Instructions file nih tables and fixes

app/assets/javascripts/components/box_batches_form.js.jsx

@@ -273,7 +273,7 @@ var BoxBatchForm = React.createClass({
         </div>
         <div className="items-concentration">
           <input type="text" name={this.fieldFor("concentrations", item.key , "concentration")} value={item.concentration} onChange={set("concentration")}/>
-          copies/ml
+          copies/mL
         </div>
       </div>
     );

app/assets/javascripts/components/samples_reports_bar_chart.js.jsx

@@ -85,7 +85,7 @@ var SamplesReportsBarChart = React.createClass({
                 ref={function(ref) { if (ref) { d3.select(ref.getDOMNode()).call(xAxis); rotateLabels(ref); }}}>
               </g>
               <text transform={"translate(" + (chartWidth) + ", "+(chartHeight+this.props.margin.bottom-10)+")"}
-                        y="6" dy=".1em" style={{textAnchor: 'end'}}>CONCENTRATION (copies/ml)</text>
+                        y="6" dy=".1em" style={{textAnchor: 'end'}}>CONCENTRATION (copies/mL)</text>
 
 
               {/* Y Axis */}

app/assets/javascripts/components/samples_reports_line_chart.js.jsx

@@ -119,7 +119,7 @@ var SamplesReportsLineChart = React.createClass({
                    ref={function(ref) { if (ref) { d3.select(ref.getDOMNode()).call(xAxis); rotateLabels(ref); }}}>
                 </g>
                 <text transform={"translate(" + (chartWidth) + ", "+(chartHeight+this.props.margin.bottom-10)+")"}
-                        y="6" dy=".1em" style={{textAnchor: 'end'}}>CONCENTRATION (copies/ml)</text>
+                        y="6" dy=".1em" style={{textAnchor: 'end'}}>CONCENTRATION (copies/mL)</text>
 
                 {/* Y Axis */}
                 <g className="y axis"

app/assets/javascripts/components/samples_selector.js.jsx

@@ -51,7 +51,7 @@ var SamplesSelector = React.createClass({
             </div>
             <div className="items-item">{sample.uuid}&nbsp;<span>{sample.batch_number}</span></div>
           </div>
-          <div className="items-concentration">{sample.concentration} copies/ml</div>
+          <div className="items-concentration">{sample.concentration} copies/mL</div>
         </div>
       </div>);
     } else {

app/views/nih_tables/nih_challenge.csv.csvbuilder

@@ -9,7 +9,7 @@ csv << [
   'pango_lineage',
   'who_label',
   'non_clinical_cutoff_min',
-  'non_clinical_cutoff_unit',
+  'non_clinical_cutoff_min_unit',
   'true_positives',
   'false_positives',
   'true_negatives',
@@ -35,19 +35,19 @@ csv << [
   @target_sample.target_organism_taxonomy_id,
   @target_sample.pango_lineage,
   @target_sample.who_label,
-  @samples_report.threshold,
-  'copies/ml',
+  params[:threshold],
+  'copies/mL',
   params[:true_positives],
   params[:false_positives],
   params[:true_negatives],
   params[:false_negatives],
-  params[:tpr],
+  params[:sensitivity],
   nil,
   nil,
-  params[:fpr],
+  params[:specificity],
   nil,
   nil,
   params[:auc],
-  params[:roc_x_values],
-  params[:roc_y_values]
+  params[:roc_x_values].to_s.gsub(",","|"),
+  params[:roc_y_values].to_s.gsub(",","|")
 ]

app/views/nih_tables/nih_results.csv.csvbuilder

@@ -11,7 +11,7 @@ csv << [
 
 @samples_report.samples.each do |sample|
   csv << [
-    sample.id,
+    sample.uuid,
     sample.box.uuid,
     "#{sample.box.purpose}-panel",
     nil,

app/views/nih_tables/nih_samples.csv.csvbuilder

@@ -29,7 +29,7 @@ csv << [
     nil,
     nil,
     sample.concentration,
-    'copies/ml',
+    'copies/mL',
     sample.reference_gene,
     sample.uuid,
     sample.batch_number,

app/views/samples/_form.haml

@@ -85,7 +85,7 @@
         - @sample_form.blinded_attribute(:concentration) do
           .row.input-unit
             = f.text_field :concentration, min:0, readonly: !@can_update, :class=> "input-medium", :value => humanize_concentration(@sample_form.concentration), :pattern => "[\\d.]+(?:[eE]\\+?\\d+)?", :title => "(examples: 120, 12e1, 1.2e2, 1.2e+2, 1.2E2, 1.2E+2, 1.2E+02)"
-            .span.unit (copies/ml)
+            .span.unit (copies/mL)
 
       = f.form_field :replicate do
         - @sample_form.blinded_attribute(:replicate) do

app/views/samples_reports/show.haml

@@ -316,11 +316,12 @@
               true_negatives: ret.confusion_matrix.true_negative || 0,
               false_positives: ret.confusion_matrix.false_positive || 0,
               false_negatives: ret.confusion_matrix.false_negative || 0,
-              tpr: (ret.confusion_matrix.true_positive || 0) / ((ret.confusion_matrix.true_positive || 0) + (ret.confusion_matrix.false_negative || 0)),
-              fpr: (ret.confusion_matrix.false_positive || 0) / ((ret.confusion_matrix.false_positive || 0) + (ret.confusion_matrix.true_negative || 0)),
-              auc: #{auc(roc_curve(@samples_report))},
-              roc_x_values: #{roc_curve(@samples_report).map{|x| x[0]}},
-              roc_y_values: #{roc_curve(@samples_report).map{|x| x[1]}},
+              sensitivity: ((ret.confusion_matrix.true_positive || 0) / ((ret.confusion_matrix.true_positive || 0) + (ret.confusion_matrix.false_negative || 0))).toFixed(3),
+              specificity: 1-((ret.confusion_matrix.false_positive || 0) / ((ret.confusion_matrix.false_positive || 0) + (ret.confusion_matrix.true_negative || 0))).toFixed(3),
+              auc: #{auc(roc_curve(@samples_report)).round(3)},
+              roc_x_values: #{roc_curve(@samples_report).map{|x| x[0].round(3)}},
+              roc_y_values: #{roc_curve(@samples_report).map{|x| x[1].round(3)}},
+              threshold: parseFloat(threshold).toFixed(3),
             };
 
             // create url params with the params dictionary

public/templates/Instructions.txt

@@ -1,2 +1,27 @@
-Instructions for the use of NIH tables.
+This compressed file contains three tables containing data elements for the RADx-rad Data Hub. The tables 
+contain pre-filled data based on the information available to the CDx LIMS system. The tables are provided 
+to the user to fill in the missing information. Please note that you need to maintain the same format as 
+the one provided in the tables (CSV file format, with identical columns and rows).
 
+The three provided tables are as follows:
+
+1. <report_name>_samples.csv
+2. <report_name>_samples_results.csv
+3. <report_name>_<purpose>.csv
+
+The first table contains one row per sample with general information about each sample. 
+
+The second table contains one row per sample result, providing information about the results obtained for 
+each sample by the user, including the readout, measurement units, used technology, etc. 
+
+The third table contains one row per panel and provides information about the aggregated results obtained 
+after the tests were performed. The <purpose> can be either "LOD" or "Challenge" depending on the type of
+test performed. 
+
+Once the developer completes the missing data, these files are ready to be submitted to the RADx-rad 
+Data Core (https://www.radxrad.org/) for quality assurance. For more information, please contact 
+Dr. Peter Rose ([email protected]). The Data Core administrator will review the data for completeness 
+and consistency and will reach out to the developer if any issues arise.
+
+After the data passes the quality check, the Data Core administrator uploads the data files, common data 
+element dictionaries, and metadata files to the NIH COVID RADx-rad Data Hub (https://radx-hub.nih.gov/).

public/templates/upload_box.csv

@@ -1,5 +1,5 @@
 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
+batch1,100,no,Add 175 ml of media,2
+batch1,1000,no,Add 175 ml of media,2
+batch2,2,yes,Add 250 ml of media,4
+batch2,200,yes,Add 100 ml of media,4

spec/controllers/nih_tables_controller_spec.rb

@@ -61,7 +61,7 @@
       samples_table = CSV.parse(Zip::File.open_buffer(response.body).entries.find{|e| e.name == "Test_results.csv"}.get_input_stream.read, headers: true)
 
       expect(samples_table.count).to eq(@samples_report.samples_report_samples.count)
-      expect(samples_table["sample_id"]).to eq(@samples_report.samples_report_samples.map{|srs| srs.sample.id.to_s})
+      expect(samples_table["sample_id"]).to eq(@samples_report.samples_report_samples.map{|srs| srs.sample.uuid.to_s})
     end
 
     it "should contain the LOD table for if the box purpose is LOD" do