Module: Resource

Extended by:
Annotation
Included in:
Scout
Defined in:
lib/scout/resource.rb,
lib/scout/resource/util.rb,
lib/scout/resource/produce.rb,
lib/scout/resource/software.rb

Class Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Annotation

extended, is_annotated?, purge, setup

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(name, prev = nil, *args) ⇒ Object 



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# File 'lib/scout/resource.rb', line 45

def method_missing(name, prev = nil, *args)
  if prev.nil?
    root.send(name, *args)
  else
    root.send(name, prev, *args)
  end
end

Class Attribute Details

.default_resource ⇒ Object

Returns the value of attribute default_resource.



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# File 'lib/scout/resource.rb', line 14

def default_resource
  @default_resource
end

Class Method Details

.default_lock_dir ⇒ Object 



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# File 'lib/scout/resource.rb', line 21

def self.default_lock_dir
  Path.setup('tmp/produce_locks').find
end

.identify(path) ⇒ Object 



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# File 'lib/scout/resource/util.rb', line 52

def self.identify(path)
  resource = path.pkgdir if Path === path
  resource = Resource.default_resource unless Resource === resource
  unlocated = resource.identify path
end

.install(content, name, software_dir = Path.setup('software'), &block) ⇒ Object 



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# File 'lib/scout/resource/software.rb', line 7

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

.install_helpers ⇒ Object 



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# File 'lib/scout/resource/software.rb', line 3

def self.install_helpers
  File.expand_path(Scout.share.software.install_helpers.find(:lib))
end

.relocate(path) ⇒ Object 



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# File 'lib/scout/resource/util.rb', line 58

def self.relocate(path)
  return path if Open.exists?(path)
  unlocated = identify(path)
  unlocated.find
end

.set_software_env(software_dir = Path.setup('software')) ⇒ Object 



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# File 'lib/scout/resource/software.rb', line 99

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

Instance Method Details

#claim(path, type, content = nil, &block) ⇒ Object 



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# File 'lib/scout/resource/produce.rb', line 6

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

#has_rake(path) ⇒ Object 



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# File 'lib/scout/resource/produce.rb', line 25

def has_rake(path)
  !! rake_for(path)
end

#identify(path) ⇒ Object 



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# File 'lib/scout/resource/util.rb', line 2

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(/\.{(PKGDIR)}/,'\.(?<\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

#lock_dir ⇒ Object 



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# File 'lib/scout/resource.rb', line 33

def lock_dir
  @lock_dir ||= Resource.default_lock_dir
end

#path_maps ⇒ Object 



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# File 'lib/scout/resource.rb', line 25

def path_maps
  @path_maps ||= Path.path_maps.dup
end

#pkgdir ⇒ Object 



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# File 'lib/scout/resource.rb', line 37

def pkgdir
  @pkgdir ||= Path.default_pkgdir
end

#produce(path, force = false) ⇒ Object 



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# File 'lib/scout/resource/produce.rb', line 52

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

#rake_for(path) ⇒ Object 



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# File 'lib/scout/resource/produce.rb', line 16

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

#root ⇒ Object 



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# File 'lib/scout/resource.rb', line 41

def root
  Path.setup(subdir.dup, self, self.libdir, @path_maps, @map_order)
end

#run_rake(path, rakefile, rake_dir) ⇒ Object 



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# File 'lib/scout/resource/produce.rb', line 29

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

#subdir ⇒ Object 



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# File 'lib/scout/resource.rb', line 29

def subdir
  @subdir ||= ""
end