Add aware_mysql_split phone data stream
JulioV
parent
daced51ca9
commit
91f4a24f65
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@ -46,13 +46,16 @@ PHONE_DATA_STREAMS:
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USE: aware_mysql
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# AVAILABLE:
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aware_mysql:
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aware_mysql: # one table per sensor with all participants' data
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DATABASE_GROUP: MY_GROUP
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aware_csv:
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aware_mysql_split: # one table per sensor per participant
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DATABASE_GROUP: MY_GROUP
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aware_csv: # one CSV file per sensor with all participants's data
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FOLDER: data/external/aware_csv
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aware_influxdb:
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aware_influxdb: # one table per sensor with all participants' data
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DATABASE_GROUP: MY_GROUP
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# Sensors ------
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@ -31,6 +31,8 @@ PHONE_DATA_STREAMS:
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DATABASE_GROUP: MY_GROUP # users define this group (user, password, host, etc.) in credentials.yaml
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```
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Secondly, update `tools/config.schema.yaml` including `[*_DATA_STREAMS][properties][USE][enum]` and `[*_DATA_STREAMS][required]`. This is needed to make sure users do not use invalid values in your data stream's `config.yaml` entry by mistake. Take the other streams' entries as examples or check this [guide](../developers/validation-schema-config.md).
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Then implement one or both of the following functions:
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=== "pull_data"
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@ -0,0 +1,15 @@
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# `aware_mysql_split`
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This [data stream](../../datastreams/data-streams-introduction) handles iOS and Android sensor data collected with the [AWARE Framework](https://awareframework.com/) and stored in a MySQL database. This stream is similar to `aware_mysql` except for the way data is stored in the database tables as explained below.
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## Container
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A MySQL database with a table per sensor **per participant**. RAPIDS assumes such tables' names follow the format `deviceid_sensorname` (for example `a748ee1a-1d0b-4ae9-9074-279a2b6ba524_accelerometer`); if this is not the case, you can modify the SQL query in this stream's `container.R`script. RAPIDS also assumes that an empty table exists for those participants that don’t have data for a specific sensor.
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The script to connect and download data from this container is at:
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```bash
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src/data/streams/aware_mysql_split/container.R
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```
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## Format
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--8<---- "docs/snippets/aware_format.md"
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@ -16,6 +16,7 @@ For reference, these are the data streams we currently support:
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| Data Stream | Device | Format | Container | Docs
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|--|--|--|--|--|
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| `aware_mysql`| Phone | AWARE app | MySQL | [link](../aware-mysql)
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| `aware_mysql_split`| Phone | AWARE app | MySQL | [link](../aware-mysql-split)
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| `aware_csv`| Phone | AWARE app | CSV files | [link](../aware-csv)
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| `aware_influxdb` (beta)| Phone | AWARE app | InfluxDB | [link](../aware-influxdb)
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| `fitbitjson_mysql`| Fitbit | JSON (per [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/)) | MySQL | [link](../fitbitjson-mysql)
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@ -476,12 +476,28 @@ Modify the following keys in your `config.yaml` depending on the [data stream](.
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--8<---- "docs/snippets/database.md"
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=== "aware_csv"
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=== "aware_mysql_split"
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| Key | Description |
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|---------------------|----------------------------------------------------------------------------------------------------------------------------|
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| `[DATABASE_GROUP]` | A database credentials group. Read the instructions below to set it up |
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--8<---- "docs/snippets/database.md"
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=== "aware_csv"
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| Key | Description|
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|---------------------|----------------------------------------------------------------------------------------------------------------------------|
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| `[FOLDER]` | Folder where you have to place a CSV file **per** phone sensor. Each file has to contain all the data from every participant you want to process. |
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=== "aware_influxdb"
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| Key | Description |
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|---------------------|----------------------------------------------------------------------------------------------------------------------------|
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| `[DATABASE_GROUP]` | A database credentials group. Read the instructions below to set it up |
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--8<---- "docs/snippets/database.md"
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@ -0,0 +1,78 @@
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# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
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library(RMariaDB)
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library(yaml)
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#' @description
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#' Auxiliary function to parse the connection credentials from a specifc group in ./credentials.yaml
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#' You can reause most of this function if you are connection to a DB or Web API.
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#' It's OK to delete this function if you don't need credentials, e.g., you are pulling data from a CSV for example.
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#' @param group the yaml key containing the credentials to connect to a database
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#' @preturn dbEngine a database engine (connection) ready to perform queries
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get_db_engine <- function(group){
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# The working dir is aways RAPIDS root folder, so your credentials file is always /credentials.yaml
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credentials <- read_yaml("./credentials.yaml")
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if(!group %in% names(credentials))
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stop(paste("The credentials group",group, "does not exist in ./credentials.yaml. The only groups that exist in that file are:", paste(names(credentials), collapse = ","), ". Did you forget to set the group in [PHONE_DATA_STREAMS][aware_mysql][DATABASE_GROUP] in config.yaml?"))
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dbEngine <- dbConnect(MariaDB(), db = credentials[[group]][["database"]],
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username = credentials[[group]][["user"]],
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password = credentials[[group]][["password"]],
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host = credentials[[group]][["host"]],
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port = credentials[[group]][["port"]])
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return(dbEngine)
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}
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# This file gets executed for each PHONE_SENSOR of each participant
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# If you are connecting to a database the env file containing its credentials is available at "./.env"
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# If you are reading a CSV file instead of a DB table, the @param sensor_container wil contain the file path as set in config.yaml
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# You are not bound to databases or files, you can query a web API or whatever data source you need.
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#' @description
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#' RAPIDS allows users to use the keyword "infer" (previously "multiple") to automatically infer the mobile Operative System a device was running.
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#' If you have a way to infer the OS of a device ID, implement this function. For example, for AWARE data we use the "aware_device" table.
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#'
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#' If you don't have a way to infer the OS, call stop("Error Message") so other users know they can't use "infer" or the inference failed,
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#' and they have to assign the OS manually in the participant file
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#'
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#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
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#' @param device A device ID string
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#' @return The OS the device ran, "android" or "ios"
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infer_device_os <- function(stream_parameters, device){
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dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
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query <- paste0("SELECT device_id,brand FROM aware_device WHERE device_id = '", device, "'")
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message(paste0("Executing the following query to infer phone OS: ", query))
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os <- dbGetQuery(dbEngine, query)
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dbDisconnect(dbEngine)
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if(nrow(os) > 0)
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return(os %>% mutate(os = ifelse(brand == "iPhone", "ios", "android")) %>% pull(os))
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else
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stop(paste("We cannot infer the OS of the following device id because it does not exist in the aware_device table:", device))
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return(os)
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}
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#' @description
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#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
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#'
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#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
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#' @param device A device ID string
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#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[CONTAINER] key in config.yaml
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#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
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#' @return A dataframe with the sensor data for device
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pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
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dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
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query <- paste0("SELECT ", paste(columns, collapse = ",")," FROM `", device, "_", sensor_container, "` WHERE ", columns$DEVICE_ID ," = '", device,"'")
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# Letting the user know what we are doing
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message(paste0("Executing the following query to download data: ", query))
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sensor_data <- dbGetQuery(dbEngine, query)
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dbDisconnect(dbEngine)
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if(nrow(sensor_data) == 0)
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warning(paste("The device '", device,"' did not have data in ", sensor_container))
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return(sensor_data)
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}
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@ -0,0 +1,337 @@
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PHONE_ACCELEROMETER:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_VALUES_0: double_values_0
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DOUBLE_VALUES_1: double_values_1
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DOUBLE_VALUES_2: double_values_2
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_VALUES_0: double_values_0
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DOUBLE_VALUES_1: double_values_1
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DOUBLE_VALUES_2: double_values_2
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_ACTIVITY_RECOGNITION:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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ACTIVITY_NAME: activity_name
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ACTIVITY_TYPE: activity_type
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CONFIDENCE: confidence
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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ACTIVITY_NAME: FLAG_TO_MUTATE
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ACTIVITY_TYPE: FLAG_TO_MUTATE
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CONFIDENCE: FLAG_TO_MUTATE
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MUTATION:
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COLUMN_MAPPINGS:
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ACTIVITIES: activities
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CONFIDENCE: confidence
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SCRIPTS: # List any python or r scripts that mutate your raw data
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- "src/data/streams/mutations/phone/aware/activity_recogniton_ios_unification.R"
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PHONE_APPLICATIONS_CRASHES:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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APPLICATION_NAME: application_name
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APPLICATION_VERSION: application_version
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ERROR_SHORT: error_short
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ERROR_LONG: error_long
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ERROR_CONDITION: error_condition
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IS_SYSTEM_APP: is_system_app
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_APPLICATIONS_FOREGROUND:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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APPLICATION_NAME: application_name
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IS_SYSTEM_APP: is_system_app
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_APPLICATIONS_NOTIFICATIONS:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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APPLICATION_NAME: application_name
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TEXT: text
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SOUND: sound
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VIBRATE: vibrate
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DEFAULTS: defaults
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FLAGS: flags
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_BATTERY:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BATTERY_STATUS: battery_status
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BATTERY_LEVEL: battery_level
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BATTERY_SCALE: battery_scale
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BATTERY_STATUS: FLAG_TO_MUTATE
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BATTERY_LEVEL: battery_level
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BATTERY_SCALE: battery_scale
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MUTATION:
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COLUMN_MAPPINGS:
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BATTERY_STATUS: battery_status
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SCRIPTS:
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- "src/data/streams/mutations/phone/aware/battery_ios_unification.R"
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PHONE_BLUETOOTH:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BT_ADDRESS: bt_address
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BT_NAME: bt_name
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BT_RSSI: bt_rssi
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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BT_ADDRESS: bt_address
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BT_NAME: bt_name
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BT_RSSI: bt_rssi
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_CALLS:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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CALL_TYPE: call_type
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CALL_DURATION: call_duration
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TRACE: trace
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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CALL_TYPE: FLAG_TO_MUTATE
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CALL_DURATION: call_duration
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TRACE: trace
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MUTATION:
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COLUMN_MAPPINGS:
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CALL_TYPE: call_type
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SCRIPTS:
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- "src/data/streams/mutations/phone/aware/calls_ios_unification.R"
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PHONE_CONVERSATION:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_ENERGY: double_energy
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INFERENCE: inference
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DOUBLE_CONVO_START: double_convo_start
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DOUBLE_CONVO_END: double_convo_end
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_ENERGY: double_energy
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INFERENCE: inference
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DOUBLE_CONVO_START: double_convo_start
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DOUBLE_CONVO_END: double_convo_end
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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- "src/data/streams/mutations/phone/aware/conversation_ios_timestamp.R"
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PHONE_KEYBOARD:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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PACKAGE_NAME: package_name
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BEFORE_TEXT: before_text
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CURRENT_TEXT: current_text
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IS_PASSWORD: is_password
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_LIGHT:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_LIGHT_LUX: double_light_lux
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ACCURACY: accuracy
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_LOCATIONS:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_LATITUDE: double_latitude
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DOUBLE_LONGITUDE: double_longitude
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DOUBLE_BEARING: double_bearing
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DOUBLE_SPEED: double_speed
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DOUBLE_ALTITUDE: double_altitude
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PROVIDER: provider
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ACCURACY: accuracy
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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DOUBLE_LATITUDE: double_latitude
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DOUBLE_LONGITUDE: double_longitude
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DOUBLE_BEARING: double_bearing
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DOUBLE_SPEED: double_speed
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DOUBLE_ALTITUDE: double_altitude
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PROVIDER: provider
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ACCURACY: accuracy
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_LOG:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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LOG_MESSAGE: log_message
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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IOS:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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LOG_MESSAGE: log_message
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
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PHONE_MESSAGES:
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ANDROID:
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RAPIDS_COLUMN_MAPPINGS:
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TIMESTAMP: timestamp
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DEVICE_ID: device_id
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MESSAGE_TYPE: message_type
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TRACE: trace
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MUTATION:
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COLUMN_MAPPINGS:
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SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
PHONE_SCREEN:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SCREEN_STATUS: screen_status
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
IOS:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SCREEN_STATUS: FLAG_TO_MUTATE
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCREEN_STATUS: screen_status
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
- "src/data/streams/mutations/phone/aware/screen_ios_unification.R"
|
||||
|
||||
PHONE_WIFI_CONNECTED:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
MAC_ADDRESS: mac_address
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
IOS:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
MAC_ADDRESS: mac_address
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
PHONE_WIFI_VISIBLE:
|
||||
ANDROID:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
SECURITY: security
|
||||
FREQUENCY: frequency
|
||||
RSSI: rssi
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
IOS:
|
||||
RAPIDS_COLUMN_MAPPINGS:
|
||||
TIMESTAMP: timestamp
|
||||
DEVICE_ID: device_id
|
||||
SSID: ssid
|
||||
BSSID: bssid
|
||||
SECURITY: security
|
||||
FREQUENCY: frequency
|
||||
RSSI: rssi
|
||||
MUTATION:
|
||||
COLUMN_MAPPINGS:
|
||||
SCRIPTS: # List any python or r scripts that mutate your raw data
|
||||
|
||||
|
|
@ -206,11 +206,32 @@ properties:
|
|||
|
||||
PHONE_DATA_STREAMS:
|
||||
type: object
|
||||
required: ["USE","aware_mysql", "aware_mysql_split", "aware_csv", "aware_influxdb"]
|
||||
properties:
|
||||
USE:
|
||||
type: string
|
||||
enum: ["aware_mysql", "aware_mysql_split", "aware_csv", "aware_influxdb"]
|
||||
aware_mysql:
|
||||
type: object
|
||||
required: ["DATABASE_GROUP"]
|
||||
properties:
|
||||
DATABASE_GROUP:
|
||||
type: string
|
||||
aware_mysql_split:
|
||||
type: object
|
||||
required: ["DATABASE_GROUP"]
|
||||
properties:
|
||||
DATABASE_GROUP:
|
||||
type: string
|
||||
aware_csv:
|
||||
type: object
|
||||
required: ["FOLDER"]
|
||||
properties:
|
||||
FOLDER:
|
||||
type: string
|
||||
aware_influxdb:
|
||||
type: object
|
||||
required: ["DATABASE_GROUP"]
|
||||
properties:
|
||||
DATABASE_GROUP:
|
||||
type: string
|
||||
|
|
@ -812,9 +833,11 @@ properties:
|
|||
|
||||
FITBIT_DATA_STREAMS:
|
||||
type: object
|
||||
required: ["USE","fitbitjson_mysql", "fitbitparsed_mysql", "fitbitjson_csv", "fitbitparsed_csv"]
|
||||
properties:
|
||||
USE:
|
||||
type: string
|
||||
enum: ["fitbitjson_mysql", "fitbitparsed_mysql", "fitbitjson_csv", "fitbitparsed_csv"]
|
||||
fitbitjson_mysql:
|
||||
type: object
|
||||
required: [DATABASE_GROUP, SLEEP_SUMMARY_LAST_NIGHT_END]
|
||||
|
|
|
|||
Loading…
Reference in New Issue