blast.rb in sequenceserver-1.1.0.beta

- old
+ new
@@ -1,168 +1,2 @@
-require 'forwardable'
-require 'tempfile'
-require 'English'
-require 'ox'
-
-require 'sequenceserver/links'
-require 'sequenceserver/blast/exceptions'
-require 'sequenceserver/blast/constants'
-require 'sequenceserver/blast/formatter'
-require 'sequenceserver/blast/report'
-require 'sequenceserver/blast/query'
-require 'sequenceserver/blast/hit'
-require 'sequenceserver/blast/hsp'
-
-module SequenceServer
-  # Simple wrapper around BLAST+ search algorithms.
-  #
-  # `BLAST::ArgumentError` and `BLAST::RuntimeError` signal errors encountered
-  # when attempting a BLAST search.
-  module BLAST
-    class << self
-      extend Forwardable
-
-      def_delegators SequenceServer, :config, :logger
-
-      # rubocop:disable Metrics/AbcSize, Metrics/CyclomaticComplexity
-      # rubocop:disable Metrics/MethodLength
-      def run(params)
-        pre_process params
-        validate_blast_params params
-
-        # Compile parameters for BLAST search into a shell executable command.
-        #
-        # BLAST method to use.
-        method  = params[:method]
-        #
-        # BLAST+ expects query sequence as a file.
-        qfile = Tempfile.new('sequenceserver_query')
-        qfile.puts(params[:sequence])
-        qfile.close
-        #
-        # Retrieve database objects from database id.
-        databases = Database[params[:databases]]
-        #
-        # Concatenate other blast options.
-        options = params[:advanced].to_s.strip + defaults
-        #
-        # blastn implies blastn, not megablast; but let's not interfere if a
-        # user specifies `task` herself.
-        options << ' -task blastn' if method == 'blastn' && !(options =~ /task/)
-
-        # Run BLAST search.
-        #
-        # Command to execute.
-        command = "#{method} -db '#{databases.map(&:name).join(' ')}'" \
-                  " -query '#{qfile.path}' #{options}"
-        #
-        # Debugging log.
-        logger.debug("Executing: #{command}")
-        #
-        # Temporary files to capture stdout and stderr.
-        rfile = Tempfile.new('sequenceserver_blast_result')
-        efile = Tempfile.new('sequenceserver_blast_error')
-        [rfile, efile].each(&:close)
-        #
-        # Execute.
-        system("#{command} > #{rfile.path} 2> #{efile.path}")
-
-        # Capture error.
-        status = $CHILD_STATUS.exitstatus
-        case status
-        when 1 # error in query sequence or options; see [1]
-          efile.open
-
-          # Most of the time BLAST+ generates a verbose error message with
-          # details we don't require.  So we parse out the relevant lines.
-          error = efile.each_line do |l|
-            break Regexp.last_match[1] if l.match(ERROR_LINE)
-          end
-
-          # But sometimes BLAST+ returns the exact/relevant error message.
-          # Trying to parse such messages returns nil, and we use the error
-          # message from BLAST+ as it is.
-          error = efile.rewind && efile.read unless error.is_a? String
-
-          efile.close
-          fail ArgumentError, error
-        when 2, 3, 4, 255 # see [1]
-          efile.open
-          error = efile.read
-          efile.close
-          fail RuntimeError.new(status, error)
-        end
-
-        Search << rfile
-        Report.new(File.basename(rfile.path), databases)
-      end
-      # rubocop:enable Metrics/AbcSize, Metrics/CyclomaticComplexity
-      # rubocop:enable Metrics/MethodLength
-
-      def pre_process(params)
-        params[:sequence].strip! unless params[:sequence].nil?
-      end
-
-      def validate_blast_params(params)
-        validate_blast_method params[:method]
-        validate_blast_sequences params[:sequence]
-        validate_blast_databases params[:databases]
-        validate_blast_options params[:advanced]
-      end
-
-      def defaults
-        " -outfmt 11 -num_threads #{config[:num_threads]}"
-      end
-
-      def validate_blast_method(method)
-        return true if ALGORITHMS.include? method
-        fail ArgumentError, 'BLAST algorithm should be one of:' \
-                            " #{ALGORITHMS.join(', ')}."
-      end
-
-      def validate_blast_sequences(sequences)
-        return true if sequences.is_a?(String) && !sequences.empty?
-        fail ArgumentError, 'Sequences should be a non-empty string.'
-      end
-
-      def validate_blast_databases(database_ids)
-        ids = Database.ids
-        return true if database_ids.is_a?(Array) && !database_ids.empty? &&
-                       (ids & database_ids).length == database_ids.length
-        fail ArgumentError, 'Database id should be one of:' \
-                            " #{ids.join("\n")}."
-      end
-
-      # Advanced options are specified by the user. Here they are checked for
-      # interference with SequenceServer operations.
-      #
-      # Raise ArgumentError if an error has occurred.
-      def validate_blast_options(options)
-        return true if !options || (options.is_a?(String) &&
-                                    options.strip.empty?)
-
-        unless allowed_chars.match(options)
-          fail ArgumentError, 'Invalid characters detected in options.'
-        end
-
-        if disallowed_options.match(options)
-          failedopt = Regexp.last_match[0]
-          fail ArgumentError, "Option \"#{failedopt}\" is prohibited."
-        end
-
-        true
-      end
-
-      def allowed_chars
-        /\A[a-z0-9\-_\. ']*\Z/i
-      end
-
-      def disallowed_options
-        /-out|-html|-outfmt|-db|-query/i
-      end
-    end
-  end
-end
-
-# References
-# ----------
-# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/
+require_relative 'blast/job'
+require_relative 'blast/report'