Merge pull request #274 from cmu-delphi/test-and-delete/jhu-nyc-support

Sanity check for linting

Author: krivard

ansible/templates/safegraph-params-prod.json.j2

@@ -0,0 +1,12 @@
+{
+  "static_file_dir": "./static",
+  "raw_data_dir": "/common/safegraph",
+  "export_dir": "./receiving",
+  "cache_dir": "./cache",
+  "n_core": "12",
+  "aws_access_key_id": "{{ safegraph_aws_access_key_id }}",
+  "aws_secret_access_key": "{{ safegraph_aws_secret_access_key }}",
+  "aws_default_region": "us-east-1",
+  "aws_endpoint": "https://s3.wasabisys.com",
+  "wip_signal": ""
+}

ansible/vars.yaml

@@ -11,4 +11,5 @@ pyenv_python_path: "/home/{{ runtime_user }}/.pyenv/versions/{{ python_version }
 google_health_api_key: "{{ vault_google_health_api_key }}"
 delphi_aws_access_key_id: "{{ vault_delphi_aws_access_key_id }}"
 delphi_aws_secret_access_key: "{{ vault_delphi_aws_secret_access_key }}"
-
+safegraph_aws_access_key_id: "{{ vault_safegraph_aws_access_key_id }}"
+safegraph_aws_secret_access_key: "{{ vault_safegraph_aws_secret_access_key }}"

ansible/vault.yaml

@@ -1,16 +1,22 @@
 $ANSIBLE_VAULT;1.1;AES256
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-6166646131623132393238336263623562373065643633310a663232373237396361623462613333
-62373663383565623263306539636431623230633065626363666531366662363065343066363031
-3738616663336665340a326138333634306137363837396366303861663064326333613662656630
-62306331646637326637363766366237663037306665343761643263646663316535343561623137
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-35663664396436313432376264316663326130306134326231303234393561643436623039613136
-63366638396262383762383336643930343661636461646162653734336334306239383132643435
-39333665643738643966356431333830646561353263353063326330643731616130396466343339
-39346437653063303336626663623835613938633834396430353634383366386237353862643766
-37393738353231666565303031393839306463373461393761653866653330646534393832303264
-30323038646166366465396235623731343539313633326539663966333437623733626131653437
-62326632656462383835656235373664366566343866383938343639613737623631616231616135
-633863383761366461363532353137323936
+39633436633363346633333638666438316131313337333132396634393538383432623239316463
+3435333238376331383439366161656639353039326163370a376363633535623363383233646533
+63363865646561323132663032383331346332373364333465643330616638623466333039623831
+6530663236313234360a336264656239383166663934303335386238386139386132626165386138
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+66353131373265373931366130383632633466363036373562363232663162333966316563373535
+65343336363732303132366335616335333334373063313562336330336661353239646533356461
+62313365633336613037626261353639323937363066363062356234653631346233373965636461
+63326237663537363338346566326232353632663463386135393535343436373335393430393865
+33393631623762636230656263363462346561323064653561393666373735313836666238323238
+66366564666266343636663666386566336637373036633966643961346636373066356632326464
+63336565656666336436383938346461646431353265353133633736363761623634346262616436
+61653633326333356330626638386665313865343233393637623662383634346534326537623662
+34326633623431343835346339656335386330333664373166313766366339663736376261343965
+63616461666230616131326537373130313239663931313330356538356161333537666237376362
+64613232333834303737323438616437303666643166383439393030316533343530363863613034
+39653761626439356133393164363561316535633230633438316137623333376633663665393634
+63333161376263613766353030616336386531303565346263366239653232333764

emr_hosp/delphi_emr_hosp/constants.py

@@ -0,0 +1,7 @@
+"""Registry for signal names and geo types"""
+SMOOTHED = "smoothed_covid19"
+SMOOTHED_ADJ = "smoothed_adj_covid19"
+SIGNALS = [SMOOTHED, SMOOTHED_ADJ]
+NA = "NA"
+HRR = "hrr"
+FIPS = "fips"

emr_hosp/delphi_emr_hosp/run.py

@@ -69,7 +69,6 @@ def run_module():
     logging.info("parallel:\t\t%s", params["parallel"])
     logging.info("weekday:\t\t%s", params["weekday"])
     logging.info("se:\t\t\t%s", params["se"])
-    logging.info("prefix:\t\t%s", params["obfuscated_prefix"])
 
     ## start generating
     for geo in params["geos"]:
@@ -85,8 +84,7 @@ def run_module():
                 geo,
                 params["parallel"],
                 weekday,
-                params["se"],
-                params["obfuscated_prefix"]
+                params["se"]
             )
             su_inst.update_sensor(
                 params["input_emr_file"],

emr_hosp/delphi_emr_hosp/update_sensor.py

@@ -1,49 +1,44 @@
 """
 Generate EMR-hosp sensors.
-
 Author: Maria Jahja
 Created: 2020-06-01
 """
-
 # standard packages
 import logging
 from datetime import timedelta
 from multiprocessing import Pool, cpu_count
+import covidcast
+from delphi_utils import read_params
 
 # third party
 import numpy as np
 import pandas as pd
-
 # first party
 from .config import Config, Constants
 from .geo_maps import GeoMaps
 from .load_data import load_combined_data
 from .sensor import EMRHospSensor
 from .weekday import Weekday
+from .constants import SIGNALS, SMOOTHED, SMOOTHED_ADJ, HRR, NA, FIPS
 
 from delphi_utils import GeoMapper
 
-
 def write_to_csv(output_dict, write_se, out_name, output_path="."):
     """Write sensor values to csv.
-
     Args:
         output_dict: dictionary containing sensor rates, se, unique dates, and unique geo_id
         write_se: boolean to write out standard errors, if true, use an obfuscated name
         out_name: name of the output file
         output_path: outfile path to write the csv (default is current directory)
     """
-
     if write_se:
         logging.info(f"========= WARNING: WRITING SEs TO {out_name} =========")
-
     geo_level = output_dict["geo_level"]
     dates = output_dict["dates"]
     geo_ids = output_dict["geo_ids"]
     all_rates = output_dict["rates"]
     all_se = output_dict["se"]
     all_include = output_dict["include"]
-
     out_n = 0
     for i, d in enumerate(dates):
         filename = "%s/%s_%s_%s.csv" % (
@@ -52,33 +47,83 @@ def write_to_csv(output_dict, write_se, out_name, output_path="."):
             geo_level,
             out_name,
         )
-
         with open(filename, "w") as outfile:
             outfile.write("geo_id,val,se,direction,sample_size\n")
-
             for geo_id in geo_ids:
                 sensor = all_rates[geo_id][i]
                 se = all_se[geo_id][i]
-
                 if all_include[geo_id][i]:
                     assert not np.isnan(sensor), "value for included sensor is nan"
                     assert not np.isnan(se), "se for included sensor is nan"
                     if sensor > 90:
                         logging.warning(f"value suspiciously high, {geo_id}: {sensor}")
                     assert se < 5, f"se suspiciously high, {geo_id}: {se}"
-
                     if write_se:
                         assert sensor > 0 and se > 0, "p=0, std_err=0 invalid"
                         outfile.write(
-                            "%s,%f,%s,%s,%s\n" % (geo_id, sensor, se, "NA", "NA"))
+                            "%s,%f,%s,%s,%s\n" % (geo_id, sensor, se, NA, NA))
                     else:
                         # for privacy reasons we will not report the standard error
                         outfile.write(
-                            "%s,%f,%s,%s,%s\n" % (geo_id, sensor, "NA", "NA", "NA")
+                            "%s,%f,%s,%s,%s\n" % (geo_id, sensor, NA, NA, NA)
                         )
                     out_n += 1
     logging.debug(f"wrote {out_n} rows for {len(geo_ids)} {geo_level}")
 
+
+def add_prefix(signal_names, wip_signal, prefix="wip_"):
+    """Adds prefix to signal if there is a WIP signal
+    Parameters
+    ----------
+    signal_names: List[str]
+        Names of signals to be exported
+    wip_signal : List[str] or bool
+        a list of wip signals: [], OR
+        all signals in the registry: True OR
+        only signals that have never been published: False
+    prefix : 'wip_'
+        prefix for new/non public signals
+    Returns
+    -------
+    List of signal names
+        wip/non wip signals for further computation
+    """
+    if wip_signal is True:
+        return [prefix + signal for signal in signal_names]
+    if isinstance(wip_signal, list):
+        make_wip = set(wip_signal)
+        return [
+            prefix + signal if signal in make_wip else signal
+            for signal in signal_names
+        ]
+    if wip_signal in {False, ""}:
+        return [
+            signal if public_signal(signal)
+            else prefix + signal
+            for signal in signal_names
+        ]
+    raise ValueError("Supply True | False or '' or [] | list()")
+
+
+def public_signal(signal_):
+    """Checks if the signal name is already public using COVIDcast
+    Parameters
+    ----------
+    signal_ : str
+        Name of the signal
+    Returns
+    -------
+    bool
+        True if the signal is present
+        False if the signal is not present
+    """
+    epidata_df = covidcast.metadata()
+    for index in range(len(epidata_df)):
+        if epidata_df['signal'][index] == signal_:
+            return True
+    return False
+
+
 class EMRHospSensorUpdator:
 
     def __init__(self,
@@ -88,10 +133,8 @@ def __init__(self,
                  geo,
                  parallel,
                  weekday,
-                 se,
-                 prefix=None):
+                 se):
         """Init Sensor Updator
-
         Args:
             startdate: first sensor date (YYYY-mm-dd)
             enddate: last sensor date (YYYY-mm-dd)
@@ -100,11 +143,8 @@ def __init__(self,
             parallel: boolean to run the sensor update in parallel
             weekday: boolean to adjust for weekday effects
             se: boolean to write out standard errors, if true, use an obfuscated name
-            prefix: string to prefix to output files (used for obfuscation in producing SEs)
-
         """
         self.startdate, self.enddate, self.dropdate = [pd.to_datetime(t) for t in (startdate, enddate, dropdate)]
-
         # handle dates
         assert (self.startdate > (Config.FIRST_DATA_DATE + Config.BURN_IN_PERIOD)
                 ), f"not enough data to produce estimates starting {self.startdate}"
@@ -114,32 +154,28 @@ def __init__(self,
         self.geo, self.parallel, self.weekday, self.se = geo.lower(), parallel, weekday, se
 
         # output file naming
-        out_name = "smoothed_adj_covid19" if self.weekday else "smoothed_covid19"
-        if se:
-            assert prefix is not None, "supply obfuscated prefix in params"
-            out_name = prefix + "_" + out_name
-        self.output_filename = out_name
-
+        signals = SIGNALS.copy()
+        signals.remove(SMOOTHED if self.weekday else SMOOTHED_ADJ)
+        signal_names = add_prefix(
+            signals,
+            wip_signal=read_params()["wip_signal"])
+        self.updated_signal_names = signal_names
 
     def shift_dates(self):
         """shift estimates forward to account for time lag, compute burnindates, sensordates
         """
-
         drange = lambda s, e: pd.date_range(start=s,periods=(e-s).days,freq='D')
         self.startdate = self.startdate - Config.DAY_SHIFT
         self.burnindate = self.startdate - Config.BURN_IN_PERIOD
         self.fit_dates = drange(Config.FIRST_DATA_DATE, self.dropdate)
         self.burn_in_dates = drange(self.burnindate, self.dropdate)
         self.sensor_dates = drange(self.startdate, self.enddate)
         return True
-
     def geo_reindex(self,data):
         """Reindex based on geography, include all date, geo pairs
-
         Args:
             data: dataframe, the output of loadcombineddata
             staticpath: path for the static geographic files
-
         Returns:
             dataframe
         """
@@ -157,92 +193,80 @@ def geo_reindex(self,data):
         else:
             logging.error(f"{geo} is invalid, pick one of 'county', 'state', 'msa', 'hrr'")
             return False
-
         self.unique_geo_ids = pd.unique(data_frame[geo])
         data_frame.set_index([geo,'date'],inplace=True)
-
         # for each location, fill in all missing dates with 0 values
         multiindex = pd.MultiIndex.from_product((self.unique_geo_ids, self.fit_dates),
                                                 names=[geo, "date"])
         assert (len(multiindex) <= (Constants.MAX_GEO[geo] * len(self.fit_dates))
                 ), "more loc-date pairs than maximum number of geographies x number of dates"
-
         # fill dataframe with missing dates using 0
         data_frame = data_frame.reindex(multiindex, fill_value=0)
         data_frame.fillna(0, inplace=True)
         return data_frame
 
 
+
     def update_sensor(self,
             emr_filepath,
             claims_filepath,
             outpath,
             staticpath):
         """Generate sensor values, and write to csv format.
-
         Args:
             emr_filepath: path to the aggregated EMR data
             claims_filepath: path to the aggregated claims data
             outpath: output path for the csv results
             staticpath: path for the static geographic files
         """
-
         self.shift_dates()
         final_sensor_idxs = (self.burn_in_dates >= self.startdate) & (self.burn_in_dates <= self.enddate)
 
         # load data
         ## JS: If the data is in fips then can we also put it into hrr?
         base_geo = "hrr" if self.geo == "hrr" else "fips"
+        base_geo = HRR if self.geo == HRR else FIPS
         data = load_combined_data(emr_filepath, claims_filepath, self.dropdate, base_geo)
 
         data.reset_index(inplace=True)
         data_frame = self.geo_reindex(data)
-
         # handle if we need to adjust by weekday
         wd_params = Weekday.get_params(data_frame) if self.weekday else None
-
         # run sensor fitting code (maybe in parallel)
         sensor_rates = {}
         sensor_se = {}
         sensor_include = {}
         if not self.parallel:
             for geo_id, sub_data in data_frame.groupby(level=0):
                 sub_data.reset_index(level=0,inplace=True)
-
                 if self.weekday:
                     sub_data = Weekday.calc_adjustment(wd_params, sub_data)
-
                 res = EMRHospSensor.fit(sub_data, self.burnindate, geo_id)
                 res = pd.DataFrame(res)
                 sensor_rates[geo_id] = np.array(res.loc[final_sensor_idxs,"rate"])
                 sensor_se[geo_id] = np.array(res.loc[final_sensor_idxs,"se"])
                 sensor_include[geo_id] = np.array(res.loc[final_sensor_idxs,"incl"])
-
         else:
             n_cpu = min(10, cpu_count())
             logging.debug(f"starting pool with {n_cpu} workers")
-
             with Pool(n_cpu) as pool:
                 pool_results = []
                 for geo_id, sub_data in data_frame.groupby(level=0,as_index=False):
                     sub_data.reset_index(level=0, inplace=True)
                     if self.weekday:
                         sub_data = Weekday.calc_adjustment(wd_params, sub_data)
-
                     pool_results.append(
                         pool.apply_async(
                             EMRHospSensor.fit, args=(sub_data, self.burnindate, geo_id,),
                         )
                     )
                 pool_results = [proc.get() for proc in pool_results]
-
                 for res in pool_results:
                     geo_id = res["geo_id"]
                     res = pd.DataFrame(res)
                     sensor_rates[geo_id] = np.array(res.loc[final_sensor_idxs, "rate"])
                     sensor_se[geo_id] = np.array(res.loc[final_sensor_idxs, "se"])
                     sensor_include[geo_id] = np.array(res.loc[final_sensor_idxs, "incl"])
-
         unique_geo_ids = list(sensor_rates.keys())
         output_dict = {
             "rates": sensor_rates,
@@ -254,6 +278,7 @@ def update_sensor(self,
         }
 
         # write out results
-        write_to_csv(output_dict, self.se, self.output_filename, outpath)
+        for signal in self.updated_signal_names:
+            write_to_csv(output_dict, self.se, signal, outpath)
         logging.debug(f"wrote files to {outpath}")
-        return True
+        return True