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
-
#libdir ⇒ Object
Returns the value of attribute libdir.
-
#original ⇒ Object
Returns the value of attribute original.
-
#pkgdir ⇒ Object
Returns the value of attribute pkgdir.
-
#resource ⇒ Object
Returns the value of attribute resource.
-
#search_order ⇒ Object
Returns the value of attribute search_order.
-
#search_paths ⇒ Object
Returns the value of attribute search_paths.
-
#where ⇒ Object
Returns the value of attribute where.
Class Method Summary collapse
- .caller_lib_dir(file = nil, relative_to = ['lib', 'bin', 'LICENSE']) ⇒ Object
- .get_extension(path) ⇒ Object
- .setup(string, pkgdir = nil, resource = nil, search_paths = nil, search_order = nil, libdir = nil) ⇒ Object
Instance Method Summary collapse
- #[](name, orig = false) ⇒ Object
- #_exists? ⇒ Boolean
- #add_search_path(name, dir) ⇒ Object
- #all_fields ⇒ Object
- #annotate(name) ⇒ Object
- #append_search_path(name, dir) ⇒ Object
- #basename ⇒ Object
- #byte(pos) ⇒ Object
- #clean_annotations ⇒ Object
- #directory? ⇒ Boolean
- #dirname ⇒ Object
- #doc_file(relative_to = 'lib') ⇒ Object
- #exists? ⇒ Boolean
- #fields ⇒ Object
- #filename ⇒ Object
- #find(where = nil, caller_lib = nil, paths = nil) ⇒ Object
- #find_all(caller_lib = nil, search_paths = nil) ⇒ Object
- #glob(pattern = '*') ⇒ Object
- #glob_all(pattern = nil, caller_lib = nil, search_paths = nil) ⇒ Object
- #identifier_file_path ⇒ Object
- #identifier_files ⇒ Object
-
#in_dir?(dir) ⇒ Boolean
{{{ Methods.
- #index(options = {}) ⇒ Object
- #join(name) ⇒ Object
- #keys(field = 0, sep = "\t") ⇒ Object
- #list ⇒ Object
- #located? ⇒ Boolean
- #method_missing(name, prev = nil, *args, &block) ⇒ Object
- #open(options = {}, &block) ⇒ Object
- #pipe_to(cmd, options = {}) ⇒ Object
- #pos_index(pos, options = {}) ⇒ Object
- #prepend_search_path(name, dir) ⇒ Object
- #produce(force = false) ⇒ Object
- #range_index(start, eend, options = {}) ⇒ Object
- #read(&block) ⇒ Object
- #remove_extension(new_extension = nil) ⇒ Object
- #replace_extension(new_extension = nil, multiple = false) ⇒ Object
- #set_extension(new_extension = nil) ⇒ Object
- #source_for_doc_file(relative_to = 'lib') ⇒ Object
- #sub(*args) ⇒ Object
- #to_s ⇒ Object
- #to_yaml(*args) ⇒ Object
- #traverse(options = {}, &block) ⇒ Object
- #tsv(*args) ⇒ Object
- #tsv_options(options = {}) ⇒ Object
- #write(*args, &block) ⇒ Object
- #yaml ⇒ Object
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', 'LICENSE']) ⇒ Object
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# File 'lib/rbbt/resource/util.rb', line 3 def self.caller_lib_dir(file = nil, relative_to = ['lib', 'bin', 'LICENSE']) #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.(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 445 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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# File 'lib/rbbt/resource/path.rb', line 298 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 413 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 339 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 493 def clean_annotations "" << self.to_s end |
#directory? ⇒ 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 461 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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# File 'lib/rbbt/resource/path.rb', line 302 def exists? begin self.produce _exists? rescue Exception false end end |
#fields ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 409 def fields TSV.parse_header(self.open).fields end |
#filename ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 294 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? path = self path = path + '.gz' if File.exist?(path + '.gz') path = path + '.bgz' if File.exist?(path + '.bgz') self.annotate(path) path.original = self return path end if where == :all || where == 'all' return find_all(caller_lib, paths) 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 275 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 pattern 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 419 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 427 def identifier_files if identifier_file_path.nil? [] else [identifier_file_path] end end |
#in_dir?(dir) ⇒ Boolean
{{{ Methods
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# File 'lib/rbbt/resource/path.rb', line 286 def in_dir?(dir) ! ! File.(self).match(/^#{Regexp.quote dir}/) end |
#index(options = {}) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 393 def index( = {}) TSV.index(self.produce, ) 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 379 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 366 def list begin path = self.produce rescue Resource::ResourceNotFound => e begin path = self.set_extension('list').produce rescue Resource::ResourceNotFound raise e end end Open.read(path).split("\n") end |
#located? ⇒ 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 330 def open( = {}, &block) file = Open.remote?(self) || Open.ssh?(self) ? self : self.produce.find Open.open(file, , &block) end |
#pipe_to(cmd, options = {}) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 389 def pipe_to(cmd, = {}) CMD.cmd(cmd, {:in => self.open, :pipe => true}.merge()) end |
#pos_index(pos, options = {}) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 401 def pos_index(pos, = {}) TSV.pos_index(self.produce, pos, ) 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 311 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 397 def range_index(start, eend, = {}) TSV.range_index(self.produce, start, eend, ) end |
#read(&block) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 321 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 440 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 449 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}$/,'') end new_path = new_path + "." + new_extension.to_s self.annotate(new_path) end |
#set_extension(new_extension = nil) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 435 def set_extension(new_extension = nil) new_path = self + "." + new_extension.to_s self.annotate(new_path) end |
#source_for_doc_file(relative_to = 'lib') ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 471 def source_for_doc_file(relative_to = 'lib') if located? lib_dir = Path.caller_lib_dir(Path.caller_lib_dir(self, 'doc'), relative_to) relative_file = self.sub(/(.*\/)doc\//, '\1').sub(lib_dir + "/",'') file = File.join(lib_dir, relative_file) if not File.exist?(file) file= Dir.glob(file.sub(/\.[^\.\/]+$/, '.*')).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 290 def to_s self.find end |
#to_yaml(*args) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 405 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 362 def traverse( = {}, &block) TSV::Parser.traverse(self.open, , &block) end |
#tsv(*args) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 343 def tsv(*args) begin path = self.produce rescue Resource::ResourceNotFound => e begin path = self.set_extension('tsv').produce rescue Resource::ResourceNotFound raise e end end TSV.open(path, *args) end |
#tsv_options(options = {}) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 356 def ( = {}) self.open do |stream| TSV::Parser.new(stream, ). end end |
#write(*args, &block) ⇒ Object
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# File 'lib/rbbt/resource/path.rb', line 325 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 383 def yaml self.open do |f| YAML.respond_to?(:unsafe_load) ? YAML.unsafe_load(f) : YAML.load(f) end end |