Light cleanup

cumulus_library/studies/core/builder_documentreference.py

@@ -56,7 +56,7 @@ def prepare_queries(
                 sql_utils.CodingConfig(
                     source_table="documentreference",
                     source_id="id",
-                    column_hierarchy=[("format", dict), ("content", dict)],
+                    column_hierarchy=[("content", list), ("format", dict)],
                     target_table="core__documentreference_dn_format",
                 ),
             ],

cumulus_library/studies/core/reference_sql/builder_documentreference.sql

@@ -98,15 +98,38 @@ CREATE TABLE core__documentreference_dn_category AS (
 
 -- ###########################################################
 
-CREATE TABLE IF NOT EXISTS "main"."core__documentreference_dn_format"
-AS (
-    SELECT * FROM (
-        VALUES
-        (cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar))
+CREATE TABLE core__documentreference_dn_format AS (
+    WITH
+
+    system_format_0 AS (
+        SELECT DISTINCT
+            s.id AS id,
+            u.parent_col.format.code,
+            u.parent_col.format.display,
+            u.parent_col.format.system AS code_system
+        FROM
+            documentreference AS s,
+            UNNEST(s.content) AS u (parent_col)
+    ), --noqa: LT07
+
+    union_table AS (
+        SELECT
+            id,
+            code_system,
+            code,
+            display
+        FROM system_format_0
+
     )
-        AS t ("id","code","code_system","display")
+    SELECT
+        id,
+        code,
+        code_system,
+        display
+    FROM union_table
 );
 
+
 -- ###########################################################
 
 

cumulus_library/template_sql/base_templates.py

@@ -74,6 +74,7 @@ def get_codeable_concept_denormalize_query(
     :param config: a CodableConeptConfig
     """
 
+    assert len(config.column_hierarchy) <= 2
     # If we get a None for code systems, we want one dummy value so the jinja
     # for loop will do a single pass. This implicitly means that we're not
     # filtering, so this parameter will be otherwise ignored
@@ -86,7 +87,7 @@ def get_codeable_concept_denormalize_query(
         parent_field=None
         if len(config.column_hierarchy) == 1
         else config.column_hierarchy[0][0],
-        is_array=True if config.column_hierarchy[0][1] == list else False,
+        is_array=(config.column_hierarchy[0][1] == list),
         target_table=config.target_table,
         filter_priority=config.filter_priority,
         code_systems=config.code_systems,
@@ -107,6 +108,7 @@ def get_coding_denormalize_query(
     :param config: a CodingConfig
     """
 
+    assert len(config.column_hierarchy) == 2
     # If we get a None for code systems, we want one dummy value so the jinja
     # for loop will do a single pass. This implicitly means that we're not
     # filtering, so this parameter will be otherwise ignored

cumulus_library/template_sql/sql_utils.py

@@ -234,7 +234,6 @@ def _check_schema_if_exists(
     cursor: databases.DatabaseCursor,
     source_table: str,
     source_col: str,
-    target_field: str,
     expected=None,
 ) -> bool:
     """Validation check for a column existing, and having the expected schema
@@ -243,9 +242,7 @@ def _check_schema_if_exists(
     :param cursor: a PEP-249 compliant database cursor
     :param source_table: The table to query against
     :param source_col: The column to check the schema against
-    :param target_field: The name of the nested value to check for inside the
-        schema of source_col
-    :param expected: a list of elements that should be present in target_field.
+    :param expected: a list of elements that should be present in source_col.
         If none, we assume it is a CodeableConcept.
     :returns: a boolean indicating if the schema was found.
     """