fix vroom problem

The issue was that the uniprot data seems to now be gziped. I handle this case now in try_query. Not sure if it is generally handled for any potential case but it at least works for uniprot.

DESCRIPTION

@@ -43,7 +43,7 @@ Imports:
     methods,
     R.utils,
     stats
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     testthat,
     covr,

NAMESPACE

@@ -116,6 +116,7 @@ importFrom(httr,modify_url)
 importFrom(httr,timeout)
 importFrom(janitor,clean_names)
 importFrom(janitor,make_clean_names)
+importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(plotly,ggplotly)
@@ -134,6 +135,7 @@ importFrom(purrr,pluck)
 importFrom(purrr,pmap)
 importFrom(purrr,reduce)
 importFrom(purrr,set_names)
+importFrom(readr,read_csv)
 importFrom(readr,read_tsv)
 importFrom(readr,write_csv)
 importFrom(readr,write_tsv)
@@ -191,3 +193,5 @@ importFrom(utils,data)
 importFrom(utils,download.file)
 importFrom(utils,head)
 importFrom(utils,untar)
+importFrom(xml2,read_html)
+importFrom(xml2,read_xml)

R/try_query.R

@@ -13,7 +13,6 @@
 #' @param type a character value that specifies the type of data at the target URL. Options are
 #' all options that can be supplied to httr::content, these include e.g.
 #' "text/tab-separated-values", "application/json" and "txt/csv". Default is "text/tab-separated-values".
-#' Default is "tab-separated-values".
 #' @param timeout a numeric value that specifies the maximum request time. Default is 60 seconds.
 #' @param accept a character value that specifies the type of data that should be sent by the API if
 #' it uses content negotiation. The default is NULL and it should only be set for APIs that use
@@ -22,6 +21,9 @@
 #'
 #' @importFrom curl has_internet
 #' @importFrom httr GET timeout http_error message_for_status http_status content accept
+#' @importFrom readr read_tsv read_csv
+#' @importFrom jsonlite fromJSON
+#' @importFrom xml2 read_html read_xml
 #'
 #' @return A data frame that contains the table from the url.
 try_query <-
@@ -88,7 +90,36 @@ try_query <-
     # Change variable to not show progress if readr is used
     options(readr.show_progress = FALSE)
 
-    result <- suppressMessages(httr::content(query_result, type = type, encoding = "UTF-8", ...))
+    # Check if the content is gzip compressed
+    if (query_result$headers[["content-encoding"]] == "gzip") {
+      # Retrieve the content as raw bytes using httr::content
+      raw_content <- httr::content(query_result, type = "raw")
+
+      # Decompress the raw content using base R's `memDecompress`
+      decompressed_content <- memDecompress(raw_content, type = "gzip")
+
+      # Convert the raw bytes to a character string
+      text_content <- rawToChar(decompressed_content)
+
+      # Read the decompressed content based on the specified type
+      if (type == "text/tab-separated-values") {
+        result <- readr::read_tsv(text_content, ...)
+      } else if (type == "text/html") {
+        result <- xml2::read_html(text_content, ...)
+      } else if (type == "text/xml") {
+        result <- xml2::read_xml(text_content, ...)
+      } else if (type == "text/csv" || type == "txt/csv") {
+        result <- readr::read_csv(text_content, ...)
+      } else if (type == "application/json") {
+        result <- jsonlite::fromJSON(text_content, ...)  # Using jsonlite for JSON parsing
+      } else if (type == "text") {
+        result <- text_content  # Return raw text as-is
+      } else {
+        stop("Unsupported content type: ", type)
+      }
+    } else {
+      result <- suppressMessages(httr::content(query_result, type = type, encoding = "UTF-8", ...))
+    }
 
     return(result)
   }