Revert "Correct the name of a field."

This reverts commit b335561a55.

It was actually correct.

.gitattributes

@@ -0,0 +1,7 @@
+# We'll let Git's auto-detection algorithm infer if a file is text. If it is,
+# enforce LF line endings regardless of OS or git configurations.
+* text=auto eol=lf
+
+# Isolate binary files in case the auto-detection algorithm fails and
+# marks them as text files (which could brick them).
+*.{png,jpg,jpeg,gif,webp,woff,woff2} binary

config.yaml

@@ -3,7 +3,7 @@
 ########################################################################################################################
 
 # See https://www.rapids.science/latest/setup/configuration/#participant-files
-PIDS: [test01]
+PIDS: [nokia_0000003]
 
 # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
 CREATE_PARTICIPANT_FILES:
@@ -28,11 +28,11 @@ TIME_SEGMENTS: &time_segments
 TIMEZONE: 
     TYPE: SINGLE
     SINGLE:
-      TZCODE: America/New_York
+      TZCODE: Europe/Ljubljana
     MULTIPLE:
       TZCODES_FILE: data/external/multiple_timezones_example.csv
       IF_MISSING_TZCODE: STOP
-      DEFAULT_TZCODE: America/New_York
+      DEFAULT_TZCODE: Europe/Ljubljana
       FITBIT: 
         ALLOW_MULTIPLE_TZ_PER_DEVICE: False
         INFER_FROM_SMARTPHONE_TZ: False
@@ -43,12 +43,15 @@ TIMEZONE:
 
 # See https://www.rapids.science/latest/setup/configuration/#data-stream-configuration
 PHONE_DATA_STREAMS:
-  USE: aware_mysql
+  USE: aware_postgresql
   
   # AVAILABLE:
   aware_mysql: 
     DATABASE_GROUP: MY_GROUP
 
+  aware_postgresql:
+    DATABASE_GROUP: PSQL_STRAW
+  
   aware_csv:
     FOLDER: data/external/aware_csv
   
@@ -177,10 +180,10 @@ PHONE_BLUETOOTH:
 
 # See https://www.rapids.science/latest/features/phone-calls/
 PHONE_CALLS:
-  CONTAINER: calls
+  CONTAINER: call
   PROVIDERS:
     RAPIDS:
-      COMPUTE: False
+      COMPUTE: True
       FEATURES_TYPE: EPISODES # EVENTS or EPISODES
       CALL_TYPES: [missed, incoming, outgoing]
       FEATURES:

renv.lock

@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.0.0",
+    "Version": "4.1.2",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -93,12 +93,19 @@
       "Repository": "CRAN",
       "Hash": "0e4f634f2bb38e325717d384a877ccc0"
     },
-    "Rcpp": {
-      "Package": "Rcpp",
-      "Version": "1.0.5",
+    "RPostgres": {
+      "Package": "RPostgres",
+      "Version": "1.4.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "125dc7a0ed375eb68c0ce533b48d291f"
+      "Hash": "dcc7c6bfb144ff8723f7d525ca4a39f0"
+    },
+    "Rcpp": {
+      "Package": "Rcpp",
+      "Version": "1.0.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "dab19adae4440ae55aa8a9d238b246bb"
     },
     "RcppArmadillo": {
       "Package": "RcppArmadillo",
@@ -354,10 +361,10 @@
     },
     "ellipsis": {
       "Package": "ellipsis",
-      "Version": "0.3.1",
+      "Version": "0.3.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a"
+      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
     },
     "entropy": {
       "Package": "entropy",
@@ -529,10 +536,10 @@
     },
     "hms": {
       "Package": "hms",
-      "Version": "0.5.3",
+      "Version": "1.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "726671f634529d470545f9fd1a9d1869"
+      "Hash": "5b8a2dd0fdbe2ab4f6081e6c7be6dfca"
     },
     "htmlTable": {
       "Package": "htmlTable",
@@ -1166,10 +1173,10 @@
     },
     "vctrs": {
       "Package": "vctrs",
-      "Version": "0.3.6",
+      "Version": "0.3.8",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "5cf1957f93076c19fdc81d01409d240b"
+      "Hash": "ecf749a1b39ea72bd9b51b76292261f1"
     },
     "viridis": {
       "Package": "viridis",

src/data/streams/aware_postgresql/container.R

@@ -0,0 +1,107 @@
+# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
+library(RPostgres)
+# Needs libpq-dev for compiling from source.
+
+# Error installing package 'RPostgres':
+#   =====================================
+#   
+#   * installing *source* package 'RPostgres' ...
+# ** package 'RPostgres' successfully unpacked and MD5 sums checked
+# ** using staged installation
+# Using PKG_CFLAGS=
+#   Using PKG_LIBS=-lpq
+# Using PKG_PLOGR=
+#   ------------------------- ANTICONF ERROR ---------------------------
+#   Configuration failed because libpq was not found. Try installing:
+#   * deb: libpq-dev (Debian, Ubuntu, etc)
+# * rpm: postgresql-devel (Fedora, EPEL)
+# * rpm: postgreql8-devel, psstgresql92-devel, postgresql93-devel, or postgresql94-devel (Amazon Linux)
+# * csw: postgresql_dev (Solaris)
+# * brew: libpq (OSX)
+# If libpq is already installed, check that either:
+#   (i)  'pkg-config' is in your PATH AND PKG_CONFIG_PATH contains
+# a libpq.pc file; or
+# (ii) 'pg_config' is in your PATH.
+# If neither can detect , you can set INCLUDE_DIR
+# and LIB_DIR manually via:
+#   R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
+# --------------------------[ ERROR MESSAGE ]----------------------------
+#   <stdin>:1:10: fatal error: libpq-fe.h: No such file or directory
+# compilation terminated.
+
+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(Postgres(), db = credentials[[group]][["database"]],
+                        user = 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$DATABASE_GROUP)
+  #query <- paste0("SELECT device_id,brand FROM aware_device WHERE device_id = '", device, "'")
+  #message(paste0("Executing the following query to infer phone OS: ", query)) 
+  #os <- dbGetQuery(dbEngine, query)
+  #dbDisconnect(dbEngine)
+  
+  #if(nrow(os) > 0)
+  #  return(os %>% mutate(os = ifelse(brand == "iPhone", "ios", "android")) %>% pull(os))
+  #else
+  stop(paste("We cannot infer the OS of the following device id because the aware_device table does not exist."))
+  
+  #return(os)
+}
+
+#' @description
+#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
+#' 
+#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
+#' @param device A device ID string
+#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[CONTAINER] key in config.yaml
+#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
+#' @return A dataframe with the sensor data for device
+
+pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
+  dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
+  query <- paste0("SELECT ", paste(columns, 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)
+}
+

src/data/streams/aware_postgresql/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
+