General nih tables exporting (#1956)

* General nih tables exporting * Lint fixes and tests added * Fixes PR review * Fix: CI can't run the analysis step (docker error) (#1957) This is a bug introduced in docker compose v2.19.0: docker/compose#10751 * General nih tables exporting * Lint fixes and tests added * Fixes PR review * Revert "Merge branch '1905-general-nih-tables' of https://github.com/instedd/cdx into 1905-general-nih-tables" This reverts commit 32366c1. * Revert "Revert "Merge branch '1905-general-nih-tables' of https://github.com/instedd/cdx into 1905-general-nih-tables"" This reverts commit 8994214. * Fixes PR review * Zip as buffer --------- Co-authored-by: Julien Portalier <[email protected]>
instedd · Jul 7, 2023 · d70369d · d70369d
1 parent cbe2039
commit d70369d
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diff --git a/app/controllers/nih_tables_controller.rb b/app/controllers/nih_tables_controller.rb
@@ -1,41 +1,37 @@
 class NihTablesController < ApplicationController
   def show
-    samples_report = SamplesReport.find(params[:id])
-    return unless authorize_resource(samples_report, READ_SAMPLES_REPORT)
+    @samples_report = SamplesReport.find(params[:id])
+    return unless authorize_resource(@samples_report, READ_SAMPLES_REPORT)
 
-    purpose = samples_report.samples[0].box.purpose
-    zip_file = create_zip_file(samples_report.name)
-
-    if purpose == "LOD"
-    add_lod_table(zip_file)
-    elsif purpose == "Challenge"
-    add_challenge_table(zip_file)
-    end
-
-    zip_file.close
-
-    send_zip_file(zip_file, samples_report.name)
+    zip_data = create_zip_file
+    send_data zip_data.read, type: 'application/zip', filename: "#{@samples_report.name}_nih_tables.zip"
   end
 
   private
 
-  def create_zip_file(filename)
-    zip_file = Tempfile.new("#{filename}_nih_tables.zip")
-    Zip::File.open(zip_file.path, Zip::File::CREATE) do |zip|
-    zip.add("Instructions.txt", Rails.root.join('public/templates/Instructions.txt'))
+  def create_zip_file
+    purpose = @samples_report.samples[0].box.purpose
+
+    zip_stream = Zip::OutputStream.write_buffer do |stream|
+      # 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"
+        #add_nih_table('lod', stream)
+      elsif purpose == "Challenge"
+        #add_nih_table('challenge', stream)
+      end
     end
-    zip_file
+    zip_stream.rewind
+    zip_stream
   end
-
-  def add_lod_table(zip_file)
-    # TODO: Add the LOD table to the zip file
-  end
-
-  def add_challenge_table(zip_file)
-    # TODO: Add the Challenge table to the zip file
-  end
-
-  def send_zip_file(zip_file, filename)
-    send_file zip_file.path, type: 'application/zip', filename: "#{filename}_nih_tables.zip"
+
+  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))
   end
 end
diff --git a/app/views/samples_reports/nih_results.csv.csvbuilder b/app/views/samples_reports/nih_results.csv.csvbuilder
@@ -0,0 +1,23 @@
+csv << [
+  'sample_id',
+  'vqa_box_id',
+  'sample_group',
+  'protocol_id',
+  'technology_platform',
+  'assay_readout',
+  'assay_readout_unit',
+  'assay_readout_description'
+]
+
+@samples_report.samples.each do |sample|
+  csv << [
+    sample.id,
+    sample.box.uuid,
+    "#{sample.box.purpose}-panel",
+    nil,
+    nil,
+    sample.measured_signal,
+    nil,
+    nil
+  ]
+end
diff --git a/app/views/samples_reports/nih_samples.csv.csvbuilder b/app/views/samples_reports/nih_samples.csv.csvbuilder
@@ -0,0 +1,44 @@
+csv << [
+  'sample_id',
+  'vqa_box_id',
+  'sample_group',
+  'sample_media',
+  'sample_media_id',
+  'sample_media_source',
+  'sample_media_source_url',
+  'sample_concentration',
+  'sample_concentration_unit',
+  'sample_concentration_reference_gene',
+  'virus_sample_id',
+  'virus_batch_number',
+  'target_analyte_type',
+  'target_organism_name',
+  'target_organism_taxonomy_id',
+  'pango_lineage',
+  'who_label',
+  'virus_sample_inactivation_method'
+]
+
+@samples_report.samples.each do |sample|
+  batch = Batch.find_by(batch_number: sample.batch_number)
+  csv << [
+    sample.id,
+    sample.box.uuid,
+    "#{sample.box.purpose}-panel",
+    nil,
+    nil,
+    nil,
+    nil,
+    sample.concentration,
+    'copies/ml',
+    batch.reference_gene,
+    sample.id,
+    sample.batch_number,
+    'inactivated virus',
+    'SARS-CoV-2',
+    batch.target_organism_taxonomy_id,
+    batch.pango_lineage,
+    batch.who_label,
+    sample.inactivation_method
+  ]
+end
diff --git a/spec/controllers/nih_tables_controller_spec.rb b/spec/controllers/nih_tables_controller_spec.rb
@@ -26,18 +26,43 @@
     it "should download a zip file on show" do
       get :show, params: { id: @samples_report.id } 
 
-      #expect sent file to be a zip file
       expect(response.headers["Content-Type"]).to eq("application/zip")
       expect(response.headers["Content-Disposition"]).to eq("attachment; filename=\"Test_nih_tables.zip\"")
     end
 
     it "should contain the Instructions.txt file" do
       get :show, params: { id: @samples_report.id }
 
-      #expect the zip file to contain the Instructions.txt file
       expect(Zip::File.open_buffer(response.body).entries.map(&:name)).to include("Instructions.txt")
     end
 
+    it "should contain the samples & results table" do
+      get :show, params: { id: @samples_report.id }
+
+      expect(Zip::File.open_buffer(response.body).entries.map(&:name)).to include("#{@samples_report.name}_samples.csv")
+      expect(Zip::File.open_buffer(response.body).entries.map(&:name)).to include("#{@samples_report.name}_results.csv")
+    end
+
+    it "should contain the samples table with the correct data" do
+      get :show, params: { id: @samples_report.id }
+
+      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
+
+    it "should contain the results table with the correct data" do
+      get :show, params: { id: @samples_report.id }
+
+      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 not allow access to user without read access" do
       sign_in @other_user
       get :show, params: { id: @samples_report.id, context: @other_institution.uuid }