generate_config script

pipelines/epinow2/generate_config.py

@@ -1,7 +1,11 @@
 import os
 from datetime import datetime
 
-from utils.epinow2.functions import generate_job_id, generate_task_configs
+from utils.epinow2.functions import (
+    generate_job_id,
+    generate_task_configs,
+    validate_args,
+)
 
 if __name__ == "__main__":
     """
@@ -17,22 +21,24 @@
     # Pull run parameters from environment
     state = os.environ.get("state", "all")
     pathogen = os.environ.get("pathogen", "all")
-    report_date = os.environ.get(
-        "report_date", datetime.today().strftime("%Y-%m-%d")
-    )
+    report_date = os.environ.get("report_date", datetime.today().strftime("%Y-%m-%d"))
     reference_date = os.environ.get("reference_date", [report_date])
     data_source = os.environ.get("data_source", "nssp")
 
+    # Validate and sanitize args
+    sanitized_args = validate_args(
+        state=state,
+        pathogen=pathogen,
+        report_date=report_date,
+        reference_date=reference_date,
+        data_source=data_source,
+    )
+
     # Generate job-specific parameters
     as_of_date = int(datetime.timestamp(datetime.now()))
     job_id = generate_job_id()
 
     # Generate task-specific configs
     task_configs = generate_task_configs(
-        state=state,
-        report_date=report_date,
-        reference_date=reference_date,
-        as_of_date=as_of_date,
-        job_id=job_id,
-        data_source=data_source,
-    )
+        **sanitized_args, as_of_date=as_of_date, job_id=job_id
+    )