studies_observationVariables_data = tryCatch({
res <- read.csv(system.file("apps/brapi/data/studies_observationVariables.csv",
package = "brapiTS"),
stringsAsFactors = FALSE)
res
}, error = function(e) {
NULL
}
)
lst2arr <- function(lst, split = ";"){
if(lst == "") lst = jsonlite::fromJSON("{}")
if(length(lst) > 0) {
lst = safe_split(lst, split)
}
lst
}
studies_observationVariables_list = function(studyDbId = "any"){
studies_observationVariables_data <- studies_observationVariables_data[studies_observationVariables_data$studyDbId == studyDbId, ]
if(nrow(studies_observationVariables_data) == 0) return(NULL)
# paging here after filtering
n = nrow(studies_observationVariables_data)
out = list(n)
cn = colnames(studies_observationVariables_data)
for(i in 1:n){
out[[i]] <- as.list(studies_observationVariables_data[i, -c(1, 2) ])
#synonyms
out[[i]]$synonyms <- lst2arr(out[[i]]$synonyms)
#context of use
out[[i]]$contextOfUse <- lst2arr(out[[i]]$contextOfUse)
#trait
xt = which(stringr::str_detect(cn, "trait\\."))
xy = studies_observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "trait\\.", "")
xy = as.list(xy)
}
names(out[[i]])[15] = "trait"
out[[i]]$trait = xy
out[[i]][16:(max(xt) - 2)] = NULL
out[[i]]$trait$synonyms <- lst2arr(out[[i]]$trait$synonyms)
out[[i]]$trait$alternativeAbbreviations <- lst2arr(out[[i]]$trait$alternativeAbbreviations)
#method
xt = which(stringr::str_detect(cn, "method\\."))
xy = studies_observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "method\\.", "")
xy = as.list(xy)
}
names(out[[i]])[16] = "method"
out[[i]]$method = xy
out[[i]][17:(max(xt) - 2)] = NULL
#scale
xt = which(stringr::str_detect(cn, "scale\\."))
xy = studies_observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "scale\\.", "")
xy = as.list(xy)
}
out[[i]]$scale = xy
out[[i]]$scale[6:8] = NULL
#scale valid values
xt = which(stringr::str_detect(cn, "scale\\.validValues\\."))
xy = studies_observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "scale\\.validValues\\.", "")
xy = as.list(xy)
}
if(jsonlite::toJSON(out[[i]]$scale) != "{}") out[[i]]$scale$validValues = xy
#scale valid values categories
if(jsonlite::toJSON(out[[i]]$scale) != "{}") out[[i]]$scale$validValues$categories = lst2arr(xy$categories, "; ")
out[[i]]$defaultValue = studies_observationVariables_data[i, "defaultValue" ]
}
attr(out, "status") = list()
#attr(out, "pagination") = pg$pagination
res = list(studyDbId = studyDbId,
trialName = studies_observationVariables_data[1, 2],
data = out)
res
}
studies_observationVariables = list(
metadata = list(
pagination = list(
pageSize = 0,
currentPage = 0,
totalCount = 0,
totalPages = 0
),
status = list(),
datafiles = list()
),
result = list()
)
process_studies_observationVariables <- function(req, res, err){
studyDbId = basename(stringr::str_replace(req$path, "/observationVariables[/]?", ""))
studies_observationVariables$result = studies_observationVariables_list(studyDbId)
if(is.null(studies_observationVariables$result$data)){
res$set_status(404)
studies_observationVariables$metadata <-
brapi_status(100,"No matching results.!"
, studies_observationVariables$metadata$status)
studies_observationVariables$result = list()
}
res$set_header("Access-Control-Allow-Methods", "GET")
res$json(studies_observationVariables)
}
mw_studies_observationVariables <<-
collector() %>%
get("/brapi/v1/studies/[0-9a-zA-Z]{1,12}/observationVariables[/]?", function(req, res, err){
process_studies_observationVariables(req, res, err)
}) %>%
put("/brapi/v1/studies/[0-9a-zA-Z]{1,12}/observationVariables[/]?", function(req, res, err){
res$set_status(405)
}) %>%
post("/brapi/v1/studies/[0-9a-zA-Z]{1,12}/observationVariables[/]?", function(req, res, err){
res$set_status(405)
}) %>%
delete("/brapi/v1/studies/[0-9a-zA-Z]{1,12}/observationVariables[/]?", function(req, res, err){
res$set_status(405)
})
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