low hanging PR fruit

cumulus_library/studies/core/builder_prereq_tables.py

@@ -21,6 +21,3 @@ 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/count_core.py

@@ -1,6 +1,6 @@
 from typing import List
 from pathlib import Path
-import cumulus_library.statistics.counts as counts
+from cumulus_library.statistics import counts
 
 
 class CoreCountsBuilder(counts.CountsBuilder):

cumulus_library/template_sql/statistics/count.sql.jinja

@@ -62,7 +62,7 @@ CREATE TABLE {{ table_name }} AS (
         {%- elif fhir_resource=='encounter' and filter_resource %}
         WHERE s.status = 'finished'
         {%- elif fhir_resource=='observation' and filter_resource %}
-        WHERE (s.status = 'final' OR status= 'amended')
+        WHERE (s.status = 'final' OR s.status= 'amended')
         {%- endif %}
     ),
     {% endif %}

cumulus_library/template_sql/utils.py

@@ -160,7 +160,6 @@ def _check_schema_if_exists(
         if cursor.fetchone() is None:
             return False
 
-        cursor.execute(query)
         schema_str = str(cursor.fetchone()[0])
         required_fields = [coding_element]
         if not allow_partial:

tests/test_counts_templates.py

@@ -169,6 +169,4 @@
 )
 def test_count_query(expected, kwargs):
     query = get_count_query("test_table", "test_source", ["age", "sex"], **kwargs)
-    with open("output.sql", "w") as f:
-        f.write(query)
     assert query == expected