Merge pull request #1169 from griffithlab/add-features-tsv-export

port gene summaries tsv exporter to feature exporter

server/app/jobs/generate_tsvs.rb

@@ -14,6 +14,15 @@ def perform
         public_path = public_file_path(e.file_name)
         FileUtils.cp(tmp_file.path, public_path)
         File.chmod(0644, public_path)
+
+        #symlink in legacy TSV names for backwards compatibility
+        if e.respond_to?(:file_aliases)
+          e.file_aliases.each do |fa|
+            link_path = public_file_path(fa)
+            FileUtils.ln_s(public_path, link_path, force: true)
+            File.chmod(0644, link_path)
+          end
+        end
       ensure
         tmp_file.unlink
       end
@@ -22,7 +31,7 @@ def perform
 
   def tsvs_to_generate
     [
-      GeneTsvFormatter,
+      FeatureTsvFormatter,
       VariantTsvFormatter,
       EvidenceItemTsvFormatter,
       VariantGroupTsvFormatter,

server/app/jobs/upload_tsvs_to_aws.rb

@@ -26,7 +26,7 @@ def perform
   def absolute_local_path(file)
     File.join(TsvRelease.downloads_path, file)
   end
-                      
+
   def bucket_name
     'civic-aws-opendata'
   end
@@ -61,7 +61,7 @@ def expected_files
     {
       "AssertionSummaries/date=#{date_string}/AssertionSummaries.tsv" => "#{date_string}/#{date_string}-AssertionSummaries.tsv",
       "ClinicalEvidenceSummaries/date=#{date_string}/ClinicalEvidenceSummaries.tsv" => "#{date_string}/#{date_string}-ClinicalEvidenceSummaries.tsv",
-      "GeneSummaries/date=#{date_string}/GeneSummaries.tsv" => "#{date_string}/#{date_string}-GeneSummaries.tsv",
+      "FeatureSummaries/date=#{date_string}/FeatureSummaries.tsv" => "#{date_string}/#{date_string}-FeatureSummaries.tsv",
       "VariantGroupSummaries/date=#{date_string}/VariantGroupSummaries.tsv"=> "#{date_string}/#{date_string}-VariantGroupSummaries.tsv",
       "VariantSummaries/date=#{date_string}/VariantSummaries.tsv" => "#{date_string}/#{date_string}-VariantSummaries.tsv",
       "MolecularProfileSummaries/date=#{date_string}/MolecularProfileSummaries.tsv" => "#{date_string}/#{date_string}-MolecularProfileSummaries.tsv",

server/app/tsv_formatters/feature_tsv_formatter.rb

@@ -0,0 +1,111 @@
+class FeatureTsvFormatter
+  def self.objects
+    Feature.joins(variants: { molecular_profiles: [:evidence_items]})
+      .includes(:feature_instance)
+      .distinct
+  end
+
+  def self.headers
+    shared_headers = [
+      'feature_id',
+      'feature_civic_url',
+      'feature_type',
+      'name',
+      'feature_aliases',
+      'description',
+      'last_review_date',
+      'is_flagged'
+    ]
+    shared_headers + gene_headers + factor_headers + fusion_headers
+  end
+
+  def self.gene_headers
+    ['entrez_id']
+  end
+
+  def self.factor_headers
+    ['ncit_id']
+  end
+
+  def self.fusion_headers
+    [
+      'five_prime_partner_status',
+      'three_prime_partner_status',
+      'five_prime_gene_id',
+      'five_prime_gene_name',
+      'five_prime_gene_entrez_id',
+      'three_prime_gene_id',
+      'three_prime_gene_name',
+      'three_prime_gene_entrez_id',
+    ]
+  end
+
+  def self.create_gene_row(feature)
+    row = [
+      feature.feature_instance.entrez_id
+    ]
+    row += Array.new(factor_headers.size)
+    row += Array.new(fusion_headers.size)
+    return row
+  end
+
+  def self.create_factor_row(feature)
+    row = Array.new(gene_headers.size)
+    row += [
+      feature.feature_instance.ncit_id
+    ]
+    row += Array.new(fusion_headers.size)
+  end
+
+  def self.create_fusion_row(feature)
+    feature_instance = feature.feature_instance
+    row = Array.new(gene_headers.size)
+    row += Array.new(factor_headers.size)
+    row += [
+      feature_instance.five_prime_partner_status,
+      feature_instance.three_prime_partner_status,
+      feature_instance.five_prime_gene_id,
+      feature_instance.five_prime_gene&.name,
+      feature_instance.five_prime_gene&.entrez_id,
+      feature_instance.three_prime_gene_id,
+      feature_instance.three_prime_gene&.name,
+      feature_instance.three_prime_gene&.entrez_id,
+    ]
+  end
+
+  def self.row_from_object(feature)
+    shared_cols = [
+      feature.id,
+      LinkAdaptors::Feature.new(feature).permalink_path(include_domain: true),
+      feature.feature_instance_type.demodulize,
+      feature.name,
+      feature.feature_aliases.map(&:name).join(","),
+      feature.description&.squish,
+      feature.updated_at,
+      feature.flagged
+    ]
+
+    feature_cols = case feature.feature_instance
+                   when Features::Gene
+                     create_gene_row(feature)
+                   when Features::Factor
+                     create_factor_row(feature)
+                   when Features::Fusion
+                     create_fusion_row(feature)
+                   else
+                     raise StandardError.new("Unknown feature type for TSV export: #{feature.feature_instance_type}")
+                   end
+    shared_cols + feature_cols
+  end
+
+  def self.file_name
+    'FeatureSummaries.tsv'
+  end
+
+  def self.file_aliases
+    [
+      'GeneSummaries.tsv'
+    ]
+  end
+end
+

server/app/tsv_formatters/variant_tsv_formatter.rb

@@ -44,7 +44,7 @@ def self.gene_headers
     ]
   end
 
-  def self.factor_headers 
+  def self.factor_headers
     [
       'ncit_id'
     ]