rbbt-util 5.28.6 → 5.28.11

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 94a6ec3c4a32e3632d59872c17b449a5c6be624cf999b2bb3469647933a0ba28
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+  data.tar.gz: d16905de756df32abacd314b8793d4792c9852d76267be7ef71b6c5e0ae4e08f8b9ce04f34f2ceba3cd36ed8cda18966e737a893439b2451a9cde43a334afcb6

data/lib/rbbt/entity.rb

@@ -38,7 +38,7 @@ module Entity
                                                    if value.to_s == k.to_s
                                                      found = k
                                                      break
-                                                   elsif value =~ /\(#{Regexp.quote k}\)/
+                                                   elsif value.to_s =~ /\(#{Regexp.quote k}\)/
                                                      found = k
                                                      break
                                                    end

data/lib/rbbt/fix_width_table.rb

@@ -67,7 +67,7 @@ class FixWidthTable
 
   def format(pos, value)
     padding = value_size - value.length
-    if range
+    if @range
       (pos  + [padding, value + ("\0" * padding)]).pack("llll#{mask}")
     else
       [pos, padding, value + ("\0" * padding)].pack("ll#{mask}")
@@ -105,7 +105,7 @@ class FixWidthTable
 
   def idx_value(index)
     return nil if index < 0 or index >= size
-    @file.seek((range ? 17 : 9 ) + (record_size) * index, IO::SEEK_SET)
+    @file.seek((@range ? 17 : 9 ) + (record_size) * index, IO::SEEK_SET)
     padding = @file.read(4).unpack("l").first+1
     txt = @file.read(value_size)
     str = txt.unpack(mask).first
@@ -277,7 +277,8 @@ class FixWidthTable
 
   def [](pos)
     return [] if size == 0
-    if range
+    self.read
+    if @range
       get_range(pos)
     else
       get_point(pos)
@@ -286,7 +287,7 @@ class FixWidthTable
   
   def overlaps(pos, value = false)
     return [] if size == 0
-    idxs = if range
+    idxs = if @range
       get_range(pos, true)
     else
       get_point(pos, true)

data/lib/rbbt/persist.rb

@@ -25,12 +25,18 @@ module Persist
   MEMORY = {} unless defined? MEMORY
   MAX_FILE_LENGTH = 150
 
-  def self.newer?(path, file)
+  # Is 'file' newer than 'path'? return non-true if path is newer than file
+  def self.newer?(path, file, by_link = false)
     return true if not Open.exists?(file)
     path = path.find if Path === path
     file = file.find if Path === file
-    patht = Open.mtime(path)
-    filet = Open.mtime(file)
+    if by_link
+      patht = File.lstat(path).mtime
+      filet = File.lstat(file).mtime
+    else
+      patht = Open.mtime(path)
+      filet = Open.mtime(file)
+    end
     return true if patht.nil? || filet.nil?
     diff = patht - filet
     return diff if diff < 0

data/lib/rbbt/persist/tsv/adapter.rb

@@ -52,7 +52,6 @@ module Persist
     def lock
       return yield if @locked
       lock_filename = Persist.persistence_path(persistence_path, {:dir => TSV.lock_dir})
-      Log.stack caller if $LOG
       Misc.lock(lock_filename) do
         begin
           @locked = true

data/lib/rbbt/persist/tsv/fix_width_table.rb

@@ -52,7 +52,7 @@ module Persist
       if TSV::ENTRY_KEYS.include? key
         set_metadata(key, value)
       else
-        if range
+        if @range
           add_range_point key, value
         else
           add key, value
@@ -61,7 +61,7 @@ module Persist
     end
      
     def add(key, value)
-      key = pos_function.call(key) if pos_function and not (range and Array === key)
+      key = pos_function.call(key) if pos_function and not (@range and Array === key)
       super(key, value)
     end
 
@@ -85,8 +85,10 @@ module Persist
     end
 
     def each
+      read
       @size.times do |i|
-        yield i, value(i)
+        v = idx_value(i)
+        yield i, v
       end
     end
 

data/lib/rbbt/resource.rb

@@ -112,13 +112,19 @@ module Resource
               end
             when Net::HTTPRedirection, Net::HTTPFound
               location = response['location']
-              Log.debug("Feching directory from: #{location}. Into: #{final_path}")
-              FileUtils.mkdir_p final_path unless File.exist? final_path
-              TmpFile.with_file do |tmp_dir|
-                Misc.in_dir tmp_dir do
-                  CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
+              if location.include? 'get_directory'
+                Log.debug("Feching directory from: #{location}. Into: #{final_path}")
+                FileUtils.mkdir_p final_path unless File.exist? final_path
+                TmpFile.with_file do |tmp_dir|
+                  Misc.in_dir tmp_dir do
+                    CMD.cmd('tar xvfz -', :in => Open.open(location, :nocache => true))
+                  end
+                  FileUtils.mv tmp_dir, final_path
+                end
+              else
+                Open.open(location, :nocache => true) do |s|
+                  Misc.sensiblewrite(final_path, s)
                 end
-                FileUtils.mv tmp_dir, final_path
               end
             when Net::HTTPInternalServerError
               @server_missing_resource_cache << url

data/lib/rbbt/tsv/accessor.rb

@@ -550,9 +550,17 @@ module TSV
         "\t" << ([""] * fields.length) * "\t" << "\n"
       end
     when Array
-      "\t" << values.collect{|v| Array === v ? v * "|" : v} * "\t" << "\n"
+      if fields.nil? or fields.empty?
+        "\n"
+      else
+        "\t" << values.collect{|v| Array === v ? v * "|" : v} * "\t" << "\n"
+      end
     else
-      "\t" << values.to_s << "\n"
+      if fields.nil? or fields.empty?
+        "\n"
+      else
+        "\t" << values.to_s << "\n"
+      end
     end
   end
 

data/lib/rbbt/tsv/dumper.rb

@@ -32,9 +32,21 @@ module TSV
           sep + ([""] * fields.length) * sep << "\n"
         end
       when Array
-        sep + (values.collect{|v| Array === v ? v * "|" : v} * sep) << "\n"
+        if fields.nil? 
+          sep + (values.collect{|v| Array === v ? v * "|" : v} * sep) << "\n"
+        elsif fields.empty?
+          "\n"
+        else
+          sep + (values.collect{|v| Array === v ? v * "|" : v} * sep) << "\n"
+        end
       else
-        sep + values.to_s << "\n"
+        if fields.nil?
+          sep + values.to_s + "\n"
+        elsif fields.empty?
+          "\n"
+        else
+          sep + values.to_s << "\n"
+        end
       end
     end
 

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

@@ -624,6 +624,8 @@ module TSV
   def self.traverse(obj, options = {}, &block)
     into = options[:into]
 
+    into = options[:into] = Open.open(into, :mode => "w") if Misc.is_filename?(into)
+
     case into
     when :stream
       sout = Misc.open_pipe false, false do |sin|                                                                                                                                           

data/lib/rbbt/tsv/util.rb

@@ -184,7 +184,11 @@ module TSV
     str = "" 
     str << preamble.strip << "\n" if preamble and not preamble.empty?
     if fields
-      str << header_hash << (key_field || "ID").to_s << sep << (fields * sep) << "\n" 
+      if fields.empty?
+        str << header_hash << (key_field || "ID").to_s << "\n" 
+      else
+        str << header_hash << (key_field || "ID").to_s << sep << (fields * sep) << "\n" 
+      end
     end
 
     str

data/lib/rbbt/util/R.rb

@@ -41,7 +41,7 @@ source('#{UTIL}');
 
     if monitor
       #io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
-      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
+      io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true, :xvfb => true))
       while line = io.gets
         case monitor
         when Proc
@@ -52,7 +52,7 @@ source('#{UTIL}');
       end
       nil
     else
-      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd))
+      CMD.cmd('R --no-save --slave --quiet', options.merge(:in => cmd, :xvfb => true))
     end
   end
 

data/lib/rbbt/util/cmd.rb

@@ -98,7 +98,9 @@ module CMD
     post       = options.delete(:post)
     log        = options.delete(:log)
     no_fail    = options.delete(:no_fail)
+    no_fail    = options.delete(:nofail) if no_fail.nil?
     no_wait    = options.delete(:no_wait)
+    xvfb       = options.delete(:xvfb)
 
     dont_close_in  = options.delete(:dont_close_in)
 
@@ -116,6 +118,14 @@ module CMD
 
     end
 
+    case xvfb
+    when TrueClass
+      cmd = "xvfb-run --server-args='-screen 0 1024x768x24' --auto-servernum #{cmd}"
+    when String
+      cmd = "xvfb-run --server-args='#{xvfb}' --auto-servernum --server-num=1 #{cmd}"
+    when String
+    end
+
     if stderr == true
       stderr = Log::HIGH
     end

data/lib/rbbt/util/config.rb

@@ -15,7 +15,7 @@ module Rbbt::Config
   end
 
   def self.load_file(file)
-    Log.debug "Loading file: #{ file }"
+    Log.debug "Loading config file: #{ file }"
     TSV.traverse file, :type => :array do |line|
       next if line =~ /^#/
       key, value, *tokens = line.strip.split(/\s/)
@@ -85,6 +85,7 @@ module Rbbt::Config
     priorities
   end
 
+  # For equal priorities the matching prioritizes tokens ealier in the list
   def self.get(key, *tokens)
     options = tokens.pop if Hash === tokens.last
     default = options.nil? ? nil : options[:default]

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

@@ -7,7 +7,7 @@ module Bgzf
 
   def self.bgzip_cmd
     @@bgzip_cmd ||= begin
-                      path = `bash -c "type -p bgzips"`.strip
+                      path = `bash -c "type -p bgzip"`.strip
                       if path.empty?
                         Rbbt.claim Rbbt.software.opt.htslib, :install, Rbbt.share.install.software.HTSLIB.find(:lib)
                         Rbbt.software.opt.htslib.produce

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

@@ -287,15 +287,19 @@ module Misc
           when Symbol 
             obj.to_s
           when (defined?(Path) and Path)
-            if obj.exists?
-              if obj.directory?
-                files = obj.glob("**/*")
-                "directory: #{Misc.fingerprint(files)}"
+            if Step === obj.resource
+              "Step file: " + obj
+            else
+              if obj.exists?
+                if obj.directory?
+                  files = obj.glob("**/*")
+                  "directory: #{Misc.fingerprint(files)}"
+                else
+                  "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
+                end
               else
-                "file: " << Open.realpath(obj) << "--" << mtime_str(obj)
+                obj + " (file missing)"
               end
-            else
-              obj + " (file missing)"
             end
           when String
             if Misc.is_filename?(obj) and ! %w(. ..).include?(obj)

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

@@ -113,7 +113,7 @@ end
   end
 
   def self.is_filename?(string)
-    return true if defined? PATH and Path === string
+    return true if defined? Path and Path === string
     return true if string.respond_to? :exists
     return true if String === string and string.length < 265 and File.exist?(string)
     return false

data/lib/rbbt/util/named_array.rb

@@ -117,7 +117,7 @@ module NamedArray
   #end
 
   def each(&block)
-    if defined?(Entity) and not @fields.nil? and not @fields.empty?
+    if defined?(Entity) && ! (@fields.nil? || @fields.empty?)
       i = 0
       super do |elem|
         field = @fields[i]

data/lib/rbbt/util/open.rb

@@ -16,9 +16,9 @@ module Open
   GREP_CMD = begin
                if ENV["GREP_CMD"] 
                  ENV["GREP_CMD"]
-               elsif File.exists?('/bin/grep')
+               elsif File.exist?('/bin/grep')
                  "/bin/grep"
-               elsif File.exists?('/usr/bin/grep')
+               elsif File.exist?('/usr/bin/grep')
                  "/usr/bin/grep"
                else
                  "grep"
@@ -262,7 +262,7 @@ module Open
     if (dir_sub_path = find_repo_dir(file))
       remove_from_repo(*dir_sub_path)
     else
-      FileUtils.rm(file) if File.exists?(file) or Open.broken_link?(file)
+      FileUtils.rm(file) if File.exist?(file) or Open.broken_link?(file)
     end
   end
 
@@ -333,7 +333,7 @@ module Open
       nil
     else
       target = target.find if Path === target
-      if ! File.exists?(target)
+      if ! File.exist?(target)
         FileUtils.mkdir_p target
       end
     end
@@ -344,8 +344,8 @@ module Open
     target = target.find if Path === target
 
     target = File.join(target, File.basename(source)) if File.directory? target
-    FileUtils.mkdir_p File.dirname(target) unless File.exists?(File.dirname(target))
-    FileUtils.rm target if File.exists?(target)
+    FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
+    FileUtils.rm target if File.exist?(target)
     FileUtils.ln_s source, target
   end
 
@@ -353,8 +353,8 @@ module Open
     source = source.find if Path === source
     target = target.find if Path === target
 
-    FileUtils.mkdir_p File.dirname(target) unless File.exists?(File.dirname(target))
-    FileUtils.rm target if File.exists?(target)
+    FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
+    FileUtils.rm target if File.exist?(target)
     FileUtils.ln source, target
   end
 
@@ -362,8 +362,8 @@ module Open
     source = source.find if Path === source
     target = target.find if Path === target
 
-    FileUtils.mkdir_p File.dirname(target) unless File.exists?(File.dirname(target))
-    FileUtils.rm target if File.exists?(target)
+    FileUtils.mkdir_p File.dirname(target) unless File.exist?(File.dirname(target))
+    FileUtils.rm target if File.exist?(target)
     begin
       CMD.cmd("ln -L '#{ source }' '#{ target }'")
     rescue ProcessFailed
@@ -397,7 +397,7 @@ module Open
     if dir_sub_path_source.nil? and dir_sub_path_target.nil?
       FileUtils.mkdir_p File.dirname(target) unless File.exist? File.dirname(target)
       tmp_target = File.join(File.dirname(target), '.tmp_mv.' + File.basename(target))
-      FileUtils.cp source, tmp_target
+      FileUtils.cp_r source, tmp_target
       FileUtils.mv tmp_target, target
       return
     end
@@ -475,6 +475,7 @@ module Open
       File.exist?(file) #|| File.symlink?(file)
     end
   end
+
   class << self
     alias exist? exists?
   end
@@ -747,7 +748,7 @@ module Open
     if (dir_sub_path = find_repo_dir(path))
       writable_repo?(*dir_sub_path)
     else
-      if File.exists?(path)
+      if File.exist?(path)
         File.writable?(path)
       else
         File.writable?(File.dirname(File.expand_path(path)))
@@ -776,14 +777,14 @@ module Open
       file = file.find if Path === file
       begin
         if File.symlink?(file) || File.stat(file).nlink > 1
-          if File.exists?(file + '.info') && defined?(Step)
+          if File.exist?(file + '.info') && defined?(Step)
             done = Step::INFO_SERIALIZER.load(Open.open(file + '.info'))[:done]
             return done if done
           end
 
           file = Pathname.new(file).realpath.to_s 
         end
-        return nil unless File.exists?(file)
+        return nil unless File.exist?(file)
         File.mtime(file)
       rescue
         nil
@@ -793,7 +794,7 @@ module Open
 
   def self.update_mtime(path, target)
     if File.symlink?(target) || File.stat(target).nlink > 1
-      if File.exists?(target + '.info')
+      if File.exist?(target + '.info')
         target = target + '.info'
       else
         target = Pathname.new(target).realpath.to_s 
@@ -801,7 +802,7 @@ module Open
     end
 
     CMD.cmd("touch -r '#{path}' '#{target}'")
-    CMD.cmd("touch -r '#{path}.info' '#{target}'") if File.exists?(path + '.info')
+    CMD.cmd("touch -r '#{path}.info' '#{target}'") if File.exist?(path + '.info')
   end
 
   def self.atime(file)
@@ -823,7 +824,7 @@ module Open
   end
 
   def self.broken_link?(path)
-    File.symlink?(path) && ! File.exists?(File.readlink(path))
+    File.symlink?(path) && ! File.exist?(File.readlink(path))
   end
 
   def self.download(url, path)