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Merge pull request #181 from kellrott/workflow-instance-data

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Re-issue of PR #176 now targeting dev, without additional commits
This commit is contained in:
Dannon Baker
2015-04-28 16:17:38 -04:00
parent 1b2cabc4b0 21a4927d4b
commit 11fe79fbc4
2 changed files with 47 additions and 12 deletions
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lib/galaxy/model/__init__.py
+42 -7
View File
@@ -551,10 +551,16 @@ class Job( object, HasJobMetrics, Dictifiable ):
input_dict = {}
for i in self.input_datasets:
if i.dataset is not None:
input_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"}
input_dict[i.name] = {
"id" : i.dataset.id, "src" : "hda",
"uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
}
for i in self.input_library_datasets:
if i.dataset is not None:
input_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"}
input_dict[i.name] = {
"id" : i.dataset.id, "src" : "ldda",
"uuid": str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
}
for k in input_dict:
if k in param_dict:
del param_dict[k]
@@ -563,10 +569,16 @@ class Job( object, HasJobMetrics, Dictifiable ):
output_dict = {}
for i in self.output_datasets:
if i.dataset is not None:
output_dict[i.name] = {"id" : i.dataset.id, "src" : "hda"}
output_dict[i.name] = {
"id" : i.dataset.id, "src" : "hda",
"uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
}
for i in self.output_library_datasets:
if i.dataset is not None:
output_dict[i.name] = {"id" : i.dataset.id, "src" : "ldda"}
output_dict[i.name] = {
"id" : i.dataset.id, "src" : "ldda",
"uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
}
rval['outputs'] = output_dict
return rval
@@ -3256,12 +3268,15 @@ class WorkflowInvocation( object, Dictifiable ):
# is relatively intutitive.
return map( lambda wi: wi.id, query.all() )
def to_dict( self, view='collection', value_mapper=None ):
def to_dict( self, view='collection', value_mapper=None, step_details=False ):
rval = super( WorkflowInvocation, self ).to_dict( view=view, value_mapper=value_mapper )
if view == 'element':
steps = []
for step in self.steps:
v = step.to_dict()
if step_details:
v = step.to_dict(view='element')
else:
v = step.to_dict(view='collection')
steps.append( v )
rval['steps'] = steps
@@ -3274,7 +3289,10 @@ class WorkflowInvocation( object, Dictifiable ):
src = "hda" if output_step_type == 'data_input' else 'hdca'
for job_input in step.job.input_datasets:
if job_input.name == step_input.input_name:
inputs[str(step_input.output_step.order_index)] = { "id": job_input.dataset_id, "src": src }
inputs[str(step_input.output_step.order_index)] = {
"id": job_input.dataset_id, "src": src,
"uuid" : str(job_input.dataset.dataset.uuid) if job_input.dataset.dataset.uuid is not None else None
}
rval['inputs'] = inputs
return rval
@@ -3313,7 +3331,24 @@ class WorkflowInvocationStep( object, Dictifiable ):
def to_dict( self, view='collection', value_mapper=None ):
rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper )
rval['order_index'] = self.workflow_step.order_index
rval['workflow_step_label'] = self.workflow_step.label
rval['workflow_step_uuid'] = str(self.workflow_step.uuid)
rval['state'] = self.job.state if self.job is not None else None
if self.job is not None and view=='element':
output_dict = {}
for i in self.job.output_datasets:
if i.dataset is not None:
output_dict[i.name] = {
"id" : i.dataset.id, "src" : "hda",
"uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
}
for i in self.job.output_library_datasets:
if i.dataset is not None:
output_dict[i.name] = {
"id" : i.dataset.id, "src" : "ldda",
"uuid" : str(i.dataset.dataset.uuid) if i.dataset.dataset.uuid is not None else None
}
rval['outputs'] = output_dict
return rval
lib/galaxy/webapps/galaxy/api/workflows.py
+5 -5
View File
@@ -213,7 +213,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
# Newer version of this API just returns the invocation as a dict, to
# facilitate migration - produce the newer style response and blend in
# the older information.
invocation_response = self.__encode_invocation( trans, invocation )
invocation_response = self.__encode_invocation( trans, invocation, step_details=kwd.get('step_details', False) )
invocation_response.update( rval )
return invocation_response
@@ -463,7 +463,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
results = self.workflow_manager.build_invocations_query( trans, stored_workflow.id )
out = []
for r in results:
out.append( self.__encode_invocation( trans, r ) )
out.append( self.__encode_invocation( trans, r, view="collection" ) )
return out
@expose_api
@@ -483,7 +483,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
decoded_workflow_invocation_id = self.decode_id( invocation_id )
workflow_invocation = self.workflow_manager.get_invocation( trans, decoded_workflow_invocation_id )
if workflow_invocation:
return self.__encode_invocation( trans, workflow_invocation )
return self.__encode_invocation( trans, workflow_invocation, step_details=kwd.get('step_details', False) )
return None
@expose_api
@@ -596,9 +596,9 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
raise exceptions.ObjectNotFound( "No such workflow found." )
return stored_workflow
def __encode_invocation( self, trans, invocation, view="element" ):
def __encode_invocation( self, trans, invocation, view="element", step_details=False ):
return self.encode_all_ids(
trans,
invocation.to_dict( view ),
invocation.to_dict( view, step_details=step_details ),
True
)