Parse and pass blast task options from help

This can be used in the front end by the Cloud version plugin to
build search params

Author: tadast

lib/sequenceserver/blast/tasks.rb

@@ -0,0 +1,38 @@
+module SequenceServer
+  module BLAST
+    # Shells out to each blast algorithm to get the help text and then parses it to extract the tasks.
+    module Tasks
+      ALGORITHMS = %w[blastn blastp blastx tblastn tblastx].freeze
+
+      def self.to_h
+        @to_h ||= ALGORITHMS.map do |algorithm|
+          help_text = `#{algorithm} -help`
+          [algorithm, extract_tasks(help_text)]
+        end.to_h
+      end
+
+      def self.extract_tasks(help_text)
+        lines = help_text.split("\n")
+
+        # Find task help paragraph start
+        task_line_index = lines.find_index { |line| line =~ /^\W-task/ }
+        return [] unless task_line_index.to_i.positive?
+
+        lines.slice!(0...task_line_index)
+
+        # Find the end of task help paragraph
+        next_option_line_index = lines.find_index { |line| line =~ /^\W-/ && !line.include?('-task') }
+        lines.slice!(next_option_line_index..-1)
+
+        extract_tasks_from_paragraph(lines)
+      end
+
+      def self.extract_tasks_from_paragraph(paragraph_lines)
+        as_one_liner = paragraph_lines.map(&:strip).join(' ')
+        as_one_liner.split('Permissible values:').last.split('>').first.split(' ').map do |task|
+          task.strip.gsub("'", '')
+        end.reject(&:empty?)
+      end
+    end
+  end
+end

lib/sequenceserver/routes.rb

@@ -5,6 +5,7 @@
 
 require 'sequenceserver/job'
 require 'sequenceserver/blast'
+require 'sequenceserver/blast/tasks'
 require 'sequenceserver/report'
 require 'sequenceserver/database'
 require 'sequenceserver/sequence'
@@ -85,7 +86,8 @@ class Routes < Sinatra::Base
       searchdata = {
         query: Database.retrieve(params[:query]),
         database: Database.all,
-        options: SequenceServer.config[:options]
+        options: SequenceServer.config[:options],
+        blastTaskMap: SequenceServer::BLAST::Tasks.to_h
       }
 
       searchdata.update(tree: Database.tree) if SequenceServer.config[:databases_widget] == 'tree'

spec/blast/tasks_spec.rb

@@ -0,0 +1,18 @@
+require 'spec_helper'
+require 'sequenceserver/blast/tasks'
+
+module SequenceServer
+  RSpec.describe BLAST::Tasks do
+    describe '#to_h' do
+      it "extracts tasks from help text" do
+        expect(described_class.to_h).to eq({
+          "blastn"=>["blastn", "blastn-short", "dc-megablast", "megablast", "rmblastn"],
+          "blastp"=>["blastp", "blastp-fast", "blastp-short"],
+          "blastx"=>["blastx", "blastx-fast"],
+          "tblastn"=>["tblastn", "tblastn-fast"],
+          "tblastx"=>[]
+        })
+      end
+    end
+  end
+end