initial draft of civic panel endpoints

app/controllers/panels_controller.rb

@@ -0,0 +1,16 @@
+class PanelsController < ApplicationController
+  actions_without_auth :index, :show
+  def index
+    render json: PipelineType.pluck(:name)
+  end
+
+  def show
+    panel = CivicPanel.new(params[:minimum_score] || 30, params[:pipeline_tech])
+    @panel = panel.presenter_classname.new(panel.variants)
+    respond_to do |format|
+      format.tsv do
+         headers['Content-Disposition'] = "attachment; filename=\"civic_panel_export_#{panel.pipeline_type}_#{panel.score_cutoff}.tsv\""
+      end
+    end
+  end
+end

app/models/civic_panel.rb

@@ -0,0 +1,28 @@
+class CivicPanel
+  attr_reader :score_cutoff, :pipeline_type
+
+  def initialize(score_cutoff = 30, pipeline_type = '')
+    @score_cutoff = score_cutoff.to_i
+    @pipeline_type = pipeline_type.downcase
+  end
+
+  def variants
+    variants = PipelineType.includes(variant_types: {variants: [:evidence_items, :gene]})
+                 .find_by('lower(pipeline_types.name) = ?', pipeline_type)
+                 .variant_types
+                 .flat_map(&:variants)
+                 .reject { |v| v.chromosome.blank? || v.start.blank? }
+                 .uniq
+
+    variants.reject do |v|
+      Actions::CalculateCivicScore.new(v).perform <= score_cutoff
+    end
+  end
+
+  def presenter_classname
+    {
+      'captureseq' => Panels::CaptureSeq,
+      'nanostring' => Panels::NanoString
+    }[pipeline_type]
+  end
+end

app/presenters/panels/capture_seq.rb

@@ -0,0 +1,91 @@
+module Panels
+  class CaptureSeq
+    attr_reader :variants, :already_tiled_genes, :genes_to_tile
+
+    def initialize(variants)
+      @variants = variants
+      @genes_to_tile = Set.new
+      @already_tiled_genes = Set.new
+    end
+
+    def partitioned_variants
+      variants.each { |v| genes_to_tile << v.gene if should_tile_gene?(v) }
+      rows = []
+      variants.each do |v|
+        tsv_variant(v).each do |row|
+          rows << row
+        end
+      end
+      rows.uniq
+    end
+
+    def headers
+      [
+        'gene',
+        'chr',
+        'start',
+        'stop',
+        'chr2',
+        'start2',
+        'stop2',
+        'gene2',
+        'variant_name',
+        'variant_types',
+        'tiling_whole_gene',
+      ]
+    end
+
+    private
+    def tsv_variant(v)
+      if genes_to_tile.include?(v.gene) && !already_tiled_genes.include?(v.gene) && !v.chromosome2.present?
+        already_tiled_genes << v.gene
+        tiled_gene(v)
+      elsif !genes_to_tile.include?(v.gene)
+        [untiled_variant(v)]
+      else
+        []
+      end
+    end
+
+    def untiled_variant(v)
+      [
+        v.gene.name,
+        v.chromosome,
+        v.start,
+        v.stop,
+        v.chromosome2 || '',
+        v.start2 || '',
+        v.stop2 || '',
+        v.representative_transcript2.present? ? Scrapers::EnsemblRest.get_gene_name_for_transcript(v.representative_transcript2) : '',
+        v.name,
+        v.variant_types.map(&:name).join(','),
+        false
+      ]
+    end
+
+    def tiled_gene(v)
+      ensembl_gene_id = Scrapers::EnsemblRest.get_gene_id_for_transcript(v.representative_transcript)
+      exon_coordinates = Scrapers::EnsemblRest.get_exon_coordinates_for_gene_id(ensembl_gene_id)
+      variants_on_gene = variants.select { |x| x.gene_id == v.gene_id }
+      exon_coordinates.map do |coordinates|
+        [
+          v.gene.name,
+          v.chromosome,
+          coordinates['start'],
+          coordinates['end'],
+          '',
+          '',
+          '',
+          '',
+          variants_on_gene.map(&:name).join(','),
+          variants_on_gene.flat_map(&:variant_types).map(&:name).uniq.join(','),
+          true
+        ]
+      end
+    end
+
+    def should_tile_gene?(v)
+      v.stop.to_i - v.start.to_i >= 1000 && v.chromosome2.blank?
+    end
+  end
+end

app/presenters/panels/nano_string.rb

@@ -0,0 +1,91 @@
+module Panels
+  class NanoString
+    attr_reader :variants, :already_tiled_genes, :genes_to_tile
+
+    def initialize(variants)
+      @variants = variants
+      @genes_to_tile = Set.new
+      @already_tiled_genes = Set.new
+    end
+
+    def partitioned_variants
+      variants.each { |v| genes_to_tile << v.gene if should_tile_gene?(v) }
+      rows = []
+      variants.each do |v|
+        tsv_variant(v).each do |row|
+          rows << row
+        end
+      end
+      rows.uniq
+    end
+
+    def headers
+      [
+        'gene',
+        'chr',
+        'start',
+        'stop',
+        'chr2',
+        'start2',
+        'stop2',
+        'gene2',
+        'variant_name',
+        'variant_types',
+        'tiling_whole_gene',
+      ]
+    end
+
+    private
+    def tsv_variant(v)
+      if genes_to_tile.include?(v.gene) && !already_tiled_genes.include?(v.gene) && !v.chromosome2.present?
+          already_tiled_genes << v.gene
+          tiled_gene(v)
+      elsif !genes_to_tile.include?(v.gene)
+        [untiled_variant(v)]
+      else
+        []
+      end
+    end
+
+    def untiled_variant(v)
+      [
+        v.gene.name,
+        v.chromosome,
+        v.start,
+        v.stop,
+        v.chromosome2 || '',
+        v.start2 || '',
+        v.stop2 || '',
+        v.representative_transcript2.present? ? Scrapers::EnsemblRest.get_gene_name_for_transcript(v.representative_transcript2) : '',
+        v.name,
+        v.variant_types.map(&:name).join(','),
+        false
+      ]
+    end
+
+    def tiled_gene(v)
+      ensembl_gene_id = Scrapers::EnsemblRest.get_gene_id_for_transcript(v.representative_transcript)
+      exon_coordinates = Scrapers::EnsemblRest.get_exon_coordinates_for_gene_id(ensembl_gene_id)
+      variants_on_gene = variants.select { |x| x.gene_id == v.gene_id }
+      exon_coordinates.map do |coordinates|
+        [
+          v.gene.name,
+          v.chromosome,
+          coordinates['start'],
+          coordinates['end'],
+          '',
+          '',
+          '',
+          '',
+          variants_on_gene.map(&:name).join(','),
+          variants_on_gene.flat_map(&:variant_types).map(&:name).uniq.join(','),
+          true,
+        ]
+      end
+    end
+
+    def should_tile_gene?(v)
+      v.stop.to_i - v.start.to_i >= 1000 && v.chromosome2.blank?
+    end
+  end
+end

app/views/panels/show.tsv.erb

@@ -0,0 +1,4 @@
+<%= @panel.headers.join("\t") %>
+<% @panel.partitioned_variants.each do |variant| %>
+<%= variant.join("\t").html_safe %>
+<% end %>

lib/importer/panel_bucket_adaptor.rb

@@ -0,0 +1,24 @@
+module Importer
+  class PanelBucketAdaptor
+    def self.valid_row?(row)
+      true
+    end
+
+    def self.create_entities_for_row(row)
+      variant_type = VariantType.find_by(soid: row['soid'])
+      if variant_type
+        existing_pipelines = variant_type.pipeline_types
+        pipeline_types.each do |type|
+          if row[type].present? && row[type].downcase == 'yes'
+            existing_pipelines << PipelineType.where(name: type).first_or_create
+          end
+        end
+        variant_type.pipeline_types = existing_pipelines.uniq
+      end
+    end
+
+    def self.pipeline_types
+      ["CaptureSeq", "NanoString"]
+    end
+  end
+end

lib/importer/panel_buckets.rb

@@ -0,0 +1,7 @@
+module Importer
+  class PanelBuckets
+    def self.import!(file = 'capture_buckets.tsv')
+      Importer::TsvReader.new(file, Importer::PanelBucketAdaptor).import!
+    end
+  end
+end

lib/scrapers/ensembl_rest.rb

@@ -0,0 +1,57 @@
+module Scrapers
+  class EnsemblRest
+    def self.get_gene_name_for_transcript(transcript)
+      resp = Util.make_get_request(url_from_transcript(transcript))
+      extract_gene_symbol_from_response(resp)
+    rescue
+      ''
+    end
+
+    def self.get_gene_id_for_transcript(transcript)
+      resp = Util.make_get_request(url_from_transcript(transcript))
+      extract_gene_id_from_response(resp)
+    rescue
+      ''
+    end
+
+    def self.get_exon_coordinates_for_gene_id(gene_id)
+      resp = Util.make_get_request(exon_url_from_gene_id(gene_id))
+      extract_exon_coordinates_from_response(resp)
+    end
+
+    def self.url_from_transcript(transcript)
+      "http://grch37.rest.ensembl.org/overlap/id/#{transcript}?feature=gene;content-type=application/json"
+    end
+
+    def self.exon_url_from_gene_id(gene_id)
+      "http://grch37.rest.ensembl.org/overlap/id/#{gene_id}.json?feature=exon"
+    end
+
+    def self.extract_exon_coordinates_from_response(text)
+      values = JSON.parse(text)
+      if values.any?
+        values.uniq { |v| v['exon_id'] }
+      else
+        []
+      end
+    end
+
+    def self.extract_gene_symbol_from_response(text)
+      values = JSON.parse(text)
+      if values.any?
+        values.select { |x| x['feature_type'] == 'gene' }.first['external_name']
+      else
+        ''
+      end
+    end
+
+    def self.extract_gene_id_from_response(text)
+      values = JSON.parse(text)
+      if values.any?
+        values.select { |x| x['feature_type'] == 'gene' }.first['id']
+      else
+        ''
+      end
+    end
+  end
+end