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}"),
  :default => :user
})
STANDARD_SEARCH = 
%w(current workflow user local global lib fast cache bulk)
SLASH = 
"/"[0]
DOT = 
"."[0]

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 87

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

#original ⇒ Object

Returns the value of attribute original.



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# File 'lib/rbbt/resource/path.rb', line 5

def original
  @original
end

#pkgdir ⇒ Object

Returns the value of attribute pkgdir.



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# File 'lib/rbbt/resource/path.rb', line 5

def pkgdir
  @pkgdir
end

#resource ⇒ Object

Returns the value of attribute resource.



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# File 'lib/rbbt/resource/path.rb', line 5

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 5

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 5

def search_paths
  @search_paths
end

Class Method Details

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



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

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

  file = File.expand_path(file)
  return Path.setup(file) if File.exist? File.join(file, relative_to)

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

    return Path.setup(dir) if File.exist? File.join(dir, relative_to)

    file = File.dirname file
  end

  return nil
end

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



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# File 'lib/rbbt/resource/path.rb', line 7

def self.setup(string, pkgdir = nil, resource = nil, search_paths = nil, search_order = 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
end

Instance Method Details

#[](name, orig = false) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 78

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

#_exists? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/resource/path.rb', line 247

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 26

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 343

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 44

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

#append_search_path(name, dir) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 35

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 287

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 83

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

#directory? ⇒ Boolean

Returns:

  • (Boolean) 


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

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 59

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 376

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

Returns:

  • (Boolean) 


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# File 'lib/rbbt/resource/path.rb', line 251

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

#fields ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 339

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

#filename ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 243

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 122

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

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

  if located?
    @path[key] = self
    return self
  end

  @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 = 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
                     raise "Did not recognize the 'where' tag: #{where}. Options: #{paths.keys}" unless paths.include? where

                     if where == :lib
                       libdir = Path.caller_lib_dir(caller_lib) || "NOLIBDIR"
                     else
                       libdir = "NOLIBDIR"
                     end
                     pwd = FileUtils.pwd
                     path = paths[where]
                     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) #, @pkgdir, @resource, @search_paths

                     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

                   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 216

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 68

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

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



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# File 'lib/rbbt/resource/path.rb', line 225

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

  search_paths.keys.
    collect{|where| Dir.glob(find(where, Path.caller_lib_dir, search_paths))}.
    compact.flatten.collect{|file| File.expand_path(file)}.uniq.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
end

#identifier_file_path ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 349

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 357

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

#in_dir?(dir) ⇒ Boolean

{{{ Methods

Returns:

  • (Boolean) 


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# File 'lib/rbbt/resource/path.rb', line 235

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 323

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

#join(name) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 50

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

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



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# File 'lib/rbbt/resource/path.rb', line 309

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 305

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

#located? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/rbbt/resource/util.rb', line 27

def located?
  self.byte(0) == SLASH or (self.byte(0) == DOT and self.byte(1) == SLASH)
end

#open(options = {}, &block) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 279

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 319

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 331

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 30

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 260

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

  self
end

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



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# File 'lib/rbbt/resource/path.rb', line 327

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 270

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

#replace_extension(new_extension = nil) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 370

def replace_extension(new_extension = nil)
  new_path = self.sub(/\.[^\.\/]{2,4}$/,'')
  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 365

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 386

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 40

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

#to_s ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 239

def to_s
  self.find
end

#to_yaml(*args) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 335

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 301

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 291

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

#tsv_options(options = {}) ⇒ Object 



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# File 'lib/rbbt/resource/path.rb', line 295

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 274

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 313

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