arg_validation.rb in genevalidator-2.1.3

- old
+ new

@@ -14,11 +14,10 @@
       extend Forwardable
       def_delegators GeneValidator, :opt
 
       def validate_args
         @opt = opt
-        assert_output_dir_does_not_exist
         assert_file_present('input file', opt[:input_fasta_file])
         assert_input_file_probably_fasta
         assert_input_sequence
         assert_BLAST_output_files
 
@@ -36,27 +35,27 @@
       end
 
       private
 
       def assert_validations_arg
-        validations = %w(lenc lenr frame merge dup orf align)
+        validations = %w[lenc lenr frame merge dup orf align]
         if @opt[:validations]
           val = @opt[:validations].collect { |v| v.strip.downcase }
           validations = val unless val.include? 'all'
         end
         @opt[:validations] = validations
       end
 
       def check_num_threads
         @opt[:num_threads] = Integer(@opt[:num_threads])
-        unless @opt[:num_threads] > 0
-          $stderr.puts 'Number of threads can not be lower than 0'
-          $stderr.puts 'Setting number of threads to 1'
+        unless @opt[:num_threads].positive?
+          warn 'Number of threads can not be lower than 0'
+          warn 'Setting number of threads to 1'
           @opt[:num_threads] = 1
         end
         return unless @opt[:num_threads] > 256
-        $stderr.puts "Number of threads set at #{@opt[:num_threads]} is" \
+        warn "Number of threads set at #{@opt[:num_threads]} is" \
                      ' unusually high.'
       end
 
       def assert_BLAST_output_files
         return unless @opt[:blast_xml_file] || @opt[:blast_tabular_file]
@@ -66,60 +65,50 @@
           assert_file_present('BLAST tabular file', @opt[:blast_tabular_file])
           assert_tabular_options_exists
         end
       end
 
-      def assert_output_dir_does_not_exist
-        output_dir = "#{@opt[:input_fasta_file]}.html"
-        return unless File.exist?(output_dir)
-        $stderr.puts 'The output directory already exists for this fasta file.'
-        $stderr.puts "\nPlease remove the following directory: #{output_dir}\n"
-        $stderr.puts "You can run the following command to remove the folder.\n"
-        $stderr.puts "\n   $ rm -r #{output_dir} \n"
-        exit 1
-      end
-
       def assert_tabular_options_exists
         return if @opt[:blast_tabular_options]
-        $stderr.puts '*** Error: BLAST tabular options (-o) have not been set.'
-        $stderr.puts '    Please set the "-o" option with the custom format'
-        $stderr.puts '    used in the BLAST -outfmt argument'
+        warn '*** Error: BLAST tabular options (-o) have not been set.'
+        warn '    Please set the "-o" option with the custom format'
+        warn '    used in the BLAST -outfmt argument'
         exit 1
       end
 
       def assert_input_file_probably_fasta
         File.open(@opt[:input_fasta_file], 'r') do |file_stream|
-          (file_stream.readline[0] == '>') ? true : false
+          file_stream.readline[0] == '>'
         end
       end
 
       def assert_file_present(desc, file, exit_code = 1)
         return if file && File.exist?(File.expand_path(file))
-        $stderr.puts "*** Error: Couldn't find the #{desc}: #{file}."
+        warn "*** Error: Couldn't find the #{desc}: #{file}."
         exit exit_code
       end
 
-      alias_method :assert_dir_present, :assert_file_present
+      alias assert_dir_present assert_file_present
 
       def assert_input_sequence
         fasta_content = IO.binread(@opt[:input_fasta_file])
         type = BlastUtils.type_of_sequences(fasta_content)
-        return if type == :nucleotide || type == :protein
-        $stderr.puts '*** Error: The input files does not contain just protein'
-        $stderr.puts '    or nucleotide data.'
-        $stderr.puts '    Please correct this and try again.'
+        return if %i[nucleotide protein].include? type
+        warn '*** Error: The input files does not contain just protein'
+        warn '    or nucleotide data.'
+        warn '    Please correct this and try again.'
         exit 1
       end
 
       def export_bin_dirs
         @opt[:bin].each do |bin|
           bin = File.expand_path(bin)
           if File.exist?(bin) && File.directory?(bin)
             add_to_path(bin)
           else
-            $stderr.puts '*** The following bin directory does not exist:'
-            $stderr.puts "    #{bin}"
+            warn '*** The following bin directory does not exist:'
+            warn "    #{bin}"
           end
         end
       end
 
       ## Checks if dir is in $PATH and if not, it adds the dir to the $PATH.
@@ -129,76 +118,58 @@
         ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
       end
 
       def assert_mafft_installation
         return if command?('mafft')
-        $stderr.puts '*** Could not find Mafft binaries.'
-        $stderr.puts '    Ignoring error and continuing - Please note that' \
+        warn '*** Could not find Mafft binaries.'
+        warn '    Ignoring error and continuing - Please note that' \
                      ' some validations may be skipped.'
-        $stderr.puts # a blank line
+        warn # a blank line
       end
     end
 
     # Validates BLAST Installation (And BLAST databases)
     class Blast
       class << self
         # Use a fixed minimum version of BLAST+
-        MINIMUM_BLAST_VERSION           = '2.2.30+'
+        MINIMUM_BLAST_VERSION           = '2.2.30+'.freeze
         # Use the following exit codes, or 1.
         EXIT_BLAST_NOT_INSTALLED        = 2
         EXIT_BLAST_NOT_COMPATIBLE       = 3
         EXIT_NO_BLAST_DATABASE          = 4
 
         def validate(opt)
           assert_blast_installation
-          warn_if_remote_database(opt)
           assert_local_blast_database_exists(opt[:db]) if opt[:db] !~ /remote/
         end
 
         def assert_blast_installation
           # Validate BLAST installation
           assert_blast_installed
           assert_blast_compatible
         end
 
-        def warn_if_remote_database(opt)
-          return if opt[:db] !~ /remote/
-          $stderr.puts # a blank line
-          if !opt[:raw_sequences] &&
-              (opt[:validations].include?('align') ||
-               opt[:validations].include?('dup'))
-            $stderr.puts 'Warning: Hit sequences will be fetched from remote' \
-                         ' server.'
-          else
-            $stderr.puts 'Warning: BLAST will be carried out on remote server.'
-          end
-          $stderr.puts 'This may take quite a bit of time.'
-          $stderr.puts 'You may want to install a local BLAST database for' \
-                       ' faster analyses.'
-          $stderr.puts # a blank line
-        end
-
         def assert_local_blast_database_exists(db)
           return if system("blastdbcmd -db #{db} -info > /dev/null 2>&1")
-          $stderr.puts '*** No BLAST database found at the provided path.'
-          $stderr.puts '    Please ensure that the provided path is correct' \
+          warn '*** No BLAST database found at the provided path.'
+          warn '    Please ensure that the provided path is correct' \
                        ' and then try again.'
           exit EXIT_NO_BLAST_DATABASE
         end
 
         private
 
         def assert_blast_installed
           return if GVArgValidation.command?('blastdbcmd')
-          $stderr.puts '*** Could not find BLAST+ binaries.'
+          warn '*** Could not find BLAST+ binaries.'
           exit EXIT_BLAST_NOT_INSTALLED
         end
 
         def assert_blast_compatible
           version = `blastdbcmd -version`.split[1]
           return if version >= MINIMUM_BLAST_VERSION
-          $stderr.puts "*** Your BLAST+ version #{version} is outdated."
-          $stderr.puts '    GeneValidator needs NCBI BLAST+ version' \
+          warn "*** Your BLAST+ version #{version} is outdated."
+          warn '    GeneValidator needs NCBI BLAST+ version' \
                        " #{MINIMUM_BLAST_VERSION} or higher."
           exit EXIT_BLAST_NOT_COMPATIBLE
         end
       end
     end