Module: Path

Defined in:
lib/rbbt/resource/path.rb,
lib/rbbt/resource/util.rb

Constant Summary collapse

SEARCH_PATHS = 
IndiferentHash.setup({
  :current => File.join("{PWD}", "{TOPLEVEL}", "{SUBPATH}"),
  :user    => File.join(ENV['HOME'], ".{PKGDIR}", "{TOPLEVEL}", "{SUBPATH}"),
  :global  => File.join('/', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
  :local   => File.join('/usr/local', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
  :fast   => File.join('/fast', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
  :cache   => File.join('/cache', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
  :bulk   => File.join('/bulk', "{TOPLEVEL}", "{PKGDIR}", "{SUBPATH}"),
  :lib     => File.join('{LIBDIR}', "{TOPLEVEL}", "{SUBPATH}"),
  :base   => File.join(caller_lib_dir(__FILE__), "{TOPLEVEL}", "{SUBPATH}"),
  :default => :user
})
STANDARD_SEARCH = 
%w(current workflow user local global lib fast cache bulk)
SLASH = 

      
        
DOT =
          
        

        

      
    

  




  
Instance Attribute Summary collapse

  




  
    

      Class Method Summary
      collapse
    


    
  
    

      Instance Method Summary
      collapse
    


    
  



  
Dynamic Method Handling

  

    This class handles dynamic methods through the method_missing method
    
  

  
    

  

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

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 121

def method_missing(name, prev = nil, *args, &block)
  if block_given?
    super name, prev, *args, &block
  else
    # Fix problem with ruby 1.9 calling methods by its own initiative. ARG
    super(name, prev, *args) if name.to_s =~ /^to_/
    if prev.nil?
      join name
    else
      join(prev).join(name)
    end
  end
end

    		
  





  



  

    
Instance Attribute Details

    
      
      
      

  

  
    #libdir  ⇒ Object 
  

  

  




  

    

Returns the value of attribute libdir.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def libdir
  @libdir
end

    		
  





    
      
      
      

  

  
    #original  ⇒ Object 
  

  

  




  

    

Returns the value of attribute original.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def original
  @original
end

    		
  





    
      
      
      

  

  
    #pkgdir  ⇒ Object 
  

  

  




  

    

Returns the value of attribute pkgdir.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def pkgdir
  @pkgdir
end

    		
  





    
      
      
      

  

  
    #resource  ⇒ Object 
  

  

  




  

    

Returns the value of attribute resource.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def resource
  @resource
end

    		
  





    
      
      
      

  

  
    #search_order  ⇒ Object 
  

  

  




  

    

Returns the value of attribute search_order.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def search_order
  @search_order
end

    		
  





    
      
      
      

  

  
    #search_paths  ⇒ Object 
  

  

  




  

    

Returns the value of attribute search_paths.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def search_paths
  @search_paths
end

    		
  





    
      
      
      

  

  
    #where  ⇒ Object 
  

  

  




  

    

Returns the value of attribute where.



  





  



  

    
      


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# File 'lib/rbbt/resource/path.rb', line 6

def where
  @where
end

    		
  





    
  



  

    
Class Method Details


    
      

  

  
    .caller_lib_dir(file = nil, relative_to = ['lib', 'bin'])  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/util.rb', line 3

def self.caller_lib_dir(file = nil, relative_to = ['lib', 'bin'])
  #file = caller.reject{|l| 
  #  l =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
  #  l =~ /rbbt\/resource\/path\.rb/ or
  #  l =~ /rbbt\/persist.rb/ or
  #  l =~ /rbbt\/util\/misc\.rb/ or
  #  l =~ /progress-monitor\.rb/ 
  #}.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
  
  
  if file.nil?
    caller_dup = caller.dup
    while file = caller_dup.shift
      break unless file =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
        file =~ /rbbt\/resource\/path\.rb/ or
        file =~ /rbbt\/persist.rb/ or
        file =~ /rbbt\/util\/misc\.rb/ or
        file =~ /progress-monitor\.rb/ 
    end
    file = file.sub(/\.rb[^\w].*/,'.rb')
  end

  relative_to = [relative_to] unless Array === relative_to
  file = File.expand_path(file)
  return Path.setup(file) if relative_to.select{|d| File.exist? File.join(file, d)}.any?

  while file != '/'
    dir = File.dirname file

    return dir if relative_to.select{|d| File.exist? File.join(dir, d)}.any?

    file = File.dirname file
  end

  return nil
end

    		
  





    
      

  

  
    .get_extension(path)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 417

def self.get_extension(path)
  path.match(/\.([^\.\/]{1,5})$/)[1]
end

    		
  





    
      

  

  
    .setup(string, pkgdir = nil, resource = nil, search_paths = nil, search_order = nil, libdir = nil)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 8

def self.setup(string, pkgdir = nil, resource = nil, search_paths = nil, search_order = nil, libdir = nil)
  return string if string.nil?
  string = string.dup if string.frozen?
  string.extend Path
  string.pkgdir = pkgdir || 'rbbt'
  string.resource = resource
  string.search_paths = search_paths
  string.search_order = search_order
  string.libdir = libdir || Path.caller_lib_dir 
  string
end

    		
  





    
  


  

    
Instance Method Details


    
      

  

  
    #[](name, orig = false)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 112

def [](name, orig = false)
  return super(name) if orig
  join name
end

    		
  





    
      

  

  
    #_exists?  ⇒ Boolean 
  

  

  




  

    

  





  

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        (Boolean)
      
      
      
    
    • 
  





  

    
      


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# File 'lib/rbbt/resource/path.rb', line 289

def _exists?
  Open.exists? self.find.to_s
end

    		
  





    
      

  

  
    #add_search_path(name, dir)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 28

def add_search_path(name, dir)
  search_paths[name.to_sym] = dir
end

    		
  





    
      

  

  
    #all_fields  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 385

def all_fields
  self.open do |stream|
    TSV.parse_header(stream).all_fields
  end
end

    		
  





    
      

  

  
    #annotate(name)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 46

def annotate(name)
  name = name.to_s
  name = Path.setup name, @pkgdir, @resource, @search_paths, @search_order, @libdir
  name
end

    		
  





    
      

  

  
    #append_search_path(name, dir)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 37

def append_search_path(name, dir)
  add_search_path(name, dir)
  search_order.push(name.to_sym)
end

    		
  





    
      

  

  
    #basename  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 329

def basename
  Path.setup(File.basename(self), self.resource, self.pkgdir)
end

    		
  





    
      

  

  
    #byte(pos)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 117

def byte(pos)
  send(:[], pos, true)
end

    		
  





    
      

  

  
    #clean_annotations  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 465

def clean_annotations
  "" << self.to_s
end

    		
  





    
      

  

  
    #directory?  ⇒ Boolean 
  

  

  




  

    

  





  

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        (Boolean)
      
      
      
    
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# File 'lib/rbbt/resource/path.rb', line 67

def directory?
  return nil unless self.exists?
  File.directory? self.find 
end

    		
  





    
      

  

  
    #dirname  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 63

def dirname
  Path.setup File.dirname(self), @pkgdir, @resource
end

    		
  





    
      

  

  
    #doc_file(relative_to = 'lib')  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 433

def doc_file(relative_to = 'lib')
  if located?
    lib_dir = Path.caller_lib_dir(self, relative_to)
    relative_file = File.join( 'doc', self.sub(lib_dir,''))
    Path.setup File.join(lib_dir, relative_file) , @pkgdir, @resource
  else
    Path.setup File.join('doc', self) , @pkgdir, @resource
  end
end

    		
  





    
      

  

  
    #exists?  ⇒ Boolean 
  

  

  




  

    

  





  

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        (Boolean)
      
      
      
    
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# File 'lib/rbbt/resource/path.rb', line 293

def exists?
  begin
    self.produce
    _exists?
  rescue Exception
    false
  end
end

    		
  





    
      

  

  
    #fields  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 381

def fields
  TSV.parse_header(self.open).fields
end

    		
  





    
      

  

  
    #filename  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 285

def filename
  self.find
end

    		
  





    
      

  

  
    #find(where = nil, caller_lib = nil, paths = nil)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 161

def find(where = nil, caller_lib = nil, paths = nil)

  if located?
    self.original ||= self
    return self
  end

  @path ||= {}
  rsearch_paths = (resource and resource.respond_to?(:search_paths)) ? resource.search_paths : nil 
  key = [where, caller_lib, rsearch_paths, paths].inspect
  self.sub!('~/', Etc.getpwuid.dir + '/') if self.include? "~"

  return @path[key] if @path[key]

  @path[key] ||= begin
                   paths = [paths, rsearch_paths, self.search_paths, SEARCH_PATHS].reverse.compact.inject({}){|acc,h| acc.merge! h; acc }
                   where = paths[:default] if where == :default
                   if self.match(/(.*?)\/(.*)/)
                     toplevel, subpath = self.match(/(.*?)\/(.*)/).values_at 1, 2
                   else
                     toplevel, subpath = "{REMOVE}", self
                   end

                   path = nil
                   search_order = self.search_order || []
                   res = nil
                   if where.nil?

                     (STANDARD_SEARCH - search_order).each do |w| 
                       w = w.to_sym
                       break if res
                       next unless paths.include? w
                       path = find(w, caller_lib, paths)
                       res = path if File.exist? path
                     end

                     search_order.each do |w| 
                       w = w.to_sym
                       next if res
                       next unless paths.include? w
                       path = find(w, caller_lib, paths)
                       res = path if File.exist?(path)
                     end if res.nil?

                     (paths.keys - STANDARD_SEARCH - search_order).each do |w|
                       w = w.to_sym
                       next if res
                       next unless paths.include? w
                       path = find(w, caller_lib, paths)
                       res = path if File.exist? path
                     end if res.nil?

                     if paths.include? :default
                       res = find((paths[:default] || :user), caller_lib, paths)
                     else
                       raise "Path '#{ path }' not found, and no default specified in search paths: #{paths.inspect}"
                     end if res.nil?

                   else
                     where = where.to_sym

                     if paths.include? where
                       path = paths[where]
                     elsif where.to_s.include?("/")
                       path = where.to_s
                     else
                       raise "Did not recognize the 'where' tag: #{where}. Options: #{paths.keys}" unless paths.include? where
                     end

                     if where == :lib 
                       libdir = @libdir || Path.caller_lib_dir(caller_lib) || "NOLIBDIR" 
                     else
                       libdir = "NOLIBDIR"
                     end

                     pwd = FileUtils.pwd
                     path = File.join(path, "{PATH}") unless path.include? "PATH}" or path.include? "{BASENAME}"
                     path = path.
                       sub('{PKGDIR}', pkgdir).
                       sub('{PWD}', pwd).
                       sub('{TOPLEVEL}', toplevel).
                       sub('{SUBPATH}', subpath).
                       sub('{BASENAME}', File.basename(self)).
                       sub('{PATH}', self).
                       sub('{LIBDIR}', libdir).
                       sub('{RESOURCE}', resource.to_s).
                       sub('{REMOVE}/', '').
                       sub('{REMOVE}', '')

                     path = path + '.gz' if File.exist?(path + '.gz')
                     path = path + '.bgz' if File.exist?(path + '.bgz')

                     self.annotate path

                     res = path
                   end

                   res.original = self.original || self
                   res.where = where

                   res
                 end
  @path[key]
end

    		
  





    
      

  

  
    #find_all(caller_lib = nil, search_paths = nil)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 266

def find_all(caller_lib = nil, search_paths = nil)
  search_paths ||= @search_paths || SEARCH_PATHS
  search_paths = search_paths.dup

  search_paths.keys.
    collect{|where| find(where, Path.caller_lib_dir, search_paths) }.
    compact.select{|file| file.exists? }.uniq
end

    		
  





    
      

  

  
    #glob(pattern = '*')  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 72

def glob(pattern = '*')
  if self.include? "*"
    self.glob_all
  else
    return [] unless self.exists? 
    found = self.find
    exp = File.join(found, pattern)
    paths = Dir.glob(exp).collect{|f| self.annotate(f) }

    paths.each do |p|
      p.original = File.join(found.original, p.sub(/^#{found}/, ''))
    end if found.original

    paths
  end
end

    		
  





    
      

  

  
    #glob_all(pattern = nil, caller_lib = nil, search_paths = nil)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 89

def glob_all(pattern = nil, caller_lib = nil, search_paths = nil)
  search_paths ||= @search_paths || SEARCH_PATHS
  search_paths = search_paths.dup

  location_paths = {}
  search_paths.keys.collect do |where| 
    found = find(where, Path.caller_lib_dir, search_paths)
    paths = pattern ? Dir.glob(File.join(found, pattern)) : Dir.glob(found) 

    paths = paths.collect{|p| self.annotate p }

    paths = paths.each do |p|
      p.original = File.join(found.original, p.sub(/^#{found}/, ''))
      p.where = where
    end if found.original and pattern

    location_paths[where] = paths
  end

  #location_paths.values.compact.flatten.collect{|file| File.expand_path(file) }.uniq.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
  location_paths.values.compact.flatten.uniq
end

    		
  





    
      

  

  
    #identifier_file_path  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 391

def identifier_file_path
  if self.dirname.identifiers.exists?
    self.dirname.identifiers
  else
    nil
  end
end

    		
  





    
      

  

  
    #identifier_files  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 399

def identifier_files
  if identifier_file_path.nil?
    []
  else
    [identifier_file_path]
  end
end

    		
  





    
      

  

  
    #in_dir?(dir)  ⇒ Boolean 
  

  

  




  

    

{{{ Methods



  





  

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        (Boolean)
      
      
      
    
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# File 'lib/rbbt/resource/path.rb', line 277

def in_dir?(dir)
  ! ! File.expand_path(self).match(/^#{Regexp.quote dir}/)
end

    		
  





    
      

  

  
    #index(options = {})  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 365

def index(options = {})
  TSV.index(self.produce, options)
end

    		
  





    
      

  

  
    #join(name)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 52

def join(name)
  raise "Invalid path: #{ self }" if self.nil?
  new = if self.empty?
          self.annotate name.to_s.dup.chomp
        else
          self.annotate File.join(self, name.to_s.chomp)
        end
  new.original = File.join(self.original, name.to_s.chomp) if self.original
  new
end

    		
  





    
      

  

  
    #keys(field = 0, sep = "\t")  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 351

def keys(field = 0, sep = "\t")
  Open.read(self.produce.find).split("\n").collect{|l| next if l =~ /^#/; l.split(sep, -1)[field]}.compact
end

    		
  





    
      

  

  
    #list  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 347

def list
  Open.read(self.produce.find).split "\n"
end

    		
  





    
      

  

  
    #located?  ⇒ Boolean 
  

  

  




  

    

  





  

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        (Boolean)
      
      
      
    
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# File 'lib/rbbt/resource/util.rb', line 42

def located?
  self.byte(0) == SLASH || (self.byte(0) == DOT && self.byte(1) == SLASH) || (resource != Rbbt && (Open.remote?(self) || Open.ssh?(self)))
end

    		
  





    
      

  

  
    #open(options = {}, &block)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 321

def open(options = {}, &block)
  Open.open(self.produce.find, options, &block)
end

    		
  





    
      

  

  
    #pipe_to(cmd, options = {})  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 361

def pipe_to(cmd, options = {})
  CMD.cmd(cmd, {:in => self.open, :pipe => true}.merge(options))
end

    		
  





    
      

  

  
    #pos_index(pos, options = {})  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 373

def pos_index(pos, options = {})
  TSV.pos_index(self.produce, pos, options)
end

    		
  





    
      

  

  
    #prepend_search_path(name, dir)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 32

def prepend_search_path(name, dir)
  add_search_path(name, dir)
  search_order.unshift(name.to_sym)
end

    		
  





    
      

  

  
    #produce(force = false)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 302

def produce(force = false)
  return self if _exists? and not force

  raise "No resource defined to produce file: #{ self }" if resource.nil?

  resource.produce self, force if Resource === resource

  self
end

    		
  





    
      

  

  
    #range_index(start, eend, options = {})  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 369

def range_index(start, eend, options = {})
  TSV.range_index(self.produce, start, eend, options)
end

    		
  





    
      

  

  
    #read(&block)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 312

def read(&block)
  Open.read(self.produce.find, &block)
end

    		
  





    
      

  

  
    #remove_extension(new_extension = nil)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 412

def remove_extension(new_extension = nil)
  self.sub(/\.[^\.\/]{1,5}$/,'')
end

    		
  





    
      

  

  
    #replace_extension(new_extension = nil, multiple = false)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 421

def replace_extension(new_extension = nil, multiple = false)
  if String === multiple
    new_path = self.sub(/(\.[^\.\/]{1,5})(.#{multiple})?$/,'')
  elsif multiple
    new_path = self.sub(/(\.[^\.\/]{1,5})+$/,'')
  else
    new_path = self.sub(/\.[^\.\/]{1,5}$/,'')
  end
  new_path = new_path + "." + new_extension.to_s
  self.annotate(new_path)
end

    		
  





    
      

  

  
    #set_extension(new_extension = nil)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 407

def set_extension(new_extension = nil)
  new_path = self + "." + new_extension.to_s
  self.annotate(new_path)
end

    		
  





    
      

  

  
    #source_for_doc_file(relative_to = 'lib')  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 443

def source_for_doc_file(relative_to = 'lib')
  if located?
    lib_dir = Path.caller_lib_dir(Path.caller_lib_dir(self, 'doc'), relative_to)
    relative_file = self.sub(/(.*\/)doc\//, '\1').sub(lib_dir + "/",'')
    file = File.join(lib_dir, relative_file)

    if not File.exist?(file)
      file= Dir.glob(file.sub(/\.[^\.\/]+$/, '.*')).first
    end

    Path.setup file, @pkgdir, @resource
  else
    relative_file = self.sub(/^doc\//, '\1')

    if not File.exist?(relative_file)
      relative_file = Dir.glob(relative_file.sub(/\.[^\.\/]+$/, '.*')).first
    end

    Path.setup relative_file , @pkgdir, @resource
  end
end

    		
  





    
      

  

  
    #sub(*args)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 42

def sub(*args)
  self.annotate super(*args)
end

    		
  





    
      

  

  
    #to_s  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 281

def to_s
  self.find
end

    		
  





    
      

  

  
    #to_yaml(*args)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 377

def to_yaml(*args)
  self.to_s.to_yaml(*args)
end

    		
  





    
      

  

  
    #traverse(options = {}, &block)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 343

def traverse(options = {}, &block)
  TSV::Parser.traverse(self.open, options, &block)
end

    		
  





    
      

  

  
    #tsv(*args)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 333

def tsv(*args)
  TSV.open(self.produce, *args)
end

    		
  





    
      

  

  
    #tsv_options(options = {})  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 337

def tsv_options(options = {})
  self.open do |stream|
    TSV::Parser.new(stream, options).options
  end
end

    		
  





    
      

  

  
    #write(*args, &block)  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 316

def write(*args, &block)
  Open.write(self.produce.find, *args, &block)
end

    		
  





    
      

  

  
    #yaml  ⇒ Object 
  

  

  




  

    
      


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# File 'lib/rbbt/resource/path.rb', line 355

def yaml
  self.open do |f|
    YAML.load f
  end
end