blast.rb in sequenceserver-1.0.0.pre.4

- old
+ new

@@ -3,10 +3,12 @@
 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'
 
@@ -14,29 +16,10 @@
   # Simple wrapper around BLAST+ search algorithms.
   #
   # `BLAST::ArgumentError` and `BLAST::RuntimeError` signal errors encountered
   # when attempting a BLAST search.
   module BLAST
-    ERROR_LINE = /\(CArgException.*\)\s(.*)/
-
-    ALGORITHMS = %w(blastn blastp blastx tblastn tblastx)
-
-    OUTFMT = {
-      'pairwise'        => [0, 'txt'],
-      'qa_identity'     => [1, 'txt'],
-      'qa_no_identity'  => [2, 'txt'],
-      'fqa_identity'    => [3, 'txt'],
-      'fqa_no_identity' => [4, 'txt'],
-      'xml'             => [5, 'xml'],
-      'tsv'             => [6, 'tsv'],
-      'tsv_commented'   => [7, 'tsv'],
-      'asn_text'        => [8, 'asn'],
-      'asn_binary'      => [9, 'asn'],
-      'csv'             => [10, 'csv'],
-      'archive'         => [11, 'txt']
-    } # See [1]
-
     class << self
       extend Forwardable
 
       def_delegators SequenceServer, :config, :logger
 
@@ -107,52 +90,20 @@
           error = efile.read
           efile.close
           fail RuntimeError.new(status, error)
         end
 
-        Report.new(File.basename(rfile), databases)
+        Search << rfile
+        Report.new(File.basename(rfile.path), databases)
       end
-
-      def format(params)
-        validate_format_params params
-
-        rfile = create_file_path params['report']
-        ofmt  = OUTFMT[params['format']]
-        type  = params['type']
-
-        oname = "seqserv_#{type}_#{Time.now.strftime('%H%M')}.#{ofmt[1]}"
-        ofile = Tempfile.new oname
-
-        command =  "blast_formatter -archive '#{rfile}' -out #{ofile.path}" \
-                   " -outfmt '#{ofmt[0]} #{params['specifiers']}' 2> /dev/null"
-
-        logger.debug("Executing: #{command}")
-        system command
-
-        {
-          :filepath => ofile.path,
-          :filename => oname,
-          :type     => ofmt[1]
-        }
-      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_format_params(params)
-        return true if params.include?('report') &&
-                       params.include?('format') &&
-                       File.exist?(create_file_path params['report'])
-        fail ArgumentError, <<MSG
-Incorrect request parameters. Please ensure that requested file name is
-correct and the file type is either xml or tsv.
-MSG
-      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]
@@ -197,15 +148,9 @@
           failedopt = Regexp.last_match[0]
           fail ArgumentError, "Option \"#{failedopt}\" is prohibited."
         end
 
         true
-      end
-
-      # Returns filename if path exists otherwise returns a path to tmp dir.
-      def create_file_path(filename)
-        return File.join(Dir.tmpdir, filename) unless File.exist? filename
-        filename
       end
 
       def allowed_chars
         /\A[a-z0-9\-_\. ']*\Z/i
       end