Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1 https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e00... Author: Martin Cech <cech.marten@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/04af1ae1c609c0b73afabaf2aeb58... Author: Nate Coraor <nate@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/2641f0af9ac84f91ea0cf3e849b6e... Author: John Chilton <jmchilton@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/bb95a65b2201509ce950d6c3c578f... Author: Aysam Guerler <aysam.guerler@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/9551fc07b475b4095b7d002315cbc... Author: Nate Coraor <nate@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/9ead68aeca6722f62d3d6fabae648... Author: Dannon Baker <dannon.baker@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/4b24d95f6f95124f357b72434a291... Author: Nate Coraor <nate@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/ada39dea6ab68be543f53feb7a30e... Author: Martin Cech <cech.marten@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/530501c682be85b595bd8115bc2fc... Author: Martin Cech <cech.marten@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/5dd839960e1ca5170b528c4c88ad8... Author: Martin Cech <cech.marten@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/edd8b222acac34cd2e35e768ab1cb... Author: Martin Cech <cech.marten@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/0398aafb1cf0aa0863d0867d20dd7... Author: Martin Cech <cech.marten@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/4b51be57d114d840112970baccb97... Author: Martin Cech <cech.marten@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/c288b43627d3da925c5fe4b2fd0eb... Author: Martin Cech <cech.marten@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/7867f3e0835a2cbd99658ad25debd... Author: Martin Cech <cech.marten@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/a4c2098da010d79a70a9425e8ccb6... Author: Martin Cech <cech.marten@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/b46636a53f579fc6ffa63fbca8881... Author: Martin Cech <cech.marten@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/170c83e6c283e97b1e399bc122ee9... Author: Martin Cech <cech.marten@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/9c7c75b7661989b5fe6f2e4819b04... Author: Nate Coraor <nate@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/c693b69b344461bd428a0ef314b3e... Author: Dannon Baker <dannon.baker@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/134d792c1fcfba5d09e2937074c32... Author: Martin Cech <cech.marten@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/e7b6b4b13bd93a8520942c94d0ed2... Author: Martin Cech <cech.marten@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/5301269fbb54753e75969ecd446b8... Author: Martin Cech <cech.marten@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/5e77af198a9b81646dbe59a02b991... Author: Nate Coraor <nate@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/ef6bd90f20394f6fb74b1bdedbd0f... Author: John Chilton <jmchilton@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/054c04f490fe5e641c1dec8c4f8af... Author: Martin Cech <cech.marten@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/308402235fe4d3d3bb85e350181ab... Author: Martin Cech <cech.marten@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/8acc7ebc048d58165d3a02b21446c... Author: Martin Cech <cech.marten@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/d331b54b99cdc9f07bf0e53f284ad... Author: Martin Cech <cech.marten@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