Specific purposes nih tables exporting (#1959)

* Specific purposes nih tables exporting

* Fixes PR review

* Lint fixes

* Fixes PR review

app/controllers/nih_tables_controller.rb

@@ -1,6 +1,7 @@
 class NihTablesController < ApplicationController
   def show
     @samples_report = SamplesReport.find(params[:id])
+    @target_batch = @samples_report.target_batch
     return unless authorize_resource(@samples_report, READ_SAMPLES_REPORT)
 
     zip_data = create_zip_file
@@ -21,9 +22,9 @@ def create_zip_file
       add_nih_table('results', stream)
 
       if purpose == "LOD"
-        #add_nih_table('lod', stream)
+        add_nih_table('lod', stream)
       elsif purpose == "Challenge"
-        #add_nih_table('challenge', stream)
+        add_nih_table('challenge', stream)
       end
     end
     zip_stream.rewind

app/models/samples_report.rb

@@ -68,6 +68,11 @@ def calculate_lod_and_lob
     self.save
   end
 
+  def target_batch
+    # The target batch for this box is the batch of any sample which distractor is false or null
+    samples_report_samples.joins(:sample).find_by("samples.distractor IS NULL OR samples.distractor = 'false'").sample.batch
+  end
+
   private
 
   def there_are_samples

app/views/samples_reports/nih_challenge.csv.csvbuilder

@@ -0,0 +1,54 @@
+csv << [
+  'protocol_id',
+  'technology_platform',
+  'vqa_box_id',
+  'sample_group',
+  'target_analyte_type',
+  'target_organism_name',
+  'target_organism_taxonomy_id',
+  'pango_lineage',
+  'who_label',
+  'non_clinical_cutoff_min',
+  'non_clinical_cutoff_unit',
+  'true_positives',
+  'false_positives',
+  'true_negatives',
+  'false_negatives',
+  'non_clinical_sensitivity',
+  'non_clinical_sensitivity_ci_percent',
+  'non_clinical_sensitivity_ci_min',
+  'non_clinical_specificity',
+  'non_clinical_specificity_ci_percent',
+  'non_clinical_specificity_ci_min',
+  'area_under_the_roc_curve',
+  'roc_x_values',
+  'roc_y_values'
+]
+
+sample = @samples_report.samples[0]
+csv << [
+  nil,
+  nil,
+  sample.box.uuid,
+  "#{sample.box.purpose}-panel",
+  'inactivated virus',
+  'SARS-CoV-2',
+  @target_batch.target_organism_taxonomy_id,
+  @target_batch.pango_lineage,
+  @target_batch.who_label,
+  @samples_report.threshold,
+  'copies/ml',
+  params[:true_positives],
+  params[:false_positives],
+  params[:true_negatives],
+  params[:false_negatives],
+  params[:tpr],
+  nil,
+  nil,
+  params[:fpr],
+  nil,
+  nil,
+  params[:auc],
+  params[:roc_x_values],
+  params[:roc_y_values]
+]

app/views/samples_reports/nih_lod.csv.csvbuilder

@@ -0,0 +1,44 @@
+csv << [
+  'protocol_id',
+  'technology_platform',
+  'vqa_box_id',
+  'sample_group',
+  'target_analyte_type',
+  'target_organism_name',
+  'target_organism_taxonomy_id',
+  'pango_lineage',
+  'who_label',
+  'limit_of_blank',
+  'limit_of_blank_unit',
+  'limit_of_detection',
+  'limit_of_detection_reference_gene',
+  'limit_of_detection_unit',
+  'limit_of_detection_sn_ratio',
+  'limit_of_detection_ci_percent',
+  'limit_of_detection_detail',
+  'analytical_sensitivity',
+  'analytical_sensitivity_unit'
+]
+
+sample = @samples_report.samples[0]
+csv << [
+  nil,
+  nil,
+  sample.box.uuid,
+  "#{sample.box.purpose}-panel",
+  'inactivated virus',
+  'SARS-CoV-2',
+  @target_batch.target_organism_taxonomy_id,
+  @target_batch.pango_lineage,
+  @target_batch.who_label,
+  @samples_report.lob,
+  nil,
+  @samples_report.lod,
+  @target_batch.reference_gene,
+  nil,
+  nil,
+  "90",
+  'linear regression',
+  nil,
+  nil
+]

app/views/samples_reports/show.haml

@@ -294,14 +294,41 @@
     document.querySelector(`.nih-report-type-modal-container`).classList.add("hidden");
   }
 
-  function downloadNIHFiles() {
+  async function downloadNIHFiles() {
     hideConfirmModal();
-
-    // Open the download_nih_tables path in a new tab
     var context = getUrlParameter('context');
-    var url = '/samples_reports/'+#{@samples_report.id}+'/nih_tables?context='+context+"";
-    window.open(url, '_blank');
-
+
+    // if purpose is challenge, then we need the live threshold calculations
+    if (#{@purpose.to_json} == "Challenge") {
+      var threshold = document.getElementById("threshold").value;
+      var url = '/samples_reports/update_threshold?context='+context+"&samples_report_id=#{@samples_report.id}&threshold="+threshold;
+      await fetch(url)
+          .then((response) => response.json())
+          .then((ret) => {
+            var params = {
+              true_positives: ret.confusion_matrix.true_positive || 0,
+              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]}},
+            };
+
+            // create url params with the params dictionary
+            var urlParams = new URLSearchParams(Object.entries(params));
+
+            // Open the download_nih_tables path in a new tab
+            var url = '/samples_reports/'+#{@samples_report.id}+'/nih_tables?context='+context+"&"+urlParams.toString();
+            window.open(url, '_blank');
+        })
+    }
+    else {
+      var url = '/samples_reports/'+#{@samples_report.id}+'/nih_tables?context='+context;
+      window.open(url, '_blank');
+    }
   }
 
   document.getElementById("print-as-csv").addEventListener("click", showConfirmModal);

spec/controllers/nih_tables_controller_spec.rb

@@ -11,6 +11,9 @@
     @box = Box.make!(:overfilled, institution: @institution, purpose: "LOD")
     @samples_report = SamplesReport.create(institution: @institution, samples_report_samples: @box.samples.map{|s| SamplesReportSample.new(sample: s)}, name: "Test")
 
+    @box2 = Box.make!(:overfilled, institution: @institution, purpose: "Challenge")
+    @samples_report2 = SamplesReport.create(institution: @institution, samples_report_samples: @box2.samples.map{|s| SamplesReportSample.new(sample: s)}, name: "TestChallenge")
+
     grant @user, @other_user, @other_institution, READ_INSTITUTION
   end
 
@@ -49,7 +52,6 @@
       samples_table = CSV.parse(Zip::File.open_buffer(response.body).entries.find{|e| e.name == "Test_samples.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})
     end
 
@@ -59,10 +61,51 @@
       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})
     end
 
+    it "should contain the LOD table for if the box purpose is LOD" do
+      get :show, params: { id: @samples_report.id }
+
+      expect(Zip::File.open_buffer(response.body).entries.map(&:name)).to include("Test_lod.csv")
+    end
+
+    it "should not contain the LOD table for if the box purpose is Challenge" do
+      get :show, params: { id: @samples_report2.id }
+
+      expect(Zip::File.open_buffer(response.body).entries.map(&:name)).not_to include("TestChallenge_lod.csv")
+    end
+
+    it "should contain the LOD table with the correct data" do
+      get :show, params: { id: @samples_report.id }
+
+      lod_table = CSV.parse(Zip::File.open_buffer(response.body).entries.find{|e| e.name == "Test_lod.csv"}.get_input_stream.read, headers: true)
+
+      expect(lod_table.count).to eq(1)
+      expect(lod_table["vqa_box_id"]).to include(@box.uuid)
+    end
+
+    it "should contain the Challenge table for if the box purpose is Challenge" do
+      get :show, params: { id: @samples_report2.id }
+
+      expect(Zip::File.open_buffer(response.body).entries.map(&:name)).to include("TestChallenge_challenge.csv")
+    end
+
+    it "should not contain the Challenge table for if the box purpose is LOD" do
+      get :show, params: { id: @samples_report.id }
+
+      expect(Zip::File.open_buffer(response.body).entries.map(&:name)).not_to include("Test_challenge.csv")
+    end
+
+    it "should contain the Challenge table with the correct data" do
+      get :show, params: { id: @samples_report2.id }
+
+      challenge_table = CSV.parse(Zip::File.open_buffer(response.body).entries.find{|e| e.name == "TestChallenge_challenge.csv"}.get_input_stream.read, headers: true)
+
+      expect(challenge_table.count).to eq(1)
+      expect(challenge_table["vqa_box_id"]).to include(@box2.uuid)
+    end
+
     it "should not allow access to user without read access" do
       sign_in @other_user
       get :show, params: { id: @samples_report.id, context: @other_institution.uuid }