rbbt-util 5.20.9 → 5.20.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: b1b7fd04c9c94d2ec1a1c16cc4e883536f7a3500
+  metadata.gz: 2c424ed8cfdf95b53803cbc976261f9542eda87d
+  data.tar.gz: 1ed15794721f06807a43e2158ec5186cdfaa6462
 SHA512:
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-  data.tar.gz: dbf542a2d17b31f6975e8d3bc1fa53739d1fcc95c9aa9f805b2609833aff38fb8d0f8851ee90791434066e9165eaab4f636632868cdab7916cb43a9dc56da8a2
+  metadata.gz: 3006d04121e96c3a1a290520a7749615a602718843c09bca87533f2f07cf412918eee6a48eedee4c12c88f751cb203ca9a996b8c6b08f0ad821ac2f56b64b35f
+  data.tar.gz: 7ca5624085d95696df0d2693e384031d7c82fc38372721fb5978c96e9e4d132abb71f9dde3f942d0f2abcf10d2b4f3f82f4fa5feab97396d23474f2ba42f9b17

data/bin/rbbt

@@ -208,7 +208,7 @@ begin
         load dir[$command].find
         exit 0
       end
-    when File.exists?($command)
+    when File.exist?($command)
       load $command
       exit 0
     else

data/bin/rbbt_query.rb

@@ -8,7 +8,7 @@ options = SOPT.get("-i--identifiers*:-f--format*:-o--organism*:-p--persistence:-
 
 file   = ARGV[0]
 
-if not File.exists? file
+if not File.exist? file
   base, path = file.match(/([^.]*)\.(.*)/).values_at 1, 2
   require 'rbbt/sources/' << base.to_s.downcase
   klass = Misc.string2const base

data/lib/rbbt/association/index.rb

@@ -128,13 +128,13 @@ module Association
                        raise "Can only reverse a TokyoCabinet::BDB dataset at the time"
                      end
 
-                     if File.exists?(reverse_filename)
+                     if File.exist?(reverse_filename)
                        new = Persist.open_tokyocabinet(reverse_filename, false, serializer, TokyoCabinet::BDB)
                        raise "Index has no info: #{reverse_filename}" if new.key_field.nil?
                        Association::Index.setup new
                        new
                      else
-                       FileUtils.mkdir_p File.dirname(reverse_filename) unless File.exists?(File.dirname(reverse_filename))
+                       FileUtils.mkdir_p File.dirname(reverse_filename) unless File.exist?(File.dirname(reverse_filename))
 
                        new = Persist.open_tokyocabinet(reverse_filename, true, serializer, TokyoCabinet::BDB)
                        
@@ -161,7 +161,7 @@ module Association
                      new
                    rescue Exception
                      Log.error "Deleting after error reversing database: #{ reverse_filename }"
-                     FileUtils.rm reverse_filename if File.exists? reverse_filename
+                     FileUtils.rm reverse_filename if File.exist? reverse_filename
                      raise $!
                    end
     end

data/lib/rbbt/fix_width_table.rb

@@ -4,7 +4,7 @@ class FixWidthTable
   def initialize(filename, value_size = nil, range = nil, update = false, in_memory = true)
     @filename = filename
 
-    if update or %w(memory stringio).include?(filename.to_s.downcase) or not File.exists?(filename)
+    if update or %w(memory stringio).include?(filename.to_s.downcase) or not File.exist?(filename)
       Log.debug "FixWidthTable create: #{ filename }"
       @value_size  = value_size
       @range       = range
@@ -15,8 +15,8 @@ class FixWidthTable
         @filename = :memory
         @file     = StringIO.new
       else
-        FileUtils.rm @filename if File.exists? @filename
-        FileUtils.mkdir_p File.dirname(@filename) unless File.exists? @filename
+        FileUtils.rm @filename if File.exist? @filename
+        FileUtils.mkdir_p File.dirname(@filename) unless File.exist? @filename
         @file = File.open(@filename, 'wb')
       end
 
@@ -57,7 +57,7 @@ class FixWidthTable
   def self.get(filename, value_size = nil, range = nil, update = false)
     return self.new(filename, value_size, range, update) if filename == :memory
     case
-    when (!File.exists?(filename) or update or not Persist::CONNECTIONS.include?(filename))
+    when (!File.exist?(filename) or update or not Persist::CONNECTIONS.include?(filename))
       Persist::CONNECTIONS[filename] = self.new(filename, value_size, range, update)
     end
 

data/lib/rbbt/persist/tsv.rb

@@ -129,7 +129,7 @@ module Persist
         end
         path = path.find if Path === path
 
-        FileUtils.rm_rf path if File.exists? path
+        FileUtils.rm_rf path if File.exist? path
 
         Log.medium "TSV persistence creating: #{ path }"
 
@@ -149,7 +149,7 @@ module Persist
           yield data
         end
 
-        FileUtils.mv data.persistence_path, path if File.exists? data.persistence_path and not File.exists? path
+        FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
         tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
         tsv.persistence_path = path
 
@@ -158,8 +158,8 @@ module Persist
         data
       rescue Exception
         Log.error "Captured error during persist_tsv. Erasing: #{path}"
-        FileUtils.rm_rf tmp_path if tmp_path and File.exists? tmp_path
-        FileUtils.rm_rf path if path and File.exists? path
+        FileUtils.rm_rf tmp_path if tmp_path and File.exist? tmp_path
+        FileUtils.rm_rf path if path and File.exist? path
         raise $!
       end
     end

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

@@ -6,7 +6,7 @@ module Persist
     include Persist::TSVAdapter
 
     def self.open(path, write)
-      write = true unless File.exists? path
+      write = true unless File.exist? path
 
      database = CONNECTIONS[path] ||= begin
                                          file = File.open(path, 'w')
@@ -126,9 +126,9 @@ module Persist
 
 
   def self.open_cdb(path, write, serializer = nil)
-    write = true unless File.exists? path
+    write = true unless File.exist? path
 
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::CDBAdapter.open(path, write)
 

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

@@ -25,7 +25,7 @@ module Persist
     end
 
     def metadata
-      return {} unless File.exists? metadata_file
+      return {} unless File.exist? metadata_file
       Open.open(metadata_file, :mode => "rb") do |f|
         Marshal.load(f)
       end
@@ -96,7 +96,7 @@ module Persist
   end
 
   def self.open_fwt(path, value_size, range = false, serializer = nil, update = false, in_memory = false, &pos_function)
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::FWTAdapter.open(path, value_size, range, update, in_memory, &pos_function)
 

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

@@ -78,9 +78,9 @@ module Persist
 
 
   def self.open_kyotocabinet(path, write, serializer = nil,  kyotocabinet_class= 'kch')
-    write = true unless File.exists? path
+    write = true unless File.exist? path
 
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::KCAdapter.open(path, write, kyotocabinet_class)
 

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

@@ -104,9 +104,9 @@ module Persist
 
 
   def self.open_leveldb(path, write, serializer = nil)
-    write = true unless File.exists? path
+    write = true unless File.exist? path
 
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::LevelDBAdapter.open(path, write)
 

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

@@ -45,9 +45,9 @@ module Persist
   end
 
   def self.open_lmdb(path, write, serializer = nil)
-    write = true unless File.exists? path
+    write = true unless File.exist? path
 
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::LMDBAdapter.open(path, write)
 

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

@@ -25,7 +25,7 @@ module Persist
     end
 
     def metadata
-      return {} unless File.exists? metadata_file
+      return {} unless File.exist? metadata_file
       Open.open(metadata_file, :mode => "rb") do |f|
         Marshal.load(f)
       end
@@ -96,7 +96,7 @@ module Persist
   end
 
   def self.open_pki(path, write, pattern, &pos_function)
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::PKIAdapter.open(path, write, pattern, &pos_function)
 

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

@@ -58,12 +58,12 @@ module Persist
         if shard == 'metadata'
           database ||= begin
                          path = File.join(persistence_path, 'shard-' << shard.to_s)
-                         (writable or File.exists?(path)) ? Persist.open_database(path, writable, :clean, "HDB", @options) : nil
+                         (writable or File.exist?(path)) ? Persist.open_database(path, writable, :clean, "HDB", @options) : nil
                      end
         else
           database ||= begin
                        path = File.join(persistence_path, 'shard-' << shard.to_s)
-                       (writable or File.exists?(path)) ? Persist.open_database(path, writable, :clean, db_type, @options) : nil
+                       (writable or File.exist?(path)) ? Persist.open_database(path, writable, :clean, db_type, @options) : nil
                      end
         end
         if database
@@ -243,9 +243,9 @@ module Persist
   end
 
   def self.open_sharder(path, write, serializer = nil, type = TokyoCabinet::HDB, options, &shard_function)
-    write = true unless File.exists? path
+    write = true unless File.exist? path
 
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::SharderAdapter.open(path, write, type, options, &shard_function)
 

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

@@ -74,9 +74,9 @@ module Persist
   end
 
   def self.open_tokyocabinet(path, write, serializer = nil, tokyocabinet_class = TokyoCabinet::HDB)
-    write = true unless File.exists? path
+    write = true unless File.exist? path
 
-    FileUtils.mkdir_p File.dirname(path) unless File.exists?(File.dirname(path))
+    FileUtils.mkdir_p File.dirname(path) unless File.exist?(File.dirname(path))
 
     database = Persist::TCAdapter.open(path, write, serializer, tokyocabinet_class)
 

data/lib/rbbt/resource.rb

@@ -92,7 +92,7 @@ module Resource
           when Net::HTTPRedirection, Net::HTTPFound
             location = response['location']
             Log.debug("Feching directory from: #{location}. Into: #{final_path}")
-            FileUtils.mkdir_p final_path unless File.exists? 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))
@@ -110,7 +110,7 @@ module Resource
     rescue
       Log.warn "Could not retrieve (#{self.to_s}) #{ path } from #{ remote_server }"
       Log.error $!.message
-      FileUtils.rm_rf final_path if File.exists? final_path
+      FileUtils.rm_rf final_path if File.exist? final_path
       return false
     end
   end
@@ -133,12 +133,12 @@ module Resource
       final_path = path
     end
 
-    if not File.exists? final_path or force
+    if not File.exist? final_path or force
       Log.medium "Producing: #{ final_path }"
       lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
       Misc.lock lock_filename do
-        FileUtils.rm_rf final_path if force and File.exists? final_path
-        if not File.exists? final_path or force
+        FileUtils.rm_rf final_path if force and File.exist? final_path
+        if not File.exist? final_path or force
           (remote_server and get_from_server(path, final_path)) or
           begin
             case type
@@ -192,7 +192,7 @@ source "$INSTALL_HELPER_FILE"
               raise "Could not produce #{ resource }. (#{ type }, #{ content })"
             end
           rescue
-            FileUtils.rm_rf final_path if File.exists? final_path
+            FileUtils.rm_rf final_path if File.exist? final_path
             raise $!
           end
         end

data/lib/rbbt/resource/path.rb

@@ -85,7 +85,7 @@ module Path
   STANDARD_SEARCH = %w(current user local global lib cache bulk)
 
   search_path_file = File.join(ENV['HOME'], '.rbbt/etc/search_paths')
-  if File.exists?(search_path_file)
+  if File.exist?(search_path_file)
     YAML.load(File.open(search_path_file)).each do |where, location|
       SEARCH_PATHS[where.to_sym] = location
     end
@@ -112,13 +112,13 @@ module Path
                          w = w.to_sym
                          next unless paths.include? w
                          path = find(w, caller_lib, paths)
-                         return path if File.exists? path
+                         return path if File.exist? 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
+                         return path if File.exist? path
                        end
 
                        if paths.include? :default
@@ -147,8 +147,8 @@ module Path
                          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'
+                       path = path + '.gz' if File.exist? path + '.gz'
+                       path = path + '.bgz' if File.exist? path + '.bgz'
 
                        self.annotate path
                      end
@@ -325,7 +325,7 @@ module Path
       relative_file = self.sub(/(.*\/)doc\//, '\1').sub(lib_dir + "/",'')
       file = File.join(lib_dir, relative_file)
 
-      if not File.exists?(file)
+      if not File.exist?(file)
         file= Dir.glob(file.sub(/\.[^\.\/]+$/, '.*')).first
       end
 
@@ -333,7 +333,7 @@ module Path
     else
       relative_file = self.sub(/^doc\//, '\1')
 
-      if not File.exists?(relative_file)
+      if not File.exist?(relative_file)
         relative_file = Dir.glob(relative_file.sub(/\.[^\.\/]+$/, '.*')).first
       end
 

data/lib/rbbt/resource/util.rb

@@ -9,12 +9,12 @@ module Path
     }.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
 
     file = File.expand_path(file)
-    return Path.setup(file) if File.exists? File.join(file, relative_to)
+    return Path.setup(file) if File.exist? File.join(file, relative_to)
 
     while file != '/'
       dir = File.dirname file
 
-      return Path.setup(dir) if File.exists? File.join(dir, relative_to)
+      return Path.setup(dir) if File.exist? File.join(dir, relative_to)
 
       file = File.dirname file
     end
@@ -38,12 +38,12 @@ module Resource
 
       Misc.env_add 'PATH', bin_dir
 
-      FileUtils.mkdir_p opt_dir unless File.exists? opt_dir
+      FileUtils.mkdir_p opt_dir unless File.exist? opt_dir
 
       %w(.ld-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
         filename = File.join(opt_dir, file)
         begin
-          FileUtils.touch filename unless File.exists? filename
+          FileUtils.touch filename unless File.exist? filename
         rescue
           Log.warn("Could not touch #{ filename }")
         end
@@ -52,25 +52,25 @@ module Resource
       Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
         Misc.env_add('LD_LIBRARY_PATH',line.chomp)
         Misc.env_add('LD_RUN_PATH',line.chomp)
-      end if File.exists? File.join(opt_dir, '.ld-paths')
+      end if File.exist? File.join(opt_dir, '.ld-paths')
 
       Open.read(File.join opt_dir, '.pkgconfig-paths').split(/\n/).each do |line|
         Misc.env_add('PKG_CONFIG_PATH',line.chomp)
-      end if File.exists? File.join(opt_dir, '.pkgconfig-paths')
+      end if File.exist? File.join(opt_dir, '.pkgconfig-paths')
 
       Open.read(File.join opt_dir, '.aclocal-paths').split(/\n/).each do |line|
         Misc.env_add('ACLOCAL_FLAGS', "-I#{File.join(opt_dir, line.chomp)}", ' ')
-      end if File.exists? File.join(opt_dir, '.aclocal-paths')
+      end if File.exist? File.join(opt_dir, '.aclocal-paths')
 
       Open.read(File.join opt_dir, '.java-classpaths').split(/\n/).each do |line|
         Misc.env_add('CLASSPATH', "#{File.join(opt_dir,'java', 'lib', line.chomp)}")
-      end if File.exists? File.join(opt_dir, '.java-classpaths')
+      end if File.exist? File.join(opt_dir, '.java-classpaths')
 
       Dir.glob(File.join opt_dir, 'jars', '*').each do |file|
         Misc.env_add('CLASSPATH', "#{File.expand_path(file)}")
       end
 
-      if File.exists?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))
+      if File.exist?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))
         Dir.glob(File.join(opt_dir, '.post_install','*')).each do |file|
           begin
             begin

data/lib/rbbt/rest/client/step.rb

@@ -250,12 +250,16 @@ class WorkflowRESTClient
           sin.write c
         end
 
-        post_thread = Thread.new do
+        post_thread = Thread.new(Thread.current) do |parent|
           bl = lambda do |rok|
-            rok.read_body do |c,_a, _b|
-              sin.write c
+            if Net::HTTPOK === rok
+              rok.read_body do |c,_a, _b|
+                sin.write c
+              end
+              sin.close
+            else
+              parent.raise "Error in RestClient: " << rok.message
             end
-            sin.close
           end
 
           Log.debug{ "RestClient execute: #{ url } - #{Misc.fingerprint task_params}" }

data/lib/rbbt/tsv/attach.rb

@@ -9,7 +9,7 @@ module TSV
     sep = options[:sep]
 
     is = case
-         when (String === input and not input.index("\n") and input.length < 250 and File.exists?(input))
+         when (String === input and not input.index("\n") and input.length < 250 and File.exist?(input))
            CMD.cmd("env LC_ALL=C sort -k1,1 -t'#{sep}' #{ input } | grep -v '^#{sep}' ", :pipe => true)
          when (String === input or StringIO === input)
            CMD.cmd("env LC_ALL=C sort -k1,1 -t'#{sep}' | grep -v '^#{sep}'", :in => input, :pipe => true)
@@ -68,7 +68,7 @@ module TSV
     sep = options[:sep] || "\t"
 
     case
-    when (String === file1 and not file1 =~ /\n/ and file1.length < 250 and File.exists?(file1))
+    when (String === file1 and not file1 =~ /\n/ and file1.length < 250 and File.exist?(file1))
       size = CMD.cmd("wc -c '#{file1}'").read.to_f if monitor
       file1 = CMD.cmd("env LC_ALL=C sort -k1,1 -t'#{sep}' #{ file1 } | grep -v '^#{sep}' ", :pipe => true)
     when (String === file1 or StringIO === file1)
@@ -80,7 +80,7 @@ module TSV
     end
 
     case
-    when (String === file2 and not file2 =~ /\n/ and file2.length < 250 and File.exists?(file2))
+    when (String === file2 and not file2 =~ /\n/ and file2.length < 250 and File.exist?(file2))
       file2 = CMD.cmd("env LC_ALL=C sort -k1,1 -t'#{sep}' #{ file2 } | grep -v '^#{sep}' ", :pipe => true)
     when (String === file2 or StringIO === file2)
       file2 = CMD.cmd("env LC_ALL=C sort -k1,1 -t'#{sep}' | grep -v '^#{sep}'", :in => file2, :pipe => true)
@@ -174,6 +174,23 @@ module TSV
     CMD.cmd("paste #{ files.collect{|f| "'#{f}'"} * " "} -d'#{delim}' |sed 's/#{delim}[^\\t]*//g'", :pipe => true)
   end
 
+  def merge_different_fields(other, options = {})
+    TmpFile.with_file do |output|
+      TSV.merge_different_fields(self, other, output, options)
+      tsv = TSV.open output, options
+      tsv.key_field = self.key_field unless self.key_field.nil?
+      tsv.fields = self.fields + other.fields unless self.fields.nil? or other.fields.nil?
+      tsv
+    end
+  end
+
+  def merge_zip(other)
+    other.each do |k,v|
+      self.zip_new k, v
+    end
+  end
+
+  
   def attach(other, options = {})
     options      = Misc.add_defaults options, :in_namespace => false, :persist_input => true
     fields, one2one, complete = Misc.process_options options, :fields, :one2one, :complete
@@ -257,20 +274,5 @@ module TSV
     self.fields.each_with_index{|field,i| detached_fields << i if file_fields.include? field.fullname}
     reorder :key, detached_fields
   end
-
-  def merge_different_fields(other, options = {})
-    TmpFile.with_file do |output|
-      TSV.merge_different_fields(self, other, output, options)
-      tsv = TSV.open output, options
-      tsv.key_field = self.key_field unless self.key_field.nil?
-      tsv.fields = self.fields + other.fields unless self.fields.nil? or other.fields.nil?
-      tsv
-    end
-  end
-
-  def merge_zip(other)
-    other.each do |k,v|
-      self.zip_new k, v
-    end
-  end
+ 
 end