Fix: upload results skips samples when CSV has whitespaces

instedd · Jul 20, 2023 · 42b2cde · 42b2cde
1 parent 3f4995b
commit 42b2cde
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Showing 2 changed files with 25 additions and 24 deletions.
diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
@@ -202,16 +202,15 @@ def bulk_destroy
   end
 
   def bulk_process_csv
-    uuid_regex = /^[0-9a-fA-F]{8}\b-[0-9a-fA-F]{4}\b-[0-9a-fA-F]{4}\b-[0-9a-fA-F]{4}\b-[0-9a-fA-F]{12}$/i
+    uuid_regex = /\b[0-9a-fA-F]{8}\b-[0-9a-fA-F]{4}\b-[0-9a-fA-F]{4}\b-[0-9a-fA-F]{4}\b-[0-9a-fA-F]{12}\b/i
 
     params[:csv_files].each do |csv_file|
       CSV.open(csv_file.path) do |csv_stream|
-        csv_stream.each do |row|
-          sample_id, measured_signal = row[0], row[1]
-          next unless sample_id&.match(uuid_regex) # non uuids are ignored
-          sample = Sample.find_by_uuid(sample_id)
-          unless sample.nil?
-            sample.measured_signal ||= Float(measured_signal) if measured_signal.present?
+        csv_stream.each do |(sample_id, measured_signal)|
+          next unless sample_id&.match(uuid_regex) && measured_signal.present?
+
+          if sample = Sample.find_by_uuid(sample_id.strip)
+            sample.measured_signal ||= Float(measured_signal.strip)
             sample.save!
           end
         end

diff --git a/app/views/samples/_upload_results_js.haml b/app/views/samples/_upload_results_js.haml
@@ -54,30 +54,32 @@
                 // Parse the input file
                 var text =  load_event.target.result
                 var lines = text.split(/\r\n|\r|\n/); // tolerate both Windows and Unix linebreaks
-                var samples_param = [] // params for GET call
                 var samples = [] // samples uuids
                 var duplicates = false
-                lines.forEach(function(line) { 
-                    var row = line.split(',');
-                    if (line != '' && isUUID(row[0])){
-                        if (samples.indexOf(row[0]) == -1){
-                            samples_param.push( 'uuids[]=' + row[0] );
-                            samples.push( row[0] );
-                        }
-                        else {
-                            duplicates = true;
-                        }
-                    } 
+
+                lines.forEach(function(line) {
+                    var row = line
+                        .split(",")
+                        .map((part) => part.trim());
+                    if (!isUUID(row[0])) return;
+
+                    if (samples.indexOf(row[0]) == -1){
+                        samples.push(row[0]);
+                    } else {
+                        duplicates = true;
+                    }
                 });
-                
+
                 // Retrieve found uuids
+                var samples_params = samples
+                    .map((uuid) => "uuids[]=" + uuid)
+                    .join("&");
                 var context = getUrlParameter('context');
-                var url = '/samples/existing_uuids?context='+context+"&"+samples_param.join("&")
+                var url = '/samples/existing_uuids?context='+context+"&"+samples_params;
                 var found = await fetch(url)
                     .then((response) => response.json())
-                    .then((r) => {
-                        return r.message;
-                })
+                    .then((r) => r.message);
+
                 // Compute not found ones
                 var not_found = samples.filter(function(x) {
                     return found.indexOf(x) < 0;