Refactored remaining core tables

cumulus_library/statistics/counts.py

@@ -122,15 +122,15 @@ def count_condition(
             filter_resource="encounter",
         )
 
-    def count_document(
+    def count_documentreference(
         self,
         table_name: str,
         source_table: str,
         table_cols: list,
         where_clauses: Union[list, None] = None,
         min_subject: int = 10,
     ) -> str:
-        """wrapper method for constructing document counts tables
+        """wrapper method for constructing documentreference counts tables
 
         :param table_name: The name of the table to create. Must start with study prefix
         :param source_table: The table to create counts data from
@@ -145,7 +145,8 @@ def count_document(
             table_cols,
             where_clauses=where_clauses,
             min_subject=min_subject,
-            fhir_resource="document",
+            fhir_resource="documentreference",
+            filter_resource="encounter",
         )
 
     def count_encounter(
@@ -174,6 +175,32 @@ def count_encounter(
             fhir_resource="encounter",
         )
 
+    def count_medicationrequest(
+        self,
+        table_name: str,
+        source_table: str,
+        table_cols: list,
+        where_clauses: Union[list, None] = None,
+        min_subject: int = 10,
+    ) -> str:
+        """wrapper method for constructing medicationrequests counts tables
+
+        :param table_name: The name of the table to create. Must start with study prefix
+        :param source_table: The table to create counts data from
+        :param table_cols: The columns from the source table to add to the count table
+        :param where_clauses: An array of where clauses to use for filtering the data
+        :param min_subject: An integer setting the minimum bin size for inclusion
+            (default: 10)
+        """
+        return self.get_count_query(
+            table_name,
+            source_table,
+            table_cols,
+            where_clauses=where_clauses,
+            min_subject=min_subject,
+            fhir_resource="medicationrequest",
+        )
+
     def count_observation(
         self,
         table_name: str,

cumulus_library/studies/core/builder_condition.py

@@ -1,7 +1,7 @@
 from cumulus_library import base_table_builder
 from cumulus_library import databases
 from cumulus_library.studies.core.core_templates import core_templates
-from cumulus_library.template_sql import templates
+from cumulus_library.template_sql import templates, utils
 
 
 expected_table_cols = {
@@ -42,8 +42,10 @@
 
 
 class CoreConditionBuilder(base_table_builder.BaseTableBuilder):
+    display_text = "Creating Condition tables..."
+
     def denormalize_codes(self):
-        preferred_config = templates.CodeableConceptConfig(
+        preferred_config = utils.CodeableConceptConfig(
             source_table="condition",
             source_id="id",
             column_name="code",
@@ -60,7 +62,7 @@ def denormalize_codes(self):
             templates.get_codeable_concept_denormalize_query(preferred_config)
         )
 
-        all_config = templates.CodeableConceptConfig(
+        all_config = utils.CodeableConceptConfig(
             source_table="condition",
             source_id="id",
             column_name="code",
@@ -72,14 +74,6 @@ def denormalize_codes(self):
             templates.get_codeable_concept_denormalize_query(all_config)
         )
 
-    def validate_schema(self, cursor: object, schema: str, expected_table_cols, parser):
-        validated_schema = {}
-        for table, cols in expected_table_cols.items():
-            query = templates.get_column_datatype_query(schema, table, cols.keys())
-            table_schema = cursor.execute(query).fetchall()
-            validated_schema[table] = parser.validate_table_schema(cols, table_schema)
-        return validated_schema
-
     def prepare_queries(
         self,
         cursor: object,
@@ -89,7 +83,7 @@ def prepare_queries(
         **kwargs,
     ):
         self.denormalize_codes()
-        validated_schema = self.validate_schema(
+        validated_schema = core_templates.validate_schema(
             cursor, schema, expected_table_cols, parser
         )
         self.queries.append(