fix cran malformat error

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: protti
 Title: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
-Version: 0.9.0
+Version: 0.9.0.9000
 Authors@R: 
     c(person(given = "Jan-Philipp",
            family = "Quast",
@@ -43,7 +43,7 @@ Imports:
     methods,
     R.utils,
     stats
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     testthat,
     covr,
@@ -67,7 +67,9 @@ Suggests:
     iq,
     scales,
     farver,
-    ggforce
+    ggforce,
+    xml2,
+    jsonlite
 Depends: 
     R (>= 4.0)
 URL: https://github.com/jpquast/protti, https://jpquast.github.io/protti/

NAMESPACE

@@ -134,6 +134,7 @@ 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)

NEWS.md

@@ -1,3 +1,8 @@
+# protti ***
+
+## Bug fixes
+* `try_query()` now correctly handles errors that don't return a response object. We also handle gzip decompression problems better since some databases compressed responses were not handled correctly. 
+
 # protti 0.9.0
 
 ## New features 

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 +21,7 @@
 #'
 #' @importFrom curl has_internet
 #' @importFrom httr GET timeout http_error message_for_status http_status content accept
+#' @importFrom readr read_tsv read_csv
 #'
 #' @return A data frame that contains the table from the url.
 try_query <-
@@ -77,18 +77,56 @@ try_query <-
       return(invisible("No internet connection"))
     }
 
-    if (httr::http_error(query_result)) {
+    # If response was an error return that error message
+    if (inherits(query_result, "response") && httr::http_error(query_result)) {
       if (!silent) httr::message_for_status(query_result)
       return(invisible(httr::http_status(query_result)$message))
     }
 
+    # Handle other types of errors separately from query errors
+    if (inherits(query_result, "character")) {
+      if (!silent) message(query_result)
+      return(invisible(query_result))
+    }
+
     # Record readr progress variable to set back later
     readr_show_progress <- getOption("readr.show_progress")
     on.exit(options(readr.show_progress = readr_show_progress))
     # 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", ...))
+    # Retrieve the content as raw bytes using httr::content
+    raw_content <- httr::content(query_result, type = "raw")
+    # Check for gzip magic number (1f 8b) before decompression
+    compressed <- length(raw_content) >= 2 && raw_content[1] == as.raw(0x1f) && raw_content[2] == as.raw(0x8b)
+
+    # Check if the content is gzip compressed
+    if (!is.null(query_result$headers[["content-encoding"]]) && query_result$headers[["content-encoding"]] == "gzip" && compressed) {
+      # 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)
   }

tests/testthat/test-fetch_extract_and_enrichment_functions.R

@@ -21,7 +21,7 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
     unis <- c("iRT", "P25437", "P30870", "P0A6P9")
     expect_warning(mobidb <- fetch_mobidb(unis))
     expect_is(mobidb, "data.frame")
-    expect_equal(nrow(mobidb), 259)
+    expect_equal(nrow(mobidb), 221)
     expect_equal(ncol(mobidb), 6)
   })