config.yaml

@@ -7,7 +7,6 @@ PIDS: [nokia_0000003]
 
 # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
 CREATE_PARTICIPANT_FILES:
-  USERNAMES_CSV: "data/external/example_usernames.csv"
   CSV_FILE_PATH: "data/external/example_participants.csv" # see docs for required format
   PHONE_SECTION:
     ADD: True

renv.lock

@@ -319,10 +319,10 @@
     },
     "dbplyr": {
       "Package": "dbplyr",
-      "Version": "2.1.1",
+      "Version": "2.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "1f37fa4ab2f5f7eded42f78b9a887182"
+      "Hash": "714005206038b1dda74cb1de85029a20"
     },
     "desc": {
       "Package": "desc",

rules/preprocessing.smk

@@ -4,19 +4,6 @@ rule create_example_participant_files:
     shell:
         "echo 'PHONE:\n  DEVICE_IDS: [a748ee1a-1d0b-4ae9-9074-279a2b6ba524]\n  PLATFORMS: [android]\n  LABEL: test-01\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\nFITBIT:\n  DEVICE_IDS: [a748ee1a-1d0b-4ae9-9074-279a2b6ba524]\n  LABEL: test-01\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\n' >> ./data/external/participant_files/example01.yaml && echo 'PHONE:\n  DEVICE_IDS: [13dbc8a3-dae3-4834-823a-4bc96a7d459d]\n  PLATFORMS: [ios]\n  LABEL: test-02\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\nFITBIT:\n  DEVICE_IDS: [13dbc8a3-dae3-4834-823a-4bc96a7d459d]\n  LABEL: test-02\n  START_DATE: 2020-04-23 00:00:00\n  END_DATE: 2020-05-04 23:59:59\n' >> ./data/external/participant_files/example02.yaml"
 
-rule prepare_participants_csv:
-    input:
-        username_list = config["CREATE_PARTICIPANT_FILES"]["USERNAMES_CSV"]
-    params:
-        data_configuration = config["PHONE_DATA_STREAMS"][config["PHONE_DATA_STREAMS"]["USE"]],
-        participants_table = "participants",
-        device_id_table = "light_sensor",
-        start_end_date_table = "esm"
-    output:
-        participants_file = config["CREATE_PARTICIPANT_FILES"]["CSV_FILE_PATH"]
-    script:
-        "../src/data/translate_usernames_into_participants_data.R"
-
 rule create_participants_files:
     input:
         participants_file = config["CREATE_PARTICIPANT_FILES"]["CSV_FILE_PATH"] 

src/data/streams/aware_postgresql/container.R

@@ -29,7 +29,6 @@ library(RPostgres)
 #   <stdin>:1:10: fatal error: libpq-fe.h: No such file or directory
 # compilation terminated.
 
-library(dbplyr)
 library(yaml)
 
 #' @description
@@ -106,101 +105,3 @@ pull_data <- function(stream_parameters, device, sensor, sensor_container, colum
   return(sensor_data)
 }
 
-#' @description
-#' Gets participants' IDs for specified usernames.
-#'
-#' @param stream_parameters The PHONE_DATA_STREAMS key in config.yaml. If you need specific parameters add them there.
-#' @param usernames A vector of usernames
-#' @param participants_container The name of the database table containing participants data, such as their username.
-#' @return A dataframe with participant IDs matching usernames
-
-pull_participants_ids <- function(stream_parameters, usernames, participants_container) {
-  dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
-  
-  query_participant_id <- tbl(dbEngine, participants_container) %>% 
-    filter(username %in% usernames) %>% 
-    select(username, id)
-  
-  message(paste0("Executing the following query to get the participant's id: \n", sql_render(query_participant_id)))
-  
-  participant_data <- query_participant_id %>% collect()
-
-  dbDisconnect(dbEngine)
-  
-  if(nrow(participant_data) == 0)
-    warning(paste("We could not find requested usernames (", usernames,  ") in ", participants_container))
-  
-  return(participant_data)
-}
-
-#' @description
-#' Gets participants' IDs for specified participant IDs
-#'
-#' @param stream_parameters The PHONE_DATA_STREAMS key in config.yaml. If you need specific parameters add them there.
-#' @param participants_ids A vector of numeric participant IDs
-#' @param device_id_container The name of the database table which will be used to determine distinct device ID. Ideally, a table that reliably contains data, but not too much.
-#' @return A dataframe with a row matching each distinct device ID with a participant ID
-
-pull_participants_device_ids <- function(stream_parameters, participants_ids, device_id_container) {
-  dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
-
-  query_device_id <- tbl(dbEngine, device_id_container) %>%
-    filter(participant_id %in% !!participants_ids) %>% 
-    group_by(participant_id) %>% 
-    distinct(device_id, .keep_all = FALSE)
-  
-  message(paste0("Executing the following query to get the distinct device IDs: \n", sql_render(query_device_id)))
-  
-  device_ids <- query_device_id %>% collect()
-  
-  dbDisconnect(dbEngine)
-  
-  if(nrow(device_ids) == 0)
-    warning(paste("We could not find device IDs for requested participant IDs (", participants_ids,  ") in ", device_id_container))
-  
-  return(device_ids)
-}
-
-#' @description
-#' Gets start and end datetimes for specified participant IDs.
-#'
-#' @param stream_parameters The PHONE_DATA_STREAMS key in config.yaml. If you need specific parameters add them there.
-#' @param participants_ids A vector of numeric participant IDs
-#' @param start_end_date_container The name of the database table which will be used to determine when a participant started and ended their participation. Briefing and debriefing EMAs can be meaningfully used here.
-#' @return A dataframe relating participant IDs with their start and end datetimes.
-
-pull_participants_start_end_dates <- function(stream_parameters, participants_ids, start_end_date_container) {
-  dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
-
-  query_timestamps <- tbl(dbEngine, start_end_date_container) %>% 
-    filter(
-      participant_id %in% !!participants_ids,
-      double_esm_user_answer_timestamp > 0
-    ) %>% 
-    group_by(participant_id) %>% 
-    summarise(
-      timestamp_min = min(double_esm_user_answer_timestamp, na.rm = TRUE),
-      timestamp_max = max(double_esm_user_answer_timestamp, na.rm = TRUE)
-    ) %>% 
-    select(participant_id, timestamp_min, timestamp_max)
-  
-  message(paste0("Executing the following query to get the starting and ending datetimes: \n", sql_render(query_timestamps)))
-  
-  start_end_timestamps <- query_timestamps %>% collect()
-  
-  if(nrow(start_end_timestamps) == 0)
-    warning(paste("We could not find datetimes for requested participant IDs (", participants_ids,  ") in ", start_end_date_container))
-
-  start_end_times <- start_end_timestamps %>% 
-    mutate(    
-      datetime_start = as_datetime(timestamp_min/1000, tz = "UTC"),
-      datetime_end = as_datetime(timestamp_max/1000, tz = "UTC")
-    ) %>% 
-    select(-c(timestamp_min, timestamp_max))
-  
-  dbDisconnect(dbEngine)
-  
-  return(start_end_times)
-}
-
-

src/data/translate_usernames_into_participants_data.R

@@ -1,62 +0,0 @@
-source("renv/activate.R")
-source("src/data/streams/aware_postgresql/container.R")
-
-library(RPostgres)
-library(magrittr)
-library(tidyverse)
-library(lubridate)
-
-prepare_participants_file <- function() {
-
-  username_list_csv_location <- snakemake@input[["username_list"]]
-
-  data_configuration <- snakemake@params[["data_configuration"]]
-  participants_container <- snakemake@params[["participants_table"]]
-  device_id_container <- snakemake@params[["device_id_table"]]
-  start_end_date_container <- snakemake@params[["start_end_date_table"]]
-
-  output_data_file <- snakemake@output[["participants_file"]]
-
-  platform <- "android"
-  pid_format <- "p%03d"
-  datetime_format <- "%Y-%m-%d %H:%M:%S"
-
-  participant_data <- read_csv(username_list_csv_location, col_types = "c", progress = FALSE)
-  usernames <- participant_data$label
-
-  participant_ids <- pull_participants_ids(data_configuration, usernames, participants_container)
-  participant_data %<>%
-    left_join(participant_ids, by = c("label" = "username")) %>%
-    rename(participant_id = id)
-
-  device_ids <- pull_participants_device_ids(data_configuration, participant_data$participant_id, device_id_container)
-  device_ids %<>%
-    group_by(participant_id) %>%
-    summarise(device_ids = list(unique(device_id)))
-  participant_data %<>%
-    left_join(device_ids, by = "participant_id")
-
-  start_end_datetimes <- pull_participants_start_end_dates(data_configuration, participant_data$participant_id, start_end_date_container)
-  participant_data %<>%
-    left_join(start_end_datetimes, by = "participant_id")
-
-  participant_data %<>%
-  mutate(
-    pid = sprintf(pid_format, participant_id),
-    start_date = strftime(datetime_start, format=datetime_format, tz = "UTC", usetz = FALSE), #TODO Check what timezone is expected
-    end_date = strftime(datetime_end, format=datetime_format, tz = "UTC", usetz = FALSE),
-    empatica_id = "placeholder", #TODO Provide in file?
-    device_id = map_chr(device_ids, str_c, collapse = ";"),
-    number_of_devices = map_int(device_ids, length),
-    fitbit_id = ""
-    ) %>%
-  rowwise() %>%
-  mutate(platform = str_c(replicate(number_of_devices, platform), collapse = ";")) %>%
-  ungroup() %>%
-  arrange(pid) %>%
-  select(pid, label, start_date, end_date, empatica_id, device_id, platform, fitbit_id)
-
-  write_csv(participant_data, output_data_file)
-}
-
-prepare_participants_file()