fixes for job submissions (#39)

* Update seurat_helpers.R

* Update R-CMD-check.yaml

* Update schema.R

* Update cytetype.R

* Update R-CMD-check.yaml

* Update R-CMD-check.yaml

* Revert "Update cytetype.R"

This reverts commit 8add6f3.

* Revert "Update seurat_helpers.R"

This reverts commit 63e4d5d.

* Update schema.R

* Update R-CMD-check.yaml

* Increment version number to 0.3.2

* fix attr to scalar

* rate limit error messages

Author: suu-yi

.github/workflows/R-CMD-check.yaml

@@ -40,10 +40,17 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        if: matrix.config.r == 'release'
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        if: matrix.config.r != 'release'
+        with:
+          extra-packages: any::rcmdcheck, cran/ggrepel@0.9.6
+          needs: check
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CyteTypeR
 Title: CyteType for R
-Version: 0.3.1
+Version: 0.3.2
 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

@@ -53,6 +53,8 @@
     ))
 
   }, error = function(e) {
+    .stop_if_rate_limited(e)
+
     # Preserve authentication/authorization errors
     if (grepl("Authentication failed|Authorization failed", e$message)) {
       stop(e)

R/artifacts.R

@@ -81,8 +81,8 @@
   on.exit(rhdf5::H5Fclose(fid), add = TRUE)
 
   rhdf5::h5createGroup(fid, "vars")
-  rhdf5::h5writeAttribute(as.integer(n_obs), h5obj = out_file, name = "n_obs", h5loc = "vars")
-  rhdf5::h5writeAttribute(as.integer(n_vars), h5obj = out_file, name = "n_vars", h5loc = "vars")
+  rhdf5::h5writeAttribute(as.integer(n_obs), h5obj = out_file, name = "n_obs", h5loc = "vars", asScalar = TRUE)
+  rhdf5::h5writeAttribute(as.integer(n_vars), h5obj = out_file, name = "n_vars", h5loc = "vars", asScalar = TRUE)
 
   # Create extensible datasets (equivalent to maxshape=(None,) in h5py)
   max_nnz <- n_obs * n_vars  # upper bound

R/client.R

@@ -41,12 +41,15 @@
   connection_timeout <- 30L
 
   # Step 1 – Initiate (empty POST; explicit empty body for compatibility)
-  init_resp <- .make_req(api_url, paste0(file_kind, "/initiate"), auth_token) |>
-    req_method("POST") |>
-    httr2::req_body_raw(raw(0), type = "application/json") |>
-    req_timeout(connection_timeout) |>
-    req_perform() |>
-    resp_body_json()
+  init_resp <- tryCatch(
+    .make_req(api_url, paste0(file_kind, "/initiate"), auth_token) |>
+      req_method("POST") |>
+      httr2::req_body_raw(raw(0), type = "application/json") |>
+      req_timeout(connection_timeout) |>
+      req_perform() |>
+      resp_body_json(),
+    error = function(e) { .stop_if_rate_limited(e); stop(e) }
+  )
 
   upload_id <- init_resp$upload_id
   chunk_size <- as.integer(init_resp$chunk_size_bytes %||% (5L * 1024L * 1024L))
@@ -86,6 +89,7 @@
           req_perform()
         list(ok = TRUE)
       }, error = function(e) {
+        .stop_if_rate_limited(e)
         list(ok = FALSE, chunk_idx = chunk_idx, message = conditionMessage(e))
       })
     }
@@ -102,12 +106,15 @@
     }
   }
   # Step 3 – Complete (empty POST; explicit empty body for compatibility)
-  complete_resp <- .make_req(api_url, paste0(upload_id, "/complete"), auth_token) |>
-    req_method("POST") |>
-    httr2::req_body_raw(raw(0), type = "application/json") |>
-    req_timeout(connection_timeout) |>
-    req_perform() |>
-    resp_body_json()
+  complete_resp <- tryCatch(
+    .make_req(api_url, paste0(upload_id, "/complete"), auth_token) |>
+      req_method("POST") |>
+      httr2::req_body_raw(raw(0), type = "application/json") |>
+      req_timeout(connection_timeout) |>
+      req_perform() |>
+      resp_body_json(),
+    error = function(e) { .stop_if_rate_limited(e); stop(e) }
+  )
 
   complete_resp
 }
@@ -167,10 +174,8 @@
     return(as.character(job_id))
 
   }, error = function(e) {
-    # Log the error
+    .stop_if_rate_limited(e)
     cat("An error occurred:", conditionMessage(e), "\n")
-
-    # Return NA for any error
     return(NA_character_)
   })
 }

R/cytetype.R

@@ -482,6 +482,5 @@ GetResults <- function(obj = NULL, job_id = NULL, results_prefix = "cytetype", a
 
 
 
-
 
 

R/errors.R

@@ -15,3 +15,27 @@ cytetype_api_error <- function(message, call = NULL) {
 print.cytetype_api_error <- function(x, ...) {
   cat("CyteType API Error: ", x$message, "\n")
 }
+
+.parse_server_error <- function(resp) {
+  body <- tryCatch(httr2::resp_body_json(resp), error = function(e) NULL)
+  if (is.null(body)) return(NULL)
+  if ("detail" %in% names(body) && is.list(body$detail)) body <- body$detail
+  if (!is.null(body$error_code) && !is.null(body$message)) {
+    return(list(error_code = body$error_code, message = body$message))
+  }
+  NULL
+}
+
+.stop_if_rate_limited <- function(e) {
+  if (inherits(e, "httr2_http") && !is.null(e$resp)) {
+    parsed <- .parse_server_error(e$resp)
+    if (!is.null(parsed) && parsed$error_code == "RATE_LIMIT_EXCEEDED") {
+      stop(
+        "Rate limit exceeded: ", parsed$message,
+        "\nUse your own LLM API key via llm_configs to bypass free-tier limits, ",
+        "or wait before retrying.",
+        call. = FALSE
+      )
+    }
+  }
+}

R/schema.R

@@ -108,6 +108,14 @@ LLMModelConfig <- function(provider,
   mask_job_details <- if (is.null(nm)) rep(TRUE, length(query_list$input_data)) else !endsWith(nm, "jobDetails")
   query_list$input_data <- query_list$input_data[mask_job_details]
 
+  # Ensure fields the server expects as JSON objects serialize to {} not []
+  dict_fields <- c("clusterMetadata", "clusterLabels", "infoTags", "expressionData")
+  for (field in dict_fields) {
+    val <- query_list$input_data[[field]]
+    if (is.list(val) && length(val) == 0 && is.null(names(val))) {
+      query_list$input_data[[field]] <- setNames(list(), character(0))
+    }
+  }
 
   return(query_list)
 }