bel 0.3.0-x86-mingw32 → 0.3.1-x86-mingw32

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data/README.md

@@ -39,29 +39,29 @@ executable commands
 
 ```bash
 
-    NAME
-        bel - Command line utilities for BEL.
-
-    SYNOPSIS
-        bel [global options] command [command options] [arguments...]
-
-    VERSION
-        0.3.0
-
-    GLOBAL OPTIONS
-        --help         - Show this message
-        --[no-]verbose - Enables verbose output.
-        --version      - Display the program version
-
-    COMMANDS
-        bel2rdf.rb   - Converts BEL to RDF.
-        compare   - Compares knowledge in two BEL script.
-        help      - Shows a list of commands or help for one command
-        parse     - Shows parse of BEL script.
-        rdfschema - Outputs the RDFS (e.g. RDF Schema) for BEL.
-        summarize - Show summary statistics. for knowledge in provided BEL script.
-        translate - Translates BEL evidence between file formats.
-        upgrade   - Upgrades BEL knowledge and annotation.
+    Usage: bel [OPTIONS]... COMMAND
+    A set of commands to process BEL knowledge.
+
+    Subcommands:
+
+      bel2rdf
+      compare
+      parse
+      rdfschema
+      summarize
+      translate
+      upgrade
+
+
+    bel 0.3.1
+    Copyright (C) 2015 OpenBEL
+    Apache License, Version 2.0, January 2004
+    http://www.apache.org/licenses/
+
+    Options:
+      -v, --verbose    Verbose output.
+      -e, --version    Print version and exit
+      -h, --help       Show this message
 ```
 
 

data/bel.gemspec

@@ -55,7 +55,6 @@ Gem::Specification.new do |spec|
 
   # runtime
   spec.add_dependency             'ffi',           '1.9.8'
-  spec.add_dependency             'gli',           '~> 2.13'
 
   # test rdf functionality
   spec.add_development_dependency 'uuid',          '~> 2.3'

data/bin/bel

@@ -1,210 +1,355 @@
 #!/usr/bin/env ruby
-require 'gli'
+require 'erb'
 require 'bel'
+require 'bel/vendor/trollop'
 
-include GLI::App
-
-# main command
-program_desc 'Command line utilities for BEL.'
-version BEL::VERSION
-
-# settings
-subcommand_option_handling :normal
-arguments :strict
-
-# global options
-desc 'Enables verbose output.'
-switch [:verbose], :default_value => false
-
-# helpers
-def which_io(input_file)
-  case input_file
-  when nil
-    $stdin
-  when '-'
-    $stdin
-  else
-    input_file
-  end
-end
+VERSION_BANNER = <<-VERSION
+bel #{BEL::VERSION}
+Copyright (C) 2015 OpenBEL
+Apache License, Version 2.0, January 2004
+http://www.apache.org/licenses/
+VERSION
 
-# Command: bel2rdf
-# ----------------
-desc      'Converts BEL to RDF.'
-long_desc <<-LONGDESC
-  Convers BEL script content into RDF triples. The RDFS schema for BEL can also be included in output.
-LONGDESC
-command :bel2rdf do |c|
-  c.flag [:b, :bel],
-    :desc => 'The BEL script file to convert to RDF.'
-  c.flag [:f, :format],
-    :desc => 'The RDF format to serialize.',
-    :default_value => 'ntriples',
-    :must_match => ['ntriples','nquads','turtle']
-  c.switch [:s, :schema], :default_value => false
-  c.action do |global_options,options,args|
-    bel_io = which_io(options[:bel])
-    ARGV.clear.concat([
-      '--format', options[:format]
-    ])
-    if bel_io != $stdin
-      ARGV.concat(['--bel', bel_io])
-    end
-    if options[:schema]
-      ARGV.concat(['--schema', options[:schema]])
-    end
+module BEL
+  module Commands
 
-    require_relative 'bel2rdf'
-  end
-end
+    class BelCommand
 
+      attr_reader :global_options
 
-# Command: compare
-# ----------------
-desc      'Compares knowledge in two BEL script.'
-long_desc <<-LONGDESC
-  Compare shows a quick breakdown of the differences between knowledge in two BEL script files.
-LONGDESC
-arg_name 'file1'
-arg_name 'file2'
-command :compare do |c|
+      def initialize(sub_commands)
+        @sub_commands = sub_commands
+      end
 
-  c.action do |global_options,options,args|
-    file1, file2 = args
+      def run
+        with_this_binding = binding
+        @global_options = Trollop::options do
+          synopsis ERB.new(
+          <<-SYNOPSIS
+A set of commands to process BEL knowledge.
 
-    raise "The first file was not specified."  unless file1
-    raise "The second file was not specified." unless file2
+Subcommands:
+<% @sub_commands.each do |cmd| %>
+  <%= cmd %><% end %>
+          SYNOPSIS
+          ).result(with_this_binding)
+          usage    "[OPTIONS]... COMMAND"
+          version  ::VERSION_BANNER
 
-    ARGV.clear.concat([file1, file2])
-    require_relative 'bel_compare'
-  end
-end
+          opt      :verbose, 'Verbose output.',
+                   :long  => :verbose,
+                   :short => :v
+          stop_on_unknown
+        end
 
+        BelCommand.fail_unless_subcommand
+      end
 
-# Command: parse
-# --------------
-desc      'Shows parse of BEL script.'
-long_desc <<-LONGDESC
-  Show parsed objects from BEL content for debugging purposes. The parsed object name is show along with the BEL script text.
-LONGDESC
-command :parse do |c|
-  c.flag [:b, :bel],
-    :desc => 'The BEL script to parse.'
-  c.action do |global_options,options,args|
-    bel_io = which_io(options[:bel])
-    if bel_io != $stdin
-      ARGV.clear.concat(['--bel', bel_io])
+      def self.fail_unless_subcommand
+        Trollop::educate if ARGV.empty?
+      end
     end
-    require_relative 'bel_parse'
-  end
-end
 
+    class Bel2rdfCommand
 
-# Command: rdfschema
-# ----------------
-desc      'Outputs the RDFS (e.g. RDF Schema) for BEL.'
-long_desc <<-LONGDESC
-  Outputs the RDFS for BEL to the chosen RDF file format.
-LONGDESC
-command :rdfschema do |c|
-  c.flag [:f, :format],
-    :desc => 'The RDF format to serialize.',
-    :default_value => 'ntriples',
-    :must_match => ['ntriples','nquads','turtle']
-  c.action do |global_options,options,args|
-    ARGV.clear.concat(['--format', options[:format]])
-    require_relative 'bel_rdfschema'
-  end
-end
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Converts BEL to RDF."
+            usage    "[OPTIONS]... bel2rdf [OPTIONS]"
+
+            opt      :bel,       'The BEL script to parse and output (Defaults to STDIN).',
+                     :type    => String,
+                     :long    => :bel,
+                     :short   => :b,
+                     :default => nil
+
+            opt      :format,    'The RDF format to output.',
+                     :type    => String,
+                     :long    => :format,
+                     :short   => :f,
+                     :default => 'ntriples'
+
+            opt      :schema,    'Includes the BEL RDFS schema in RDF output.',
+                     :long    => :schema,
+                     :short   => :s,
+                     :default => false
+          end
 
+        ARGV.concat(['--bel',    parsed_options[:bel]])    if parsed_options[:bel]
+        ARGV.concat(['--format', parsed_options[:format]]) if parsed_options[:format]
+        ARGV.concat(['--schema', parsed_options[:schema]]) if parsed_options[:schema]
 
-# Command: summarize
-# ------------------
-desc      'Show summary statistics. for knowledge in provided BEL script.'
-long_desc <<-LONGDESC
-  Show summary statistics for knowledge in provided BEL script. The output is provided in CSV with an initial header row.
-LONGDESC
-command :summarize do |c|
-  c.flag [:b, :bel],
-    :desc => 'The BEL script to parse.'
-  c.action do |global_options,options,args|
-    bel_io = which_io(options[:bel])
-    if bel_io != $stdin
-      ARGV.clear.concat(['--bel', bel_io])
+        require_relative 'bel2rdf'
+      end
     end
-    require_relative 'bel_summarize'
-  end
-end
 
+    class CompareCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Compares knowledge in two BEL script files."
+            usage    "[OPTIONS]... compare FILE1 FILE2"
+          end
 
-# Command: translate
-# ------------------
-desc      'Translates BEL evidence between file formats.'
-long_desc <<-LONGDESC
-  Translates BEL evidence from one format (e.g. <from_format>) to another format (e.g. <to_format>). If --input-file was not provided then evidence data is read from STDIN (e.g. -).
-LONGDESC
-arg_name 'from_format'
-arg_name 'to_format'
-command :translate do |c|
+        # Error if two file arguments were not provided.
+        Trollop::educate unless ARGV.size == 2
 
-  c.flag [:i, :"input-file"],
-    :desc          => 'The file to read evidence data from.'
-  c.action do |global_options,options,args|
-    input_io = which_io(options[:'input-file'])
+        # Error if file arguments are not readable.
+        missing = ARGV.select { |arg|
+          !File.readable?(arg)
+        }
+        if !missing.empty?
+          missing.each do |arg|
+            $stderr.puts %Q{File "#{arg}" is not readable.}
+          end
+          $stderr.puts
+          Trollop::educate
+        end
 
-    if ![$stdin, '-'].include?(input_io)
-      unless File.readable?(input_io)
-        raise "File #{input_io} does not exist or is not readable."
+        ARGV.insert(0, '--verbose') if @global_options[:verbose]
+        require_relative 'bel_compare'
       end
     end
 
-    from_format, to_format = args
+    class ParseCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Shows parse of BEL script."
+            usage    "[OPTIONS]... parse [OPTIONS]"
+
+            opt      :bel,       'The BEL script to parse and output. If not provided the default is to read from standard in (STDIN).',
+                     :type    => String,
+                     :long    => :bel,
+                     :short   => :b,
+                     :default => nil
+          end
 
-    from = BEL::Extension::Format.formatters(from_format)
-    unless from
-      from_format ?
-        (raise %Q{The format "#{from_format}" is not available.}) :
-        (raise "The from_format argument was not specified.")
+        if parsed_options[:bel]
+          ARGV.concat(['--bel', parsed_options[:bel]])
+        else
+          Trollop::educate if !ARGV.empty?
+        end
+
+        require_relative 'bel_parse'
+      end
     end
-    to   = BEL::Extension::Format.formatters(to_format)
-    unless to
-      to_format ?
-        (raise %Q{The format "#{to_format}" is not available."}) :
-        (raise "The to_format argument was not specified.")
+
+    class RdfschemaCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Outputs the RDFS (e.g. RDF Schema) for BEL."
+            usage    "[OPTIONS]... rdfschema [OPTIONS]"
+
+            opt      :format,    'The RDF format to output.',
+                     :type    => String,
+                     :long    => :format,
+                     :short   => :f,
+                     :default => 'ntriples'
+          end
+
+        formats = ['nquads', 'ntriples', 'turtle']
+        unless formats.include? parsed_options[:format]
+          fmt = parsed_options[:format]
+          $stderr.puts %Q{Format "#{fmt}" must be one of #{formats.join(' ')}.}
+          $stderr.puts
+          Trollop::educate
+        end
+
+        ARGV.concat(['--format', parsed_options[:format]]) if parsed_options[:format]
+        require_relative 'bel_rdfschema'
+      end
     end
 
-    begin
-      BEL::Format.translate(input_io, from_format, to_format, $stdout)
-    ensure
-      $stdout.close
+    class SummarizeCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Show summary statistics. for knowledge in provided BEL script."
+            usage    "[OPTIONS]... summarize [OPTIONS]"
+
+            opt      :bel,       'The BEL script to parse and output. If not provided the default is to read from standard in (STDIN).',
+                     :type    => String,
+                     :long    => :bel,
+                     :short   => :b,
+                     :default => nil
+          end
+
+        if parsed_options[:bel]
+          ARGV.concat(['--bel', parsed_options[:bel]])
+        else
+          Trollop::educate if !ARGV.empty?
+        end
+
+        require_relative 'bel_summarize'
+      end
     end
-  end
-end
 
+    class TranslateCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def which_io(input_file)
+        case input_file
+        when nil
+          $stdin
+        when '-'
+          $stdin
+        else
+          input_file
+        end
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Translates BEL evidence between file formats."
+            usage    "[OPTIONS]... translate [OPTIONS] FROM_FORMAT TO_FORMAT"
+
+            opt      :'input-file', 'The file containing evidence data to translate. If not specified the default is to read from STDIN.',
+                     :type    => String,
+                     :long    => :'input-file',
+                     :short   => :i,
+                     :default => nil
+          end
+
+        input_io = which_io(parsed_options[:'input-file'])
+
+        if ![$stdin, '-'].include?(input_io)
+          unless File.readable?(input_io)
+            $stderr.puts %Q{File "#{input_io}" is not readable.}
+            $stderr.puts
+            Trollop::educate
+          end
+        end
+
+        unless ARGV.size == 2
+          $stderr.puts %Q{Formats were not provided.}
+          $stderr.puts
+          Trollop::educate
+        end
 
-# Command: upgrade
-# ----------------
-desc      'Upgrades BEL knowledge and annotation.'
-long_desc <<-LONGDESC
-  Upgrades BEL knowledge, including annotations ane namespaces, by applying changelog file. A changelog file is published with new resource versions to allow for the upgrade.
-LONGDESC
-command :upgrade do |c|
-  c.flag [:b, :bel],
-    :desc          => 'The BEL script to parse.'
-  c.flag [:c, :changelog],
-    :desc     => 'The changelog JSON file or URL.',
-    :required => true
-  c.action do |global_options,options,args|
-    ARGV.clear.concat([
-      '--changelog', options[:changelog]
-    ])
-    bel_io = which_io(options[:bel])
-    if bel_io != $stdin
-      ARGV.concat(['--bel', bel_io])
+        from_format, to_format = ARGV
+
+        from = BEL::Extension::Format.formatters(from_format)
+        unless from
+          $stderr.puts(
+            from_format ?
+              %Q{The format "#{from_format}" is not available.} :
+              "The from_format argument was not specified."
+          )
+          $stderr.puts
+          Trollop::educate
+        end
+
+        to   = BEL::Extension::Format.formatters(to_format)
+        unless to
+          $stderr.puts(
+            to_format ?
+              %Q{The format "#{to_format}" is not available."} :
+              "The to_format argument was not specified."
+          )
+          $stderr.puts
+          Trollop::educate
+        end
+
+        begin
+          BEL::Format.translate(input_io, from_format, to_format, $stdout)
+        ensure
+          $stdout.close
+        end
+      end
     end
 
-    require_relative 'bel_upgrade'
+    class UpgradeCommand
+
+      def initialize(global_options)
+        @global_options = global_options
+      end
+
+      def run
+        parsed_options =
+          Trollop::options do
+            synopsis "Upgrades BEL knowledge and annotation."
+            usage    "[OPTIONS]... upgrade [OPTIONS]"
+
+            opt      :bel,       'The BEL script to parse and output. If not provided the default is to read from standard in (STDIN).',
+                     :type    => String,
+                     :long    => :bel,
+                     :short   => :b,
+                     :default => nil
+
+            opt      :changelog, 'The changelog JSON file or URL.',
+                     :type    => String,
+                     :long    => :changelog,
+                     :short   => :c,
+                     :default => 'http://resource.belframework.org/belframework/latest-release/change_log.json'
+          end
+
+        if parsed_options[:bel]
+          ARGV.concat(['--bel', parsed_options[:bel]])
+        else
+          Trollop::educate if !ARGV.empty?
+        end
+
+        ARGV.concat(['--changelog', parsed_options[:changelog]])
+
+        require_relative 'bel_upgrade'
+      end
+    end
   end
 end
 
-exit run(ARGV)
+def find_subcommands_in_module(mod)
+  mod.constants.map(&:to_s).select { |constant|
+    constant.end_with?('Command')
+  }.map { |cmd|
+    cmd.sub(/Command$/, '').downcase
+  }
+end
+
+# Run bel command
+bel_command     = BEL::Commands::BelCommand.new(
+  find_subcommands_in_module(BEL::Commands) - ['bel']
+)
+bel_command.run
+
+global_options  = bel_command.global_options
+
+# Run subcommand
+sub_command     = ARGV.shift
+sub_class       = :"#{sub_command.capitalize}Command"
+if BEL::Commands.const_defined?(sub_class)
+  BEL::Commands.const_get(sub_class).new(global_options).run
+else
+  $stderr.puts "error: The command #{sub_command} is not valid.\n\n"
+  Trollop::educate
+end