Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4602d413cc80e7478eaa8de164aa8fde014de500 https://github.com/galaxyproject/galaxy/commit/4602d413cc80e7478eaa8de164aa8... Author: Helena Rasche <hxr@hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Implement dataset permissions api Commit: 409d5fcc8057309df71e2baa1b9bd37b16a5883a https://github.com/galaxyproject/galaxy/commit/409d5fcc8057309df71e2baa1b9bd... Author: Helena Rasche <hxr@hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- remove unnecessary doc Commit: fe5794916496364dbabfd97f7ad3fba6d91f7336 https://github.com/galaxyproject/galaxy/commit/fe5794916496364dbabfd97f7ad3f... Author: Helena Rasche <hxr@hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- fix linting Commit: 19523352ced554868fa6979dfe37161be7c864dd https://github.com/galaxyproject/galaxy/commit/19523352ced554868fa6979dfe371... Author: Helena Rasche <hxr@hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Correct documentation URL Commit: f7176dcfc9c63c7230c3ddc127e4e7718be49b9e https://github.com/galaxyproject/galaxy/commit/f7176dcfc9c63c7230c3ddc127e4e... Author: Helena Rasche <hxr@hx42.org> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py Log Message: ----------- Allow exception to bubble up naturally Commit: 6067fee3d44e6106217012ed9d7f029691e5d99f https://github.com/galaxyproject/galaxy/commit/6067fee3d44e6106217012ed9d7f0... Author: John Chilton <jmchilton@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/managers/datasets.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Remove unused dataset deserializer stuff. An unfinished thread left in the code base. It was a fine idea but I don't think anyone is left to pick it up and run with it. Commit: 18148a9656242369220d2ba1f0f10d89f2d44f2e https://github.com/galaxyproject/galaxy/commit/18148a9656242369220d2ba1f0f10... Author: John Chilton <jmchilton@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Refactor dataset_is_private_to_user to consume dataset instead of LibraryDataset. More consistent with other methods in that file and allows for use without knowledge of how to go from a LD -> Dataset. Commit: 49693814a9702a855d7df166d27c7a6f4f1faba1 https://github.com/galaxyproject/galaxy/commit/49693814a9702a855d7df166d27c7... Author: John Chilton <jmchilton@gmail.com> Date: 2018-08-10 (Fri, 10 Aug 2018) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py A test/api/test_roles.py M test/api/test_tools.py M test/base/api.py M test/base/populators.py Log Message: ----------- Unified dataset permission API. There was an existing library dataset permission API and one proposed for HDAs in #6461. This tries to reconcile the two approaches and move toward managers. - Proper treatment of "master_api_key" throughout the manager layers related to this. - Use PUT instead of POST, since that is more appropriate for updates I believe. - Use a similar URL pattern for library datasets, history contents, and dataset APIs. - Generalize the dataset API to allow HDA or LDDA inputs (the proposal for the new API in #6461 added an HDA-only option to the dataset API - this isn't how that API layer is meant to be used I believe). - Add an HDA only endpoint in the history contents API for this functionality to mirror the library dataset API. - Use consistent and backward compatible payload parsing for these endpoints. - Use consistent serialization for the result of these changes. - Generalize the HDA variant of this to allow different actions - such as make public and make private that were available in the library dataset variant. - Test cases for the new API endpoints, the roles API, tests for permissions during collection creation and running tools with both dataset and collection inputs. Commit: 53b8f08752edc35839f1ed9a8bc6355a528c99b4 https://github.com/galaxyproject/galaxy/commit/53b8f08752edc35839f1ed9a8bc63... Author: Helena Rasche <erasche@users.noreply.github.com> Date: 2018-08-22 (Wed, 22 Aug 2018) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/lddas.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/users.py M lib/galaxy/security/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py A test/api/test_roles.py M test/api/test_tools.py M test/base/api.py M test/base/populators.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge pull request #6568 from jmchilton/dataset-permissions-api-2 Unified dataset permission API. Compare: https://github.com/galaxyproject/galaxy/compare/fc167c068c9d...53b8f08752ed **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.