Merge pull request #49 from linkml/mongo-select

Allowing paths to be used for select queries with mongodb

Author: cmungall

src/linkml_store/api/stores/mongodb/mongodb_collection.py

@@ -7,6 +7,7 @@
 from linkml_store.api import Collection
 from linkml_store.api.collection import DEFAULT_FACET_LIMIT, OBJECT
 from linkml_store.api.queries import Query, QueryResult
+from linkml_store.utils.object_utils import object_path_get
 
 logger = logging.getLogger(__name__)
 
@@ -130,7 +131,15 @@ def upsert(
     def query(self, query: Query, limit: Optional[int] = None, offset: Optional[int] = None, **kwargs) -> QueryResult:
         mongo_filter = self._build_mongo_filter(query.where_clause)
         limit = limit or query.limit
-        cursor = self.mongo_collection.find(mongo_filter)
+        
+        # Build projection if select_cols are provided
+        projection = None
+        if query.select_cols:
+            projection = {"_id": 0}
+            for col in query.select_cols:
+                projection[col] = 1
+        
+        cursor = self.mongo_collection.find(mongo_filter, projection)
         if limit and limit >= 0:
             cursor = cursor.limit(limit)
         offset = offset or query.offset
@@ -141,9 +150,19 @@ def query(self, query: Query, limit: Optional[int] = None, offset: Optional[int]
 
         def _as_row(row: dict):
             row = copy(row)
-            del row["_id"]
+            if "_id" in row:
+                del row["_id"]
+                
             if select_cols:
-                row = {k: row[k] for k in select_cols if k in row}
+                # For nested fields, ensure we handle them properly
+                result = {}
+                for col in select_cols:
+                    # If it's a nested field (contains dots)
+                    if "." in col or "[" in col:
+                        result[col]  = object_path_get(row, col)
+                    elif col in row:
+                        result[col] = row[col]
+                return result
             return row
 
         rows = [_as_row(row) for row in cursor]

src/linkml_store/utils/object_utils.py

@@ -83,15 +83,21 @@ def object_path_get(obj: Union[BaseModel, Dict[str, Any]], path: str, default_va
     'NA'
     """
     if isinstance(obj, BaseModel):
-        obj = obj.dict()
+        obj = obj.model_dump()
     parts = path.split(".")
     for part in parts:
         if "[" in part:
             key, index = part[:-1].split("[")
             index = int(index)
-            obj = obj[key][index]
+            if key in obj and obj[key] is not None:
+                obj = obj[key][index]
+            else:
+                return default_value
         else:
-            obj = obj.get(part, default_value)
+            if isinstance(obj, list):
+                obj = [v1.get(part, default_value) for v1 in obj]
+            else:
+                obj = obj.get(part, default_value)
     return obj