observationVariables_data = tryCatch({
res <- read.csv(system.file("apps/brapi/data/studies_observationVariables.csv",
package = "brapiTS"),
stringsAsFactors = FALSE)
res[, -c(1, 2)]
}, error = function(e) {
NULL
}
)
lst2arr <- function(lst, split = ";"){
if(lst == "") lst = jsonlite::fromJSON("{}")
if(length(lst) > 0) {
lst = safe_split(lst, split)
}
lst
}
observationVariables_list = function(
page = 0, pageSize = 10000,
observationVariableDbId = "any", ontologyXref = "any", ontologyDbId = "any",
methodDbId = "any", scaleDbId = "any",
name = "any", scale.datatype = "any", trait.class = "any"){
if (observationVariableDbId[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$observationVariableDbId %in% observationVariableDbId, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (ontologyXref[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$ontologyXref %in% ontologyXref, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (ontologyDbId[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$ontologyDbId %in% ontologyDbId, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (methodDbId[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$methodDbId %in% methodDbId, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (scaleDbId[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$scaleDbId %in% scaleDbId, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (name[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$name %in% name, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (scale.datatype[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$scale.datatype %in% scale.datatype, ]
if(nrow(observationVariables_data) == 0) return(NULL)
if (trait.class[1] != "any")
observationVariables_data <- observationVariables_data[
observationVariables_data$trait.class %in% trait.class, ]
if(nrow(observationVariables_data) == 0) return(NULL)
observationVariables_data <- observationVariables_data[
!duplicated(observationVariables_data$observationVariableDbId), ]
# paging here after filtering
pg = paging(observationVariables_data, page, pageSize)
observationVariables_data <- observationVariables_data[pg$recStart:pg$recEnd, ]
n = nrow(observationVariables_data)
out = list(n)
cn = colnames(observationVariables_data)
for(i in 1:n){
#out[[i]] <- as.list(observationVariables_data[i, -c(1, 2) ])
out[[i]] <- as.list(observationVariables_data[i, ])
#synonyms
out[[i]]$synonyms <- lst2arr(out[[i]]$synonyms)
#context of use
out[[i]]$contextOfUse <- lst2arr(out[[i]]$contextOfUse)
#trait
xt = which(stringr::str_detect(cn, "trait\\."))
xy = observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "trait\\.", "")
xy = as.list(xy)
}
names(out[[i]])[15] = "trait"
out[[i]]$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 = 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]]$method = xy
out[[i]][17:(max(xt) - 2)] = NULL
#scale
xt = which(stringr::str_detect(cn, "scale\\."))
xy = observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "scale\\.", "")
xy = as.list(xy)
}
out[[i]]$scale = xy
out[[i]]$scale[6:8] = NULL
#scale valid values
xt = which(stringr::str_detect(cn, "scale\\.validValues\\."))
xy = observationVariables_data[i, xt]
if (all(xy == "" | is.na(xy)) | is.null(xy)) xy = jsonlite::fromJSON("{}")
if (any(xy != "" | !is.na(xy) | !is.null(xy))) {
colnames(xy) = stringr::str_replace(colnames(xy), "scale\\.validValues\\.", "")
xy = as.list(xy)
}
if(jsonlite::toJSON(out[[i]]$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 = observationVariables_data[i, "defaultValue" ]
}
attr(out, "status") = list()
attr(out, "pagination") = pg$pagination
out
}
observationVariables = list(
metadata = list(
pagination = list(
pageSize = 0,
currentPage = 0,
totalCount = 0,
totalPages = 0
),
status = list(),
datafiles = list()
),
result = list()
)
process_observationVariables <- function(req, res, err){
#message("Hi")
prms <- names(req$params)
#message(str(req$params$observationVariableDbIds))
page <- ifelse('page' %in% prms, as.integer(req$params$page), 0)
pageSize <- ifelse('pageSize' %in% prms, as.integer(req$params$pageSize), 10000)
observationVariableDbId <- ifelse('observationVariableDbIds' %in% prms,
req$params$observationVariableDbIds %>% paste(collapse = ";"), "any")
ontologyXref <- ifelse('ontologyXrefs' %in% prms,
req$params$ontologyXrefs %>% paste(collapse = ";"), "any")
ontologyDbId <- ifelse('ontologyDbIds' %in% prms,
req$params$ontologyDbIds %>% paste(collapse = ";"), "any")
methodDbId <- ifelse('methodDbIds' %in% prms,
req$params$methodDbIds %>% paste(collapse = ";"), "any")
scaleDbId <- ifelse('scaleDbIds' %in% prms,
req$params$scaleDbIds %>% paste(collapse = ";"), "any")
name <- ifelse('names' %in% prms,
req$params$names %>% paste(collapse = ";"), "any")
scale.datatype <- ifelse('datatypes' %in% prms,
req$params$datatypes %>% paste(collapse = ";"), "any")
trait.class <- ifelse('traitClasses' %in% prms,
req$params$traitClasses %>% paste(collapse = ";"), "any")
observationVariableDbId <- safe_split(observationVariableDbId)
ontologyXref <- safe_split(ontologyXref)
ontologyDbId <- safe_split(ontologyDbId)
methodDbId <- safe_split(methodDbId)
scaleDbId <- safe_split(scaleDbId)
name <- safe_split(name)
scale.datatype <- safe_split(scale.datatype)
trait.class <- safe_split(trait.class)
observationVariables$result$data = observationVariables_list(
page, pageSize, observationVariableDbId, ontologyXref, ontologyDbId, methodDbId, scaleDbId,
name, scale.datatype, trait.class)
observationVariables$metadata$pagination = attr(observationVariables$result$data, "pagination")
if (is.null(observationVariables$result$data)) {
res$set_status(404)
observationVariables$metadata <-
brapi_status(100, "No matching results!"
, observationVariables$metadata$status)
observationVariables$result = list()
}
res$set_header("Access-Control-Allow-Methods", "POST")
res$json(observationVariables)
}
mw_observationVariables <<-
collector() %>%
get("/brapi/v1/variables-search[/]?", function(req, res, err){
res$set_status(405)
}) %>%
put("/brapi/v1/variables-search[/]?", function(req, res, err){
res$set_status(405)
}) %>%
post("/brapi/v1/variables-search[/]?", function(req, res, err){
process_observationVariables(req, res, err)
}) %>%
delete("/brapi/v1/variables-search[/]?", function(req, res, err){
res$set_status(405)
})
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