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}"),
  :lib     => File.join('{LIBDIR}', "{TOPLEVEL}", "{SUBPATH}"),
  :default => :user
})
STANDARD_SEARCH = 
%w(current user local global lib 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 



61
62
63
64
65
66
67
68
69
70
71
72
73
 
# File 'lib/rbbt/resource/path.rb', line 61

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

#pkgdir ⇒ Object

Returns the value of attribute pkgdir.



5
6
7
 
# File 'lib/rbbt/resource/path.rb', line 5

def pkgdir
  @pkgdir
end

#resource ⇒ Object

Returns the value of attribute resource.



5
6
7
 
# File 'lib/rbbt/resource/path.rb', line 5

def resource
  @resource
end

#search_paths ⇒ Object

Returns the value of attribute search_paths.



5
6
7
 
# 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 



3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
 
# 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?

  return Path.setup(file) if File.exists? File.join(file, relative_to)

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

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

    file = File.dirname file
  end

  return nil
end

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



7
8
9
10
11
12
13
14
 
# File 'lib/rbbt/resource/path.rb', line 7

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

Instance Method Details

#[](name, orig = false) ⇒ Object 



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

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

#_exists? ⇒ Boolean

Returns:

  • (Boolean) 


186
187
188
 
# File 'lib/rbbt/resource/path.rb', line 186

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

#all_fields ⇒ Object 



282
283
284
285
286
 
# File 'lib/rbbt/resource/path.rb', line 282

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

#annotate(name) ⇒ Object 



20
21
22
 
# File 'lib/rbbt/resource/path.rb', line 20

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

#basename ⇒ Object 



226
227
228
 
# File 'lib/rbbt/resource/path.rb', line 226

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

#byte(pos) ⇒ Object 



57
58
59
 
# File 'lib/rbbt/resource/path.rb', line 57

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

#directory? ⇒ Boolean

Returns:

  • (Boolean) 


37
38
39
40
 
# File 'lib/rbbt/resource/path.rb', line 37

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

#dirname ⇒ Object 



33
34
35
 
# File 'lib/rbbt/resource/path.rb', line 33

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

#doc_file(relative_to = 'lib') ⇒ Object 



309
310
311
312
313
314
315
316
317
 
# File 'lib/rbbt/resource/path.rb', line 309

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) 


190
191
192
193
194
195
196
197
 
# File 'lib/rbbt/resource/path.rb', line 190

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

#fields ⇒ Object 



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

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

#filename ⇒ Object 



182
183
184
 
# File 'lib/rbbt/resource/path.rb', line 182

def filename
  self.find
end

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



93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
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
 
# File 'lib/rbbt/resource/path.rb', line 93

def find(where = nil, caller_lib = nil, paths = nil)
  @path ||= {}
  rsearch_paths = (resource and resource.respond_to?(:search_paths)) ? resource.search_paths : nil 
  key = Misc.digest([where, caller_lib, rsearch_paths, paths].inspect)
  @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
                   return self if located?
                   if self.match(/(.*?)\/(.*)/)
                     toplevel, subpath = self.match(/(.*?)\/(.*)/).values_at 1, 2
                   else
                     toplevel, subpath = self, ""
                   end

                   path = nil
                   if where.nil?
                     STANDARD_SEARCH.each do |w| 
                       w = w.to_sym
                       next unless paths.include? w
                       path = find(w, caller_lib, paths)
                       return path if File.exists? path
                     end
                     (SEARCH_PATHS.keys - STANDARD_SEARCH).each do |w|
                       w = w.to_sym
                       next unless paths.include? w
                       path = find(w, caller_lib, paths)
                       return path if File.exists? path
                     end
                     if paths.include? :default
                       find((paths[:default] || :user), caller_lib, paths)
                     else
                       raise "Path '#{ path }' not found, and no default specified in search paths: #{paths.inspect}"
                     end
                   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.exists? path + '.gz'
                     path = path + '.bgz' if File.exists? path + '.bgz'

                     self.annotate path
                   end
                 end
end

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



155
156
157
158
159
160
161
162
 
# File 'lib/rbbt/resource/path.rb', line 155

def find_all(caller_lib = nil, search_paths = nil)
  search_paths ||= self.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 



42
43
44
45
46
47
48
49
50
 
# File 'lib/rbbt/resource/path.rb', line 42

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 



164
165
166
167
168
169
170
171
 
# File 'lib/rbbt/resource/path.rb', line 164

def glob_all(caller_lib = nil, search_paths = nil)
  search_paths ||= self.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{|path| Path.setup(path, self.resource, self.pkgdir)}
end

#identifier_file_path ⇒ Object 



288
289
290
291
292
293
294
 
# File 'lib/rbbt/resource/path.rb', line 288

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

#identifier_files ⇒ Object 



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

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

#in_dir?(dir) ⇒ Boolean

{{{ Methods

Returns:

  • (Boolean) 


174
175
176
 
# File 'lib/rbbt/resource/path.rb', line 174

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

#index(options = {}) ⇒ Object 



262
263
264
 
# File 'lib/rbbt/resource/path.rb', line 262

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

#join(name) ⇒ Object 



24
25
26
27
28
29
30
31
 
# File 'lib/rbbt/resource/path.rb', line 24

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 



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

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 



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

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

#located? ⇒ Boolean

Returns:

  • (Boolean) 


26
27
28
 
# File 'lib/rbbt/resource/util.rb', line 26

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

#open(options = {}, &block) ⇒ Object 



218
219
220
 
# File 'lib/rbbt/resource/path.rb', line 218

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

#pipe_to(cmd, options = {}) ⇒ Object 



258
259
260
 
# File 'lib/rbbt/resource/path.rb', line 258

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

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



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

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

#produce(force = false) ⇒ Object 



199
200
201
202
203
204
205
206
207
 
# File 'lib/rbbt/resource/path.rb', line 199

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 



266
267
268
 
# File 'lib/rbbt/resource/path.rb', line 266

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

#read(&block) ⇒ Object 



209
210
211
 
# File 'lib/rbbt/resource/path.rb', line 209

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

#set_extension(new_extension = nil) ⇒ Object 



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

def set_extension(new_extension = nil)
  new_path = self.sub(/\.[^\.\/]+$/, "." << new_extension.to_s)
  Path.setup new_path, @pkgdir, @resource
end

#source_for_doc_file(relative_to = 'lib') ⇒ Object 



319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
 
# File 'lib/rbbt/resource/path.rb', line 319

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.exists?(file)
      file= Dir.glob(file.sub(/\.[^\.\/]+$/, '.*')).first
    end

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

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

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

#sub(*args) ⇒ Object 



16
17
18
 
# File 'lib/rbbt/resource/path.rb', line 16

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

#to_s ⇒ Object 



178
179
180
 
# File 'lib/rbbt/resource/path.rb', line 178

def to_s
  self.find
end

#to_yaml(*args) ⇒ Object 



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

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

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



240
241
242
 
# File 'lib/rbbt/resource/path.rb', line 240

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

#tsv(*args) ⇒ Object 



230
231
232
 
# File 'lib/rbbt/resource/path.rb', line 230

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

#tsv_options(options = {}) ⇒ Object 



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

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

#write(*args, &block) ⇒ Object 



213
214
215
 
# File 'lib/rbbt/resource/path.rb', line 213

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

#yaml ⇒ Object 



252
253
254
255
256
 
# File 'lib/rbbt/resource/path.rb', line 252

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