Implement the necessary functions for PSQL.

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)
+}
+