Merge pull request #1975: various fixes for boxes & samples reports

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

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}

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)
 

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
+end

app/controllers/samples_controller.rb

@@ -201,22 +201,32 @@ 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
         end
       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
 

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
 

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

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 = @box.institution.batches.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

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