Fix unstructured logging variable formatting

_delphi_utils_python/README.md

@@ -22,13 +22,22 @@ 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
+- signal
+- issue_date
+- filename
+
 Single-thread usage.
 
 ```py
 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.

_delphi_utils_python/delphi_utils/export.py

@@ -22,8 +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 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:

_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("FLaSH: worth inspecting", signal=signal, lag=lag, payload=p_text)
 
 
 def evd_ranking_fn(ts_streams, EVD_max, EVD_min):

_delphi_utils_python/delphi_utils/logger.py

@@ -1,11 +1,11 @@
 """Structured logger utility for creating JSON logs.
 
-See the delphi_utils README.md for usage examples.
+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)
 
-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
+See the delphi_utils README.md for usage examples.
 """
 
 import contextlib

_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:
@@ -59,9 +60,15 @@ 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(f"Started {ind_name} with covidcast-indicators version {current_version}")
-    else: logger.info(f"Started {ind_name} without version.cfg")
+        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
+        )
 
     indicator_fn(params)
     validator = validator_fn(params)
@@ -77,8 +84,10 @@ def run_indicator_pipeline(indicator_fn:  Callable[[Params], None],
             break
         time.sleep(1)
     else:
-        logger.error(f"Flash step timed out ({timer} s), 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:

_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):

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)
@@ -157,28 +157,30 @@ 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 = []
     for geo in params["indicator"]["geos"]:
         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,
@@ -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_type=geo)
 
     elapsed_time_in_seconds = round(time.time() - start_time, 2)
     min_max_date = stats and min(s[0] for s in stats)

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(
+            ".fit() DEBUG - last rate/se for geo",
+            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}

changehc/delphi_changehc/update_sensor.py

@@ -41,17 +41,15 @@ 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
 
     assert not df["val"].isna().any(), " val contains nan values"
     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_value=geo, filename=out_name)
 
     dates = create_export_csv(
         df,
@@ -62,10 +60,8 @@ 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, num_geo_ids=df["geo_id"].unique().size)
+    logger.debug("Wrote files", export_dir=output_path)
     return dates
 
 
@@ -148,8 +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("{0} is invalid, pick one of 'county', "
-                          "'state', 'msa', 'hrr', 'hss','nation'".format(geo))
+            self.logger.error(
+                "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,
@@ -224,7 +221,7 @@ 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_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):

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."""

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()

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(
+            ".fit() DEBUG - last rate/se for geo",
+            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}

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("Wrote modified csv", filename=out_path)
     return files, dfs_list

claims_hosp/delphi_claims_hosp/run.py

@@ -116,17 +116,17 @@ 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"]:
                 assert params["indicator"]["obfuscated_prefix"] is not None, \
                     "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,
@@ -135,16 +135,16 @@ 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))
-        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"]):