Merge pull request #35 from USEPA/34-api-key-check-helper-function

34 api key check helper function
USEPA · Nov 21, 2024 · cfac9c6 · cfac9c6
2 parents 3d57d54 + 33f1207
commit cfac9c6
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diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -41,6 +41,7 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
         uses: JamesIves/[email protected]

diff --git a/R/bioactivity-APIs-batch.R b/R/bioactivity-APIs-batch.R
@@ -27,14 +27,11 @@ get_bioactivity_details_batch <- function(DTXSID = NULL,
                                           Server = NULL,
                                           rate_limit = 0L,
                                           verbose = FALSE){
-  if (is.null(API_key) || !is.character(API_key)){
-    if (has_ctx_key()) {
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
+
   if (!is.numeric(rate_limit) | (rate_limit < 0)){
     warning('Setting rate limit to 0 seconds between requests!')
     rate_limit <- 0L
@@ -218,14 +215,11 @@ get_bioactivity_summary_batch <- function(AEID = NULL,
                                           Server = NULL,
                                           rate_limit = 0L,
                                           verbose = FALSE){
-  if (is.null(API_key) || !is.character(API_key)){
-    if (has_ctx_key()) {
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
+
   if (!is.numeric(rate_limit) | (rate_limit < 0)){
     warning('Setting rate limit to 0 seconds between requests!')
     rate_limit <- 0L
@@ -296,14 +290,11 @@ get_annotation_by_aeid_batch <- function(AEID = NULL,
                                          Server = NULL,
                                          rate_limit = 0L,
                                          verbose = FALSE){
-  if (is.null(API_key) || !is.character(API_key)){
-    if (has_ctx_key()) {
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
+
   if (!is.numeric(rate_limit) | (rate_limit < 0)){
     warning('Setting rate limit to 0 seconds between requests!')
     rate_limit <- 0L

diff --git a/R/bioactivity-APIs.R b/R/bioactivity-APIs.R
@@ -29,13 +29,10 @@ get_bioactivity_details <- function(DTXSID = NULL,
   #else if (!is.null(DTXSID) & !is.null(AEID))
   else if (length(which(!sapply(list(DTXSID, AEID, SPID, m4id), is.null))) > 1)
     stop('Please input a value for only one of DTXSID, AEID, SPID, or m4id, but not multiple!')
-  else if (is.null(API_key)){
-    if (has_ctx_key()) {
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
 
   data_index <- which(!sapply(list(DTXSID, AEID, SPID, m4id), is.null))
@@ -140,13 +137,10 @@ get_bioactivity_summary <- function(AEID = NULL,
   #return()
   if (is.null(AEID))
     stop('Please input an AEID!')
-  else if (is.null(API_key)){
-    if (has_ctx_key()){
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
 
   response <- httr::GET(url = paste0(Server, '/data/summary/search/by-aeid/', AEID),
@@ -203,13 +197,9 @@ get_all_assays <- function(API_key = NULL,
                            Server = bioactivity_api_server,
                            verbose = FALSE){
 
-  if (is.null(API_key)){
-    if (has_ctx_key()){
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
 
   response <-  httr::GET(url = paste0(Server, '/assay/'),
@@ -255,13 +245,10 @@ get_annotation_by_aeid <- function(AEID = NULL,
                                    verbose = FALSE){
   if (is.null(AEID))
     stop('Please input an AEID!')
-  else if (is.null(API_key)){
-    if (has_ctx_key()){
-      API_key <- ctx_key()
-      if (verbose) {
-        message('Using stored API key!')
-      }
-    }
+
+  API_key <- check_api_key(API_key = API_key, verbose = verbose)
+  if (is.null(API_key) & verbose){
+    warning('Missing API key. Please supply during function call or save using `register_ctx_api_key()`!')
   }
 
   response <- httr::GET(url = paste0(Server, '/assay/search/by-aeid/', AEID),