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 = 
"/"[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 



120
121
122
123
124
125
126
127
128
129
130
131
132
 
# File 'lib/rbbt/resource/path.rb', line 120

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 dir if File.exist? File.join(dir, relative_to)

    file = File.dirname file
  end

  return nil
end

.get_extension(path) ⇒ Object 



410
411
412
 
# File 'lib/rbbt/resource/path.rb', line 410

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 



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 || Path.caller_lib_dir
  string
end

Instance Method Details

#[](name, orig = false) ⇒ Object 



111
112
113
114
 
# File 'lib/rbbt/resource/path.rb', line 111

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

#_exists? ⇒ Boolean

Returns:

  • (Boolean) 


282
283
284
 
# File 'lib/rbbt/resource/path.rb', line 282

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 



378
379
380
381
382
 
# File 'lib/rbbt/resource/path.rb', line 378

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 



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

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

#byte(pos) ⇒ Object 



116
117
118
 
# File 'lib/rbbt/resource/path.rb', line 116

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

#directory? ⇒ Boolean

Returns:

  • (Boolean) 


67
68
69
70
 
# File 'lib/rbbt/resource/path.rb', line 67

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

#dirname ⇒ Object 



63
64
65
 
# File 'lib/rbbt/resource/path.rb', line 63

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

#doc_file(relative_to = 'lib') ⇒ Object 



424
425
426
427
428
429
430
431
432
 
# File 'lib/rbbt/resource/path.rb', line 424

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) 


286
287
288
289
290
291
292
293
 
# File 'lib/rbbt/resource/path.rb', line 286

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

#fields ⇒ Object 



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

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

#filename ⇒ Object 



278
279
280
 
# File 'lib/rbbt/resource/path.rb', line 278

def filename
  self.find
end

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



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
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
 
# File 'lib/rbbt/resource/path.rb', line 160

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.obj2digest(key_elems.inspect)
  self.sub!('~/', Etc.getpwuid.dir + '/') if self.include? "~"

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

  if located?
    @path[key] = self
    self.original ||= 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('{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
                 end
  @path[key]
end

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



259
260
261
262
263
264
265
266
 
# File 'lib/rbbt/resource/path.rb', line 259

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 



72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
 
# 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| Path.setup(f, self.resource, self.pkgdir)}

    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 



89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
 
# 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}/, ''))
    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 



384
385
386
387
388
389
390
 
# File 'lib/rbbt/resource/path.rb', line 384

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

#identifier_files ⇒ Object 



392
393
394
395
396
397
398
 
# File 'lib/rbbt/resource/path.rb', line 392

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

#in_dir?(dir) ⇒ Boolean

{{{ Methods

Returns:

  • (Boolean) 


270
271
272
 
# File 'lib/rbbt/resource/path.rb', line 270

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

#index(options = {}) ⇒ Object 



358
359
360
 
# File 'lib/rbbt/resource/path.rb', line 358

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

#join(name) ⇒ Object 



52
53
54
55
56
57
58
59
60
61
 
# 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
        else
          self.annotate File.join(self, name.to_s)
        end
  new.original = File.join(self.original, name.to_s) if self.original
  new
end

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



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

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 



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

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

#open(options = {}, &block) ⇒ Object 



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

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

#pipe_to(cmd, options = {}) ⇒ Object 



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

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

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



366
367
368
 
# File 'lib/rbbt/resource/path.rb', line 366

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 



295
296
297
298
299
300
301
302
303
 
# File 'lib/rbbt/resource/path.rb', line 295

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 



362
363
364
 
# File 'lib/rbbt/resource/path.rb', line 362

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

#read(&block) ⇒ Object 



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

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

#remove_extension(new_extension = nil) ⇒ Object 



405
406
407
 
# File 'lib/rbbt/resource/path.rb', line 405

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

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



414
415
416
417
418
419
420
421
422
 
# File 'lib/rbbt/resource/path.rb', line 414

def replace_extension(new_extension = nil, multiple = false)
  if 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 



400
401
402
403
 
# File 'lib/rbbt/resource/path.rb', line 400

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 



434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
 
# File 'lib/rbbt/resource/path.rb', line 434

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 



274
275
276
 
# File 'lib/rbbt/resource/path.rb', line 274

def to_s
  self.find
end

#to_yaml(*args) ⇒ Object 



370
371
372
 
# File 'lib/rbbt/resource/path.rb', line 370

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

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



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

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

#tsv(*args) ⇒ Object 



326
327
328
 
# File 'lib/rbbt/resource/path.rb', line 326

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

#tsv_options(options = {}) ⇒ Object 



330
331
332
333
334
 
# File 'lib/rbbt/resource/path.rb', line 330

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

#write(*args, &block) ⇒ Object 



309
310
311
 
# File 'lib/rbbt/resource/path.rb', line 309

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

#yaml ⇒ Object 



348
349
350
351
352
 
# File 'lib/rbbt/resource/path.rb', line 348

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