Fix the RCurl::url.exists() to httr::http_error() transition

LieberInstitute · May 6, 2023 · 82f45ce · 82f45ce
1 parent 2c3d29e
commit 82f45ce
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Showing 2 changed files with 41 additions and 26 deletions.
diff --git a/R/file_retrieve.R b/R/file_retrieve.R
@@ -56,17 +56,23 @@ file_retrieve <-
         ## In case the url is a local file, there's no need to cache it then
         if (file.exists(url)) {
             return(url)
-        } else if (http_error(url)) {
-            if (!grepl("tcga\\.recount_pred|gtex\\.recount_pred", url)) {
-                warning("The 'url' <",
-                    url,
-                    "> does not exist or is not available.",
-                    call. = FALSE
-                )
+        } else {
+            url_failed <- tryCatch(
+                http_error(url),
+                error = function(e) { return (TRUE)}
+            )
+            if (url_failed) {
+                if (!grepl("tcga\\.recount_pred|gtex\\.recount_pred", url)) {
+                    warning("The 'url' <",
+                        url,
+                        "> does not exist or is not available.",
+                        call. = FALSE
+                    )
+                }
+                res <- as.character(NA)
+                names(res) <- names(url)
+                return(res)
             }
-            res <- as.character(NA)
-            names(res) <- names(url)
-            return(res)
         }
 
         if (!methods::is(bfc, "BiocFileCache")) {

diff --git a/R/project_homes.R b/R/project_homes.R
@@ -38,23 +38,10 @@ project_homes <-
         homes <- getOption(option_name)
         if (!is.null(homes)) {
               return(homes)
-          }
-
-        ## Construct the URL for the homes_index file
-        homes_url <-
-            paste(recount3_url, organism, "homes_index", sep = "/")
-        if (!http_error(homes_url)) {
-            homes_from_url <- readLines(homes_url)
-
-            ## Cache the result for the resulting organism so we don't need
-            ## to check this again in this R session
-            options_list <- list(homes_from_url)
-            names(options_list) <- option_name
-            options(options_list)
+        }
 
-            ## Return result found
-            return(homes_from_url)
-        } else if (recount3_url == "http://snaptron.cs.jhu.edu/data/temp/recount3") {
+        ## For the recount3 test case
+        if (recount3_url == "http://snaptron.cs.jhu.edu/data/temp/recount3") {
             if (organism == "mouse") {
                 return("data_sources/sra")
             } else if (organism == "human") {
@@ -68,6 +55,28 @@ project_homes <-
                     )
                 )
             }
+        }
+
+        url_failed <- tryCatch(
+            http_error(homes_url),
+            error = function(e) { return (TRUE)}
+        )
+
+
+        ## Construct the URL for the homes_index file
+        homes_url <-
+            paste(recount3_url, organism, "homes_index", sep = "/")
+        if (!url_failed) {
+            homes_from_url <- readLines(homes_url)
+
+            ## Cache the result for the resulting organism so we don't need
+            ## to check this again in this R session
+            options_list <- list(homes_from_url)
+            names(options_list) <- option_name
+            options(options_list)
+
+            ## Return result found
+            return(homes_from_url)
         } else if (!file.exists(recount3_url)) {
             stop(
                 "'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.",