Merge pull request #105 from nationalparkservice/EMLeditor_DataStore_…

…v6_dev

DataStore v6 dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: EMLeditor
 Title: View and Edit EML Metadata
-Version: 0.1.0.7
+Version: 0.1.1
 Authors@R: c(
     person(given="Robert", family="Baker", email="robert_baker@nps.gov",
            role = c("aut", "cre"),

NEWS.md

@@ -1,4 +1,7 @@
-# EMLeditor v0.1.0.8 "Work in progress"
+EMLeditor v0.1.1 "Big South Fork"
+
+## 29 August 2023
+  Updated all rest API services from v4/v5 to v6. Units services remain at v2.
 
 ## 15 August 2023
   * Fix bugs in `get_authors()`

R/datastore_interactions.R

@@ -43,7 +43,7 @@ set_datastore_doi <- function(eml_object, force = FALSE, NPS = TRUE){
     if(length(seq_along(doc)) == 1){
       #get Datastore Reference ID:
       DS_ref <- get_ds_id(eml_object)
-      url <- paste0("https://irmaservices.nps.gov/datastore-secure/v4/rest/ReferenceCodeSearch?q=", DS_ref)
+      url <- paste0(.ds_secure_api(), "ReferenceCodeSearch?q=", DS_ref)
       #API call to look for an existing reference:
       test_req <- httr::GET(url, httr::authenticate(":", ":", "ntlm"))
       status_code <- httr::stop_for_status(test_req)$status_code
@@ -105,7 +105,8 @@ set_datastore_doi <- function(eml_object, force = FALSE, NPS = TRUE){
                                    precision = ""))
   bdy <- jsonlite::toJSON(mylist, pretty = TRUE, auto_unbox = TRUE)
   #Create empty draft reference:
-  req <- httr::POST("https://irmaservices.nps.gov/datastore-secure/v4/rest/Reference/CreateDraft",
+  post_url <- paste0(.ds_secure_api(), "Reference/CreateDraft")
+  req <- httr::POST(post_url,
                 httr::authenticate(":", "", "ntlm"),
                 httr::add_headers('Content-Type'='application/json'),
                 body = bdy)
@@ -187,7 +188,7 @@ upload_data_package <- function(directory = here::here(), force = FALSE){
   #list files in data package
 
   #test whether reference already exists or the DOI:
-  url <- paste0("https://irmaservices.nps.gov/datastore-secure/v4/rest/ReferenceCodeSearch?q=", DS_ref)
+  url <- paste0(.ds_secure_api(), "ReferenceCodeSearch?q=", DS_ref)
   #verbose approach:
   if(force == FALSE){
     #API call to look for an existing reference:
@@ -264,9 +265,7 @@ upload_data_package <- function(directory = here::here(), force = FALSE){
           stop()
         }
         if(is.null(file_size_error)){
-          api_url <- paste0(
-            "https://irmaservices.nps.gov/datastore-secure/v4/rest/Reference/",
-              DS_ref, "/UploadFile")
+          api_url <- paste0(.ds_secure_api(), "Reference/", DS_ref, "/UploadFile")
           #upload the files
           for(i in seq_along(files)){
             req <- httr::POST(
@@ -339,9 +338,7 @@ upload_data_package <- function(directory = here::here(), force = FALSE){
       stop()
     }
     if(is.null(file_size_error)){
-      api_url <- paste0(
-        "https://irmaservices.nps.gov/datastore-secure/v4/rest/Reference/",
-          DS_ref, "/UploadFile")
+      api_url <- paste0(.ds_secure_api(), "Reference/", DS_ref, "/UploadFile")
       #upload the files
       for(i in seq_along(files)){
         req <- httr::POST(

R/editEMLfunctions.R

@@ -1065,7 +1065,7 @@ set_language <- function(eml_object, lang, force = FALSE, NPS = TRUE) {
 #'
 #' @description set_protocol adds a metadata link to the protocol under which the data being described were collected. It automatically inserts a link to the DataStore landing page for the protocol as well as ?????
 #'
-#' @details set_protocol requires that you have your protocols and projects organized in a specific fashion in DataStore. Errors generated by this function my stem from either a protocol that has not been published (or is not publicly available) or an obsolete protocol/project organization within DataStore.
+#' @details set_protocol requires that you have your protocols and projects organized in a specific fashion in DataStore. Errors generated by this function may stem from either a protocol that has not been published (or is not publicly available) or an obsolete protocol/project organization within DataStore.
 #'
 #' @inheritParams set_title
 #' @param protocol_id a string. The 7-digit number identifying the DataStore reference number for the Project that describes your inventory or monitoring project.
@@ -1082,7 +1082,7 @@ set_protocol <- function(eml_object, protocol_id, force = FALSE, NPS = TRUE) {
   # get data to construct project:
 
   # get protocol profile via rest services:
-  ds_reference <- httr::content(httr::GET(paste0("https://irmaservices.nps.gov/datastore/v4/rest/Profile/", protocol_id)))
+  ds_reference <- httr::content(httr::GET(paste0(.ds_api(), "Profile/", protocol_id)))
 
   # extract project title
   proj_title <- ds_reference$bibliography$title
@@ -1094,7 +1094,8 @@ set_protocol <- function(eml_object, protocol_id, force = FALSE, NPS = TRUE) {
   ref <- ds_reference$series$referenceId
 
   # rest services call to get organization name info:
-  org_name <- httr::content(httr::GET(paste0("https://irmaservices.nps.gov/datastore/v4/rest/Profile/", ref)))$bibliography$title
+  org_name <- httr::content(
+    httr::GET(paste0(.ds_api(), "Profile/", ref)))$bibliography$title
 
   # Construct a project to inject into EML. Note 'role' is required but not sure what to put there.
   # Also i find it confusing that onlineURL references projTitle not orgName but hopefully we will hash that out soon.

R/utils.R

@@ -1,3 +1,22 @@
+## assign global package variables
+
+#initiate new environment accessible from within package:
+.pkgglobalenv <- new.env(parent=emptyenv())
+
+#data_store API base URL:
+assign("ds_api", "https://irmaservices.nps.gov/datastore/v6/rest/", envir=.pkgglobalenv)
+
+#data_store secure API base URL:
+assign("ds_secure_api", "https://irmaservices.nps.gov/datastore-secure/v6/rest/", envir=.pkgglobalenv)
+
+.ds_api <- function(x){
+  get("ds_api", envir = .pkgglobalenv)
+}
+
+.ds_secure_api <- function(x){
+  get("ds_secure_api", envir = .pkgglobalenv)
+}
+
 #this gets rid of the "no visible binding for global variable 'x'" error in build checks:
 globalVariables(c("UnitCode",
                   "Name",