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 



89
90
91
92
93
94
95
96
97
98
99
100
101
 
# File 'lib/rbbt/resource/path.rb', line 89

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.



6
7
8
 
# File 'lib/rbbt/resource/path.rb', line 6

def libdir
  @libdir
end

#original ⇒ Object

Returns the value of attribute original.



6
7
8
 
# File 'lib/rbbt/resource/path.rb', line 6

def original
  @original
end

#pkgdir ⇒ Object

Returns the value of attribute pkgdir.



6
7
8
 
# File 'lib/rbbt/resource/path.rb', line 6

def pkgdir
  @pkgdir
end

#resource ⇒ Object

Returns the value of attribute resource.



6
7
8
 
# File 'lib/rbbt/resource/path.rb', line 6

def resource
  @resource
end

#search_order ⇒ Object

Returns the value of attribute search_order.



6
7
8
 
# File 'lib/rbbt/resource/path.rb', line 6

def search_order
  @search_order
end

#search_paths ⇒ Object

Returns the value of attribute search_paths.



6
7
8
 
# File 'lib/rbbt/resource/path.rb', line 6

def search_paths
  @search_paths
end

Class Method Details

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



3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
 
# 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, libdir = nil) ⇒ Object 



8
9
10
11
12
13
14
15
16
17
18
 
# 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
  string
end

Instance Method Details

#[](name, orig = false) ⇒ Object 



80
81
82
83
 
# File 'lib/rbbt/resource/path.rb', line 80

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

#_exists? ⇒ Boolean

Returns:

  • (Boolean) 


256
257
258
 
# File 'lib/rbbt/resource/path.rb', line 256

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

#add_search_path(name, dir) ⇒ Object 



28
29
30
 
# File 'lib/rbbt/resource/path.rb', line 28

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

#all_fields ⇒ Object 



352
353
354
355
356
 
# File 'lib/rbbt/resource/path.rb', line 352

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

#annotate(name) ⇒ Object 



46
47
48
49
50
 
# 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 



37
38
39
40
 
# 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 



296
297
298
 
# File 'lib/rbbt/resource/path.rb', line 296

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

#byte(pos) ⇒ Object 



85
86
87
 
# File 'lib/rbbt/resource/path.rb', line 85

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

#directory? ⇒ Boolean

Returns:

  • (Boolean) 


65
66
67
68
 
# File 'lib/rbbt/resource/path.rb', line 65

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

#dirname ⇒ Object 



61
62
63
 
# File 'lib/rbbt/resource/path.rb', line 61

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

#doc_file(relative_to = 'lib') ⇒ Object 



385
386
387
388
389
390
391
392
393
 
# File 'lib/rbbt/resource/path.rb', line 385

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) 


260
261
262
263
264
265
266
267
 
# File 'lib/rbbt/resource/path.rb', line 260

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

#fields ⇒ Object 



348
349
350
 
# File 'lib/rbbt/resource/path.rb', line 348

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

#filename ⇒ Object 



252
253
254
 
# File 'lib/rbbt/resource/path.rb', line 252

def filename
  self.find
end

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



128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
 
# File 'lib/rbbt/resource/path.rb', line 128

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

                     if where == :lib 
                       libdir = @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).
                       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

                   res
                 end
  @path[key]
end

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



225
226
227
228
229
230
231
232
 
# File 'lib/rbbt/resource/path.rb', line 225

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 



70
71
72
73
74
75
76
77
78
 
# File 'lib/rbbt/resource/path.rb', line 70

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



234
235
236
237
238
239
240
241
 
# File 'lib/rbbt/resource/path.rb', line 234

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

  search_paths.keys.
    collect{|where| pattern ? Dir.glob(File.join(find(where, Path.caller_lib_dir, search_paths), pattern)) : 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 



358
359
360
361
362
363
364
 
# File 'lib/rbbt/resource/path.rb', line 358

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

#identifier_files ⇒ Object 



366
367
368
369
370
371
372
 
# File 'lib/rbbt/resource/path.rb', line 366

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

#in_dir?(dir) ⇒ Boolean

{{{ Methods

Returns:

  • (Boolean) 


244
245
246
 
# File 'lib/rbbt/resource/path.rb', line 244

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

#index(options = {}) ⇒ Object 



332
333
334
 
# File 'lib/rbbt/resource/path.rb', line 332

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

#join(name) ⇒ Object 



52
53
54
55
56
57
58
59
 
# File 'lib/rbbt/resource/path.rb', line 52

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 



318
319
320
 
# File 'lib/rbbt/resource/path.rb', line 318

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 



314
315
316
 
# File 'lib/rbbt/resource/path.rb', line 314

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

#located? ⇒ Boolean

Returns:

  • (Boolean) 


27
28
29
 
# 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 



288
289
290
 
# File 'lib/rbbt/resource/path.rb', line 288

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

#pipe_to(cmd, options = {}) ⇒ Object 



328
329
330
 
# File 'lib/rbbt/resource/path.rb', line 328

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

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



340
341
342
 
# File 'lib/rbbt/resource/path.rb', line 340

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

#prepend_search_path(name, dir) ⇒ Object 



32
33
34
35
 
# 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 



269
270
271
272
273
274
275
276
277
 
# File 'lib/rbbt/resource/path.rb', line 269

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 



336
337
338
 
# File 'lib/rbbt/resource/path.rb', line 336

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

#read(&block) ⇒ Object 



279
280
281
 
# File 'lib/rbbt/resource/path.rb', line 279

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

#replace_extension(new_extension = nil) ⇒ Object 



379
380
381
382
383
 
# File 'lib/rbbt/resource/path.rb', line 379

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 



374
375
376
377
 
# File 'lib/rbbt/resource/path.rb', line 374

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 



395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
 
# File 'lib/rbbt/resource/path.rb', line 395

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 



42
43
44
 
# File 'lib/rbbt/resource/path.rb', line 42

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

#to_s ⇒ Object 



248
249
250
 
# File 'lib/rbbt/resource/path.rb', line 248

def to_s
  self.find
end

#to_yaml(*args) ⇒ Object 



344
345
346
 
# File 'lib/rbbt/resource/path.rb', line 344

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

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



310
311
312
 
# File 'lib/rbbt/resource/path.rb', line 310

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

#tsv(*args) ⇒ Object 



300
301
302
 
# File 'lib/rbbt/resource/path.rb', line 300

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

#tsv_options(options = {}) ⇒ Object 



304
305
306
307
308
 
# File 'lib/rbbt/resource/path.rb', line 304

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

#write(*args, &block) ⇒ Object 



283
284
285
 
# File 'lib/rbbt/resource/path.rb', line 283

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

#yaml ⇒ Object 



322
323
324
325
326
 
# File 'lib/rbbt/resource/path.rb', line 322

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