Download MCPD and PDCI data in Excel for the specified institute

DESCRIPTION

 Package: genesysr
-Version: 0.9.2
+Version: 0.9.3
 Title: Genesys PGR Client
 Description: Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>).
   Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
+export(api1_url)
 export(api_url)
 export(authorization)
 export(client_login)
+export(download_mcpd)
+export(download_pdci)
 export(fetch_accessions)
 export(filter_DOI)
 export(filter_ORIGCTY)

R/api-client.R

@@ -18,6 +18,7 @@
 #' 
 #' @param libname Library name
 #' @param pkgname Package name
+#' @keywords internal
 .onLoad <- function(libname, pkgname) {
   setup_production()
 }
@@ -80,6 +81,7 @@ authorization <- function(authorization) {
 }
 
 #' Ensure that environment has OAuth token
+#' @keywords internal
 .check_auth <- function() {
   if (is.null(.genesysEnv$Authorization)) {
     warning("You must first authorize with Genesys with user_login() or client_login(...).");
@@ -158,6 +160,7 @@ client_login <- function() {
 }
 
 
+#' @keywords internal
 .api_call <- function(path, method = "get") {
   .check_auth()
   resp <- httr::GET(api_url(path), httr::add_headers(
@@ -187,6 +190,21 @@ api_url <- function(path) {
   paste0(.genesysEnv$server, "/api/v0", path)
 }
 
+
+#' Get full Genesys API v1 URL for a specific path
+#'
+#' @param path relative path of the API v1 endpoint (e.g. \code{/me})
+#'
+#' @return Absolute URL to an API call
+#' @export
+#'
+#' @examples
+#'  api1_url("/me")
+api1_url <- function(path) {
+  paste0(.genesysEnv$server, "/api/v1", path)
+}
+
+#' @keywords internal
 .get <- function(path, query = NULL) {
   .check_auth()
   resp <- httr::GET(api_url(path), query = query, httr::add_headers(
@@ -206,6 +224,7 @@ api_url <- function(path) {
 #' @param content.type Content-Type of the body
 #'
 #' @return httr response
+#' @keywords internal
 .post <- function(path, query = NULL, body = NULL, content.type = "application/json") {
   .check_auth()
   content <- jsonlite::toJSON(body)

R/genesys.R

@@ -13,6 +13,7 @@
 # limitations under the License.
 
 #' Max pages to retrieve
+#' @keywords internal
 .MAX_ALLOWED_PAGES <- 500
 
 #' Who am i?
@@ -40,6 +41,7 @@ me <- function() {
 #' }
 #' 
 #' @return Paged data structure
+#' @keywords internal
 .fetch_accessions_page <- function(filters = list(), page = 0, size = 1000, selector = NULL) {
   start_time <- as.numeric(as.numeric(Sys.time())*1000, digits=15)
   resp <- .post(path = "/acn/filter", query=list(p = page, l = size), body = filters)
@@ -115,3 +117,76 @@ fetch_accessions <- function(filters = list(), page = NULL, size = 1000, selecto
   
   paged
 }
+
+
+#' Download all passport data for one genebank in Excel format and save it to disk
+#'
+#' @param instituteCode FAO WIEWS institute code
+#' @param file Target file name. Defaults to Genesys-provided file name in the current working directory.
+#'
+#' @examples
+#' \dontrun{
+#'   # Download MCPD passport data for NGA039
+#'   excelData <- download_mcpd("NGA039")
+#' }
+#' 
+#' @export
+#' @return HTTP response data
+download_mcpd <- function(instituteCode, file = NULL) {
+  if (is.na(instituteCode)) {
+    stop("instituteCode parameter is required")
+  }
+
+  if (is.null(file)) {
+    file <- paste0("genesys-accessions-", instituteCode, ".xlsx")
+  }
+
+  resp <- httr::POST(
+    api1_url(paste0("/wiews/", instituteCode, "/download")),
+    body = list(mcpd = "mcpd"), encode = "form",
+    httr::write_disk(file),
+    httr::add_headers(
+      Authorization = .genesysEnv$Authorization
+    )) # , httr::verbose())
+  if (httr::status_code(resp) != 200) {
+    stop("Genesys responded with HTTP status code ", httr::status_code(resp), ". Expected 200.")
+  }
+  invisible(resp)
+}
+
+
+#' Download PDCI data for one genebank in Excel format and save it to disk.
+#'
+#' @param instituteCode FAO WIEWS institute code
+#' @param file Target file name. Defaults to Genesys-provided file name in the current working directory.
+#'
+#' @examples
+#' \dontrun{
+#'   # Download PDCI  data for NGA039
+#'   excelData <- download_pdci("NGA039")
+#' }
+#' 
+#' @export
+#' @return HTTP response data
+download_pdci <- function(instituteCode, file = NULL) {
+  if (is.na(instituteCode)) {
+    stop("instituteCode parameter is required")
+  }
+  
+  if (is.null(file)) {
+    file <- paste0("genesys-pdci-", instituteCode, ".xlsx")
+  }
+  
+  resp <- httr::POST(
+    api1_url(paste0("/wiews/", instituteCode, "/download")),
+    body = list(pdci = "pdci"), encode = "form",
+    httr::write_disk(file),
+    httr::add_headers(
+      Authorization = .genesysEnv$Authorization
+    )) # , httr::verbose())
+  if (httr::status_code(resp) != 200) {
+    stop("Genesys responded with HTTP status code ", httr::status_code(resp), ". Expected 200.")
+  }
+  invisible(resp)
+}
+