fix bug in processing of in-param of tools

graph_creation/cwl_processing.py

@@ -29,8 +29,9 @@ def process_cwl_inputs(driver: Driver, cwl_entity: dict) -> None:
                 process_in_param(driver, input['id'], component_id, input['type'], cwl_entity['class'])
     elif isinstance(cwl_entity['inputs'], dict):
         # If 'inputs' is a dictionary, iterate over the keys (which are the input IDs)
-        for key in cwl_entity['inputs'].keys():
-            process_in_param(driver, key, component_id, None, cwl_entity['class'])
+        input_dict = cwl_entity['inputs']
+        for key in input_dict.keys():
+            process_in_param(driver, key, component_id, input_dict[key]['type'], cwl_entity['class'])
 
 def process_cwl_outputs(driver: Driver, cwl_entity: dict, step_lookup) -> None:
     """

graph_creation/utils.py

@@ -30,7 +30,7 @@ def process_step_lookup(cwl_entity: dict) -> dict:
         step_lookup[step['id']] = step_path
     return step_lookup
 
-def process_in_param(driver: Driver, param_id: str, component_id: str, param_type: str = None, entity_type: str = None):
+def process_in_param(driver: Driver, param_id: str, component_id: str, param_type: str, entity_type: str):
     """
     Processes an input parameter by ensuring its node exists and optionally creating a relationship 
     between the component and the parameter node.
@@ -46,7 +46,7 @@ def process_in_param(driver: Driver, param_id: str, component_id: str, param_typ
     """
 
     param_node = ensure_in_parameter_node(driver, param_id, component_id, param_type, entity_type)
-    if entity_type == "Workflow":
+    if entity_type != "Workflow":
         create_in_param_relationship(driver, component_id, param_node[0])
 
 def process_parameter_source(driver: Driver, param_node_internal_id: int, source_id: str, workflow_id: str, step_lookup: dict) -> None:
@@ -119,7 +119,6 @@ def process_control_dependencies(driver: Driver, source_id: str, workflow_id: st
     with driver.session() as session:
         in_parameters = get_all_in_parameter_nodes_of_entity(session, component_id)
         node_ids = [record["nodeId"] for record in in_parameters]
-        print(node_ids)
         for node_id in node_ids:
             create_control_relationship(driver, node_id, source_param_node, workflow_id, source_id)
         

neo4j_dependency_queries/create_edge_queries.py

@@ -21,7 +21,7 @@ def create_in_param_relationship(driver: Driver, prefixed_component_id: str, par
     query = """
     MATCH (c:Component {component_id: $component_id}), (p:InParameter)
     WHERE elementId(p) = $parameter_internal_id
-    MERGE (c)<-[r:DATA_FLOW {component_id: $component_id}]->(p)
+    MERGE (c)<-[r:DATA_FLOW {component_id: $component_id}]-(p)
     SET r.data_ids = 
         CASE 
             WHEN r.data_ids IS NULL THEN [p.parameter_id]

neo4j_dependency_queries/processing_queries.py

@@ -104,7 +104,6 @@ def get_all_outermost_workflow_ids(session: Session):
         """
     result = session.run(query)
     unique_component_ids = result.single()["unique_component_ids"]
-    print(unique_component_ids)
     return unique_component_ids
 
 def get_all_out_parameter_nodes_of_entity(session: Session, component_id: str):