Add data stream for AWARE Micro server (#173)

* Add data stream for AWARE Micro server * Fix one documentation typo and one ommission
4 months ago · 10e896ca1d
5 changed files with 439 additions and 0 deletions
--- a/docs/datastreams/aware-micro-mysql.md
+++ b/docs/datastreams/aware-micro-mysql.md
@ -0,0 +1,15 @@
+# `aware_micro_mysql`
+
+This [data stream](../../datastreams/data-streams-introduction) handles iOS and Android sensor data collected with the [AWARE Framework's](https://awareframework.com/) [AWARE Micro](https://github.com/denzilferreira/aware-micro) server and stored in a MySQL database.
+
+## Container
+A MySQL database with a table per sensor, each containing the data for all participants. Sensor data is stored in a JSON field within each table called `data`
+
+The script to connect and download data from this container is at:
+```bash
+src/data/streams/aware_micro_mysql/container.R
+```
+
+## Format
+
+--8<---- "docs/snippets/aware_format.md"
--- a/docs/datastreams/data-streams-introduction.md
+++ b/docs/datastreams/data-streams-introduction.md
@ -16,6 +16,7 @@ For reference, these are the data streams we currently support:
 | Data Stream | Device | Format | Container | Docs
 |--|--|--|--|--|
 | `aware_mysql`| Phone | AWARE app | MySQL | [link](../aware-mysql)
+| `aware_micro_mysql`| Phone | AWARE Micro server | MySQL | [link](../aware-micro-mysql)
 | `aware_csv`| Phone | AWARE app | CSV files | [link](../aware-csv)
 | `aware_influxdb` (beta)| Phone | AWARE app | InfluxDB | [link](../aware-influxdb)
 | `fitbitjson_mysql`| Fitbit | JSON (per [Fitbit's API](https://dev.fitbit.com/build/reference/web-api/)) | MySQL | [link](../fitbitjson-mysql)
--- a/mkdocs.yml
+++ b/mkdocs.yml
@ -85,6 +85,7 @@ nav:
      - Introduction: datastreams/data-streams-introduction.md
      - Phone:
        - aware_mysql: datastreams/aware-mysql.md
+        - aware_micro_mysql: datastreams/aware-micro-mysql.md
        - aware_csv: datastreams/aware-csv.md
        - aware_influxdb (beta): datastreams/aware-influxdb.md
        - Mandatory Phone Format: datastreams/mandatory-phone-format.md
--- a/src/data/streams/aware_micro_mysql/container.R
+++ b/src/data/streams/aware_micro_mysql/container.R
@ -0,0 +1,85 @@
+# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
+library(RMariaDB)
+library(yaml)
+
+#' @description
+#' Auxiliary function to parse the connection credentials from a specifc group in ./credentials.yaml
+#' You can reause most of this function if you are connection to a DB or Web API.
+#' It's OK to delete this function if you don't need credentials, e.g., you are pulling data from a CSV for example.
+#' @param group the yaml key containing the credentials to connect to a database
+#' @preturn dbEngine a database engine (connection) ready to perform queries
+get_db_engine <- function(group){
+  # The working dir is aways RAPIDS root folder, so your credentials file is always /credentials.yaml
+  credentials <- read_yaml("./credentials.yaml")
+  if(!group %in% names(credentials))
+    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?"))
+  dbEngine <- dbConnect(MariaDB(), db = credentials[[group]][["database"]],
+                                    username = credentials[[group]][["user"]],
+                                    password = credentials[[group]][["password"]],
+                                    host = credentials[[group]][["host"]],
+                                    port = credentials[[group]][["port"]])
+  return(dbEngine)
+}
+
+# This file gets executed for each PHONE_SENSOR of each participant
+# If you are connecting to a database the env file containing its credentials is available at "./.env"
+# 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
+# You are not bound to databases or files, you can query a web API or whatever data source you need.
+
+#' @description
+#' RAPIDS allows users to use the keyword "infer" (previously "multiple") to automatically infer the mobile Operative System a device was running.
+#' 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.
+#'  
+#' 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, 
+#' and they have to assign the OS manually in the participant file
+#' 
+#' @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
+#' @return The OS the device ran, "android" or "ios"
+
+infer_device_os <- function(stream_parameters, device){
+  dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
+  query <- paste0("SELECT device_id,brand FROM aware_device WHERE device_id = '", device, "'")
+  message(paste0("Executing the following query to infer phone OS: ", query)) 
+  os <- dbGetQuery(dbEngine, query)
+  dbDisconnect(dbEngine)
+  
+  if(nrow(os) > 0)
+    return(os %>% mutate(os = ifelse(brand == "iPhone", "ios", "android")) %>% pull(os))
+  else
+    stop(paste("We cannot infer the OS of the following device id because it does not exist in the aware_device table:", device))
+  
+  return(os)
+}
+
+#' @description
+#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
+#' 
+#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
+#' @param device A device ID string
+#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[CONTAINER] key in config.yaml
+#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
+#' @return A dataframe with the sensor data for device
+
+pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
+  dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
+
+  select_items <- c()
+  for (column in columns) {
+    select_items <- append(select_items, paste0("data->>'$.", column, "' ", column))
+  }
+
+  query <- paste0("SELECT ", paste(select_items, collapse = ",")," FROM ", sensor_container, " WHERE ", columns$DEVICE_ID ," = '", device,"'")
+
+  # Letting the user know what we are doing
+  message(paste0("Executing the following query to download data: ", query)) 
+  sensor_data <- dbGetQuery(dbEngine, query)
+  
+  dbDisconnect(dbEngine)
+  
+  if(nrow(sensor_data) == 0)
+    warning(paste("The device '", device,"' did not have data in ", sensor_container))
+
+  return(sensor_data)
+}
+
--- a/src/data/streams/aware_micro_mysql/format.yaml
+++ b/src/data/streams/aware_micro_mysql/format.yaml
@ -0,0 +1,337 @@
+PHONE_ACCELEROMETER:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      DOUBLE_VALUES_0: double_values_0
+      DOUBLE_VALUES_1: double_values_1
+      DOUBLE_VALUES_2: double_values_2
+    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
+      DOUBLE_VALUES_0: double_values_0
+      DOUBLE_VALUES_1: double_values_1
+      DOUBLE_VALUES_2: double_values_2
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_ACTIVITY_RECOGNITION:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      ACTIVITY_NAME: activity_name
+      ACTIVITY_TYPE: activity_type
+      CONFIDENCE: confidence
+    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
+      ACTIVITY_NAME: FLAG_TO_MUTATE
+      ACTIVITY_TYPE: FLAG_TO_MUTATE
+      CONFIDENCE: FLAG_TO_MUTATE
+    MUTATION:
+      COLUMN_MAPPINGS:
+        ACTIVITIES: activities
+        CONFIDENCE: confidence
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+        - "src/data/streams/mutations/phone/aware/activity_recogniton_ios_unification.R"
+
+PHONE_APPLICATIONS_CRASHES:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      PACKAGE_NAME: package_name
+      APPLICATION_NAME: application_name
+      APPLICATION_VERSION: application_version
+      ERROR_SHORT: error_short
+      ERROR_LONG: error_long
+      ERROR_CONDITION: error_condition
+      IS_SYSTEM_APP: is_system_app
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_APPLICATIONS_FOREGROUND:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      PACKAGE_NAME: package_name
+      APPLICATION_NAME: application_name
+      IS_SYSTEM_APP: is_system_app
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_APPLICATIONS_NOTIFICATIONS:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      PACKAGE_NAME: package_name
+      APPLICATION_NAME: application_name
+      TEXT: text
+      SOUND: sound
+      VIBRATE: vibrate
+      DEFAULTS: defaults
+      FLAGS: flags
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_BATTERY:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      BATTERY_STATUS: battery_status
+      BATTERY_LEVEL: battery_level
+      BATTERY_SCALE: battery_scale
+    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
+      BATTERY_STATUS: FLAG_TO_MUTATE
+      BATTERY_LEVEL: battery_level
+      BATTERY_SCALE: battery_scale
+    MUTATION:
+      COLUMN_MAPPINGS:
+        BATTERY_STATUS: battery_status
+      SCRIPTS:
+        - "src/data/streams/mutations/phone/aware/battery_ios_unification.R"
+
+PHONE_BLUETOOTH:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      BT_ADDRESS: bt_address
+      BT_NAME: bt_name
+      BT_RSSI: bt_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
+      BT_ADDRESS: bt_address
+      BT_NAME: bt_name
+      BT_RSSI: bt_rssi
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_CALLS:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      CALL_TYPE: call_type
+      CALL_DURATION: call_duration
+      TRACE: trace
+    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
+      CALL_TYPE: FLAG_TO_MUTATE
+      CALL_DURATION: call_duration
+      TRACE: trace
+    MUTATION:
+      COLUMN_MAPPINGS:
+        CALL_TYPE: call_type
+      SCRIPTS:
+        - "src/data/streams/mutations/phone/aware/calls_ios_unification.R"
+
+PHONE_CONVERSATION:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      DOUBLE_ENERGY: double_energy
+      INFERENCE: inference
+      DOUBLE_CONVO_START: double_convo_start
+      DOUBLE_CONVO_END: double_convo_end
+    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
+      DOUBLE_ENERGY: double_energy
+      INFERENCE: inference
+      DOUBLE_CONVO_START: double_convo_start
+      DOUBLE_CONVO_END: double_convo_end
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+        - "src/data/streams/mutations/phone/aware/conversation_ios_timestamp.R"
+
+PHONE_KEYBOARD:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      PACKAGE_NAME: package_name
+      BEFORE_TEXT: before_text
+      CURRENT_TEXT: current_text
+      IS_PASSWORD: is_password
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_LIGHT:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      DOUBLE_LIGHT_LUX: double_light_lux
+      ACCURACY: accuracy
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_LOCATIONS:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      DOUBLE_LATITUDE: double_latitude
+      DOUBLE_LONGITUDE: double_longitude
+      DOUBLE_BEARING: double_bearing
+      DOUBLE_SPEED: double_speed
+      DOUBLE_ALTITUDE: double_altitude
+      PROVIDER: provider
+      ACCURACY: accuracy
+    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
+      DOUBLE_LATITUDE: double_latitude
+      DOUBLE_LONGITUDE: double_longitude
+      DOUBLE_BEARING: double_bearing
+      DOUBLE_SPEED: double_speed
+      DOUBLE_ALTITUDE: double_altitude
+      PROVIDER: provider
+      ACCURACY: accuracy
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_LOG:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      LOG_MESSAGE: log_message
+    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
+      LOG_MESSAGE: log_message
+    MUTATION:
+      COLUMN_MAPPINGS:
+      SCRIPTS: # List any python or r scripts that mutate your raw data
+
+PHONE_MESSAGES:
+  ANDROID:
+    RAPIDS_COLUMN_MAPPINGS:
+      TIMESTAMP: timestamp
+      DEVICE_ID: device_id
+      MESSAGE_TYPE: message_type
+      TRACE: trace
+    MUTATION:
+      COLUMN_MAPPINGS:
+      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
+