scout-gear 9.1.0 → 10.0.1

data/lib/scout/resource/produce.rb

@@ -1,151 +0,0 @@
-require_relative '../open'
-require_relative '../tmpfile'
-require_relative 'produce/rake'
-
-module Resource
-  def claim(path, type, content = nil, &block)
-    if type == :rake
-      @rake_dirs ||= {}
-      @rake_dirs[path] = content || block
-    else
-      @resources ||= {}
-      @resources[path] = [type, content || block]
-    end
-  end
-
-  def rake_for(path)
-    @rake_dirs ||= {}
-    @rake_dirs.select{|dir, content|
-      Misc.path_relative_to(dir, path)
-    }.sort_by{|dir, content|
-      dir.length
-    }.last
-  end
-
-  def has_rake(path)
-    !! rake_for(path)
-  end
-
-  def run_rake(path, rakefile, rake_dir)
-    task = Misc.path_relative_to rake_dir, path
-    rakefile = rakefile.produce if rakefile.respond_to? :produce
-    rakefile = rakefile.find if rakefile.respond_to? :find
-
-    rake_dir = rake_dir.find(:user) if rake_dir.respond_to? :find
-
-    begin
-      if Proc === rakefile
-        ScoutRake.run(nil, rake_dir, task, &rakefile)
-      else
-        ScoutRake.run(rakefile, rake_dir, task)
-      end
-    rescue ScoutRake::TaskNotFound
-      if rake_dir.nil? or rake_dir.empty? or rake_dir == "/" or rake_dir == "./"
-        raise $! 
-      end
-      task = File.join(File.basename(rake_dir), task)
-      rake_dir = File.dirname(rake_dir)
-      retry
-    end
-  end
-
-  def produce(path, force = false)
-    case
-    when (@resources && @resources.include?(path))
-      type, content = @resources[path]
-    when (Path === path && @resources && @resources.include?(path.original))
-      type, content = @resources[path.original]
-    when has_rake(path)
-      type = :rake
-      rake_dir, content = rake_for(path)
-      rake_dir = Path.setup(rake_dir.dup, self.pkgdir, self)
-    else
-      if path !~ /\.(gz|bgz)$/
-        begin
-          produce(path.annotate(path + '.gz'), force)
-        rescue ResourceNotFound
-          begin
-            produce(path.annotate(path + '.bgz'), force)
-          rescue ResourceNotFound
-            raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
-          end
-        end
-      else
-        raise ResourceNotFound, "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
-      end
-    end
-
-    if path.respond_to?(:find) 
-      final_path = force ? path.find(:default) : path.find
-    else
-      final_path = path
-    end
-
-    if type and not File.exist?(final_path) or force
-      Log.medium "Producing: (#{self.to_s}) #{ final_path }"
-      lock_filename = TmpFile.tmp_for_file(final_path, :dir => lock_dir)
-
-      Open.lock lock_filename do
-        FileUtils.rm_rf final_path if force and File.exist? final_path
-
-        if ! File.exist?(final_path) || force 
-
-          begin
-            case type
-            when :string
-              Open.sensible_write(final_path, content)
-            when :csv
-              raise "TSV/CSV Not implemented yet"
-              #require 'rbbt/tsv/csv'
-              #tsv = TSV.csv Open.open(content)
-              #Open.sensible_write(final_path, tsv.to_s)
-            when :url
-              options = {}
-              options[:noz] = true if Open.gzip?(final_path) || Open.bgzip?(final_path) || Open.zip?(final_path)
-              Open.sensible_write(final_path, Open.open(content, options))
-            when :proc
-              data = case content.arity
-                     when 0
-                       content.call
-                     when 1
-                       content.call final_path
-                     end
-              case data
-              when String, IO, StringIO
-                Open.sensible_write(final_path, data) 
-              when Array
-                Open.sensible_write(final_path, data * "\n")
-              when TSV
-                Open.sensible_write(final_path, data.dumper_stream) 
-              when TSV::Dumper
-                Open.sensible_write(final_path, data.stream) 
-              when nil
-              else
-                raise "Unkown object produced: #{Log.fingerprint data}"
-              end
-            when :rake
-              run_rake(path, content, rake_dir)
-            when :install
-              software_dir = self.root.software
-              name = File.basename(path)
-              Resource.install(content, name, software_dir)
-              set_software_env(software_dir)
-            else
-              raise "Could not produce #{ resource }. (#{ type }, #{ content })"
-            end
-          rescue
-            FileUtils.rm_rf final_path if File.exist? final_path
-            raise $!
-          end
-        end
-      end
-    end
-
-    # After producing a file, make sure we recheck all locations, the file
-    # might have appeared with '.gz' extension for instance
-    path.instance_variable_set("@path", {})
-
-    path
-  end
-
-end

data/lib/scout/resource/scout.rb

@@ -1,3 +0,0 @@
-module Scout
-  extend Resource
-end

data/lib/scout/resource/software.rb

@@ -1,178 +0,0 @@
-module Resource
-
-  def self.install_helpers
-    File.expand_path(Scout.share.software.install_helpers.find(:lib))
-  end
-
-  def self.install(content, name, software_dir = Path.setup('software'), &block)
-    software_dir ||= Path.setup('software')
-    software_dir = software_dir.find(:user) if Path === software_dir
-
-    content = block if block_given?
-
-    preamble = <<-EOF
-#!/bin/bash
-
-SOFTWARE_DIR="#{software_dir}"
-
-INSTALL_HELPER_FILE="#{install_helpers}"
-source "$INSTALL_HELPER_FILE"
-    EOF
-
-    content = content.call if Proc === content
-
-    name = content[:name] if Hash === content && content.include?(:name)
-    content = 
-      if content =~ /git:|\.git$/
-        {:git => content}
-      else
-        {:src => content}
-      end if String === content and Open.remote?(content)
-
-      script_text = 
-        case content
-        when nil
-          raise "No way to install #{name}"
-        when Path
-          Open.read(content) 
-        when String
-          if Path.is_filename?(content) and Open.exists?(content)
-            Open.read(content) 
-          else
-            content
-          end
-        when Hash
-          name = content[:name] || name
-          git = content[:git]
-          src = content[:src]
-          url = content[:url]
-          jar = content[:jar]
-          extra = content[:extra]
-          commands = content[:commands]
-          if git
-            <<-EOF
-
-name='#{name}'
-url='#{git}'
-
-install_git "$name" "$url" #{extra}
-
-#{commands}
-            EOF
-          elsif src
-            <<-EOF
-
-name='#{name}'
-url='#{src}'
-
-install_src "$name" "$url" #{extra}
-
-#{commands}
-            EOF
-          elsif jar
-            <<-EOF
-
-name='#{name}'
-url='#{jar}'
-
-install_jar "$name" "$url" #{extra}
-
-#{commands}
-            EOF
-          else
-            <<-EOF
-
-name='#{name}'
-url='#{url}'
-
-#{commands}
-            EOF
-          end
-        end
-
-      script = preamble + "\n" + script_text
-      Log.debug "Installing software #{name} into #{software_dir} with script:\n" << script
-      CMD.cmd_log('bash', :in => script)
-      Resource.set_software_env(software_dir)
-  end
-
-  def self.set_software_env(software_dir = Path.setup('software'))
-    software_dir.opt.find_all.collect{|d| d.annotate(File.dirname(d)) }.reverse.each do |software_dir|
-      next unless software_dir.exists?
-      Log.medium "Preparing software env at #{software_dir}"
-
-      software_dir = File.expand_path(software_dir)
-      opt_dir = File.join(software_dir, 'opt')
-      bin_dir = File.join(opt_dir, 'bin')
-
-      Misc.env_add 'PATH', bin_dir
-
-      FileUtils.mkdir_p opt_dir unless File.exist? opt_dir
-
-      %w(.ld-paths .c-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
-        filename = File.join(opt_dir, file)
-        begin
-          FileUtils.touch filename unless File.exist? filename
-        rescue
-          Log.warn("Could not touch #{ filename }")
-        end
-      end
-
-      Open.read(File.join opt_dir, '.c-paths').split(/\n/).each do |line|
-        dir = line.chomp
-        dir = File.join(opt_dir, dir) unless dir[0] == "/"
-        Misc.env_add('CPLUS_INCLUDE_PATH',dir)
-        Misc.env_add('C_INCLUDE_PATH',dir)
-      end if File.exist? File.join(opt_dir, '.c-paths')
-
-      Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
-        dir = line.chomp
-        dir = File.join(opt_dir, dir) unless dir[0] == "/"
-        Misc.env_add('LIBRARY_PATH',dir)
-        Misc.env_add('LD_LIBRARY_PATH',dir)
-        Misc.env_add('LD_RUN_PATH',dir)
-      end if File.exist? File.join(opt_dir, '.ld-paths')
-
-      Open.read(File.join opt_dir, '.pkgconfig-paths').split(/\n/).each do |line|
-        dir = line.chomp
-        dir = File.join(opt_dir, dir) unless dir[0] == "/"
-        Misc.env_add('PKG_CONFIG_PATH',dir)
-      end if File.exist? File.join(opt_dir, '.pkgconfig-paths')
-
-      Open.read(File.join opt_dir, '.aclocal-paths').split(/\n/).each do |line|
-        dir = line.chomp
-        dir = File.join(opt_dir, dir) unless dir[0] == "/"
-        Misc.env_add('ACLOCAL_FLAGS', "-I #{dir}", ' ')
-      end if File.exist? File.join(opt_dir, '.aclocal-paths')
-
-      Open.read(File.join opt_dir, '.java-classpaths').split(/\n/).each do |line|
-        dir = line.chomp
-        dir = File.join(opt_dir, dir) unless dir[0] == "/"
-        Misc.env_add('CLASSPATH', "#{dir}")
-      end if File.exist? File.join(opt_dir, '.java-classpaths')
-
-      Dir.glob(File.join opt_dir, 'jars', '*.jar').each do |file|
-        Misc.env_add('CLASSPATH', "#{file}")
-      end
-
-      if File.exist?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))
-        Dir.glob(File.join(opt_dir, '.post_install','*')).each do |file|
-
-          # Load exports
-          Open.read(file).split("\n").each do |line|
-            next unless line =~ /^\s*export\s+([^=]+)=(.*)/
-            var = $1.strip
-            value = $2.strip
-            value.sub!(/^['"]/,'')
-            value.sub!(/['"]$/,'')
-            value.gsub!(/\$[a-z_0-9]+/i){|var| ENV[var[1..-1]] }
-            Log.debug "Set variable export from .post_install: #{Log.fingerprint [var,value]*"="}"
-            ENV[var] = value
-          end
-        end
-      end
-    end
-  end
-
-  self.set_software_env
-end

data/lib/scout/resource/util.rb

@@ -1,59 +0,0 @@
-module Resource
-  def identify(path)
-    return path unless path.start_with?("/")
-    path_maps = path.path_maps if Path === path
-    path_maps ||= self.path_maps || Path.path_maps
-    path = File.expand_path(path)
-    path += "/" if File.directory?(path)
-
-    map_order ||= (path_maps.keys & Path.basic_map_order) + (path_maps.keys - Path.basic_map_order)
-    map_order -= [:current, "current"]
-
-    choices = []
-    map_order.uniq.each do |name|
-      pattern = path_maps[name]
-      pattern = path_maps[pattern] while Symbol === pattern
-      next if pattern.nil?
-
-      pattern = pattern.sub('{PWD}', Dir.pwd)
-      pattern = pattern.sub('{HOME}', ENV["HOME"])
-      if String ===  pattern and pattern.include?('{')
-        regexp = "^" + pattern
-          .gsub(/{(TOPLEVEL)}/,'(?<\1>[^/]+)')
-          .gsub(/{([^}]+)}/,'(?<\1>[^/]+)?') +
-        "(?:/(?<REST>.*))?/?$"
-        if m = path.match(regexp) 
-          if ! m.named_captures.include?("PKGDIR") || m["PKGDIR"] == self.pkgdir
-            unlocated = %w(TOPLEVEL SUBPATH PATH REST).collect{|c| 
-              m.named_captures.include?(c) ? m[c] : nil
-            }.compact * "/"
-            unlocated.gsub!(/\/+/,'/')
-            if self.subdir && ! self.subdir.empty?
-              subdir = self.subdir
-              subdir += "/" unless subdir.end_with?("/")
-              unlocated[subdir] = "" 
-            end
-            choices << self.annotate(unlocated)
-          end
-        end
-      end
-    end
-
-    identified = choices.sort_by{|s| s.length }.first
-
-    Path.setup(identified || path, self, nil, path_maps)
-  end
-
-  def self.identify(path)
-    resource = path.pkgdir if Path === path
-    resource = Scout unless Resource === resource
-    unlocated = resource.identify path
-  end
-
-  def self.relocate(path)
-    return path if Open.exists?(path)
-    unlocated = identify(path)
-    unlocated.find
-  end
-end
-

data/lib/scout/resource.rb

@@ -1,41 +0,0 @@
-require_relative 'log'
-require_relative 'path'
-require_relative 'resource/produce'
-require_relative 'resource/path'
-require_relative 'resource/open'
-require_relative 'resource/util'
-require_relative 'resource/software'
-
-module Resource
-  extend MetaExtension
-  extension_attr :pkgdir, :libdir, :subdir, :resources, :rake_dirs, :path_maps, :lock_dir
-
-  def self.default_lock_dir
-    Path.setup('tmp/produce_locks').find
-  end
-
-  def subdir
-    @subdir ||= ""
-  end
-
-  def lock_dir
-    @lock_dir ||= Resource.default_lock_dir
-  end
-
-  def pkgdir
-    @pkgdir ||= Path.default_pkgdir
-  end
-
-  def root
-    Path.setup(subdir, self, self.libdir, @path_maps)
-  end
-
-  def method_missing(name, prev = nil, *args)
-    if prev.nil?
-      root.send(name, *args)
-    else
-      root.send(name, prev, *args)
-    end
-  end
-end
-

data/lib/scout/simple_opt/accessor.rb

@@ -1,54 +0,0 @@
-module SOPT
-  class << self
-    attr_writer :inputs, :input_shortcuts, :input_types, :input_descriptions, :input_defaults
-  end
-
-  def self.all
-    @all ||= {}
-  end
-
-  def self.shortcuts
-    @shortcuts ||= {}
-  end
-  
-  def self.inputs 
-    @inputs ||= []
-  end
-
-  def self.input_shortcuts 
-    @input_shortcuts ||= {}
-  end
-
-  def self.input_types 
-    @input_types ||= {}
-  end
-
-  def self.input_descriptions 
-    @input_descriptions ||= {}
-  end
-
-  def self.input_defaults 
-    @input_defaults ||= {}
-  end
-
-  def self.reset
-    @shortcuts = {}
-    @all = {}
-  end
-
-  def self.delete_inputs(inputs)
-    inputs.each do |input|
-      input = input.to_s
-      self.shortcuts.delete self.input_shortcuts.delete(input)
-      self.inputs.delete input
-      self.input_types.delete input
-      self.input_defaults.delete input
-      self.input_descriptions.delete input
-    end
-  end
-
-  def self.usage
-    puts SOPT.doc
-    exit 0
-  end
-end

data/lib/scout/simple_opt/doc.rb

@@ -1,126 +0,0 @@
-require_relative '../log'
-module SOPT
-
-  class << self
-    attr_writer :command, :summary, :synopsys, :description
-  end
-
-  def self.command
-    @command ||= File.basename($0)
-  end
-
-  def self.summary
-    @summary ||= ""
-  end
-
-  def self.synopsys
-    @synopsys ||= begin
-                    "#{command} " <<
-                    inputs.collect{|name|
-                      "[" << input_format(name, input_types[name] || :string, input_defaults[name], input_shortcuts[name]).sub(/:$/,'') << "]"
-                    } * " "
-                  end
-  end
-
-  def self.description
-    @description ||= "Missing"
-  end
-
-  def self.input_format(name, type = nil, default = nil, short = nil)
-    input_str = (short.nil? or short.empty?) ? "--#{name}" : "-#{short},--#{name}"
-    input_str = Log.color(:blue, input_str)
-    extra = case type
-    when nil
-      ""
-    when :boolean
-      "[=false]" 
-    when :tsv, :text
-      "=<file|->"
-    when :array
-      "=<list|file|->"
-    else
-      "=<#{ type }>"
-    end
-    #extra << " (default: #{Array === default ? (default.length > 3 ? default[0..2]*", " + ', ...' : default*", " ): default})" if default != nil
-    extra << " (default: #{Log.fingerprint(default)})" if default != nil
-    input_str << Log.color(:green, extra)
-  end
-
-  def self.input_array_doc(input_array)
-    input_array.collect do |name,type,description,default,options|
-      type = :string if type.nil?
-
-      name = name.to_s
-      shortcut, options = options, nil if String === options || Symbol === options
-
-      case options && options[:shortcut]
-      when FalseClass
-        shortcut = nil
-      when TrueClass, nil
-        shortcut = fix_shortcut(name[0], name)
-      else
-        shortcut = options[:shortcut]
-      end unless shortcut
-
-      shortcut = fix_shortcut(shortcut, name)
-      register(shortcut, name, type, description) unless self.inputs.include? name
-      name  = SOPT.input_format(name, type.to_sym, default, shortcut ) 
-      Misc.format_definition_list_item(name, description)
-    end * "\n"
-  end
-
-  def self.input_doc(inputs, input_types = nil, input_descriptions = nil, input_defaults = nil, input_shortcuts = nil)
-    type = description = default = nil
-    shortcut = ""
-    seen = []
-    inputs.collect do |name|
-      next if seen.include? name
-      seen << name
-
-      type = input_types[name] unless input_types.nil?
-      description = input_descriptions[name] unless input_descriptions.nil?
-      default = input_defaults[name] unless input_defaults.nil?
-
-      name = name.to_s
-
-      case input_shortcuts
-      when nil, FalseClass
-        shortcut = nil
-      when Hash
-        shortcut = input_shortcuts[name] 
-      when TrueClass
-        shortcut = fix_shortcut(name[0], name)
-      end
-
-      type = :string if type.nil?
-      register(shortcut, name, type, description) unless self.inputs.include? name
-
-      name  = SOPT.input_format(name, type.to_sym, default, shortcut) 
-      Misc.format_definition_list_item(name, description)
-    end * "\n"
-  end
-
-
-  def self.doc
-    doc =<<-EOF
-#{Log.color :magenta}#{command}(1) -- #{summary}
-#{"=" * (command.length + summary.length + 7)}#{Log.color :reset}
-
-    EOF
-
-    if synopsys and not synopsys.empty?
-      doc << Log.color(:magenta, "## SYNOPSYS") << "\n\n"
-      doc << Log.color(:blue, synopsys) << "\n\n"
-    end
-
-    if description and not description.empty?
-      doc << Log.color(:magenta, "## DESCRIPTION") << "\n\n"
-      doc << Misc.format_paragraph(description) << "\n\n"
-    end
-
-    doc << Log.color(:magenta, "## OPTIONS") << "\n\n"
-    doc << input_doc(inputs, input_types, input_descriptions, input_defaults, input_shortcuts)
-
-    doc
-  end
-end

data/lib/scout/simple_opt/get.rb

@@ -1,57 +0,0 @@
-module SOPT
-  GOT_OPTIONS= IndiferentHash.setup({})
-  def self.current_options=(options)
-    @@current_options = options
-  end
-  def self.consume(args = ARGV)
-    i = 0
-    @@current_options ||= {}
-    while i < args.length do
-      current = args[i]
-      break if current == "--"
-      if m = current.match(/--?(.+?)(?:=(.+))?$/)
-        key = $1
-        value = $2
-
-        input = inputs.include?(key)? key : shortcuts[key]
-
-        if input.nil?
-          i += 1
-          next
-        else
-          args.delete_at i
-        end
-      else
-        i += 1
-        next
-      end
-
-      if input_types[input] == :string
-        value = args.delete_at(i) if value.nil?
-        @@current_options[input] = value
-      else
-        if value.nil? and %w(F false FALSE no).include?(args[i])
-          Log.warn "Boolean values are best specified as #{current}=[true|false], not #{ current } [true|false]. Token '#{args[i]}' following '#{current}' automatically assigned as value" 
-          value = args.delete_at(i)
-        end
-        @@current_options[input] = %w(F false FALSE no).include?(value)? false : true
-      end
-    end
-
-    IndiferentHash.setup @@current_options
-    GOT_OPTIONS.merge! @@current_options
-
-    @@current_options
-  end
-  
-  def self.get(opt_str)
-    SOPT.parse(opt_str)
-    SOPT.consume(ARGV)
-  end
-
-  def self.require(options, *parameters)
-    parameters.flatten.each do |parameter|
-      raise ParameterException, "Parameter '#{ Log.color :blue, parameter }' not given" if options[parameter].nil?
-    end
-  end
-end