#' ba_phenotypes_search
#'
#' Retrieve a list of observation units with the observed Phenotypes using a GET
#' method.
#'
#' @param con list, brapi connection object
#' @param germplasmDbId character, search for observation units where the
#' specified germplasm has been used/tested; e.g. "CML123";
#' default: ""
#' @param observationVariableDbId character, search for observation units where
#' the specified observation variable, supplied as
#' a character string of the internal observation
#' variable database identifier e.g. "CO-PH-123",
#' has been measured; default: ""
#' @param studyDbId character, search for observation units by an internal study
#' database identifier e.g. "1001"; default: ""
#' @param locationDbId character, search for observation units with the observed
#' Phenotypes by an internal location database identifier;
#' default: ""
#' @param trialDbId character, search for observation units with the observed
#' Phenotypes by an internal trial database identifier;
#' default: ""
#' @param programDbId character, search for observation units with the observed
#' Phenotypes by an internal program database identifier;
#' default: ""
#' @param seasonDbId character, search for observation units with the observed
#' Phenotypes by an internal season database identifier;
#' default: ""
#' @param observationLevel character, search for observation units with the
#' observed Phenotypes by specifying observation level
#' e.g. "plant"/"plot"; default: ""
#' @param observationTimeStampRangeStart chararcter, specifying the time stamp
#' range start from which to search for the
#' observation units with the observed
#' Phenotypes; default: ""
#' @param observationTimeStampRangeEnd character, specifying the time stamp range
#' end to which to search for the observation
#' units with the observed Phenotypes;
#' default: ""
#' @param pageSize integer, items per page to be returned; default: 1000
#' @param page integer, the requested page to be returned; default: 0 (1st page)
#' @param rclass character, class of the object to be returned; default: "tibble"
#' , possible other values: "json"/"list"/"data.frame"
#'
#' @return An object of class as defined by rclass containing the observation
#' units with the observed Phenotypes.
#'
#' @note Tested against: test-server
#' @note BrAPI Version: 1.2
#' @note BrAPI Status: active
#'
#' @author Reinhard Simon, Maikel Verouden
#' @references \href{https://github.com/plantbreeding/API/blob/V1.2/Specification/Phenotypes/PhenotypesSearch_GET.md}{github}
#'
#' @family studies
#' @family phenotyping
#' @import tibble
#' @export
### to be put in front of @import #' @example inst/examples/ex-ba_studies_search.R
ba_phenotypes_search <- function(con = NULL,
germplasmDbId = "",
observationVariableDbId = "",
studyDbId = "",
locationDbId = "",
trialDbId = "",
programDbId = "",
seasonDbId = "",
observationLevel = "",
observationTimeStampRangeStart = "",
observationTimeStampRangeEnd = "",
pageSize = 1000,
page = 0,
rclass = c("tibble", "data.frame",
"list", "json")) {
ba_check(con = con, verbose = FALSE, brapi_calls = "phenotypes-search-get")
check_character(germplasmDbId, observationVariableDbId, studyDbId,
locationDbId, trialDbId, programDbId, seasonDbId,
observationLevel, observationTimeStampRangeStart,
observationTimeStampRangeEnd)
rclass <- match.arg(rclass)
brp <- get_brapi(con) %>% paste0("phenotypes-search")
callurl <- get_endpoint(brp,
germplasmDbId = germplasmDbId,
observationVariableDbId = observationVariableDbId,
studyDbId = studyDbId,
locationDbId = locationDbId,
trialDbId = trialDbId,
programDbId = programDbId,
seasonDbId = seasonDbId,
observationLevel = observationLevel,
observationTimeStampRangeStart = observationTimeStampRangeStart,
observationTimeStampRangeEnd = observationTimeStampRangeEnd,
page = page,
pageSize = pageSize)
out <- NULL
out <- try({
resp <- brapiGET(url = callurl, con = con)
cont <- httr::content(x = resp, as = "text", encoding = "UTF-8")
if (rclass != "json") {
out <- baps2rclass(cont, rclass)
} else {
out <- cont
}
out
})
if (!is.null(out)) {
class(out) <- c(class(out), "ba_phenotypes_search_get")
} else {
message("Server did not return a result!
Check your query parameters or contact the server administrator.")
}
show_metadata(resp)
return(out)
}
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