Add steps intraday to fitbitjson_mysql
JulioV
parent
9a276c1c66
commit
72f6b2d621
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@ -276,8 +276,7 @@ for provider in config["FITBIT_STEPS_SUMMARY"]["PROVIDERS"].keys():
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for provider in config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"].keys():
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if config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["COMPUTE"]:
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_raw.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_parsed.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_parsed_with_datetime.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/raw/{pid}/fitbit_steps_intraday_with_datetime.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/interim/{pid}/fitbit_steps_intraday_features/fitbit_steps_intraday_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
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files_to_compute.extend(expand("data/processed/features/{pid}/fitbit_steps_intraday.csv", pid=config["PIDS"]))
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files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
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@ -83,3 +83,40 @@ If you want RAPIDS to process Fitbit sensor data using this stream, you will nee
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|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |"activities-steps":[{"dateTime":"2020-10-08","value":"3201"}],"activities-steps-intraday":{"dataset":[{"time":"00:00:00","value":14},{"time":"00:01:00","value":11},{"time":"00:02:00","value":10},...],"datasetInterval":1,"datasetType":"minute"}}
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|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |"activities-steps":[{"dateTime":"2020-10-09","value":"998"}],"activities-steps-intraday":{"dataset":[{"time":"00:00:00","value":0},{"time":"00:01:00","value":0},{"time":"00:02:00","value":0},...],"datasetInterval":1,"datasetType":"minute"}}
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??? info "FITBIT_STEPS_INTRADAY"
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**RAPIDS_COLUMN_MAPPINGS**
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| RAPIDS column | Stream column |
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|-----------------|-----------------|
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| TIMESTAMP | FLAG_TO_MUTATE |
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| DEVICE_ID | device_id |
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| LOCAL_DATE_TIME | FLAG_TO_MUTATE |
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| STEPS | FLAG_TO_MUTATE |
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**MUTATION**
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- **COLUMN_MAPPINGS**
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| Script column | Stream column |
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|-----------------|-----------------|
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| JSON_FITBIT_COLUMN | fitbit_data |
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- **SCRIPTS**
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```bash
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src/data/streams/mutations/fitbit/parse_steps_intraday_json.py
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```
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!!! note
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`TIMESTAMP`, `LOCAL_DATE_TIME`, and `STEPS` are parsed from `JSON_FITBIT_COLUMN`. `JSON_FITBIT_COLUMN` is a string column containing the JSON objects returned by [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/activity/#get-activity-intraday-time-series). See an example of the raw data RAPIDS expects for this data stream:
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??? example "Example of the expected raw data"
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|device_id |fitbit_data |
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|---------------------------------------- |--------------------------------------------------------- |
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|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |"activities-steps":[{"dateTime":"2020-10-07","value":"1775"}],"activities-steps-intraday":{"dataset":[{"time":"00:00:00","value":5},{"time":"00:01:00","value":3},{"time":"00:02:00","value":0},...],"datasetInterval":1,"datasetType":"minute"}}
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|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |"activities-steps":[{"dateTime":"2020-10-08","value":"3201"}],"activities-steps-intraday":{"dataset":[{"time":"00:00:00","value":14},{"time":"00:01:00","value":11},{"time":"00:02:00","value":10},...],"datasetInterval":1,"datasetType":"minute"}}
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|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |"activities-steps":[{"dateTime":"2020-10-09","value":"998"}],"activities-steps-intraday":{"dataset":[{"time":"00:00:00","value":0},{"time":"00:01:00","value":0},{"time":"00:02:00","value":0},...],"datasetInterval":1,"datasetType":"minute"}}
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@ -21,4 +21,13 @@ This is a description of the format RAPIDS needs to process data for the followi
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| TIMESTAMP | An UNIX timestamp (13 digits) when a row of data was logged |
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| LOCAL_DATE_TIME | Date time string with format `yyyy-mm-dd hh:mm:ss` |
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| DEVICE_ID | A string that uniquely identifies a device |
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| STEPS | Daily step count |
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| STEPS | Daily step count |
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??? info "FITBIT_STEPS_INTRADAY"
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| RAPIDS column | Description |
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|-----------------|-----------------|
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| TIMESTAMP | An UNIX timestamp (13 digits) when a row of data was logged |
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| LOCAL_DATE_TIME | Date time string with format `yyyy-mm-dd hh:mm:ss` |
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| DEVICE_ID | A string that uniquely identifies a device |
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| STEPS | Intraday step count (usually every minute)|
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@ -610,7 +610,7 @@ rule fitbit_steps_summary_r_features:
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rule fitbit_steps_intraday_python_features:
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input:
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sensor_data = "data/raw/{pid}/fitbit_steps_intraday_parsed_with_datetime.csv",
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sensor_data = "data/raw/{pid}/fitbit_steps_intraday_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
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provider = lambda wildcards: config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
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@ -623,7 +623,7 @@ rule fitbit_steps_intraday_python_features:
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rule fitbit_steps_intraday_r_features:
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input:
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sensor_data = "data/raw/{pid}/fitbit_steps_intraday_parsed_with_datetime.csv",
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sensor_data = "data/raw/{pid}/fitbit_steps_intraday_with_datetime.csv",
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time_segments_labels = "data/interim/time_segments/{pid}_time_segments_labels.csv"
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params:
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provider = lambda wildcards: config["FITBIT_STEPS_INTRADAY"]["PROVIDERS"][wildcards.provider_key.upper()],
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@ -9,3 +9,15 @@ FITBIT_STEPS_SUMMARY:
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JSON_FITBIT_COLUMN: fitbit_data # text column with JSON objects
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SCRIPTS: # List any python or r scripts that mutate your raw data
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- src/data/streams/mutations/fitbit/parse_steps_summary_json.py
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FITBIT_STEPS_INTRADAY:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: FLAG_TO_MUTATE
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DEVICE_ID: device_id
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LOCAL_DATE_TIME: FLAG_TO_MUTATE
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STEPS: FLAG_TO_MUTATE
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MUTATION:
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COLUMN_MAPPINGS:
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JSON_FITBIT_COLUMN: fitbit_data # text column with JSON objects
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SCRIPTS: # List any python or r scripts that mutate your raw data
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- src/data/streams/mutations/fitbit/parse_steps_intraday_json.py
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@ -13,7 +13,7 @@ def parseStepsData(steps_data):
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records = []
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# Parse JSON into individual records
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for record in steps_data.fitbit_data:
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for record in steps_data.json_fitbit_column:
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record = json.loads(record) # Parse text into JSON
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if "activities-steps" in record.keys():
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curr_date = datetime.strptime(record["activities-steps"][0]["dateTime"], "%Y-%m-%d")
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@ -39,5 +39,6 @@ def parseStepsData(steps_data):
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def main(json_raw, stream_parameters):
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parsed_data = parseStepsData(json_raw)
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parsed_data["timestamp"] = None # this column is added at readable_datetime.R because we neeed to take into account multiple timezones
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parsed_data["timestamp"] = 0 # this column is added at readable_datetime.R because we neeed to take into account multiple timezones
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parsed_data['local_date_time'] = parsed_data['local_date_time'].dt.strftime('%Y-%m-%d %H:%M:%S')
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return(parsed_data)
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@ -98,6 +98,12 @@ FITBIT_STEPS_SUMMARY:
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- LOCAL_DATE_TIME
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- STEPS
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FITBIT_STEPS_INTRADAY:
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- TIMESTAMP
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- DEVICE_ID
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- LOCAL_DATE_TIME
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- STEPS
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EMPATICA_ACCELEROMETER:
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- TIMESTAMP
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- DEVICE_ID
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