Fix failing test. Adapt to general dbxref requirements

dbxref/retrieve/cdd.py

@@ -43,7 +43,7 @@ def main():
     print(json.dumps(documents, sort_keys=True, indent=4))
 
 
-def retrieve(dbxrefs, basics, abstract, date, pssmlength, structure, status):
+def retrieve(dbxrefs, basics=True, abstract=False, date=False, pssmlength=False, structure=False, status=False):
     """Retrieve json document from InterPro REST api, filter information by selected Options and parse into new json"""
     resolved = dbxref.resolver.resolve(dbxrefs, check_existence=False)
     documents = []
@@ -56,22 +56,24 @@ def retrieve(dbxrefs, basics, abstract, date, pssmlength, structure, status):
         cdd_json = json.loads(r.text)
 
         # parse retrieved json file by selected options
-        output = {}
+        output = {"id": entry["dbxref"]}
         acc_id = str(resolved[0]["dbxref"][4:])
         if basics:
             try:
-                output.update({"dbxref_id": "CDD:" + acc_id, "accession_id": cdd_json["result"][acc_id]["accession"],
+                output.update({"dbxref": "CDD:" + acc_id, "accession": cdd_json["result"][acc_id]["accession"],
                                "scientific_name": cdd_json["result"][acc_id]["title"],
                                "database": cdd_json["result"][acc_id]["database"],
                                "associated_organism": cdd_json["result"][acc_id]["organism"]
                                })
             except KeyError:
                 print("One or more basic information were not available for the given entry. Please check your data.")
+                raise
         if abstract:
             try:
                 output.update({"abstract": cdd_json["result"][acc_id]["abstract"]})
             except KeyError:
                 print("An abstract was not available for the given entry.")
+                raise
         if date:
             try:
                 output.update({"publication_date": cdd_json["result"][acc_id]["pubdate"],
@@ -79,21 +81,25 @@ def retrieve(dbxrefs, basics, abstract, date, pssmlength, structure, status):
             except KeyError:
                 print("The date of publishment and/or day of addition to Entrez were not available for the given "
                       "entry.")
+                raise
         if pssmlength:
             try:
                 output.update({"pssmlength": cdd_json["result"][acc_id]["pssmlength"]})
             except KeyError:
                 print("Information about PSSM was not available for the given entry.")
+                raise
         if structure:
             try:
                 output.update({"representative_structure": cdd_json["result"][acc_id]["structurerepresentative"]})
             except KeyError:
                 print("There was no representative structure available for the given entry.")
+                raise
         if status:
             try:
                 output.update({"status": cdd_json["result"][acc_id]["status"]})
             except KeyError:
                 print("Status information was not available for the given entry. Please check your data.")
+                raise
         documents.append(output)
     return documents
 

tests/test_cdd.py

@@ -4,7 +4,7 @@ from dbxref.retrieve import cdd
 class TestCDD(unittest.TestCase):
 
     def test_output(self):
-        documents = cdd.retrieve({"db": "CDD", "id": "351793"}, basics=True, abstract=True, date=True, pssmlength=True,
+        documents = cdd.retrieve([{"db": "CDD", "id": "351793"}], basics=True, abstract=True, date=True, pssmlength=True,
                                  status=True, structure=True)
         self.assertTrue(documents)