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fix: export summaries and quiet warning about output mode #56

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merged 1 commit into from
Jul 16, 2024
Merged

fix: export summaries and quiet warning about output mode #56

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2 changes: 1 addition & 1 deletion cumulus_library_data_metrics/__init__.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
"""Data Metrics study for Cumulus Library"""

__version__ = "4.0.0"
__version__ = "4.0.1"
9 changes: 5 additions & 4 deletions cumulus_library_data_metrics/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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6 changes: 6 additions & 0 deletions cumulus_library_data_metrics/manifest.toml
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
]