Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85751ebb163eb5474d6ba18b7bf9d75097d53e15 https://github.com/galaxyproject/galaxy/commit/85751ebb163eb5474d6ba18b7bf9d... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Add tag and group tag rule to history level rule builder Commit: 1e7ce13b4773ffeaea169b03963a2a252187dfee https://github.com/galaxyproject/galaxy/commit/1e7ce13b4773ffeaea169b03963a2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py Log Message: ----------- Reuse HDA copy method in HDAManager Should benefit from smarter flush strategy in HDA.copy() Commit: d1f9ab88e4637d00c6c5c3c2290f6a19dd369456 https://github.com/galaxyproject/galaxy/commit/d1f9ab88e4637d00c6c5c3c2290f6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Always copy HDAs when creating a new collection from exisitng datasets, and allow setting tags Commit: 91438996df29caac56bb7a6fe8dc25e52815caf8 https://github.com/galaxyproject/galaxy/commit/91438996df29caac56bb7a6fe8dc2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test creation of collection from existing dataset, with a new tag Commit: eb4b878f3f5e9a898d5048c917ce2d379d7bf20f https://github.com/galaxyproject/galaxy/commit/eb4b878f3f5e9a898d5048c917ce2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/hdas.py Log Message: ----------- Simplify hda manager usage Commit: 5dd63dd6d077e9836f126d97a3c50b8a25ea66cc https://github.com/galaxyproject/galaxy/commit/5dd63dd6d077e9836f126d97a3c50... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Include tags in element_identifier when building collection from datasets Commit: ce892a028cb9d65aa19f8a4333626b421a184ec9 https://github.com/galaxyproject/galaxy/commit/ce892a028cb9d65aa19f8a4333626... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Restore hiding of dataset instances Commit: d4a80e61e13fbeeda43a65874910d85cfc1c8b29 https://github.com/galaxyproject/galaxy/commit/d4a80e61e13fbeeda43a65874910d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Adapt unit tests to copying HDAs when creating collections Commit: a9cb290754f09a1ea3073e8858df6f9a9e45b147 https://github.com/galaxyproject/galaxy/commit/a9cb290754f09a1ea3073e8858df6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Adjust API tests to copying HDAs when creating collection Commit: 711016ab9aac78c96fa65cd04f9421fbb6473b49 https://github.com/galaxyproject/galaxy/commit/711016ab9aac78c96fa65cd04f942... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Treat LDDA as HDA when creating collection This avoids copying the LDDA to HDA and then copying the HDA again. Commit: 34cfdcac6a583c84c8641ac8e26243769d09598d https://github.com/galaxyproject/galaxy/commit/34cfdcac6a583c84c8641ac8e2624... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Test for proper 403 response Coincidentally fixed by e013f2fbd1596b103ef195afcba8cbd787c49b33. Commit: c00ae9f81b953df7909aa591e411ebd6298a6f7c https://github.com/galaxyproject/galaxy/commit/c00ae9f81b953df7909aa591e411e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/webapps/galaxy/api/history_contents.py Log Message: ----------- Default to not copying source HDAs when creating new collections via API Commit: 9409322a730d431344d4438e379e61559632812d https://github.com/galaxyproject/galaxy/commit/9409322a730d431344d4438e379e6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_CollectionManager.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Revert "Adapt unit tests to copying HDAs when creating collections" This reverts commit 408a003f171be73e4b347579ee6f662a18fc1990. Commit: b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161 https://github.com/galaxyproject/galaxy/commit/b13cce0a1340a5f9b7a77ab7eda1c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py M test/api/test_tools.py M test/api/test_workflows.py Log Message: ----------- Revert "Adjust API tests to copying HDAs when creating collection" This reverts commit f120390a63700ff0ec6c09185aad26b91ad8f842. Commit: cfd8379917703ce03b631fd48b5a2bcecc30bbea https://github.com/galaxyproject/galaxy/commit/cfd8379917703ce03b631fd48b5a2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/api/test_history_contents.py Log Message: ----------- Send copy_elements=True in new create collection test Commit: 43ee13a0ce43ae5b29ffa1e317df1db645cb93a8 https://github.com/galaxyproject/galaxy/commit/43ee13a0ce43ae5b29ffa1e317df1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Default to copying HDAs when creating collections via the UI Commit: 50a524496a4ed52184967ede53094e5c8243d93d https://github.com/galaxyproject/galaxy/commit/50a524496a4ed52184967ede53094... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Add unit test for copy_element option Commit: ddb0c74b9bd9f534691a93911f10903da3609927 https://github.com/galaxyproject/galaxy/commit/ddb0c74b9bd9f534691a93911f109... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Original HDA must be owned by user if hiding source elements Commit: 366701cfb23d8de31eac3c4312c6accca2e74ef1 https://github.com/galaxyproject/galaxy/commit/366701cfb23d8de31eac3c4312c6a... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-26 (Sun, 26 Aug 2018) Changed paths: M lib/galaxy/managers/tags.py M lib/galaxy/util/__init__.py A test/unit/managers/test_TagManager.py Log Message: ----------- Strip unicode control characters from tags Leaving them in can trip up postgresql: ``` Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 396, in create return self.__create_dataset_collection(trans, history, payload, **kwd) File "lib/galaxy/webapps/galaxy/api/history_contents.py", line 525, in __create_dataset_collection **create_params File "lib/galaxy/managers/collections.py", line 108, in create copy_elements=copy_elements, File "lib/galaxy/managers/collections.py", line 181, in create_dataset_collection copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 217, in _element_identifiers_to_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 389, in __load_elements copy_elements=copy_elements) File "lib/galaxy/managers/collections.py", line 434, in __load_element self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str) File "lib/galaxy/managers/tags.py", line 182, in apply_item_tags self.apply_item_tag(user, item, name, value) File "lib/galaxy/managers/tags.py", line 154, in apply_item_tag tag = self._get_or_create_tag(lc_name) File "lib/galaxy/managers/tags.py", line 233, in _get_or_create_tag tag = self.get_tag_by_name(scrubbed_tag_str) File "lib/galaxy/managers/tags.py", line 205, in get_tag_by_name return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first() File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2789, in first ret = list(self[0:1]) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2581, in __getitem__ return list(res) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1416, in _handle_dbapi_exception util.reraise(*exc_info) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) ValueError: A string literal cannot contain NUL (0x00) characters. ``` Commit: 2adae6c4ca77067f2f45f3f101218d411fec7e25 https://github.com/galaxyproject/galaxy/commit/2adae6c4ca77067f2f45f3f101218... Author: John Chilton <jmchilton@gmail.com> Date: 2018-08-28 (Tue, 28 Aug 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/managers/collections.py M lib/galaxy/managers/collections_util.py M lib/galaxy/managers/hdas.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/history_contents.py M test/api/test_history_contents.py M test/unit/managers/test_HistoryContentsManager.py A test/unit/managers/test_TagManager.py Log Message: ----------- Merge pull request #6572 from mvdbeek/add_group_tags_to_history_rule_builder Add tagging rule to history level rule builder, copy HDAs when building collection Compare: https://github.com/galaxyproject/galaxy/compare/3121d9f0a468...2adae6c4ca77 **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.