From 9d7d4c5d9717a65252e011ec922e7574418a4adf Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 20 Aug 2024 18:01:41 -0400 Subject: [PATCH 01/47] first implementation --- changehc/delphi_changehc/run.py | 34 +++++++++--------- changehc/delphi_changehc/update_sensor.py | 2 +- .../download_claims_ftp_files.py | 2 +- .../delphi_claims_hosp/modify_claims_drops.py | 2 +- claims_hosp/delphi_claims_hosp/run.py | 6 ++-- .../download_claims_ftp_files.py | 2 +- .../modify_claims_drops.py | 2 +- doctor_visits/delphi_doctor_visits/patch.py | 11 +++--- doctor_visits/delphi_doctor_visits/run.py | 36 ++++++++++--------- .../delphi_doctor_visits/update_sensor.py | 2 +- .../delphi_google_symptoms/date_utils.py | 2 +- .../delphi_google_symptoms/patch.py | 11 +++--- google_symptoms/delphi_google_symptoms/run.py | 7 ++-- nssp/delphi_nssp/run.py | 2 +- nwss_wastewater/delphi_nwss/run.py | 2 +- .../delphi_quidel_covidtest/pull.py | 6 ++-- 16 files changed, 68 insertions(+), 61 deletions(-) diff --git a/changehc/delphi_changehc/run.py b/changehc/delphi_changehc/run.py index 92a03e6c5..61c1f0e20 100644 --- a/changehc/delphi_changehc/run.py +++ b/changehc/delphi_changehc/run.py @@ -25,7 +25,7 @@ def retrieve_files(params, filedate, logger): if files["denom"] is None: ## download recent files from FTP server - logger.info("downloading recent files through SFTP") + logger.info("Downloading recent files through SFTP") download_counts(filedate, params["indicator"]["input_cache_dir"], params["indicator"]["ftp_conn"]) denom_file = "%s/%s_Counts_Products_Denom.dat.gz" % (params["indicator"]["input_cache_dir"],filedate) @@ -157,18 +157,20 @@ def run_module(params: Dict[str, Dict[str, Any]]): startdate, enddate = process_dates(params, startdate_dt, enddate_dt) - logger.info("generating signal and exporting to CSV", - first_sensor_date = startdate, - last_sensor_date = enddate, - drop_date = dropdate, - n_backfill_days = n_backfill_days, - n_waiting_days = n_waiting_days, - geos = params["indicator"]["geos"], - export_dir = params["common"]["export_dir"], - parallel = params["indicator"]["parallel"], - weekday = params["indicator"]["weekday"], - types = params["indicator"]["types"], - se = params["indicator"]["se"]) + logger.info( + "Generating signal and exporting to CSV", + first_sensor_date=startdate, + last_sensor_date=enddate, + drop_date=dropdate, + n_backfill_days=n_backfill_days, + n_waiting_days=n_waiting_days, + geos=params["indicator"]["geos"], + export_dir=params["common"]["export_dir"], + parallel=params["indicator"]["parallel"], + weekday=params["indicator"]["weekday"], + types=params["indicator"]["types"], + se=params["indicator"]["se"], + ) ## start generating stats = [] @@ -176,9 +178,9 @@ def run_module(params: Dict[str, Dict[str, Any]]): for numtype in params["indicator"]["types"]: for weekday in params["indicator"]["weekday"]: if weekday: - logger.info("starting weekday adj", geo = geo, numtype = numtype) + logger.info("Starting weekday adj", geo=geo, numtype=numtype) else: - logger.info("starting no adj", geo = geo, numtype = numtype) + logger.info("Starting no adj", geo=geo, numtype=numtype) su_inst = CHCSensorUpdater( startdate, enddate, @@ -211,7 +213,7 @@ def run_module(params: Dict[str, Dict[str, Any]]): ) stats.extend(more_stats) - logger.info("finished processing", geo = geo) + logger.info("Finished processing", geo=geo) elapsed_time_in_seconds = round(time.time() - start_time, 2) min_max_date = stats and min(s[0] for s in stats) diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index edae85517..6b77427dd 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -41,7 +41,7 @@ def write_to_csv(df, geo_level, write_se, day_shift, out_name, logger, output_pa assert df[suspicious_se_mask].empty, " se contains suspiciously large values" assert not df["se"].isna().any(), " se contains nan values" if write_se: - logger.info("========= WARNING: WRITING SEs TO {0} =========".format(out_name)) + logger.info("WARNING: WRITING SEs", filename=out_name) else: df["se"] = np.nan diff --git a/claims_hosp/delphi_claims_hosp/download_claims_ftp_files.py b/claims_hosp/delphi_claims_hosp/download_claims_ftp_files.py index 2ce093488..ee6e98286 100644 --- a/claims_hosp/delphi_claims_hosp/download_claims_ftp_files.py +++ b/claims_hosp/delphi_claims_hosp/download_claims_ftp_files.py @@ -57,7 +57,7 @@ def download(ftp_credentials, out_path, logger): """Pull the latest raw files.""" current_time = datetime.datetime.now() seconds_in_day = 24 * 60 * 60 - logger.info("starting download", time=current_time) + logger.info("Starting download") # open client client = paramiko.SSHClient() diff --git a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py index 0ab93ebcc..667274da8 100644 --- a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py +++ b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py @@ -57,5 +57,5 @@ def modify_and_write(data_path, logger, test_mode=False): dfs_list.append(dfs) else: dfs.to_csv(out_path, index=False) - logger.info(f"Wrote {out_path}") + logger.info(f"Wrote modified csv", filename=out_path) return files, dfs_list diff --git a/claims_hosp/delphi_claims_hosp/run.py b/claims_hosp/delphi_claims_hosp/run.py index 53c4cd33b..d64420b1f 100644 --- a/claims_hosp/delphi_claims_hosp/run.py +++ b/claims_hosp/delphi_claims_hosp/run.py @@ -116,9 +116,9 @@ def run_module(params): for geo in params["indicator"]["geos"]: for weekday in params["indicator"]["weekday"]: if weekday: - logger.info("starting weekday adj", geo = geo) + logger.info("Starting weekday adj", geo=geo) else: - logger.info("starting no weekday adj", geo = geo) + logger.info("Starting no weekday adj", geo=geo) signal_name = Config.signal_weekday_name if weekday else Config.signal_name if params["indicator"]["write_se"]: @@ -144,7 +144,7 @@ def run_module(params): ) max_dates.append(updater.output_dates[-1]) n_csv_export.append(len(updater.output_dates)) - logger.info("finished updating", geo = geo) + logger.info("Finished updating", geo=geo) # Remove all the raw files for fn in os.listdir(params["indicator"]["input_dir"]): diff --git a/doctor_visits/delphi_doctor_visits/download_claims_ftp_files.py b/doctor_visits/delphi_doctor_visits/download_claims_ftp_files.py index 9d51768be..6cb42364a 100644 --- a/doctor_visits/delphi_doctor_visits/download_claims_ftp_files.py +++ b/doctor_visits/delphi_doctor_visits/download_claims_ftp_files.py @@ -59,7 +59,7 @@ def download(ftp_credentials, out_path, logger, issue_date=None): else: current_time = datetime.datetime.strptime(issue_date, "%Y-%m-%d").replace(hour=23, minute=59, second=59) - logger.info("starting download", time=current_time) + logger.info("Starting download") seconds_in_day = 24 * 60 * 60 # open client diff --git a/doctor_visits/delphi_doctor_visits/modify_claims_drops.py b/doctor_visits/delphi_doctor_visits/modify_claims_drops.py index daed93d58..3900f68d7 100644 --- a/doctor_visits/delphi_doctor_visits/modify_claims_drops.py +++ b/doctor_visits/delphi_doctor_visits/modify_claims_drops.py @@ -48,5 +48,5 @@ def modify_and_write(f, logger, test_mode=False): if not test_mode: dfs.to_csv(out_path, index=False) - logger.info(f"Wrote {out_path}") + logger.info(f"Wrote modified csv", filename=out_path) return dfs diff --git a/doctor_visits/delphi_doctor_visits/patch.py b/doctor_visits/delphi_doctor_visits/patch.py index 32b6d308f..80ad7c518 100644 --- a/doctor_visits/delphi_doctor_visits/patch.py +++ b/doctor_visits/delphi_doctor_visits/patch.py @@ -45,16 +45,19 @@ def patch(): start_issue = datetime.strptime(params["patch"]["start_issue"], "%Y-%m-%d") end_issue = datetime.strptime(params["patch"]["end_issue"], "%Y-%m-%d") - logger.info(f"""Start patching {params["patch"]["patch_dir"]}""") - logger.info(f"""Start issue: {start_issue.strftime("%Y-%m-%d")}""") - logger.info(f"""End issue: {end_issue.strftime("%Y-%m-%d")}""") + logger.info( + "Start patching", + filename=params["patch"]["patch_dir"], + start_date=start_issue.strftime("%Y-%m-%d"), + end_date=end_issue.strftime("%Y-%m-%d"), + ) makedirs(params["patch"]["patch_dir"], exist_ok=True) current_issue = start_issue while current_issue <= end_issue: - logger.info(f"""Running issue {current_issue.strftime("%Y-%m-%d")}""") + logger.info("Running issue", issue_date=current_issue.strftime("%Y-%m-%d")) params["patch"]["current_issue"] = current_issue.strftime("%Y-%m-%d") diff --git a/doctor_visits/delphi_doctor_visits/run.py b/doctor_visits/delphi_doctor_visits/run.py index 3c941534a..f9c3c9fe3 100644 --- a/doctor_visits/delphi_doctor_visits/run.py +++ b/doctor_visits/delphi_doctor_visits/run.py @@ -88,32 +88,34 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements startdate_dt = enddate_dt - timedelta(days=n_backfill_days) enddate = str(enddate_dt.date()) startdate = str(startdate_dt.date()) - logger.info("drop date:\t\t%s", dropdate) - logger.info("first sensor date:\t%s", startdate) - logger.info("last sensor date:\t%s", enddate) - logger.info("n_backfill_days:\t%s", n_backfill_days) - logger.info("n_waiting_days:\t%s", n_waiting_days) + + logger.info( + "Loaded params", + startdate=startdate, + enddate=enddate, + dropdate=dropdate, + n_backfill_days=params["indicator"]["n_backfill_days"], + n_waiting_days=params["indicator"]["n_waiting_days"], + geos=params["indicator"]["geos"], + outpath=params["common"]["export_dir"], + parallel=params["indicator"]["parallel"], + weekday=params["indicator"]["weekday"], + write_se=params["indicator"]["write_se"], + prefix=prefix, + ) ## geographies geos = ["state", "msa", "hrr", "county", "hhs", "nation"] - - ## print out other vars - logger.info("outpath:\t\t%s", export_dir) - logger.info("parallel:\t\t%s", params["indicator"]["parallel"]) - logger.info("weekday:\t\t%s", params["indicator"]["weekday"]) - logger.info("write se:\t\t%s", se) - logger.info("obfuscated prefix:\t%s", prefix) - max_dates = [] n_csv_export = [] ## start generating for geo in geos: for weekday in params["indicator"]["weekday"]: if weekday: - logger.info("starting %s, weekday adj", geo) + logger.info("Starting with weekday adj", geo=geo) else: - logger.info("starting %s, no adj", geo) + logger.info("Starting with no adj", geo=geo) sensor = update_sensor( filepath=claims_file, startdate=startdate, @@ -137,8 +139,8 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements write_to_csv(sensor, geo, se, out_name, logger, export_dir) max_dates.append(sensor.date.max()) n_csv_export.append(sensor.date.unique().shape[0]) - logger.debug(f"wrote files to {export_dir}") - logger.info("finished updating", geo = geo) + logger.debug("Wrote files", filename=export_dir) + logger.info("Finished updating", geo=geo) # Remove all the raw files for fn in os.listdir(params["indicator"]["input_dir"]): diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index 125c0df18..d8ad9f48a 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -34,7 +34,7 @@ def write_to_csv(output_df: pd.DataFrame, geo_level, se, out_name, logger, outpu output_path: outfile path to write the csv (default is current directory) """ if se: - logger.info(f"========= WARNING: WRITING SEs TO {out_name} =========") + logger.info("Warning SE is enabled", filename=out_name) out_n = 0 for d in set(output_df["date"]): diff --git a/google_symptoms/delphi_google_symptoms/date_utils.py b/google_symptoms/delphi_google_symptoms/date_utils.py index ebfe5109a..2ad6244e9 100644 --- a/google_symptoms/delphi_google_symptoms/date_utils.py +++ b/google_symptoms/delphi_google_symptoms/date_utils.py @@ -98,7 +98,7 @@ def generate_num_export_days(params: Dict, logger) -> [int]: expected_date_diff += global_max_expected_lag if latest_date_diff > expected_date_diff: - logger.info(f"Missing dates from: {to_datetime(min(gs_metadata.max_time)).date()}") + logger.info("Missing date", date=to_datetime(min(gs_metadata.max_time)).date()) num_export_days = expected_date_diff diff --git a/google_symptoms/delphi_google_symptoms/patch.py b/google_symptoms/delphi_google_symptoms/patch.py index 01d099c4f..ac79394e4 100755 --- a/google_symptoms/delphi_google_symptoms/patch.py +++ b/google_symptoms/delphi_google_symptoms/patch.py @@ -58,16 +58,19 @@ def patch(params): issue_date = datetime.strptime(params["patch"]["start_issue"], "%Y-%m-%d") end_issue = datetime.strptime(params["patch"]["end_issue"], "%Y-%m-%d") - logger.info(f"""Start patching {params["patch"]["patch_dir"]}""") - logger.info(f"""Start issue: {issue_date.strftime("%Y-%m-%d")}""") - logger.info(f"""End issue: {end_issue.strftime("%Y-%m-%d")}""") + logger.info( + "Start patching", + filename=params["patch"]["patch_dir"], + start_date=issue_date.strftime("%Y-%m-%d"), + end_date=end_issue.strftime("%Y-%m-%d"), + ) makedirs(params["patch"]["patch_dir"], exist_ok=True) patch_dates = generate_patch_dates(params) while issue_date <= end_issue: - logger.info(f"""Running issue {issue_date.strftime("%Y-%m-%d")}""") + logger.info("Running issue", issue_date=issue_date.strftime("%Y-%m-%d")) # Output dir setup current_issue_yyyymmdd = issue_date.strftime("%Y%m%d") diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 8303a9a8a..4e75ec5c6 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,10 +80,7 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info("generating signal and exporting to CSV", - geo_res=geo_res, - metric=metric, - smoother=smoother) + logger.info("Generating signal and exporting to CSV", geo_res=geo_res, metric=metric, smoother=smoother) df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( @@ -96,7 +93,7 @@ def run_module(params, logger=None): df = df.reset_index() sensor_name = "_".join([smoother, "search"]) if len(df) == 0: - logger.info("No data for %s_%s_%s", geo_res, metric.lower(), sensor_name) + logger.info("No data for signal", signal=f"{geo_res}_{metric.lower()}_{sensor_name}") continue exported_csv_dates = create_export_csv( df, diff --git a/nssp/delphi_nssp/run.py b/nssp/delphi_nssp/run.py index 7c5a3ffac..ff83c1497 100644 --- a/nssp/delphi_nssp/run.py +++ b/nssp/delphi_nssp/run.py @@ -90,7 +90,7 @@ def run_module(params): for geo in GEOS: df = df_pull.copy() df["val"] = df[signal] - logger.info("Generating signal and exporting to CSV", metric=signal) + logger.info("Generating signal and exporting to CSV", signal=signal) if geo == "nation": df = df[df["geography"] == "United States"] df["geo_id"] = "us" diff --git a/nwss_wastewater/delphi_nwss/run.py b/nwss_wastewater/delphi_nwss/run.py index 378849ba5..13045fbfc 100644 --- a/nwss_wastewater/delphi_nwss/run.py +++ b/nwss_wastewater/delphi_nwss/run.py @@ -146,7 +146,7 @@ def run_module(params): df = generate_weights(df, sensor) for geo in GEOS: - logger.info("Generating signal and exporting to CSV", metric=sensor) + logger.info("Generating signal and exporting to CSV", geo=geo, sensor=sensor) if geo == "nation": agg_df = weighted_nation_sum(df, sensor) else: diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py index d9f23f2ec..d06a44ff3 100644 --- a/quidel_covidtest/delphi_quidel_covidtest/pull.py +++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py @@ -56,7 +56,7 @@ def get_from_s3(start_date, end_date, bucket, logger): seen_files = set() for search_date in [start_date + timedelta(days=x) for x in range(n_days)]: if search_date in s3_files.keys(): - logger.info(f"Pulling data received on {search_date.date()}") + logger.info("Pulling data received", search_date=search_date.date()) # Fetch data received on the same day for fn in s3_files[search_date]: @@ -110,11 +110,11 @@ def fix_date(df, logger): df.insert(2, "timestamp", df["TestDate"]) mask = df["TestDate"] <= df["StorageDate"] - logger.info(f"Removing {((len(df) - np.sum(mask)) * 100 / len(df)):.2f}% of unusual data") + logger.info("Removing unusual data", percent=((len(df) - np.sum(mask)) * 100 / len(df))) df = df[mask] mask = df["StorageDate"] - df["TestDate"] > pd.Timedelta(days=90) - logger.info(f"Fixing {(np.sum(mask) * 100 / len(df)):.2f}% of outdated data") + logger.info("Fixing outdated data", percent=(np.sum(mask) * 100 / len(df))) df["timestamp"].values[mask] = df["StorageDate"].values[mask] return df From 2c6623c05714330f81aaadd0df5531024ee1cac5 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 20 Aug 2024 18:13:55 -0400 Subject: [PATCH 02/47] found missing and making msg consistent --- claims_hosp/delphi_claims_hosp/run.py | 4 ++-- .../delphi_claims_hosp/update_indicator.py | 23 ++++++++----------- .../delphi_doctor_visits/update_sensor.py | 2 +- 3 files changed, 13 insertions(+), 16 deletions(-) diff --git a/claims_hosp/delphi_claims_hosp/run.py b/claims_hosp/delphi_claims_hosp/run.py index d64420b1f..b2718fed8 100644 --- a/claims_hosp/delphi_claims_hosp/run.py +++ b/claims_hosp/delphi_claims_hosp/run.py @@ -135,12 +135,12 @@ def run_module(params): params["indicator"]["parallel"], weekday, params["indicator"]["write_se"], - signal_name + signal_name, + logger, ) updater.update_indicator( claims_file, params["common"]["export_dir"], - logger, ) max_dates.append(updater.output_dates[-1]) n_csv_export.append(len(updater.output_dates)) diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index df3f3308f..beee5f958 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -28,8 +28,7 @@ class ClaimsHospIndicatorUpdater: # pylint: disable=too-many-instance-attributes, too-many-arguments # all variables are used - def __init__(self, startdate, enddate, dropdate, geo, parallel, weekday, - write_se, signal_name): + def __init__(self, startdate, enddate, dropdate, geo, parallel, weekday, write_se, signal_name, logger): """ Initialize updater for the claims-based hospitalization indicator. @@ -53,6 +52,7 @@ def __init__(self, startdate, enddate, dropdate, geo, parallel, weekday, # init in shift_dates, declared here for pylint self.burnindate, self.fit_dates, self.burn_in_dates, self.output_dates = \ [None] * 4 + self.logger = logger assert ( self.startdate > (Config.FIRST_DATA_DATE + Config.BURN_IN_PERIOD) @@ -114,9 +114,7 @@ def geo_reindex(self, data): elif self.geo == "hrr": data_frame = data # data is already adjusted in aggregation step above else: - logging.error( - "%s is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", - self.geo) + self.logger.error("%s is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", self.geo) return False unique_geo_ids = pd.unique(data_frame[self.geo]) @@ -133,7 +131,7 @@ def geo_reindex(self, data): data_frame.fillna(0, inplace=True) return data_frame - def update_indicator(self, input_filepath, outpath, logger): + def update_indicator(self, input_filepath, outpath): """ Generate and output indicator values. @@ -159,7 +157,7 @@ def update_indicator(self, input_filepath, outpath, logger): ["num"], Config.DATE_COL, [1, 1e5], - logger, + self.logger, ) if self.weekday else None @@ -182,7 +180,7 @@ def update_indicator(self, input_filepath, outpath, logger): valid_inds[geo_id] = np.array(res.loc[final_output_inds, "incl"]) else: n_cpu = min(Config.MAX_CPU_POOL, cpu_count()) - logging.debug("starting pool with %d workers", n_cpu) + self.logger.debug("Starting pool", n_cpu=n_cpu) with Pool(n_cpu) as pool: pool_results = [] for geo_id, sub_data in data_frame.groupby(level=0, as_index=False): @@ -217,7 +215,7 @@ def update_indicator(self, input_filepath, outpath, logger): } self.write_to_csv(output_dict, outpath) - logging.debug("wrote files to %s", outpath) + self.logger.debug("Wrote files", filename=outpath) def write_to_csv(self, output_dict, output_path="./receiving"): """ @@ -229,8 +227,7 @@ def write_to_csv(self, output_dict, output_path="./receiving"): """ if self.write_se: - logging.info("========= WARNING: WRITING SEs TO %s =========", - self.signal_name) + self.logger.info("WARNING: WRITING SEs", signal=self.signal_name) geo_level = output_dict["geo_level"] dates = output_dict["dates"] @@ -255,7 +252,7 @@ def write_to_csv(self, output_dict, output_path="./receiving"): assert not np.isnan(val), "value for included value is nan" assert not np.isnan(se), "se for included rate is nan" if val > 90: - logging.warning("value suspicious, %s: %d", geo_id, val) + self.logger.warning("value suspicious, %s: %d", geo=geo_id, value=val) assert se < 5, f"se suspicious, {geo_id}: {se}" if self.write_se: assert val > 0 and se > 0, "p=0, std_err=0 invalid" @@ -267,4 +264,4 @@ def write_to_csv(self, output_dict, output_path="./receiving"): "%s,%f,%s,%s,%s\n" % (geo_id, val, "NA", "NA", "NA")) out_n += 1 - logging.debug("wrote %d rows for %d %s", out_n, len(geo_ids), geo_level) + self.logger.debug("wrote %d rows for %d %s", out_n, len(geo_ids), geo_level) diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index d8ad9f48a..1da1e82a4 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -34,7 +34,7 @@ def write_to_csv(output_df: pd.DataFrame, geo_level, se, out_name, logger, outpu output_path: outfile path to write the csv (default is current directory) """ if se: - logger.info("Warning SE is enabled", filename=out_name) + logger.info("WARNING: WRITING SEs", filename=out_name) out_n = 0 for d in set(output_df["date"]): From b10f0e59188ed37af7996fb6ee24b6f55c7f219c Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 22 Aug 2024 10:35:06 -0400 Subject: [PATCH 03/47] suggested changes --- .../delphi_claims_hosp/modify_claims_drops.py | 2 +- claims_hosp/delphi_claims_hosp/update_indicator.py | 13 +++++++------ .../delphi_doctor_visits/modify_claims_drops.py | 2 +- doctor_visits/delphi_doctor_visits/patch.py | 8 ++++---- doctor_visits/delphi_doctor_visits/run.py | 13 ++++++------- google_symptoms/delphi_google_symptoms/patch.py | 8 ++++---- nssp/delphi_nssp/run.py | 2 +- nwss_wastewater/delphi_nwss/run.py | 2 +- quidel_covidtest/delphi_quidel_covidtest/pull.py | 2 +- 9 files changed, 26 insertions(+), 26 deletions(-) diff --git a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py index 667274da8..19a962884 100644 --- a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py +++ b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py @@ -57,5 +57,5 @@ def modify_and_write(data_path, logger, test_mode=False): dfs_list.append(dfs) else: dfs.to_csv(out_path, index=False) - logger.info(f"Wrote modified csv", filename=out_path) + logger.info("Wrote modified csv", filename=out_path) return files, dfs_list diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index beee5f958..4b052b9cf 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -7,7 +7,6 @@ """ # standard packages -import logging from multiprocessing import Pool, cpu_count # third party @@ -114,7 +113,9 @@ def geo_reindex(self, data): elif self.geo == "hrr": data_frame = data # data is already adjusted in aggregation step above else: - self.logger.error("%s is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", self.geo) + self.logger.error( + "geo is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", geo=self.geo + ) return False unique_geo_ids = pd.unique(data_frame[self.geo]) @@ -180,7 +181,7 @@ def update_indicator(self, input_filepath, outpath): valid_inds[geo_id] = np.array(res.loc[final_output_inds, "incl"]) else: n_cpu = min(Config.MAX_CPU_POOL, cpu_count()) - self.logger.debug("Starting pool", n_cpu=n_cpu) + self.logger.debug("Starting pool", n_workers=n_cpu) with Pool(n_cpu) as pool: pool_results = [] for geo_id, sub_data in data_frame.groupby(level=0, as_index=False): @@ -215,7 +216,7 @@ def update_indicator(self, input_filepath, outpath): } self.write_to_csv(output_dict, outpath) - self.logger.debug("Wrote files", filename=outpath) + self.logger.debug("Wrote files", directory=outpath) def write_to_csv(self, output_dict, output_path="./receiving"): """ @@ -252,7 +253,7 @@ def write_to_csv(self, output_dict, output_path="./receiving"): assert not np.isnan(val), "value for included value is nan" assert not np.isnan(se), "se for included rate is nan" if val > 90: - self.logger.warning("value suspicious, %s: %d", geo=geo_id, value=val) + self.logger.warning("value suspicious", geo=geo_id, value=val) assert se < 5, f"se suspicious, {geo_id}: {se}" if self.write_se: assert val > 0 and se > 0, "p=0, std_err=0 invalid" @@ -264,4 +265,4 @@ def write_to_csv(self, output_dict, output_path="./receiving"): "%s,%f,%s,%s,%s\n" % (geo_id, val, "NA", "NA", "NA")) out_n += 1 - self.logger.debug("wrote %d rows for %d %s", out_n, len(geo_ids), geo_level) + self.logger.debug("Wrote rows", num_rows=out_n, num_geo_ids=len(geo_ids), geo_level=geo_level) diff --git a/doctor_visits/delphi_doctor_visits/modify_claims_drops.py b/doctor_visits/delphi_doctor_visits/modify_claims_drops.py index 3900f68d7..3be9393e4 100644 --- a/doctor_visits/delphi_doctor_visits/modify_claims_drops.py +++ b/doctor_visits/delphi_doctor_visits/modify_claims_drops.py @@ -48,5 +48,5 @@ def modify_and_write(f, logger, test_mode=False): if not test_mode: dfs.to_csv(out_path, index=False) - logger.info(f"Wrote modified csv", filename=out_path) + logger.info("Wrote modified csv", filename=out_path) return dfs diff --git a/doctor_visits/delphi_doctor_visits/patch.py b/doctor_visits/delphi_doctor_visits/patch.py index 80ad7c518..32c62dd6b 100644 --- a/doctor_visits/delphi_doctor_visits/patch.py +++ b/doctor_visits/delphi_doctor_visits/patch.py @@ -46,10 +46,10 @@ def patch(): end_issue = datetime.strptime(params["patch"]["end_issue"], "%Y-%m-%d") logger.info( - "Start patching", - filename=params["patch"]["patch_dir"], - start_date=start_issue.strftime("%Y-%m-%d"), - end_date=end_issue.strftime("%Y-%m-%d"), + "Starting patching", + patch_directory=params["patch"]["patch_dir"], + start_issue=start_issue.strftime("%Y-%m-%d"), + end_issue=end_issue.strftime("%Y-%m-%d"), ) makedirs(params["patch"]["patch_dir"], exist_ok=True) diff --git a/doctor_visits/delphi_doctor_visits/run.py b/doctor_visits/delphi_doctor_visits/run.py index f9c3c9fe3..db7506660 100644 --- a/doctor_visits/delphi_doctor_visits/run.py +++ b/doctor_visits/delphi_doctor_visits/run.py @@ -90,17 +90,16 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements startdate = str(startdate_dt.date()) logger.info( - "Loaded params", + "Using params", startdate=startdate, enddate=enddate, dropdate=dropdate, - n_backfill_days=params["indicator"]["n_backfill_days"], - n_waiting_days=params["indicator"]["n_waiting_days"], - geos=params["indicator"]["geos"], - outpath=params["common"]["export_dir"], + n_backfill_days=n_backfill_days, + n_waiting_days=n_waiting_days, + outpath=export_dir, parallel=params["indicator"]["parallel"], weekday=params["indicator"]["weekday"], - write_se=params["indicator"]["write_se"], + write_se=se, prefix=prefix, ) @@ -139,7 +138,7 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements write_to_csv(sensor, geo, se, out_name, logger, export_dir) max_dates.append(sensor.date.max()) n_csv_export.append(sensor.date.unique().shape[0]) - logger.debug("Wrote files", filename=export_dir) + logger.debug("Wrote files", directory=export_dir) logger.info("Finished updating", geo=geo) # Remove all the raw files diff --git a/google_symptoms/delphi_google_symptoms/patch.py b/google_symptoms/delphi_google_symptoms/patch.py index ac79394e4..85df89394 100755 --- a/google_symptoms/delphi_google_symptoms/patch.py +++ b/google_symptoms/delphi_google_symptoms/patch.py @@ -59,10 +59,10 @@ def patch(params): end_issue = datetime.strptime(params["patch"]["end_issue"], "%Y-%m-%d") logger.info( - "Start patching", - filename=params["patch"]["patch_dir"], - start_date=issue_date.strftime("%Y-%m-%d"), - end_date=end_issue.strftime("%Y-%m-%d"), + "Starting patching", + patch_directory=params["patch"]["patch_dir"], + start_issue=issue_date.strftime("%Y-%m-%d"), + end_issue=end_issue.strftime("%Y-%m-%d"), ) makedirs(params["patch"]["patch_dir"], exist_ok=True) diff --git a/nssp/delphi_nssp/run.py b/nssp/delphi_nssp/run.py index ff83c1497..23fae9cdc 100644 --- a/nssp/delphi_nssp/run.py +++ b/nssp/delphi_nssp/run.py @@ -90,7 +90,7 @@ def run_module(params): for geo in GEOS: df = df_pull.copy() df["val"] = df[signal] - logger.info("Generating signal and exporting to CSV", signal=signal) + logger.info("Generating signal and exporting to CSV", geo=geo, signal=signal) if geo == "nation": df = df[df["geography"] == "United States"] df["geo_id"] = "us" diff --git a/nwss_wastewater/delphi_nwss/run.py b/nwss_wastewater/delphi_nwss/run.py index 13045fbfc..5104de7a1 100644 --- a/nwss_wastewater/delphi_nwss/run.py +++ b/nwss_wastewater/delphi_nwss/run.py @@ -146,7 +146,7 @@ def run_module(params): df = generate_weights(df, sensor) for geo in GEOS: - logger.info("Generating signal and exporting to CSV", geo=geo, sensor=sensor) + logger.info("Generating signal and exporting to CSV", geo=geo, signal=sensor) if geo == "nation": agg_df = weighted_nation_sum(df, sensor) else: diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py index d06a44ff3..09611225d 100644 --- a/quidel_covidtest/delphi_quidel_covidtest/pull.py +++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py @@ -56,7 +56,7 @@ def get_from_s3(start_date, end_date, bucket, logger): seen_files = set() for search_date in [start_date + timedelta(days=x) for x in range(n_days)]: if search_date in s3_files.keys(): - logger.info("Pulling data received", search_date=search_date.date()) + logger.info("Pulling data received on date", search_date=search_date.date()) # Fetch data received on the same day for fn in s3_files[search_date]: From a2339aed49ddd7ea42b5813eafc8828566562d9b Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 22 Aug 2024 14:08:21 -0400 Subject: [PATCH 04/47] suggested change and making params more consistent --- changehc/delphi_changehc/run.py | 6 +++--- claims_hosp/delphi_claims_hosp/update_indicator.py | 2 +- doctor_visits/delphi_doctor_visits/run.py | 8 ++++---- doctor_visits/delphi_doctor_visits/update_sensor.py | 2 +- google_symptoms/delphi_google_symptoms/run.py | 4 ++-- 5 files changed, 11 insertions(+), 11 deletions(-) diff --git a/changehc/delphi_changehc/run.py b/changehc/delphi_changehc/run.py index 61c1f0e20..9c15b221d 100644 --- a/changehc/delphi_changehc/run.py +++ b/changehc/delphi_changehc/run.py @@ -178,9 +178,9 @@ def run_module(params: Dict[str, Dict[str, Any]]): for numtype in params["indicator"]["types"]: for weekday in params["indicator"]["weekday"]: if weekday: - logger.info("Starting weekday adj", geo=geo, numtype=numtype) + logger.info("Starting weekday adj", geo_type=geo, numtype=numtype) else: - logger.info("Starting no adj", geo=geo, numtype=numtype) + logger.info("Starting no adj", geo_type=geo, numtype=numtype) su_inst = CHCSensorUpdater( startdate, enddate, @@ -213,7 +213,7 @@ def run_module(params: Dict[str, Dict[str, Any]]): ) stats.extend(more_stats) - logger.info("Finished processing", geo=geo) + logger.info("Finished processing", geo_type=geo) elapsed_time_in_seconds = round(time.time() - start_time, 2) min_max_date = stats and min(s[0] for s in stats) diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index 4b052b9cf..4ce116cc4 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -216,7 +216,7 @@ def update_indicator(self, input_filepath, outpath): } self.write_to_csv(output_dict, outpath) - self.logger.debug("Wrote files", directory=outpath) + self.logger.debug("Wrote files", export_dir=outpath) def write_to_csv(self, output_dict, output_path="./receiving"): """ diff --git a/doctor_visits/delphi_doctor_visits/run.py b/doctor_visits/delphi_doctor_visits/run.py index db7506660..711e1bddb 100644 --- a/doctor_visits/delphi_doctor_visits/run.py +++ b/doctor_visits/delphi_doctor_visits/run.py @@ -112,9 +112,9 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements for geo in geos: for weekday in params["indicator"]["weekday"]: if weekday: - logger.info("Starting with weekday adj", geo=geo) + logger.info("Starting with weekday adj", geo_type=geo) else: - logger.info("Starting with no adj", geo=geo) + logger.info("Starting with no adj", geo_type=geo) sensor = update_sensor( filepath=claims_file, startdate=startdate, @@ -138,8 +138,8 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements write_to_csv(sensor, geo, se, out_name, logger, export_dir) max_dates.append(sensor.date.max()) n_csv_export.append(sensor.date.unique().shape[0]) - logger.debug("Wrote files", directory=export_dir) - logger.info("Finished updating", geo=geo) + logger.debug("Wrote files", export_dir=export_dir) + logger.info("Finished updating", geo_type=geo) # Remove all the raw files for fn in os.listdir(params["indicator"]["input_dir"]): diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index 1da1e82a4..e41e7281f 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -64,7 +64,7 @@ def write_to_csv(output_df: pd.DataFrame, geo_level, se, out_name, logger, outpu outfile.write( "%s,%f,%s,%s,%s\n" % (geo_id, sensor, "NA", "NA", "NA")) out_n += 1 - logger.debug(f"wrote {out_n} rows for {geo_level}") + logger.debug(f"Wrote rows", num_rows=out_n, geo_type=geo_level) def update_sensor( diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 4e75ec5c6..994aad2e5 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,7 +80,7 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info("Generating signal and exporting to CSV", geo_res=geo_res, metric=metric, smoother=smoother) + logger.info("Generating signal and exporting to CSV", geo_type=geo_res, metric=metric, smoother=smoother) df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( @@ -93,7 +93,7 @@ def run_module(params, logger=None): df = df.reset_index() sensor_name = "_".join([smoother, "search"]) if len(df) == 0: - logger.info("No data for signal", signal=f"{geo_res}_{metric.lower()}_{sensor_name}") + logger.info("No data for signal", geo_type=geo_res, metric=metric, sensor=sensor_name) continue exported_csv_dates = create_export_csv( df, From 114feb08b55272a1cb7cfe52c0cef583142ff902 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 22 Aug 2024 14:12:47 -0400 Subject: [PATCH 05/47] more suggested change --- quidel_covidtest/delphi_quidel_covidtest/pull.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py index 09611225d..54fc76222 100644 --- a/quidel_covidtest/delphi_quidel_covidtest/pull.py +++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py @@ -110,11 +110,11 @@ def fix_date(df, logger): df.insert(2, "timestamp", df["TestDate"]) mask = df["TestDate"] <= df["StorageDate"] - logger.info("Removing unusual data", percent=((len(df) - np.sum(mask)) * 100 / len(df))) + logger.info("Removing unusual data", percent= "%.2f" % (len(df) - np.sum(mask)) * 100 / len(df)) df = df[mask] mask = df["StorageDate"] - df["TestDate"] > pd.Timedelta(days=90) - logger.info("Fixing outdated data", percent=(np.sum(mask) * 100 / len(df))) + logger.info("Fixing outdated data", percent="%.2f" % (np.sum(mask) * 100 / len(df))) df["timestamp"].values[mask] = df["StorageDate"].values[mask] return df From 43eff035f9975be36d4e6b50bcc5a18c5e1df47a Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 22 Aug 2024 15:32:20 -0400 Subject: [PATCH 06/47] test and fix tests --- claims_hosp/tests/test_update_indicator.py | 21 ++++++++++++------- .../delphi_doctor_visits/update_sensor.py | 2 +- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/claims_hosp/tests/test_update_indicator.py b/claims_hosp/tests/test_update_indicator.py index 1471be655..5ca527287 100644 --- a/claims_hosp/tests/test_update_indicator.py +++ b/claims_hosp/tests/test_update_indicator.py @@ -51,7 +51,8 @@ def test_shift_dates(self): self.parallel, self.weekday, self.write_se, - Config.signal_name + Config.signal_name, + TEST_LOGGER ) ## Test init assert updater.startdate.month == 2 @@ -72,7 +73,8 @@ def test_geo_reindex(self): self.parallel, self.weekday, self.write_se, - Config.signal_name + Config.signal_name, + TEST_LOGGER ) updater.shift_dates() data_frame = updater.geo_reindex(self.small_test_data.reset_index()) @@ -90,13 +92,13 @@ def test_update_indicator(self): self.parallel, self.weekday, self.write_se, - Config.signal_name + Config.signal_name, + TEST_LOGGER ) updater.update_indicator( DATA_FILEPATH, - td.name, - TEST_LOGGER + td.name ) assert len(os.listdir(td.name)) == len( @@ -112,7 +114,8 @@ def test_write_to_csv_results(self): self.parallel, self.weekday, self.write_se, - Config.signal_name + Config.signal_name, + TEST_LOGGER ) res0 = { @@ -192,7 +195,8 @@ def test_write_to_csv_with_se_results(self): self.parallel, True, True, - signal_name + signal_name, + TEST_LOGGER ) res0 = { @@ -243,7 +247,8 @@ def test_write_to_csv_wrong_results(self): self.parallel, self.weekday, self.write_se, - Config.signal_name + Config.signal_name, + TEST_LOGGER ) res0 = { diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index e41e7281f..28484ff67 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -64,7 +64,7 @@ def write_to_csv(output_df: pd.DataFrame, geo_level, se, out_name, logger, outpu outfile.write( "%s,%f,%s,%s,%s\n" % (geo_id, sensor, "NA", "NA", "NA")) out_n += 1 - logger.debug(f"Wrote rows", num_rows=out_n, geo_type=geo_level) + logger.debug("Wrote rows", num_rows=out_n, geo_type=geo_level) def update_sensor( From 0c60b41c303bac02ce07209e4859679427ce0ca9 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 22 Aug 2024 15:47:54 -0400 Subject: [PATCH 07/47] lint --- quidel_covidtest/delphi_quidel_covidtest/pull.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py index 54fc76222..0ce17c1d6 100644 --- a/quidel_covidtest/delphi_quidel_covidtest/pull.py +++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py @@ -110,11 +110,11 @@ def fix_date(df, logger): df.insert(2, "timestamp", df["TestDate"]) mask = df["TestDate"] <= df["StorageDate"] - logger.info("Removing unusual data", percent= "%.2f" % (len(df) - np.sum(mask)) * 100 / len(df)) + logger.info("Removing unusual data", percent= round((len(df) - np.sum(mask)) * 100 / len(df), 2)) df = df[mask] mask = df["StorageDate"] - df["TestDate"] > pd.Timedelta(days=90) - logger.info("Fixing outdated data", percent="%.2f" % (np.sum(mask) * 100 / len(df))) + logger.info("Fixing outdated data", percent=round((np.sum(mask) * 100 / len(df)), 2)) df["timestamp"].values[mask] = df["StorageDate"].values[mask] return df From a53c2f1517f98f7a0b5b1700bcaf88fef6ca6fa8 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 27 Aug 2024 10:11:46 -0400 Subject: [PATCH 08/47] lint --- quidel_covidtest/delphi_quidel_covidtest/pull.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py index 0ce17c1d6..560f89456 100644 --- a/quidel_covidtest/delphi_quidel_covidtest/pull.py +++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py @@ -110,7 +110,7 @@ def fix_date(df, logger): df.insert(2, "timestamp", df["TestDate"]) mask = df["TestDate"] <= df["StorageDate"] - logger.info("Removing unusual data", percent= round((len(df) - np.sum(mask)) * 100 / len(df), 2)) + logger.info("Removing unusual data", percent=round((len(df) - np.sum(mask)) * 100 / len(df), 2)) df = df[mask] mask = df["StorageDate"] - df["TestDate"] > pd.Timedelta(days=90) From 39f26a2a9b3a6e94f999cae7271714f3973bc01d Mon Sep 17 00:00:00 2001 From: aysim319 Date: Tue, 27 Aug 2024 11:34:52 -0400 Subject: [PATCH 09/47] Update doctor_visits/delphi_doctor_visits/run.py Co-authored-by: george --- doctor_visits/delphi_doctor_visits/run.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doctor_visits/delphi_doctor_visits/run.py b/doctor_visits/delphi_doctor_visits/run.py index 711e1bddb..2dccffc8c 100644 --- a/doctor_visits/delphi_doctor_visits/run.py +++ b/doctor_visits/delphi_doctor_visits/run.py @@ -96,7 +96,7 @@ def run_module(params, logger=None): # pylint: disable=too-many-statements dropdate=dropdate, n_backfill_days=n_backfill_days, n_waiting_days=n_waiting_days, - outpath=export_dir, + export_dir=export_dir, parallel=params["indicator"]["parallel"], weekday=params["indicator"]["weekday"], write_se=se, From 7262d2927db41a1ff03a14cbdcc5f09450941541 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 29 Aug 2024 15:49:38 -0400 Subject: [PATCH 10/47] suggested change --- google_symptoms/delphi_google_symptoms/run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 994aad2e5..9a3fc3cf9 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,7 +80,7 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info("Generating signal and exporting to CSV", geo_type=geo_res, metric=metric, smoother=smoother) + logger.info("Generating signal and exporting to CSV", signal=f"{geo_res}_{metric}_{sensor}") df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( @@ -93,7 +93,7 @@ def run_module(params, logger=None): df = df.reset_index() sensor_name = "_".join([smoother, "search"]) if len(df) == 0: - logger.info("No data for signal", geo_type=geo_res, metric=metric, sensor=sensor_name) + logger.info("No data for signal", signal=f"{geo_res}_{metric}_{sensor}") continue exported_csv_dates = create_export_csv( df, From 8033bd645b866484260917e54cd52a112326c13b Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 29 Aug 2024 15:55:13 -0400 Subject: [PATCH 11/47] suggested change --- google_symptoms/delphi_google_symptoms/run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 9a3fc3cf9..5e1ded703 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,7 +80,7 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info("Generating signal and exporting to CSV", signal=f"{geo_res}_{metric}_{sensor}") + logger.info("Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor}") df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( @@ -93,7 +93,7 @@ def run_module(params, logger=None): df = df.reset_index() sensor_name = "_".join([smoother, "search"]) if len(df) == 0: - logger.info("No data for signal", signal=f"{geo_res}_{metric}_{sensor}") + logger.info("No data for signal", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor}") continue exported_csv_dates = create_export_csv( df, From 43e19856a7181ffd72acfd7bb766395dfc076d2a Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 29 Aug 2024 15:56:47 -0400 Subject: [PATCH 12/47] suggested change --- google_symptoms/delphi_google_symptoms/run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 5e1ded703..4da021932 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,7 +80,7 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info("Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor}") + logger.info("Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor_name}") df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( @@ -93,7 +93,7 @@ def run_module(params, logger=None): df = df.reset_index() sensor_name = "_".join([smoother, "search"]) if len(df) == 0: - logger.info("No data for signal", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor}") + logger.info("No data for signal", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor_name}") continue exported_csv_dates = create_export_csv( df, From 68a56d8e10e52391a075b2120ecba9063f6cad7d Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 29 Aug 2024 15:57:03 -0400 Subject: [PATCH 13/47] suggested change --- google_symptoms/delphi_google_symptoms/run.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 4da021932..6b7acd337 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,7 +80,9 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info("Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor_name}") + logger.info( + "Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor_name}" + ) df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( From 49af0b894d1eef19259708c570d1f52cfc18db17 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Thu, 29 Aug 2024 17:56:59 -0400 Subject: [PATCH 14/47] suggested changes --- _delphi_utils_python/README.md | 10 +++++++++- _delphi_utils_python/delphi_utils/export.py | 3 +-- .../delphi_utils/flash_eval/eval_day.py | 3 +-- _delphi_utils_python/delphi_utils/runner.py | 5 +++-- google_symptoms/delphi_google_symptoms/run.py | 4 ++-- 5 files changed, 16 insertions(+), 9 deletions(-) diff --git a/_delphi_utils_python/README.md b/_delphi_utils_python/README.md index 0ac6350bf..efaebe18a 100644 --- a/_delphi_utils_python/README.md +++ b/_delphi_utils_python/README.md @@ -21,6 +21,14 @@ Source code can be found here: [https://github.com/cmu-delphi/covidcast-indicators/](https://github.com/cmu-delphi/covidcast-indicators/) ## Logger Usage +To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, the event argument (typically the first unnamed arg) should be a static string (to make filtering easier), and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument to the logger call (for use in filtering, thresholding, grouping, visualization, etc). + +### Commonly used argument: +- data_source +- geo_type +- signal +- issue_date +- filename Single-thread usage. @@ -28,7 +36,7 @@ Single-thread usage. from delphi_utils.logger import get_structured_logger logger = get_structured_logger('my_logger') -logger.info('Hello, world!') +logger.info('Hello', name="World") ``` Multi-thread usage. diff --git a/_delphi_utils_python/delphi_utils/export.py b/_delphi_utils_python/delphi_utils/export.py index 37f8faf98..bcf9130db 100644 --- a/_delphi_utils_python/delphi_utils/export.py +++ b/_delphi_utils_python/delphi_utils/export.py @@ -22,8 +22,7 @@ def filter_contradicting_missing_codes(df, sensor, metric, date, logger=None): for mask in masks: if not logger is None and df.loc[mask].size > 0: logger.info( - "Filtering contradictory missing code in " + - "{0}_{1}_{2}.".format(sensor, metric, date.strftime(format="%Y-%m-%d")) + "Filtering contradictory missing code", sensor=sensor, metric=metric, date=date.strftime(format="%Y-%m-%d") ) df = df.loc[~mask] elif logger is None and df.loc[mask].size > 0: diff --git a/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py b/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py index 660fca042..490c47f4e 100644 --- a/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py +++ b/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py @@ -153,8 +153,7 @@ def output(evd_ranking, day, lag, signal, logger): p_text += f"\t{start_link}|*{index}*, {'{:.2f}'.format(value)}>\n" else: break - name = f"Signal: {signal} Lag: {lag}" - logger.info(name, payload=p_text) + logger.info(f"Signal: {signal} Lag: {lag}", signal=signal, lag=lag, payload=p_text) def evd_ranking_fn(ts_streams, EVD_max, EVD_min): diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index abc28ba19..d9d0cfd24 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -51,6 +51,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], #Get version and indicator name for startup ind_name = indicator_fn.__module__.replace(".run", "") + #Check for version.cfg in indicator directory if os.path.exists("version.cfg"): with open("version.cfg") as ver_file: @@ -60,8 +61,8 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], current_version = str.strip(line) current_version = current_version.replace("current_version = ", "") #Logging - Starting Indicator - logger.info(f"Started {ind_name} with covidcast-indicators version {current_version}") - else: logger.info(f"Started {ind_name} without version.cfg") + logger.info(f"Started with covidcast-indicators", indicator_name=ind_name, current_version=current_version) + else: logger.info(f"Started without version.cfg", indicator_name=ind_name) indicator_fn(params) validator = validator_fn(params) diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index 6b7acd337..bfbaa8451 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -81,7 +81,7 @@ def run_module(params, logger=None): continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): logger.info( - "Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor_name}" + "Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{metric}_{sensor_name}" ) df = df_pull df["val"] = df[metric].astype(float) @@ -95,7 +95,7 @@ def run_module(params, logger=None): df = df.reset_index() sensor_name = "_".join([smoother, "search"]) if len(df) == 0: - logger.info("No data for signal", geo_type=geo_res, signal=f"{geo_res}_{metric}_{sensor_name}") + logger.info("No data for signal", geo_type=geo_res, signal=f"{metric}_{sensor_name}") continue exported_csv_dates = create_export_csv( df, From 539f0de864b4d8f9ee3a3c46f34b9527ec7e3ddd Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 30 Aug 2024 10:16:28 -0400 Subject: [PATCH 15/47] fixing order --- google_symptoms/delphi_google_symptoms/run.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/google_symptoms/delphi_google_symptoms/run.py b/google_symptoms/delphi_google_symptoms/run.py index bfbaa8451..8ad1d6d10 100644 --- a/google_symptoms/delphi_google_symptoms/run.py +++ b/google_symptoms/delphi_google_symptoms/run.py @@ -80,9 +80,8 @@ def run_module(params, logger=None): if len(df_pull) == 0: continue for metric, smoother in product(COMBINED_METRIC, SMOOTHERS): - logger.info( - "Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{metric}_{sensor_name}" - ) + sensor_name = "_".join([smoother, "search"]) + logger.info("Generating signal and exporting to CSV", geo_type=geo_res, signal=f"{metric}_{sensor_name}") df = df_pull df["val"] = df[metric].astype(float) df["val"] = df[["geo_id", "val"]].groupby( @@ -93,7 +92,6 @@ def run_module(params, logger=None): # Drop early entries where data insufficient for smoothing df = df.loc[~df["val"].isnull(), :] df = df.reset_index() - sensor_name = "_".join([smoother, "search"]) if len(df) == 0: logger.info("No data for signal", geo_type=geo_res, signal=f"{metric}_{sensor_name}") continue From 3bb80a96182814c51caf0ecaca76a6b822c0b598 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 30 Aug 2024 10:26:01 -0400 Subject: [PATCH 16/47] lint --- _delphi_utils_python/delphi_utils/export.py | 5 ++++- _delphi_utils_python/delphi_utils/runner.py | 5 +++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/export.py b/_delphi_utils_python/delphi_utils/export.py index bcf9130db..8ac5de48e 100644 --- a/_delphi_utils_python/delphi_utils/export.py +++ b/_delphi_utils_python/delphi_utils/export.py @@ -22,7 +22,10 @@ def filter_contradicting_missing_codes(df, sensor, metric, date, logger=None): for mask in masks: if not logger is None and df.loc[mask].size > 0: logger.info( - "Filtering contradictory missing code", sensor=sensor, metric=metric, date=date.strftime(format="%Y-%m-%d") + "Filtering contradictory missing code", + sensor=sensor, + metric=metric, + date=date.strftime(format="%Y-%m-%d"), ) df = df.loc[~mask] elif logger is None and df.loc[mask].size > 0: diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index d9d0cfd24..f511aa252 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -61,8 +61,9 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], current_version = str.strip(line) current_version = current_version.replace("current_version = ", "") #Logging - Starting Indicator - logger.info(f"Started with covidcast-indicators", indicator_name=ind_name, current_version=current_version) - else: logger.info(f"Started without version.cfg", indicator_name=ind_name) + logger.info("Started with covidcast-indicators", indicator_name=ind_name, current_version=current_version) + else: + logger.info("Started without version.cfg", indicator_name=ind_name) indicator_fn(params) validator = validator_fn(params) From 1ae613c04e4338ad38ffd05b98492cc097fa3dc5 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 30 Aug 2024 11:16:05 -0400 Subject: [PATCH 17/47] make change to test --- _delphi_utils_python/tests/test_export.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/_delphi_utils_python/tests/test_export.py b/_delphi_utils_python/tests/test_export.py index 3e72f1d7f..960fe1dba 100644 --- a/_delphi_utils_python/tests/test_export.py +++ b/_delphi_utils_python/tests/test_export.py @@ -323,12 +323,13 @@ def test_export_df_with_missingness(self, tmp_path): @mock.patch("delphi_utils.logger") def test_export_df_with_contradictory_missingness(self, mock_logger, tmp_path): - + sensor="test" + geo_res = "state" create_export_csv( df=self.DF3.copy(), export_dir=tmp_path, - geo_res="state", - sensor="test", + sensor=sensor, + geo_res=geo_res, logger=mock_logger ) assert set(listdir(tmp_path)) == set( @@ -339,8 +340,9 @@ def test_export_df_with_contradictory_missingness(self, mock_logger, tmp_path): ] ) assert pd.read_csv(join(tmp_path, "20200315_state_test.csv")).size > 0 + date_str = datetime.strftime(self.TIMES[0], "%Y-%m-%d") mock_logger.info.assert_called_once_with( - "Filtering contradictory missing code in test_None_2020-02-15." + "Filtering contradictory missing code", sensor=sensor, metric=None, date=date_str ) def test_export_sort(self, tmp_path): From 4d7a6d002c6fb9a85fef8ec76b33512b1001ae00 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 30 Aug 2024 12:43:16 -0400 Subject: [PATCH 18/47] rename argument --- claims_hosp/delphi_claims_hosp/modify_claims_drops.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py index 19a962884..3d046178b 100644 --- a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py +++ b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py @@ -57,5 +57,5 @@ def modify_and_write(data_path, logger, test_mode=False): dfs_list.append(dfs) else: dfs.to_csv(out_path, index=False) - logger.info("Wrote modified csv", filename=out_path) + logger.info("Wrote modified csv", output_path=out_path) return files, dfs_list From bd89a300930883bed9189b48687280d35d61abf3 Mon Sep 17 00:00:00 2001 From: aysim319 Date: Fri, 30 Aug 2024 13:58:07 -0400 Subject: [PATCH 19/47] Update _delphi_utils_python/README.md Co-authored-by: minhkhul <118945681+minhkhul@users.noreply.github.com> --- _delphi_utils_python/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/_delphi_utils_python/README.md b/_delphi_utils_python/README.md index efaebe18a..134743974 100644 --- a/_delphi_utils_python/README.md +++ b/_delphi_utils_python/README.md @@ -22,6 +22,7 @@ Source code can be found here: ## Logger Usage To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, the event argument (typically the first unnamed arg) should be a static string (to make filtering easier), and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument to the logger call (for use in filtering, thresholding, grouping, visualization, etc). +Note that for some older implementations, you might find historical info hidden in arguments that are no longer used currently. ### Commonly used argument: - data_source From d0859546abe67ca073c45c2766ef7bb2f9ddd16e Mon Sep 17 00:00:00 2001 From: aysim319 Date: Fri, 30 Aug 2024 14:11:38 -0400 Subject: [PATCH 20/47] Update _delphi_utils_python/README.md Co-authored-by: george --- _delphi_utils_python/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_delphi_utils_python/README.md b/_delphi_utils_python/README.md index 134743974..4f998406c 100644 --- a/_delphi_utils_python/README.md +++ b/_delphi_utils_python/README.md @@ -21,7 +21,7 @@ Source code can be found here: [https://github.com/cmu-delphi/covidcast-indicators/](https://github.com/cmu-delphi/covidcast-indicators/) ## Logger Usage -To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, the event argument (typically the first unnamed arg) should be a static string (to make filtering easier), and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument to the logger call (for use in filtering, thresholding, grouping, visualization, etc). +To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, the `event` argument (typically the first unnamed arg) should be a static string (to make filtering easier), and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument to the logger call (for use in filtering, thresholding, grouping, visualization, etc). Note that for some older implementations, you might find historical info hidden in arguments that are no longer used currently. ### Commonly used argument: From b35a91ee82064282442554d2c1df6ee7d34cf2bb Mon Sep 17 00:00:00 2001 From: aysim319 Date: Fri, 30 Aug 2024 14:13:11 -0400 Subject: [PATCH 21/47] Update _delphi_utils_python/delphi_utils/flash_eval/eval_day.py Co-authored-by: george --- _delphi_utils_python/delphi_utils/flash_eval/eval_day.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py b/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py index 490c47f4e..52bfbdc4c 100644 --- a/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py +++ b/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py @@ -153,7 +153,7 @@ def output(evd_ranking, day, lag, signal, logger): p_text += f"\t{start_link}|*{index}*, {'{:.2f}'.format(value)}>\n" else: break - logger.info(f"Signal: {signal} Lag: {lag}", signal=signal, lag=lag, payload=p_text) + logger.info(f"FLaSH: worth inspecting", signal=signal, lag=lag, payload=p_text) def evd_ranking_fn(ts_streams, EVD_max, EVD_min): From 3ddd35d7509f35a13a6711f585481a1ba9694a37 Mon Sep 17 00:00:00 2001 From: aysim319 Date: Fri, 30 Aug 2024 14:13:32 -0400 Subject: [PATCH 22/47] Update _delphi_utils_python/delphi_utils/runner.py Co-authored-by: george --- _delphi_utils_python/delphi_utils/runner.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index f511aa252..1e1e5f540 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -61,9 +61,9 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], current_version = str.strip(line) current_version = current_version.replace("current_version = ", "") #Logging - Starting Indicator - logger.info("Started with covidcast-indicators", indicator_name=ind_name, current_version=current_version) + logger.info("Started a covidcast-indicator", indicator_name=ind_name, current_version=current_version) else: - logger.info("Started without version.cfg", indicator_name=ind_name) + logger.info("Started a covidcast-indicator without version.cfg", indicator_name=ind_name) indicator_fn(params) validator = validator_fn(params) From 18f40af7b93aaa20b872b3acb1f6b1cca729c8d4 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 3 Sep 2024 09:26:33 -0400 Subject: [PATCH 23/47] suggested changes --- _delphi_utils_python/README.md | 6 ++---- _delphi_utils_python/tests/test_export.py | 2 +- claims_hosp/delphi_claims_hosp/modify_claims_drops.py | 2 +- claims_hosp/delphi_claims_hosp/run.py | 8 ++++---- claims_hosp/delphi_claims_hosp/update_indicator.py | 4 ++-- 5 files changed, 10 insertions(+), 12 deletions(-) diff --git a/_delphi_utils_python/README.md b/_delphi_utils_python/README.md index 4f998406c..63d9e70ff 100644 --- a/_delphi_utils_python/README.md +++ b/_delphi_utils_python/README.md @@ -21,10 +21,8 @@ Source code can be found here: [https://github.com/cmu-delphi/covidcast-indicators/](https://github.com/cmu-delphi/covidcast-indicators/) ## Logger Usage -To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, the `event` argument (typically the first unnamed arg) should be a static string (to make filtering easier), and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument to the logger call (for use in filtering, thresholding, grouping, visualization, etc). -Note that for some older implementations, you might find historical info hidden in arguments that are no longer used currently. -### Commonly used argument: +### Commonly used argument names: - data_source - geo_type - signal @@ -37,7 +35,7 @@ Single-thread usage. from delphi_utils.logger import get_structured_logger logger = get_structured_logger('my_logger') -logger.info('Hello', name="World") +logger.info('Hello', name='World') ``` Multi-thread usage. diff --git a/_delphi_utils_python/tests/test_export.py b/_delphi_utils_python/tests/test_export.py index 960fe1dba..c9c1f8483 100644 --- a/_delphi_utils_python/tests/test_export.py +++ b/_delphi_utils_python/tests/test_export.py @@ -323,7 +323,7 @@ def test_export_df_with_missingness(self, tmp_path): @mock.patch("delphi_utils.logger") def test_export_df_with_contradictory_missingness(self, mock_logger, tmp_path): - sensor="test" + sensor = "test" geo_res = "state" create_export_csv( df=self.DF3.copy(), diff --git a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py index 3d046178b..19a962884 100644 --- a/claims_hosp/delphi_claims_hosp/modify_claims_drops.py +++ b/claims_hosp/delphi_claims_hosp/modify_claims_drops.py @@ -57,5 +57,5 @@ def modify_and_write(data_path, logger, test_mode=False): dfs_list.append(dfs) else: dfs.to_csv(out_path, index=False) - logger.info("Wrote modified csv", output_path=out_path) + logger.info("Wrote modified csv", filename=out_path) return files, dfs_list diff --git a/claims_hosp/delphi_claims_hosp/run.py b/claims_hosp/delphi_claims_hosp/run.py index b2718fed8..a9752072c 100644 --- a/claims_hosp/delphi_claims_hosp/run.py +++ b/claims_hosp/delphi_claims_hosp/run.py @@ -116,9 +116,9 @@ def run_module(params): for geo in params["indicator"]["geos"]: for weekday in params["indicator"]["weekday"]: if weekday: - logger.info("Starting weekday adj", geo=geo) + logger.info("Starting weekday adj", geo_type=geo) else: - logger.info("Starting no weekday adj", geo=geo) + logger.info("Starting no weekday adj", geo_type=geo) signal_name = Config.signal_weekday_name if weekday else Config.signal_name if params["indicator"]["write_se"]: @@ -126,7 +126,7 @@ def run_module(params): "supply obfuscated prefix in params.json" signal_name = params["indicator"]["obfuscated_prefix"] + "_" + signal_name - logger.info("Updating signal name", signal_name = signal_name) + logger.info("Updating signal name", signal=signal_name) updater = ClaimsHospIndicatorUpdater( startdate, enddate, @@ -144,7 +144,7 @@ def run_module(params): ) max_dates.append(updater.output_dates[-1]) n_csv_export.append(len(updater.output_dates)) - logger.info("Finished updating", geo=geo) + logger.info("Finished updating", geo_type=geo) # Remove all the raw files for fn in os.listdir(params["indicator"]["input_dir"]): diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index 4ce116cc4..1ac75ebda 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -253,7 +253,7 @@ def write_to_csv(self, output_dict, output_path="./receiving"): assert not np.isnan(val), "value for included value is nan" assert not np.isnan(se), "se for included rate is nan" if val > 90: - self.logger.warning("value suspicious", geo=geo_id, value=val) + self.logger.warning("value suspicious", geo_type=geo_id, value=val) assert se < 5, f"se suspicious, {geo_id}: {se}" if self.write_se: assert val > 0 and se > 0, "p=0, std_err=0 invalid" @@ -265,4 +265,4 @@ def write_to_csv(self, output_dict, output_path="./receiving"): "%s,%f,%s,%s,%s\n" % (geo_id, val, "NA", "NA", "NA")) out_n += 1 - self.logger.debug("Wrote rows", num_rows=out_n, num_geo_ids=len(geo_ids), geo_level=geo_level) + self.logger.debug("Wrote rows", num_rows=out_n, num_geo_ids=len(geo_ids)) From 29c927ba88fae36cbe5868ac1495a530e766d4e6 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 3 Sep 2024 10:38:22 -0400 Subject: [PATCH 24/47] more suggeseted changes --- nssp/delphi_nssp/run.py | 2 +- nwss_wastewater/delphi_nwss/run.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nssp/delphi_nssp/run.py b/nssp/delphi_nssp/run.py index 23fae9cdc..dfd987f89 100644 --- a/nssp/delphi_nssp/run.py +++ b/nssp/delphi_nssp/run.py @@ -90,7 +90,7 @@ def run_module(params): for geo in GEOS: df = df_pull.copy() df["val"] = df[signal] - logger.info("Generating signal and exporting to CSV", geo=geo, signal=signal) + logger.info("Generating signal and exporting to CSV", geo_type=geo, signal=signal) if geo == "nation": df = df[df["geography"] == "United States"] df["geo_id"] = "us" diff --git a/nwss_wastewater/delphi_nwss/run.py b/nwss_wastewater/delphi_nwss/run.py index 5104de7a1..60bfc84c7 100644 --- a/nwss_wastewater/delphi_nwss/run.py +++ b/nwss_wastewater/delphi_nwss/run.py @@ -146,7 +146,7 @@ def run_module(params): df = generate_weights(df, sensor) for geo in GEOS: - logger.info("Generating signal and exporting to CSV", geo=geo, signal=sensor) + logger.info("Generating signal and exporting to CSV", geo_type=geo, signal=sensor) if geo == "nation": agg_df = weighted_nation_sum(df, sensor) else: From fc2fa46c99066dcb5364f427597101d5dfa8115c Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Wed, 4 Sep 2024 11:51:10 -0400 Subject: [PATCH 25/47] lint --- _delphi_utils_python/delphi_utils/flash_eval/eval_day.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py b/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py index 52bfbdc4c..3c8012803 100644 --- a/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py +++ b/_delphi_utils_python/delphi_utils/flash_eval/eval_day.py @@ -153,7 +153,7 @@ def output(evd_ranking, day, lag, signal, logger): p_text += f"\t{start_link}|*{index}*, {'{:.2f}'.format(value)}>\n" else: break - logger.info(f"FLaSH: worth inspecting", signal=signal, lag=lag, payload=p_text) + logger.info("FLaSH: worth inspecting", signal=signal, lag=lag, payload=p_text) def evd_ranking_fn(ts_streams, EVD_max, EVD_min): From d0ef8aa37ce4bc8dba469d65e36ce366574a8c12 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 6 Sep 2024 10:25:28 -0400 Subject: [PATCH 26/47] lint --- claims_hosp/delphi_claims_hosp/update_indicator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index 1ac75ebda..cc9e1b59a 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -114,7 +114,7 @@ def geo_reindex(self, data): data_frame = data # data is already adjusted in aggregation step above else: self.logger.error( - "geo is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", geo=self.geo + "geo is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", geo_type=self.geo ) return False From dd9e5fcde86ffd9f4a61cc2a64a7901ff31c2d5d Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 6 Sep 2024 10:29:26 -0400 Subject: [PATCH 27/47] suggested change --- claims_hosp/delphi_claims_hosp/update_indicator.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index cc9e1b59a..f6e9db522 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -253,7 +253,7 @@ def write_to_csv(self, output_dict, output_path="./receiving"): assert not np.isnan(val), "value for included value is nan" assert not np.isnan(se), "se for included rate is nan" if val > 90: - self.logger.warning("value suspicious", geo_type=geo_id, value=val) + self.logger.warning("value suspicious", geo_type=geo_level, geo_value=geo_id, value=val) assert se < 5, f"se suspicious, {geo_id}: {se}" if self.write_se: assert val > 0 and se > 0, "p=0, std_err=0 invalid" @@ -265,4 +265,4 @@ def write_to_csv(self, output_dict, output_path="./receiving"): "%s,%f,%s,%s,%s\n" % (geo_id, val, "NA", "NA", "NA")) out_n += 1 - self.logger.debug("Wrote rows", num_rows=out_n, num_geo_ids=len(geo_ids)) + self.logger.debug("Wrote rows", num_rows=out_n, geo_type=geo_level, num_geo_ids=len(geo_ids)) From 5a27f338e8740a7e98c66166688b66619b0318f2 Mon Sep 17 00:00:00 2001 From: aysim319 Date: Fri, 6 Sep 2024 14:00:17 -0400 Subject: [PATCH 28/47] Update _delphi_utils_python/README.md Co-authored-by: george --- _delphi_utils_python/README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_delphi_utils_python/README.md b/_delphi_utils_python/README.md index 63d9e70ff..e1b091cae 100644 --- a/_delphi_utils_python/README.md +++ b/_delphi_utils_python/README.md @@ -22,6 +22,8 @@ Source code can be found here: ## Logger Usage +To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, the `event` argument (typically the first unnamed arg) should be a static string (to make filtering easier), and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument to the logger call (for use in filtering, thresholding, grouping, visualization, etc). + ### Commonly used argument names: - data_source - geo_type From 6db7d611149cc5d70ff2f8053462c4984b3fa20c Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 6 Sep 2024 14:04:57 -0400 Subject: [PATCH 29/47] suggesed changes --- _delphi_utils_python/delphi_utils/runner.py | 2 +- changehc/delphi_changehc/update_sensor.py | 8 +++----- doctor_visits/delphi_doctor_visits/update_sensor.py | 2 +- doctor_visits/tests/receiving/.gitignore | 1 - quidel_covidtest/delphi_quidel_covidtest/run.py | 2 +- 5 files changed, 6 insertions(+), 9 deletions(-) delete mode 100644 doctor_visits/tests/receiving/.gitignore diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index 1e1e5f540..58057382c 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -79,7 +79,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], break time.sleep(1) else: - logger.error(f"Flash step timed out ({timer} s), terminating", + logger.error("Flash step timed out, terminating", elapsed_time_in_seconds = round(time.time() - start, 2)) t1.terminate() t1.join() diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index 6b77427dd..42ad346ef 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -62,10 +62,8 @@ def write_to_csv(df, geo_level, write_se, day_shift, out_name, logger, output_pa sensor=out_name, write_empty_days=True ) - logger.debug("wrote {0} rows for {1} {2}".format( - df.size, df["geo_id"].unique().size, geo_level - )) - logger.debug("wrote files to {0}".format(output_path)) + logger.debug("Wrote rows", num_rows=df.size, geo_type=geo_level) + logger.debug("Wrote files", file_name=output_path) return dates @@ -224,7 +222,7 @@ def update_sensor(self, dfs.append(res) else: n_cpu = min(10, cpu_count()) - self.logger.debug("starting pool with {0} workers".format(n_cpu)) + self.logger.debug("Starting pool", n_worker=n_cpu) with Pool(n_cpu) as pool: pool_results = [] for geo_id, sub_data in data_frame.groupby(level=0,as_index=False): diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index 28484ff67..4f6ba0057 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -177,7 +177,7 @@ def update_sensor( else: n_cpu = min(10, cpu_count()) - logger.debug(f"starting pool with {n_cpu} workers") + logger.debug(f"Starting pool", n_workers=n_cpu) with Pool(n_cpu) as pool: pool_results = [] diff --git a/doctor_visits/tests/receiving/.gitignore b/doctor_visits/tests/receiving/.gitignore deleted file mode 100644 index 16f2dc5fa..000000000 --- a/doctor_visits/tests/receiving/.gitignore +++ /dev/null @@ -1 +0,0 @@ -*.csv \ No newline at end of file diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py index a59e0c101..e6974b6aa 100644 --- a/quidel_covidtest/delphi_quidel_covidtest/run.py +++ b/quidel_covidtest/delphi_quidel_covidtest/run.py @@ -164,7 +164,7 @@ def run_module(params: Dict[str, Any]): n_cpu = min(8, cpu_count()) # for parallelization with pool_and_threadedlogger(logger, n_cpu) as (pool, threaded_logger): # for using loggers in multiple threads - logger.info("Parallelizing sensor generation", n_cpu=n_cpu) + logger.info("Parallelizing sensor generation", n_workers=n_cpu) pool_results = [] for geo_res in NONPARENT_GEO_RESOLUTIONS: geo_data, res_key = geo_map(geo_res, data) From 89e7245246e630346fb8d80a173ee2a566d1ea8d Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 6 Sep 2024 14:27:14 -0400 Subject: [PATCH 30/47] lint --- doctor_visits/delphi_doctor_visits/update_sensor.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index 4f6ba0057..4cac1e81c 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -177,7 +177,7 @@ def update_sensor( else: n_cpu = min(10, cpu_count()) - logger.debug(f"Starting pool", n_workers=n_cpu) + logger.debug("Starting pool", n_workers=n_cpu) with Pool(n_cpu) as pool: pool_results = [] From e050a51334cd2d26c072c0ccd0f689e7f5551193 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Fri, 6 Sep 2024 17:11:28 -0400 Subject: [PATCH 31/47] suggested changes --- _delphi_utils_python/delphi_utils/logger.py | 5 +++++ _delphi_utils_python/delphi_utils/runner.py | 3 +-- changehc/delphi_changehc/update_sensor.py | 6 +++--- doctor_visits/tests/receiving/.gitignore | 1 + 4 files changed, 10 insertions(+), 5 deletions(-) create mode 100644 doctor_visits/tests/receiving/.gitignore diff --git a/_delphi_utils_python/delphi_utils/logger.py b/_delphi_utils_python/delphi_utils/logger.py index c0e4502a8..4eaf703ee 100644 --- a/_delphi_utils_python/delphi_utils/logger.py +++ b/_delphi_utils_python/delphi_utils/logger.py @@ -1,5 +1,10 @@ """Structured logger utility for creating JSON logs. +To make our structured logging as useful as it can be, particularly within the context of how we use logs in Elastic, +the `event` argument (typically the first unnamed arg) should be a static string (to make filtering easier), +and each dynamic/varying value should be specified in an individual meaningfully- and consistently-named argument +to the logger call (for use in filtering, thresholding, grouping, visualization, etc) + See the delphi_utils README.md for usage examples. The Delphi group uses two ~identical versions of this file. diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index 58057382c..d8004abca 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -79,8 +79,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], break time.sleep(1) else: - logger.error("Flash step timed out, terminating", - elapsed_time_in_seconds = round(time.time() - start, 2)) + logger.error("Flash step timed out, terminating", elapsed_time_in_seconds=round(time.time() - start, 2)) t1.terminate() t1.join() if validator: diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index 42ad346ef..9a09bffd6 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -62,8 +62,8 @@ def write_to_csv(df, geo_level, write_se, day_shift, out_name, logger, output_pa sensor=out_name, write_empty_days=True ) - logger.debug("Wrote rows", num_rows=df.size, geo_type=geo_level) - logger.debug("Wrote files", file_name=output_path) + logger.debug("Wrote rows", num_rows=df.size, geo_type=geo_level, num_geo_ids=df["geo_id"].unique().size) + logger.debug("Wrote files", export_dir=output_path) return dates @@ -222,7 +222,7 @@ def update_sensor(self, dfs.append(res) else: n_cpu = min(10, cpu_count()) - self.logger.debug("Starting pool", n_worker=n_cpu) + self.logger.debug("Starting pool", n_workers=n_cpu) with Pool(n_cpu) as pool: pool_results = [] for geo_id, sub_data in data_frame.groupby(level=0,as_index=False): diff --git a/doctor_visits/tests/receiving/.gitignore b/doctor_visits/tests/receiving/.gitignore new file mode 100644 index 000000000..16f2dc5fa --- /dev/null +++ b/doctor_visits/tests/receiving/.gitignore @@ -0,0 +1 @@ +*.csv \ No newline at end of file From 37122f4c116fa407f76933db5700e7df519ab627 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Mon, 9 Sep 2024 16:15:10 -0400 Subject: [PATCH 32/47] suggested changes --- changehc/delphi_changehc/update_sensor.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index 9a09bffd6..a915a7eb6 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -49,9 +49,7 @@ def write_to_csv(df, geo_level, write_se, day_shift, out_name, logger, output_pa suspicious_val_mask = df["val"].gt(90) if not df[suspicious_val_mask].empty: for geo in df.loc[suspicious_val_mask, "geo_id"]: - logger.warning("value suspiciously high, {0}: {1}".format( - geo, out_name - )) + logger.warning("value suspiciously high", geo_type=geo, filename=out_name) dates = create_export_csv( df, @@ -146,8 +144,8 @@ def geo_reindex(self, data): geo = self.geo gmpr = GeoMapper() if geo not in {"county", "state", "msa", "hrr", "nation", "hhs"}: - self.logger.error("{0} is invalid, pick one of 'county', " - "'state', 'msa', 'hrr', 'hss','nation'".format(geo)) + self.logger.error(f"{geo} is invalid, pick one of 'county', " + "'state', 'msa', 'hrr', 'hss','nation'", geo_type=geo) return False if geo == "county": data_frame = gmpr.fips_to_megacounty(data, From e8631f800794ea5b88083c23bdebb5a7bf784069 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 10:21:39 -0400 Subject: [PATCH 33/47] more changes --- _delphi_utils_python/delphi_utils/logger.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/logger.py b/_delphi_utils_python/delphi_utils/logger.py index 4eaf703ee..30fd78059 100644 --- a/_delphi_utils_python/delphi_utils/logger.py +++ b/_delphi_utils_python/delphi_utils/logger.py @@ -6,11 +6,6 @@ to the logger call (for use in filtering, thresholding, grouping, visualization, etc) See the delphi_utils README.md for usage examples. - -The Delphi group uses two ~identical versions of this file. -Try to keep them in sync with edits, for sanity. - https://github.com/cmu-delphi/covidcast-indicators/blob/main/_delphi_utils_python/delphi_utils/logger.py - https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/common/logger.py """ import contextlib From 7a31f8e0820f8dfed242e361a11d71a349698185 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 10:21:57 -0400 Subject: [PATCH 34/47] more changes --- changehc/delphi_changehc/update_sensor.py | 2 +- changehc/tests/test_update_sensor.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index a915a7eb6..4df326012 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -49,7 +49,7 @@ def write_to_csv(df, geo_level, write_se, day_shift, out_name, logger, output_pa suspicious_val_mask = df["val"].gt(90) if not df[suspicious_val_mask].empty: for geo in df.loc[suspicious_val_mask, "geo_id"]: - logger.warning("value suspiciously high", geo_type=geo, filename=out_name) + logger.warning("Value suspiciously high", geo_value=geo, filename=out_name) dates = create_export_csv( df, diff --git a/changehc/tests/test_update_sensor.py b/changehc/tests/test_update_sensor.py index 7ef25a608..d2e7ee2f3 100644 --- a/changehc/tests/test_update_sensor.py +++ b/changehc/tests/test_update_sensor.py @@ -9,6 +9,7 @@ import pandas as pd import numpy as np from boto3 import Session +from delphi_utils import get_structured_logger from moto import mock_s3 import pytest @@ -28,7 +29,7 @@ DENOM_FILEPATH = PARAMS["indicator"]["input_denom_file"] DROP_DATE = pd.to_datetime(PARAMS["indicator"]["drop_date"]) OUTPATH="test_data/" -TEST_LOGGER = logging.getLogger() +TEST_LOGGER = get_structured_logger() class TestCHCSensorUpdater: """Tests for updating the sensors.""" From 79b1ede34670edd7f2c91ba991ee715ed1cdaeee Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 12:16:25 -0400 Subject: [PATCH 35/47] lint --- changehc/delphi_changehc/update_sensor.py | 5 +++-- claims_hosp/delphi_claims_hosp/update_indicator.py | 4 ++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index 4df326012..f1337a464 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -144,8 +144,9 @@ def geo_reindex(self, data): geo = self.geo gmpr = GeoMapper() if geo not in {"county", "state", "msa", "hrr", "nation", "hhs"}: - self.logger.error(f"{geo} is invalid, pick one of 'county', " - "'state', 'msa', 'hrr', 'hss','nation'", geo_type=geo) + self.logger.error( + f"{geo} is invalid, pick one of 'county', " "'state', 'msa', 'hrr', 'hss','nation'", geo_type=geo + ) return False if geo == "county": data_frame = gmpr.fips_to_megacounty(data, diff --git a/claims_hosp/delphi_claims_hosp/update_indicator.py b/claims_hosp/delphi_claims_hosp/update_indicator.py index f6e9db522..5ba8ddd22 100644 --- a/claims_hosp/delphi_claims_hosp/update_indicator.py +++ b/claims_hosp/delphi_claims_hosp/update_indicator.py @@ -114,7 +114,7 @@ def geo_reindex(self, data): data_frame = data # data is already adjusted in aggregation step above else: self.logger.error( - "geo is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", geo_type=self.geo + "Geo is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', nation'", geo_type=self.geo ) return False @@ -253,7 +253,7 @@ def write_to_csv(self, output_dict, output_path="./receiving"): assert not np.isnan(val), "value for included value is nan" assert not np.isnan(se), "se for included rate is nan" if val > 90: - self.logger.warning("value suspicious", geo_type=geo_level, geo_value=geo_id, value=val) + self.logger.warning("Value suspicious", geo_type=geo_level, geo_value=geo_id, value=val) assert se < 5, f"se suspicious, {geo_id}: {se}" if self.write_se: assert val > 0 and se > 0, "p=0, std_err=0 invalid" From f8220a5735486a1c898d0634178ea740f2a97420 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 14:19:58 -0400 Subject: [PATCH 36/47] lint --- _delphi_utils_python/delphi_utils/runner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index d8004abca..0466d9bb6 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -60,7 +60,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], if "current_version" in line: current_version = str.strip(line) current_version = current_version.replace("current_version = ", "") - #Logging - Starting Indicator + # Logging - Starting Indicator logger.info("Started a covidcast-indicator", indicator_name=ind_name, current_version=current_version) else: logger.info("Started a covidcast-indicator without version.cfg", indicator_name=ind_name) From 3d44e679bdcdcc52892e9314b7de886567b0d53e Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 14:29:13 -0400 Subject: [PATCH 37/47] lint conflict --- _delphi_utils_python/delphi_utils/runner.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index 0466d9bb6..9e3bd487b 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -60,10 +60,16 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], if "current_version" in line: current_version = str.strip(line) current_version = current_version.replace("current_version = ", "") - # Logging - Starting Indicator - logger.info("Started a covidcast-indicator", indicator_name=ind_name, current_version=current_version) + #Logging - Starting Indicator + logger.info( + "Started a covidcast-indicator", + indicator_name=ind_name, + current_version=current_version + ) else: - logger.info("Started a covidcast-indicator without version.cfg", indicator_name=ind_name) + logger.info( + "Started a covidcast-indicator without version.cfg", indicator_name=ind_name + ) indicator_fn(params) validator = validator_fn(params) @@ -79,7 +85,9 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], break time.sleep(1) else: - logger.error("Flash step timed out, terminating", elapsed_time_in_seconds=round(time.time() - start, 2)) + logger.error("Flash step timed out, terminating", + elapsed_time_in_seconds=round(time.time() - start, 2) + ) t1.terminate() t1.join() if validator: From a3d0aabcf358c00a00da06b9cfad489c24b7d27c Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 14:39:44 -0400 Subject: [PATCH 38/47] lint --- _delphi_utils_python/delphi_utils/runner.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index 9e3bd487b..a824505a1 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -64,7 +64,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], logger.info( "Started a covidcast-indicator", indicator_name=ind_name, - current_version=current_version + current_version=current_version, ) else: logger.info( @@ -86,7 +86,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], time.sleep(1) else: logger.error("Flash step timed out, terminating", - elapsed_time_in_seconds=round(time.time() - start, 2) + elapsed_time_in_seconds=round(time.time() - start, 2), ) t1.terminate() t1.join() From 0b8d527a0660f764c203cc9631142138106f76b6 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 14:46:12 -0400 Subject: [PATCH 39/47] lint --- _delphi_utils_python/delphi_utils/runner.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index a824505a1..ceac6196a 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -87,7 +87,7 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], else: logger.error("Flash step timed out, terminating", elapsed_time_in_seconds=round(time.time() - start, 2), - ) + ) t1.terminate() t1.join() if validator: From 10df87ade0a117b50326acf1635fe8c5c9031433 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 10 Sep 2024 14:49:20 -0400 Subject: [PATCH 40/47] lint --- _delphi_utils_python/delphi_utils/runner.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index ceac6196a..731d501ed 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -85,8 +85,9 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], break time.sleep(1) else: - logger.error("Flash step timed out, terminating", - elapsed_time_in_seconds=round(time.time() - start, 2), + logger.error( + "Flash step timed out, terminating", + elapsed_time_in_seconds=round(time.time() - start, 2), ) t1.terminate() t1.join() From 9947332bf55b8cf0aab07046fb897a84ec5fbcb7 Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Wed, 11 Sep 2024 17:56:19 -0400 Subject: [PATCH 41/47] suggested changes --- changehc/delphi_changehc/sensor.py | 14 +++++++------- claims_hosp/delphi_claims_hosp/indicator.py | 11 +++++++---- doctor_visits/delphi_doctor_visits/sensor.py | 2 +- 3 files changed, 15 insertions(+), 12 deletions(-) diff --git a/changehc/delphi_changehc/sensor.py b/changehc/delphi_changehc/sensor.py index 0449f07df..effcf39bf 100644 --- a/changehc/delphi_changehc/sensor.py +++ b/changehc/delphi_changehc/sensor.py @@ -118,10 +118,10 @@ def fit(y_data, first_sensor_date, geo_id, logger, num_col="num", den_col="den") se_valid = valid_rates.eval('sqrt(rate * (1 - rate) / den)') rate_data['se'] = se_valid - logger.debug("{0}: {1:.3f},[{2:.3f}]".format( - geo_id, rate_data['rate'][-1], rate_data['se'][-1] - )) - return {"geo_id": geo_id, - "rate": 100 * rate_data['rate'], - "se": 100 * rate_data['se'], - "incl": include} + logger.debug( + "{0}: {1:.3f},[{2:.3f}]".format(geo_id, rate_data["rate"][-1], rate_data["se"][-1]), + geo_value=geo_id, + value=rate_data["rate"][-1], + se=rate_data["se"][-1], + ) + return {"geo_id": geo_id, "rate": 100 * rate_data["rate"], "se": 100 * rate_data["se"], "incl": include} diff --git a/claims_hosp/delphi_claims_hosp/indicator.py b/claims_hosp/delphi_claims_hosp/indicator.py index 4ad3ef7df..467772801 100644 --- a/claims_hosp/delphi_claims_hosp/indicator.py +++ b/claims_hosp/delphi_claims_hosp/indicator.py @@ -143,7 +143,10 @@ def fit(y_data, first_date, geo_id, num_col="num", den_col="den"): se_valid = valid_rates.eval('sqrt(rate * (1 - rate) / den)') rate_data['se'] = se_valid - logging.debug("%s: %05.3f, [%05.3f]", - geo_id, rate_data['rate'][-1], rate_data['se'][-1]) - return {"geo_id": geo_id, "rate": 100 * rate_data['rate'], - "se": 100 * rate_data['se'], "incl": include} + logging.debug( + "%s: %05.3f, [%05.3f]".format(geo_id, rate_data["rate"][-1], rate_data["se"][-1]), + geo_value=geo_id, + value=rate_data["rate"][-1], + se=rate_data["se"][-1], + ) + return {"geo_id": geo_id, "rate": 100 * rate_data["rate"], "se": 100 * rate_data["se"], "incl": include} diff --git a/doctor_visits/delphi_doctor_visits/sensor.py b/doctor_visits/delphi_doctor_visits/sensor.py index b5a645ea8..c9986d0ad 100644 --- a/doctor_visits/delphi_doctor_visits/sensor.py +++ b/doctor_visits/delphi_doctor_visits/sensor.py @@ -239,7 +239,7 @@ def fit(y_data, se[include] = np.sqrt( np.divide((new_rates[include] * (1 - new_rates[include])), den[include])) - logger.debug(f"{geo_id}: {new_rates[-1]:.3f},[{se[-1]:.3f}]") + logger.debug(f"{geo_id}: {new_rates[-1]:.3f},[{se[-1]:.3f}]", geo_value=geo_id, value=new_rates[-1], se=se[-1]) included_indices = [x for x in final_sensor_idxs if include[x]] From dcdbed827a17df44aaf5405f236ee7d02b63eb7d Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Wed, 11 Sep 2024 18:03:42 -0400 Subject: [PATCH 42/47] lint --- claims_hosp/delphi_claims_hosp/indicator.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/claims_hosp/delphi_claims_hosp/indicator.py b/claims_hosp/delphi_claims_hosp/indicator.py index 467772801..e2d9b48dc 100644 --- a/claims_hosp/delphi_claims_hosp/indicator.py +++ b/claims_hosp/delphi_claims_hosp/indicator.py @@ -144,7 +144,7 @@ def fit(y_data, first_date, geo_id, num_col="num", den_col="den"): rate_data['se'] = se_valid logging.debug( - "%s: %05.3f, [%05.3f]".format(geo_id, rate_data["rate"][-1], rate_data["se"][-1]), + f"{geo_id}: %05.3f, [%05.3f]".format(rate_data["rate"][-1], rate_data["se"][-1]), geo_value=geo_id, value=rate_data["rate"][-1], se=rate_data["se"][-1], From b0c31ae9795f5695d097703de6cf050010976a5b Mon Sep 17 00:00:00 2001 From: Amaris Sim Date: Tue, 17 Sep 2024 10:15:04 -0400 Subject: [PATCH 43/47] suggested changes --- _delphi_utils_python/delphi_utils/runner.py | 5 +- changehc/delphi_changehc/sensor.py | 2 +- changehc/delphi_changehc/update_sensor.py | 2 +- claims_hosp/delphi_claims_hosp/indicator.py | 2 +- doctor_visits/delphi_doctor_visits/sensor.py | 2 +- fluview/delphi_fluview/pull.py | 0 fluview/tests/conftest.py | 0 fluview/tests/test_data/flu_metadata.json | 14657 +++++++++++++++++ 8 files changed, 14662 insertions(+), 8 deletions(-) create mode 100644 fluview/delphi_fluview/pull.py create mode 100644 fluview/tests/conftest.py create mode 100644 fluview/tests/test_data/flu_metadata.json diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index 731d501ed..8e5912b06 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -60,16 +60,13 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], if "current_version" in line: current_version = str.strip(line) current_version = current_version.replace("current_version = ", "") - #Logging - Starting Indicator logger.info( "Started a covidcast-indicator", indicator_name=ind_name, current_version=current_version, ) else: - logger.info( - "Started a covidcast-indicator without version.cfg", indicator_name=ind_name - ) + logger.info("Started a covidcast-indicator without version.cfg", indicator_name=ind_name) indicator_fn(params) validator = validator_fn(params) diff --git a/changehc/delphi_changehc/sensor.py b/changehc/delphi_changehc/sensor.py index effcf39bf..9a1fd29e0 100644 --- a/changehc/delphi_changehc/sensor.py +++ b/changehc/delphi_changehc/sensor.py @@ -119,7 +119,7 @@ def fit(y_data, first_sensor_date, geo_id, logger, num_col="num", den_col="den") rate_data['se'] = se_valid logger.debug( - "{0}: {1:.3f},[{2:.3f}]".format(geo_id, rate_data["rate"][-1], rate_data["se"][-1]), + ".fit() DEBUG - last rate/se for geo", geo_value=geo_id, value=rate_data["rate"][-1], se=rate_data["se"][-1], diff --git a/changehc/delphi_changehc/update_sensor.py b/changehc/delphi_changehc/update_sensor.py index f1337a464..7c78dc020 100644 --- a/changehc/delphi_changehc/update_sensor.py +++ b/changehc/delphi_changehc/update_sensor.py @@ -145,7 +145,7 @@ def geo_reindex(self, data): gmpr = GeoMapper() if geo not in {"county", "state", "msa", "hrr", "nation", "hhs"}: self.logger.error( - f"{geo} is invalid, pick one of 'county', " "'state', 'msa', 'hrr', 'hss','nation'", geo_type=geo + "Geo is invalid, pick one of 'county', " "'state', 'msa', 'hrr', 'hss','nation'", geo_type=geo ) return False if geo == "county": diff --git a/claims_hosp/delphi_claims_hosp/indicator.py b/claims_hosp/delphi_claims_hosp/indicator.py index e2d9b48dc..c5ac4e886 100644 --- a/claims_hosp/delphi_claims_hosp/indicator.py +++ b/claims_hosp/delphi_claims_hosp/indicator.py @@ -144,7 +144,7 @@ def fit(y_data, first_date, geo_id, num_col="num", den_col="den"): rate_data['se'] = se_valid logging.debug( - f"{geo_id}: %05.3f, [%05.3f]".format(rate_data["rate"][-1], rate_data["se"][-1]), + ".fit() DEBUG - last rate/se for geo", geo_value=geo_id, value=rate_data["rate"][-1], se=rate_data["se"][-1], diff --git a/doctor_visits/delphi_doctor_visits/sensor.py b/doctor_visits/delphi_doctor_visits/sensor.py index c9986d0ad..91faa20cf 100644 --- a/doctor_visits/delphi_doctor_visits/sensor.py +++ b/doctor_visits/delphi_doctor_visits/sensor.py @@ -239,7 +239,7 @@ def fit(y_data, se[include] = np.sqrt( np.divide((new_rates[include] * (1 - new_rates[include])), den[include])) - logger.debug(f"{geo_id}: {new_rates[-1]:.3f},[{se[-1]:.3f}]", 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The volume of tested specimens has greatly increased during this time due to increased participation and increased testing. During the 1997-98 season 43 state public health laboratories participated in surveillance, and by the 2004-05 season all state public health laboratories were participating in surveillance. The addition of NREVSS data during the 1997-98 season roughly doubled the amount of virologic data reported each week.

The number of specimens tested and % positive rate vary by region and season based on different testing practices including triaging of specimens by the reporting labs, therefore it is not appropriate to compare the magnitude of positivity rates or the number of positive specimens between regions or seasons.

The U.S. WHO and NREVSS collaborating laboratories report the total number of respiratory specimens tested and the number positive for influenza types A and B each week to CDC. Most of the U.S. WHO collaborating laboratories also report the influenza A subtype (H1 or H3) of the viruses they have isolated, but the majority of NREVSS laboratories do not report the influenza A subtype.

For more information on virologic surveillance please visit:http://www.cdc.gov/flu/weekly/overview.htm#Viral

Outpatient Illness Surveillance — Information on patient visits to health care providers for influenza-like illness is collected through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). This collaborative effort between CDC, state and local health departments, and health care providers started during the 1997-98 influenza season when approximately 250 providers were enrolled. Enrollment in the system has increased over time and there were >3,000 providers enrolled during the 2010-11 season.

The number and percent of patients presenting with ILI each week will vary by region and season due to many factors, including having different provider type mixes (children present with higher rates of ILI than adults, and therefore regions with a higher percentage of pediatric practices will have higher numbers of cases). Therefore it is not appropriate to compare the magnitude of the percent of visits due to ILI between regions and seasons.

Baseline levels are calculated both nationally and for each region. Percentages at or above the baseline level are considered to be elevated.

For more information on ILI surveillance and baselines please visit:http://www.cdc.gov/flu/weekly/overview.htm#Outpatient", + "ili_elevated": [ + { + "ili_elevated_value": 1, + "colorname": "Orange", + "color_hexvalue": "#C85837", + "displaylabel": "ILI Elevated" + }, + { + "ili_elevated_value": 0, + "colorname": "vanilla", + "color_hexvalue": "#FFFBF2", + "displaylabel": "ILI Normal" + } + ], + "ili_line_chart": [ + { + "key": "Percent_Weighted_ILI_Color", + "value": "#FF0000" + }, + { + "key": "Percent_Weighted_ILI_Label", + "value": "Percent Weighted ILI" + }, + { + "key": "National_Baseline_Color", + "value": "#376092" + }, + { + "key": "National_Baseline_Label", + "value": "National Baseline" + }, + { + "key": "Regional_Baseline_Color", + "value": "#376092" + }, + { + "key": "Regional_Baseline_Label", + "value": "Regional Baseline" + } + ], + "mmwr": [ + { + "mmwrid": 3223, + "weekend": "2023-10-07", + "weekendlabel": "Oct 07, 2023", + "weekendlabel2": "Oct-07-2023", + 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Label", - "value": "Percent Positive for Influenza A" - }, - { - "id": 3, - "description": "Percent B Line Color", - "value": "#64DD17" - }, - { - "id": 2, - "description": "Percent A Line Color", - "value": "#FFC107" - }, - { - "id": 1, - "description": "Percent Positive Line Color", - "value": "#000000" - } - ], - "labtypes": [ - { - "labtypeid": 2, - "labname": "Clinical Labs" - }, - { - "labtypeid": 1, - "labname": "Public Health Labs" - } - ], - "disclaimer": "Viral Surveillance — Data collection from both the U.S. World Health Organization (WHO) Collaborating Laboratories and National Respiratory and Enteric Virus Surveillance System (NREVSS) laboratories began during the 1997-98 season. The volume of tested specimens has greatly increased during this time due to increased participation and increased testing. During the 1997-98 season 43 state public health laboratories participated in surveillance, and by the 2004-05 season all state public health laboratories were participating in surveillance. The addition of NREVSS data during the 1997-98 season roughly doubled the amount of virologic data reported each week.

The number of specimens tested and % positive rate vary by region and season based on different testing practices including triaging of specimens by the reporting labs, therefore it is not appropriate to compare the magnitude of positivity rates or the number of positive specimens between regions or seasons.

The U.S. WHO and NREVSS collaborating laboratories report the total number of respiratory specimens tested and the number positive for influenza types A and B each week to CDC. Most of the U.S. WHO collaborating laboratories also report the influenza A subtype (H1 or H3) of the viruses they have isolated, but the majority of NREVSS laboratories do not report the influenza A subtype.

For more information on virologic surveillance please visit:http://www.cdc.gov/flu/weekly/overview.htm#Viral

Outpatient Illness Surveillance — Information on patient visits to health care providers for influenza-like illness is collected through the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). This collaborative effort between CDC, state and local health departments, and health care providers started during the 1997-98 influenza season when approximately 250 providers were enrolled. Enrollment in the system has increased over time and there were >3,000 providers enrolled during the 2010-11 season.

The number and percent of patients presenting with ILI each week will vary by region and season due to many factors, including having different provider type mixes (children present with higher rates of ILI than adults, and therefore regions with a higher percentage of pediatric practices will have higher numbers of cases). Therefore it is not appropriate to compare the magnitude of the percent of visits due to ILI between regions and seasons.

Baseline levels are calculated both nationally and for each region. Percentages at or above the baseline level are considered to be elevated.

For more information on ILI surveillance and baselines please visit:http://www.cdc.gov/flu/weekly/overview.htm#Outpatient", - "ili_elevated": [ - { - "ili_elevated_value": 1, - "colorname": "Orange", - "color_hexvalue": "#C85837", - "displaylabel": "ILI Elevated" - }, - { - "ili_elevated_value": 0, - "colorname": "vanilla", - "color_hexvalue": "#FFFBF2", - "displaylabel": "ILI Normal" - } - ], - "ili_line_chart": [ - { - "key": "Percent_Weighted_ILI_Color", - "value": "#FF0000" - }, - { - "key": "Percent_Weighted_ILI_Label", - "value": "Percent Weighted ILI" - }, - { - "key": "National_Baseline_Color", - "value": "#376092" - }, - { - "key": "National_Baseline_Label", - "value": "National Baseline" - }, - { - "key": "Regional_Baseline_Color", - "value": "#376092" - }, - { - "key": "Regional_Baseline_Label", - "value": "Regional Baseline" - } - ], - "mmwr": [ - { - "mmwrid": 3223, - "weekend": "2023-10-07", - "weekendlabel": "Oct 07, 2023", - "weekendlabel2": "Oct-07-2023", - "weeknumber": 40, - 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"color_hexvalue": "#200CF7", - "labtypeid": 1 - } - ] -} \ No newline at end of file From bc6a1dcc6d08c0d02bc9c75ea74d3163b7c6993b Mon Sep 17 00:00:00 2001 From: george Date: Wed, 18 Sep 2024 17:03:08 -0400 Subject: [PATCH 45/47] Delete fluview/delphi_fluview/pull.py --- fluview/delphi_fluview/pull.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 fluview/delphi_fluview/pull.py diff --git a/fluview/delphi_fluview/pull.py b/fluview/delphi_fluview/pull.py deleted file mode 100644 index e69de29bb..000000000 From 54d183ff3585cba1c39165430e9db5b77e043dae Mon Sep 17 00:00:00 2001 From: george Date: Wed, 18 Sep 2024 17:03:25 -0400 Subject: [PATCH 46/47] Delete fluview/tests/conftest.py --- fluview/tests/conftest.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 fluview/tests/conftest.py diff --git a/fluview/tests/conftest.py b/fluview/tests/conftest.py deleted file mode 100644 index e69de29bb..000000000 From 7c7f15a211c539c763216e02605c8479cf66a501 Mon Sep 17 00:00:00 2001 From: george Date: Wed, 18 Sep 2024 17:24:03 -0400 Subject: [PATCH 47/47] Update runner.py --- _delphi_utils_python/delphi_utils/runner.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/_delphi_utils_python/delphi_utils/runner.py b/_delphi_utils_python/delphi_utils/runner.py index 8e5912b06..9083371aa 100644 --- a/_delphi_utils_python/delphi_utils/runner.py +++ b/_delphi_utils_python/delphi_utils/runner.py @@ -66,7 +66,9 @@ def run_indicator_pipeline(indicator_fn: Callable[[Params], None], current_version=current_version, ) else: - logger.info("Started a covidcast-indicator without version.cfg", indicator_name=ind_name) + logger.info( + "Started a covidcast-indicator without version.cfg", indicator_name=ind_name + ) indicator_fn(params) validator = validator_fn(params)