{"push_id":2831966883,"size":20,"distinct_size":20,"ref":"refs/heads/dev","head":"2adae6c4ca77067f2f45f3f101218d411fec7e25","before":"3121d9f0a468d23f6619e3496cf46c627560d90c","commits":[{"sha":"85751ebb163eb5474d6ba18b7bf9d75097d53e15","author":{"name":"Marius van den Beek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Add tag and group tag rule to history level rule builder","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/85751ebb163eb5474d6ba18b7bf9d75097d53e15"},{"sha":"1e7ce13b4773ffeaea169b03963a2a252187dfee","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Reuse HDA copy method in HDAManager\n\nShould benefit from smarter flush strategy in HDA.copy()","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/1e7ce13b4773ffeaea169b03963a2a252187dfee"},{"sha":"d1f9ab88e4637d00c6c5c3c2290f6a19dd369456","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Always copy HDAs when creating a new collection from exisitng datasets, and allow setting tags","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/d1f9ab88e4637d00c6c5c3c2290f6a19dd369456"},{"sha":"91438996df29caac56bb7a6fe8dc25e52815caf8","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Test creation of collection from existing dataset, with a new tag","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/91438996df29caac56bb7a6fe8dc25e52815caf8"},{"sha":"eb4b878f3f5e9a898d5048c917ce2d379d7bf20f","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Simplify hda manager usage","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/eb4b878f3f5e9a898d5048c917ce2d379d7bf20f"},{"sha":"5dd63dd6d077e9836f126d97a3c50b8a25ea66cc","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Include tags in element_identifier when building collection from datasets","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/5dd63dd6d077e9836f126d97a3c50b8a25ea66cc"},{"sha":"ce892a028cb9d65aa19f8a4333626b421a184ec9","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Restore hiding of dataset instances","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/ce892a028cb9d65aa19f8a4333626b421a184ec9"},{"sha":"d4a80e61e13fbeeda43a65874910d85cfc1c8b29","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Adapt unit tests to copying HDAs when creating collections","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/d4a80e61e13fbeeda43a65874910d85cfc1c8b29"},{"sha":"a9cb290754f09a1ea3073e8858df6f9a9e45b147","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Adjust API tests to copying HDAs when creating collection","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/a9cb290754f09a1ea3073e8858df6f9a9e45b147"},{"sha":"711016ab9aac78c96fa65cd04f9421fbb6473b49","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Treat LDDA as HDA when creating collection\n\nThis avoids copying the LDDA to HDA and then copying the HDA again.","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/711016ab9aac78c96fa65cd04f9421fbb6473b49"},{"sha":"34cfdcac6a583c84c8641ac8e26243769d09598d","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Test for proper 403 response\n\nCoincidentally fixed by e013f2fbd1596b103ef195afcba8cbd787c49b33.","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/34cfdcac6a583c84c8641ac8e26243769d09598d"},{"sha":"c00ae9f81b953df7909aa591e411ebd6298a6f7c","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Default to not copying source HDAs when creating new collections via API","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/c00ae9f81b953df7909aa591e411ebd6298a6f7c"},{"sha":"9409322a730d431344d4438e379e61559632812d","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Revert \"Adapt unit tests to copying HDAs when creating collections\"\n\nThis reverts commit 408a003f171be73e4b347579ee6f662a18fc1990.","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/9409322a730d431344d4438e379e61559632812d"},{"sha":"b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Revert \"Adjust API tests to copying HDAs when creating collection\"\n\nThis reverts commit f120390a63700ff0ec6c09185aad26b91ad8f842.","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/b13cce0a1340a5f9b7a77ab7eda1ceb0930ed161"},{"sha":"cfd8379917703ce03b631fd48b5a2bcecc30bbea","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Send copy_elements=True in new create collection test","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/cfd8379917703ce03b631fd48b5a2bcecc30bbea"},{"sha":"43ee13a0ce43ae5b29ffa1e317df1db645cb93a8","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Default to copying HDAs when  creating collections via the UI","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/43ee13a0ce43ae5b29ffa1e317df1db645cb93a8"},{"sha":"50a524496a4ed52184967ede53094e5c8243d93d","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Add unit test for copy_element option","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/50a524496a4ed52184967ede53094e5c8243d93d"},{"sha":"ddb0c74b9bd9f534691a93911f10903da3609927","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Original HDA must be owned by user if hiding source elements","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/ddb0c74b9bd9f534691a93911f10903da3609927"},{"sha":"366701cfb23d8de31eac3c4312c6accca2e74ef1","author":{"name":"mvdbeek","email":"b9a99571b072a850cc7863a4db1e2f9c85574c4c@gmail.com"},"message":"Strip unicode control characters from tags\n\nLeaving them in can trip up postgresql:\n```\nTraceback (most recent call last):\n  File \"lib/galaxy/web/framework/decorators.py\", line 283, in decorator\n    rval = func(self, trans, *args, **kwargs)\n  File \"lib/galaxy/webapps/galaxy/api/history_contents.py\", line 396, in create\n    return self.__create_dataset_collection(trans, history, payload, **kwd)\n  File \"lib/galaxy/webapps/galaxy/api/history_contents.py\", line 525, in __create_dataset_collection\n    **create_params\n  File \"lib/galaxy/managers/collections.py\", line 108, in create\n    copy_elements=copy_elements,\n  File \"lib/galaxy/managers/collections.py\", line 181, in create_dataset_collection\n    copy_elements=copy_elements)\n  File \"lib/galaxy/managers/collections.py\", line 217, in _element_identifiers_to_elements\n    copy_elements=copy_elements)\n  File \"lib/galaxy/managers/collections.py\", line 389, in __load_elements\n    copy_elements=copy_elements)\n  File \"lib/galaxy/managers/collections.py\", line 434, in __load_element\n    self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)\n  File \"lib/galaxy/managers/tags.py\", line 182, in apply_item_tags\n    self.apply_item_tag(user, item, name, value)\n  File \"lib/galaxy/managers/tags.py\", line 154, in apply_item_tag\n    tag = self._get_or_create_tag(lc_name)\n  File \"lib/galaxy/managers/tags.py\", line 233, in _get_or_create_tag\n    tag = self.get_tag_by_name(scrubbed_tag_str)\n  File \"lib/galaxy/managers/tags.py\", line 205, in get_tag_by_name\n    return self.sa_session.query(galaxy.model.Tag).filter_by(name=tag_name.lower()).first()\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py\", line 2789, in first\n    ret = list(self[0:1])\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py\", line 2581, in __getitem__\n    return list(res)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py\", line 2889, in __iter__\n    return self._execute_and_instances(context)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py\", line 2912, in _execute_and_instances\n    result = conn.execute(querycontext.statement, self._params)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py\", line 948, in execute\n    return meth(self, multiparams, params)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py\", line 269, in _execute_on_connection\n    return connection._execute_clauseelement(self, multiparams, params)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py\", line 1060, in _execute_clauseelement\n    compiled_sql, distilled_params\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py\", line 1200, in _execute_context\n    context)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py\", line 1416, in _handle_dbapi_exception\n    util.reraise(*exc_info)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py\", line 1193, in _execute_context\n    context)\n  File \"/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py\", line 507, in do_execute\n    cursor.execute(statement, parameters)\nValueError: A string literal cannot contain NUL (0x00) characters.\n```","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/366701cfb23d8de31eac3c4312c6accca2e74ef1"},{"sha":"2adae6c4ca77067f2f45f3f101218d411fec7e25","author":{"name":"John Chilton","email":"e361bfc8c8526c02f5efd3e71aa466615402f28f@gmail.com"},"message":"Merge pull request #6572 from mvdbeek/add_group_tags_to_history_rule_builder\n\nAdd tagging rule to history level rule builder, copy HDAs when building collection","distinct":true,"url":"https://api.github.com/repos/galaxyproject/galaxy/commits/2adae6c4ca77067f2f45f3f101218d411fec7e25"}]}
{"actor":{"display_login":"jmchilton"}}