search_biomodel 0.1.2 → 1.0.0

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/classic_namespace.rb

@@ -0,0 +1,9 @@
+# The following classes used to be in the top level namespace.
+# Loading this file enables compatibility with older Rakefile that
+# referenced Task from the top level.
+
+warn "WARNING: Classic namespaces are deprecated and will be removed from future versions of Rake."
+Task = Rake::Task
+FileTask = Rake::FileTask
+FileCreationTask = Rake::FileCreationTask
+RakeApp = Rake::Application

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/clean.rb

@@ -0,0 +1,31 @@
+# The 'rake/clean' file defines two file lists (CLEAN and CLOBBER) and
+# two rake tasks (:clean and :clobber).
+#
+# [:clean] Clean up the project by deleting scratch files and backup
+#          files.  Add files to the CLEAN file list to have the :clean
+#          target handle them.
+#
+# [:clobber] Clobber all generated and non-source files in a project.
+#            The task depends on :clean, so all the clean files will
+#            be deleted as well as files in the CLOBBER file list.
+#            The intent of this task is to return a project to its
+#            pristine, just unpacked state.
+
+require 'rake'
+
+CLEAN = Rake::FileList["**/*~", "**/*.bak", "**/core"]
+CLEAN.clear_exclude.exclude { |fn|
+  fn.pathmap("%f") == 'core' && File.directory?(fn)
+}
+
+desc "Remove any temporary products."
+task :clean do
+  CLEAN.each { |fn| rm_r fn rescue nil }
+end
+
+CLOBBER = Rake::FileList.new
+
+desc "Remove any generated file."
+task :clobber => [:clean] do
+  CLOBBER.each { |fn| rm_r fn rescue nil }
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/cloneable.rb

@@ -0,0 +1,25 @@
+module Rake
+  # ##########################################################################
+  # Mixin for creating easily cloned objects.
+  #
+  module Cloneable
+    # Clone an object by making a new object and setting all the instance
+    # variables to the same values.
+    def dup
+      sibling = self.class.new
+      instance_variables.each do |ivar|
+        value = self.instance_variable_get(ivar)
+        new_value = value.clone rescue value
+        sibling.instance_variable_set(ivar, new_value)
+      end
+      sibling.taint if tainted?
+      sibling
+    end
+
+    def clone
+      sibling = dup
+      sibling.freeze if frozen?
+      sibling
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/contrib/compositepublisher.rb

@@ -0,0 +1,21 @@
+module Rake
+
+  # Manage several publishers as a single entity.
+  class CompositePublisher
+    def initialize
+      @publishers = []
+    end
+
+    # Add a publisher to the composite.
+    def add(pub)
+      @publishers << pub
+    end
+
+    # Upload all the individual publishers.
+    def upload
+      @publishers.each { |p| p.upload }
+    end
+  end
+
+end
+

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/contrib/ftptools.rb

@@ -0,0 +1,150 @@
+# = Tools for FTP uploading.
+#
+# This file is still under development and is not released for general
+# use.
+
+require 'date'
+require 'net/ftp'
+
+module Rake # :nodoc:
+
+  ####################################################################
+  # <b>Note:</b> <em> Not released for general use.</em>
+  class FtpFile
+    attr_reader :name, :size, :owner, :group, :time
+
+    def self.date
+      @date_class ||= Date
+    end
+
+    def self.time
+      @time_class ||= Time
+    end
+
+    def initialize(path, entry)
+      @path = path
+      @mode, _, @owner, @group, size, d1, d2, d3, @name = entry.split(' ')
+      @size = size.to_i
+      @time = determine_time(d1, d2, d3)
+    end
+
+    def path
+      File.join(@path, @name)
+    end
+
+    def directory?
+      @mode[0] == ?d
+    end
+
+    def mode
+      parse_mode(@mode)
+    end
+
+    def symlink?
+      @mode[0] == ?l
+    end
+
+    private # --------------------------------------------------------
+
+    def parse_mode(m)
+      result = 0
+      (1..9).each do |i|
+        result = 2*result + ((m[i]==?-) ? 0 : 1)
+      end
+      result
+    end
+
+    def determine_time(d1, d2, d3)
+      now = self.class.time.now
+      if /:/ =~ d3
+        result = Time.parse("#{d1} #{d2} #{now.year} #{d3}")
+        if result > now
+          result = Time.parse("#{d1} #{d2} #{now.year-1} #{d3}")
+        end
+      else
+        result = Time.parse("#{d1} #{d2} #{d3}")
+      end
+      result
+#       elements = ParseDate.parsedate("#{d1} #{d2} #{d3}")
+#       if elements[0].nil?
+#         today = self.class.date.today
+#         if elements[1] > today.month
+#           elements[0] = today.year - 1
+#         else
+#           elements[0] = today.year
+#         end
+#       end
+#       elements = elements.collect { |el| el.nil? ? 0 : el }
+#       Time.mktime(*elements[0,7])
+    end
+  end
+
+  ####################################################################
+  # Manage the uploading of files to an FTP account.
+  class FtpUploader
+
+    # Log uploads to standard output when true.
+    attr_accessor :verbose
+
+    class << FtpUploader
+      # Create an uploader and pass it to the given block as +up+.
+      # When the block is complete, close the uploader.
+      def connect(path, host, account, password)
+        up = self.new(path, host, account, password)
+        begin
+          yield(up)
+        ensure
+          up.close
+        end
+      end
+    end
+
+    # Create an FTP uploader targeting the directory +path+ on +host+
+    # using the given account and password.  +path+ will be the root
+    # path of the uploader.
+    def initialize(path, host, account, password)
+      @created = Hash.new
+      @path = path
+      @ftp = Net::FTP.new(host, account, password)
+      makedirs(@path)
+      @ftp.chdir(@path)
+    end
+
+    # Create the directory +path+ in the uploader root path.
+    def makedirs(path)
+      route = []
+      File.split(path).each do |dir|
+        route << dir
+        current_dir = File.join(route)
+        if @created[current_dir].nil?
+          @created[current_dir] = true
+          $stderr.puts "Creating Directory  #{current_dir}" if @verbose
+          @ftp.mkdir(current_dir) rescue nil
+        end
+      end
+    end
+
+    # Upload all files matching +wildcard+ to the uploader's root
+    # path.
+    def upload_files(wildcard)
+      Dir[wildcard].each do |fn|
+        upload(fn)
+      end
+    end
+
+    # Close the uploader.
+    def close
+      @ftp.close
+    end
+
+    private # --------------------------------------------------------
+
+    # Upload a single file to the uploader's root path.
+    def upload(file)
+      $stderr.puts "Uploading #{file}" if @verbose
+      dir = File.dirname(file)
+      makedirs(dir)
+      @ftp.putbinaryfile(file, file) unless File.directory?(file)
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/contrib/publisher.rb

@@ -0,0 +1,69 @@
+# Copyright 2003-2010 by Jim Weirich (jim.weirich@gmail.com)
+# All rights reserved.
+
+# Configuration information about an upload host system.
+# * name   :: Name of host system.
+# * webdir :: Base directory for the web information for the
+#             application.  The application name (APP) is appended to
+#             this directory before using.
+# * pkgdir :: Directory on the host system where packages can be
+#             placed.
+HostInfo = Struct.new(:name, :webdir, :pkgdir)
+
+# Manage several publishers as a single entity.
+class CompositePublisher
+  def initialize
+    @publishers = []
+  end
+
+  # Add a publisher to the composite.
+  def add(pub)
+    @publishers << pub
+  end
+
+  # Upload all the individual publishers.
+  def upload
+    @publishers.each { |p| p.upload }
+  end
+end
+
+# Publish an entire directory to an existing remote directory using
+# SSH.
+class SshDirPublisher
+  def initialize(host, remote_dir, local_dir)
+    @host = host
+    @remote_dir = remote_dir
+    @local_dir = local_dir
+  end
+
+  def upload
+    run %{scp -rq #{@local_dir}/* #{@host}:#{@remote_dir}}
+  end
+end
+
+# Publish an entire directory to a fresh remote directory using SSH.
+class SshFreshDirPublisher < SshDirPublisher
+  def upload
+    run %{ssh #{@host} rm -rf #{@remote_dir}} rescue nil
+    run %{ssh #{@host} mkdir #{@remote_dir}}
+    super
+  end
+end
+
+# Publish a list of files to an existing remote directory.
+class SshFilePublisher
+  # Create a publisher using the give host information.
+  def initialize(host, remote_dir, local_dir, *files)
+    @host = host
+    @remote_dir = remote_dir
+    @local_dir = local_dir
+    @files = files
+  end
+
+  # Upload the local directory to the remote directory.
+  def upload
+    @files.each do |fn|
+      run %{scp -q #{@local_dir}/#{fn} #{@host}:#{@remote_dir}}
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/contrib/rubyforgepublisher.rb

@@ -0,0 +1,16 @@
+require 'rake/contrib/sshpublisher'
+
+module Rake
+
+  class RubyForgePublisher < SshDirPublisher
+    attr_reader :project, :proj_id, :user
+
+    def initialize(projname, user)
+      super(
+        "#{user}@rubyforge.org",
+        "/var/www/gforge-projects/#{projname}",
+        "html")
+    end
+  end
+
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/contrib/sshpublisher.rb

@@ -0,0 +1,45 @@
+require 'rake/contrib/compositepublisher'
+
+module Rake
+
+  # Publish an entire directory to an existing remote directory using
+  # SSH.
+  class SshDirPublisher
+    def initialize(host, remote_dir, local_dir)
+      @host = host
+      @remote_dir = remote_dir
+      @local_dir = local_dir
+    end
+
+    def upload
+      sh %{scp -rq #{@local_dir}/* #{@host}:#{@remote_dir}}
+    end
+  end
+
+  # Publish an entire directory to a fresh remote directory using SSH.
+  class SshFreshDirPublisher < SshDirPublisher
+    def upload
+      sh %{ssh #{@host} rm -rf #{@remote_dir}} rescue nil
+      sh %{ssh #{@host} mkdir #{@remote_dir}}
+      super
+    end
+  end
+
+  # Publish a list of files to an existing remote directory.
+  class SshFilePublisher
+    # Create a publisher using the give host information.
+    def initialize(host, remote_dir, local_dir, *files)
+      @host = host
+      @remote_dir = remote_dir
+      @local_dir = local_dir
+      @files = files
+    end
+
+    # Upload the local directory to the remote directory.
+    def upload
+      @files.each do |fn|
+        sh %{scp -q #{@local_dir}/#{fn} #{@host}:#{@remote_dir}}
+      end
+    end
+  end
+end

data/search_biomodel/ruby/1.8/gems/rake-0.9.2/lib/rake/contrib/sys.rb

@@ -0,0 +1,191 @@
+warn 'Sys has been deprecated in favor of FileUtils'
+
+#--
+# Copyright 2003-2010 by Jim Weirich (jim.weirich@gmail.com)
+# All rights reserved.
+#++
+#
+begin
+  require 'ftools'
+rescue LoadError
+end
+require 'rbconfig'
+
+######################################################################
+# Sys provides a number of file manipulation tools for the convenience
+# of writing Rakefiles.  All commands in this module will announce
+# their activity on standard output if the $verbose flag is set
+# ($verbose = true is the default).  You can control this by globally
+# setting $verbose or by using the +verbose+ and +quiet+ methods.
+#
+# Sys has been deprecated in favor of the FileUtils module available
+# in Ruby 1.8.
+#
+module Sys
+  RUBY = RbConfig::CONFIG['ruby_install_name']
+
+  # Install all the files matching +wildcard+ into the +dest_dir+
+  # directory.  The permission mode is set to +mode+.
+  def install(wildcard, dest_dir, mode)
+    Dir[wildcard].each do |fn|
+      File.install(fn, dest_dir, mode, $verbose)
+    end
+  end
+
+  # Run the system command +cmd+.
+  def run(cmd)
+    log cmd
+    system(cmd) or fail "Command Failed: [#{cmd}]"
+  end
+
+  # Run a Ruby interpreter with the given arguments.
+  def ruby(*args)
+    run "#{RUBY} #{args.join(' ')}"
+  end
+
+  # Copy a single file from +file_name+ to +dest_file+.
+  def copy(file_name, dest_file)
+    log "Copying file #{file_name} to #{dest_file}"
+    File.copy(file_name, dest_file)
+  end
+
+  # Copy all files matching +wildcard+ into the directory +dest_dir+.
+  def copy_files(wildcard, dest_dir)
+    for_matching_files(wildcard, dest_dir) { |from, to| copy(from, to) }
+  end
+
+  # Link +file_name+ to +dest_file+.
+  def link(file_name, dest_file)
+    log "Linking file #{file_name} to #{dest_file}"
+    File.link(file_name, dest_file)
+  end
+
+  # Link all files matching +wildcard+ into the directory +dest_dir+.
+  def link_files(wildcard, dest_dir)
+    for_matching_files(wildcard, dest_dir) { |from, to| link(from, to) }
+  end
+
+  # Symlink +file_name+ to +dest_file+.
+  def symlink(file_name, dest_file)
+    log "Symlinking file #{file_name} to #{dest_file}"
+    File.symlink(file_name, dest_file)
+  end
+
+  # Symlink all files matching +wildcard+ into the directory +dest_dir+.
+  def symlink_files(wildcard, dest_dir)
+    for_matching_files(wildcard, dest_dir) { |from, to| link(from, to) }
+  end
+
+  # Remove all files matching +wildcard+.  If a matching file is a
+  # directory, it must be empty to be removed.  used +delete_all+ to
+  # recursively delete directories.
+  def delete(*wildcards)
+    wildcards.each do |wildcard|
+      Dir[wildcard].each do |fn|
+        if File.directory?(fn)
+          log "Deleting directory #{fn}"
+          Dir.delete(fn)
+        else
+          log "Deleting file #{fn}"
+          File.delete(fn)
+        end
+      end
+    end
+  end
+
+  # Recursively delete all files and directories matching +wildcard+.
+  def delete_all(*wildcards)
+    wildcards.each do |wildcard|
+      Dir[wildcard].each do |fn|
+        next if ! File.exist?(fn)
+        if File.directory?(fn)
+          Dir["#{fn}/*"].each do |subfn|
+            next if subfn=='.' || subfn=='..'
+            delete_all(subfn)
+          end
+          log "Deleting directory #{fn}"
+          Dir.delete(fn)
+        else
+          log "Deleting file #{fn}"
+          File.delete(fn)
+        end
+      end
+    end
+  end
+
+  # Make the directories given in +dirs+.
+  def makedirs(*dirs)
+    dirs.each do |fn|
+      log "Making directory #{fn}"
+      File.makedirs(fn)
+    end
+  end
+
+  # Make +dir+ the current working directory for the duration of
+  # executing the given block.
+  def indir(dir)
+    olddir = Dir.pwd
+    Dir.chdir(dir)
+    yield
+  ensure
+    Dir.chdir(olddir)
+  end
+
+  # Split a file path into individual directory names.
+  #
+  # For example:
+  #   split_all("a/b/c") =>  ['a', 'b', 'c']
+  def split_all(path)
+    head, tail = File.split(path)
+    return [tail] if head == '.' || tail == '/'
+    return [head, tail] if head == '/'
+    return split_all(head) + [tail]
+  end
+
+  # Write a message to standard error if $verbose is enabled.
+  def log(msg)
+    print "  " if $trace && $verbose
+    $stderr.puts msg if $verbose
+  end
+
+  # Perform a block with $verbose disabled.
+  def quiet(&block)
+    with_verbose(false, &block)
+  end
+
+  # Perform a block with $verbose enabled.
+  def verbose(&block)
+    with_verbose(true, &block)
+  end
+
+  # Perform a block with each file matching a set of wildcards.
+  def for_files(*wildcards)
+    wildcards.each do |wildcard|
+      Dir[wildcard].each do |fn|
+        yield(fn)
+      end
+    end
+  end
+
+  extend(self)
+
+  private # ----------------------------------------------------------
+
+  def for_matching_files(wildcard, dest_dir)
+    Dir[wildcard].each do |fn|
+      dest_file = File.join(dest_dir, fn)
+      parent = File.dirname(dest_file)
+      makedirs(parent) if ! File.directory?(parent)
+      yield(fn, dest_file)
+    end
+  end
+
+  def with_verbose(v)
+    oldverbose = $verbose
+    $verbose = v
+    yield
+  ensure
+    $verbose = oldverbose
+  end
+
+end