studies_search_data = tryCatch({
res <- read.csv(system.file("apps/brapi/data/studies.csv", package = "brapiTS"),
stringsAsFactors = FALSE)[, 1:13]
colnames(res)[2] = "name"
res
}, error = function(e) {
NULL
}
)
studies_search_additionalInfo_data = tryCatch({
res <- read.csv(system.file("apps/brapi/data/studies_additionalinfo.csv",
package = "brapiTS"),
stringsAsFactors = FALSE)
}, error = function(e) {
NULL
}
)
studies_search_list = function(studyType = "any", programDbId = "any",
locationDbId = "any", seasonDbId = "any",
germplasmDbIds = "any", observationVariableDbIds = "any",
active = "any",
sortBy = "none", sortOrder = "asc",
page = 0, pageSize = 100){
if(studyType != "any") {
studies_search_data <- studies_search_data[studies_search_data$studyType == studyType, ]
if(nrow(studies_search_data) == 0) return(NULL)
}
if(programDbId != "any") {
studies_search_data <- studies_search_data[studies_search_data$programDbId == programDbId, ]
if(nrow(studies_search_data) == 0) return(NULL)
}
if(active != "any") {
studies_search_data <- studies_search_data[studies_search_data$active == active, ]
if(nrow(studies_search_data) == 0) return(NULL)
}
if(locationDbId != "any" ) {
studies_search_data <- studies_search_data[studies_search_data$locationDbId == locationDbId, ]
if(nrow(studies_search_data) == 0) return(NULL)
}
if(seasonDbId != "any" ) {
studies_search_data <- studies_search_data[studies_search_data$seasons == seasonDbId, ]
if(nrow(studies_search_data) == 0) return(NULL)
}
# TODO germplasmDbIds
# TODO observationVariableDbIds
if(sortBy != "none" & sortBy %in% colnames(studies_search_data)){
dcr = ifelse(sortOrder == "asc", FALSE, TRUE)
studies_search_data <- studies_search_data[ order( studies_search_data[, sortBy], decreasing = dcr), ]
}
# paging here after filtering
pg = paging(studies_search_data, page, pageSize)
studies_search_data <- studies_search_data[pg$recStart:pg$recEnd, ]
n = nrow(studies_search_data)
out = list(n)
for(i in 1:n){
out[[i]] <- studies_search_data[i, ] %>% as.list
out[[i]]$seasons = safe_split(out[[i]]$seasons, ";") %>% as.list
additionalInfo =
studies_search_additionalInfo_data[studies_search_additionalInfo_data$studyDbId == studies_search_data$studyDbId[i],
-c(1)]
if(nrow(additionalInfo) == 0) {
#out[[i]] = as.list(out[[i]], additionalInfo = "") ### Challenge: how to get the empty object NOT the array!
additionalInfo = jsonlite::fromJSON("{}")
} else {
additionalInfo = additionalInfo[, !is.na(additionalInfo) %>% as.logical() ] %>% as.list
#additionalInfo = as.list(out[[i]], additionalInfo)
}
out[[i]]$additionalInfo = additionalInfo
#out[[i]] = list(out[[i]], additionalInfo = additionalInfo)
}
attr(out, "status") = list()
attr(out, "pagination") = pg$pagination
out
}
studies_search = list(
metadata = list(
pagination = list(
pageSize = 1000,
currentPage = 0,
totalCount = nrow(studies_search_data),
totalPages = 1
),
status = list(),
datafiles = list()
),
result = list()
)
process_studies_search <- function(req, res, err){
prms <- names(req$params)
studyType = ifelse('studyType' %in% prms, req$params$studyType, "any")
seasonDbId = ifelse('seasonDbId' %in% prms, req$params$seasonDbId, "any")
programDbId = ifelse('programDbId' %in% prms, req$params$programDbId, "any")
locationDbId = ifelse('locationDbId' %in% prms, req$params$locationDbId, "any")
active = ifelse('active' %in% prms, req$params$active, "any")
#germplasmDbIds = ifelse('germplasmDbIds' %in% prms, req$params$germplasmDbIds, "any")
germplasmDbIds = req$params[stringr::str_detect(names(req$params), "germplasmDbIds")] %>% paste(collapse = ",")
germplasmDbIds = safe_split(germplasmDbIds, ",")
#observationVariableDbIds = ifelse('observationVariableDbIds' %in% prms, req$params$observationVariableDbIds, "any")
observationVariableDbIds = req$params[stringr::str_detect(names(req$params), "observationVariableDbIds")] %>% paste(collapse = ",")
observationVariableDbIds = safe_split(observationVariableDbIds, ",")
sortBy = ifelse('sortBy' %in% prms, req$params$sortBy, "none")
sortOrder = ifelse('sortOrder' %in% prms, req$params$sortOrder, "asc")
page = ifelse('page' %in% prms, as.integer(req$params$page), 0)
pageSize = ifelse('pageSize' %in% prms, as.integer(req$params$pageSize), 1000)
studies_search$result$data = studies_search_list(
studyType, programDbId, locationDbId, seasonDbId,
germplasmDbIds, observationVariableDbIds,
active, sortBy, sortOrder,
page, pageSize)
studies_search$metadata$pagination = attr(studies_search$result$data, "pagination")#,
#status = attr(studies_search$result, "status"),
#datafiles = list())
if(is.null(studies_search$result$data)){
res$set_status(404)
studies_search$metadata <-
brapi_status(100,"No matching results.!"
, studies_search$metadata$status)
studies_search$result = list()
}
res$set_header("Access-Control-Allow-Methods", "GET")
res$json(studies_search)
}
mw_studies_search <<-
collector() %>%
get("/brapi/v1/studies-search[/]?", function(req, res, err){
process_studies_search(req, res, err)
}) %>%
put("/brapi/v1/studies-search[/]?", function(req, res, err){
res$set_status(405)
}) %>%
post("/brapi/v1/studies-search[/]?", function(req, res, err){
process_studies_search(req, res, err)
}) %>%
delete("/brapi/v1/studies-search[/]?", function(req, res, err){
res$set_status(405)
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.