rbbt-util 5.20.9 → 5.20.10

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -22,7 +22,7 @@ module TSV
         if obj.done?
           path = obj.path
           path = path.find if path.respond_to? :find
-          if File.exists? path
+          if File.exist? path
             CMD.cmd("wc -l '#{path}'").read.to_i 
           else
             nil
@@ -39,7 +39,7 @@ module TSV
         CMD.cmd("wc -l '#{obj.path}'").read.to_i
       when Path, String
         obj = obj.find if Path === obj
-        if File.exists? obj
+        if File.exist? obj
           return nil if Open.gzip?(obj) or Open.bgzip?(obj)
           CMD.cmd("wc -l '#{obj}'").read.to_i
         else

data/lib/rbbt/tsv/util.rb

@@ -127,7 +127,7 @@ module TSV
       end
       file
     when String
-      if Open.remote?(file) or File.exists? file
+      if Open.remote?(file) or File.exist? file
         Open.open(file, open_options)
       else
         StringIO.new file

data/lib/rbbt/util/R.rb

@@ -31,7 +31,7 @@ source('#{UTIL}');
     case
     when IO === command
       cmd << command.read
-    when File.exists?(command)
+    when File.exist?(command)
       cmd << File.open(command, 'r') do |f| f.read end
     else
       cmd << command

data/lib/rbbt/util/R/eval.rb

@@ -5,7 +5,7 @@ require 'rserve'
 module Rserve
   module TCPSocket 
     def self.new(hostname, port_number)
-      raise "Socket at #{hostname} not found" unless File.exists? hostname
+      raise "Socket at #{hostname} not found" unless File.exist? hostname
       @s = Socket.unix hostname
     end
   end
@@ -50,16 +50,16 @@ module R
         Log.warn "Error killing Rserve (#{@@instance_process}): #{$!.message}"
       end
     end
-    FileUtils.rm_rf pid_file if File.exists? pid_file
-    FileUtils.rm_rf socket_file if File.exists? socket_file
-    FileUtils.rm_rf lockfile if File.exists? lockfile
-    FileUtils.rm_rf workdir if File.exists? workdir
+    FileUtils.rm_rf pid_file if File.exist? pid_file
+    FileUtils.rm_rf socket_file if File.exist? socket_file
+    FileUtils.rm_rf lockfile if File.exist? lockfile
+    FileUtils.rm_rf workdir if File.exist? workdir
   end
 
   def self.instance
     @@instance ||= begin
 
-                     clear if File.exists? pid_file and ! Misc.pid_exists?(Open.read(pid_file).strip.to_i)
+                     clear if File.exist? pid_file and ! Misc.pid_exists?(Open.read(pid_file).strip.to_i)
 
                      FileUtils.mkdir_p File.dirname(socket_file) unless File.directory?(File.dirname(socket_file))
                      FileUtils.mkdir_p workdir unless File.directory? workdir
@@ -70,7 +70,7 @@ module R
 
                      begin
 
-                       if not File.exists? socket_file
+                       if not File.exist? socket_file
 
                          sh_pid = Process.fork do
                            #args = %w(CMD Rserve --vanilla --quiet --RS-socket)
@@ -90,7 +90,7 @@ module R
                            $stdout.reopen File.new('/dev/null', 'w')
                            exec(ENV, cmd)
                          end
-                         while not File.exists? pid_file
+                         while not File.exist? pid_file
                            sleep 0.5
                          end
                          @@instance_process = Open.read(pid_file).to_i
@@ -100,7 +100,7 @@ module R
                        i = Rserve::Connection.new :hostname => socket_file
 
                        begin
-                        FileUtils.mkdir workdir unless File.exists? workdir
+                        FileUtils.mkdir workdir unless File.exist? workdir
                         i.eval "setwd('#{workdir}');"
                         i.eval "source('#{UTIL}');" 
                         i
@@ -111,7 +111,7 @@ module R
                      rescue Exception
                        Log.exception $!
                        Process.kill :INT, @@instance_process if defined? @@instance_process and @@instance_process
-                       FileUtils.rm socket_file if File.exists? socket_file
+                       FileUtils.rm socket_file if File.exist? socket_file
                        retry if TryAgain === $!
                        raise $!
                      end

data/lib/rbbt/util/R/model.rb

@@ -122,7 +122,7 @@ predict(model, data.frame(#{field} = #{R.ruby2R tsv}));
     end
 
     def exists?
-      File.exists? model_file
+      File.exist? model_file
     end
 
     def fit(tsv, method='lm', args = {})
@@ -132,7 +132,7 @@ predict(model, data.frame(#{field} = #{R.ruby2R tsv}));
 
       tsv = Model.groom(tsv, formula)
 
-      FileUtils.mkdir_p File.dirname(model_file) unless File.exists?(File.dirname(model_file))
+      FileUtils.mkdir_p File.dirname(model_file) unless File.exist?(File.dirname(model_file))
       roptions = r_options(tsv)
       tsv.R <<-EOF, roptions
 model = rbbt.model.fit(data, #{formula}, method=#{method}#{args_str})

data/lib/rbbt/util/docker.rb

@@ -3,7 +3,7 @@ module Docker
     mounts, job_inputs, directory, pipe = Misc.process_options options, :mounts, :job_inputs, :directory, :pipe
 
     if mounts
-      mounts.each{|t,s| FileUtils.mkdir_p s unless File.exists? s}
+      mounts.each{|t,s| FileUtils.mkdir_p s unless File.exist? s}
       mount_cmd = mounts.sort.collect{|t,s| "-v " + ["'" + s + "'", "'" + t + "'"] * ":" } * " "
     else
       mount_cmd = ""
@@ -26,7 +26,7 @@ module Docker
             obj.join if obj.respond_to?(:join) and not obj.joined?
           end
         when String
-          if obj.length < 256 and File.exists?(obj)
+          if obj.length < 256 and File.exist?(obj)
             FileUtils.cp obj, directory[name]
           else
             Open.write(directory[name], obj)
@@ -49,7 +49,7 @@ module Docker
               obj.join if obj.respond_to?(:join) and not obj.joined?
             end
           when String
-            if obj.length < 256 and File.exists?(obj)
+            if obj.length < 256 and File.exist?(obj)
               FileUtils.cp obj, tmpfile[name]
             else
               Open.write(tmpfile[name], obj)

data/lib/rbbt/util/filecache.rb

@@ -39,13 +39,13 @@ module FileCache
   end
 
   def self.found(filename)
-    File.exists? FileCache.path(filename)
+    File.exist? FileCache.path(filename)
   end
 
   def self.get(filename)
     path = path(filename)
 
-    return nil if ! File.exists? path
+    return nil if ! File.exist? path
 
     File.open(path)
   end

data/lib/rbbt/util/misc/development.rb

@@ -63,7 +63,7 @@ module Misc
       result = RubyProf.stop
       printer = RubyProf::MultiPrinter.new(result)
       TmpFile.with_file do |dir|
-        FileUtils.mkdir_p dir unless File.exists? dir
+        FileUtils.mkdir_p dir unless File.exist? dir
         printer.print(:path => dir, :profile => 'profile')
         CMD.cmd("firefox  -no-remote  '#{ dir }'")
       end
@@ -284,7 +284,9 @@ module Misc
     num = :current if num.nil?
     cpus = case num
            when :current
-            10
+            n = 10
+            n = elems.length / 2 if n > elems.length/2
+            n
            when String
              num.to_i
            when Integer
@@ -363,7 +365,7 @@ module Misc
                      ENV["PUSHBULLET_KEY"] 
                    else
                      config_api = File.join(ENV['HOME'], 'config/apps/pushbullet/apikey')
-                     if File.exists? config_api
+                     if File.exist? config_api
                        File.read(config_api).strip
                      else
                        nil
@@ -386,7 +388,7 @@ module Misc
   end
 
   def self.unzip_in_dir(file, dir)
-    raise "Target is not a directory: #{file}" if File.exists?(dir) and not File.directory?(dir)
+    raise "Target is not a directory: #{file}" if File.exist?(dir) and not File.directory?(dir)
     if Open.remote? file
       file = file.find if Path === file
       Open.open(file) do |stream|

data/lib/rbbt/util/misc/lock.rb

@@ -23,7 +23,7 @@ module Misc
     return yield if file.nil? and not Lockfile === options[:lock]
 
     file = file.find if Path === file
-    FileUtils.mkdir_p File.dirname(File.expand_path(file)) unless File.exists? File.dirname(File.expand_path(file))
+    FileUtils.mkdir_p File.dirname(File.expand_path(file)) unless File.exist? File.dirname(File.expand_path(file))
 
 
     case options[:lock]

data/lib/rbbt/util/misc/multipart_payload.rb

@@ -69,7 +69,7 @@ module RbbtMutiplartPayload
         next if stream_input and input == stream_input.to_s
         content_str = case content
                       when String
-                        if Misc.is_filename?(content) and File.exists?(content)
+                        if Misc.is_filename?(content) and File.exist?(content)
                           File.read(content)
                         else
                           content

data/lib/rbbt/util/misc/pipes.rb

@@ -331,7 +331,7 @@ module Misc
         Misc.consume_stream content 
       else
         FileUtils.mkdir_p File.dirname(tmp_path) unless File.directory? File.dirname(tmp_path)
-        FileUtils.rm_f tmp_path if File.exists? tmp_path
+        FileUtils.rm_f tmp_path if File.exist? tmp_path
         begin
           case
           when block_given?
@@ -355,7 +355,7 @@ module Misc
               Open.mv tmp_path, path, lock_options
             end
           rescue Exception
-            raise $! unless File.exists? path
+            raise $! unless File.exist? path
           end
 
           content.join if content.respond_to? :join and not content.joined?  
@@ -363,23 +363,23 @@ module Misc
           if Lockfile === lock_options[:lock] and lock_options[:lock].locked?
             lock_options[:lock].unlock
           end
-          FileUtils.touch path if File.exists? path
+          FileUtils.touch path if File.exist? path
           Open.notify_write(path) 
         rescue Aborted
           Log.medium "Aborted sensiblewrite -- #{ Log.reset << Log.color(:blue, path) }"
           content.abort if content.respond_to? :abort
-          Open.rm path if File.exists? path
+          Open.rm path if File.exist? path
         rescue Exception
           Log.medium "Exception in sensiblewrite: [#{Process.pid}] #{$!.message} -- #{ Log.color :blue, path }"
           Log.exception $!
           content.abort if content.respond_to? :abort
-          Open.rm path if File.exists? path
+          Open.rm path if File.exist? path
           raise $!
         rescue
           Log.exception $!
           raise $!
         ensure
-          FileUtils.rm_f tmp_path if File.exists? tmp_path
+          FileUtils.rm_f tmp_path if File.exist? tmp_path
         end
       end
     end
@@ -607,7 +607,7 @@ module Misc
     else
       erase = []
 
-      if Path === stream1 or (String === stream1 and File.exists? stream1)
+      if Path === stream1 or (String === stream1 and File.exist? stream1)
         file1 = stream1
       else
         file1 = TmpFile.tmp_file
@@ -615,7 +615,7 @@ module Misc
         Open.write(file1, TSV.get_stream(stream1))
       end
 
-      if Path === stream2 or (String === stream2 and File.exists? stream2)
+      if Path === stream2 or (String === stream2 and File.exist? stream2)
         file2 = stream2
       else
         file2 = TmpFile.tmp_file

data/lib/rbbt/util/misc/system.rb

@@ -78,7 +78,7 @@ end
     old_pwd = FileUtils.pwd
     res = nil
     begin
-      FileUtils.mkdir_p dir unless File.exists? dir
+      FileUtils.mkdir_p dir unless File.exist? dir
       FileUtils.cd dir
       res = yield
     ensure
@@ -88,12 +88,12 @@ end
   end
 
   def self.filename?(string)
-    String === string and string.length > 0 and string.length < 250 and File.exists?(string)
+    String === string and string.length > 0 and string.length < 250 and File.exist?(string)
   end
 
   def self.is_filename?(string)
     return true if string.respond_to? :exists
-    return true if String === string and string.length < 265 and File.exists? string
+    return true if String === string and string.length < 265 and File.exist? string
     return false
   end
 

data/lib/rbbt/util/open.rb

@@ -17,7 +17,7 @@ module Open
 
     def repository_dirs
       @repository_dirs ||= begin
-                             File.exists?(Rbbt.etc.repository_dirs.find) ? 
+                             File.exist?(Rbbt.etc.repository_dirs.find) ? 
                                File.read(Rbbt.etc.repository_dirs.find).split("\n") :
                                []
                            rescue
@@ -100,7 +100,7 @@ module Open
   #
   def self.in_cache(url, options = {})
     filename = File.join(REMOTE_CACHEDIR, digest_url(url, options))
-    if File.exists? filename
+    if File.exist? filename
       return filename 
     else
       nil
@@ -111,7 +111,7 @@ module Open
     digest = Misc.digest([url, options.values_at("--post-data", "--post-data="), (options.include?("--post-file")? Open.read(options["--post-file"]) : "")].inspect)
 
     filename = File.join(REMOTE_CACHEDIR, digest)
-    if File.exists? filename
+    if File.exist? filename
       FileUtils.rm filename 
     else
       nil
@@ -239,7 +239,7 @@ module Open
     dir_sub_path_target = find_repo_dir(target)
 
     if dir_sub_path_source.nil? and dir_sub_path_target.nil?
-      FileUtils.mkdir_p File.dirname(target) unless File.exists? File.dirname(target)
+      FileUtils.mkdir_p File.dirname(target) unless File.exist? File.dirname(target)
       return FileUtils.mv source, target 
     end
 
@@ -271,7 +271,7 @@ module Open
       exists_in_repo(*dir_sub_path)
     else
       file = file.find if Path === file
-      File.exists? file
+      File.exist? file
     end
   end
 
@@ -409,7 +409,7 @@ module Open
   end
 
   def self.can_open?(file)
-    String === file and (File.exists?(file) or remote?(file))
+    String === file and (File.exist?(file) or remote?(file))
   end
 
   def self.read(file, options = {}, &block)
@@ -431,7 +431,7 @@ module Open
   def self.notify_write(file)
     begin
       notification_file = file + '.notify'
-      if File.exists? notification_file
+      if File.exist? notification_file
         key = Open.read(notification_file).strip
         key = nil if key.empty?
         Misc.notify("Wrote " << file, nil, key)
@@ -456,7 +456,7 @@ module Open
           yield f
         end
       rescue Exception
-        FileUtils.rm file if File.exists? file
+        FileUtils.rm file if File.exist? file
         raise $!
       end
     when content.nil?
@@ -473,7 +473,7 @@ module Open
           f.flock(File::LOCK_UN)
         end
       rescue Exception
-        FileUtils.rm_rf file if File.exists? file
+        FileUtils.rm_rf file if File.exist? file
         raise $!
       end
       content.close

data/lib/rbbt/util/simpleDSL.rb

@@ -49,7 +49,7 @@ module SimpleDSL
       end
       
       instance_eval &actions
-    elsif File.exists?(actions)
+    elsif File.exist?(actions)
       
       @config[@@method_name] = File.open(actions).read
 
@@ -67,7 +67,7 @@ module SimpleDSL
   def load_config(method = nil, file = nil, &block)
     @config = {}
     if file
-      raise ConfigFileMissingError.new "Config file '#{ file }' is missing" unless File.exists? file
+      raise ConfigFileMissingError.new "Config file '#{ file }' is missing" unless File.exist? file
       parse(method, file)
     end
 

data/lib/rbbt/util/tar.rb

@@ -84,7 +84,7 @@ module Misc
   end
 
   def self._untar_cmd(io, destination)
-    FileUtils.mkdir_p destination unless File.exists? destination
+    FileUtils.mkdir_p destination unless File.exist? destination
     CMD.cmd("tar xvf - -C '#{destination}'", :in => io)
     nil
   end

data/lib/rbbt/util/tmpfile.rb

@@ -42,7 +42,7 @@ module TmpFile
 
     result = yield(tmpfile)
 
-    FileUtils.rm_rf tmpfile if File.exists?(tmpfile) and erase
+    FileUtils.rm_rf tmpfile if File.exist?(tmpfile) and erase
 
     result
   end
@@ -54,7 +54,7 @@ module TmpFile
 
     result = yield(tmpdir)
 
-    FileUtils.rm_rf tmpdir if File.exists?(tmpdir) and erase
+    FileUtils.rm_rf tmpdir if File.exist?(tmpdir) and erase
 
     result
   end

data/lib/rbbt/workflow.rb

@@ -39,14 +39,18 @@ module Workflow
     eval "Object::#{wf_name} = WorkflowRESTClient.new '#{ url }', '#{wf_name}'"
   end
 
+  def self.load_workflow_libdir(filename)
+    workflow_lib_dir = File.join(File.dirname(File.expand_path(filename)), 'lib')
+    if File.directory? workflow_lib_dir
+      Log.debug "Adding workflow lib directory to LOAD_PATH: #{workflow_lib_dir}"
+      $LOAD_PATH.unshift(workflow_lib_dir)
+    end
+  end
+
   def self.load_workflow_file(filename)
     begin
-      workflow_lib_dir = File.join(File.dirname(File.expand_path(filename)), 'lib')
-      #$LOAD_PATH.unshift(File.join(File.dirname(File.expand_path(filename)), 'lib'))
-      if File.directory? workflow_lib_dir
-        Log.debug "Adding workflow lib directory to LOAD_PATH: #{workflow_lib_dir}"
-        $LOAD_PATH.unshift(workflow_lib_dir)
-      end
+
+      load_workflow_libdir(filename)
 
       filename = File.expand_path(filename)
 
@@ -81,29 +85,40 @@ module Workflow
                       end
   end
 
-  def self.require_local_workflow(wf_name)
+  def self.local_workflow_filename(wf_name)
     filename = nil
 
     if Path === wf_name
       case
         # Points to workflow file
-      when ((File.exists?(wf_name.find) and not File.directory?(wf_name.find)) or File.exists?(wf_name.find + '.rb')) 
+      when ((File.exist?(wf_name.find) and not File.directory?(wf_name.find)) or File.exist?(wf_name.find + '.rb')) 
         filename = wf_name.find
 
         # Points to workflow dir
-      when (File.exists?(wf_name.find) and File.directory?(wf_name.find) and File.exists?(File.join(wf_name.find, 'workflow.rb')))
+      when (File.exist?(wf_name.find) and File.directory?(wf_name.find) and File.exist?(File.join(wf_name.find, 'workflow.rb')))
         filename = wf_name['workflow.rb'].find
       end
 
     else
-      if ((File.exists?(wf_name) and not File.directory?(wf_name)) or File.exists?(wf_name + '.rb'))
+      if ((File.exist?(wf_name) and not File.directory?(wf_name)) or File.exist?(wf_name + '.rb'))
         filename = (wf_name =~ /\.?\//) ? wf_name : "./" << wf_name 
       else
         filename = workflow_dir[wf_name]['workflow.rb'].find
       end
     end
 
-    if filename and File.exists? filename
+    if filename.nil? or not File.exist?(filename)
+      wf_name_snake = Misc.snake_case(wf_name)
+      return local_workflow_filename(wf_name_snake) if wf_name_snake != wf_name
+    end
+
+    filename
+  end
+
+  def self.require_local_workflow(wf_name)
+    filename = local_workflow_filename(wf_name)
+
+    if filename and File.exist? filename
       load_workflow_file filename
     else
       return false
@@ -153,7 +168,6 @@ module Workflow
 
     Log.info{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) or 
-    require_local_workflow(Misc.snake_case(wf_name)) or 
     (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)}` and require_local_workflow(Misc.snake_case(wf_name))) or
     raise("Workflow not found or could not be loaded: #{ wf_name }")
     begin