Fix error catching

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CyteTypeR
 Title: CyteType for R
-Version: 0.4.1
+Version: 0.4.2
 Description: CyteTypeR is the R version of CyteType python package.
 Authors@R: 
     person("Nygen Analytics AB", , ,"contact@nygen.io", role = c("aut", "cre"))

R/api.R

@@ -59,6 +59,10 @@
 
     # Check for other non-success status codes
     if (status_code < 200 || status_code >= 300) {
+      parsed <- .parse_server_error(response)
+      if (!is.null(parsed)) {
+        stop(paste0("HTTP ", status_code, " [", parsed$error_code, "] ", parsed$message))
+      }
       error_body <- tryCatch(resp_body_string(response), error = function(e) "Unknown error")
       stop(paste("HTTP", status_code, "error:", error_body))
     }
@@ -117,7 +121,7 @@
     req_perform()
 
   status <- resp_status(resp)
-  if (status >= 400L) {
+  if (status >= 400) {
     stop(cytetype_api_error(
       message = paste0("Presigned upload rejected with HTTP ", status),
       call = "api"

R/client.R

@@ -30,7 +30,7 @@
       req_timeout(connection_timeout) |>
       req_perform() |>
       resp_body_json(),
-    error = function(e) { .stop_if_rate_limited(e); stop(e) }
+    error = function(e) .stop_with_server_error(e, "Upload initiate failed")
   )
 
   upload_id <- init_resp$upload_id
@@ -82,7 +82,9 @@
         list(ok = TRUE)
       }, error = function(e) {
         .stop_if_rate_limited(e)
-        list(ok = FALSE, chunk_idx = chunk_idx, message = conditionMessage(e))
+        detail <- .format_server_error(e)
+        list(ok = FALSE, chunk_idx = chunk_idx,
+             message = detail %||% conditionMessage(e))
       })
     }
 
@@ -99,7 +101,9 @@
         list(ok = TRUE, etag = etag, part_number = chunk_idx + 1L)
       }, error = function(e) {
         .stop_if_rate_limited(e)
-        list(ok = FALSE, chunk_idx = chunk_idx, message = conditionMessage(e))
+        detail <- .format_server_error(e)
+        list(ok = FALSE, chunk_idx = chunk_idx,
+             message = detail %||% conditionMessage(e))
       })
     }
 
@@ -167,7 +171,7 @@
       req_timeout(connection_timeout) |>
       req_perform() |>
       resp_body_json(),
-    error = function(e) { .stop_if_rate_limited(e); stop(e) }
+    error = function(e) .stop_with_server_error(e, "Upload complete failed")
   )
 
   complete_resp
@@ -216,6 +220,10 @@
     # Check status
     status <- resp_status(response)
     if (status != 200) {
+      parsed <- .parse_server_error(response)
+      if (!is.null(parsed)) {
+        stop(paste0("HTTP ", status, " [", parsed$error_code, "] ", parsed$message))
+      }
       stop("HTTP ", status, ": ", resp_body_string(response))
     }
 
@@ -232,9 +240,7 @@
     return(as.character(job_id))
 
   }, error = function(e) {
-    .stop_if_rate_limited(e)
-    cat("An error occurred:", conditionMessage(e), "\n")
-    return(NA_character_)
+    .stop_with_server_error(e, "Job submission failed")
   })
 }
 

R/cytetype.R

@@ -363,12 +363,13 @@ CyteTypeR <- function(obj,
       )
     }, error = function(e) {
       if (require_artifacts) {
-        log_error("Uploading artifacts failed: {conditionMessage(e)}")
+        log_error(paste("Uploading artifacts failed:", conditionMessage(e),
+        "Set `require_artifacts=FALSE` to continue without uploading artifacts."))
         stop(e)
       } else {
         log_warn(paste(
           "Uploading artifacts failed. Continuing without artifacts.",
-          "Set `require_artifacts=TRUE` to raise this as an error.",
+          "Set `require_artifacts=TRUE` to stop on upload failures.",
           "Original error:", conditionMessage(e)
         ))
       }
@@ -382,8 +383,8 @@ CyteTypeR <- function(obj,
 
   job_id <- .submit_job(query_for_json, api_url, auth_token)
 
-  if (is.na(job_id)) {
-    stop("Job submission failed.")
+  if (is.na(job_id) || is.null(job_id)) {
+    stop("Job submission failed: no job ID returned.", call. = FALSE)
   }
 
   obj <- .store_job_details_seurat(obj, job_id, api_url, results_prefix, group_key, prepped_data$clusterLabels)

R/errors.R

@@ -26,6 +26,13 @@ print.cytetype_api_error <- function(x, ...) {
   NULL
 }
 
+.format_server_error <- function(e) {
+  if (!inherits(e, "httr2_http") || is.null(e$resp)) return(NULL)
+  parsed <- .parse_server_error(e$resp)
+  if (is.null(parsed)) return(NULL)
+  paste0("[", parsed$error_code, "] ", parsed$message)
+}
+
 .stop_if_rate_limited <- function(e) {
   if (inherits(e, "httr2_http") && !is.null(e$resp)) {
     parsed <- .parse_server_error(e$resp)
@@ -39,3 +46,11 @@ print.cytetype_api_error <- function(x, ...) {
     }
   }
 }
+
+.stop_with_server_error <- function(e, context = NULL) {
+  .stop_if_rate_limited(e)
+  detail <- .format_server_error(e)
+  msg <- detail %||% conditionMessage(e)
+  if (!is.null(context)) msg <- paste0(context, ": ", msg)
+  stop(msg, call. = FALSE)
+}