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

@@ -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_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/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

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

app/views/samples_reports/nih_challenge.csv.csvbuilder → 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]
-]
+]

app/views/samples_reports/nih_lod.csv.csvbuilder → 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
-]
+]

app/views/samples_reports/nih_samples.csv.csvbuilder → 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.id, # FIXME: 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.id, # FIXME: ??
     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
+end