Handle 'None' string in fence config

fence/config-default.yaml

@@ -557,7 +557,7 @@ dbGaP:
     #
     # If `parse_consent_code` is true, then a user will be given access to the exact
     # same consent codes in the child studies
-    parent_to_child_studies_mapping:
+    parent_to_child_studies_mapping: {}
       # 'phs001194': ['phs000571', 'phs001843']
     # A consent of "c999" can indicate access to that study's "exchange area data"
     # and when a user has access to one study's exchange area data, they

fence/config.py

@@ -6,6 +6,8 @@
 from gen3config import Config
 
 from cdislogging import get_logger
+from collections import Counter
+from typing import List, Dict, Any
 
 logger = get_logger(__name__)
 
@@ -150,28 +152,39 @@ def post_process(self):
                 logger.warning(
                     f"IdP '{idp_id}' is using multifactor_auth_claim_info '{mfa_info['claim']}', which is neither AMR or ACR. Unable to determine if a user used MFA. Fence will continue and assume they have not used MFA."
                 )
+        dbgap_configs = self._configs["dbGaP"]
+        if isinstance(dbgap_configs, list):
+            corrected_dbgap_configs = dbgap_configs
+        elif isinstance(dbgap_configs, dict):
+            corrected_dbgap_configs = [dbgap_configs]
+        else:
+            raise Exception("The dbgap configuration is not a recognized data structure, aborting!")
+        self._validate_parent_child_studies(corrected_dbgap_configs)
 
-        self._validate_parent_child_studies(self._configs["dbGaP"])
+    @staticmethod
+    def find_duplicates(collection):
+        item_with_occurrences = Counter(collection)
+        duplicates = {item
+                      for item, occurrences in item_with_occurrences.items()
+                      if occurrences > 1}
+        return duplicates
 
     @staticmethod
-    def _validate_parent_child_studies(dbgap_configs):
-        if isinstance(dbgap_configs, list):
-            configs = dbgap_configs
-        else:
-            configs = [dbgap_configs]
-
-        all_parent_studies = set()
-        for dbgap_config in configs:
-            parent_studies = dbgap_config.get(
-                "parent_to_child_studies_mapping", {}
-            ).keys()
-            conflicts = parent_studies & all_parent_studies
-            if len(conflicts) > 0:
-                raise Exception(
-                    f"{conflicts} are duplicate parent study ids found in parent_to_child_studies_mapping for "
-                    f"multiple dbGaP configurations."
-                )
-            all_parent_studies.update(parent_studies)
+    def _validate_parent_child_studies(dbgap_configs: List[Dict[str, Any]]) -> None:
+        def get_parent_studies_safely(dbgap_config):
+            study_mapping = dbgap_config.get('parent_to_child_studies_mapping', {})
+            # study mapping could be 'None'
+            return list(study_mapping.keys()) if isinstance(study_mapping, dict) else []
+
+        safe_list_of_parent_studies = [safe_parent_studies
+                                       for dbgap_config in dbgap_configs
+                                       for safe_parent_studies in get_parent_studies_safely(dbgap_config)]
+
+        duplicates = FenceConfig.find_duplicates(safe_list_of_parent_studies)
+        if len(duplicates) > 0:
+            raise Exception(
+                f"{duplicates} are duplicate parent study ids found in parent_to_child_studies_mapping for "
+                f"multiple dbGaP configurations.")
 
 
 config = FenceConfig(DEFAULT_CFG_PATH)

tests/test_app_config.py

@@ -122,6 +122,14 @@ def test_app_config():
 
 
 def test_app_config_parent_child_study_mapping(monkeypatch):
+
+    none_string_config = [{"parent_to_child_studies_mapping": 'None'},
+                          {"parent_to_child_studies_mapping": 'None'},]
+    try:
+        FenceConfig._validate_parent_child_studies(none_string_config)
+    except Exception:
+        pytest.fail("Study validation failed when given 'None' mapping!")
+
     invalid_dbgap_configs = [
         {
             "parent_to_child_studies_mapping": {
@@ -138,3 +146,22 @@ def test_app_config_parent_child_study_mapping(monkeypatch):
     ]
     with pytest.raises(Exception):
         FenceConfig._validate_parent_child_studies(invalid_dbgap_configs)
+
+    valid_dbgap_configs = [
+        {
+            "parent_to_child_studies_mapping": {
+                "phs001194": ["phs000571", "phs001843"],
+                "phs001193": ["phs000572", "phs001844"],
+            }
+        },
+        {
+            "parent_to_child_studies_mapping": {
+                "phs001195": ["phs0015623"],
+                "phs001192": ["phs0001", "phs002"],
+            }
+        },
+    ]
+    try:
+        FenceConfig._validate_parent_child_studies(valid_dbgap_configs)
+    except Exception:
+        pytest.fail("Study validation failed when it should have passed!")