Fix bugs in Fitbit data parsing

- Fix the script that was breaking with an empty file
- Fix the script that was breaking when start/end dates were empty
- Ambigous and nonexistent DST times are handled now
- Remove unnecessary else clause

docs/change-log.md

@@ -5,6 +5,8 @@
 - Update CI to create a release on a tagged push that passes the tests
 - Clarify in DB credential configuration that we only support MySQL
 - Add Windows installation instructions
+- Fix bugs in the create_participants_file script
+- Fix bugs in Fitbit data parsing.
 ## v0.3.1
 - Update installation docs for RAPIDS' docker container
 - Fix example analysis use of accelerometer data in a plot

src/data/fitbit_parse_calories.py

@@ -41,10 +41,14 @@ elif table_format == "CSV":
     summary = pd.read_csv(snakemake.input[0], parse_dates=["local_date_time"], date_parser=lambda col: pd.to_datetime(col).tz_localize(None))
     intraday = pd.read_csv(snakemake.input[1], parse_dates=["local_date_time"], date_parser=lambda col: pd.to_datetime(col).tz_localize(None))
 
+#    if not pd.isnull(local_start_date) and not pd.isnull(local_end_date):
+
 if summary.shape[0] > 0:
-    summary["timestamp"] = summary["local_date_time"].dt.tz_localize(timezone).astype(np.int64) // 10**6
+    summary["timestamp"] = summary["local_date_time"].dt.tz_localize(timezone, ambiguous=False, nonexistent="NaT").dropna().astype(np.int64) // 10**6
+    summary.dropna(subset=['timestamp'], inplace=True)
 if intraday.shape[0] > 0:
-    intraday["timestamp"] = intraday["local_date_time"].dt.tz_localize(timezone).astype(np.int64) // 10**6
+    intraday["timestamp"] = intraday["local_date_time"].dt.tz_localize(timezone, ambiguous=False, nonexistent="NaT").dropna().astype(np.int64) // 10**6
+    intraday.dropna(subset=['timestamp'], inplace=True)
 
 summary.to_csv(snakemake.output["summary_data"], index=False)
 intraday.to_csv(snakemake.output["intraday_data"], index=False)

src/data/fitbit_parse_heartrate.py

@@ -97,7 +97,11 @@ def parseHeartrateIntradayData(records_intraday, dataset, device_id, curr_date,
 
 def parseHeartrateData(heartrate_data, fitbit_data_type):
     if heartrate_data.empty:
-        return pd.DataFrame(columns=HR_SUMMARY_COLUMNS), pd.DataFrame(columns=HR_INTRADAY_COLUMNS)
+        if fitbit_data_type == "summary":
+            return pd.DataFrame(columns=HR_SUMMARY_COLUMNS)
+        elif fitbit_data_type == "intraday":
+            return pd.DataFrame(columns=HR_INTRADAY_COLUMNS)
+
     device_id = heartrate_data["device_id"].iloc[0]
     records_summary, records_intraday = [], []
 
@@ -121,8 +125,6 @@ def parseHeartrateData(heartrate_data, fitbit_data_type):
         parsed_data = pd.DataFrame(data=records_summary, columns=HR_SUMMARY_COLUMNS)
     elif fitbit_data_type == "intraday":
         parsed_data = pd.DataFrame(data=records_intraday, columns=HR_INTRADAY_COLUMNS)
-    else:
-        raise ValueError("fitbit_data_type can only be one of ['summary', 'intraday'].")
     return parsed_data
     
 
@@ -145,9 +147,11 @@ else:
     raise ValueError("column_format can only be one of ['JSON', 'PLAIN_TEXT'].")
 
 # Only keep dates in the range of [local_start_date, local_end_date)
+if not pd.isnull(local_start_date) and not pd.isnull(local_end_date):
     parsed_data = parsed_data.loc[(parsed_data["local_date_time"] >= local_start_date) & (parsed_data["local_date_time"] < local_end_date)]
 
 if parsed_data.shape[0] > 0:
-    parsed_data["timestamp"] = parsed_data["local_date_time"].dt.tz_localize(timezone).astype(np.int64) // 10**6
+    parsed_data["timestamp"] = parsed_data["local_date_time"].dt.tz_localize(timezone, ambiguous=False, nonexistent="NaT").dropna().astype(np.int64) // 10**6
+    parsed_data.dropna(subset=['timestamp'], inplace=True)
 
 parsed_data.to_csv(snakemake.output[0], index=False)

src/data/fitbit_parse_sleep.py

@@ -188,7 +188,10 @@ def parseOneRecordForV12(record, device_id, d_is_main_sleep, records_summary, re
 def parseSleepData(sleep_data, fitbit_data_type):
     SLEEP_SUMMARY_COLUMNS = SLEEP_SUMMARY_COLUMNS_V1_2
     if sleep_data.empty:
-        return pd.DataFrame(columns=SLEEP_SUMMARY_COLUMNS), pd.DataFrame(columns=SLEEP_INTRADAY_COLUMNS)
+        if fitbit_data_type == "summary":
+            return pd.DataFrame(columns=SLEEP_SUMMARY_COLUMNS)
+        elif fitbit_data_type == "intraday":
+            return pd.DataFrame(columns=SLEEP_INTRADAY_COLUMNS)
     device_id = sleep_data["device_id"].iloc[0]
     records_summary, records_intraday = [], []
     # Parse JSON into individual records
@@ -210,13 +213,9 @@ def parseSleepData(sleep_data, fitbit_data_type):
         parsed_data = pd.DataFrame(data=records_summary, columns=SLEEP_SUMMARY_COLUMNS)
     elif fitbit_data_type == "intraday":
         parsed_data = pd.DataFrame(data=records_intraday, columns=SLEEP_INTRADAY_COLUMNS)
-    else:
-        raise ValueError("fitbit_data_type can only be one of ['summary', 'intraday'].")
 
     return parsed_data
 
-
-
 timezone = snakemake.params["timezone"]
 column_format = snakemake.params["column_format"]
 fitbit_data_type = snakemake.params["fitbit_data_type"]
@@ -235,31 +234,26 @@ elif column_format == "PLAIN_TEXT":
         parsed_data = pd.read_csv(snakemake.input["raw_data"], parse_dates=["local_start_date_time", "local_end_date_time"], date_parser=lambda col: pd.to_datetime(col).tz_localize(None))
     elif fitbit_data_type == "intraday":
         parsed_data = pd.read_csv(snakemake.input["raw_data"], parse_dates=["local_date_time"], date_parser=lambda col: pd.to_datetime(col).tz_localize(None))
-    else:
-        raise ValueError("fitbit_data_type can only be one of ['summary', 'intraday'].")
 else:
     raise ValueError("column_format can only be one of ['JSON', 'PLAIN_TEXT'].")
 
 if parsed_data.shape[0] > 0 and fitbit_data_type == "summary":
-    
     if sleep_episode_timestamp != "start" and sleep_episode_timestamp != "end":
         raise ValueError("SLEEP_EPISODE_TIMESTAMP can only be one of ['start', 'end'].")
-
     # Column name to be considered as the event datetime
     datetime_column = "local_" + sleep_episode_timestamp + "_date_time"
-    # Only keep dates in the range of [local_start_date, local_end_date)
+    
+    if not pd.isnull(local_start_date) and not pd.isnull(local_end_date):
         parsed_data = parsed_data.loc[(parsed_data[datetime_column] >= local_start_date) & (parsed_data[datetime_column] < local_end_date)]
-    # Convert datetime to timestamp
+    parsed_data["timestamp"] = parsed_data[datetime_column].dt.tz_localize(timezone, ambiguous=False, nonexistent="NaT").dropna().astype(np.int64) // 10**6
-    parsed_data["timestamp"] = parsed_data[datetime_column].dt.tz_localize(timezone).astype(np.int64) // 10**6
+    parsed_data.dropna(subset=['timestamp'], inplace=True)
-    # Drop useless columns: local_start_date_time and local_end_date_time
     parsed_data.drop(["local_start_date_time", "local_end_date_time"], axis = 1, inplace=True)
 
 if parsed_data.shape[0] > 0 and fitbit_data_type == "intraday":
-    # Only keep dates in the range of [local_start_date, local_end_date)
+    if not pd.isnull(local_start_date) and not pd.isnull(local_end_date):
         parsed_data = parsed_data.loc[(parsed_data["local_date_time"] >= local_start_date) & (parsed_data["local_date_time"] < local_end_date)]
-    # Convert datetime to timestamp
+    parsed_data["timestamp"] = parsed_data["local_date_time"].dt.tz_localize(timezone, ambiguous=False, nonexistent="NaT").dropna().astype(np.int64) // 10**6
-    parsed_data["timestamp"] = parsed_data["local_date_time"].dt.tz_localize(timezone).astype(np.int64) // 10**6
+    parsed_data.dropna(subset=['timestamp'], inplace=True)
-    # Unifying level
     parsed_data["unified_level"] = np.where(parsed_data["level"].isin(["awake", "wake", "restless"]), 0, 1)
 
 parsed_data.to_csv(snakemake.output[0], index=False)

src/data/fitbit_parse_steps.py

@@ -9,9 +9,10 @@ STEPS_COLUMNS = ("device_id", "steps", "local_date_time", "timestamp")
 
 def parseStepsData(steps_data, fitbit_data_type):
     if steps_data.empty:
-        return pd.DataFrame(), pd.DataFrame(columns=STEPS_INTRADAY_COLUMNS)
+        return pd.DataFrame(columns=STEPS_COLUMNS)
+
     device_id = steps_data["device_id"].iloc[0]
-    records_summary, records_intraday = [], []
+    records = []
     
     # Parse JSON into individual records
     for record in steps_data.fitbit_data:
@@ -26,7 +27,7 @@ def parseStepsData(steps_data, fitbit_data_type):
                 curr_date,
                 0)
             
-            records_summary.append(row_summary)
+            records.append(row_summary)
 
         # Parse intraday data
         if fitbit_data_type == "intraday":
@@ -40,14 +41,9 @@ def parseStepsData(steps_data, fitbit_data_type):
                     d_datetime,
                     0)
 
-                records_intraday.append(row_intraday)
+                records.append(row_intraday)
     
-    if fitbit_data_type == "summary":
+        parsed_data = pd.DataFrame(data=records, columns=STEPS_COLUMNS)
-        parsed_data = pd.DataFrame(data=records_summary, columns=STEPS_COLUMNS)
-    elif fitbit_data_type == "intraday":
-        parsed_data = pd.DataFrame(data=records_intraday, columns=STEPS_COLUMNS)
-    else:
-        raise ValueError("fitbit_data_type can only be one of ['summary', 'intraday'].")
 
     return parsed_data
 
@@ -71,9 +67,11 @@ else:
     raise ValueError("column_format can only be one of ['JSON', 'PLAIN_TEXT'].")
 
 # Only keep dates in the range of [local_start_date, local_end_date)
+if not pd.isnull(local_start_date) and not pd.isnull(local_end_date):
     parsed_data = parsed_data.loc[(parsed_data["local_date_time"] >= local_start_date) & (parsed_data["local_date_time"] < local_end_date)]
 
 if parsed_data.shape[0] > 0:
-    parsed_data["timestamp"] = parsed_data["local_date_time"].dt.tz_localize(timezone).astype(np.int64) // 10**6
+    parsed_data["timestamp"] = parsed_data["local_date_time"].dt.tz_localize(timezone, ambiguous=False, nonexistent="NaT").dropna().astype(np.int64) // 10**6
+    parsed_data.dropna(subset=['timestamp'], inplace=True)
 
 parsed_data.to_csv(snakemake.output[0], index=False)