bin/bel2rdf.rb in bel-0.6.0 vs bin/bel2rdf.rb in bel-0.7.0

@@ -44,19 +44,39 @@
 
   opts.on('-f', '--format FORMAT', 'RDF file format. The default output format is N-Triples.') do |format|
     options[:format] = format.downcase
   end
 
+
+  opts.on('-p', '--rdf-prefix-file FILE', "A YAML file mapping prefix containing key/value pairs. The key is an RDF prefix to use in the RDF output; the value is the RDF URI for that prefix. For example, belv: 'http://www.openbel.org/vocabulary/'.") do |prefix_file|
+    options[:rdf_prefix_file] = prefix_file
+  end
+
   opts.on('-s', '--[no-]schema', 'Write BEL RDF schema? The default is to include the schema in the output.') do |schema|
     options[:schema] = schema
   end
+
+  opts.on('-r', '--remap-file FILE', 'A YAML file that remaps annotation and namespace definitions. Run "bel remapfile" to get an example of the YAML format.') do |remap_file|
+    options[:remap_file] = remap_file
+  end
 end.parse!
 
 if options[:bel] and not File.exists? options[:bel]
   $stderr.puts "No file for bel, #{options[:bel]}"
   exit 1
 end
+
+if options[:rdf_prefix_file] and not File.exists? options[:rdf_prefix_file]
+  $stderr.puts "No file for rdf_prefix_file, #{options[:rdf_prefix_file]}"
+  exit 1
+end
+
+if options[:remap_file] and not File.exist? options[:remap_file]
+  $stderr.puts "No file for remap_file, #{options[:remap_file]}"
+  exit 1
+end
+
 unless RDF_TRANSLATORS.include? options[:format]
   $stderr.puts "Format must be one of: #{RDF_TRANSLATORS.join(', ')}"
   exit 1
 end
 
@@ -75,20 +95,22 @@
 end
 
 # read bel content
 input_io =
   if options[:bel]
-    File.open(options[:bel], :external_encoding => 'UTF-8')
+    File.open(options[:bel], external_encoding: 'UTF-8')
   else
     $stdin
   end
 
 validate_translator!(:bel)
 validate_translator!(options[:format])
 begin
   BEL.translate(input_io, :bel, options[:format], $stdout,
     {
-      :write_schema => options[:schema]
+      write_schema:    options[:schema],
+      rdf_prefix_file: options[:rdf_prefix_file],
+      remap_file:      options[:remap_file]
     }
   )
 ensure
   $stdout.close
 end