add return of file instead of stream

bin/validate.py

@@ -340,19 +340,19 @@ def make_products(dataset, gaf_path, products, ontology_graph):
 @tools.gzips
 def make_gpads(dataset, gaf_path, products, ontology_graph, noctua_gpad_file):
 
+    gpad_file_path = os.path.join(os.path.split(gaf_path)[0], f"{dataset}_gpad.gpad")
+
     product_files = {
         "gpad": open(os.path.join(os.path.split(gaf_path)[0], "{}_gpad.gpad".format(dataset)), "wb")
     }
 
     if not products["gpad"]:
-        # Bail if we have no products
         return []
 
     # logger.info("AssocParserConfig used: {}".format(config))
 
-    validated_gpad_path = product_files["gpad"]
-    outfile = open(validated_gpad_path, "w")
-    gpadwriter = GpadWriter(file=outfile, version="GPAD_2_0")
+    with open(gpad_file_path, "w") as outfile:
+        gpadwriter = GpadWriter(file=outfile, version="GPAD_2_0")
 
     print("noctua-gpad-file: {}".format(noctua_gpad_file))
     if noctua_gpad_file is not None:
@@ -386,10 +386,8 @@ def make_gpads(dataset, gaf_path, products, ontology_graph, noctua_gpad_file):
                 gpadwriter.write_assoc(association)
 
         # After we run through associations
-        for f in product_files.values():
-            f.close()
+    return [gpad_file_path] if products["gpad"] else []
 
-    return [product_files["gpad"].name for prod in sorted(product_files.keys()) if products[prod]]
 
 @tools.gzips
 def produce_gpi(dataset, target_dir, gaf_path, ontology_graph):