rename pathogen -> disease

pipelines/epinow2/generate_config.py

@@ -1,5 +1,6 @@
 import os
-from datetime import date, datetime
+from datetime import date, datetime, timezone
+
 
 from utils.epinow2.functions import (
     generate_job_id,
@@ -20,24 +21,22 @@
 
     # Pull run parameters from environment
     state = os.environ.get("state", "all")
-    pathogen = os.environ.get("pathogen", "all")
+    disease = os.environ.get("disease", "all")
     report_date = os.environ.get("report_date", date.today())
     reference_dates = os.environ.get("reference_date", [report_date])
     data_source = os.environ.get("data_source", "nhsn")
 
     # Validate and sanitize args
     sanitized_args = validate_args(
         state=state,
-        pathogen=pathogen,
+        disease=disease,
         report_date=report_date,
         reference_dates=reference_dates,
         data_source=data_source,
     )
-
     # Generate job-specific parameters
-    as_of_date = int(datetime.timestamp(datetime.now()))
+    as_of_date = int(datetime.timestamp(datetime.now(timezone.utc)))
     job_id = generate_job_id()
-
     # Generate task-specific configs
     task_configs = generate_task_configs(
         **sanitized_args, as_of_date=as_of_date, job_id=job_id

utils/epinow2/constants.py

@@ -14,7 +14,7 @@
     },
 }
 
-states = [
+all_states = [
     "AK",
     "AL",
     "AR",
@@ -71,5 +71,5 @@
 ]
 
 nssp_states_omit = ["AS", "FM", "MH", "NP", "PR", "PW", "VI", "MO", "GU"]
-pathogens = ["COVID-19", "Influenza"]
+all_diseases = ["COVID-19", "Influenza"]
 data_sources = ["nhsn", "nssp"]

utils/epinow2/functions.py

@@ -3,9 +3,9 @@
 
 from utils.epinow2.constants import (
     nssp_states_omit,
-    pathogens,
+    all_diseases,
     shared_params,
-    states,
+    all_states,
 )
 
 
@@ -19,7 +19,7 @@ def generate_job_id() -> UUID:
 
 def validate_args(
     state: str | None = None,
-    pathogen: str | None = None,
+    disease: str | None = None,
     report_date: date | None = None,
     reference_dates: list[date] | None = None,
     data_source: str | None = None,
@@ -28,7 +28,7 @@ def validate_args(
     in a standardized format for downstream use.
     Parameters:
         state: geography to run model
-        pathogen: pathogen to run
+        disease: disease to run
         report_date: date of model run
         reference_dates: array of reference (event) dates
         data_source: source of input data
@@ -38,27 +38,30 @@ def validate_args(
     args_dict = {}
     if state == "all":
         if data_source == "nssp":
-            args_dict["state"] = list(set(states) - set(nssp_states_omit))
+            args_dict["state"] = list(set(all_states) - set(nssp_states_omit))
         elif data_source == "nhsn":
-            args_dict["state"] = states
+            args_dict["state"] = all_states
         else:
-            raise ValueError(f"Data source {data_source} not recognized.")
-    elif state not in states:
+            raise ValueError(
+                f"Data source {data_source} not recognized. Valid options are 'nssp' or 'nhsn'."
+            )
+    elif state not in all_states:
         raise ValueError(f"State {state} not recognized.")
     else:
         args_dict["state"] = [state]
 
-    if pathogen == "all":
-        args_dict["pathogen"] = pathogens
-    elif pathogen not in pathogens:
-        raise ValueError(f"Pathogen {pathogen} not recognized.")
+    if disease == "all":
+        args_dict["disease"] = all_diseases
+    elif disease not in all_diseases:
+        raise ValueError(
+            f"Disease {disease} not recognized. Valid options are 'COVID-19' or 'Influenza'."
+        )
     else:
-        args_dict["pathogen"] = [pathogen]
+        args_dict["disease"] = [disease]
 
     # Standardize reference_dates
     reference_dates = [
-        date.fromisoformat(x) if isinstance(x, str) else x
-        for x in reference_dates
+        date.fromisoformat(x) if isinstance(x, str) else x for x in reference_dates
     ]
 
     # Check valid reference_date
@@ -74,21 +77,21 @@ def validate_args(
 def generate_task_id(
     job_id: UUID | None = None,
     state: str | None = None,
-    pathogen: str | None = None,
+    disease: str | None = None,
 ) -> str:
     """Generates a task_id which consists of the hex code of the job_id
     and information on the state and pathogen.
     Parameters:
         job_id: UUID of job
         state: state being run
-        pathogen: pathogen being run
+        disease: disease being run
     """
-    return f"{job_id.hex}_{state}_{pathogen}"
+    return f"{job_id.hex}_{state}_{disease}"
 
 
 def generate_task_configs(
     state: list | None = None,
-    pathogen: list | None = None,
+    disease: list | None = None,
     report_date: date | None = None,
     reference_dates: list[date] | None = None,
     as_of_date: int | None = None,
@@ -99,7 +102,7 @@ def generate_task_configs(
     supplied parameters.
     Parameters:
         state: geography to run model
-        pathogen: pathogen to run
+        disease: pathogen to run
         report_date: date of model run
         reference_dates: array of reference (event) dates
         as_of_date: timestamp of model run
@@ -110,14 +113,12 @@ def generate_task_configs(
     configs = []
     # Create tasks for each state-pathogen combination
     for s in state:
-        for p in pathogen:
+        for d in disease:
             task_config = {
                 "job_id": str(job_id),
-                "task_id": generate_task_id(
-                    job_id=job_id, state=s, pathogen=p
-                ),
+                "task_id": generate_task_id(job_id=job_id, state=s, disease=d),
                 "as_of_date": as_of_date,
-                "disease": p,
+                "disease": d,
                 "geo_value": [s],
                 "geo_type": "state" if s != "US" else "country",
                 "parameters": shared_params["parameters"],