2 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/fa67fbfa58e1/ Changeset: fa67fbfa58e1 User: jmchilton Date: 2014-05-29 03:25:53 Summary: Bugfix for a06c6c9. With improved testing :). Affected #: 2 files

diff -r 85aa79e9ab9a87a5b5fea0ed1039aeb9a5c23642 -r fa67fbfa58e16ad2f1a18c9e53fac2b02c7ab7f0 lib/galaxy/dataset_collections/__init__.py --- a/lib/galaxy/dataset_collections/__init__.py +++ b/lib/galaxy/dataset_collections/__init__.py @@ -147,7 +147,10 @@ ): assert source == "hdca" # for now source_hdca = self.__get_history_collection_instance( trans, encoded_source_id ) - parent.add_dataset_collection( source_hdca.copy() ) + new_hdca = source_hdca.copy() + parent.add_dataset_collection( new_hdca ) + trans.sa_session.add( new_hdca ) + trans.sa_session.flush() return source_hdca

def _set_from_dict( self, trans, dataset_collection_instance, new_data ):

diff -r 85aa79e9ab9a87a5b5fea0ed1039aeb9a5c23642 -r fa67fbfa58e16ad2f1a18c9e53fac2b02c7ab7f0 test/api/test_history_contents.py --- a/test/api/test_history_contents.py +++ b/test/api/test_history_contents.py @@ -150,8 +150,10 @@ source='hdca', content=hdca_id, ) + assert len( self._get( "histories/%s/contents/dataset_collections" % second_history_id ).json() ) == 0 create_response = self._post( "histories/%s/contents/dataset_collections" % second_history_id, create_data ) self.__check_create_collection_response( create_response ) + assert len( self._get( "histories/%s/contents/dataset_collections" % second_history_id ).json() ) == 1

def __check_create_collection_response( self, response ): self._assert_status_code_is( response, 200 )

https://bitbucket.org/galaxy/galaxy-central/commits/f415f6c5ecf2/ Changeset: f415f6c5ecf2 User: jmchilton Date: 2014-05-29 03:25:53 Summary: More extract functional tests. Add test for extracting copied, mapped datasets and copied input dataset collections from history. Affected #: 2 files

diff -r fa67fbfa58e16ad2f1a18c9e53fac2b02c7ab7f0 -r f415f6c5ecf22720f5bc8d8ae983cbc713831890 lib/galaxy/workflow/extract.py --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -2,6 +2,7 @@ histories. """ from galaxy.util.odict import odict +from galaxy import exceptions from galaxy import model from galaxy.tools.parameters.basic import ( DataToolParameter, @@ -88,6 +89,8 @@ for hid in dataset_collection_ids: step = model.WorkflowStep() step.type = 'data_collection_input' + if hid not in summary.collection_types: + raise exceptions.RequestParameterInvalidException( "hid %s does not appear to be a collection" % hid ) collection_type = summary.collection_types[ hid ] step.tool_inputs = dict( name="Input Dataset Collection", collection_type=collection_type ) hid_to_output_pair[ hid ] = ( step, 'output' )

diff -r fa67fbfa58e16ad2f1a18c9e53fac2b02c7ab7f0 -r f415f6c5ecf22720f5bc8d8ae983cbc713831890 test/api/test_workflows.py --- a/test/api/test_workflows.py +++ b/test/api/test_workflows.py @@ -106,12 +106,7 @@ offset = 0 old_contents = self._get( "histories/%s/contents" % old_history_id ).json() for old_dataset in old_contents: - payload = dict( - source="hda", - content=old_dataset["id"] - ) - response = self._post( "histories/%s/contents/datasets" % history_id, payload ) - self._assert_status_code_is( response, 200 ) + self.__copy_content_to_history( history_id, old_dataset ) new_contents = self._get( "histories/%s/contents" % history_id ).json() input_hids = map( lambda c: c[ "hid" ], new_contents[ (offset + 0):(offset + 2) ] ) cat1_job_id = self.__job_id( history_id, new_contents[ (offset + 2) ][ "id" ] ) @@ -186,40 +181,33 @@ @skip_without_tool( "random_lines1" ) def test_extract_mapping_workflow_from_history( self ): history_id = self.dataset_populator.new_history() - hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() - hdca_id = hdca[ "id" ] - inputs1 = { - "input|__collection_multirun__": hdca_id, - "num_lines": 2 - } - implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) - inputs2 = { - "input|__collection_multirun__": implicit_hdca1[ "id" ], - "num_lines": 1 - } - _, job_id2 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs2 ) + hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( history_id ) downloaded_workflow = self._extract_and_download_workflow( from_history_id=history_id, dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), job_ids=dumps( [ job_id1, job_id2 ] ), workflow_name="test import from mapping history", ) - # Assert workflow is input connected to a tool step with one output - # connected to another tool step. - assert len( downloaded_workflow[ "steps" ] ) == 3 - collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) - tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 ) - tool_step_idxs = [] - tool_input_step_idxs = [] - for tool_step in tool_steps: - self._assert_has_key( tool_step[ "input_connections" ], "input" ) - input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ] - tool_step_idxs.append( tool_step[ "id" ] ) - tool_input_step_idxs.append( input_step_idx ) + self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )

- assert collect_step_idx not in tool_step_idxs - assert tool_input_step_idxs[ 0 ] == collect_step_idx - assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ] + def test_extract_copied_mapping_from_history( self ): + old_history_id = self.dataset_populator.new_history() + hdca, job_id1, job_id2 = self.__run_random_lines_mapped_over_pair( old_history_id ) + + history_id = self.dataset_populator.new_history() + old_contents = self._get( "histories/%s/contents" % old_history_id ).json() + for old_content in old_contents: + self.__copy_content_to_history( history_id, old_content ) + # API test is somewhat contrived since there is no good way + # to retrieve job_id1, job_id2 like this for copied dataset + # collections I don't think. + downloaded_workflow = self._extract_and_download_workflow( + from_history_id=history_id, + dataset_collection_ids=dumps( [ hdca[ "hid" ] ] ), + job_ids=dumps( [ job_id1, job_id2 ] ), + workflow_name="test import from history", + ) + self.__assert_looks_like_randomlines_mapping_workflow( downloaded_workflow )

@skip_without_tool( "random_lines1" ) @skip_without_tool( "multi_data_param" ) @@ -259,6 +247,56 @@ reduction_step_input = reduction_step[ "input_connections" ][ "f1" ] assert reduction_step_input[ "id"] == random_lines_map_step[ "id" ]

+ def __copy_content_to_history( self, history_id, content ): + if content[ "history_content_type" ] == "dataset": + payload = dict( + source="hda", + content=content["id"] + ) + response = self._post( "histories/%s/contents/datasets" % history_id, payload ) + + else: + payload = dict( + source="hdca", + content=content["id"] + ) + response = self._post( "histories/%s/contents/dataset_collections" % history_id, payload ) + self._assert_status_code_is( response, 200 ) + return response.json() + + def __run_random_lines_mapped_over_pair( self, history_id ): + hdca = self.dataset_collection_populator.create_pair_in_history( history_id, contents=["1 2 3\n4 5 6", "7 8 9\n10 11 10"] ).json() + hdca_id = hdca[ "id" ] + inputs1 = { + "input|__collection_multirun__": hdca_id, + "num_lines": 2 + } + implicit_hdca1, job_id1 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs1 ) + inputs2 = { + "input|__collection_multirun__": implicit_hdca1[ "id" ], + "num_lines": 1 + } + _, job_id2 = self._run_tool_get_collection_and_job_id( history_id, "random_lines1", inputs2 ) + return hdca, job_id1, job_id2 + + def __assert_looks_like_randomlines_mapping_workflow( self, downloaded_workflow ): + # Assert workflow is input connected to a tool step with one output + # connected to another tool step. + assert len( downloaded_workflow[ "steps" ] ) == 3 + collect_step_idx = self._assert_first_step_is_paired_input( downloaded_workflow ) + tool_steps = self._get_steps_of_type( downloaded_workflow, "tool", expected_len=2 ) + tool_step_idxs = [] + tool_input_step_idxs = [] + for tool_step in tool_steps: + self._assert_has_key( tool_step[ "input_connections" ], "input" ) + input_step_idx = tool_step[ "input_connections" ][ "input" ][ "id" ] + tool_step_idxs.append( tool_step[ "id" ] ) + tool_input_step_idxs.append( input_step_idx ) + + assert collect_step_idx not in tool_step_idxs + assert tool_input_step_idxs[ 0 ] == collect_step_idx + assert tool_input_step_idxs[ 1 ] == tool_step_idxs[ 0 ] + def _run_tool_get_collection_and_job_id( self, history_id, tool_id, inputs ): run_output1 = self.dataset_populator.run_tool( tool_id=tool_id,

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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