galaxy-commits January 2016

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[galaxyproject/galaxy] 1b43e8: Logging fix.
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 1b43e8d68ffd44780f552e2472010d02dbc274b6 https://github.com/galaxyproject/galaxy/commit/1b43e8d68ffd44780f552e247201… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Logging fix. Commit: 2fc982027cb3de555afbd1650b52dbd84897956a https://github.com/galaxyproject/galaxy/commit/2fc982027cb3de555afbd1650b52… Author: Dannon Baker <dannon.baker(a)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. Compare: https://github.com/galaxyproject/galaxy/compare/17abd4a30d41...2fc982027cb3

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[galaxyproject/galaxy] eca2c3: Failing test case to exhibit #1514.
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: eca2c3bcee2c9f05dee062c60607251a589a93fd https://github.com/galaxyproject/galaxy/commit/eca2c3bcee2c9f05dee062c60607… Author: John Chilton <jmchilton(a)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/f1394d250db103eda0bc88044eaa… Author: John Chilton <jmchilton(a)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: 17abd4a30d41ff070202c1818ad84c015a642733 https://github.com/galaxyproject/galaxy/commit/17abd4a30d41ff070202c1818ad8… Author: Aysam Guerler <aysam.guerler(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/a00faba4fefa...17abd4a30d41

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[galaxyproject/galaxy] 035a67: Keep track of hidden datasets
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 035a67d0b5a1deeb54592937150a9ae82fab997e https://github.com/galaxyproject/galaxy/commit/035a67d0b5a1deeb54592937150a… Author: guerler <aysam.guerler(a)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: a00faba4fefabd1e28f3ce58603c9f99abf9a4f8 https://github.com/galaxyproject/galaxy/commit/a00faba4fefabd1e28f3ce58603c… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/58d75f4bc2e4...a00faba4fefa

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[galaxyproject/galaxy] bbff72: Fix upgrade messages
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bbff72e0ce9876b495971d20223780f1244d1f03 https://github.com/galaxyproject/galaxy/commit/bbff72e0ce9876b495971d202237… Author: guerler <aysam.guerler(a)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: 58d75f4bc2e4e52b9f4541d20c1253e49735a22f https://github.com/galaxyproject/galaxy/commit/58d75f4bc2e4e52b9f4541d20c12… Author: John Chilton <jmchilton(a)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 Compare: https://github.com/galaxyproject/galaxy/compare/16e0bc08c833...58d75f4bc2e4

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[galaxyproject/galaxy] bb1524: repack static scripts
by GitHub 20 Jan '16

20 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb152429031b4beb7a70f73b0c2722ccfab25c0f https://github.com/galaxyproject/galaxy/commit/bb152429031b4beb7a70f73b0c27… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- repack static scripts Commit: ce3f2b9cd18c0160ae198fe2482cd056c5449e86 https://github.com/galaxyproject/galaxy/commit/ce3f2b9cd18c0160ae198fe2482c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #1548 from martenson/repack-static repack static scripts Compare: https://github.com/galaxyproject/galaxy/compare/747c981a25de...ce3f2b9cd18c

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[galaxyproject/galaxy] 66c941: Copy workflow objects when importing them.
by GitHub 20 Jan '16

20 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66c94125ee258baf6578b439e9fb4b33f2bd5499 https://github.com/galaxyproject/galaxy/commit/66c94125ee258baf6578b439e9fb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-11 (Mon, 11 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Copy workflow objects when importing them. If not anywhere workflow.stored_workflow is checked will be broken. Commit: 95d00b4174efd23b0ad9c350d3463bf9d696d8cc https://github.com/galaxyproject/galaxy/commit/95d00b4174efd23b0ad9c350d346… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix MIMEText usage in galaxy.util Commit: e397ebba585ed578798645ee9352b891e3055372 https://github.com/galaxyproject/galaxy/commit/e397ebba585ed578798645ee9352… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1509 from dannon/release_16.01 Fix MIMEText usage in galaxy.util Commit: c143d659d4f7b598bc89a9d06b8040dff39a1b85 https://github.com/galaxyproject/galaxy/commit/c143d659d4f7b598bc89a9d06b80… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Revise tool caching to be less broken. Just switch the default for tool caching and only cache during initial loads of tool panels - as during a toolbox refresh. This should mean that all code from tool shed will ignore the cache and should fix #1515. Additionally, reloading the tool was broken since if would call the load tool code and then just trust the cache. This should fix tool reloading as well. Commit: 3d1ad5ad8dab30aa6c6372fbe85a0c3c7d198d61 https://github.com/galaxyproject/galaxy/commit/3d1ad5ad8dab30aa6c6372fbe85a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1511 from martenson/log-user-exceptions-properly [16.01] catch Exception and properly log errors Commit: ae2ee4a4432b55a4b0fbdd218bc34f88f7ad1b2b https://github.com/galaxyproject/galaxy/commit/ae2ee4a4432b55a4b0fbdd218bc3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1517 from jmchilton/tool_cache_fixes [16.01] Tool cache fixes Commit: 817f36626d7e720b0dbb63d0071f2889146c1c41 https://github.com/galaxyproject/galaxy/commit/817f36626d7e720b0dbb63d0071f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge pull request #1474 from jmchilton/workflow_copy [16.01] Copy workflow objects when importing them. Commit: fc434d62e971df92bc51b296d119030ca85af303 https://github.com/galaxyproject/galaxy/commit/fc434d62e971df92bc51b296d119… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Handle unvalidated values in depth Commit: 0e9302127f4478611170dee237d811e072100e99 https://github.com/galaxyproject/galaxy/commit/0e9302127f4478611170dee237d8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-01-16 (Sat, 16 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- sourcing Conda will write to stderr, we need to redirect it to stdout Commit: a77403cc9e6ef2d90ba78822afca601eed09e6ec https://github.com/galaxyproject/galaxy/commit/a77403cc9e6ef2d90ba78822afca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1527 from bgruening/release_16.01 Sourcing Conda will write to stderr Commit: 16e0bc08c8333c75c05a1a47de57eed8196bf9d9 https://github.com/galaxyproject/galaxy/commit/16e0bc08c8333c75c05a1a47de57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-15 (Fri, 15 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1526 from guerler/fix_unvalidated_001 [16.01] Handle unvalidated values in depth Commit: 151c90183bd0b0003048b706f91a835b8606a7ed https://github.com/galaxyproject/galaxy/commit/151c90183bd0b0003048b706f91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_1 Commit: 747c981a25ded3689a9fa454fa1cd9d1f7990cca https://github.com/galaxyproject/galaxy/commit/747c981a25ded3689a9fa454fa1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/web/base/controller.py M test/api/test_workflows.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge pull request #1547 from jmchilton/dev_merge_1 Merge release_16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/1b8f52807435...747c981a25de

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[galaxyproject/galaxy] 988bfc: add minor styling to tour popover
by GitHub 20 Jan '16

20 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 988bfc7730c14706e5ee7ff7a29dc766bf2deb39 https://github.com/galaxyproject/galaxy/commit/988bfc7730c14706e5ee7ff7a29d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/galaxy/style/less/base.less A client/galaxy/style/less/tour.less M static/style/blue/base.css Log Message: ----------- add minor styling to tour popover Commit: 1b8f5280743526ac420280557067460d40362da5 https://github.com/galaxyproject/galaxy/commit/1b8f5280743526ac420280557067… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M client/galaxy/style/less/base.less A client/galaxy/style/less/tour.less M static/style/blue/base.css Log Message: ----------- Merge, rebuild style. Compare: https://github.com/galaxyproject/galaxy/compare/fe6d22e1a7e4...1b8f52807435

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[galaxyproject/infrastructure-playbook] 4732bc: Ignore workspaces rotated by ws-cleanup when backi...
by GitHub 20 Jan '16

20 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4732bc296efd0687f1c3063aef16de8f7ec0da05 https://github.com/galaxyproject/infrastructure-playbook/commit/4732bc296ef… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M galaxyenv/host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- Ignore workspaces rotated by ws-cleanup when backing up Jenkins

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[galaxyproject/galaxy] 1bd193: Revert "Remove handlebars and rely solely on under...
by GitHub 20 Jan '16

20 Jan '16

Branch: refs/heads/revert-1537-handlebars.removal Home: https://github.com/galaxyproject/galaxy Commit: 1bd19314bbabe61353597eb8bf92aba6fe88d7f0 https://github.com/galaxyproject/galaxy/commit/1bd19314bbabe61353597eb8bf92… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-19 (Tue, 19 Jan 2016) Changed paths: M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js A client/galaxy/scripts/libs/handlebars.runtime.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/templates/compiled/panel_section.js A client/galaxy/scripts/templates/compiled/tool_form.js A client/galaxy/scripts/templates/compiled/tool_link.js A client/galaxy/scripts/templates/compiled/tool_search.js A client/galaxy/scripts/templates/panel_section.handlebars A client/galaxy/scripts/templates/tool_form.handlebars A client/galaxy/scripts/templates/tool_link.handlebars A client/galaxy/scripts/templates/tool_search.handlebars M client/galaxy/style/less/base.less M client/grunt-tasks/install-libs.js M client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json M client/webpack.config.js M config/plugins/visualizations/scatterplot/Gruntfile.js M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/handlebars/chartcontrol.handlebars A config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars A config/plugins/visualizations/scatterplot/src/handlebars/editor.handlebars M config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M lib/galaxy/webapps/galaxy/controllers/root.py A static/maps/libs/handlebars.runtime.js.map M static/maps/mvc/tool/tools.js.map M static/maps/onload.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/tool/tools.js M static/scripts/onload.js A static/scripts/templates/compiled/panel_section.js A static/scripts/templates/compiled/tool_form.js A static/scripts/templates/compiled/tool_link.js A static/scripts/templates/compiled/tool_search.js M static/style/blue/base.css M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/visualization/sweepster.mako Log Message: ----------- Revert "Remove handlebars and rely solely on underscore templates"

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[galaxyproject/galaxy]
by GitHub 20 Jan '16

20 Jan '16

Branch: refs/heads/revert-1537-handlebars.removal Home: https://github.com/galaxyproject/galaxy

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galaxy-commits January 2016