Update user-side processing

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AzimuthAPI
 Title: Pan-Azimuth Web API Interface
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: 
     person("Satija", "Lab", email = "satijalabnygc@gmail.com", role = c("aut", "cre"))
 Description: An R package providing an interface to the Pan-Azimuth Web API for single-cell RNA sequencing analysis.

R/api_interface.R

@@ -2,7 +2,7 @@
 #'
 #' @param url API endpoint URL
 #' @param file_path Path to the file being processed
-#' @return NULL
+#' @return Logical indicating success (TRUE) or failure (FALSE)
 #' @importFrom curl new_handle handle_setform curl_fetch_stream
 #' @importFrom jsonlite fromJSON
 #' @export
@@ -21,6 +21,8 @@ listen_to_progress <- function(url, file_path, ...) {
 
   # Buffer to store partial messages
   buffer <- ""
+  # Track whether processing succeeded
+  success <- NULL
 
   # Process the SSE stream in real time
   curl_fetch_stream(
@@ -51,6 +53,11 @@ listen_to_progress <- function(url, file_path, ...) {
           tryCatch({
             parsed <- fromJSON(json_message)
 
+            # Check for success flag
+            if (!is.null(parsed$success)) {
+              success <<- parsed$success
+            }
+
             # Print messages based on content
             if (!is.null(parsed$message)) {
               cat(parsed$message, "\n")
@@ -78,6 +85,8 @@ listen_to_progress <- function(url, file_path, ...) {
       }
     }
   )
+
+  return(success)
 }
 
 #' Download output file from the API

R/cloud.R

@@ -2,23 +2,23 @@
 #'
 #' @param object Seurat object to annotate
 #' @param assay Name of the assay to use (default: 'RNA')
-#' @param ip IP address of the cloud server (default: '34.222.135.233')
+#' @param ip Hostname or IP address of the cloud server (default: 'azimuthapi.satijalab.org')
 #' @param port Port number for the API (default: 5000)
 #' @return Annotated Seurat object
 #' @importFrom httr POST GET upload_file content status_code
 #' @importFrom RCurl url.exists
 #' @export
-CloudAzimuth <- function(object = object, assay = 'RNA', ip = '34.222.135.233', 
+CloudAzimuth <- function(object = object, assay = 'RNA', ip = 'azimuthapi.satijalab.org', 
                          port = 5000, ...) {
   message("Running Pan-Human Azimuth on the cloud!")
 
   layer_name <- 'data'
   data <- LayerData(object, assay = assay, layer = layer_name)
 
-  # check if data has been normalized, just using the first 5 cells
+  # if data exists, check if normalized, just using the first 5 cells
   # throw an error if large values, or all integer values, are detected
-  data_check <- data[,1:min(5,ncol(data))]
-  if ((max(data_check) > 15) || isTRUE(all.equal(data_check,floor(data_check)))) {
+  data_check <- if (!IsMatrixEmpty(data)) data[,1:min(5,ncol(data))] else NULL
+  if (is.null(data_check) || (max(data_check) > 15 || isTRUE(all.equal(data_check, floor(data_check))))) {
     stop("Please run NormalizeData on the data before running Azimuth")
   }
 
@@ -46,13 +46,22 @@ CloudAzimuth <- function(object = object, assay = 'RNA', ip = '34.222.135.233',
     object[[i]] <- srt[[i]]
   }
 
-  # Copy metadata columns except QC ones
+  # Copy metadata columns except QC ones, matching by cell names
   md_cols <- grep("nCount_RNA|nFeature_RNA", 
                  colnames(srt@meta.data), 
                  invert = TRUE, 
                  value = TRUE)
+
+  # Only update metadata for cells that were processed (objects can have multiple assays w/ cell IDs formatted differently)
+  assay_cells <- Cells(srt)
+
   for (i in md_cols) {
-    object@meta.data[, i] <- srt@meta.data[, i]
+    # Initialize column with NA only if it doesn't exist
+    if (!i %in% colnames(object@meta.data)) {
+      object@meta.data[, i] <- NA
+    }
+    # Update only the processed cells
+    object@meta.data[assay_cells, i] <- srt@meta.data[assay_cells, i]
   }
 
   Idents(object) <- 'azimuth_label'
@@ -68,7 +77,12 @@ CloudAzimuth <- function(object = object, assay = 'RNA', ip = '34.222.135.233',
 process_rds_file <- function(api_base_url, file_path, ...) {
   progress_url <- paste0(api_base_url, "/process_rds")
   cat("Uploading file and listening for updates...\n")
-  listen_to_progress(progress_url, file_path, ...)
+  success <- listen_to_progress(progress_url, file_path, ...)
+
+  if (isFALSE(success)) {
+    stop("Processing failed on the server. Please check the error messages above.")
+  }
+
   output_file_name <- gsub("\\.rds$", "_ANN.rds", basename(file_path))
   download_url <- paste0(api_base_url, "/download_output?output_file=/tmp/", 
                          output_file_name)