#' get_data_from_num
#' @export
get_data_from_num <- function(cohorte_num,
num_type,
cohort,
progress = NULL,
icd_prefix = '',
neg ,
config,
step_p) {
if(!is.null(progress)) {
step_p<-step_p+1
progress$set(step_p, detail = stringr::str_interp('Loading ${cohort} patients') )
} else {
cat('Loading cases...')
}
cohort_data <- list()
#cases$patients <- get_patients(base_url, token, num = cohorte_num, num_type = "cohorte", only_num = "false", count = "true" )
cohort_data$patients <- DWHtools2::get_patients(num = cohorte_num, num_type = num_type, only_num = FALSE, count = TRUE, config)
#cases$concepts <- get_concepts(base_url, token, num = cohorte_num, num_type = "cohorte")
cohort_data$concepts <- DWHtools2::get_concepts(num = cohorte_num, num_type = num_type, config)
if(!is.null(progress)) {
step_p<-step_p
progress$set(step_p, detail = stringr::str_interp('Loading ${cohort} concepts') )
} else {
cat('concepts...')
}
if (!is.null(cohort_data$concepts)) {
cohort_data$concepts <- modify_code_given_certitude(cohort_data$concepts, neg)
cohort_data$concepts$group = cohort
}
cohort_data$patients$group = cohort
if(!is.null(progress)) {
step_p<-step_p+1
progress$set(step_p, detail = stringr::str_interp('Loading ${cohort} bio') )
} else {
cat('bio...')
}
#cases$bio <- get_data(base_url, token, num = cohorte_num, num_type = "cohorte", data_type = 'bio_num')
cohort_data$bio <- DWHtools2::get_data(num = cohorte_num, num_type = num_type, data_type = 'bio_num', config = config)
if (!is.null(cohort_data$bio)) {
cohort_data$bio$group = cohort
#cohort_data$bio <- preprocess_bio_concepts(cohort_data$bio, type = 'iep', nb_occurrences =1, map_loinc = TRUE)
}
if(!is.null(progress)) {
step_p<-step_p+1
progress$set(step_p, detail = stringr::str_interp('Loading ${cohort} cim10') )
} else {
cat('cim10...')
}
#cases$cim <- get_data(base_url, token, num = cohorte_num, num_type = "cohorte", data_type = 'cim10')
cohort_data$cim <- DWHtools2::get_data(num = cohorte_num, num_type = num_type, data_type = 'cim10', config = config)
if (!is.null(cohort_data$cim)) {
cohort_data$cim$group = cohort
#cohort_data$cim <- preprocess_cim(cohort_data$cim, scale1, icd_prefix = icd_prefix, nb_occurrences = 1)
}
if(is.null(progress)) {
cat('Done\n')
}
return (cohort_data)
}
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