rbbt 1.2.5 → 2.0.0

data/lib/rbbt/util/open.rb

@@ -1,251 +0,0 @@
-require 'rbbt'
-require 'rbbt/util/tmpfile'
-
-
-# Provides with a few helper functions to read and write files, as well # as
-# for accessing remote files. It supports caching the files.
-module Open
-
-  # Return a Proc to use in the :select parameter of the Open.to_hash method.
-  # It selects those lines with the content of the first field present on the
-  # entities array. The field can be chosen to be a different one in the
-  # options hash, also the separation string or regexp to determine fields.
-  def self.func_match_field(entities, options = {})
-    field, sep = {:field => 0, :sep => "\t"}.merge(options).values_at(:field, :sep)
-
-    Proc.new {|line| entities.include? line.split(sep)[field] }
-  end
-
-  def self.fields(line, sep = "\t")
-    line << sep
-    line << "PLACEHOLDER"
-    chunks = line.split(/(#{sep})/).select{|c| c !~ /^#{sep}$/ }
-    if line =~ /#{sep}$/
-      chunks << ""
-    end
-    chunks.pop
-    chunks
-  end
-
-  class DirectoryNotFoundError < StandardError; end
-  class OpenURLError < StandardError; end
-
-  private 
-
-  @@remote_cachedir =  File.join(Rbbt.cachedir, 'open-remote/')
-  FileUtils.mkdir @@remote_cachedir unless File.exist? @@remote_cachedir
-
-  # If no data is specified and the url is found in the cache the saved
-  # contents are returned, if not found, the url is opened and the contents of
-  # that are returned. If +data+ is specified then it is saved in the
-  # cache under +url+. To match +url+ in the cache a MD5 digest is used.
-  # The location of the cache directory is bu default
-  # File.join(Rbbt.cachedir, 'open-remote/').
-  def self.cache(url, data = nil)
-    require 'digest/md5'
-    digest = Digest::MD5.hexdigest(url)
-
-    if data
-      Open.write(File.join(@@remote_cachedir, digest), data)
-      return nil
-    else
-      if File.exist? File.join(@@remote_cachedir, digest)
-        return File.open(File.join(@@remote_cachedir, digest)){|file| file.read }
-      else
-        return nil
-      end
-    end
-  end
-
-  # Checks if +url+ is a remote file.
-  def self.remote(url)
-    url =~ /^(?:http|ssh|https|ftp):\/\//
-  end
-
-
-  # Checks if +url+ is a gzip file.
-  def self.gziped(url)
-    if remote(url)
-      return url =~ /\.gz$/ || url =~ /\.gz\?.*$/
-    else
-      return url =~ /\.gz$/ 
-    end
-  end
-
-
-  @@last_time = Time.now   
-  def self.wait(lag = 0)
-    time = Time.now   
-
-    if time < @@last_time + lag
-      sleep @@last_time + lag - time
-    end
-
-    @@last_time = Time.now   
-  end
-
-  public
-  # Reads the file specified by url. If the url es local it just opens
-  # the file, if it is remote if checks the cache first. In any case, it
-  # unzips gzip files automatically.
-  #
-  # Options: 
-  # * :quiet    => Do not print the progress of downloads
-  # * :nocache  => do not use the cache.
-  # * :nice     => secconds to wait between online queries
-  #
-  def self.read(url, options = {})
-
-    case
-    when remote(url)
-      if !options[:nocache] && data = cache(url)
-        return data
-      end
-
-      wait(options[:nice]) if options[:nice]
-      tmp = TmpFile.tmp_file("open-")
-      `wget --user-agent=firefox -O #{tmp} '#{url}' #{options[:quiet] ? '-q' : '' }`
-
-      if $?.success?
-        if gziped(url)
-        `mv #{tmp} #{tmp}.gz; gunzip #{tmp}`
-        end
-
-        cache(url, File.open(tmp){|file| file.read}) unless options[:nocache]
-
-        data = File.open(tmp){|file| file.read}
-        FileUtils.rm tmp
-        return data
-      else
-        raise OpenURLError, "Error reading remote url: #{ url }"
-      end
-    
-    when IO === url
-      url.read
-    else
-      return  File.open(url){|file| file.read}
-    end
-
-  end
-
-  # Writes the contents on the path specified by filename
-  #
-  # Options: 
-  # * :force => Create directories if missing.
-  def self.write(filename, content, options = {})
-    if !File.exist? File.dirname(filename) 
-      if options[:force] 
-        FileUtils.makedirs(File.dirname(filename))
-      else
-        raise Open::DirectoryNotFoundError, "Directory #{File.dirname(filename)} was not found"
-      end
-    end
-
-    File.open(filename,'w'){|f|
-      f.write content
-    }
-
-    nil
-  end
-
-  # Writes the contents on the path specified by filename. If the file
-  # is present it appends the contents.
-  #
-  # Options: 
-  # * :force => Create directories if missing.
-  def self.append(filename, content, options ={})
-    if !File.exist? File.dirname(filename) 
-      if options[:force] 
-        FileUtils.makedirs(File.dirname(filename))
-      else
-        raise Open::DirectoryNotFoundError, "Directory #{File.dirname(filename)} was not found"
-      end
-    end
-
-    f = File.open(filename,'a')
-    f.write content
-    f.close
-
-    nil
-  end
-
-
-
-  # Reads a file with rows with elementes separated by a given pattern
-  # and builds a hash with it. The keys of the hash are the elements in
-  # the :native positions, by default the first (0). The value for each
-  # key is an array with one position for each of the rest possible
-  # positions specified in :extra, by default all but the :native. Since
-  # the native key may be repeated, each of the positions of the values
-  # is in itself an array. There are a number of options to change this
-  # behaviour.
-  #
-  # Options:
-  # * :native => position of the elements that will constitute the keys. By default 0.
-  # * :extra => positions of the rest of elements. By default all but :native. It can be an array of positions or a single position.
-  # * :sep =>  pattern to use in splitting the lines into elements, by default "\t"
-  # * :sep2 =>  pattern to use in splitting the elements into subelements, by default "|"
-  # * :flatten => flatten the array of arrays that hold the values for each key into a simple array.
-  # * :single => for each key select only the first of the values, instead of the complete array.
-  # * :fix  => A Proc that is called to pre-process the line
-  # * :exclude => A Proc that is called to check if the line must be excluded from the process.
-  # * :select => A Proc that is called to check if the line must be selected to process.
-  def self.to_hash(input, options = {})
-    native  = options[:native]  || 0
-    extra   = options[:extra]
-    exclude = options[:exclude]
-    select  = options[:select]
-    fix     = options[:fix]
-    sep     = options[:sep]     || "\t"
-    sep2    = options[:sep2]    || "|"
-    single  = options[:single]  
-    single  = false if single.nil?
-    flatten = options[:flatten]
-    flatten = single if flatten.nil?
-
-    extra = [extra] if extra && ! extra.is_a?( Array)
-
-    if StringIO === input
-      content = input
-    else
-      content = Open.read(input)
-    end
-
-    data = {}
-    content.each_line{|l|
-      l = fix.call(l) if fix
-      next if exclude and exclude.call(l)
-      next if select  and ! select.call(l)
-
-      row_fields = self.fields(l.chomp, sep)
-      id = row_fields[native]
-      next if id.nil? || id == ""
-
-      data[id] ||= []
-
-      if extra
-        row_fields = row_fields.values_at(*extra)
-      else
-        row_fields.delete_at(native)
-      end
-
-
-      if flatten
-        data[id] += row_fields.compact.collect{|v| 
-          v.split(sep2)
-        }.flatten
-      else
-        row_fields.each_with_index{|value, i|
-          next if value.nil?
-          data[id][i] ||= []
-          data[id][i] += value.split(sep2)
-        }
-      end
-    }
-
-    data = Hash[*(data.collect{|key,values| [key, values.first]}).flatten] if single
-
-    data
-  end
-
-end

data/lib/rbbt/util/rake.rb

@@ -1,183 +0,0 @@
-require 'rake'
-
-# Include the step_def and step methods to simplify Pipelines. Steps depend on
-# the step strictly above by default. The output of the step is save marshaled,
-# except for Strings which are save as text. The input of the step, the output
-# of the previous step if availabe is accessed with the input method
-#
-# Example::
-#
-#     step :text do 
-#       "Text to revert"
-#     end
-#
-#     step :revert do
-#       text = input
-#       text.reverse
-#     end
-#
-module Rake::Pipeline
-
-  module Rake::Pipeline::Step
-
-    class << self
-
-      @@step_descriptions = {}
-      def step_descriptions
-        @@step_descriptions
-      end
-
-      def add_description(re, step, message)
-        @@step_descriptions[re] = "#{ step }: #{ message }"                       
-      end
-
-      @@last_step = nil
-      def step_def(name, dependencies = nil)
-
-        re = Regexp.new(/(?:^|\/)#{name}\/.*$/)
-
-        # Take the last_description and associate it with the name
-        if Rake.application.last_description
-          add_description(re, name, Rake.application.last_description)
-        end
-
-        if dependencies.nil? && ! @@last_step.nil?
-          dependencies = @@last_step
-        end
-        @@last_step = name
-
-        # Generate the Hash definition
-        case 
-        when dependencies.nil?
-          re
-        when String === dependencies || Symbol === dependencies
-          {re => lambda{|filename| filename.sub(name.to_s,dependencies.to_s) }}
-        when Array === dependencies
-          {re => lambda{|filename| dependencies.collect{|dep| filename.sub(name.to_s, dep.to_s) } }}
-        when Proc === dependencies
-          {re => dependencies}
-        end
-
-      end
-
-    end
-  end
-
-  module Rake::Pipeline::Info
-
-    def self.info_file(filename)
-      filename.sub(/^(.*?)(?:[^\/]*)\/([^\/]*)$/, '\1.info/\2.yaml')
-    end
-
-    def self.load_info(t)
-      filename = t.name
-      info_filename = info_file(filename)
-
-      if File.exists? info_filename
-        YAML.load(File.open(info_filename))
-      else
-        {}
-      end
-    end
-
-    def self.save_info(t, info = {})
-      filename = t.name
-      info_filename = info_file(filename)
-
-      FileUtils.mkdir_p File.dirname(info_filename) unless File.exists? File.dirname(info_filename)
-      File.open(info_filename,'w'){|file|
-        file.write YAML.dump info
-      }
-    end
-
-  end
-
-
-  NON_ASCII_PRINTABLE = /[^\x20-\x7e\s]/
-  def is_binary?(file)
-    binary = file.read(1024) =~ NON_ASCII_PRINTABLE
-    file.rewind
-    binary
-  end
-
-  def step_descriptions
-    Rake::Pipeline::Step.step_descriptions
-  end
-
-
-  def step_def(*args)
-    Rake::Pipeline::Step.step_def(*args)
-  end
-
-  def infile(t, &block)
-    File.open(t.prerequisites.first) do |f|
-      block.call(f)
-    end
-  end
-
-  def outfile(t, &block)
-    File.open(t.name, 'w') do |f|
-      block.call(f)
-    end
-  end
-
-  def load_input(t)
-    return nil if t.prerequisites.first.nil?
-    infile(t){|f| 
-      if is_binary?(f)
-        Marshal.load(f) 
-      else
-        f.read
-      end
-    }
-  end
-
-  def save_output(t, output)
-    case 
-    when output.nil?
-      nil
-    when String === output
-      outfile(t){|f| f.write output } 
-    else
-      outfile(t){|f| f.write Marshal.dump(output) } 
-    end
-
-  end
-
-  # We cannot load the input variable before the block.call, so we need another method
-
-  # Load the input data from the previous step
-  def input
-    load_input(@@current_task) if @@current_task
-  end
-
-  # Add values to the info file
-  def info(values = {})
-    info = Rake::Pipeline::Info.load_info(@@current_task)
-    info = info.merge values
-    Rake::Pipeline::Info.save_info(@@current_task, info)
-    info
-  end
-  
-  
-  # Define a new step, it depends on the previously defined by default. It
-  # saves the output of the block so it can be loaded by the input method of
-  # the next step
-  def step(name, dependencies = nil, &block)
-    rule step_def(name, dependencies) do |t| 
-
-      # Save the task object to be able to load the input
-      @@current_task = t
-      
-      output = block.call(t)
-      
-      save_output(t, output)
-    end
-
-  end
-end
-
-if __FILE__ == $0
-
-  p Rake::Pipeline::Info.info_file('work/diseases/t')
-end

data/lib/rbbt/util/simpleDSL.rb

@@ -1,87 +0,0 @@
-require 'parse_tree_extensions'
-require 'parse_tree'
-require 'ruby2ruby'
-
-# This class helps designing DSL in ruby based on method_missing. Class
-# is initialize with a block of code or a file with the code, and it is
-# given a method to be invoked instead of method missing. This class
-# deals simply with making the method_missing alias and removing it and
-# executing the block of file with code.
-class SimpleDSL
-
-  class ConfigFileMissingError < StandardError; end
-
-  private
-
-  def hook_method(method = nil)
-    method ||= :DSL_action 
-    @@restore_name = ("restore_DSL_" + method.to_s).to_sym
-    @@method_name = method.to_sym
-    
-    class << self
-      @restore_stack ||= []
-      @restore_stack << @@restore_name
-      alias_method(@@restore_name, :method_missing)
-      alias_method(:method_missing, @@method_name)
-    end
-  end
-
-  def unhook_method
-    class << self
-      alias_method(:method_missing, @restore_stack.pop)
-    end
-  end
-
-  public
-
-  def parse(method = nil, actions = nil, &block)
-
-    actions ||= block
-    
-    hook_method(method)
-
-    # Execute
-    if actions.is_a? Proc
-     
-      @config[@@method_name] = actions.to_ruby.collect[1..-2].join
-
-      instance_eval &actions
-    elsif File.exists?(actions)
-
-      @config[@@method_name] = File.open(actions).read
-
-      eval File.open(actions).read
-    end
-
-    unhook_method
-
-  end
-
-
-  # Processes a DSL. +method+ is the name of the method executed instead
-  # of method_missing. The code to be evaluated as a DSL is either
-  # specified in +&block+ or in the file pointed by +file+.
-  def initialize(method = nil, file = nil, &block)
-    @config = {}
-    if file
-      raise ConfigFileMissingError.new "File '#{ file }' is missing. Have you installed the config files? (use rbbt_config)." unless File.exists? file
-      parse(method, file)
-    end
-
-    if block
-      parse(method, block)
-    end
-  end
-
-  # Returns the code with the DSL that was executed. If it came from a
-  # block it was turned to string using ruby2ruby.
-  def config(action = nil)
-    if action
-      @config[action.to_sym]
-    else
-      @config[:DSL_action]
-    end
-  end
-end
-
-