February 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 539310: Copy over element_identifier to HDA.
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5393107a42fe6ef2a5942e56a870939026322b5c https://github.com/galaxyproject/galaxy/commit/5393107a42fe6ef2a5942e56a870… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Copy over element_identifier to HDA. Commit: 19efb1a99d5b46056392826324507fa952872591 https://github.com/galaxyproject/galaxy/commit/19efb1a99d5b4605639282632450… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Test if element_identifer is defined. Commit: e6dc96def3b91e76d6c772fedced0e4d455f8a52 https://github.com/galaxyproject/galaxy/commit/e6dc96def3b91e76d6c772fedced… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1693 from mvdbeek/better_fix_for_missing_element_identifier Better fix for missing element identifier Compare: https://github.com/galaxyproject/galaxy/compare/f4c3177717c0...e6dc96def3b9

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[galaxyproject/galaxy] bf4e73: Update david identifier types
by GitHub 09 Feb '16

09 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bf4e736c3ca8e129ff8c75f8261c08f303c76080 https://github.com/galaxyproject/galaxy/commit/bf4e736c3ca8e129ff8c75f8261c… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server.

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[galaxyproject/galaxy] e468c9: Update david identifier types
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e468c9882f1a8ca85f303c1f1e878a042207b3b0 https://github.com/galaxyproject/galaxy/commit/e468c9882f1a8ca85f303c1f1e87… Author: pavanvidem <videmp(a)informatik.uni-freiburg.de> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Update david identifier types David identifier types seem to be changed. Some of them are no more available on david web server. Commit: f4c3177717c0c673720fc40961467f9c0e45678a https://github.com/galaxyproject/galaxy/commit/f4c3177717c0c673720fc4096146… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M tools/phenotype_association/linkToDavid.xml Log Message: ----------- Merge pull request #1696 from pavanvidem/patch-1 Update david identifier types Compare: https://github.com/galaxyproject/galaxy/compare/d331b54b99cd...f4c3177717c0

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[galaxyproject/usegalaxy-playbook] be043f: update Test and mutable confs
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: be043f30573a4e205f3a0801307dcc674a38ffd3 https://github.com/galaxyproject/usegalaxy-playbook/commit/be043f30573a4e20… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version A stage/files/interactive_environments/plugins/phinch/config/phinch.ini.sample A stage/files/interactive_environments/plugins/phinch/config/phinch.xml A stage/files/interactive_environments/plugins/phinch/static/js/phinch.js A stage/files/interactive_environments/plugins/phinch/templates/phinch.mako M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/all.yml Log Message: ----------- update Test and mutable confs

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[galaxyproject/galaxy] bf989f: correct typo in text datatype
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1 https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- correct typo in text datatype Commit: 04af1ae1c609c0b73afabaf2aeb58110043847e6 https://github.com/galaxyproject/galaxy/commit/04af1ae1c609c0b73afabaf2aeb5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always use the python hashlib for verifying the virtualenv download in common_startup.sh rather than attempting to use sha256sum. Older versions of coreutils (such as in RHEL 6) did not include the --strict argument to sha256sum. Commit: 2641f0af9ac84f91ea0cf3e849b6e8348da8909d https://github.com/galaxyproject/galaxy/commit/2641f0af9ac84f91ea0cf3e849b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1668 from natefoo/venv-checksum [16.01] Always use the python hashlib method for verifying the virtualenv download Commit: bb95a65b2201509ce950d6c3c578f8d417f83cc4 https://github.com/galaxyproject/galaxy/commit/bb95a65b2201509ce950d6c3c578… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1666 from martenson/correct-datatype-typo [16.01] correct typo in text datatype Commit: 9551fc07b475b4095b7d002315cbc05bdf0925b5 https://github.com/galaxyproject/galaxy/commit/9551fc07b475b4095b7d002315cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL. Commit: 9ead68aeca6722f62d3d6fabae6484aa00246615 https://github.com/galaxyproject/galaxy/commit/9ead68aeca6722f62d3d6fabae64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1669 from natefoo/scientificlinux-tag-compat [16.01] Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL Commit: 4b24d95f6f95124f357b72434a29113fa9bacf73 https://github.com/galaxyproject/galaxy/commit/4b24d95f6f95124f357b72434a29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Improve documentation about binary-compatibility.cfg. Resolves #1672. Commit: ada39dea6ab68be543f53feb7a30e97167d96013 https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- handle correctly application/json pased in POST Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0 https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix setting library permissions to accept JSON correctly Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- unify api for library creation; support POST with url params Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824 https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- catch value errors from id decoding Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85 https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix updating library API to not require payload and to properly handle optional params Commit: 4b51be57d114d840112970baccb979ec1876663b https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- allow specifying DELETE params in JSON Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2 https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow creating folders with JSON payload Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2 https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folders.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- accept json as input for setting permissions; fix inconsistency by leveraging role_manager Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442 https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py Log Message: ----------- allow PATCHing with payload in urlparams Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6 https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- remove deletion of the payload dict item it is not necessary and the key does not have to exist Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4 https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- fix unused imports and unused vars Commit: 9c7c75b7661989b5fe6f2e4819b04ae6e7b901a1 https://github.com/galaxyproject/galaxy/commit/9c7c75b7661989b5fe6f2e4819b0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Typo Commit: c693b69b344461bd428a0ef314b3ec985e1a60d9 https://github.com/galaxyproject/galaxy/commit/c693b69b344461bd428a0ef314b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Merge pull request #1677 from natefoo/admin-docs [16.01] Improve documentation about binary-compatibility.cfg Commit: 134d792c1fcfba5d09e2937074c3263792bea991 https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- delete the 'payload' if it is in kwd so it is not supplied twice Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- Revert "delete the 'payload' if it is in kwd so it is not supplied twice" This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991. Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6 https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py Log Message: ----------- update docs of the data libraries API Commit: 5e77af198a9b81646dbe59a02b991d496b334967 https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018 https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M static/maps/mvc/library/library-folder-view.js.map M static/scripts/mvc/library/library-folder-view.js Log Message: ----------- Merge pull request #1641 from martenson/libraries-load-handle-payload [16.01] libraries: handle correctly application/json pased in POST Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Merge pull request #1695 from natefoo/help-message-css [16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: 308402235fe4d3d3bb85e350181ab5ab11df87f2 https://github.com/galaxyproject/galaxy/commit/308402235fe4d3d3bb85e350181a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/base.less M doc/source/admin/framework_dependencies.rst M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M scripts/binary_compatibility.py M scripts/common_startup.sh M static/maps/mvc/library/library-folder-view.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/mvc/library/library-folder-view.js M static/style/blue/base.css Log Message: ----------- Merge release_16.01 into dev Commit: 8acc7ebc048d58165d3a02b21446cc5674f6aefd https://github.com/galaxyproject/galaxy/commit/8acc7ebc048d58165d3a02b21446… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: 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/style/blue/base.css Log Message: ----------- repack client Commit: d331b54b99cdc9f07bf0e53f284adf1fa4398ce0 https://github.com/galaxyproject/galaxy/commit/d331b54b99cdc9f07bf0e53f284a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/style/less/base.less M doc/source/admin/framework_dependencies.rst M lib/galaxy/datatypes/text.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M scripts/binary_compatibility.py M scripts/common_startup.sh M static/maps/mvc/library/library-folder-view.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-folder-view.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1697 from martenson/merge-1601-dev merge 16.01 into dev Compare: https://github.com/galaxyproject/galaxy/compare/ae372ae33b67...d331b54b99cd

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[galaxyproject/galaxy] 055f18: Managers: fix sharable.list_published's incorrect ...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 055f180d20bfe70c0edd7f550e0332b0a79e228f https://github.com/galaxyproject/galaxy/commit/055f180d20bfe70c0edd7f550e03… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/visualizations.py M lib/galaxy/webapps/galaxy/api/histories.py Log Message: ----------- Managers: fix sharable.list_published's incorrect use of query, add manager getter to base serializer, deserializer, and filter parser; Managers, ratable: implement and attach to history Commit: de42737c44d93684f3b6e83b385beab2c0a5ea21 https://github.com/galaxyproject/galaxy/commit/de42737c44d93684f3b6e83b385b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M static/maps/mvc/list/list-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/list/list-view.js M templates/show_params.mako M test/docker/base/run_test_wrapper.sh A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.ratable Commit: 4d75d1c6418a363f56700b2f3afd9c32c6d60516 https://github.com/galaxyproject/galaxy/commit/4d75d1c6418a363f56700b2f3afd… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/ratable.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Managers, ratable: clean up, test, and fix Commit: 05a3d04b60bf9512a2fd9ebe07bc978a295e6865 https://github.com/galaxyproject/galaxy/commit/05a3d04b60bf9512a2fd9ebe07bc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/managers/annotatable.py M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/deletable.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/pages.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/visualizations.py Log Message: ----------- Managers: extract manager() code and move into class with property accessor Commit: d07677bba16d535a67a2e4517f29ab28a8bb6c04 https://github.com/galaxyproject/galaxy/commit/d07677bba16d535a67a2e4517f29… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py Log Message: ----------- Managers: bit of cleanup for 05a3d04b Commit: 427909929296ccf5c24389aace39057225f4b2da https://github.com/galaxyproject/galaxy/commit/427909929296ccf5c24389aace39… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A .ci/first_startup.sh M .travis.yml M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.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-libraryrow-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/tour.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/__init__.py M lib/galaxy/util/heartbeat.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/layout/menu.js.map M static/maps/layout/page.js.map R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.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 M static/scripts/layout/menu.js M static/scripts/layout/page.js R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-select-content.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-libraryrow-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/user/info.mako M templates/user/username.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test-data/3.bam M test/api/test_workflows.py M test/api/workflows_format_2/converter.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 A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.ratable Commit: ae372ae33b67fb2b50d45f79dfed1e54452d60d0 https://github.com/galaxyproject/galaxy/commit/ae372ae33b67fb2b50d45f79dfed… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/ratable.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/managers/visualizations.py M lib/galaxy/webapps/galaxy/api/histories.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #1618 from carlfeberhard/managers.ratable Implement the ratable mixin Compare: https://github.com/galaxyproject/galaxy/compare/eab2f1ff5c53...ae372ae33b67

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[galaxyproject/galaxy] e10660: Add a more correct zip file type.
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e106609c1c1eebca693e20bbe36e6597d5e6574a https://github.com/galaxyproject/galaxy/commit/e106609c1c1eebca693e20bbe36e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Add a more correct zip file type. Commit: 87f3ee48b026628506afeb2b8f99b0b0e37c74a8 https://github.com/galaxyproject/galaxy/commit/87f3ee48b026628506afeb2b8f99… Author: Gildas Le Corguillé <lecorguille(a)MacBook.local> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add a zip datatype which won't be extracted Commit: b81f3149bfb624b26e84c95b4efd519850045981 https://github.com/galaxyproject/galaxy/commit/b81f3149bfb624b26e84c95b4efd… Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1 from jmchilton/zip_datatype I take :) Commit: eab2f1ff5c53a733bd4b0ecf5718f3a53274f413 https://github.com/galaxyproject/galaxy/commit/eab2f1ff5c53a733bd4b0ecf5718… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #1665 from lecorguille/zip_datatype add a zip datatype which won't be extracted Compare: https://github.com/galaxyproject/galaxy/compare/7a60f669fa5f...eab2f1ff5c53

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[galaxyproject/galaxy] 20f187: added resolver dependency display to the tool view...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20f18793cd53c6c0c5c43838b7368eb14809188e https://github.com/galaxyproject/galaxy/commit/20f18793cd53c6c0c5c43838b736… Author: Zipho Mashologu <zipho(a)trustpay.biz> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- added resolver dependency display to the tool view page Commit: 95cb53a2fb28c214a9191ba2f8758914efe1d151 https://github.com/galaxyproject/galaxy/commit/95cb53a2fb28c214a9191ba2f875… Author: Zipho Mashologu <zipho(a)trustpay.biz> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/form/form-select-content.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-libraryrow-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/library.less M client/galaxy/style/less/tour.less M config/galaxy.ini.sample M config/plugins/visualizations/charts/Gruntfile.js M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/visualizations/scatterplot/templates/scatterplot.mako A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/project/issues.rst A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/datatypes/interval.py A lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/special_tools.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/heartbeat.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/scheduling_manager.py M lib/tool_shed/galaxy_install/install_manager.py M scripts/bootstrap_history.py M scripts/common_startup.sh R static/maps/libs/backbone/backbone.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/maps/mvc/list/list-view.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/mvc/workflow/workflow-view.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 R static/scripts/libs/backbone/backbone.js M static/scripts/mvc/form/form-select-content.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-libraryrow-view.js M static/scripts/mvc/list/list-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/visualization/visualization-model.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/show_params.mako M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/api/test_workflows.py M test/api/workflows_format_2/converter.py M test/docker/base/run_test_wrapper.sh 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 A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge branch 'dev' into resolver_dependencies Commit: 0a440f60ae3f9443599eb234f32fa3c149f05c61 https://github.com/galaxyproject/galaxy/commit/0a440f60ae3f9443599eb234f32f… Author: Zipho Mashologu <zipho(a)trustpay.biz> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- fixed variable names and making user feedback friendlier Commit: 7a60f669fa5fd9603ddbf30153cb8e17dbe8a1a8 https://github.com/galaxyproject/galaxy/commit/7a60f669fa5fd9603ddbf30153cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M templates/admin/tool_shed_repository/manage_repository.mako M templates/webapps/tool_shed/repository/common.mako Log Message: ----------- Merge pull request #1632 from zipho/resolver_dependencies added resolver dependency display to the tool view page Compare: https://github.com/galaxyproject/galaxy/compare/6a3452afff49...7a60f669fa5f

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[galaxyproject/galaxy] ebb412: added Phinch interactive environment
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebb41225bef68042d7725bbff2f75721f23f0e66 https://github.com/galaxyproject/galaxy/commit/ebb41225bef68042d7725bbff2f7… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- added Phinch interactive environment Commit: 87b5ba458fe574deb8c6200d8f12a8c329af98a1 https://github.com/galaxyproject/galaxy/commit/87b5ba458fe574deb8c6200d8f12… Author: shiltemann <s.hiltemann(a)erasmusmc.nl> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M config/plugins/interactive_environments/phinch/config/phinch.ini.sample Log Message: ----------- changed docker tag to fit with Galaxy release Commit: 1b04ba3833597f2ebdc2e4f527044906ab7a4e7d https://github.com/galaxyproject/galaxy/commit/1b04ba3833597f2ebdc2e4f52704… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- use bioblend for dataset import instead of mount Commit: 674bf530c65c05fea3e77a82404a77dc03f645ca https://github.com/galaxyproject/galaxy/commit/674bf530c65c05fea3e77a82404a… Author: Saskia Hiltemann <zazkia(a)gmail.com> Date: 2016-02-05 (Fri, 05 Feb 2016) Changed paths: M config/plugins/interactive_environments/phinch/static/js/phinch.js M config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- fix window height issue Commit: 6a3452afff49ec14fecc919e23a6012832ed3429 https://github.com/galaxyproject/galaxy/commit/6a3452afff49ec14fecc919e23a6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: A config/plugins/interactive_environments/phinch/config/phinch.ini.sample A config/plugins/interactive_environments/phinch/config/phinch.xml A config/plugins/interactive_environments/phinch/static/js/phinch.js A config/plugins/interactive_environments/phinch/templates/phinch.mako Log Message: ----------- Merge pull request #1647 from shiltemann/dev Phinch interactive environment Compare: https://github.com/galaxyproject/galaxy/compare/faeedd6f824f...6a3452afff49

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[galaxyproject/galaxy] 5e77af: Update help text rST note/warning/error box stylin...
by GitHub 08 Feb '16

08 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5e77af198a9b81646dbe59a02b991d496b334967 https://github.com/galaxyproject/galaxy/commit/5e77af198a9b81646dbe59a02b99… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Commit: 054c04f490fe5e641c1dec8c4f8af53cf02daffd https://github.com/galaxyproject/galaxy/commit/054c04f490fe5e641c1dec8c4f8a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M client/galaxy/style/less/base.less 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/style/blue/base.css Log Message: ----------- Merge pull request #1695 from natefoo/help-message-css [16.01] Update help text rST note/warning/error box styling for change in div class from toolHelpBody to ui-form-help. Compare: https://github.com/galaxyproject/galaxy/compare/ef6bd90f2039...054c04f490fe

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