From 4f5fd096026bbbb5e9f24894d94a44d8d08cae6f Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Thu, 20 Jul 2023 12:39:22 +0200
Subject: [PATCH 1/7] Fix: Box CSV validation fails when CSV has whitespaces

---
 .../components/upload_csv_box.js.jsx          | 29 ++++-------
 app/controllers/boxes_controller.rb           | 29 ++++++++++-
 app/controllers/csv_validations_controller.rb | 36 -------------
 app/models/box_form.rb                        | 37 ++++++-------
 app/views/boxes/_form.haml                    |  4 +-
 app/views/boxes/_upload_csv_box.haml          | 48 -----------------
 app/views/boxes/validate.json.jbuilder        |  4 ++
 config/routes.rb                              |  9 ++--
 spec/controllers/boxes_controller_spec.rb     | 52 +++++++++++++++++++
 spec/support/blueprints.rb                    | 18 +++----
 10 files changed, 128 insertions(+), 138 deletions(-)
 delete mode 100644 app/controllers/csv_validations_controller.rb
 delete mode 100644 app/views/boxes/_upload_csv_box.haml
 create mode 100644 app/views/boxes/validate.json.jbuilder

diff --git a/app/assets/javascripts/components/upload_csv_box.js.jsx b/app/assets/javascripts/components/upload_csv_box.js.jsx
index a0637255a..d672a1508 100644
--- a/app/assets/javascripts/components/upload_csv_box.js.jsx
+++ b/app/assets/javascripts/components/upload_csv_box.js.jsx
@@ -2,7 +2,7 @@ var UploadCsvBox = React.createClass({
   getInitialState: function() {
     return {
       csrfToken: this.props.csrf_token,
-      url: "/csv_validation/" + this.props.context,
+      url: this.props.validate_url,
       fieldName: this.props.name, // Initial fieldName value
       uploadRows: [], // Array to store upload rows
       hideListItems: "hidden",
@@ -16,7 +16,7 @@ var UploadCsvBox = React.createClass({
     this.setState({ fileValue: event.target.value });
     const file = event.target.files[0];
     const formData = new FormData();
-    formData.append('csv_file', file);
+    formData.append('csv_box', file);
 
     fetch(this.state.url, {
       method: "POST",
@@ -33,25 +33,19 @@ var UploadCsvBox = React.createClass({
         }
       })
       .then(responseJson => {
-        const not_found_batches = responseJson.not_found_batches;
-        const samples_nbr = responseJson.samples_nbr;
-        const error_message = responseJson.error_message;
-
         // Create row from template with filename and upload info
-        const filename = file.name;
-        const uploadInfo =  {
-          uploadedSamplesCount: samples_nbr,
-          notFoundUuids: not_found_batches,
-          errorMessage: error_message
+        const uploadInfo = {
+          uploadedSamplesCount: responseJson.samples_count,
+          notFoundUuids: responseJson.not_found_batches,
+          errorMessage: responseJson.error_message,
         };
 
         // Add the new row to the state
         this.setState(prevState => ({
-          uploadRows: [...prevState.uploadRows, {filename, uploadInfo, showTooltip: false}]
+          uploadRows: [...prevState.uploadRows, {filename: file.name, uploadInfo, showTooltip: false}]
         }));
 
         this.setState({ hideListItems: "" });
-
       })
       .catch(error => {
         this.setState({ errorMessage: error });
@@ -97,7 +91,7 @@ var UploadCsvBox = React.createClass({
 
   const tooltipText = notFoundUuids.slice(0, 5).map((batch_number) => <div>{batch_number}</div>);
 
-  const rowContent = errorMessage == "" ?
+  const rowContent = errorMessage ?
     <div className="uploaded-samples-count">
       {uploadedSamplesCount} {samplesText}
       {batchesNotFound > 0 && (
@@ -110,17 +104,16 @@ var UploadCsvBox = React.createClass({
       {errorMessage}
     </div>;
 
-
   return (
     <div className="items-row" key={filename}>
       <div className="items-item gap-5">
         <div className="icon-circle-minus icon-gray remove_file" onClick={() => this.handleRemove(index)}></div>
         <div className="file-name">{filename}</div>
       </div>
-      <div className={`items-row-action gap-5 not_found_message ${batchesNotFound > 0 ? ' ttip ' : ' '} ${batchesNotFound > 0 || errorMessage != "" ? ' input-required ' : ' '}}`}
+      <div className={`items-row-action gap-5 not_found_message ${batchesNotFound > 0 ? ' ttip ' : ' '} ${batchesNotFound > 0 || errorMessage ? ' input-required ' : ' '}}`}
            onClick={() => this.handleClick(index)}>
-        {rowContent}  
-        <div className={`upload-icon bigger ${batchesNotFound > 0 || errorMessage != "" ? 'icon-alert icon-red' : 'icon-check'}`}></div>
+        {rowContent}
+        <div className={`upload-icon bigger ${batchesNotFound > 0 || errorMessage ? 'icon-alert icon-red' : 'icon-check'}`}></div>
         {batchesNotFound > 0 && (
           <div className={`ttext not-found-uuids ${showTooltip ? '' : 'hidden'}`}>
             {tooltipText}
diff --git a/app/controllers/boxes_controller.rb b/app/controllers/boxes_controller.rb
index 6b7d2d350..63c268f87 100644
--- a/app/controllers/boxes_controller.rb
+++ b/app/controllers/boxes_controller.rb
@@ -1,5 +1,5 @@
 class BoxesController < ApplicationController
-  before_action :load_box, except: %i[index new create bulk_destroy]
+  before_action :load_box, except: %i[index new validate create bulk_destroy]
 
   def index
     @can_create = has_access?(@navigation_context.institution, CREATE_INSTITUTION_BOX)
@@ -51,6 +51,33 @@ def new
     @box_form = BoxForm.build(@navigation_context)
   end
 
+  def validate
+    @samples_count = 0
+    batch_numbers = Set.new
+
+    # 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
+
+      unless csv.headers == ["Batch", "Concentration", "Distractor", "Instructions"]
+        @error_message = "Invalid columns"
+        return # rubocop:disable Lint/NonLocalExitFromIterator
+      end
+
+      csv.each do |row|
+        if batch_number = row["Batch"].presence&.strip
+          batch_numbers << batch_number
+          @samples_count += 1
+        end
+      end
+    end
+
+    @found_batches = @navigation_context.institution.batches.where(batch_number: batch_numbers.to_a).pluck(:batch_number)
+    @not_found_batches = (batch_numbers - @found_batches)
+  end
+
   def create
     return unless authorize_resource(@navigation_context.institution, CREATE_INSTITUTION_BOX)
 
diff --git a/app/controllers/csv_validations_controller.rb b/app/controllers/csv_validations_controller.rb
deleted file mode 100644
index de54201d8..000000000
--- a/app/controllers/csv_validations_controller.rb
+++ /dev/null
@@ -1,36 +0,0 @@
-class CsvValidationsController < ApplicationController
-  def create
-    uploaded_file = params[:csv_file]
-    if uploaded_file.content_type == "text/csv"
-      csv_text = uploaded_file.read
-      institution = @navigation_context.institution
-      csv_table = CSV.parse(csv_text, headers: true)
-
-      unless csv_table.headers == ["Batch", "Concentration", "Distractor", "Instructions"]
-        render_invalid_format
-        return
-      end
-
-      batch_values = csv_table.map { |row| row["Batch"] }
-      found_batches = institution.batches.where(batch_number: batch_values).pluck(:batch_number)
-      not_found_batches = (batch_values - found_batches).uniq
-
-      render json: { found_batches: found_batches,
-                     not_found_batches: not_found_batches,
-                     samples_nbr: csv_table.size,
-                     error_message: "" }
-    else
-      render_invalid_format
-    end
-  end
-
-  private
-
-  def render_invalid_format
-    render json: { found_batches: [],
-                   not_found_batches: [],
-                   samples_nbr: 0, 
-                   error_message: "Invalid file format." }
-  end
-
-end
diff --git a/app/models/box_form.rb b/app/models/box_form.rb
index 2eafc0f30..d2e524ce0 100644
--- a/app/models/box_form.rb
+++ b/app/models/box_form.rb
@@ -22,8 +22,9 @@ def initialize(box, params)
     @option = params[:option]
     @media = params[:media].presence
     @batches_data = params[:batches].presence.to_h
-    @csv_box = params[:csv_box].presence
-    initialize_csv_box if @csv_box
+    if uploaded_file = params[:csv_box].presence
+      parse_csv(uploaded_file.path)
+    end
     @batch_uuids = @batches_data.transform_values { |v| v[:batch_uuid] }
     @sample_uuids = params[:sample_uuids].presence.to_h
   end
@@ -204,23 +205,23 @@ def have_distractor_sample?
     @samples.any? { |_, sample| sample.distractor }
   end
 
-  def initialize_csv_box
-    CSV.open(@csv_box.path) do |csv_stream|
-      i = 0
-      csv_stream.each do |row|
-        batch_number, concentration, distractor, instruction = row[0..3]
-        batch_uuid = Batch.find_by(batch_number: batch_number)&.uuid
-        next if batch_uuid.blank?
-        @batches_data[i] = {
-          batch_uuid: batch_uuid,
-          distractor: distractor.downcase == "yes",
-          instruction: instruction,
-          concentrations: {"0" => {
-            replicate: 1,
-            concentration: Integer(Float(concentration)),
-          }},
+  def parse_csv(path)
+    CSV.open(path, headers: true) do |csv|
+      csv.each do |row|
+        next unless batch_number = row["Batch"]&.strip.presence
+        next unless batch = Batch.find_by(batch_number: batch_number)
+
+        @batches_data[@batches_data.size] = {
+          batch_uuid: batch.uuid,
+          distractor: row["Distractor"]&.strip&.downcase == "yes",
+          instruction: row["Instructions"],
+          concentrations: {
+            "0" => {
+              replicate: 1,
+              concentration: Integer(Float(row["Concentration"]&.strip)),
+            },
+          },
         }
-        i += 1
       end
     end
   end
diff --git a/app/views/boxes/_form.haml b/app/views/boxes/_form.haml
index 6d0f7b626..18593bf7c 100644
--- a/app/views/boxes/_form.haml
+++ b/app/views/boxes/_form.haml
@@ -42,7 +42,7 @@
 
             .row
               .col
-                = react_component "UploadCsvBox", { name: "box[csv_box]", context: @navigation_context.uuid, csrf_token: form_authenticity_token}
+                = react_component "UploadCsvBox", { name: "box[csv_box]", validate_url: validate_boxes_url(context: @navigation_context.institution.uuid + "-*"), csrf_token: form_authenticity_token}
             .row
               =link_to '/templates/upload_box.csv', class: 'btn-link', target: "_blank" do
                 .icon-download.icon-gray
@@ -74,8 +74,6 @@
                       showCloseButton: false,
                       message: "If you change the sample source, the box contents will be emptied. ")
 
-= render 'upload_csv_box'
-
 :javascript
   var sourcesRadio = document.querySelectorAll(".radiotoggle input");
   var oldSource = null;
diff --git a/app/views/boxes/_upload_csv_box.haml b/app/views/boxes/_upload_csv_box.haml
deleted file mode 100644
index 8c6edb2ac..000000000
--- a/app/views/boxes/_upload_csv_box.haml
+++ /dev/null
@@ -1,48 +0,0 @@
-
-%template{:id => "csvFileRow"}
-  .list-items.upload_info
-    .items-row
-      .items-item.gap-5
-        .icon-circle-minus.icon-gray.remove_file
-        .file-name
-      .items-row-action.gap-5.not_found_message
-        .uploaded-samples-count
-        .upload-icon.bigger
-        .ttext.not-found-uuids.hidden
-
-%template{:id => "csvInputFile"}
-  = file_field_tag "box[csv_box]", hidden: true, class: "csv_file", accept: "text/csv"
-
-:javascript
-  var getUrlParameter = function getUrlParameter(sParam) {
-      var sPageURL = window.location.search.substring(1),
-          sURLVariables = sPageURL.split('&'),
-          sParameterName,
-          i;
-
-      for (i = 0; i < sURLVariables.length; i++) {
-          sParameterName = sURLVariables[i].split('=');
-
-          if (sParameterName[0] === sParam) {
-              return sParameterName[1] === undefined ? true : decodeURIComponent(sParameterName[1]);
-          }
-      }
-      return false;
-  };
-
-  var context = getUrlParameter('context');
-  var isUUID = function(str) {
-    const regexExp = /^[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}$/gi;
-    return regexExp.test(str);
-  };
-
-  var showToolTip = function(evt) {
-    var tooltip = evt.currentTarget.tooltip
-    if (tooltip.classList.contains("hidden")) {
-        tooltip.classList.remove("hidden")
-        setTimeout(() => tooltip.classList.add("hidden"), 5000)
-    }
-    else {
-        tooltip.classList.toggle("hidden")
-    }
-  }
diff --git a/app/views/boxes/validate.json.jbuilder b/app/views/boxes/validate.json.jbuilder
new file mode 100644
index 000000000..a97c84fd2
--- /dev/null
+++ b/app/views/boxes/validate.json.jbuilder
@@ -0,0 +1,4 @@
+json.found_batches @found_batches || []
+json.not_found_batches @not_found_batches || []
+json.samples_count @samples_count
+json.error_message @error_message if @error_message
diff --git a/config/routes.rb b/config/routes.rb
index b381474a7..b8d8938be 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -166,16 +166,15 @@
     member do
       post :unblind
       post :blind
-      get 'print'
-      get 'inventory', constraints: { format: 'csv' }
+      get :print
+      get :inventory, constraints: { format: 'csv' }
     end
     collection do
-      post 'bulk_action', constraints: lambda { |request| request.params[:bulk_action] == 'destroy' }, action: :bulk_destroy
+      post :validate
+      post :bulk_action, constraints: lambda { |request| request.params[:bulk_action] == 'destroy' }, action: :bulk_destroy
     end
   end
 
-  post '/csv_validation/:context', to: 'csv_validations#create', as: 'csv_validation'
-
   resources :qc_infos
   resources :test_results , only: [:index, :show]
   resources :filters, format: 'html'
diff --git a/spec/controllers/boxes_controller_spec.rb b/spec/controllers/boxes_controller_spec.rb
index 7aee7f6fe..6c54f9037 100644
--- a/spec/controllers/boxes_controller_spec.rb
+++ b/spec/controllers/boxes_controller_spec.rb
@@ -260,6 +260,58 @@
     end
   end
 
+  describe "validate (CSV)" do
+    let!(:batch) do
+      Batch.make!(institution: institution, site: site, batch_number: "DISTRACTOR")
+    end
+
+    it "validates CSV headers" do
+      csv_file = fixture_file_upload(Rails.root.join("spec/fixtures/csvs/samples_results_1.csv"), "text/csv")
+
+      expect do
+        post :validate, params: { csv_box: csv_file }, format: "json"
+        expect(response).to have_http_status(:ok)
+      end.to change(institution.boxes, :count).by(0)
+
+      expect(JSON.parse(response.body)).to eq({
+        "found_batches" => [],
+        "not_found_batches" => [],
+        "samples_count" => 0,
+        "error_message" => "Invalid columns"
+      })
+    end
+
+    it "finds all batches" do
+      csv_file = fixture_file_upload(Rails.root.join("spec/fixtures/csvs/csv_box_1.csv"), "text/csv")
+
+      expect do
+        post :validate, params: { csv_box: csv_file }, format: "json"
+        expect(response).to have_http_status(:ok)
+      end.to change(institution.boxes, :count).by(0)
+
+      expect(JSON.parse(response.body)).to eq({
+        "found_batches" => ["DISTRACTOR"],
+        "not_found_batches" => [],
+        "samples_count" => 3,
+      })
+    end
+
+    it "fails to find some batches" do
+      csv_file = fixture_file_upload(Rails.root.join("spec/fixtures/csvs/csv_box_2.csv"), "text/csv")
+
+      expect do
+        post :validate, params: { csv_box: csv_file }, format: "json"
+        expect(response).to have_http_status(:ok)
+      end.to change(institution.boxes, :count).by(0)
+
+      expect(JSON.parse(response.body)).to eq({
+        "found_batches" => ["DISTRACTOR"],
+        "not_found_batches" => ["VIRUS"],
+        "samples_count" => 5,
+      })
+    end
+  end
+
   describe "create" do
     let :batch do
       Batch.make!(institution: institution, site: site)
diff --git a/spec/support/blueprints.rb b/spec/support/blueprints.rb
index 5c69219fc..53d6724a9 100644
--- a/spec/support/blueprints.rb
+++ b/spec/support/blueprints.rb
@@ -271,15 +271,15 @@ def first_or_make_site_unless_manufacturer(institution)
   @batch_two = Batch.make!
 
   samples { [
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 30, replicate: 1),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 200, replicate: 2),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 1000, replicate: 3),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 30, replicate: 4),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 200, replicate: 5),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 1000, replicate: 6),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 30, replicate: 7),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 200, replicate: 8),
-    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 1000, replicate: 9),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 30, replicate: 1, distractor: true),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 200, replicate: 2, distractor: false),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 1000, replicate: 3, distractor: true),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 30, replicate: 4, distractor: false),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 200, replicate: 5, distractor: true),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 1000, replicate: 6, distractor: false),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 30, replicate: 7, distractor: true),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_two, concentration: 200, replicate: 8, distractor: false),
+    Sample.make(:filled, box: object, institution: object.institution, site: object.site, batch: @batch_one, concentration: 1000, replicate: 9, distractor: true),
   ] }
 end
 

From d1f761da8682d546065b39ab269dd39e08dbe5ba Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Thu, 20 Jul 2023 14:43:48 +0200
Subject: [PATCH 2/7] Fix: alignment of sample/batch uuids in edit sample form

---
 app/views/samples/_form.haml | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/app/views/samples/_form.haml b/app/views/samples/_form.haml
index f709f0005..38c000549 100644
--- a/app/views/samples/_form.haml
+++ b/app/views/samples/_form.haml
@@ -8,20 +8,22 @@
             = "VIEW QC INFO"
 
       = f.form_field :uuid do
-        %span.copy-content
-          = f.object.uuid
-        %button.btn-copy.ttip
-          = icon_tag "copy", class: "btn-icon"
+        .value
+          %span.copy-content
+            = f.object.uuid
+          %button.btn-copy.ttip
+            = icon_tag "copy", class: "btn-icon"
       - if f.object.batch_number
         = f.form_field :batch_id, value: @sample_form.batch_number
 
       - if box = @sample_form.box
         = f.fields_for :box, box do |g|
           = g.form_field :uuid, label: { text: "Box ID" } do
-            %span.copy-content
-              = g.object.uuid
-            %button.btn-copy.ttip
-              = icon_tag "copy", class: "btn-icon"
+            .value
+              %span.copy-content
+                = g.object.uuid
+              %button.btn-copy.ttip
+                = icon_tag "copy", class: "btn-icon"
           = g.form_field :purpose, value: box.purpose, label: { text: "Box Purpose" }
 
     .col.pe-5

From e391535d971293a828dbcfe7261e59fb99e4aceb Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Thu, 20 Jul 2023 15:02:28 +0200
Subject: [PATCH 3/7] Fix: larger width for autocomplete text fields

closes #1963
---
 .../components/cdx_select_autocomplete.js.jsx    | 10 ++++++++--
 app/helpers/autocomplete_field_helper.rb         | 16 +++++++++-------
 app/views/batches/_form.haml                     | 15 ++++++++++-----
 app/views/samples/_form.haml                     | 15 ++++++++++-----
 4 files changed, 37 insertions(+), 19 deletions(-)

diff --git a/app/assets/javascripts/components/cdx_select_autocomplete.js.jsx b/app/assets/javascripts/components/cdx_select_autocomplete.js.jsx
index e94b34390..b4fa8ec9a 100644
--- a/app/assets/javascripts/components/cdx_select_autocomplete.js.jsx
+++ b/app/assets/javascripts/components/cdx_select_autocomplete.js.jsx
@@ -1,6 +1,8 @@
 var CdxSelectAutocomplete = React.createClass({
-  componentWillMount: function () {
-    this.asyncOptions = _.debounce(this.asyncOptions.bind(this), 100, { maxWait: 250 });
+  getDefaultProps: function() {
+    return {
+      className: "input-large"
+    };
   },
 
   getInitialState: function () {
@@ -9,6 +11,10 @@ var CdxSelectAutocomplete = React.createClass({
     };
   },
 
+  componentWillMount: function () {
+    this.asyncOptions = _.debounce(this.asyncOptions.bind(this), 100, { maxWait: 250 });
+  },
+
   // Since <Select> uses a different INPUT we must copy the value when the
   // user is typing from the visible to the hidden INPUT, otherwise when the
   // user enters free-text of validates with an invalid value, the backend won't
diff --git a/app/helpers/autocomplete_field_helper.rb b/app/helpers/autocomplete_field_helper.rb
index 0c174ca28..56c5ad364 100644
--- a/app/helpers/autocomplete_field_helper.rb
+++ b/app/helpers/autocomplete_field_helper.rb
@@ -1,11 +1,13 @@
 module AutocompleteFieldHelper
-  def autocomplete_field(f, field, institution)
-    field_name = field.match(/\[(.*?)\]/)[1]
-    react_component "CdxSelectAutocomplete", {
-      name: field,
-      value: f.object.public_send(field_name.to_sym),
+  def autocomplete_field(f, name, field_name, institution, **attributes)
+    class_name = attributes.delete(:class)
+    props = attributes.merge(
+      name: name,
+      value: f.object.public_send(field_name),
       url: institution_autocomplete_path(institution_id: institution.id, field_name: field_name),
-      combobox: true,
-    }
+      combobox: true
+    )
+    props[:className] = class_name if class_name
+    react_component("CdxSelectAutocomplete", props)
   end
 end
diff --git a/app/views/batches/_form.haml b/app/views/batches/_form.haml
index b87d8bd12..ce4fba715 100644
--- a/app/views/batches/_form.haml
+++ b/app/views/batches/_form.haml
@@ -36,14 +36,19 @@
         .row.input-unit
           = f.number_field :volume, min: 0, step: :any, :class => "input-small", readonly: !@can_update
           .span.unit (μl)
+
       = f.form_field :reference_gene do
-        = autocomplete_field(f, "batch[reference_gene]", @navigation_context.institution)
-      = f.form_field :target_organism_taxonomy do
-        = autocomplete_field(f, "batch[target_organism_taxonomy_id]", @navigation_context.institution)
+        = autocomplete_field(f, "batch[reference_gene]", :reference_gene, @navigation_context.institution, class: "input-x-large")
+
+      = f.form_field :target_organism_taxonomy_id do
+        = autocomplete_field(f, "batch[target_organism_taxonomy_id]", :target_organism_taxonomy_id, @navigation_context.institution, class: "input-x-large")
+
       = f.form_field :pango_lineage do
-        = autocomplete_field(f, "batch[pango_lineage]", @navigation_context.institution)
+        = autocomplete_field(f, "batch[pango_lineage]", :pango_lineage, @navigation_context.institution, class: "input-x-large")
+
       = f.form_field :who_label do
-        = autocomplete_field(f, "batch[who_label]", @navigation_context.institution)
+        = autocomplete_field(f, "batch[who_label]", :who_label, @navigation_context.institution, class: "input-x-large")
+
       - if @can_edit_sample_quantity
         = f.form_field :samples_quantity do
           = f.number_field :samples_quantity, min: 0, :class => "input-small"
diff --git a/app/views/samples/_form.haml b/app/views/samples/_form.haml
index 38c000549..237bc4e16 100644
--- a/app/views/samples/_form.haml
+++ b/app/views/samples/_form.haml
@@ -64,14 +64,19 @@
         .row.input-unit
           = f.number_field :volume, min: 0, step: :any, :class => "input-small", readonly: !@can_update
           .span.unit (μl)
+
       = f.form_field :reference_gene do
-        = autocomplete_field(f, "sample[reference_gene]", @navigation_context.institution)
-      = f.form_field :target_organism_taxonomy do
-        = autocomplete_field(f, "sample[target_organism_taxonomy_id]", @navigation_context.institution)
+        = autocomplete_field(f, "sample[reference_gene]", :reference_gene, @navigation_context.institution, class: "input-x-large")
+
+      = f.form_field :target_organism_taxonomy_id do
+        = autocomplete_field(f, "sample[target_organism_taxonomy_id]", :target_organism_taxonomy_id, @navigation_context.institution, class: "input-x-large")
+
       = f.form_field :pango_lineage do
-        = autocomplete_field(f, "sample[pango_lineage]", @navigation_context.institution)
+        = autocomplete_field(f, "sample[pango_lineage]", :pango_lineage, @navigation_context.institution, class: "input-x-large")
+
       = f.form_field :who_label do
-        = autocomplete_field(f, "sample[who_label]", @navigation_context.institution)
+        = autocomplete_field(f, "sample[who_label]", :who_label, @navigation_context.institution, class: "input-x-large")
+
       = f.form_field :concentration do
         - @sample_form.blinded_attribute(:concentration) do
           .row.input-unit

From 7666ac97b9fbd7c2e2acf17b7edde3003780d585 Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Thu, 20 Jul 2023 17:19:29 +0200
Subject: [PATCH 4/7] Fix: use data from samples directly in samples reports

This is a required change because after a transfer the sample <-> batch
relationship is severed. This is actually not a problem because the data
is already on the samples.
---
 app/controllers/nih_tables_controller.rb      | 26 +++++++--------
 app/controllers/samples_reports_controller.rb |  5 ++-
 app/models/sample.rb                          |  3 +-
 app/models/samples_report.rb                  | 32 +++++++++++--------
 .../nih_challenge.csv.csvbuilder              | 13 ++++----
 .../nih_lod.csv.csvbuilder                    | 15 ++++-----
 .../nih_results.csv.csvbuilder                |  0
 .../nih_samples.csv.csvbuilder                | 15 ++++-----
 .../controllers/nih_tables_controller_spec.rb |  2 +-
 9 files changed, 57 insertions(+), 54 deletions(-)
 rename app/views/{samples_reports => nih_tables}/nih_challenge.csv.csvbuilder (83%)
 rename app/views/{samples_reports => nih_tables}/nih_lod.csv.csvbuilder (75%)
 rename app/views/{samples_reports => nih_tables}/nih_results.csv.csvbuilder (100%)
 rename app/views/{samples_reports => nih_tables}/nih_samples.csv.csvbuilder (78%)

diff --git a/app/controllers/nih_tables_controller.rb b/app/controllers/nih_tables_controller.rb
index 53dcddf76..eee5ed0d0 100644
--- a/app/controllers/nih_tables_controller.rb
+++ b/app/controllers/nih_tables_controller.rb
@@ -1,29 +1,29 @@
 class NihTablesController < ApplicationController
   def show
-    @samples_report = SamplesReport.find(params[:id])
-    @target_batch = @samples_report.target_batch
+    @samples_report = SamplesReport.preload(:samples => :box).find(params[:id])
     return unless authorize_resource(@samples_report, READ_SAMPLES_REPORT)
-    
-    zip_data = create_zip_file
+
+    @target_box = @samples_report.boxes.take
+    @target_sample = @samples_report.target_sample
+    zip_data = create_zip_file(@target_box.purpose)
     send_data zip_data.read, type: 'application/zip', filename: "#{@samples_report.name}_nih_tables.zip"
   end
-  
+
   private
-  
-  def create_zip_file
-    purpose = @samples_report.samples[0].box.purpose
 
+  def create_zip_file(purpose)
     zip_stream = Zip::OutputStream.write_buffer do |stream|
-      # Read public/templates/Instructions.txt contents and write to zip
+      # TODO: read public/templates/Instructions.txt contents and write to zip
       stream.put_next_entry('Instructions.txt')
       stream.write(File.read(Rails.root.join('public/templates/Instructions.txt')))
 
       add_nih_table('samples', stream)
       add_nih_table('results', stream)
 
-      if purpose == "LOD"
+      case purpose
+      when "LOD"
         add_nih_table('lod', stream)
-      elsif purpose == "Challenge"
+      when "Challenge"
         add_nih_table('challenge', stream)
       end
     end
@@ -33,6 +33,6 @@ def create_zip_file
 
   def add_nih_table(table_name, stream)
     stream.put_next_entry("#{@samples_report.name}_#{table_name}.csv")
-    stream.write(render_to_string('samples_reports/nih_'+table_name, formats: :csv))
+    stream.write(render_to_string("nih_#{table_name}", formats: :csv))
   end
-end
\ No newline at end of file
+end
diff --git a/app/controllers/samples_reports_controller.rb b/app/controllers/samples_reports_controller.rb
index 93c73bb96..e99c4285f 100644
--- a/app/controllers/samples_reports_controller.rb
+++ b/app/controllers/samples_reports_controller.rb
@@ -14,14 +14,13 @@ def index
     @samples_reports = SamplesReport.where(institution: @navigation_context.institution)
     @samples_reports = check_access(@samples_reports, READ_SAMPLES_REPORT).order('samples_reports.created_at DESC')
 
-    # Filter by search params
-
+    # filter by search params
     @samples_reports = @samples_reports.partial_name(params[:name])
     @samples_reports = @samples_reports.partial_sample_uuid(params[:sample_uuid])
     @samples_reports = @samples_reports.partial_box_uuid(params[:box_uuid])
     @samples_reports = @samples_reports.partial_batch_number(params[:batch_number])
 
-    #paginate samples report
+    # paginate samples report
     @samples_reports = perform_pagination(@samples_reports)
   end
 
diff --git a/app/models/sample.rb b/app/models/sample.rb
index 523b4d788..f5768ca27 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -19,7 +19,8 @@ def self.institution_is_required
   has_many :sample_identifiers, inverse_of: :sample, dependent: :destroy
   has_many :test_results, through: :sample_identifiers
 
-  has_many :samples_reports, through: :samples_report_sample
+  has_many :samples_reports, through: :samples_report_samples
+  has_many :samples_report_samples, dependent: :destroy
 
   has_many :assay_attachments, dependent: :destroy
   accepts_nested_attributes_for :assay_attachments, allow_destroy: true
diff --git a/app/models/samples_report.rb b/app/models/samples_report.rb
index 0d11f8520..cbfee960a 100644
--- a/app/models/samples_report.rb
+++ b/app/models/samples_report.rb
@@ -7,6 +7,7 @@ class SamplesReport < ApplicationRecord
 
   has_many :samples_report_samples, dependent: :destroy
   has_many :samples, through: :samples_report_samples
+  has_many :boxes, through: :samples
 
   def self.entity_scope
     "samples_report"
@@ -30,19 +31,24 @@ def self.entity_scope
   }
 
   scope :partial_box_uuid, ->(box_uuid) {
-    joins("LEFT JOIN samples_report_samples ON samples_report_samples.samples_report_id = samples_reports.id
-      LEFT JOIN samples ON samples_report_samples.sample_id = samples.id
-      LEFT JOIN boxes ON boxes.id = samples.box_id")
-      .where("boxes.uuid LIKE ?", "%#{sanitize_sql_like(box_uuid)}%")
-      .group(:samples_report_id) unless box_uuid.blank?
+    unless box_uuid.blank?
+      where(id: SamplesReportSample
+        .select(:samples_report_id)
+        .joins(:sample => :box)
+        .where("boxes.uuid LIKE ?", "%#{sanitize_sql_like(box_uuid)}%"))
+    end
   }
 
   scope :partial_batch_number, ->(batch_number) {
-    joins("LEFT JOIN samples_report_samples ON samples_report_samples.samples_report_id = samples_reports.id
-      LEFT JOIN samples ON samples_report_samples.sample_id = samples.id
-      LEFT JOIN batches ON batches.id = samples.batch_id")
-      .where("batches.batch_number LIKE ?", "%#{sanitize_sql_like(batch_number)}%")
-      .group(:samples_report_id) unless batch_number.blank?
+    # after box transfer, the sample <-> batch relationship will be severed,
+    # hence the coalesce to match the old batch number (valid after transfer)
+    # then the original batch number (valid before transfer)
+    unless batch_number.blank?
+      where(id: SamplesReportSample
+        .select(:samples_report_id)
+        .left_joins(:sample => :batch)
+        .where("COALESCE(samples.old_batch_number, batches.batch_number) LIKE ?", "%#{sanitize_sql_like(batch_number)}%"))
+    end
   }
 
   def calculate_lod_and_lob
@@ -68,9 +74,9 @@ 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
+  # Returns any sample that isn't a distractor.
+  def target_sample
+    samples.where.not(distractor: true).take!
   end
 
   private
diff --git a/app/views/samples_reports/nih_challenge.csv.csvbuilder b/app/views/nih_tables/nih_challenge.csv.csvbuilder
similarity index 83%
rename from app/views/samples_reports/nih_challenge.csv.csvbuilder
rename to app/views/nih_tables/nih_challenge.csv.csvbuilder
index 8abfc22ad..ccc7cda87 100644
--- a/app/views/samples_reports/nih_challenge.csv.csvbuilder
+++ b/app/views/nih_tables/nih_challenge.csv.csvbuilder
@@ -25,17 +25,16 @@ csv << [
   'roc_y_values'
 ]
 
-sample = @samples_report.samples[0]
 csv << [
   nil,
   nil,
-  sample.box.uuid,
-  "#{sample.box.purpose}-panel",
+  @target_box.uuid,
+  "#{@target_box.purpose}-panel",
   'inactivated virus',
   'SARS-CoV-2',
-  @target_batch.target_organism_taxonomy_id,
-  @target_batch.pango_lineage,
-  @target_batch.who_label,
+  @target_sample.target_organism_taxonomy_id,
+  @target_sample.pango_lineage,
+  @target_sample.who_label,
   @samples_report.threshold,
   'copies/ml',
   params[:true_positives],
@@ -51,4 +50,4 @@ csv << [
   params[:auc],
   params[:roc_x_values],
   params[:roc_y_values]
-]
\ No newline at end of file
+]
diff --git a/app/views/samples_reports/nih_lod.csv.csvbuilder b/app/views/nih_tables/nih_lod.csv.csvbuilder
similarity index 75%
rename from app/views/samples_reports/nih_lod.csv.csvbuilder
rename to app/views/nih_tables/nih_lod.csv.csvbuilder
index ab093fd00..eba288e6d 100644
--- a/app/views/samples_reports/nih_lod.csv.csvbuilder
+++ b/app/views/nih_tables/nih_lod.csv.csvbuilder
@@ -20,25 +20,24 @@ csv << [
   'analytical_sensitivity_unit'
 ]
 
-sample = @samples_report.samples[0]
 csv << [
   nil,
   nil,
-  sample.box.uuid,
-  "#{sample.box.purpose}-panel",
+  @target_box.uuid,
+  "#{@target_box.purpose}-panel",
   'inactivated virus',
   'SARS-CoV-2',
-  @target_batch.target_organism_taxonomy_id,
-  @target_batch.pango_lineage,
-  @target_batch.who_label,
+  @target_sample.target_organism_taxonomy_id,
+  @target_sample.pango_lineage,
+  @target_sample.who_label,
   @samples_report.lob,
   nil,
   @samples_report.lod,
-  @target_batch.reference_gene,
+  @target_sample.reference_gene,
   nil,
   nil,
   "90",
   'linear regression',
   nil,
   nil
-]
\ No newline at end of file
+]
diff --git a/app/views/samples_reports/nih_results.csv.csvbuilder b/app/views/nih_tables/nih_results.csv.csvbuilder
similarity index 100%
rename from app/views/samples_reports/nih_results.csv.csvbuilder
rename to app/views/nih_tables/nih_results.csv.csvbuilder
diff --git a/app/views/samples_reports/nih_samples.csv.csvbuilder b/app/views/nih_tables/nih_samples.csv.csvbuilder
similarity index 78%
rename from app/views/samples_reports/nih_samples.csv.csvbuilder
rename to app/views/nih_tables/nih_samples.csv.csvbuilder
index ed0f40d6c..78486991f 100644
--- a/app/views/samples_reports/nih_samples.csv.csvbuilder
+++ b/app/views/nih_tables/nih_samples.csv.csvbuilder
@@ -20,9 +20,8 @@ csv << [
 ]
 
 @samples_report.samples.each do |sample|
-  batch = Batch.find_by(batch_number: sample.batch_number)
   csv << [
-    sample.id,
+    sample.uuid,
     sample.box.uuid,
     "#{sample.box.purpose}-panel",
     nil,
@@ -31,14 +30,14 @@ csv << [
     nil,
     sample.concentration,
     'copies/ml',
-    batch.reference_gene,
-    sample.id,
+    sample.reference_gene,
+    sample.uuid,
     sample.batch_number,
     'inactivated virus',
     'SARS-CoV-2',
-    batch.target_organism_taxonomy_id,
-    batch.pango_lineage,
-    batch.who_label,
+    sample.target_organism_taxonomy_id,
+    sample.pango_lineage,
+    sample.who_label,
     sample.inactivation_method
   ]
-end
\ No newline at end of file
+end
diff --git a/spec/controllers/nih_tables_controller_spec.rb b/spec/controllers/nih_tables_controller_spec.rb
index cfe69961a..b14b655f6 100644
--- a/spec/controllers/nih_tables_controller_spec.rb
+++ b/spec/controllers/nih_tables_controller_spec.rb
@@ -52,7 +52,7 @@
       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})
+      expect(samples_table["sample_id"]).to eq(@samples_report.samples_report_samples.map{|srs| srs.sample.uuid})
     end
 
     it "should contain the results table with the correct data" do

From a6966ea3b44eb0e7c722f690aa6e36e601287f07 Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Thu, 20 Jul 2023 17:23:37 +0200
Subject: [PATCH 5/7] Fix: scope to current institution when creating box from
 CSV

---
 app/models/box_form.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/box_form.rb b/app/models/box_form.rb
index d2e524ce0..5ece9b0ff 100644
--- a/app/models/box_form.rb
+++ b/app/models/box_form.rb
@@ -209,7 +209,7 @@ def parse_csv(path)
     CSV.open(path, headers: true) do |csv|
       csv.each do |row|
         next unless batch_number = row["Batch"]&.strip.presence
-        next unless batch = Batch.find_by(batch_number: batch_number)
+        next unless batch = @box.institution.batches.find_by(batch_number: batch_number)
 
         @batches_data[@batches_data.size] = {
           batch_uuid: batch.uuid,

From 0c6aa69dd8d5e32432e08979daadf3a55b66b1d7 Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Fri, 21 Jul 2023 13:09:00 +0200
Subject: [PATCH 6/7] Fix: can't create samples report with partial results

The linear regression calculation was crashing because we tried to
compare all samples vs some samples (with measured signals).

closes #1965
---
 app/models/samples_report.rb | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/app/models/samples_report.rb b/app/models/samples_report.rb
index cbfee960a..d3c01ed8c 100644
--- a/app/models/samples_report.rb
+++ b/app/models/samples_report.rb
@@ -52,25 +52,25 @@ def self.entity_scope
   }
 
   def calculate_lod_and_lob
+    samples = self.samples.select { |sample| sample.measured_signal.present? }
     concentrations = samples.map(&:concentration)
-    signals = Numo::DFloat[*samples.select { |sample| sample.measured_signal.present? }.map(&:measured_signal)]
-    concentrations_matrix = Numo::DFloat[*concentrations.map { |c| [c] }]
-    lr = Rumale::LinearModel::LinearRegression.new(fit_bias: true)
-    lr.fit(concentrations_matrix, signals)
 
-    lod = lr.bias_term
+    concentrations_matrix = Numo::DFloat[*concentrations.map { |c| [c] }]
+    signals = Numo::DFloat[*samples.map(&:measured_signal)]
+    linear_regression = Rumale::LinearModel::LinearRegression.new(fit_bias: true)
+    linear_regression.fit(concentrations_matrix, signals)
+    lod = linear_regression.bias_term
     blank_samples = signals[Numo::DFloat.cast(concentrations).eq(0)]
-    if blank_samples.size > 0
-      blank_samples_mean = blank_samples.mean
-      blank_samples_sd = blank_samples.stddev
-      lod = [lod, 3 * blank_samples_sd].max
-      lob = blank_samples_mean + 1.645 * blank_samples_sd
-    else
-      lob = nil
+
+    unless blank_samples.empty?
+      stddev = blank_samples.stddev
+      lod = [lod, 3 * stddev].max
+      lob = blank_samples.mean + 1.645 * stddev
     end
 
-    self.lod = lod.try(:round, 3)
-    self.lob = lob.try(:round, 3)
+    self.lod = lod&.round(3)
+    self.lob = lob&.round(3)
+
     self.save
   end
 

From f22d6b2c220cf4400419d25f7d2540f0c873f025 Mon Sep 17 00:00:00 2001
From: Julien Portalier <julien@portalier.com>
Date: Fri, 21 Jul 2023 17:07:42 +0200
Subject: [PATCH 7/7] Fix: unblind box when all samples have a measurement

closes #1961
---
 app/controllers/samples_controller.rb       | 12 +++-
 spec/controllers/samples_controller_spec.rb | 67 ++++++++++++++++-----
 spec/spec_helper.rb                         |  1 +
 spec/support/uploaded_file_helper.rb        | 17 ++++++
 4 files changed, 80 insertions(+), 17 deletions(-)
 create mode 100644 spec/support/uploaded_file_helper.rb

diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb
index 74cdfaf80..be41e1cdd 100644
--- a/app/controllers/samples_controller.rb
+++ b/app/controllers/samples_controller.rb
@@ -201,15 +201,21 @@ def bulk_destroy
     redirect_to samples_path, notice: "Samples were successfully deleted."
   end
 
+  def upload_results
+  end
+
   def bulk_process_csv
     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
+    samples = check_access(@navigation_context.institution.samples, UPDATE_SAMPLE)
+    box_ids = Set.new
 
     params[:csv_files].each do |csv_file|
       CSV.open(csv_file.path) do |csv_stream|
         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)
+          if sample = samples.find_by_uuid(sample_id.strip)
+            box_ids << sample.box_id
             sample.measured_signal ||= Float(measured_signal.strip)
             sample.save!
           end
@@ -217,6 +223,10 @@ def bulk_process_csv
       end
     end
 
+    Box.where(blinded: true, id: box_ids.to_a).each do |box|
+      box.unblind! if box.samples.all?(&:measured_signal)
+    end
+
     redirect_to samples_path, notice: "Sample's results uploaded successfully."
   end
 
diff --git a/spec/controllers/samples_controller_spec.rb b/spec/controllers/samples_controller_spec.rb
index 820ba0e21..557d4fdee 100644
--- a/spec/controllers/samples_controller_spec.rb
+++ b/spec/controllers/samples_controller_spec.rb
@@ -646,30 +646,65 @@ def build_sample_form_plan(options)
   end
 
   context "upload_results" do
-    let!(:sample1) { Sample.make!(institution: institution, sample_identifiers: [SampleIdentifier.make!(uuid: '01234567-8ce1-a0c8-ac1b-58bed3633e88')], date_produced: Time.zone.local(2018, 1, 1)) }
+    it "renders form" do
+      get :upload_results
+      expect(response).to have_http_status(:ok)
+    end
+  end
 
-    it "should write measurement results for samples" do
-      file_path = File.join(Rails.root, 'spec', 'fixtures', 'csvs', 'samples_results_1.csv')
-      file = fixture_file_upload(file_path, 'text/csv')
-      post :bulk_process_csv, params: { "csv_files": [file] }
-      sample1.reload
+  context "bulk_process_csv" do
+    let(:sample) { Sample.make! :filled, institution: institution }
 
-      expect(sample1.measured_signal).to eq(10.0)
+    it "should write measurement results for samples" do
+      uploaded_file("#{sample.uuid},10", "text/csv") do |file|
+        post :bulk_process_csv, params: { "csv_files": [file] }
+        expect(response).to redirect_to(samples_path)
+      end
+      expect(sample.reload.measured_signal).to eq(10.0)
     end
 
     it "shouldn't overwrite measurement results for samples with measurements" do
-      file_path = File.join(Rails.root, 'spec', 'fixtures', 'csvs', 'samples_results_1.csv')
-      file = fixture_file_upload(file_path, 'text/csv')
-      post :bulk_process_csv, params: { "csv_files": [file] }
-      sample1.reload
+      uploaded_file("#{sample.uuid},10", "text/csv") do |file|
+        post :bulk_process_csv, params: { "csv_files": [file] }
+        expect(response).to redirect_to(samples_path)
+      end
 
-      file_path = File.join(Rails.root, 'spec', 'fixtures', 'csvs', 'samples_results_2.csv')
-      file = fixture_file_upload(file_path, 'text/csv')
-      post :bulk_process_csv, params: { "csv_files": [file] }
-      sample1.reload
+      uploaded_file("#{sample.uuid},20", "text/csv") do |file|
+        post :bulk_process_csv, params: { "csv_files": [file] }
+        expect(response).to redirect_to(samples_path)
+      end
 
-      expect(sample1.measured_signal).to eq(10.0)
+      expect(sample.reload.measured_signal).to eq(10.0)
     end
 
+    describe "box" do
+      let(:box) do
+        Box.make! :filled_without_measurements, institution: institution, blinded: true
+      end
+
+      it "unblinds box with complete results" do
+        contents = <<~CSV
+          #{box.samples[0].uuid},10
+          #{box.samples[1].uuid},20
+        CSV
+        uploaded_file(contents, "text/csv") do |file|
+          post :bulk_process_csv, params: { "csv_files": [file] }
+          expect(response).to redirect_to(samples_path)
+          expect(box.reload.blinded).to be(false)
+        end
+        expect(box.samples[0].reload.measured_signal).to eq(10.0)
+        expect(box.samples[1].reload.measured_signal).to eq(20.0)
+      end
+
+      it "won't unblind box with partial results" do
+        uploaded_file("#{box.samples[1].uuid},20", "text/csv") do |file|
+          post :bulk_process_csv, params: { "csv_files": [file] }
+          expect(response).to redirect_to(samples_path)
+          expect(box.reload.blinded).to be(true)
+        end
+        expect(box.samples[0].reload.measured_signal).to be_nil
+        expect(box.samples[1].reload.measured_signal).to eq(20.0)
+      end
+    end
   end
 end
diff --git a/spec/spec_helper.rb b/spec/spec_helper.rb
index c87a88a1e..6ba683b17 100644
--- a/spec/spec_helper.rb
+++ b/spec/spec_helper.rb
@@ -72,6 +72,7 @@ def primary_key_name
 
   config.include Devise::TestHelpers, :type => :controller
   config.include DefaultParamsHelper, :type => :controller
+  config.include UploadedFileHelper, :type => :controller
   config.extend SpecFixtures
   config.include ManifestSpecHelper
   config.include CdxFieldsHelper
diff --git a/spec/support/uploaded_file_helper.rb b/spec/support/uploaded_file_helper.rb
new file mode 100644
index 000000000..6385e0cba
--- /dev/null
+++ b/spec/support/uploaded_file_helper.rb
@@ -0,0 +1,17 @@
+require 'active_support/concern'
+
+module UploadedFileHelper
+  extend ActiveSupport::Concern
+
+  def uploaded_file(contents, type, binary = false, &block)
+    tempfile = Tempfile.new("uploaded_file")
+    begin
+      tempfile.write(contents)
+      tempfile.rewind
+      yield Rack::Test::UploadedFile.new(tempfile, type, binary)
+    ensure
+      tempfile.close
+      tempfile.unlink
+    end
+  end
+end