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

[galaxyproject/galaxy] 092ad6: Fix quota function name
by GitHub 21 Aug '17

21 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 092ad6d67fe63a8b8895c003e2ad6ce54a612878 https://github.com/galaxyproject/galaxy/commit/092ad6d67fe63a8b8895c003e2ad… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Fix quota function name Commit: 63d1d428a1d98f3f607381c84e501030481eadbf https://github.com/galaxyproject/galaxy/commit/63d1d428a1d98f3f607381c84e50… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge pull request #4469 from guerler/fix_quota_api Fix quota function name Compare: https://github.com/galaxyproject/galaxy/compare/e3b3457b1fbe...63d1d428a1d9

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[galaxyproject/galaxy] 912da2: Fix checking WorkflowInvocation for published work...
by GitHub 21 Aug '17

21 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 912da2f3b93e7ae655725b6619febf0dbbcc4455 https://github.com/galaxyproject/galaxy/commit/912da2f3b93e7ae655725b6619fe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows.py Log Message: ----------- Fix checking WorkflowInvocation for published workflows Commit: 413233eec3ce9b3f930db8e40413856831dfc0cb https://github.com/galaxyproject/galaxy/commit/413233eec3ce9b3f930db8e40413… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Correctly raise Exception if invocation not found Commit: 0a4203ed92acb795a2f32c5ca095146b388a2ec2 https://github.com/galaxyproject/galaxy/commit/0a4203ed92acb795a2f32c5ca095… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix test to use invocation_id instead of history_id Commit: 80e264d35ffbf9eecacf37918fab7f7dbfa27cc7 https://github.com/galaxyproject/galaxy/commit/80e264d35ffbf9eecacf37918fab… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check ownership of invocation, instead of stored_workflow Commit: 2d16470132b86fb04bd67665bbdaf20e55874170 https://github.com/galaxyproject/galaxy/commit/2d16470132b86fb04bd67665bbda… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Allow admin user to view workflow invocation (thx @nsoranzo) Commit: cff306b86bc6368b4489805b96f92da04761c013 https://github.com/galaxyproject/galaxy/commit/cff306b86bc6368b4489805b96f9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Only skip check_security checks if check_ownership and check_accessible are false Commit: 64f8e74adeb5f46e781fb3cf54294097c6301880 https://github.com/galaxyproject/galaxy/commit/64f8e74adeb5f46e781fb3cf5429… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M test/unit/workflows/workflow_support.py Log Message: ----------- Fix subworkflow tests Commit: e3b3457b1fbeac31e1837be18f96a2e4d795902f https://github.com/galaxyproject/galaxy/commit/e3b3457b1fbeac31e1837be18f96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-21 (Mon, 21 Aug 2017) Changed paths: M lib/galaxy/managers/workflows.py M test/api/test_workflows.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #4465 from mvdbeek/workflow_invocation_security_check Fix checking WorkflowInvocation for published workflows Compare: https://github.com/galaxyproject/galaxy/compare/2346c0aa7e66...e3b3457b1fbe

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[galaxyproject/galaxy] 0e4688: Show up to 15 histories by default in saved histor...
by GitHub 20 Aug '17

20 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0e46888eed5412a85439f82907f58f540d9963d9 https://github.com/galaxyproject/galaxy/commit/0e46888eed5412a85439f82907f5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show up to 15 histories by default in saved histories menu Commit: a9d5c7c59c6b1bf2b656ec58d6ae3cea5a94d6ca https://github.com/galaxyproject/galaxy/commit/a9d5c7c59c6b1bf2b656ec58d6ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M templates/tagging_common.mako Log Message: ----------- Show tag if < 3 tags on history Commit: 2346c0aa7e66580792b4cd2d0bd48656421c5352 https://github.com/galaxyproject/galaxy/commit/2346c0aa7e66580792b4cd2d0bd4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-20 (Sun, 20 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py M templates/tagging_common.mako Log Message: ----------- Merge pull request #4467 from mvdbeek/saved_history_tags More items per page in saved history and directly show tags Compare: https://github.com/galaxyproject/galaxy/compare/fd51a61d014c...2346c0aa7e66

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[galaxyproject/galaxy] 1342c2: Integrated File Browsing and Workflow support for ...
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1342c2bd706b353038871a73992ae1a19878a694 https://github.com/galaxyproject/galaxy/commit/1342c2bd706b353038871a73992a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Integrated File Browsing and Workflow support for GenomeSpace Commit: e39901ef0695d6e7828d81ce3d1a9a230fda1569 https://github.com/galaxyproject/galaxy/commit/e39901ef0695d6e7828d81ce3d1a… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M client/galaxy/style/less/ui.less M lib/galaxy/dependencies/pinned-requirements.txt M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Moved back some code to wrapper and added back data type sniffing. Commit: ad1b61344557b53af10fae91011ec4a7be5d4a67 https://github.com/galaxyproject/galaxy/commit/ad1b61344557b53af10fae91011e… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M config/tool_conf.xml.main M config/tool_conf.xml.sample M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml Log Message: ----------- Added support for pushing multiple files from GenomeSpace to Galaxy. Commit: b04ccbe55b33ffca1aa09668885bceea61951dfe https://github.com/galaxyproject/galaxy/commit/b04ccbe55b33ffca1aa09668885b… Author: slugger70 <slugger70(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M tools/genomespace/genomespace_importer.xml Log Message: ----------- Fixed genomespace_importer.xml command block Commit: cb1b086324b1625d4f5ac0087e00971f3048afd4 https://github.com/galaxyproject/galaxy/commit/cb1b086324b1625d4f5ac0087e00… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Fixed pylint errors Commit: 46c04dcbd4eb47a2f3a2ff559c9ba4e280621750 https://github.com/galaxyproject/galaxy/commit/46c04dcbd4eb47a2f3a2ff559c9b… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M tools/genomespace/genomespace_importer.py Log Message: ----------- Fix incorrect reference when determining file type through file ext Commit: 678d575a7ae2cf7056564b525971396dc16d9b39 https://github.com/galaxyproject/galaxy/commit/678d575a7ae2cf7056564b525971… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M tools/genomespace/genomespace_importer.py Log Message: ----------- Improved recognition of compressed files Commit: ae6ae8ffe2c1558513737b5fab77840a22cea0a8 https://github.com/galaxyproject/galaxy/commit/ae6ae8ffe2c1558513737b5fab77… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-genomespace.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/managers/configuration.py Log Message: ----------- Added new config setting for GenomeSpace UI URL Commit: 517fd23fc8cd84c5277ccadc33222fa913230cc8 https://github.com/galaxyproject/galaxy/commit/517fd23fc8cd84c5277ccadc3322… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M tools/genomespace/genomespace_exporter.xml Log Message: ----------- Fixed typo in exporter help text Commit: b73e21b584dc13716460f550ed80108634adca37 https://github.com/galaxyproject/galaxy/commit/b73e21b584dc13716460f550ed80… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Formatting and linting fixes for GenomeSpace tool Commit: b995e551d408bd192322de530db89ddd08d35db2 https://github.com/galaxyproject/galaxy/commit/b995e551d408bd192322de530db8… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less Log Message: ----------- Fixed alignment of buttons in Genomespace Importer Commit: 46dc4a252cf6144672053864b16e52a85c810e34 https://github.com/galaxyproject/galaxy/commit/46dc4a252cf6144672053864b16e… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml Log Message: ----------- Fixed template formatting according to review comments Commit: 3e8bf3c4e72ca035f98142b3dc153de0a8e9d6a1 https://github.com/galaxyproject/galaxy/commit/3e8bf3c4e72ca035f98142b3dc15… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_push.xml Log Message: ----------- Moved genomespace token to environment variable Commit: 52b26f45a2bd3bcb0155553bf6e3e765d3bd4b2c https://github.com/galaxyproject/galaxy/commit/52b26f45a2bd3bcb0155553bf6e3… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Registered genomespace_importer as a tool needing Galaxy's python env Commit: 32401978234c46aeef80bc0ee144a478820468dc https://github.com/galaxyproject/galaxy/commit/32401978234c46aeef80bc0ee144… Author: Nuwan Goonasekera <nuwan.ag(a)gmail.com> Date: 2017-08-19 (Sat, 19 Aug 2017) Changed paths: M static/maps/mvc/form/form-parameters.js.map A static/maps/mvc/tool/tool-genomespace.js.map A static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/mvc/form/form-parameters.js A static/scripts/mvc/tool/tool-genomespace.js A static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css Log Message: ----------- Rebuilt galaxy client files Commit: fd51a61d014c4d3affe146b69fc3ed097037d2a1 https://github.com/galaxyproject/galaxy/commit/fd51a61d014c4d3affe146b69fc3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js A client/galaxy/scripts/mvc/tool/tool-genomespace.js A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/style/less/ui.less M config/galaxy.ini.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/config.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/form_builder.py M static/maps/mvc/form/form-parameters.js.map A static/maps/mvc/tool/tool-genomespace.js.map A static/maps/mvc/ui/ui-select-genomespace.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/mvc/form/form-parameters.js A static/scripts/mvc/tool/tool-genomespace.js A static/scripts/mvc/ui/ui-select-genomespace.js M static/style/blue/base.css M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py R tools/genomespace/genomespace_file_browser_dev.xml R tools/genomespace/genomespace_file_browser_prod.xml R tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml A tools/genomespace/genomespace_push.xml Log Message: ----------- Merge pull request #1814 from gvlproject/genomespace_workflows Galaxy Workflow support for GenomeSpace Compare: https://github.com/galaxyproject/galaxy/compare/263018326895...fd51a61d014c

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[galaxyproject/galaxy] dd27c1: Client rebuild, @guerler and I were trying to figu...
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd27c1edccb06b54ef5d503749ce51f79abcfcf0 https://github.com/galaxyproject/galaxy/commit/dd27c1edccb06b54ef5d503749ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map 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.map Log Message: ----------- Client rebuild, @guerler and I were trying to figure out what changed in the recently merged #4438 but don't see anything obvious. Commit: 263018326895c3f6e36288dcdeb242a056580892 https://github.com/galaxyproject/galaxy/commit/263018326895c3f6e36288dcdeb2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M static/scripts/bundled/admin.bundled.js.map 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.map Log Message: ----------- Merge pull request #4464 from dannon/rebuild_000 Client rebuild, @guerler and I were trying to figure out what changed… Compare: https://github.com/galaxyproject/galaxy/compare/7f50a8a29f53...263018326895

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[galaxyproject/galaxy] a078ee: Move form augmentation to form handler
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a078ee025f02732e108cf2d790e18cc826829ac5 https://github.com/galaxyproject/galaxy/commit/a078ee025f02732e108cf2d790e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.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/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move form augmentation to form handler Commit: abe8117b650bb9ab6575294d2892d33daeb32e4b https://github.com/galaxyproject/galaxy/commit/abe8117b650bb9ab6575294d2892… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-15 (Tue, 15 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix Fix Commit: 338abee984c6915a3f32f60ff1c448245c030376 https://github.com/galaxyproject/galaxy/commit/338abee984c6915a3f32f60ff1c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Separate input augmentation helpers from form views, augment inputs for regular form Commit: 7af41d472f360c02d41e9113307385141e85ade6 https://github.com/galaxyproject/galaxy/commit/7af41d472f360c02d41e91133073… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) 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: ----------- Simplify form wrapper calling Commit: 73d6bd09d30859ca3dfd14debc8f20ed750598a9 https://github.com/galaxyproject/galaxy/commit/73d6bd09d30859ca3dfd14debc8f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.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/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Restore build model bypass Pack Commit: 1fc4bb1a62d493412f9b28a30c806d10c56474cf https://github.com/galaxyproject/galaxy/commit/1fc4bb1a62d493412f9b28a30c80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/job/job-params.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/toolshed/categories-view.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repositories-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/util.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/ui/ui-drilldown.js M client/galaxy/scripts/mvc/ui/ui-popover.js M 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config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js M config/plugins/visualizations/charts/static/client/components/screenshot.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js M config/plugins/webhooks/demo/search/static/script.js M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py M 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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/galaxy.pages.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-library-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/scripts/mvc/library/library-model.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/toolshed/categories-view.js M static/scripts/mvc/toolshed/repo-status-view.js M static/scripts/mvc/toolshed/repositories-view.js M static/scripts/mvc/toolshed/repository-queue-view.js M static/scripts/mvc/toolshed/repository-view.js M static/scripts/mvc/toolshed/util.js M static/scripts/mvc/toolshed/workflows-view.js M static/scripts/mvc/ui/ui-drilldown.js M static/scripts/mvc/ui/ui-popover.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-ftp.js M static/scripts/mvc/upload/upload-view.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/reports_webapp/run_stats.js M static/scripts/ui/scroll-panel.js M static/scripts/utils/graph.js M static/scripts/utils/uploadbox.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/tracks.js R templates/admin/dataset_security/group/group.mako R templates/admin/dataset_security/group/group_create.mako R templates/admin/dataset_security/group/group_rename.mako A templates/webapps/tool_shed/admin/dataset_security/group/group.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako M test/unit/tools/test_actions.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge branch 'dev' into improve_form_modules Commit: a0217cb2372bfd83bee833299b3ea956a4d9b5b1 https://github.com/galaxyproject/galaxy/commit/a0217cb2372bfd83bee833299b3e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.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/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Attempt to customize build model Commit: 5b64e6d0032f515093a2e2d589839da451081546 https://github.com/galaxyproject/galaxy/commit/5b64e6d0032f515093a2e2d58983… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form.js M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Decouple model building Commit: 3c4e8927e398e8468b232c2d6a5e49b3206c19b9 https://github.com/galaxyproject/galaxy/commit/3c4e8927e398e8468b232c2d6a5e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.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/tool/tool-form-base.js Log Message: ----------- Hide initial tool version message Commit: 8b43348b676161d7d1aa799dd6988040767c7f6f https://github.com/galaxyproject/galaxy/commit/8b43348b676161d7d1aa799dd698… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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 M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Move workflow tool form model rebuilding to workflow forms Commit: 192c4b1141a5a58b45d42afad93f1565579b31e0 https://github.com/galaxyproject/galaxy/commit/192c4b1141a5a58b45d42afad93f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Properly update workflow tool module Commit: 6d87448b45074b52298c71dfbca562d8c1950343 https://github.com/galaxyproject/galaxy/commit/6d87448b45074b52298c71dfbca5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/workflow/workflow-forms.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/tool/tool-form-base.js M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Add optional initial model caller Pack Commit: 409867230cac37572779199d5210210a37663145 https://github.com/galaxyproject/galaxy/commit/409867230cac37572779199d5210… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Remove form dom removal through workflow manager Commit: 0092600cf384df8888fcb982aadfe1964b4d7a37 https://github.com/galaxyproject/galaxy/commit/0092600cf384df8888fcb982aadf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/actions/admin.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-wrapper.js.map M static/maps/mvc/ui/ui-select-content.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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-parameters.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/ui/ui-select-content.js M static/scripts/mvc/ui/ui-select-default.js R templates/admin/quota/quota.mako R templates/admin/quota/quota_create.mako R templates/admin/quota/quota_edit.mako R templates/admin/quota/quota_rename.mako R templates/admin/quota/quota_set_default.mako Log Message: ----------- Merge branch 'dev' into improve_form_modules Commit: d8925d73c5ba7b4e0bcbb36c98d45e45bb3b9e78 https://github.com/galaxyproject/galaxy/commit/d8925d73c5ba7b4e0bcbb36c98d4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-16 (Wed, 16 Aug 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix message style Commit: 56c1f25bf385fa3610e447ddc6fad0f063cc2de1 https://github.com/galaxyproject/galaxy/commit/56c1f25bf385fa3610e447ddc6fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix help text style Commit: 5a913700221c3734364d70546abfa1b9342d8c1b https://github.com/galaxyproject/galaxy/commit/5a913700221c3734364d70546abf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.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/tool/tool-form-composite.js Log Message: ----------- Fix title Commit: 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lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M 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test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py M test/shed_functional/functional/test_0530_repository_admin_feature.py M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py M test/shed_functional/functional/test_1000_install_basic_repository.py M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py M test/shed_functional/functional/test_1060_install_repository_with_workflow.py M test/shed_functional/functional/test_1070_invalid_tool.py M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py M test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/shed_functional/functional/test_1160_tool_help_images.py M test/shed_functional/functional/test_1170_prior_installation_required.py M test/shed_functional/functional/test_1180_circular_prior_installation_required.py M test/shed_functional/functional/test_1190_complex_prior_installation_required.py M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional/test_1400_review_migration_stages.py M test/shed_functional/functional/test_1410_update_manager.py M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py M test/shed_functional/functional/test_1430_repair_installed_repository.py M test/shed_functional/functional/test_1440_missing_env_sh_files.py M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py M test/shed_functional/functional/test_1460_data_managers.py M test/shed_functional/functional/test_1470_updating_installed_repositories.py M test/shed_functional/functional_tests.py M test/unit/dataset_collections/test_matching.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/datatypes/test_data.py M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_datasets.py M test/unit/jobs/test_job_configuration.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_job_wrapper.py M test/unit/jobs/test_mapper.py M test/unit/jobs/test_rule_helper.py M test/unit/jobs/test_rules/10_site.py M test/unit/jobs/test_runner_local.py M test/unit/jobs/test_runner_params.py M test/unit/managers/base.py M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/shed_unit/test_fabric_util.py M test/unit/shed_unit/test_td_common_util.py M test/unit/shed_unit/test_tool_panel_manager.py M test/unit/test_galaxy_mapping.py M test/unit/test_galaxy_transactions.py M test/unit/test_routes.py M test/unit/test_security_helper.py M test/unit/test_sqlite_utils.py M test/unit/test_topsort.py M test/unit/tools/filter_modules/filtermod.py M test/unit/tools/test_actions.py M test/unit/tools/test_citations.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parameter_parsing.py M test/unit/tools/test_select_parameters.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_panel.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_toolbox_filters.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/unittest_utils/utility.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_run_parameters.py M test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py M tool_list.py M tools/data_source/data_source.py M tools/data_source/fetch.py M tools/data_source/genbank.py M tools/data_source/hbvar_filter.py M tools/data_source/import.py M tools/data_source/microbial_import.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/evolution/add_scores.py M tools/evolution/codingSnps_filter.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_lav.py M tools/filters/axt_to_lav_code.py M tools/filters/bed_to_gff_converter.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/gtf_filter_by_attribute_values_list.py M tools/filters/gff_to_bed_converter.py M tools/filters/grep.py M tools/filters/gtf_to_bedgraph_converter.py M tools/filters/join.py M tools/filters/joinWrapper.py M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed_code.py M tools/filters/mergeCols.py M tools/filters/random_lines_two_pass.py M tools/filters/randomlines.py M tools/filters/secure_hash_message_digest.py M tools/filters/sorter.py M tools/filters/trimmer.py M tools/filters/ucsc_gene_bed_to_exon_bed.py M tools/filters/ucsc_gene_bed_to_intron_bed.py M tools/filters/ucsc_gene_table_to_intervals.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py M tools/maf/interval2maf.py M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/meme/fimo_wrapper.py M tools/metag_tools/blat_wrapper.py M tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/plotting/bar_chart.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_assembly/velveth_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/sr_mapping/srma_wrapper.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ.py M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'dev' into improve_form_modules Commit: 7f50a8a29f53c7fa86e5b0c7a57d2d898c6c4650 https://github.com/galaxyproject/galaxy/commit/7f50a8a29f53c7fa86e5b0c7a57d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-manager.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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-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/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-manager.js M static/scripts/mvc/workflow/workflow-node.js M static/scripts/mvc/workflow/workflow-view.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4438 from guerler/improve_form_modules Augment form module separation Compare: https://github.com/galaxyproject/galaxy/compare/cd22de114c20...7f50a8a29f53

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[galaxyproject/galaxy] 8d132b: More detailed sentry reports
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d132b2bca0dab22f7e028773dd31aa553cae668 https://github.com/galaxyproject/galaxy/commit/8d132b2bca0dab22f7e028773dd3… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- More detailed sentry reports Commit: e987b9b9e48bfa2f5ee69c013f991eb8bec70a2d https://github.com/galaxyproject/galaxy/commit/e987b9b9e48bfa2f5ee69c013f99… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- swap id to username Commit: cd22de114c2098ecbf2ab2108f3526abe70f00e6 https://github.com/galaxyproject/galaxy/commit/cd22de114c2098ecbf2ab2108f35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #4457 from erasche/sentry-extra-info More detailed sentry reports Compare: https://github.com/galaxyproject/galaxy/compare/9c6fd670cf20...cd22de114c20

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[galaxyproject/galaxy] cff929: Uniform indentation of multiline if conditionals
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cff9292f07d1318ce789bcfdab7dbf3e67c8d162 https://github.com/galaxyproject/galaxy/commit/cff9292f07d1318ce789bcfdab7d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Uniform indentation of multiline if conditionals Use 8-spaces indentation for the conditional continuation lines of an `if`-statement where the conditional part spans multiple lines. According to PEP-8, using 4-spaces "can produce a visual conflict with the indented suite of code nested inside the `if`-statement", but the PEP "takes no explicit position". There were only 2 places in the whole codebase where 8 spaces were not used, this will make it uniform. Commit: d2d1f857bbc2b7528e2e17cc8fcfdaad7d79fa75 https://github.com/galaxyproject/galaxy/commit/d2d1f857bbc2b7528e2e17cc8fcf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Fix import order and Python3 compatibility for lib/galaxy/util/pastescript/serve.py Commit: 9c6fd670cf201b9b3fed67cd5f100d75a24cb5f6 https://github.com/galaxyproject/galaxy/commit/9c6fd670cf201b9b3fed67cd5f10… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/pastescript/serve.py Log Message: ----------- Merge pull request #4455 from nsoranzo/multiline_if_conditionals Uniform indentation of multiline if conditionals Compare: https://github.com/galaxyproject/galaxy/compare/e4924942825c...9c6fd670cf20

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[galaxyproject/galaxy] 4e7563: Use log.warning() instead of deprecated warn()
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e75635d629f654f7b9d203fa6b6c1bc61495aa6 https://github.com/galaxyproject/galaxy/commit/4e75635d629f654f7b9d203fa6b6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/config.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/execute.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py Log Message: ----------- Use log.warning() instead of deprecated warn() Commit: e32ad2864f6b4ea05a347602b19202b94ae0ea81 https://github.com/galaxyproject/galaxy/commit/e32ad2864f6b4ea05a347602b192… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/containers/__init__.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py Log Message: ----------- Remove container config log message from cleanup scripts logs Commit: bd88524a109e6695a68f57e55ace64c21f907089 https://github.com/galaxyproject/galaxy/commit/bd88524a109e6695a68f57e55ace… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/containers/__init__.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py Log Message: ----------- Fix import order and Python3 compatibility Commit: e4924942825c6ea2d472d8ccff45222f165fa6bf https://github.com/galaxyproject/galaxy/commit/e4924942825c6ea2d472d8ccff45… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/config.py M lib/galaxy/containers/__init__.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/execute.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/api/users.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/communication/communication_server.py M scripts/secret_decoder_ring.py Log Message: ----------- Merge pull request #4456 from nsoranzo/logging_fixes Logging fixes Compare: https://github.com/galaxyproject/galaxy/compare/dd89a9c65f72...e4924942825c

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[galaxyproject/galaxy] 517f24: Overhaul of tool provided job metadata.
by GitHub 18 Aug '17

18 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 517f248ac49caca3f0933c4b1f48cd4d74cf89fe https://github.com/galaxyproject/galaxy/commit/517f248ac49caca3f0933c4b1f48… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Overhaul of tool provided job metadata. - Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID. - Add a bit more documentation to test tools. - Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata. - Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version. Commit: 72e361bcf14191dae58af8e3963b89a4e8acd38a https://github.com/galaxyproject/galaxy/commit/72e361bcf14191dae58af8e3963b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/collection_creates_dynamic_nested_from_json.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_7.xml Log Message: ----------- Allow discovering datasets directly from galaxy.json... without needing to specify a discovered dataset pattern. If the ``discovered_datasets`` tag includes ``from_tool_provided_metadata="true"`` the datsets listed in galaxy.json will just be used directly without needing to be "discovered" using a dataset pattern. Metadata and such can continue to be specified either in that file or on the discovered_dataset element except things like pattern (which is not used) and sort_by (since the json should describe the order I suppose). Commit: 6563e387a5d001bb6078469b7ad6a13f9bbed8aa https://github.com/galaxyproject/galaxy/commit/6563e387a5d001bb6078469b7ad6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Allow discovering dataset collections in galaxy.json in a nested fashion. Fixes #2658. Commit: 39d4411f8c21b307a86340fc5438ed2193abd766 https://github.com/galaxyproject/galaxy/commit/39d4411f8c21b307a86340fc5438… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_8.xml Log Message: ----------- Move determining tool provided metadata style to tool parser. Allow override by specifying "provided_metadata_style=" attribute on outputs in tool XML - this should allow newer profile tools to use the older style JSON providing a clear path for upgrades. Commit: a8bec7a275b5bd387daddf6555b6ff382851e8e8 https://github.com/galaxyproject/galaxy/commit/a8bec7a275b5bd387daddf6555b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_9.xml Log Message: ----------- Allow override of provided metadata location. Eliminates that terrible circular dependency between tools and jobs. Commit: 1e1df6786aeb6d02fba1ad84cceb204aa745ea62 https://github.com/galaxyproject/galaxy/commit/1e1df6786aeb6d02fba1ad84cceb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-17 (Thu, 17 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Variety of fixes for #4437. Commit: dd89a9c65f7297d4da5f0c0f7b6fea884a9698e6 https://github.com/galaxyproject/galaxy/commit/dd89a9c65f7297d4da5f0c0f7b6f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-18 (Fri, 18 Aug 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/collection_creates_dynamic_nested_from_json.xml A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/tool_provided_metadata_1.xml M test/functional/tools/tool_provided_metadata_2.xml M test/functional/tools/tool_provided_metadata_3.xml A test/functional/tools/tool_provided_metadata_4.xml A test/functional/tools/tool_provided_metadata_5.xml A test/functional/tools/tool_provided_metadata_6.xml A test/functional/tools/tool_provided_metadata_7.xml A test/functional/tools/tool_provided_metadata_8.xml A test/functional/tools/tool_provided_metadata_9.xml M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- Merge pull request #4437 from jmchilton/galaxy_json_rev Enhanced tool options for dataset discovery Compare: https://github.com/galaxyproject/galaxy/compare/b459399edebb...dd89a9c65f72

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