[DC-1022] updates required_labs query to include concept_ancestor_extension

Signed-off-by: Krishna Kalluri <[email protected]>

Author: ksdkalluri

data_steward/tools/generate_concept_ancestor_extension.py

@@ -1,7 +1,7 @@
 """
 concept_relationship stores two types of relationships 
 1) hierarchical relationships: 'is_a' / 'subsume' that defines the hierarchy of the vocabulary;
-2.) associative relationships:  relationships across the hierarchy such as Drug A
+2) associative relationships:  relationships across the hierarchy such as Drug A
 'is an indication of' Condition B. The concept_ancestor table is built based on 'Is A' and 'Subsume' relationships
 recursively so any ancestor/descendent pairs (regardless of the levels of separation) are pre-computed for us.
 
@@ -20,7 +20,7 @@
 
 LOGGER = logging.getLogger(__name__)
 
-CONCEPT_ANCESTOR_EXT = 'concept_ancestor_extension'
+CONCEPT_ANCESTOR_EXTENSION = 'concept_ancestor_extension'
 
 CONCEPT_ANCESTOR_EXT_QUERY = '''
 DECLARE
@@ -129,7 +129,7 @@
 
 def generate_concept_ancestor_extension(project_id, dataset_id):
     """
-    generates concept ancestor extension table from the concept relationship table for for LOINC hierarchy
+    generates concept ancestor extension table from the concept relationship table for LOINC hierarchy
     :param project_id: identifier for project id
     :param dataset_id: identifier for dataset
     :return: Bq job result

data_steward/validation/metrics/required_labs_sql.py

@@ -17,6 +17,19 @@
   FROM UNNEST([36208978, 36206173, 36208195, 36207527, 36210656, 40782521, 40779250, 40772590]) AS excluded_ancestor_concept_id
 ),
 
+concept_ancestor AS
+(
+SELECT
+  *
+FROM
+  `{project_id}.{vocab_dataset_id}.concept_ancestor`
+UNION ALL
+SELECT
+  *
+FROM
+  `{project_id}.{vocab_dataset_id}.concept_ancestor_extension`
+)
+
 get_direct_parents_loinc_group AS
 (
   -- We use left joins because there are concepts that don`t have a LONIC_Group type ancestor in concept_ancestor
@@ -36,7 +49,7 @@
   ON 
     m.Measurement_OMOP_ID = c1.concept_id
   LEFT JOIN
-    `{project_id}.{vocab_dataset_id}.concept_ancestor` AS ca
+    concept_ancestor AS ca
   ON
     m.Measurement_OMOP_ID = ca.descendant_concept_id 
     AND ca.min_levels_of_separation = 1
@@ -70,7 +83,7 @@
   ON 
     m.Measurement_OMOP_ID = c1.concept_id
   LEFT JOIN
-    `{project_id}.{vocab_dataset_id}.concept_ancestor` AS ca
+    concept_ancestor AS ca
   ON
     m.Measurement_OMOP_ID = ca.descendant_concept_id 
       AND ca.min_levels_of_separation IN (1, 2)
@@ -138,7 +151,7 @@
     COALESCE(ca1.min_levels_of_separation, -1) AS distance
   FROM get_direct_parents_loinc_group AS lg
   LEFT JOIN 
-    `{project_id}.{vocab_dataset_id}.concept_ancestor` AS ca1
+    concept_ancestor AS ca1
   ON
     lg.parent_concept_id = ca1.ancestor_concept_id 
       AND ca1.min_levels_of_separation <> 0
@@ -164,7 +177,7 @@
     COALESCE(ca1.min_levels_of_separation, -1) AS distance
   FROM get_ancestors_loinc_hierarchy_distinct AS lh
   LEFT JOIN 
-    `{project_id}.{vocab_dataset_id}.concept_ancestor` AS ca1
+    concept_ancestor AS ca1
   ON
     lh.ancestor_concept_id = ca1.ancestor_concept_id
       AND ca1.min_levels_of_separation <> 0