Merge pull request #1897 from cmu-delphi/release/indicators_v0.3.47_u…

…tils_v0.3.21

Release covidcast-indicators 0.3.47

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.46
+current_version = 0.3.47
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.20
+current_version = 0.3.21
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.3.20"
+__version__ = "0.3.21"

_delphi_utils_python/delphi_utils/runner.py

@@ -72,9 +72,13 @@ def run_indicator_pipeline(indicator_fn:  Callable[[Params], None],
     start = time.time()
     while time.time()-start < timer:
         if not t1.is_alive():
+            logger.info("Completed flash step",
+                    elapsed_time_in_seconds = round(time.time() - start, 2))
             break
-        time.sleep(10)
+        time.sleep(1)
     else:
+        logger.error(f"Flash step timed out ({timer} s), terminating",
+                elapsed_time_in_seconds = round(time.time() - start, 2))
         t1.terminate()
         t1.join()
     if validator:

_delphi_utils_python/delphi_utils/validator/dynamic.py

@@ -237,7 +237,9 @@ def check_min_allowed_max_date(self, max_date, geo_type, signal_type, report):
                 ValidationFailure("check_min_max_date",
                                   geo_type=geo_type,
                                   signal=signal_type,
-                                  message="date of most recent generated file seems too long ago"))
+                                  date=max_date,
+                                  message="date of most recent generated file seems too long ago "
+                                  f"({max_date} < {self.params.generation_date} - {min_thres})"))
 
         report.increment_total_checks()
 
@@ -263,7 +265,9 @@ def check_max_allowed_max_date(self, max_date, geo_type, signal_type, report):
                 ValidationFailure("check_max_max_date",
                                   geo_type=geo_type,
                                   signal=signal_type,
-                                  message="date of most recent generated file seems too recent"))
+                                  date=max_date,
+                                  message="date of most recent generated file seems too recent "
+                                  f"({max_date} > {self.params.generation_date} - {max_thres})"))
 
         report.increment_total_checks()
 
@@ -307,7 +311,9 @@ def create_dfs(self, geo_sig_df, api_df_or_error, checking_date, geo_type, signa
                                     signal_type,
                                     "test data for a given checking date-geo type-signal type"
                                     " combination is missing. Source data may be missing"
-                                    " for one or more dates"))
+                                    " for one or more dates "
+                                    f"({checking_date} < {self.params.generation_date} "
+                                    f"- {min_thres})"))
             return False
 
         # Reference dataframe runs backwards from the recent_cutoff_date
@@ -418,7 +424,9 @@ def check_max_date_vs_reference(self, df_to_test, df_to_reference, checking_date
                                   checking_date,
                                   geo_type,
                                   signal_type,
-                                  "reference df has days beyond the max date in the =df_to_test="))
+                                  "reference df has days beyond the max date in the =df_to_test= "
+                                  f"{df_to_test['time_value'].max()} < "
+                                  f"{df_to_reference['time_value'].max().date()}"))
 
         report.increment_total_checks()
 
@@ -459,7 +467,8 @@ def check_rapid_change_num_rows(self, df_to_test, df_to_reference, checking_date
                                   geo_type,
                                   signal_type,
                                   "Number of rows per day seems to have changed rapidly (reference "
-                                  "vs test data)"))
+                                  "vs test data); "
+                                  f"relative difference: {abs(compare_rows)} > 0.35"))
         report.increment_total_checks()
 
     def check_positive_negative_spikes(self, source_df, api_frames, geo, sig, report):

_delphi_utils_python/delphi_utils/validator/report.py

@@ -35,6 +35,8 @@ def __init__(self, errors_to_suppress: List[ValidationFailure],
             Warnings raised from validation execution
         unsuppressed_errors: List[Exception]
             Errors raised from validation failures not found in `self.errors_to_suppress`
+        elapsed_time_in_seconds: float
+            Elapsed time of validation run, rounded down
         """
         self.errors_to_suppress = errors_to_suppress
         self.data_source = data_source
@@ -44,6 +46,7 @@ def __init__(self, errors_to_suppress: List[ValidationFailure],
         self.raised_warnings = []
         self.unsuppressed_errors = []
         self.dry_run = dry_run
+        self.elapsed_time_in_seconds = -1
     # pylint: enable=R0902
 
     def add_raised_error(self, error):
@@ -68,6 +71,10 @@ def increment_total_checks(self):
         """Record a check."""
         self.total_checks += 1
 
+    def set_elapsed_time_in_seconds(self, time):
+        """Set elapsed runtime in seconds for later logging."""
+        self.elapsed_time_in_seconds = time
+
     def add_raised_warning(self, warning):
         """Add a warning to the report.
 
@@ -94,15 +101,17 @@ def log(self, logger=None):
                 checks_failed = len(self.unsuppressed_errors),
                 checks_suppressed = self.num_suppressed,
                 warnings = len(self.raised_warnings),
-                phase = "validation")
+                phase = "validation",
+                elapsed_time_in_seconds=self.elapsed_time_in_seconds)
         else:
             logger.info("Validation run unsuccessful",
                 data_source = self.data_source,
                 checks_run = self.total_checks,
                 checks_failed = len(self.unsuppressed_errors),
                 checks_suppressed = self.num_suppressed,
                 warnings = len(self.raised_warnings),
-                phase="validation")
+                phase="validation",
+                elapsed_time_in_seconds=self.elapsed_time_in_seconds)
         # Threshold for slack alerts if warnings are excessive,
         # Currently extremely strict, set by observation of 1 month's logs
         excessive_warnings = self.total_checks > 0 and \

_delphi_utils_python/delphi_utils/validator/static.py

@@ -178,17 +178,17 @@ def check_bad_geo_id_value(self, df_to_test, filename, geo_type, report):
             - report: ValidationReport; report where results are added
         """
         valid_geos = self._get_valid_geo_values(geo_type)
-        unexpected_geos = [geo for geo in df_to_test['geo_id']
-                           if geo.lower() not in valid_geos]
+        unexpected_geos = {geo for geo in df_to_test['geo_id']
+                           if geo.lower() not in valid_geos}
         if len(unexpected_geos) > 0:
             report.add_raised_error(
                 ValidationFailure(
                     "check_bad_geo_id_value",
                     filename=filename,
                     message=f"Unrecognized geo_ids (not in historical data) {unexpected_geos}"))
         report.increment_total_checks()
-        upper_case_geos = [
-            geo for geo in df_to_test['geo_id'] if geo.lower() != geo]
+        upper_case_geos = {
+            geo for geo in df_to_test['geo_id'] if geo.lower() != geo}
         if len(upper_case_geos) > 0:
             report.add_raised_warning(
                 ValidationFailure(
@@ -218,8 +218,8 @@ def find_all_unexpected_geo_ids(df_to_test, geo_regex, geo_type):
             if geo_type in numeric_geo_types:
                 # Check if geo_ids were stored as floats (contain decimal point) and
                 # contents before decimal match the specified regex pattern.
-                leftover = [geo[1] for geo in df_to_test["geo_id"].str.split(
-                    ".") if len(geo) > 1 and re.match(geo_regex, geo[0])]
+                leftover = {geo[1] for geo in df_to_test["geo_id"].str.split(
+                    ".") if len(geo) > 1 and re.match(geo_regex, geo[0])}
 
                 # If any floats found, remove decimal and anything after.
                 if len(leftover) > 0:
@@ -230,7 +230,7 @@ def find_all_unexpected_geo_ids(df_to_test, geo_regex, geo_type):
                         ValidationFailure(
                             "check_geo_id_type",
                             filename=nameformat,
-                            message="geo_ids saved as floats; strings preferred"))
+                            message=f"geo_ids saved as floats; strings preferred: {leftover}"))
 
             if geo_type in fill_len.keys():
                 # Left-pad with zeroes up to expected length. Fixes missing leading zeroes
@@ -281,29 +281,35 @@ def check_bad_val(self, df_to_test, nameformat, signal_type, report):
 
         if percent_option:
             if not df_to_test[(df_to_test['val'] > 100)].empty:
+                bad_values = df_to_test[(df_to_test['val'] > 100)]['val'].unique()
                 report.add_raised_error(
                     ValidationFailure(
                         "check_val_pct_gt_100",
                         filename=nameformat,
-                        message="val column can't have any cell greater than 100 for percents"))
+                        message="val column can't have any cell greater than 100 for percents; "
+                                f"invalid values: {bad_values}"))
 
             report.increment_total_checks()
 
         if proportion_option:
             if not df_to_test[(df_to_test['val'] > 100000)].empty:
+                bad_values = df_to_test[(df_to_test['val'] > 100000)]['val'].unique()
                 report.add_raised_error(
                     ValidationFailure("check_val_prop_gt_100k",
                                       filename=nameformat,
                                       message="val column can't have any cell greater than 100000 "
-                                              "for proportions"))
+                                              "for proportions; "
+                                              f"invalid values: {bad_values}"))
 
             report.increment_total_checks()
 
         if not df_to_test[(df_to_test['val'] < 0)].empty:
+            bad_values = df_to_test[(df_to_test['val'] < 0)]['val'].unique()
             report.add_raised_error(
                 ValidationFailure("check_val_lt_0",
                                   filename=nameformat,
-                                  message="val column can't have any cell smaller than 0"))
+                                  message="val column can't have any cell smaller than 0; "
+                                          f"invalid values: {bad_values}"))
 
         report.increment_total_checks()
 
@@ -346,10 +352,12 @@ def check_bad_se(self, df_to_test, nameformat, report):
             report.increment_total_checks()
 
             if df_to_test["se"].isnull().mean() > 0.5:
+                bad_mean = round(df_to_test["se"].isnull().mean() * 100, 2)
                 report.add_raised_error(
                     ValidationFailure("check_se_many_missing",
                                       filename=nameformat,
-                                      message='Recent se values are >50% NA'))
+                                      message='Recent se values are >50% NA: '
+                                              f'{bad_mean}%'))
 
             report.increment_total_checks()
 

_delphi_utils_python/delphi_utils/validator/validate.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Tools to validate CSV source data, including various check methods."""
+import time
 from .datafetcher import load_all_files
 from .dynamic import DynamicValidator
 from .errors import ValidationFailure
@@ -54,11 +55,13 @@ def validate(self):
         Returns:
             - ValidationReport collating the validation outcomes
         """
+        start_time = time.time()
         report = ValidationReport(self.suppressed_errors, self.data_source, self.dry_run)
         frames_list = load_all_files(self.export_dir, self.time_window.start_date,
                                      self.time_window.end_date)
         self.static_validation.validate(frames_list, report)
         # Dynamic Validation only performed when frames_list is populated
         if len(frames_list) > 0:
             self.dynamic_validation.validate(aggregate_frames(frames_list), report)
+        report.set_elapsed_time_in_seconds(round(time.time() - start_time, 2))
         return report

_delphi_utils_python/setup.py

@@ -27,7 +27,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.3.20",
+    version="0.3.21",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",

changehc/delphi_changehc/update_sensor.py

@@ -162,6 +162,8 @@ def geo_reindex(self, data):
                                                  date_col=Config.DATE_COL)
             # this line should be removed once the fix is implemented for megacounties
             data_frame = data_frame[~((data_frame['county'].str.len() > 5) | (data_frame['county'].str.contains('_')))]
+            # handle rogue \N:
+            data_frame = data_frame[data_frame['county'] != r'\N']
         elif geo == "state":
             data_frame = gmpr.replace_geocode(data, "fips", "state_id", new_col="state",
                                               date_col=Config.DATE_COL)

changehc/tests/test_update_sensor.py

@@ -89,9 +89,14 @@ def test_geo_reindex(self):
                 "fips": ['01001'] * 7 + ['04007'] * 6,
                 "den": [1000] * 7 + [2000] * 6,
                 "timestamp": [pd.Timestamp(f'03-{i}-2020') for i in range(1, 14)]})
+            if geo == "county": # test for rogue \N
+                row_contain_N = {"num": 700, "fips": r"\N", "den": 2000, "timestamp": pd.Timestamp("03-15-2020")}
+                test_data = test_data.append(row_contain_N, ignore_index=True)
             data_frame = su_inst.geo_reindex(test_data)
             assert data_frame.shape[0] == multiple*len(su_inst.fit_dates)
             assert (data_frame.sum(numeric_only=True) == (4200,19000)).all()
+            if geo == "county":
+                assert r'\N' not in data_frame.index.get_level_values('county')
 
     def test_update_sensor(self):
         """Tests that the sensors are properly updated."""

changehc/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

claims_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

doctor_visits/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

google_symptoms/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

hhs_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

nchs_mortality/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

nowcast/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

quidel_covidtest/delphi_quidel_covidtest/pull.py

@@ -2,6 +2,7 @@
 """Collect and process Quidel export files."""
 from os.path import join
 import os
+import time
 from datetime import datetime, timedelta
 import boto3
 
@@ -369,7 +370,7 @@ def check_export_start_date(export_start_date, export_end_date,
         return datetime(2020, 5, 26)
     return export_start_date
 
-def update_cache_file(df, _end_date, cache_dir):
+def update_cache_file(df, _end_date, cache_dir, logger):
     """
     Update cache file. Remove the old one, export the new one.
 
@@ -380,8 +381,14 @@ def update_cache_file(df, _end_date, cache_dir):
             The most recent date when the raw data is received
         cache_dir:
             ./cache where the cache file is stored
+        logger: logging.Logger
+            Structured logger.
     """
+    start_time = time.time()
     for fn in os.listdir(cache_dir):
         if ".csv" in fn:
             os.remove(join(cache_dir, fn))
     df.to_csv(join(cache_dir, "pulled_until_%s.csv") % _end_date.strftime("%Y%m%d"), index=False)
+    logger.info("Completed cache file update",
+                end_date = _end_date.strftime('%Y-%m-%d'),
+                elapsed_time_in_seconds = round(time.time() - start_time, 2))

quidel_covidtest/delphi_quidel_covidtest/run.py

@@ -121,6 +121,7 @@ def run_module(params: Dict[str, Any]):
         __name__, filename=params["common"].get("log_filename"),
         log_exceptions=params["common"].get("log_exceptions", True))
     stats = []
+    # Log at program exit in case of an exception, otherwise after successful completion
     atexit.register(log_exit, start_time, stats, logger)
     cache_dir = params["indicator"]["input_cache_dir"]
     export_dir = params["common"]["export_dir"]
@@ -223,4 +224,7 @@ def run_module(params: Dict[str, Any]):
 
     # Export the cache file if the pipeline runs successfully.
     # Otherwise, don't update the cache file
-    update_cache_file(df, _end_date, cache_dir)
+    update_cache_file(df, _end_date, cache_dir, logger)
+    # Log stats now instead of at program exit
+    atexit.unregister(log_exit)
+    log_exit(start_time, stats, logger)

quidel_covidtest/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47

sir_complainsalot/version.cfg

@@ -1 +1 @@
-current_version = 0.3.46
+current_version = 0.3.47