Added column replicates in CSV box creation (#1983)

* Added column replicates in CSV box creation * Specs fixed * Update app/models/box_form.rb Co-authored-by: Julien Portalier <[email protected]> --------- Co-authored-by: Julien Portalier <[email protected]>
instedd · Aug 4, 2023 · 792b728 · 792b728
1 parent 171f6dd
commit 792b728
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Showing 8 changed files with 41 additions and 43 deletions.
diff --git a/app/assets/javascripts/components/upload_csv_box.js.jsx b/app/assets/javascripts/components/upload_csv_box.js.jsx
@@ -92,17 +92,17 @@ var UploadCsvBox = React.createClass({
   const tooltipText = notFoundUuids.slice(0, 5).map((batch_number) => <div>{batch_number}</div>);
 
   const rowContent = errorMessage ?
-    <div className="uploaded-samples-count">
-      {uploadedSamplesCount} {samplesText}
-      {batchesNotFound > 0 && (
-        <span className="dashed-underline">
-          {" ("}{batchesNotFound} {batchesText} not found{")"}
-        </span>
-      )}
-    </div> :
     <div className="uploaded-samples-count">
       {errorMessage}
-    </div>;
+    </div>:
+    <div className="uploaded-samples-count">
+     {uploadedSamplesCount} {samplesText}
+     {batchesNotFound > 0 && (
+       <span className="dashed-underline">
+         {" ("}{batchesNotFound} {batchesText} not found{")"}
+       </span>
+     )}
+   </div>;
 
   return (
     <div className="items-row" key={filename}>

diff --git a/app/controllers/boxes_controller.rb b/app/controllers/boxes_controller.rb
@@ -57,19 +57,23 @@ def validate
 
     # TODO: should be handled by BoxForm (& duplicates BoxForm#parse_csv)
     CSV.open(params[:csv_box].path, headers: true) do |csv|
-      while csv.headers == true
-        csv.readline
-      end
+      unique_rows = Set.new
+      csv.each do |row|
 
-      unless csv.headers == ["Batch", "Concentration", "Distractor", "Instructions"]
-        @error_message = "Invalid columns"
-        return # rubocop:disable Lint/NonLocalExitFromIterator
-      end
+        unless csv.headers == ["Batch", "Concentration", "Distractor", "Instructions", "Replicates"]
+          @error_message = "Invalid columns"
+          return # rubocop:disable Lint/NonLocalExitFromIterator
+        end
+
+        if unique_rows.include?([row["Batch"], row["Concentration"], row["Distractor"], row["Instructions"]])
+          @error_message = "Batch, Concentration, Distractor, Instructions must be unique"
+          return # rubocop:disable Lint/NonLocalExitFromIterator
+        end
+        unique_rows << [row["Batch"], row["Concentration"], row["Distractor"], row["Instructions"]]
 
-      csv.each do |row|
         if batch_number = row["Batch"].presence&.strip
           batch_numbers << batch_number
-          @samples_count += 1
+          @samples_count += row["Replicates"].to_i
         end
       end
     end

diff --git a/app/models/box_form.rb b/app/models/box_form.rb
@@ -217,7 +217,7 @@ def parse_csv(path)
           instruction: row["Instructions"],
           concentrations: {
             "0" => {
-              replicate: 1,
+              replicate: row["Replicates"].to_i,
               concentration: Integer(Float(row["Concentration"]&.strip)),
             },
           },

diff --git a/public/templates/upload_box.csv b/public/templates/upload_box.csv
@@ -1,9 +1,5 @@
-Batch,Concentration,Distractor,Instructions
-batch1,100,no,Add 175 ml of media
-batch1,100,no,Add 175 ml of media
-batch1,1000,no,Add 175 ml of media
-batch1,1000,no,Add 175 ml of media
-batch2,2,yes,Add 250 ml of media
-batch2,2,yes,Add 250 ml of media
-batch2,200,yes,Add 100 ml of media
-batch2,200,yes,Add 100 ml of media
+Batch,Concentration,Distractor,Instructions,Replicates
+borrar,100,no,Add 175 ml of media,2
+borrar,1000,no,Add 175 ml of media,2
+Blank,2,yes,Add 250 ml of media,4
+Blank,200,yes,Add 100 ml of media,4
diff --git a/spec/controllers/boxes_controller_spec.rb b/spec/controllers/boxes_controller_spec.rb
@@ -266,7 +266,7 @@
     end
 
     it "validates CSV headers" do
-      csv_file = fixture_file_upload(Rails.root.join("spec/fixtures/csvs/samples_results_1.csv"), "text/csv")
+      csv_file = fixture_file_upload(Rails.root.join("spec/fixtures/csvs/csv_box_no_headers.csv"), "text/csv")
 
       expect do
         post :validate, params: { csv_box: csv_file }, format: "json"
@@ -292,7 +292,7 @@
       expect(JSON.parse(response.body)).to eq({
         "found_batches" => ["DISTRACTOR"],
         "not_found_batches" => [],
-        "samples_count" => 3,
+        "samples_count" => 4,
       })
     end
 
@@ -307,7 +307,7 @@
       expect(JSON.parse(response.body)).to eq({
         "found_batches" => ["DISTRACTOR"],
         "not_found_batches" => ["VIRUS"],
-        "samples_count" => 5,
+        "samples_count" => 6,
       })
     end
   end

diff --git a/spec/fixtures/csvs/csv_box_1.csv b/spec/fixtures/csvs/csv_box_1.csv
@@ -1,5 +1,3 @@
-Batch,Concentration,Distractor,Instructions
-DISTRACTOR,10,no,Add 10ml
-DISTRACTOR,10,no,Add 10ml
-DISTRACTOR,20,no,Add 10ml
-DISTRACTOR,20,no,Add 10ml
+Batch,Concentration,Distractor,Instructions,Replicates
+DISTRACTOR,10,no,Add 10ml,2
+DISTRACTOR,20,no,Add 10ml,2
diff --git a/spec/fixtures/csvs/csv_box_2.csv b/spec/fixtures/csvs/csv_box_2.csv
@@ -1,7 +1,4 @@
-Batch,Concentration,Distractor,Instructions
-VIRUS,10,no,Add 10ml
-VIRUS,10,no,Add 10ml
-DISTRACTOR,10,yes,Add 10ml
-DISTRACTOR,10,yes,Add 10ml
-DISTRACTOR,20,yes,Add 10ml
-DISTRACTOR,20,yes,Add 10ml
+Batch,Concentration,Distractor,Instructions,Replicates
+VIRUS,10,no,Add 10ml,2
+DISTRACTOR,10,yes,Add 10ml,2
+DISTRACTOR,20,yes,Add 10ml,2
diff --git a/spec/fixtures/csvs/csv_box_no_headers.csv b/spec/fixtures/csvs/csv_box_no_headers.csv
@@ -0,0 +1,3 @@
+VIRUS,10,no,Add 10ml,2
+DISTRACTOR,10,yes,Add 10ml,2
+DISTRACTOR,20,yes,Add 10ml,2