Merge pull request #736 from hubmapconsortium/Derek-Furst/constraints…

…-allow-non-donors

Added a bypass in metadata_constraints.py for any non-donor entries i…

src/app.py

@@ -35,7 +35,7 @@
 from schema.schema_constants import DataVisibilityEnum
 from schema.schema_constants import MetadataScopeEnum
 from schema.schema_constants import TriggerTypeEnum
-from metadata_constraints import get_constraints
+from metadata_constraints import get_constraints, constraints_json_is_valid
 # from lib.ontology import initialize_ubkg, init_ontology, Ontology, UbkgSDK
 
 
@@ -2329,9 +2329,7 @@ def validate_constraints():
         'name': "ok"
     }
 
-    index = 0
     for constraint in json_entry:
-        index += 1
         if order == 'descendants':
             result = get_constraints(constraint, 'descendants', 'ancestors', is_match)
         else:
@@ -4599,35 +4597,6 @@ def internal_server_error(err_msg):
     abort(500, description = err_msg)
 
 
-"""
-Validates the incoming json for the endpoint /constraints. 
-Returns true if the json matches the required format. If 
-invalid, returns a string explaining why.
-"""
-def constraints_json_is_valid(json_entry):
-    if not isinstance(json_entry, list):
-        return "JSON body expects a list."
-
-    for constraint in json_entry:
-        if not isinstance(constraint, dict):
-            return "Each constraint in the list must be a JSON object."
-
-        for key in constraint:
-            if key not in ["ancestors", "descendants"]:
-                return f"Invalid key '{key}'. Allowed keys are 'ancestors' and 'descendants'."
-
-            value = constraint[key]
-            if isinstance(value, dict):
-                continue
-            elif isinstance(value, list):
-                for item in value:
-                    if not isinstance(item, dict):
-                        return f"The value for '{key}' must be represented as a JSON object or as a list of objects"
-            else:
-                return f"The value for '{key}' must be a JSON object or a list of JSON objects."
-    return True
-
-
 """
 Parse the token from Authorization header
 

src/metadata_constraints.py

@@ -151,6 +151,36 @@ def validate_exclusions(entry, constraint, key) -> bool:
             return True
     else:
         return False
+
+
+"""
+Validates the incoming json for the endpoint /constraints. 
+Returns true if the json matches the required format. If 
+invalid, returns a string explaining why.
+"""
+def constraints_json_is_valid(json_entry):
+    if not isinstance(json_entry, list):
+        return "JSON body expects a list."
+
+    for constraint in json_entry:
+        if not isinstance(constraint, dict):
+            return "Each constraint in the list must be a JSON object."
+
+        for key in constraint:
+            if key not in ["ancestors", "descendants"]:
+                return f"Invalid key '{key}'. Allowed keys are 'ancestors' and 'descendants'."
+
+            value = constraint[key]
+            if isinstance(value, dict):
+                continue
+            elif isinstance(value, list):
+                for item in value:
+                    if not isinstance(item, dict):
+                        return f"The value for '{key}' must be represented as a JSON object or as a list of objects"
+            else:
+                return f"The value for '{key}' must be a JSON object or a list of JSON objects."
+    return True
+
 
 
 def get_constraints(entry, key1, key2, is_match=False) -> dict:
@@ -159,37 +189,44 @@ def get_constraints(entry, key1, key2, is_match=False) -> dict:
     result = {'code': 400, 'name': "Bad Request"} if is_match else {'code': 200, 'name': 'OK', 'description': 'Nothing to validate.'}
 
     if entry_key1 is not None:
-        report = determine_constraint_from_entity(entry_key1)
-        constraints = report.get('constraints')
-        if report.get('error') is not None and not constraints:
-            result = {'code': 400, 'name': "Bad Request", 'description': report.get('error')}
-
-        for constraint in constraints:
-            const_key1 = get_constraint_unit(constraint.get(key1))
-
-            if DeepDiff(entry_key1, const_key1, ignore_string_case=True, exclude_types=[type(None)]) == {}: # or validate_exclusions(entry_key1, const_key1, 'sub_type_val'):
-                const_key2 = constraint.get(key2)
-
-                if is_match:
-                    entry_key2 = entry.get(key2)
-                    v = validate_constraint_units_to_entry_units(entry_key2, const_key2) 
-                    if entry_key2 is not None and v:
-                        result = {'code': 200, 'name': 'OK', 'description': const_key2}
+        """
+        We only are interested in validating the constraints of donors to verify that their descendants are Organ samples. 
+        For any other entity type, we are passing automatically with the message "Nothing to valiate". For donors, validation
+        Occurs as normal, with the constraint requiring a descendant that is an organ. 
+        """
+        if entry_key1.get('entity_type') and entry_key1.get('entity_type').lower() == 'donor':
+            report = determine_constraint_from_entity(entry_key1)
+            constraints = report.get('constraints')
+            if report.get('error') is not None and not constraints:
+                result = {'code': 400, 'name': "Bad Request", 'description': report.get('error')}
+
+            for constraint in constraints:
+                const_key1 = get_constraint_unit(constraint.get(key1))
+
+                if DeepDiff(entry_key1, const_key1, ignore_string_case=True, exclude_types=[type(None)]) == {}: # or validate_exclusions(entry_key1, const_key1, 'sub_type_val'):
+                    const_key2 = constraint.get(key2)
+
+                    if is_match:
+                        entry_key2 = entry.get(key2)
+                        v = validate_constraint_units_to_entry_units(entry_key2, const_key2) 
+                        if entry_key2 is not None and v:
+                            result = {'code': 200, 'name': 'OK', 'description': const_key2}
+                        else:
+                            entity_type = entry_key1.get('entity_type')
+                            entity_type = entity_type.title() if entity_type is not None else entity_type
+                            sub_type = entry_key1.get('sub_type')
+                            sub_type = ', '.join(sub_type) if sub_type is not None else ''
+                            msg = (
+                                f"This `{entity_type}` `{sub_type}` cannot be associated with the provided `{key1}` due to entity constraints. "
+                                f"Click the link to view valid entity types that can be `{key2}`"
+                            )
+                            result = {'code' :404, 'name': msg, 'description': const_key2}
                     else:
-                        entity_type = entry_key1.get('entity_type')
-                        entity_type = entity_type.title() if entity_type is not None else entity_type
-                        sub_type = entry_key1.get('sub_type')
-                        sub_type = ', '.join(sub_type) if sub_type is not None else ''
-                        msg = (
-                            f"This `{entity_type}` `{sub_type}` cannot be associated with the provided `{key1}` due to entity constraints. "
-                            f"Click the link to view valid entity types that can be `{key2}`"
-                        )
-                        result = {'code' :404, 'name': msg, 'description': const_key2}
-                else:
-                    result = {'code': 200, 'name': 'OK', 'description': const_key2}
-                break
-
-            else:
-                result = {'code' :404, 'name': f"No matching constraints on given '{key1}"}
+                        result = {'code': 200, 'name': 'OK', 'description': const_key2}
+                    break
 
+                else:
+                    result = {'code' :404, 'name': f"No matching constraints on given '{key1}"}
+        else:
+            result = {'code': 200, 'name': 'OK', 'description': 'Nothing to validate.'}
     return result