1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/170e2294712a/ Changeset: 170e2294712a User: jmchilton Date: 2014-05-14 23:06:33 Summary: Bugfixes: More bug fixes for extracting collection-y workflows from a history. The embarrassment continues... Affected #: 1 file
diff -r c0eb8b472f3ccabdfd1b0396dbf92c34f3140200 -r 170e2294712a2db7a703df8df62ace9a27fa1c9c lib/galaxy/workflow/extract.py --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -5,6 +5,7 @@ from galaxy import model from galaxy.tools.parameters.basic import ( DataToolParameter, + DataCollectionToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue @@ -98,6 +99,8 @@ raise AssertionError( "Attempt to create workflow with job not connected to current history" ) job = jobs_by_id[ job_id ] tool_inputs, associations = step_inputs( trans, job ) + log.info("job %s has tool_inputs %s" % (job.id, tool_inputs) ) + log.info("associations are %s" % associations) step = model.WorkflowStep() step.type = 'tool' step.tool_id = job.tool_id @@ -111,6 +114,7 @@ input_collection = an_implicit_output_collection.find_implicit_input_collection( input_name ) if input_collection: other_hid = input_collection.hid + log.info("For input_name %s, have hid %s" % ( input_name, other_hid ) ) if other_hid in hid_to_output_pair: other_step, other_name = hid_to_output_pair[ other_hid ] conn = model.WorkflowStepConnection() @@ -190,7 +194,6 @@ # just grab the implicitly mapped jobs and handle in second pass. Second pass is # needed because cannot allow selection of individual datasets from an implicit # mapping during extraction - you get the collection or nothing. - implicit_outputs = [] for content in self.history.active_contents: if content.history_content_type == "dataset_collection": hid = content.hid @@ -200,34 +203,32 @@ job = DatasetCollectionCreationJob( content ) self.jobs[ job ] = [ ( None, content ) ] else: - implicit_outputs.append( content ) + dataset_collection = content + # TODO: Optimize db call + # TODO: Ensure this is deterministic, must get same job + # for each dataset collection. + dataset_instance = dataset_collection.collection.dataset_instances[ 0 ] + if not self.__check_state( dataset_instance ): + # Just checking the state of one instance, don't need more but + # makes me wonder if even need this check at all? + continue + + job_hda = self.__original_hda( dataset_instance ) + if not job_hda.creating_job_associations: + log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" ) + job = DatasetCollectionCreationJob( dataset_collection ) + self.jobs[ job ] = [ ( None, dataset_collection ) ] + + for assoc in job_hda.creating_job_associations: + job = assoc.job + if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": + self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ] + self.implicit_map_jobs.append( job ) + else: + self.jobs[ job ].append( ( assoc.name, dataset_collection ) ) else: self.__append_dataset( content )
- for dataset_collection in implicit_outputs: - # TODO: Optimize db call - # TODO: Ensure this is deterministic, must get same job - # for each dataset collection. - dataset_instance = dataset_collection.collection.dataset_instances[ 0 ] - if not self.__check_state( dataset_instance ): - # Just checking the state of one instance, don't need more but - # makes me wonder if even need this check at all? - continue - - job_hda = self.__original_hda( dataset_instance ) - if not job_hda.creating_job_associations: - log.warn( "An implicitly create output dataset collection doesn't have a creating_job_association, should not happen!" ) - job = DatasetCollectionCreationJob( dataset_collection ) - self.jobs[ job ] = [ ( None, dataset_collection ) ] - - for assoc in job_hda.creating_job_associations: - job = assoc.job - if job not in self.jobs or self.jobs[ job ][ 0 ][ 1 ].history_content_type == "dataset": - self.jobs[ job ] = [ ( assoc.name, dataset_collection ) ] - self.implicit_map_jobs.append( job ) - else: - self.jobs[ job ].append( ( assoc.name, dataset_collection ) ) - def __append_dataset( self, dataset ): if not self.__check_state( dataset ): return @@ -289,7 +290,7 @@ if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): values[key] = UnvalidatedValue( values[key] ) - if isinstance( input, DataToolParameter ): + if isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter ): tmp = values[key] values[key] = None # HACK: Nested associations are not yet working, but we
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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