fixed germplasm pedigree endpoint

Author: mlm483

initdb/113__germplasm_pedigree_get.sql

@@ -3,7 +3,11 @@ CREATE OR REPLACE FUNCTION get_pedigree(
     "germplasmDbId" text
 )
     RETURNS json AS $$
+DECLARE
+    pedigree_node_id text;
 BEGIN
+    SELECT id INTO pedigree_node_id FROM pedigree_node WHERE germplasm_id = "germplasmDbId";
+
     RETURN (
         SELECT json_build_object(
             '@context', '[]'::json,
@@ -15,49 +19,57 @@ BEGIN
                     'familyCode', node.family_code,
                     'germplasmDbId', "germplasmDbId",
                     'germplasmName', germ.germplasm_name,
-                    'parents', json_agg(
+                    'parents', COALESCE(
                         (
-                            SELECT json_build_object(
-                                'germplasmDbId', parent.id,
-                                'germplasmName', parent.germplasm_name,
-                                'parentType', to_parent_type(e.parent_type)
-                            )
+                            SELECT
+                                json_agg(
+                                    json_build_object(
+                                        'germplasmDbId', parent.id,
+                                        'germplasmName', parent.germplasm_name,
+                                        'parentType', to_parent_type(e.parent_type)
+                                    )
+                                )
                             FROM
                                 pedigree_node parent_node
                                 JOIN
-                                pedigree_edge e ON parent_node.id = e.connceted_node_id AND e.edge_type = edge_type_to_int('parent') -- TODO: hardcoded EdgeType (parent=0, child=1, sibling=2)
+                                pedigree_edge e ON parent_node.id = e.connceted_node_id AND e.edge_type = edge_type_to_int('parent')
                                 JOIN
                                 germplasm parent ON parent_node.germplasm_id = parent.id
-                            WHERE e.this_node_id = (SELECT child_node.id
+                            WHERE
+                                e.this_node_id = (SELECT child_node.id
                                                  FROM pedigree_node child_node
                                                  WHERE child_node.germplasm_id = "germplasmDbId")
-                        )
+                        ),
+                        '[]'::json
                     ),
                     'pedigree', node.pedigree_string,
-                    'siblings', json_agg(
+                    'siblings', COALESCE(
                         (
                             SELECT
-                            json_build_object(
-                                    'germplasmDbId', sibling.id,
-                                    'germplasmName', sibling.germplasm_name
-                            )
+                                json_agg(
+                                    json_build_object(
+                                        'germplasmDbId', sibling.id,
+                                        'germplasmName', sibling.germplasm_name
+                                    )
+                                )
                             FROM
-                            pedigree_node sibling_node
-                            JOIN
-                            pedigree_edge pe ON sibling_node.id = pe.this_node_id AND pe.edge_type = edge_type_to_int('parent')
-                            JOIN
-                            germplasm sibling ON sibling_node.germplasm_id = sibling.id
+                                pedigree_node sibling_node
+                                JOIN
+                                pedigree_edge pe ON sibling_node.id = pe.this_node_id AND pe.edge_type = edge_type_to_int('parent')
+                                JOIN
+                                germplasm sibling ON sibling_node.germplasm_id = sibling.id
                             WHERE
-                            pe.connceted_node_id IN
-                            (
-                                SELECT parent_node.id
-                                FROM
-                                    pedigree_node parent_node
-                                    JOIN
-                                    pedigree_edge e ON parent_node.id = e.connceted_node_id AND e.edge_type = edge_type_to_int('parent')
-                                WHERE e.this_node_id = (SELECT id FROM pedigree_node WHERE germplasm_id = "germplasmDbId")
-                            )
-                        )
+                                pe.connceted_node_id IN
+                                (
+                                    SELECT parent_node.id
+                                    FROM
+                                        pedigree_node parent_node
+                                        JOIN
+                                        pedigree_edge e ON parent_node.id = e.connceted_node_id AND e.edge_type = edge_type_to_int('parent')
+                                    WHERE e.this_node_id = pedigree_node_id
+                                )
+                        ),
+                        '[]'::json
                     )
                 )
                 FROM

server.py

@@ -204,7 +204,7 @@ def get_progeny(germplasmDbId: str):
 
 
 @app.get("/brapi/v2/germplasm/<germplasmDbId>/pedigree")
-def get_progeny(germplasmDbId: str):
+def get_pedigree(germplasmDbId: str):
     with psycopg.connect(CONN_STR) as conn:
         with conn.cursor() as cur:
             cur.execute("SELECT get_pedigree(%s);", (germplasmDbId,))