Patch up validators later

Author: jlubken

defaults/cli.cfg

@@ -1,11 +1,11 @@
 --current-hospitalized 69
---doubling_time 4.0
+--doubling-time 4.0
 --hospitalized-days 7
 --hospitalized-rate 0.025
 --icu-days 9
 --icu-rate 0.0075
 --infectious-days 14
---market_share 0.15
+--market-share 0.15
 --n-days 100
 --population 3600000
 --recovered 0

defaults/webapp.cfg

@@ -6,7 +6,7 @@
 --icu-days 9
 --icu-rate 0.0075
 --infectious-days 14
---market_share 0.15
+--market-share 0.15
 --n-days 100
 --population 3600000
 --recovered 0

src/penn_chime/cli.py

@@ -9,7 +9,7 @@
 
 def main():
     """Main."""
-    p = Parameters.create(os.environ, sys.argv)
+    p = Parameters.create(os.environ, sys.argv[1:])
     m = Model(p)
 
     for df, name in (

src/penn_chime/parameters.py

@@ -67,8 +67,8 @@ class Disposition(_Disposition):
     @classmethod
     def create(cls, *, days: int, rate: float):
         """Mandate key word arguments."""
-        Positive(key='days', value=days)
-        Rate(key='rate', value=rate)
+        Positive(key="days", value=days)
+        Rate(key="rate", value=rate)
         return cls(days, rate)
 
 
@@ -124,8 +124,6 @@ def validate(string):
     "current_date": (OptionalDate, cast_date, "Date on which the forecast should be based"),
     "date_first_hospitalized": (OptionalDate, cast_date, "Date the first patient was hospitalized"),
     "doubling_time": (OptionalStrictlyPositive, float, "Doubling time before social distancing (days)"),
-    "hospitalized": (ValDisposition, None, None),
-    "icu": (ValDisposition, None, None),
     "infectious_days": (StrictlyPositive, int, "Infectious days"),
     "mitigation_date": (OptionalDate, cast_date, "Date on which social distancing measures too effect"),
     "market_share": (Rate, float, "Hospital market share (0.00001 - 1.0)"),
@@ -136,16 +134,166 @@ def validate(string):
     "region": (OptionalValue, None, "No help available"),
     "relative_contact_rate": (Rate, float, "Social distancing reduction rate: 0.0 - 1.0"),
     "ventilated": (ValDisposition, None, None),
+    "hospitalized": (ValDisposition, None, None),
+    "icu": (ValDisposition, None, None),
 }
 
 
-class FromFile(Action):
-    """From File."""
-
-    def __call__(self, parser, namespace, values, option_string=None):
-        logger.info('Using file: %s', values)
-        with values as f:
-            parser.parse_args(f.read().split(), namespace)
+def cli_args():
+    return (
+        (
+            "parameters",
+            str,
+            None,
+            None,
+            "Parameters file.",
+            False,
+        ),
+        (
+            "current_hospitalized",
+            int,
+            0,
+            None,
+            "Currently hospitalized COVID-19 patients (>= 0)",
+            True,
+        ),
+        (
+            "current_date",
+            cast_date,
+            None,
+            None,
+            "Current date (default is today)",
+            False,
+        ),
+        (
+            "date_first_hospitalized",
+            cast_date,
+            None,
+            None,
+            "Date of first hospitalization",
+            False,
+        ),
+        (
+            "doubling_time",
+            float,
+            0.0,
+            None,
+            "Doubling time before social distancing (days)",
+            True,
+        ),
+        (
+            "hospitalized_days",
+            int,
+            0,
+            None,
+            "Average hospital length of stay (in days)",
+            True,
+        ),
+        (
+            "hospitalized_rate",
+            float,
+            0.00001,
+            1.0,
+            "Hospitalized Rate: 0.00001 - 1.0",
+            True,
+        ),
+        (
+            "icu_days",
+            int,
+            0,
+            None,
+            "Average days in ICU",
+            True,
+        ),
+        (
+            "icu_rate",
+            float,
+            0.0,
+            1.0,
+            "ICU rate: 0.0 - 1.0",
+            True,
+        ),
+        (
+            "market_share",
+            float,
+            0.00001,
+            1.0,
+            "Hospital market share (0.00001 - 1.0)",
+            True,
+        ),
+        (
+            "infectious_days",
+            int,
+            0.0,
+            None,
+            "Infectious days",
+            True,
+        ),
+        (
+            "mitigation_date",
+            cast_date,
+            None,
+            None,
+            "Mitigation date for social distancing.",
+            False,
+        ),
+        (
+            "max_y_axis",
+            int,
+            0,
+            None,
+            "Maximum y axis",
+            True,
+        ),
+        (
+            "n-days",
+            int,
+            0,
+            None,
+            "Number of days to project >= 0",
+            True,
+        ),
+        (
+            "recovered",
+            int,
+            0,
+            None,
+            "Initial recovered >= 0",
+            True,
+        ),
+        (
+            "relative-contact-rate",
+            float,
+            0.0,
+            1.0,
+            "Social distancing reduction rate: 0.0 - 1.0",
+            True,
+        ),
+        (
+            "population",
+            int,
+            1,
+            None,
+            "Regional population >= 1",
+            True,
+        ),
+        (
+            "ventilated_days",
+            int,
+            0,
+            None,
+            "Average days on ventilator",
+            True,
+        ),
+        (
+            "ventilated_rate",
+            float,
+            0.0,
+            1.0,
+            "Ventilated Rate: 0.0 - 1.0",
+            True,
+        ),
+    )
 
 
 def to_cli(name):
@@ -156,43 +304,11 @@ class Parameters:
     """Parameters."""
 
     @classmethod
-    def parser(cls, environ: Dict[str, str]):
+    def parser(cls):
         parser = ArgumentParser(
             description=f"penn_chime: {VERSION} {CHANGE_DATE}")
-        parser.add_argument(
-            "--parameters",
-            type=open,
-            action=FromFile,
-            default=environ.get("PARAMETERS"),
-            help='Parameters file.'
-        )
-
-        for name, (params_validator, cast, help) in ACCEPTED_PARAMETERS.items():
-            if cast is None:
-                continue
-
-            parser.add_argument(
-                to_cli(name),
-                type=declarative_validator(cast),
-                help=help
-            )
 
-        for name, cast, min_value, max_value, help, required in (
-            ("hospitalized_days", int, 0, None, "Average hospital length of stay (in days)", True),
-            (
-                "hospitalized_rate",
-                float,
-                0.00001,
-                1.0,
-                "Hospitalized Rate: 0.00001 - 1.0",
-                True,
-            ),
-            ("icu_days", int, 0, None, "Average days in ICU", True),
-            ("icu_rate", float, 0.0, 1.0, "ICU rate: 0.0 - 1.0", True),
-
-            ("ventilated_days", int, 0, None, "Average days on ventilator", True),
-            ("ventilated_rate", float, 0.0, 1.0, "Ventilated Rate: 0.0 - 1.0", True),
-        ):
+        for name, cast, min_value, max_value, help, required in cli_args():
             arg = to_cli(name)
             parser.add_argument(
                 arg,
@@ -204,14 +320,32 @@ def parser(cls, environ: Dict[str, str]):
     @classmethod
     def create(
         cls,
-        environ: Dict[str, str],
+        env: Dict[str, str],
         argv: List[str],
     ) -> Parameters:
-        parser = cls.parser(environ)
+        parser = cls.parser()
         a = parser.parse_args(argv)
 
+        if a.parameters is None:
+            a.parameters = env.get("PARAMETERS")
+
+        if a.parameters is not None:
+            logger.info('Using file: %s', a.parameters)
+            with open(a.parameters, 'r') as fin:
+                parser.parse_args(fin.read().split(), a)
+
         del a.parameters
 
+        logger.info(vars(a))
+
+        Positive(key='hospitalized_days', value=a.hospitalized_days)
+        Positive(key='icu_days', value=a.icu_days)
+        Positive(key='ventilated_days', value=a.ventilated_days)
+
+        Rate(key='hospitalized_rate', value=a.hospitalized_rate)
+        Rate(key='icu_rate', value=a.icu_rate)
+        Rate(key='ventilated_rate', value=a.ventilated_rate)
+
         hospitalized = Disposition.create(
             days=a.hospitalized_days,
             rate=a.hospitalized_rate,
@@ -239,7 +373,6 @@ def create(
             **vars(a),
         )
 
-
     def __init__(self, **kwargs):
         today = date.today()
 
@@ -272,7 +405,8 @@ def __init__(self, **kwargs):
             try:
                 validator(key=key, value=value)
             except TypeError as ve:
-                raise ValueError(f"For parameter '{key}', with value '{value}', validation returned error \"{ve}\"")
+                raise ValueError(
+                    f"For parameter '{key}', with value '{value}', validation returned error \"{ve}\"")
             setattr(self, key, value)
 
         if self.region is None and self.population is None:
@@ -282,7 +416,7 @@ def __init__(self, **kwargs):
             self.current_date = today
 
         if self.mitigation_date is None:
-            self.mitigation_Date = today
+            self.mitigation_date = today
 
         Date(key='current_date', value=self.current_date)
         Date(key='mitigation_date', value=self.mitigation_date)

src/penn_chime/presentation.py

@@ -353,19 +353,26 @@ def display_sidebar(st, d: Parameters) -> Parameters:
 
     return Parameters(
         current_hospitalized=current_hospitalized,
-        hospitalized=Disposition(hospitalized_rate, hospitalized_days),
-        icu=Disposition(icu_rate, icu_days),
-        relative_contact_rate=relative_contact_rate,
-        mitigation_date=mitigation_date,
-        ventilated=Disposition(ventilated_rate, ventilated_days),
         current_date=current_date,
         date_first_hospitalized=date_first_hospitalized,
         doubling_time=doubling_time,
+        hospitalized=Disposition.create(
+            rate=hospitalized_rate,
+            days=hospitalized_days),
+        icu=Disposition.create(
+            rate=icu_rate,
+            days=icu_days),
         infectious_days=infectious_days,
         market_share=market_share,
         max_y_axis=max_y_axis,
+        mitigation_date=mitigation_date,
         n_days=n_days,
         population=population,
+        recovered=d.recovered,
+        relative_contact_rate=relative_contact_rate,
+        ventilated=Disposition.create(
+            rate=ventilated_rate,
+            days=ventilated_days),
     )