Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a4a104dcc2f020ed4100ed7edda75dd1d2857578 https://github.com/galaxyproject/galaxy/commit/a4a104dcc2f020ed4100ed7edda75... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API: allow filtering by date using string format YYYY-MM-DDTHH:MM (by removing the 'T' from when parsing the filter), allow filtering by hybrid properties and not just columns; API, history contents: allow filtering, order, and limit/offset of contents (in the same format as histories) Commit: 1cb1c48975e915ab98a0776a6a37dca914c542d4 https://github.com/galaxyproject/galaxy/commit/1cb1c48975e915ab98a0776a6a37d... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Managers, history contents: use text fn to wrap history_content_type filters; API, history contents: correct default order Commit: d4374bd0617d162db1a7b2803f1cc42880e0a9c7 https://github.com/galaxyproject/galaxy/commit/d4374bd0617d162db1a7b2803f1cc... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- Managers, history contents: remove model_class column, remove content_type from allowed filters (does not work on postgres), general cleanup Commit: 31e252743e633ffb48c655a3a12f4640a90c155e https://github.com/galaxyproject/galaxy/commit/31e252743e633ffb48c655a3a12f4... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/history_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: provide support for deleted and visible filters as bare keywords (e.g. 'deleted=True') Commit: 81b4eb484d55c30b386cce0af3141d6e5d4ee565 https://github.com/galaxyproject/galaxy/commit/81b4eb484d55c30b386cce0af3141... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: remove unreadable preceding binary operator, add blank line Commit: 120fef8cd09c4b158e5577833d89db60e7da3caf https://github.com/galaxyproject/galaxy/commit/120fef8cd09c4b158e5577833d89d... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/managers/history_contents.py Log Message: ----------- API, History contents: allow filtering by state, history_content_type Commit: d95c7c9d2b25d8b27d342f94c28d5c967c4af47a https://github.com/galaxyproject/galaxy/commit/d95c7c9d2b25d8b27d342f94c28d5... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-02-04 (Thu, 04 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- API, history contents: split code path in index to prevent backwards incompatibility Commit: c423f1eaa5f17190bf79f5f97b4f8a41903f5e3b https://github.com/galaxyproject/galaxy/commit/c423f1eaa5f17190bf79f5f97b4f8... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-02-09 (Tue, 09 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- API, history_contents: allow filtering by update/create times, inclusion in type_id list; models: add type_id as sql property on HDCAs and HDAs; managers: allow count; testing Commit: 1561759919073caa77d25eec9930b0f2235a82a1 https://github.com/galaxyproject/galaxy/commit/1561759919073caa77d25eec9930b... Author: carlfeberhard <carlfeberhard@gmail.com> Date: 2016-02-09 (Tue, 09 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/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-libraryrow-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M config/datatypes_conf.xml.sample M config/galaxy.ini.sample 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 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 M lib/galaxy/datatypes/text.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/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/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/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/folders.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/tool_dependencies.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.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/binary_compatibility.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 M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/library/library-folder-view.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/upload/default/default-row.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 M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.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-libraryrow-view.js M static/scripts/mvc/tours.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/admin/tool_shed_repository/manage_repository.mako 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 templates/webapps/tool_shed/repository/common.mako M test-data/3.bam M test/api/test_workflows.py M test/api/workflows_format_2/converter.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml 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 M tools/phenotype_association/linkToDavid.xml M tox.ini Log Message: ----------- (merge conflicts with dev) Commit: 1e46198becdba27f98f7ce93bb27f21ae59392a1 https://github.com/galaxyproject/galaxy/commit/1e46198becdba27f98f7ce93bb27f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2016-02-10 (Wed, 10 Feb 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/datasets.py M lib/galaxy/managers/hdas.py A lib/galaxy/managers/hdcas.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py A test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Merge pull request #1602 from carlfeberhard/history.contents API, history contents: allow filters, limit/offset, and ordering Compare: https://github.com/galaxyproject/galaxy/compare/6a5d2653a706...1e46198becdb