junos
/
rapids
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity

Validate participant files without device ids

pull/130/head
JulioV 2021-03-28 14:31:44 -04:00
parent 87fbbbe402
commit 30ad3cd586
3 changed files with 41 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
src/data/datetime/process_time_segments.R
View File

@ -173,15 +173,10 @@ validate_event_segments <- function(segments){
return(segments)
}
prepare_event_segments <- function(segments, participant_data){
participant_devices <- get_devices_ids(participant_data)
if(length(participant_devices) == 0)
stop("There are no devices in the participant file.")
prepare_event_segments <- function(segments, participant_devices){
new_segments <- segments%>%
validate_event_segments() %>%
filter(device_id %in% participant_devices)
return(new_segments)
}
compute_time_segments <- function(){
@ -191,6 +186,11 @@ compute_time_segments <- function(){
participant_file <- snakemake@input[["participant_file"]]
message("Processing ",type, " time segments for ", pid,"'s ", participant_file)
participant_data <- yaml::read_yaml(participant_file)
participant_devices <- get_devices_ids(participant_data)
if(length(participant_devices) == 0)
stop("There are no device ids in this participant file for smartphones or wearables: ", participant_file)
if(type == "FREQUENCY"){
segments <- read_csv(segments_file, col_types = cols_only(label = "c", length = "i"), trim_ws = TRUE)
new_segments <- prepare_frequency_segments(segments)
@ -198,9 +198,8 @@ compute_time_segments <- function(){
segments <- read_csv(segments_file, col_types = cols_only(label = "c", start_time = "c",length = "c",repeats_on = "c",repeats_value = "i"), trim_ws = TRUE)
new_segments <- prepare_periodic_segments(segments)
} else if(type == "EVENT"){
participant_data <- yaml::read_yaml(participant_file)
segments <- read_csv(segments_file, col_types = cols_only(label = "c", event_timestamp = "d",length = "c",shift = "c",shift_direction = "i", device_id = "c"), trim_ws = TRUE)
new_segments <- prepare_event_segments(segments, participant_data)
new_segments <- prepare_event_segments(segments, participant_devices)
}
write.csv(new_segments %>% select(label) %>% distinct(label), snakemake@output[["segments_labels_file"]], row.names = FALSE, quote = FALSE)

17
src/data/streams/pull_phone_data.R
View File

@ -100,6 +100,22 @@ load_container_script <- function(stream_container){
}
}
get_devices_ids <- function(participant_data){
devices_ids = c()
for(device in participant_data)
for(attribute in names(device))
if(attribute == "DEVICE_IDS")
devices_ids <- c(devices_ids, device[[attribute]])
return(devices_ids)
}
validate_participant_file_without_device_ids <- function(participant_file){
participant_data <- yaml::read_yaml(participant_file)
participant_devices <- get_devices_ids(participant_data)
if(length(participant_devices) == 0)
stop("There are no device ids in this participant file for smartphones or wearables: ", participant_file)
}
pull_phone_data <- function(){
participant_file <- snakemake@input[["participant_file"]]
stream_format <- snakemake@input[["stream_format"]]
@ -111,6 +127,7 @@ pull_phone_data <- function(){
device_type <- "phone"
output_data_file <- snakemake@output[[1]]
validate_participant_file_without_device_ids(participant_file)
participant_data <- read_yaml(participant_file)
stream_schema <- read_yaml(stream_format)
rapids_schema <- read_yaml(rapids_schema_file)

17
src/data/streams/pull_wearable_data.R
View File

@ -68,6 +68,22 @@ load_container_script <- function(stream_container){
}
}
get_devices_ids <- function(participant_data){
devices_ids = c()
for(device in participant_data)
for(attribute in names(device))
if(attribute == "DEVICE_IDS")
devices_ids <- c(devices_ids, device[[attribute]])
return(devices_ids)
}
validate_participant_file_without_device_ids <- function(participant_file){
participant_data <- yaml::read_yaml(participant_file)
participant_devices <- get_devices_ids(participant_data)
if(length(participant_devices) == 0)
stop("There are no device ids in this participant file for smartphones or wearables: ", participant_file)
}
pull_wearable_data_main <- function(){
participant_file <- snakemake@input[["participant_file"]]
stream_format <- snakemake@input[["stream_format"]]
@ -81,6 +97,7 @@ pull_wearable_data_main <- function(){
output_data_file <- snakemake@output[[1]]
validate_participant_file_without_device_ids(participant_file)
participant_data <- read_yaml(participant_file)
stream_schema <- read_yaml(stream_format)
rapids_schema <- read_yaml(rapids_schema_file)