search_biomodel 1.0.0 → 1.0.1

data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/lib.rb

@@ -1,719 +0,0 @@
-require 'tempfile'
-
-module Git
-  
-  class GitExecuteError < StandardError 
-  end
-  
-  class Lib
-      
-    def initialize(base = nil, logger = nil)
-      @git_dir = nil
-      @git_index_file = nil
-      @git_work_dir = nil
-      @path = nil
-      
-      if base.is_a?(Git::Base)
-        @git_dir = base.repo.path
-        @git_index_file = base.index.path if base.index
-        @git_work_dir = base.dir.path if base.dir
-      elsif base.is_a?(Hash)
-        @git_dir = base[:repository]
-        @git_index_file = base[:index] 
-        @git_work_dir = base[:working_directory]
-      end
-      @logger = logger
-    end
-    
-    def init
-      command('init')
-    end
-    
-    # tries to clone the given repo
-    #
-    # returns {:repository} (if bare)
-    #         {:working_directory} otherwise
-    #
-    # accepts options:
-    #  :remote:: name of remote (rather than 'origin')
-    #  :bare::   no working directory
-    #  :depth::  the number of commits back to pull
-    # 
-    # TODO - make this work with SSH password or auth_key
-    #
-    def clone(repository, name, opts = {})
-      @path = opts[:path] || '.'
-      clone_dir = opts[:path] ? File.join(@path, name) : name
-      
-      arr_opts = []
-      arr_opts << "--bare" if opts[:bare]
-      arr_opts << "-o" << opts[:remote] if opts[:remote]
-      arr_opts << "--depth" << opts[:depth].to_i if opts[:depth] && opts[:depth].to_i > 0
-
-      arr_opts << '--'
-      arr_opts << repository
-      arr_opts << clone_dir
-      
-      command('clone', arr_opts)
-      
-      opts[:bare] ? {:repository => clone_dir} : {:working_directory => clone_dir}
-    end
-    
-    
-    ## READ COMMANDS ##
-    
-    
-    def log_commits(opts = {})
-      arr_opts = ['--pretty=oneline']
-      arr_opts << "-#{opts[:count]}" if opts[:count]
-      arr_opts << "--since=#{opts[:since]}" if opts[:since].is_a? String
-      arr_opts << "--until=#{opts[:until]}" if opts[:until].is_a? String
-      arr_opts << "--grep=#{opts[:grep]}" if opts[:grep].is_a? String
-      arr_opts << "--author=#{opts[:author]}" if opts[:author].is_a? String
-      arr_opts << "#{opts[:between][0].to_s}..#{opts[:between][1].to_s}" if (opts[:between] && opts[:between].size == 2)
-      arr_opts << opts[:object] if opts[:object].is_a? String
-      arr_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
-
-      command_lines('log', arr_opts, true).map { |l| l.split.first }
-    end
-    
-    def full_log_commits(opts = {})
-      arr_opts = ['--pretty=raw']
-      arr_opts << "-#{opts[:count]}" if opts[:count]
-      arr_opts << "--skip=#{opts[:skip]}" if opts[:skip]
-      arr_opts << "--since=#{opts[:since]}" if opts[:since].is_a? String
-      arr_opts << "--until=#{opts[:until]}" if opts[:until].is_a? String
-      arr_opts << "--grep=#{opts[:grep]}" if opts[:grep].is_a? String
-      arr_opts << "--author=#{opts[:author]}" if opts[:author].is_a? String
-      arr_opts << "#{opts[:between][0].to_s}..#{opts[:between][1].to_s}" if (opts[:between] && opts[:between].size == 2)
-      arr_opts << opts[:object] if opts[:object].is_a? String
-      arr_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
-      
-      full_log = command_lines('log', arr_opts, true)
-      process_commit_data(full_log)
-    end
-    
-    def revparse(string)
-      return string if string =~ /[A-Fa-f0-9]{40}/  # passing in a sha - just no-op it
-      rev = ['head', 'remotes', 'tags'].map do |d|
-        File.join(@git_dir, 'refs', d, string)
-      end.find do |path|
-        File.file?(path)
-      end
-      return File.read(rev).chomp if rev
-      command('rev-parse', string)
-    end
-    
-    def namerev(string)
-      command('name-rev', string).split[1]
-    end
-    
-    def object_type(sha)
-      command('cat-file', ['-t', sha])
-    end
-    
-    def object_size(sha)
-      command('cat-file', ['-s', sha]).to_i
-    end
-    
-    # returns useful array of raw commit object data
-    def commit_data(sha)
-      sha = sha.to_s
-      cdata = command_lines('cat-file', ['commit', sha])
-      process_commit_data(cdata, sha, 0)
-    end
-    
-    def process_commit_data(data, sha = nil, indent = 4)
-      in_message = false
-            
-      if sha
-        hsh = {'sha' => sha, 'message' => '', 'parent' => []}
-      else
-        hsh_array = []        
-      end
-    
-      data.each do |line|
-        line = line.chomp
-        if line == ''
-          in_message = !in_message
-        elsif in_message
-          hsh['message'] << line[indent..-1] << "\n"
-        else
-          data = line.split
-          key = data.shift
-          value = data.join(' ')
-          if key == 'commit'
-            sha = value
-            hsh_array << hsh if hsh
-            hsh = {'sha' => sha, 'message' => '', 'parent' => []}
-          end
-          if key == 'parent'
-            hsh[key] << value
-          else
-            hsh[key] = value
-          end
-        end
-      end
-      
-      if hsh_array
-        hsh_array << hsh if hsh
-        hsh_array
-      else
-        hsh
-      end
-    end
-    
-    def object_contents(sha, &block)
-      command('cat-file', ['-p', sha], &block)
-    end
-
-    def ls_tree(sha)
-      data = {'blob' => {}, 'tree' => {}}
-      
-      command_lines('ls-tree', sha).each do |line|
-        (info, filenm) = line.split("\t")
-        (mode, type, sha) = info.split
-        data[type][filenm] = {:mode => mode, :sha => sha}
-      end
-      
-      data
-    end
-
-    def mv(file1, file2)
-      command_lines('mv', ['--', file1, file2])
-    end
-        
-    def full_tree(sha)
-      command_lines('ls-tree', ['-r', sha])
-    end
-            
-    def tree_depth(sha)
-      full_tree(sha).size
-    end
-
-    def change_head_branch(branch_name)
-      command('symbolic-ref', ['HEAD', "refs/heads/#{branch_name}"])
-    end
-    
-    def branches_all
-      arr = []
-      command_lines('branch', '-a').each do |b| 
-        current = (b[0, 2] == '* ')
-        arr << [b.gsub('* ', '').strip, current]
-      end
-      arr
-    end
-
-    def list_files(ref_dir)
-      dir = File.join(@git_dir, 'refs', ref_dir)
-      files = []
-      Dir.chdir(dir) { files = Dir.glob('**/*').select { |f| File.file?(f) } } rescue nil
-      files
-    end
-    
-    def branch_current
-      branches_all.select { |b| b[1] }.first[0] rescue nil
-    end
-
-
-    # returns hash
-    # [tree-ish] = [[line_no, match], [line_no, match2]]
-    # [tree-ish] = [[line_no, match], [line_no, match2]]
-    def grep(string, opts = {})
-      opts[:object] ||= 'HEAD'
-
-      grep_opts = ['-n']
-      grep_opts << '-i' if opts[:ignore_case]
-      grep_opts << '-v' if opts[:invert_match]
-      grep_opts << '-e'
-      grep_opts << string
-      grep_opts << opts[:object] if opts[:object].is_a?(String)
-      grep_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
-
-      hsh = {}
-      command_lines('grep', grep_opts).each do |line|
-        if m = /(.*)\:(\d+)\:(.*)/.match(line)        
-          hsh[m[1]] ||= []
-          hsh[m[1]] << [m[2].to_i, m[3]] 
-        end
-      end
-      hsh
-    end
-    
-    def diff_full(obj1 = 'HEAD', obj2 = nil, opts = {})
-      diff_opts = ['-p']
-      diff_opts << obj1
-      diff_opts << obj2 if obj2.is_a?(String)
-      diff_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
-
-      command('diff', diff_opts)
-    end
-    
-    def diff_stats(obj1 = 'HEAD', obj2 = nil, opts = {})
-      diff_opts = ['--numstat']
-      diff_opts << obj1
-      diff_opts << obj2 if obj2.is_a?(String)
-      diff_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
-
-      hsh = {:total => {:insertions => 0, :deletions => 0, :lines => 0, :files => 0}, :files => {}}
-      
-      command_lines('diff', diff_opts).each do |file|
-        (insertions, deletions, filename) = file.split("\t")
-        hsh[:total][:insertions] += insertions.to_i
-        hsh[:total][:deletions] += deletions.to_i
-        hsh[:total][:lines] = (hsh[:total][:deletions] + hsh[:total][:insertions])
-        hsh[:total][:files] += 1
-        hsh[:files][filename] = {:insertions => insertions.to_i, :deletions => deletions.to_i}
-      end
-            
-      hsh
-    end
-
-    # compares the index and the working directory
-    def diff_files
-      hsh = {}
-      command_lines('diff-files').each do |line|
-        (info, file) = line.split("\t")
-        (mode_src, mode_dest, sha_src, sha_dest, type) = info.split
-        hsh[file] = {:path => file, :mode_file => mode_src.to_s[1, 7], :mode_index => mode_dest, 
-                      :sha_file => sha_src, :sha_index => sha_dest, :type => type}
-      end
-      hsh
-    end
-    
-    # compares the index and the repository
-    def diff_index(treeish)
-      hsh = {}
-      command_lines('diff-index', treeish).each do |line|
-        (info, file) = line.split("\t")
-        (mode_src, mode_dest, sha_src, sha_dest, type) = info.split
-        hsh[file] = {:path => file, :mode_repo => mode_src.to_s[1, 7], :mode_index => mode_dest, 
-                      :sha_repo => sha_src, :sha_index => sha_dest, :type => type}
-      end
-      hsh
-    end
-            
-    def ls_files(location=nil)
-      hsh = {}
-      command_lines('ls-files', ['--stage', location]).each do |line|
-        (info, file) = line.split("\t")
-        (mode, sha, stage) = info.split
-        file = eval(file) if file =~ /^\".*\"$/ # This takes care of quoted strings returned from git
-        hsh[file] = {:path => file, :mode_index => mode, :sha_index => sha, :stage => stage}
-      end
-      hsh
-    end
-
-
-    def ignored_files
-      command_lines('ls-files', ['--others', '-i', '--exclude-standard'])
-    end
-
-
-    def config_remote(name)
-      hsh = {}
-      config_list.each do |key, value|
-        if /remote.#{name}/.match(key)
-          hsh[key.gsub("remote.#{name}.", '')] = value
-        end
-      end
-      hsh
-    end
-
-    def config_get(name)
-      do_get = lambda do
-        command('config', ['--get', name])
-      end
-
-      if @git_dir
-        Dir.chdir(@git_dir, &do_get)
-      else
-        build_list.call
-      end
-    end
-
-    def global_config_get(name)
-      command('config', ['--global', '--get', name], false)
-    end
-    
-    def config_list
-      build_list = lambda do |path|
-        parse_config_list command_lines('config', ['--list'])
-      end
-      
-      if @git_dir
-        Dir.chdir(@git_dir, &build_list)
-      else
-        build_list.call
-      end
-    end
-
-    def global_config_list
-      parse_config_list command_lines('config', ['--global', '--list'], false)
-    end
-    
-    def parse_config_list(lines)
-      hsh = {}
-      lines.each do |line|
-        (key, *values) = line.split('=')
-        hsh[key] = values.join('=')
-      end
-      hsh
-    end
-
-    def parse_config(file)
-      hsh = {}
-      parse_config_list command_lines('config', ['--list', '--file', file], false)
-      #hsh = {}
-      #file = File.expand_path(file)
-      #if File.file?(file)
-      #  current_section = nil
-      #  File.readlines(file).each do |line|
-      #    if m = /\[(\w+)\]/.match(line)
-      #      current_section = m[1]
-      #    elsif m = /\[(\w+?) "(.*?)"\]/.match(line)
-      #      current_section = "#{m[1]}.#{m[2]}"
-      #    elsif m = /(\w+?) = (.*)/.match(line)
-      #      key = "#{current_section}.#{m[1]}"
-      #      hsh[key] = m[2] 
-      #    end
-      #  end
-      #end
-      #hsh
-    end
-    
-    ## WRITE COMMANDS ##
-        
-    def config_set(name, value)
-      command('config', [name, value])
-    end
-
-    def global_config_set(name, value)
-      command('config', ['--global', name, value], false)
-    end
-          
-    def add(path = '.')
-      arr_opts = ['--']
-      if path.is_a?(Array)
-        arr_opts += path
-      else
-        arr_opts << path
-      end
-      command('add', arr_opts)
-    end
-    
-    def remove(path = '.', opts = {})
-      arr_opts = ['-f']  # overrides the up-to-date check by default
-      arr_opts << ['-r'] if opts[:recursive]
-      arr_opts << '--'
-      if path.is_a?(Array)
-        arr_opts += path
-      else
-        arr_opts << path
-      end
-
-      command('rm', arr_opts)
-    end
-
-    def commit(message, opts = {})
-      arr_opts = ['-m', message]
-      arr_opts << '-a' if opts[:add_all]
-      arr_opts << '--allow-empty' if opts[:allow_empty]
-      arr_opts << "--author" << opts[:author] if opts[:author]
-      command('commit', arr_opts)
-    end
-
-    def reset(commit, opts = {})
-      arr_opts = []
-      arr_opts << '--hard' if opts[:hard]
-      arr_opts << commit if commit
-      command('reset', arr_opts)
-    end
-    
-    def apply(patch_file)
-      arr_opts = []
-      arr_opts << '--' << patch_file if patch_file
-      command('apply', arr_opts)
-    end
-    
-    def apply_mail(patch_file)
-      arr_opts = []
-      arr_opts << '--' << patch_file if patch_file
-      command('am', arr_opts)
-    end
-    
-    def stashes_all
-      arr = []
-      filename = File.join(@git_dir, 'logs/refs/stash')
-      if File.exist?(filename)
-        File.open(filename).each_with_index { |line, i|
-          m = line.match(/:(.*)$/)
-          arr << [i, m[1].strip]
-        }
-      end
-      arr
-    end
-    
-    def stash_save(message)
-      output = command('stash save', ['--', message])
-      output =~ /HEAD is now at/
-    end
-
-    def stash_apply(id = nil)
-      if id
-        command('stash apply', [id])
-      else
-        command('stash apply')
-      end
-    end
-    
-    def stash_clear
-      command('stash clear')
-    end
-    
-    def stash_list
-      command('stash list')
-    end
-    
-    def branch_new(branch)
-      command('branch', branch)
-    end
-    
-    def branch_delete(branch)
-      command('branch', ['-D', branch])
-    end
-    
-    def checkout(branch, opts = {})
-      arr_opts = []
-      arr_opts << '-f' if opts[:force]
-      arr_opts << '-b' << opts[:new_branch] if opts[:new_branch]
-      arr_opts << branch
-      
-      command('checkout', arr_opts)
-    end
-
-    def checkout_file(version, file)
-      arr_opts = []
-      arr_opts << version
-      arr_opts << file
-      command('checkout', arr_opts)
-    end
-    
-    def merge(branch, message = nil)      
-      arr_opts = []
-      arr_opts << '-m' << message if message
-      arr_opts += [branch]
-      command('merge', arr_opts)
-    end
-
-    def unmerged
-      unmerged = []
-      command_lines('diff', ["--cached"]).each do |line|
-        unmerged << $1 if line =~ /^\* Unmerged path (.*)/
-      end
-      unmerged
-    end
-
-    def conflicts # :yields: file, your, their
-      self.unmerged.each do |f|
-        your = Tempfile.new("YOUR-#{File.basename(f)}").path
-        command('show', ":2:#{f}", true, "> #{escape your}") 
-
-        their = Tempfile.new("THEIR-#{File.basename(f)}").path
-        command('show', ":3:#{f}", true, "> #{escape their}") 
-        yield(f, your, their)
-      end
-    end
-
-    def remote_add(name, url, opts = {})
-      arr_opts = ['add']
-      arr_opts << '-f' if opts[:with_fetch]
-      arr_opts << '--'
-      arr_opts << name
-      arr_opts << url
-      
-      command('remote', arr_opts)
-    end
-    
-    # this is documented as such, but seems broken for some reason
-    # i'll try to get around it some other way later
-    def remote_remove(name)
-      command('remote', ['rm', '--', name])
-    end
-    
-    def remotes
-      command_lines('remote')
-    end
-
-    def tags
-      command_lines('tag')
-    end
-
-    def tag(tag)
-      command('tag', tag)
-    end
-
-    
-    def fetch(remote)
-      command('fetch', remote)
-    end
-    
-    def push(remote, branch = 'master', tags = false)
-      command('push', [remote, branch])
-      command('push', ['--tags', remote]) if tags
-    end
-    
-    def tag_sha(tag_name)
-      head = File.join(@git_dir, 'refs', 'tags', tag_name)
-      return File.read(head).chomp if File.exists?(head)
-      
-      command('show-ref',  ['--tags', '-s', tag_name])
-    end  
-    
-    def repack
-      command('repack', ['-a', '-d'])
-    end
-    
-    def gc
-      command('gc', ['--prune', '--aggressive', '--auto'])
-    end
-    
-    # reads a tree into the current index file
-    def read_tree(treeish, opts = {})
-      arr_opts = []
-      arr_opts << "--prefix=#{opts[:prefix]}" if opts[:prefix]
-      arr_opts += [treeish]
-      command('read-tree', arr_opts)
-    end
-    
-    def write_tree
-      command('write-tree')
-    end
-    
-    def commit_tree(tree, opts = {})
-      opts[:message] ||= "commit tree #{tree}"
-      t = Tempfile.new('commit-message')
-      t.write(opts[:message])
-      t.close
-      
-      arr_opts = []
-      arr_opts << tree
-      arr_opts << '-p' << opts[:parent] if opts[:parent]
-      arr_opts += [opts[:parents]].map { |p| ['-p', p] }.flatten if opts[:parents]
-      command('commit-tree', arr_opts, true, "< #{escape t.path}")
-    end
-    
-    def update_ref(branch, commit)
-      command('update-ref', [branch, commit])
-    end
-    
-    def checkout_index(opts = {})
-      arr_opts = []
-      arr_opts << "--prefix=#{opts[:prefix]}" if opts[:prefix]
-      arr_opts << "--force" if opts[:force]
-      arr_opts << "--all" if opts[:all]
-      arr_opts << '--' << opts[:path_limiter] if opts[:path_limiter].is_a? String
-
-      command('checkout-index', arr_opts)
-    end
-    
-    # creates an archive file
-    #
-    # options
-    #  :format  (zip, tar)
-    #  :prefix
-    #  :remote
-    #  :path
-    def archive(sha, file = nil, opts = {})
-      opts[:format] ||= 'zip'
-      
-      if opts[:format] == 'tgz'
-        opts[:format] = 'tar' 
-        opts[:add_gzip] = true
-      end
-      
-      file ||= Tempfile.new('archive').path
-      
-      arr_opts = []
-      arr_opts << "--format=#{opts[:format]}" if opts[:format]
-      arr_opts << "--prefix=#{opts[:prefix]}" if opts[:prefix]
-      arr_opts << "--remote=#{opts[:remote]}" if opts[:remote]
-      arr_opts << sha
-      arr_opts << '--' << opts[:path] if opts[:path]
-      command('archive', arr_opts, true, (opts[:add_gzip] ? '| gzip' : '') + " > #{escape file}")
-      return file
-    end
-
-    # returns the current version of git, as an Array of Fixnums.
-    def current_command_version
-      output = command('version', [], false)
-      version = output[/\d+\.\d+(\.\d+)+/]
-      version.split('.').collect {|i| i.to_i}
-    end
-
-    def required_command_version
-      [1, 6, 0, 0]
-    end
-
-    def meets_required_version?
-      current_version  = self.current_command_version
-      required_version = self.required_command_version
-
-      return current_version[0] >= required_version[0] && 
-             current_version[1] >= required_version[1] &&
-             (current_version[2] ? current_version[2] >= required_version[2] : true) &&
-             (current_version[3] ? current_version[3] >= required_version[3] : true)
-    end
-
-
-    private
-    
-    def command_lines(cmd, opts = [], chdir = true, redirect = '')
-      command(cmd, opts, chdir).split("\n")
-    end
-    
-    def command(cmd, opts = [], chdir = true, redirect = '', &block)
-      ENV['GIT_DIR'] = @git_dir
-      ENV['GIT_INDEX_FILE'] = @git_index_file
-      ENV['GIT_WORK_TREE'] = @git_work_dir
-      path = @git_work_dir || @git_dir || @path
-
-      opts = [opts].flatten.map {|s| escape(s) }.join(' ')
-      git_cmd = "git #{cmd} #{opts} #{redirect} 2>&1"
-
-      out = nil
-      if chdir && (Dir.getwd != path)
-        Dir.chdir(path) { out = run_command(git_cmd, &block) } 
-      else
-        out = run_command(git_cmd, &block)
-      end
-      
-      if @logger
-        @logger.info(git_cmd)
-        @logger.debug(out)
-      end
-            
-      if $?.exitstatus > 0
-        if $?.exitstatus == 1 && out == ''
-          return ''
-        end
-        raise Git::GitExecuteError.new(git_cmd + ':' + out.to_s) 
-      end
-      out
-    end
-    
-    def run_command(git_cmd, &block)
-      if block_given?
-        IO.popen(git_cmd, &block)
-      else
-        `#{git_cmd}`.chomp
-      end
-    end
-
-    def escape(s)
-      escaped = s.to_s.gsub('\'', '\'\\\'\'')
-      %Q{"#{escaped}"}
-    end
-
-  end
-end