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added brapi_post_search_studies() and brapi_post_search_trials()
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,171 @@ | ||
| #' @title | ||
| #' post /search/studies | ||
| #' | ||
| #' @description | ||
| #' Submit a search request for Studies | ||
| #' | ||
| #' @param con list; required: TRUE; BrAPI connection object | ||
| #' @param active logical; required: FALSE; Is this study currently active; | ||
| #' default: NA, other possible values: TRUE | FALSE | ||
| #' @param commonCropNames vector of type character; required: FALSE; Common crop | ||
| #' name(s) of the studies to search for; default: "", when using | ||
| #' multiple values supply as c("value1", "value2"). | ||
| #' @param externalReferenceIDs vector of type character; required: FALSE; | ||
| #' External reference identifier(s) to search for. Could be a simple strings | ||
| #' or a URIs (use with `externalReferenceSources` parameter).; default: | ||
| #' "", when using multiple values supply as c("value1", | ||
| #' "value2"). | ||
| #' @param externalReferenceSources vector of type character; required: FALSE; | ||
| #' Source system or database identifier(s) of an external reference(s) to | ||
| #' search for (use with `externalReferenceIDs` parameter); default: | ||
| #' "", when using multiple values supply as c("value1", | ||
| #' "value2"). | ||
| #' @param germplasmDbIds vector of type character; required: FALSE; Unique | ||
| #' germplasm indentifier(s) to search for; default: "", when using | ||
| #' multiple values supply as c("value1", "value2"). | ||
| #' @param germplasmNames vector of type character; required: FALSE; Human | ||
| #' readable germplasm name(s) to search for; default: "", when | ||
| #' using multiple values supply as c("value1", "value2"). | ||
| #' @param locationDbIds vector of type character; required: FALSE; The unique | ||
| #' location identifier(s) to search for; default: "", when using | ||
| #' multiple values supply as c("value1", "value2"). | ||
| #' @param locationNames vector of type character; required: FALSE; A human | ||
| #' readable location name(s) to search for; default: "", when using | ||
| #' multiple values supply as c("value1", "value2"). | ||
| #' @param observationVariableDbIds vector of type character; required: FALSE; | ||
| #' Unique observation variable indentifier(s) to search for; default: | ||
| #' "", when using multiple values supply as c("value1", | ||
| #' "value2"). | ||
| #' @param observationVariableNames vector of type character; required: FALSE; | ||
| #' Observation variable name(s) to search for; default: "", when | ||
| #' using multiple values supply as c("value1", "value2"). | ||
| #' @param programDbIds vector of type character; required: FALSE; Unique program | ||
| #' identifier(s) to search for; default: "", when using multiple | ||
| #' values supply as c("value1", "value2"). | ||
| #' @param programNames vector of type character; required: FALSE; Program | ||
| #' name(s) to search for; default: "", when using multiple values | ||
| #' supply as c("value1", "value2"). | ||
| #' @param seasonDbIds vector of type character; required: FALSE; Unique season | ||
| #' identifier(s) to search for; default: "", when using multiple | ||
| #' values supply as c("value1", "value2"). | ||
| #' @param sortBy character; required: FALSE; Name of one of the fields within | ||
| #' the study object on which results can be sorted; default: "". | ||
| #' @param sortOrder character; required: FALSE; Order results should be sorted, | ||
| #' e.g. "ASC" or "DESC"; default: "". | ||
| #' @param studyCodes vector of type character; required: FALSE; Short human | ||
| #' readable study code(s) to search for; default: "", when using | ||
| #' multiple values supply as c("value1", "value2"). | ||
| #' @param studyDbIds vector of type character; required: FALSE; Unique study | ||
| #' identifier(s) to search for; default: "", when using multiple | ||
| #' values supply as c("value1", "value2"). | ||
| #' @param studyNames vector of type character; required: FALSE; Study name(s) to | ||
| #' filter search results for; default: "", when using multiple | ||
| #' values supply as c("value1", "value2"). | ||
| #' @param studyPUIs vector of type character; required: FALSE; Study permanent | ||
| #' unique identifier(s) to search for. For example, a URI or DOI; default: | ||
| #' "", when using multiple values supply as c("value1", | ||
| #' "value2"). | ||
| #' @param studyTypes vector of type character; required: FALSE; Study type(s) | ||
| #' being performed to search for, e.g. "Yield Trial", *etc.*; | ||
| #' default: "", when using multiple values supply as | ||
| #' c("value1", "value2"). | ||
| #' @param trialDbIds vector of type character; required: FALSE; Unique trial | ||
| #' identifier(s) to search for; default: "", when using multiple | ||
| #' values supply as c("value1", "value2"). | ||
| #' @param trialNames vector of type character; required: FALSE; Human readable | ||
| #' trial name(s) to search for; default: "", when using multiple | ||
| #' values supply as c("value1", "value2"). | ||
| #' @param page integer; required: FALSE; Used to request a specific page of data | ||
| #' to be returned. The page indexing starts at 0 (the first page is | ||
| #' `page = 0`). Default is `0`. | ||
| #' @param pageSize integer; required: FALSE; The size of the pages to be | ||
| #' returned. Default is `1000`. | ||
| #' | ||
| #' @details Advanced searching for the studies resource. Function will return | ||
| #' either the search results (Status 200 for an immediate response) or a | ||
| #' `searchResultsDbId` (Status 202 for both a saved and an asynchronous | ||
| #' search). | ||
| #' | ||
| #' @return data.frame | ||
| #' | ||
| #' @author Maikel Verouden | ||
| #' | ||
| #' @references \href{https://app.swaggerhub.com/apis/PlantBreedingAPI/BrAPI-Core/2.0#/Studies/post_search_studies }{BrAPI SwaggerHub} | ||
| #' | ||
| #' @family brapi_2.0 | ||
| #' @family brapi-core | ||
| #' @family Studies | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' con <- brapi_db()$testserver | ||
| #' con[["token"]] <- "YYYY" | ||
| #' | ||
| #' TO BE ADDED STILL | ||
| #' } | ||
| #' | ||
| #' @export | ||
| brapi_post_search_studies <- function(con = NULL, | ||
| active = NA, | ||
| commonCropNames = '', | ||
| externalReferenceIDs = '', | ||
| externalReferenceSources = '', | ||
| germplasmDbIds = '', | ||
| germplasmNames = '', | ||
| locationDbIds = '', | ||
| locationNames = '', | ||
| observationVariableDbIds = '', | ||
| observationVariableNames = '', | ||
| programDbIds = '', | ||
| programNames = '', | ||
| seasonDbIds = '', | ||
| sortBy = '', | ||
| sortOrder = '', | ||
| studyCodes = '', | ||
| studyDbIds = '', | ||
| studyNames = '', | ||
| studyPUIs = '', | ||
| studyTypes = '', | ||
| trialDbIds = '', | ||
| trialNames = '', | ||
| page = 0, | ||
| pageSize = 1000) { | ||
| ## Create a list of used arguments | ||
| usedArgs <- brapirv2:::brapi_usedArgs(origValues = FALSE) | ||
| ## Check if BrAPI server can be reached given the connection details | ||
| brapi_checkCon(con = usedArgs[["con"]], verbose = FALSE) | ||
| ## Check validity of used and required arguments | ||
| brapirv2:::brapi_checkArgs(usedArgs, reqArgs = "") | ||
| ## Obtain the call url | ||
| callurl <- brapirv2:::brapi_POST_callURL(usedArgs = usedArgs, | ||
| callPath = "/search/studies", | ||
| reqArgs = "", | ||
| packageName = "BrAPI-Core", | ||
| callVersion = 2.0) | ||
| ## Build the Body | ||
| callbody <- brapirv2:::brapi_POST_callBody(usedArgs = usedArgs, | ||
| reqArgs = "") | ||
|
|
||
| try({ | ||
| ## Make the call and receive the response | ||
| resp <- brapirv2:::brapi_POST(url = callurl, body = callbody, usedArgs = usedArgs) | ||
| ## Message about call status | ||
| if (httr::status_code(resp) == 200) { | ||
| message(paste0("Immediate Response.", "\n")) | ||
| } else if (httr::status_code(resp) == 202) { | ||
| message(paste0("Saved or Asynchronous Response has provided a searchResultsDbId.", "\n")) | ||
| message(paste0("Use the GET /search/studies/{searchResultsDbId} call to retrieve the paginated output.", "\n")) | ||
| } else { | ||
| stop(paste0("The POST /search/studies call resulted in Server status, ", httr::http_status(resp)[["message"]])) | ||
| } | ||
| ## Extract the content from the response object in human readable form | ||
| cont <- httr::content(x = resp, as = "text", encoding = "UTF-8") | ||
| ## Convert the content object into a data.frame | ||
| out <- brapirv2:::brapi_result2df(cont, usedArgs) | ||
| }) | ||
| ## Set class of output | ||
| class(out) <- c(class(out), "brapi_post_search_studies") | ||
| ## Show pagination information from metadata | ||
| brapirv2:::brapi_serverinfo_metadata(cont) | ||
| return(out) | ||
| } |
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