f552e2472010... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Logging fix. Commit: 093f1f2712eeaa3c4a23952e2488a9a7a6731b17 https://github.com/galaxyproject/galaxy/commit/093f1f2712eeaa3c4a23952e2488a... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Make sciex sniffer tighter. Otherwise a bed file easily could sniff as sciex. Commit: 58d75f4bc2e4e52b9f4541d20c1253e49735a22f https://github.com/galaxyproject/galaxy/commit/58d75f4bc2e4e52b9f4541d20c125... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 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: ----------- Merge pull request #1550 from guerler/fix_upgrade_000 [16.01] Fix upgrade messages Commit: a00faba4fefabd1e28f3ce58603c9f99abf9a4f8 https://github.com/galaxyproject/galaxy/commit/a00faba4fefabd1e28f3ce58603c9... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/ui/ui-select-default.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-select-content.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #1551 from guerler/fix_hidden_rerun_000 [16.01] Keep track of hidden datasets Commit: 17abd4a30d41ff070202c1818ad84c015a642733 https://github.com/galaxyproject/galaxy/commit/17abd4a30d41ff070202c1818ad84... Author: Aysam Guerler <aysam.guerler@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/validation.py M test/api/test_workflows.py A test/functional/tools/for_workflows/1.bam A test/functional/tools/for_workflows/mapper.xml A test/functional/tools/for_workflows/pileup.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1536 from jmchilton/issue_1514 [16.01] Test case and fix for issue #1514 Commit: 2fc982027cb3de555afbd1650b52dbd84897956a https://github.com/galaxyproject/galaxy/commit/2fc982027cb3de555afbd1650b52d... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Merge pull request #1553 from jmchilton/logging_fix [16.01] Logging fix. Commit: e48388ef6cca6505d47b3daf3c2e0c4a5041b3f4 https://github.com/galaxyproject/galaxy/commit/e48388ef6cca6505d47b3daf3c2e0... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1545 from jmchilton/subcollection_mapping_problem [16.01] Fix #1538. Commit: 8ceb4d8ee495d21a664e3faece1e072a88048494 https://github.com/galaxyproject/galaxy/commit/8ceb4d8ee495d21a664e3faece1e0... Author: Nate Coraor <nate@bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Force --skip-venv if we can detect that Python is Conda Python. Commit: fe96255022f4fdf72f39be959a15993d014a0d38 https://github.com/galaxyproject/galaxy/commit/fe96255022f4fdf72f39be959a159... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1554 from natefoo/conda-interop [16.01] Force --skip-venv if we can detect that Python is Conda Python. Commit: f5fbe1c5020fb432346ce6340833937d13cbf6d0 https://github.com/galaxyproject/galaxy/commit/f5fbe1c5020fb432346ce63408339... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Client: remove older compiled backbone/backbone.js, update scatterplot and charts for same; Visualizations: fix visualization-model url; Scatterplot: fix title bug and Galaxy var Commit: 1b7462644d0352d44b36e2d790d6d10d906e7be4 https://github.com/galaxyproject/galaxy/commit/1b7462644d0352d44b36e2d790d6d... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/visualization/visualization-model.js M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/visualization/visualization-model.js.map R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/visualization/visualization-model.js Log Message: ----------- Merge pull request #1558 from carlfeberhard/release_16.01 [16.01] Fix redundant backbone and visualizations Commit: c117d400506e605c41e3837b83d79593733c5af0 https://github.com/galaxyproject/galaxy/commit/c117d400506e605c41e3837b83d79... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1557 from jmchilton/sciex_sniff [16.01] Tighten up ScIdx sniffer. Commit: 35f90da20ca21a8f82d1650c0cf520a064b6bd8a https://github.com/galaxyproject/galaxy/commit/35f90da20ca21a8f82d1650c0cf52... Author: Martin Cech <cech.marten@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge pull request #1542 from jmchilton/did_fix [16.01] Attempt to fix #1531. Commit: 11654a0950ee89f643893de119f55314ac626217 https://github.com/galaxyproject/galaxy/commit/11654a0950ee89f643893de119f55... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge release_16.01 into dev. Commit: f725e964333d084798410d90a522eadfcdecd540 https://github.com/galaxyproject/galaxy/commit/f725e964333d084798410d90a522e... Author: John Chilton <jmchilton@gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/jobs/actions/post.py M test/api/test_workflows.py M test/api/workflows_format_2/converter.py Log Message: ----------- Merge pull request #1591 from jmchilton/dev_merge_3 Merge 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/217e38eae30f...f725e964333d