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Add fitbitparsed_csv

pull/128/head
JulioV 2021-03-11 12:19:44 -05:00
parent b97b70e3a1
commit d48194fc07
9 changed files with 386 additions and 246 deletions
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4
config.yaml
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@ -350,6 +350,10 @@ FITBIT_DATA_STREAMS:
FOLDER: data/external/fitbit_csv FOLDER: data/external/fitbit_csv
SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: end # summary sleep episodes are considered as events based on either the start timestamp or end timestamp. SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: end # summary sleep episodes are considered as events based on either the start timestamp or end timestamp.
fitbitparsed_csv:
FOLDER: data/external/fitbit_csv
SLEEP_SUMMARY_EPISODE_DAY_ANCHOR: end # summary sleep episodes are considered as events based on either the start timestamp or end timestamp.
# Sensors ------ # Sensors ------
# See https://www.rapids.science/latest/features/fitbit-data-yield/ # See https://www.rapids.science/latest/features/fitbit-data-yield/

18
docs/datastreams/data-streams-introduction.md
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@ -15,14 +15,10 @@ For reference, these are the data streams we currently support:
| Data Stream | Device | Format | Container | Docs | Data Stream | Device | Format | Container | Docs
|--|--|--|--|--| |--|--|--|--|--|
| `aware_mysql`| Phone | AWARE app | MySQL | [link]() | `aware_mysql`| Phone | AWARE app | MySQL | [link](../aware-mysql)
| `aware_csv`| Phone | AWARE app | CSV files | [link]() | `aware_csv`| Phone | AWARE app | CSV files | [link](../aware-csv)
| `fitbitjson_mysql`| Fitbit | JSON (per Fitbit's API) | MySQL | [link]() | `fitbitjson_mysql`| Fitbit | JSON (per [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/)) | MySQL | [link](../fitbitjson-mysql)
| `fitbitjson_csv`| Fitbit | JSON (per Fitbit's API) | CSV files | [link]() | `fitbitjson_csv`| Fitbit | JSON (per [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/)) | CSV files | [link](../fitbitjson-csv)
| `fitbitparsed_mysql`| Fitbit | Parsed (parsed API data) | MySQL | [link]() | `fitbitparsed_mysql`| Fitbit | Parsed (parsed API data) | MySQL | [link](../fitbitparsed-mysql)
| `fitbitparsed_csv`| Fitbit | Parsed (parsed API data) | CSV files | [link]() | `fitbitparsed_csv`| Fitbit | Parsed (parsed API data) | CSV files | [link](../fitbitparsed-csv)
| `empatica_zip`| Empatica | E4 Connect | ZIP files | [link]() | `empatica_zip`| Empatica | [E4 Connect](https://support.empatica.com/hc/en-us/articles/201608896-Data-export-and-formatting-from-E4-connect-) | ZIP files | [link](../empatica-zip)
!!! hint
- Fitbit data can be processed from the JSON object produced by Fitbit's API (recommended) or from parsed tabular data (if you only have access to parsed data).
- Empatica data can only be accessed through the [E4 Connect website](https://support.empatica.com/hc/en-us/articles/201608896-Data-export-and-formatting-from-E4-connect-) that produces zip files with a CSV file per sensor which can be processed directly in RAPIDS.

17
docs/datastreams/fitbitparsed-csv.md 100644
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@ -0,0 +1,17 @@
# `fitbitparsed_csv`
This [data stream](../../datastreams/data-streams-introduction) handles Fitbit sensor data downloaded using the [Fitbit Web API](https://dev.fitbit.com/build/reference/web-api/), **parsed**, and stored in a CSV file. Please note that RAPIDS cannot query the API directly; you need to use other available tools or implement your own. Once you have your parsed sensor data in a CSV file, RAPIDS can process it.
!!! info "What is the difference between JSON and plain data streams"
Most people will only need `fitbitjson_*` because they downloaded and stored their data directly from Fitbit's API. However, if, for some reason, you don't have access to that JSON data and instead only have the parsed data (columns and rows), you can use this data stream.
## Container
The container should be a CSV file per sensor, each containing all participants' data.
The script to connect and download data from this container is at:
```bash
src/data/streams/fitbitparsed_csv/container.R
```
## Format
--8<---- "docs/snippets/parsedfitbit_format.md"

235
docs/datastreams/fitbitparsed-mysql.md
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@ -2,7 +2,7 @@
This [data stream](../../datastreams/data-streams-introduction) handles Fitbit sensor data downloaded using the [Fitbit Web API](https://dev.fitbit.com/build/reference/web-api/), **parsed**, and stored in a MySQL database. Please note that RAPIDS cannot query the API directly; you need to use other available tools or implement your own. Once you have your parsed sensor data in a MySQL database, RAPIDS can process it. This [data stream](../../datastreams/data-streams-introduction) handles Fitbit sensor data downloaded using the [Fitbit Web API](https://dev.fitbit.com/build/reference/web-api/), **parsed**, and stored in a MySQL database. Please note that RAPIDS cannot query the API directly; you need to use other available tools or implement your own. Once you have your parsed sensor data in a MySQL database, RAPIDS can process it.
!!! info "What is the difference between JSON and plain data streams" !!! info "What is the difference between JSON and plain data streams"
Most people will only need `fitbitjson_mysql` because they downloaded and stored their data directly from Fitbit's API. However, if, for some reason, you don't have access to that JSON data and instead only have the parsed data (columns and rows), you can use this data stream. Most people will only need `fitbitjson_*` because they downloaded and stored their data directly from Fitbit's API. However, if, for some reason, you don't have access to that JSON data and instead only have the parsed data (columns and rows), you can use this data stream.
## Container ## Container
The container should be a MySQL database with a table per sensor, each containing all participants' data. The container should be a MySQL database with a table per sensor, each containing all participants' data.
@ -14,235 +14,4 @@ src/data/streams/fitbitparsed_mysql/container.R
## Format ## Format
The `format.yaml` maps and transforms columns in your raw data stream to the [mandatory columns RAPIDS needs for Fitbit sensors](../mandatory-fitbit-format). This file is at: --8<---- "docs/snippets/parsedfitbit_format.md"
```bash
src/data/streams/fitbitparsed_mysql/format.yaml
```
If you want to use this stream with your data, modify every sensor in `format.yaml` to map all columns except `TIMESTAMP` in `[RAPIDS_COLUMN_MAPPINGS]` to your raw data column names.
All columns are mandatory; however, all except `device_id` and `local_date_time` can be empty if you don't have that data. Just have in mind that some features will be empty if some of these columns are empty.
??? info "FITBIT_HEARTRATE_SUMMARY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP| FLAG_TO_MUTATE |
| LOCAL_DATE_TIME | local_date_time |
| DEVICE_ID | device_id |
| HEARTRATE_DAILY_RESTINGHR | heartrate_daily_restinghr |
| HEARTRATE_DAILY_CALORIESOUTOFRANGE | heartrate_daily_caloriesoutofrange |
| HEARTRATE_DAILY_CALORIESFATBURN | heartrate_daily_caloriesfatburn |
| HEARTRATE_DAILY_CALORIESCARDIO | heartrate_daily_caloriescardio |
| HEARTRATE_DAILY_CALORIESPEAK | heartrate_daily_caloriespeak |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the raw data RAPIDS expects for this data stream"
|device_id |local_date_time |heartrate_daily_restinghr |heartrate_daily_caloriesoutofrange |heartrate_daily_caloriesfatburn |heartrate_daily_caloriescardio |heartrate_daily_caloriespeak |
|-------------------------------------- |----------------- |------- |-------------- |------------- |------------ |-------|
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 |72 |1200.6102 |760.3020 |15.2048 |0 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-08 |70 |1100.1120 |660.0012 |23.7088 |0 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-09 |69 |750.3615 |734.1516 |131.8579 |0 |
??? info "FITBIT_HEARTRATE_INTRADAY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP| FLAG_TO_MUTATE |
| LOCAL_DATE_TIME | local_date_time |
| DEVICE_ID | device_id |
| HEARTRATE | heartrate |
| HEARTRATE_ZONE | heartrate_zone |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the raw data RAPIDS expects for this data stream"
|device_id |local_date_time |heartrate |heartrate_zone |
|-------------------------------------- |---------------------- |--------- |--------------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:00:00 |68 |outofrange |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:01:00 |67 |outofrange |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:02:00 |67 |outofrange |
??? info "FITBIT_SLEEP_SUMMARY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP| FLAG_TO_MUTATE |
| LOCAL_DATE_TIME| local_date_time |
| LOCAL_START_DATE_TIME| local_start_date_time |
| LOCAL_END_DATE_TIME| local_end_date_time |
| DEVICE_ID| device_id |
| EFFICIENCY| efficiency |
| MINUTES_AFTER_WAKEUP| minutes_after_wakeup |
| MINUTES_ASLEEP| minutes_asleep |
| MINUTES_AWAKE| minutes_awake |
| MINUTES_TO_FALL_ASLEEP| minutes_to_fall_asleep |
| MINUTES_IN_BED| minutes_in_bed |
| IS_MAIN_SLEEP| is_main_sleep |
| TYPE| type |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
Fitbit API has two versions for sleep data, v1 and v1.2. We support both but ignore v1's `count_awake`, `duration_awake`, and `count_awakenings`, `count_restless`, `duration_restless` columns.
??? example "Example of the expected raw data"
|device_id |local_start_date_time |local_end_date_time |efficiency |minutes_after_wakeup |minutes_asleep |minutes_awake |minutes_to_fall_asleep |minutes_in_bed |is_main_sleep |type |
|-------------------------------------- |---------------------- |---------------------- |----------- |--------------------- |--------------- |-------------- |----------------------- |--------------- |-------------- |-------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-10 15:36:30 |2020-10-10 16:37:00 |92 |0 |55 |5 |0 |60 |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-10 01:46:30 |2020-10-10 08:10:00 |88 |0 |318 |65 |0 |383 |1 |stages |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-11 00:12:30 |2020-10-11 11:47:00 |89 |1 |562 |132 |0 |694 |1 |stages |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-12 01:31:00 |2020-10-12 09:34:30 |93 |0 |415 |68 |0 |483 |1 |stages |
??? info "FITBIT_SLEEP_INTRADAY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP | FLAG_TO_MUTATE |
| LOCAL_DATE_TIME | local_date_time |
| DEVICE_ID | device_id |
| TYPE_EPISODE_ID | type_episode_id |
| DURATION | duration |
| IS_MAIN_SLEEP | is_main_sleep |
| TYPE | type |
| LEVEL | level |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
Fitbit API has two versions for sleep data, v1 and v1.2, we support both.
??? example "Example of the expected raw data"
|device_id |type_episode_id |local_date_time |duration |level |is_main_sleep |type |
|------------------------------------ |---------------- |------------------- |--------- |---------- |-------------- |-------------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |0 |2020-10-10 15:36:30 |60 |restless |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |0 |2020-10-10 15:37:30 |660 |asleep |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |0 |2020-10-10 15:48:30 |60 |restless |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |... |... |... |... |... |... |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |1 |2020-10-10 01:46:30 |420 |light |1 |stages |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |1 |2020-10-10 01:53:30 |1230 |deep |1 |stages |
??? info "FITBIT_STEPS_SUMMARY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP | FLAG_TO_MUTATE |
| DEVICE_ID | device_id |
| LOCAL_DATE_TIME | local_date_time |
| STEPS | steps |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the expected raw data"
|device_id |local_date_time |steps |
|-------------------------------------- |---------------------- |--------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 |1775 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-08 |3201 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-09 |998 |
??? info "FITBIT_STEPS_INTRADAY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP | FLAG_TO_MUTATE |
| DEVICE_ID | device_id |
| LOCAL_DATE_TIME | local_date_time |
| STEPS | steps |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the expected raw data"
|device_id |local_date_time |steps |
|-------------------------------------- |---------------------- |--------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:00:00 |5 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:01:00 |3 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:02:00 |0 |

233
docs/snippets/parsedfitbit_format.md 100644
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@ -0,0 +1,233 @@
The `format.yaml` maps and transforms columns in your raw data stream to the [mandatory columns RAPIDS needs for Fitbit sensors](../mandatory-fitbit-format). This file is at:
```bash
src/data/streams/fitbitparsed_mysql/format.yaml
```
If you want to use this stream with your data, modify every sensor in `format.yaml` to map all columns except `TIMESTAMP` in `[RAPIDS_COLUMN_MAPPINGS]` to your raw data column names.
All columns are mandatory; however, all except `device_id` and `local_date_time` can be empty if you don't have that data. Just have in mind that some features will be empty if some of these columns are empty.
??? info "FITBIT_HEARTRATE_SUMMARY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP| FLAG_TO_MUTATE |
| LOCAL_DATE_TIME | local_date_time |
| DEVICE_ID | device_id |
| HEARTRATE_DAILY_RESTINGHR | heartrate_daily_restinghr |
| HEARTRATE_DAILY_CALORIESOUTOFRANGE | heartrate_daily_caloriesoutofrange |
| HEARTRATE_DAILY_CALORIESFATBURN | heartrate_daily_caloriesfatburn |
| HEARTRATE_DAILY_CALORIESCARDIO | heartrate_daily_caloriescardio |
| HEARTRATE_DAILY_CALORIESPEAK | heartrate_daily_caloriespeak |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the raw data RAPIDS expects for this data stream"
|device_id |local_date_time |heartrate_daily_restinghr |heartrate_daily_caloriesoutofrange |heartrate_daily_caloriesfatburn |heartrate_daily_caloriescardio |heartrate_daily_caloriespeak |
|-------------------------------------- |----------------- |------- |-------------- |------------- |------------ |-------|
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 |72 |1200.6102 |760.3020 |15.2048 |0 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-08 |70 |1100.1120 |660.0012 |23.7088 |0 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-09 |69 |750.3615 |734.1516 |131.8579 |0 |
??? info "FITBIT_HEARTRATE_INTRADAY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP| FLAG_TO_MUTATE |
| LOCAL_DATE_TIME | local_date_time |
| DEVICE_ID | device_id |
| HEARTRATE | heartrate |
| HEARTRATE_ZONE | heartrate_zone |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the raw data RAPIDS expects for this data stream"
|device_id |local_date_time |heartrate |heartrate_zone |
|-------------------------------------- |---------------------- |--------- |--------------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:00:00 |68 |outofrange |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:01:00 |67 |outofrange |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:02:00 |67 |outofrange |
??? info "FITBIT_SLEEP_SUMMARY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP| FLAG_TO_MUTATE |
| LOCAL_DATE_TIME| local_date_time |
| LOCAL_START_DATE_TIME| local_start_date_time |
| LOCAL_END_DATE_TIME| local_end_date_time |
| DEVICE_ID| device_id |
| EFFICIENCY| efficiency |
| MINUTES_AFTER_WAKEUP| minutes_after_wakeup |
| MINUTES_ASLEEP| minutes_asleep |
| MINUTES_AWAKE| minutes_awake |
| MINUTES_TO_FALL_ASLEEP| minutes_to_fall_asleep |
| MINUTES_IN_BED| minutes_in_bed |
| IS_MAIN_SLEEP| is_main_sleep |
| TYPE| type |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
Fitbit API has two versions for sleep data, v1 and v1.2. We support both but ignore v1's `count_awake`, `duration_awake`, and `count_awakenings`, `count_restless`, `duration_restless` columns.
??? example "Example of the expected raw data"
|device_id |local_start_date_time |local_end_date_time |efficiency |minutes_after_wakeup |minutes_asleep |minutes_awake |minutes_to_fall_asleep |minutes_in_bed |is_main_sleep |type |
|-------------------------------------- |---------------------- |---------------------- |----------- |--------------------- |--------------- |-------------- |----------------------- |--------------- |-------------- |-------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-10 15:36:30 |2020-10-10 16:37:00 |92 |0 |55 |5 |0 |60 |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-10 01:46:30 |2020-10-10 08:10:00 |88 |0 |318 |65 |0 |383 |1 |stages |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-11 00:12:30 |2020-10-11 11:47:00 |89 |1 |562 |132 |0 |694 |1 |stages |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-12 01:31:00 |2020-10-12 09:34:30 |93 |0 |415 |68 |0 |483 |1 |stages |
??? info "FITBIT_SLEEP_INTRADAY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP | FLAG_TO_MUTATE |
| LOCAL_DATE_TIME | local_date_time |
| DEVICE_ID | device_id |
| TYPE_EPISODE_ID | type_episode_id |
| DURATION | duration |
| IS_MAIN_SLEEP | is_main_sleep |
| TYPE | type |
| LEVEL | level |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
Fitbit API has two versions for sleep data, v1 and v1.2, we support both.
??? example "Example of the expected raw data"
|device_id |type_episode_id |local_date_time |duration |level |is_main_sleep |type |
|------------------------------------ |---------------- |------------------- |--------- |---------- |-------------- |-------------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |0 |2020-10-10 15:36:30 |60 |restless |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |0 |2020-10-10 15:37:30 |660 |asleep |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |0 |2020-10-10 15:48:30 |60 |restless |0 |classic |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |... |... |... |... |... |... |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |1 |2020-10-10 01:46:30 |420 |light |1 |stages |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |1 |2020-10-10 01:53:30 |1230 |deep |1 |stages |
??? info "FITBIT_STEPS_SUMMARY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP | FLAG_TO_MUTATE |
| DEVICE_ID | device_id |
| LOCAL_DATE_TIME | local_date_time |
| STEPS | steps |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the expected raw data"
|device_id |local_date_time |steps |
|-------------------------------------- |---------------------- |--------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 |1775 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-08 |3201 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-09 |998 |
??? info "FITBIT_STEPS_INTRADAY"
**RAPIDS_COLUMN_MAPPINGS**
| RAPIDS column | Stream column |
|-----------------|-----------------|
| TIMESTAMP | FLAG_TO_MUTATE |
| DEVICE_ID | device_id |
| LOCAL_DATE_TIME | local_date_time |
| STEPS | steps |
**MUTATION**
- **COLUMN_MAPPINGS** (None)
- **SCRIPTS**
```bash
src/data/streams/mutations/fitbit/add_zero_timestamp.py
```
!!! note
`add_zero_timestamp` adds an all-zero column called `timestamp` that will be filled in later in the pipeline by `readable_time.R` converting LOCAL_DATE_TIME to a unix timestamp taking into account single or multiple time zones.
??? example "Example of the expected raw data"
|device_id |local_date_time |steps |
|-------------------------------------- |---------------------- |--------- |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:00:00 |5 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:01:00 |3 |
|a748ee1a-1d0b-4ae9-9074-279a2b6ba524 |2020-10-07 00:02:00 |0 |

2
src/data/streams/fitbitjson_csv/container.R
View File

@ -12,7 +12,7 @@ library(readr)
pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){ pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
if(!dir.exists(stream_parameters$FOLDER)) if(!dir.exists(stream_parameters$FOLDER))
stop("[FITBIT_DATA_STREAMS][fitbit_json_csv][FOLDER] does not exist: ", stream_parameters$FOLDER) stop("[FITBIT_DATA_STREAMS][fitbitjson_csv][FOLDER] does not exist: ", stream_parameters$FOLDER)
data_file <- file.path(stream_parameters$FOLDER, sensor_container) data_file <- file.path(stream_parameters$FOLDER, sensor_container)
if(!file.exists(data_file)) if(!file.exists(data_file))

37
src/data/streams/fitbitparsed_csv/container.R 100644
View File

@ -0,0 +1,37 @@
# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
library(readr)
#' @description
#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
#'
#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
#' @param device A device ID string
#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[TABLE] key in config.yaml
#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
#' @return A dataframe with the sensor data for device
pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
if(!dir.exists(stream_parameters$FOLDER))
stop("[FITBIT_DATA_STREAMS][fitbitparsed_csv][FOLDER] does not exist: ", stream_parameters$FOLDER)
data_file <- file.path(stream_parameters$FOLDER, sensor_container)
if(!file.exists(data_file))
stop("The data container should be a CSV file but it does not exist: ", data_file)
if(!endsWith(data_file, ".csv"))
stop("The data container should be a CSV file: ", data_file)
# Letting the user know what we are doing
message(paste0("Reading this CSV file: ", data_file))
sensor_data <- read_csv_chunked(data_file,
callback = DataFrameCallback$new(function(x, pos) subset(x,x[[columns$DEVICE_ID]] == device, select = unlist(columns))), progress = T, chunk_size = 50000)
if(is.null(sensor_data)) # emtpy file
sensor_data <- read.csv(data_file)
if(nrow(sensor_data) == 0)
warning("The device '", device,"' did not have data in ", sensor_container)
return(sensor_data)
}

83
src/data/streams/fitbitparsed_csv/format.yaml 100644
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@ -0,0 +1,83 @@
FITBIT_HEARTRATE_SUMMARY:
RAPIDS_COLUMN_MAPPINGS:
TIMESTAMP: FLAG_TO_MUTATE
DEVICE_ID: device_id
LOCAL_DATE_TIME: local_date_time
HEARTRATE_DAILY_RESTINGHR: heartrate_daily_restinghr
HEARTRATE_DAILY_CALORIESOUTOFRANGE: heartrate_daily_caloriesoutofrange
HEARTRATE_DAILY_CALORIESFATBURN: heartrate_daily_caloriesfatburn
HEARTRATE_DAILY_CALORIESCARDIO: heartrate_daily_caloriescardio
HEARTRATE_DAILY_CALORIESPEAK: heartrate_daily_caloriespeak
MUTATION:
COLUMN_MAPPINGS:
SCRIPTS: # List any python or r scripts that mutate your raw data
- src/data/streams/mutations/fitbit/add_zero_timestamp.py
FITBIT_HEARTRATE_INTRADAY:
RAPIDS_COLUMN_MAPPINGS:
TIMESTAMP: FLAG_TO_MUTATE
DEVICE_ID: device_id
LOCAL_DATE_TIME: local_date_time
HEARTRATE: heartrate
HEARTRATE_ZONE: heartrate_zone
MUTATION:
COLUMN_MAPPINGS:
SCRIPTS: # List any python or r scripts that mutate your raw data
- src/data/streams/mutations/fitbit/add_zero_timestamp.py
FITBIT_SLEEP_SUMMARY:
RAPIDS_COLUMN_MAPPINGS:
TIMESTAMP: FLAG_TO_MUTATE
DEVICE_ID: device_id
LOCAL_DATE_TIME: local_date_time
LOCAL_START_DATE_TIME: local_start_date_time
LOCAL_END_DATE_TIME: local_end_date_time
EFFICIENCY: efficiency
MINUTES_AFTER_WAKEUP: minutes_after_wakeup
MINUTES_ASLEEP: minutes_asleep
MINUTES_AWAKE: minutes_awake
MINUTES_TO_FALL_ASLEEP: minutes_to_fall_asleep
MINUTES_IN_BED: minutes_in_bed
IS_MAIN_SLEEP: is_main_sleep
TYPE: type
MUTATION:
COLUMN_MAPPINGS:
SCRIPTS: # List any python or r scripts that mutate your raw data
- src/data/streams/mutations/fitbit/add_zero_timestamp.py
FITBIT_SLEEP_INTRADAY:
RAPIDS_COLUMN_MAPPINGS:
TIMESTAMP: FLAG_TO_MUTATE
DEVICE_ID: device_id
LOCAL_DATE_TIME: local_date_time
TYPE_EPISODE_ID: type_episode_id
DURATION: duration
IS_MAIN_SLEEP: is_main_sleep
TYPE: type
LEVEL: level
MUTATION:
COLUMN_MAPPINGS:
SCRIPTS: # List any python or r scripts that mutate your raw data
- src/data/streams/mutations/fitbit/add_zero_timestamp.py
FITBIT_STEPS_SUMMARY:
RAPIDS_COLUMN_MAPPINGS:
TIMESTAMP: FLAG_TO_MUTATE
DEVICE_ID: device_id
LOCAL_DATE_TIME: local_date_time
STEPS: steps
MUTATION:
COLUMN_MAPPINGS:
SCRIPTS: # List any python or r scripts that mutate your raw data
- src/data/streams/mutations/fitbit/add_zero_timestamp.py
FITBIT_STEPS_INTRADAY:
RAPIDS_COLUMN_MAPPINGS:
TIMESTAMP: FLAG_TO_MUTATE
DEVICE_ID: device_id
LOCAL_DATE_TIME: local_date_time
STEPS: steps
MUTATION:
COLUMN_MAPPINGS:
SCRIPTS: # List any python or r scripts that mutate your raw data
- src/data/streams/mutations/fitbit/add_zero_timestamp.py

3
src/data/streams/mutations/fitbit/add_zero_timestamp.py
View File

@ -2,5 +2,6 @@ import pandas as pd
def main(parsed_data, stream_parameters): def main(parsed_data, stream_parameters):
parsed_data["timestamp"] = 0 # this column is added at readable_datetime.R because we neeed to take into account multiple timezones parsed_data["timestamp"] = 0 # this column is added at readable_datetime.R because we neeed to take into account multiple timezones
# parsed_data['local_date_time'] = parsed_data['local_date_time'].dt.strftime('%Y-%m-%d %H:%M:%S') if pd.api.types.is_datetime64_any_dtype( parsed_data['local_date_time']):
parsed_data['local_date_time'] = parsed_data['local_date_time'].dt.strftime('%Y-%m-%d %H:%M:%S')
return(parsed_data) return(parsed_data)