Merge pull request #56 from smart-on-fhir/mikix/export-summaries

fix: export summaries and quiet warning about output mode

cumulus_library_data_metrics/__init__.py

@@ -1,3 +1,3 @@
 """Data Metrics study for Cumulus Library"""
 
-__version__ = "4.0.0"
+__version__ = "4.0.1"

cumulus_library_data_metrics/base.py

@@ -117,11 +117,12 @@ def get_output_mode(self, config: base_utils.StudyConfig) -> str:
             or os.environ.get("DATA_METRICS_OUTPUT_MODE")
         )
         if output_mode not in {"aggregate", "cube"}:
+            if output_mode:
+                print(
+                    f"Did not understand output mode '{output_mode}'. Using 'cube' instead.",
+                    file=sys.stderr,
+                )
             output_mode = "cube"
-            print(
-                f"Did not understand output mode '{output_mode}'. Using 'cube' instead.",
-                file=sys.stderr,
-            )
         return output_mode
 
     def render_sql(self, template: str, **kwargs) -> str:

cumulus_library_data_metrics/manifest.toml

@@ -41,6 +41,7 @@ export_list = [
     "data_metrics__count_c_resource_count_patient_all",
     "data_metrics__count_c_resource_count_procedure_month",
     "data_metrics__count_c_resource_count_procedure_year",
+    "data_metrics__c_resources_per_pt_summary",
     "data_metrics__count_c_system_use_allergyintolerance_code",
     "data_metrics__count_c_system_use_condition_code",
     "data_metrics__count_c_system_use_device_type",
@@ -86,4 +87,9 @@ export_list = [
     "data_metrics__count_c_us_core_v4_count_patient_must_support",
     "data_metrics__count_c_us_core_v4_count_procedure_mandatory",
     "data_metrics__count_c_us_core_v4_count_procedure_must_support",
+    "data_metrics__q_date_recent_summary",
+    "data_metrics__q_ref_target_pop_summary",
+    "data_metrics__q_ref_target_valid_summary",
+    "data_metrics__q_system_use_summary",
+    "data_metrics__q_valid_us_core_v4_summary",
 ]