Merge pull request #685 from TGAC/plant_trial_export_download

Plant trial export download

Gemfile

@@ -35,6 +35,7 @@ gem 'hashie'
 gem 'draper', '~> 2.1.0'
 gem 'kaminari'
 gem 'paperclip', '~> 4.3'
+gem 'rubyzip'
 gem 'typhoeus'
 gem 'squeel'
 

Gemfile.lock

@@ -318,6 +318,7 @@ GEM
     rspec-support (3.5.0)
     ruby_parser (3.6.4)
       sexp_processor (~> 4.1)
+    rubyzip (1.2.0)
     safe_yaml (0.9.7)
     sass (3.2.19)
     sass-rails (4.0.5)
@@ -419,6 +420,7 @@ DEPENDENCIES
   reform (~> 1.2.6)
   rspec-html-matchers
   rspec-rails (~> 3.5.0)
+  rubyzip
   sass-rails (~> 4.0.3)
   shoulda-matchers
   spring

app/assets/javascripts/data_grid_specific_columns.js.coffee

@@ -152,7 +152,15 @@ window.configs =
       ,
         targets: 'plant_trials_id_column'
         render: (data, type, full, meta) ->
-          '<a href="trial_scorings/' + data + '">Show</a>'
+          '<a href="trial_scorings/' + data + '" ' +
+            'title="See all trial\'s trait scorings in a single table." data-toggle="tooltip">' +
+            'Show' +
+          '</a>' +
+          '</br>' +
+          '<a href="trial_scorings/' + data + '.zip" ' +
+            'title="Download zip file with full trial information." data-toggle="tooltip">' +
+            'Download' +
+          '</a>'
       ]
 
   'population-loci':

app/controllers/trial_scorings_controller.rb

@@ -16,13 +16,18 @@ def show
         end
         render json: grid_data
       end
+      format.zip do
+        send_data Submission::PlantTrialZipExporter.new.call(@plant_trial).read,
+                  filename: "plant_trial_#{@plant_trial.plant_trial_name.parameterize('_')}.zip",
+                  type: 'application/zip'
+      end
     end
   end
 
   private
 
   def prepare_grid_data
-    objects = @plant_trial.scoring_table_data(current_user.try(:id))
+    objects = @plant_trial.scoring_table_data(user_id: current_user.try(:id))
     ApplicationDecorator.decorate(objects).as_grid_data
   end
 

app/models/plant_trial.rb

@@ -44,35 +44,67 @@ class PlantTrial < ActiveRecord::Base
   include TableData
 
   # NOTE: this one works per-trial and provides data for so-called 'pivot' trial scoring table
-  def scoring_table_data(uid = nil)
+  def scoring_table_data(user_id: nil, extended: false)
     ts = TraitScore.arel_table
 
-    psu_subquery = PlantScoringUnit.visible(uid)
-    td_subquery = TraitDescriptor.visible(uid)
+    psu_subquery = PlantScoringUnit.visible(user_id)
+    td_subquery = TraitDescriptor.visible(user_id)
+    pa_subquery = PlantAccession.visible(user_id)
+    if extended
+      pl_subquery = PlantLine.visible(user_id)
+      df_subquery = DesignFactor.visible(user_id)
+    end
 
     all_scores = TraitScore.
-      joins {[
-        psu_subquery.as('plant_scoring_units').on { plant_scoring_unit_id == plant_scoring_units.id }.outer,
-        td_subquery.as('trait_descriptors').on { trait_descriptor_id == trait_descriptors.id }.outer
-      ]}
+      joins {
+        [
+          psu_subquery.as('plant_scoring_units').on { plant_scoring_unit_id == plant_scoring_units.id }.outer,
+          pa_subquery.as('plant_accessions').on { plant_accessions.id == plant_scoring_units.plant_accession_id }.outer,
+          td_subquery.as('trait_descriptors').on { trait_descriptor_id == trait_descriptors.id }.outer
+        ] +
+        (
+          extended ? [
+            pl_subquery.as('plant_lines').on { plant_lines.id == plant_accessions.plant_line_id }.outer,
+            df_subquery.as('design_factors').on { design_factors.id == plant_scoring_units.design_factor_id }.outer
+          ] : []
+        )
+      }
     all_scores = all_scores.
       where(plant_scoring_units: { plant_trial_id: self.id }).
-      where(ts[:user_id].eq(uid).or(ts[:published].eq(true))).
+      where(ts[:user_id].eq(user_id).or(ts[:published].eq(true))).
       order('plant_scoring_units.scoring_unit_name asc, trait_descriptors.id asc').
       group_by(&:plant_scoring_unit_id)
 
-    plant_scoring_units.visible(uid).order('scoring_unit_name asc').map do |unit|
-      scores = all_scores[unit.id] || []
-
-      [unit.scoring_unit_name] +
+    plant_scoring_units.visible(user_id).order('scoring_unit_name asc').map do |plant_scoring_unit|
+      scores = all_scores[plant_scoring_unit.id] || []
+      plant_accession = plant_scoring_unit.plant_accession
+      plant_line = extended ? plant_scoring_unit.plant_accession.try(:plant_line) : nil
+
+      [plant_scoring_unit.scoring_unit_name,
+       plant_accession.try(:plant_accession)] +
+        (
+          extended ? [
+            plant_accession.try(:plant_line).try(:plant_line_name),
+            (plant_accession.try(:plant_variety) || plant_line.try(:plant_variety)).try(:plant_variety_name),
+            plant_accession.try(:plant_accession_derivation),
+            plant_accession.try(:originating_organisation),
+            plant_accession.try(:year_produced),
+            plant_accession.try(:date_harvested),
+            plant_scoring_unit.number_units_scored,
+            plant_scoring_unit.scoring_unit_sample_size,
+            plant_scoring_unit.scoring_unit_frame_size,
+            plant_scoring_unit.design_factor.try(:design_factors),
+            plant_scoring_unit.date_planted
+          ] : []
+        ) +
         trait_descriptors.pluck(:id).map do |td_id|
           scores_for_trait = scores.select{ |s| s.trait_descriptor_id == td_id.to_i}
           (1..replicate_numbers[td_id.to_i]).map do |replicate_number|
             replicate = scores_for_trait.detect{ |s| s.technical_replicate_number == replicate_number }
             replicate ? replicate.score_value : '-'
           end
         end.flatten +
-        [unit.id]
+        [plant_scoring_unit.id]
     end
   end
 

app/services/submission/exporter.rb

@@ -13,19 +13,22 @@ def submitted_object
     @submission.submitted_object
   end
 
-  def generate_document(klass, query)
+  def generate_document(klass, query, column_names: nil)
+    column_names ||= klass.table_columns
     data = klass.table_data(query: query).
-                 map{ |r| r[0, klass.table_columns.size] }
+                 map{ |r| r[0, column_names.size] }
     return nil if data.empty?
     CSV.generate(headers: true) do |csv|
-      csv << humanize_columns(klass.table_columns)
+      csv << humanize_columns(klass, column_names)
       data.each { |row| csv << row }
     end
   end
 
-  def humanize_columns(column_names)
+  def humanize_columns(klass, column_names)
     column_names.map do |column_name|
-      column_name.split(/ as /i)[-1]
+      column_name = column_name.split(/ as /i)[-1]
+      column_name = "#{klass.table_name}.#{column_name}" unless column_name.include? '.'
+      I18n.t("tables.#{column_name}")
     end
   end
 end

app/services/submission/plant_trial_exporter.rb

@@ -2,8 +2,6 @@ class Submission::PlantTrialExporter < Submission::Exporter
   def documents
     {
       plant_trial: plant_trial,
-      plant_scoring_units: plant_scoring_units,
-      plant_accessions: plant_accessions,
       trait_descriptors: trait_descriptors,
       trait_scoring: trait_scoring
     }.reject { |_,v| v.nil? }
@@ -13,17 +11,8 @@ def documents
 
   def plant_trial
     generate_document PlantTrial,
-                      { id: submitted_object.id }
-  end
-
-  def plant_scoring_units
-    generate_document PlantScoringUnit,
-                      { id: submitted_object.plant_scoring_units.pluck(:id) }
-  end
-
-  def plant_accessions
-    generate_document PlantAccession,
-                      { id: submitted_object.plant_scoring_units.pluck(:plant_accession_id) }
+                      { id: submitted_object.id },
+                      column_names: PlantTrial.table_columns[0..-3]
   end
 
   def trait_descriptors
@@ -32,10 +21,24 @@ def trait_descriptors
   end
 
   def trait_scoring
-    data = submitted_object.scoring_table_data(@submission.user.id)
+    data = submitted_object.scoring_table_data(user_id: @submission.user.id, extended: true)
     return nil if data.empty?
     CSV.generate(headers: true) do |csv|
-      csv << ['Scoring unit name'] + submitted_object.decorate.trait_headers
+      csv << [
+        I18n.t('tables.plant_scoring_units.scoring_unit_name'),
+        I18n.t('tables.plant_accessions.plant_accession'),
+        I18n.t('tables.plant_lines.plant_line_name'),
+        I18n.t('tables.plant_varieties.plant_variety_name'),
+        I18n.t('tables.plant_accessions.plant_accession_derivation'),
+        I18n.t('tables.plant_accessions.originating_organisation'),
+        I18n.t('tables.plant_accessions.year_produced'),
+        I18n.t('tables.plant_accessions.date_harvested'),
+        I18n.t('tables.plant_scoring_units.number_units_scored'),
+        I18n.t('tables.plant_scoring_units.scoring_unit_sample_size'),
+        I18n.t('tables.plant_scoring_units.scoring_unit_frame_size'),
+        I18n.t('tables.design_factors.design_factors'),
+        I18n.t('tables.plant_scoring_units.date_planted')
+      ] + submitted_object.decorate.trait_headers
       data.each { |row| csv << row[0...-1] }  # Drop the BIP internal id
     end
   end

app/services/submission/plant_trial_zip_exporter.rb

@@ -0,0 +1,18 @@
+require 'zip'
+
+class Submission::PlantTrialZipExporter
+  def call(plant_trial)
+    exporter = Submission::PlantTrialExporter.new(
+      OpenStruct.new(submitted_object: plant_trial, user: plant_trial.user)
+    )
+    compressed_filestream = Zip::OutputStream.write_buffer do |zos|
+      exporter.documents.each do |document_name, content|
+        filename = "#{document_name}.csv"
+        zos.put_next_entry filename
+        zos.print content
+      end
+    end
+    compressed_filestream.rewind
+    compressed_filestream
+  end
+end

app/views/trial_scorings/show.html.haml

@@ -17,6 +17,8 @@
       %tr
         %th.plant_scoring_units_scoring_unit_name_column
           = t 'tables.plant_scoring_units.scoring_unit_name'
+        %th.plant_accessions_plant_accession_column
+          = t 'tables.plant_accessions.plant_accession'
         - @plant_trial.decorate.trait_headers.each do |header|
           %th.trait_scores_score_value_column= header
     %tbody

config/locales/data_tables.en.yml

@@ -75,7 +75,7 @@ en:
       scoring_unit_frame_size: Frame size
       date_planted: Date planted
     plant_trials:
-      id: Scoring
+      id: Trait scoring
       plant_trial_name: Trial name
       plant_trial_description: Description
       project_descriptor: Project

spec/controllers/trial_scorings_controller_spec.rb

@@ -46,5 +46,44 @@
         get :show, format: :json, id: plant_trial.id
       end
     end
+
+    context 'when called for zip format' do
+      let(:tds) { create_list(:trait_descriptor, 2) }
+      before(:each) {
+        psus = [
+          create(:plant_scoring_unit,
+                 plant_accession: create(:plant_accession, plant_line: create(:plant_line, :with_variety)),
+                 plant_trial: plant_trial,
+                 scoring_unit_name: 'a'),
+          create(:plant_scoring_unit,
+                 plant_accession: create(:plant_accession, :with_variety),
+                 plant_trial: plant_trial,
+                 scoring_unit_name: 'b')
+        ]
+        create(:trait_score, trait_descriptor: tds[0], plant_scoring_unit: psus[0])
+        create(:trait_score, trait_descriptor: tds[1], plant_scoring_unit: psus[0])
+        create(:trait_score, trait_descriptor: tds[1], plant_scoring_unit: psus[1])
+      }
+
+      it 'produces a zip file' do
+        get :show, format: :zip, id: plant_trial.id
+        expect(response.content_type).to eq 'application/zip'
+      end
+
+      it 'compress three files in the zip file' do
+        get :show, format: :zip, id: plant_trial.id
+        file = Tempfile.new('plant_trial')
+        file.write(response.body)
+        file.close
+        Zip::File.open(file.path) do |zfile|
+          data = zfile.map do |entry|
+            [entry.name, entry.get_input_stream.read]
+          end
+          expect(data.map(&:first)).
+            to match_array %w(plant_trial.csv trait_descriptors.csv trait_scoring.csv)
+          expect(data.map{ |d| d[1].lines.size }).to match_array [2,3,3]
+        end
+      end
+    end
   end
 end

spec/factories/plant_line.rb

@@ -27,5 +27,9 @@
         plant_line.update_column(:user_id, nil)
       end
     end
+
+    trait :with_variety do
+      plant_variety
+    end
   end
 end