linting, sqlfluff

cumulus_library/.sqlfluff

@@ -15,6 +15,9 @@ ignore_comment_lines = true
 [sqlfluff:rules:capitalisation.keywords]
 capitalisation_policy = upper
 
+[sqlfluff:templater:jinja]
+load_macros_from_path = cumulus_library/studies/core/core_templates
+
 [sqlfluff:templater:jinja:context]
 code_systems = ["http://snomed.info/sct", "http://hl7.org/fhir/sid/icd-10-cm"]
 col_type_list = ["a string","b string"]
@@ -44,6 +47,7 @@ prefix = Test
 primary_ref = encounter_ref
 pos_source_table = pos_source_table
 schema_name = test_schema
+schema = {'condition': {'category': {'coding': True, 'code': True, 'display': True, 'system': True, 'userSelected': True, 'version': True, 'text': True}, 'clinicalstatus': {'coding': True, 'code': True, 'display': True, 'system': True, 'userSelected': True, 'version': True, 'text': True}, 'id': True, 'recordeddate': True, 'verificationstatus': {'coding': True, 'code': True, 'display': True, 'system': True, 'userSelected': True, 'version': True, 'text': True}, 'subject': {'reference': True, 'display': False, 'type': True}, 'encounter': {'reference': True, 'display': False, 'type': True}}}
 source_table = source_table
 source_id = source_id
 table_cols = ["a","b"]

cumulus_library/studies/core/builder_prereq_tables.py

@@ -21,3 +21,6 @@ def prepare_queries(self, cursor: object, schema: str, *args, **kwargs):
             with open(dir_path / sql_file) as file:
                 queries = sqlparse.split(file.read())
                 self.queries += queries
+        self.comment_queries()
+        self.write_queries()
+        exit()

cumulus_library/studies/core/core_templates/condition.sql.jinja

@@ -38,7 +38,7 @@ SELECT
     tc.display AS code_display,
     tc.subject_ref,
     tc.encounter_ref,
-    tc.id as condition_id,
+    tc.id AS condition_id,
     tc.condition_ref,
     tc.recordeddate,
     date_trunc('week', date(tc.recordeddate)) AS recorded_week,
@@ -48,4 +48,4 @@ FROM temp_condition AS tc,
     unnest(category) AS t_category (category_coding),
     unnest(category_coding.coding) AS t_category_coding (category_row)
 
-WHERE tc.recordeddate BETWEEN date('2016-01-01') AND current_date;
+WHERE tc.recordeddate BETWEEN date('2016-01-01') AND current_date;

cumulus_library/studies/core/fhir_lookup_tables.sql

@@ -51,4 +51,4 @@ FROM
             'virtual'
         )
     )
-        AS t (code, display)
+        AS t (code, display);

cumulus_library/studies/core/fhir_mapping_tables.sql

@@ -137,4 +137,4 @@ SELECT * FROM
         ('PRENC', 'PRENC'),
         ('SS', 'SS'),
         ('VR', 'VR')
-    ) AS t (expected, found)
+    ) AS t (expected, found);