rbbt-util 4.0.2 → 4.1.0

data/test/rbbt/tsv/test_util.rb

@@ -0,0 +1,25 @@
+require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
+require 'rbbt/tsv'
+require 'rbbt/tsv/util'
+require 'rbbt/util/tmpfile'
+require 'test/unit'
+
+class TestTSVUtil < Test::Unit::TestCase
+
+  def test_field_counts
+   content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b    Id1|Id2
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+
+      assert_equal 2, TSV.field_match_counts(tsv, ["a","A","a","b","Id3"])["ValueA"]
+
+    end
+  
+  end
+
+end

data/test/rbbt/util/test_misc.rb

@@ -133,6 +133,14 @@ class TestMisc < Test::Unit::TestCase
     end
   end
 
+  def test_positions2hash
+    inputs = Misc.positional2hash([:one, :two, :three], 1, :two => 2, :four => 4)
+    assert_equal 1, inputs[:one]
+    assert_equal 2, inputs[:two]
+    assert_equal nil, inputs[:three]
+    assert_equal nil, inputs[:four]
+  end
+
 #  def test_divide
 #    assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
 #  end

metadata

@@ -5,9 +5,9 @@ version: !ruby/object:Gem::Version
   prerelease: 
   segments: 
   - 4
+  - 1
   - 0
-  - 2
-  version: 4.0.2
+  version: 4.1.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-10-03 00:00:00 +02:00
+date: 2011-11-17 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -161,7 +161,6 @@ files:
 - lib/rbbt/util/log.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/open.rb
-- lib/rbbt/util/persistence.rb
 - lib/rbbt/util/simpleDSL.rb
 - lib/rbbt/util/simpleopt.rb
 - lib/rbbt/util/task/job.rb
@@ -197,9 +196,11 @@ files:
 - test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_util.rb
 - test/rbbt/workflow/test_soap.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
+- test/rbbt/test_persist.rb
 - test/test_rbbt.rb
 - bin/tsv.rb
 - bin/tchash.rb
@@ -264,7 +265,9 @@ test_files:
 - test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_util.rb
 - test/rbbt/workflow/test_soap.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
+- test/rbbt/test_persist.rb
 - test/test_rbbt.rb

data/lib/rbbt/util/persistence.rb

@@ -1,406 +0,0 @@
-require 'rbbt/util/tsv'
-require 'rbbt/util/misc'
-require 'rbbt/util/open'
-require 'digest/md5'
-require 'yaml'
-
-module Persistence
-  require 'rbbt/util/tc_hash'
-  TSV = TCHash
-
-  CACHEDIR="/tmp/tsv_persistent_cache"
-  FileUtils.mkdir CACHEDIR unless File.exist? CACHEDIR
-
-  def self.cachedir=(cachedir)
-    CACHEDIR.replace cachedir
-    FileUtils.mkdir_p CACHEDIR unless File.exist? CACHEDIR
-  end
-
-  def self.cachedir
-    CACHEDIR
-  end
- 
-  def self.get_persistence_file(file, prefix, options = {})
-    persistence_dir = Misc.process_options options, :dir
-    persistence_dir ||= CACHEDIR
-
-    if options.include? :filters
-      options[:filters].each do |match,value|
-        file = file + "&F[#{match}=#{Misc.digest(value.inspect)}]"
-      end
-    end
-
-    name = prefix.to_s.dup << ":" << file.to_s << ":"
-
-    options_md5 = Misc.hash2md5 options
-    File.join(persistence_dir, name.to_s.gsub(/\s/,'_').gsub(/\//,'>') + options_md5)
-  end
-
-  def self.get_filename(file)
-    case
-    when (String === file and File.exists? file)
-      File.expand_path file
-    when File === file
-      File.expand_path file.path
-    when Object::TSV === file
-      file.filename
-    when String === file
-      file
-    else
-      file.class.to_s
-    end
-  end
-
-  def self.persist_string(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists? persistence_file
-      Log.debug "Creating #{ persistence_file }. Prefix = #{prefix}"
-
-      res = yield file, options, filename, persistence_file
-      Open.write(persistence_file, res.to_s)
-      res
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-
-      Open.read(persistence_file)
-    end
-  end
-
-  def self.persist_marshal(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists? persistence_file
-      Log.debug "Creating #{ persistence_file }. Prefix = #{prefix}"
-      res = yield file, options
-      Open.write(persistence_file, Marshal.dump(res))
-      res
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-      Marshal.load(Open.open(persistence_file))
-    end
-  end
-
-  def self.persist_yaml(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists? persistence_file
-      Log.debug "Creating #{ persistence_file }. Prefix = #{prefix}"
-      res = yield file, options, filename, persistence_file
-      Open.write(persistence_file, YAML.dump(res))
-      res
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-      YAML.load(Open.open(persistence_file))
-    end
-  end
-
-  def self.persist_tsv_string(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists? persistence_file
-      Log.debug "Creating #{ persistence_file }. Prefix = #{prefix}"
-      res = yield file, options, filename, persistence_file
-      Open.write(persistence_file, res.to_s)
-      res
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-      tsv = Object::TSV.new persistence_file
-      tsv.filename = filename
-      tsv
-    end
-  end
-
-  def self.tsv_serializer(data, extra = nil)
-    return data.serializer if Persistence::TSV === data
-    if Object::TSV === data 
-      return :integer if (data.cast == "to_i" or data.cast == :to_i) and data.type == :single
-      return :integer_array if (data.cast == "to_i" or data.cast == :to_i) and (data.type == :list or data.type == :flat)
-
-      case
-      when (data.type == :list or data.type == :flat)
-        :list
-      when data.type == :single
-        :single
-      else
-        :double
-      end
-    else
-      return :marshal if extra.nil?
-      return :integer if (extra[:cast] == "to_i" or extra[:cast] == :to_i) and extra[:type] == :single
-      return :integer_array if (extra[:cast] == "to_i" or extra[:cast] == :to_i) and (extra[:type] == :list or extra[:type] == :flat)
-
-      case
-      when (extra[:type] == :list or extra[:type] == :flat)
-        :list
-      when extra[:type] == :single
-        :single
-      else
-        :double
-      end
-    end
-  end
-
-  def self.persist_tsv(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists? persistence_file
-      Log.debug "Creating #{ persistence_file }. Prefix = #{prefix}"
-
-      res = yield file, options, filename, persistence_file
-
-      serializer = tsv_serializer res
-
-      if TCHash === res
-        per = res
-      else
-
-        if File.exists? persistence_file
-          Log.debug "Erasing old #{ persistence_file }. Prefix = #{prefix}"
-          FileUtils.rm persistence_file
-        end
-
-        Log.debug "Dump data into '#{persistence_file}'"
-        per = Persistence::TSV.get persistence_file, true, serializer
-
-        per.write
-        per.merge! res
-
-        Persistence::TSV::FIELD_INFO_ENTRIES.keys.each do |key| 
-          if res.respond_to?(key.to_sym) and per.respond_to?("#{key}=".to_sym)
-            per.send "#{key}=".to_sym, res.send(key.to_sym) 
-          end
-        end
-      end
-
-      tsv = Object::TSV.new per
-
-      per.read
-
-      tsv
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-
-      per = Persistence::TSV.get persistence_file, false, serializer
-      tsv = Object::TSV.new per
-      Persistence::TSV::FIELD_INFO_ENTRIES.keys.each do |key| 
-        if tsv.respond_to?(key.to_sym)  and per.respond_to?(key.to_sym)
-          tsv.send "#{key}=".to_sym, per.send(key.to_sym) 
-        end
-      end
-      
-      per.read
-
-      tsv
-    end
-  end
-
-  def self.persist_tsv_extra(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists?(persistence_file)
-      Log.debug "Creating #{ persistence_file }. Prefix = #{prefix}"
-      res, extra = yield file, options, filename, persistence_file
-
-      serializer = tsv_serializer res, extra
-
-      per = nil
-      if not Persistence::TSV === res
-        begin
-          per = Persistence::TSV.get persistence_file, true, serializer
-
-          per.write
-          per.merge! res
-          Persistence::TSV::FIELD_INFO_ENTRIES.keys.each do |key| 
-            if extra.include?(key.to_sym)  and per.respond_to?(key.to_sym)
-              per.send "#{key}=".to_sym, extra[key.to_sym]
-            end
-          end
-
-        rescue Exception
-          per.close
-          raise $!
-        end
-      else
-        per = res
-      end
-
-     [ per, extra ]
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-      begin
-        per = Persistence::TSV.get persistence_file, false, serializer
-
-        extra = {}
-        Persistence::TSV::FIELD_INFO_ENTRIES.keys.each do |key| 
-          if per.respond_to?(key.to_sym)
-            extra[key] = per.send(key.to_sym)
-          end
-        end
-
-      rescue Interrupt
-        raise "Interrupted"
-      rescue Exception
-        per.close unless per.nil?
-        raise $!
-      end
-
-      [ per, extra ]
-    end
-  end
-
-  def self.persist_fwt(file, prefix = "", options = {})
-    options = 
-      Misc.add_defaults options, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_file, filename =
-      Misc.process_options options, :persistence_update, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, options)
-
-    if persistence_update or not File.exists? persistence_file
-      Log.debug "Creating FWT #{ persistence_file }. Prefix = #{prefix}"
-
-      range = options[:range]
-
-      res = yield file, options, filename, persistence_file
-
-      if File.exists? persistence_file
-        Log.debug "Erasing old #{ persistence_file }. Prefix = #{prefix}"
-        FileUtils.rm persistence_file
-      end
-
-
-      if FixWidthTable === res and res.filename == :memory 
-        Log.debug "Dumping memory FWT into #{ persistence_file }. Prefix = #{prefix}"
-        FileUtils.mkdir_p File.dirname(persistence_file) unless File.exists? File.dirname(persistence_file)
-        Open.write(persistence_file, res.dump)
-        fwt = FixWidthTable.get persistence_file
-      else
-
-        max_length = res.collect{|k,v| k.length}.max
-
-        if range
-          begin
-            fwt = FixWidthTable.get persistence_file, max_length, true
-            fwt.add_range res
-          rescue
-            FileUtils.rm persistence_file if File.exists? persistence_file
-            raise $!
-          end
-        else
-          begin
-            fwt = FixWidthTable.get persistence_file, max_length, false
-            fwt.add_point res
-          rescue
-            FileUtils.rm persistence_file
-            raise $!
-          end
-        end
-
-        fwt.read
-      end
-
-      fwt
-    else
-      Log.debug "Loading #{ persistence_file }. Prefix = #{prefix}"
-
-      fwt = FixWidthTable.new persistence_file, nil, nil
-
-      fwt
-    end
-  end
-
-  def self.persist(file, prefix = "", persistence_type = :string, options = {}, &block)
-    options = Misc.add_defaults options, :persistence => true
-
-    persistence =
-      Misc.process_options options, :persistence
-
-    filename = get_filename(file)
-
-    o = options.dup
-    o = 
-      Misc.add_defaults o, :persistence_update => false, :persistence_file => nil, :filename => nil
-    persistence_update, persistence_dir, persistence_file, filename =
-      Misc.process_options o, :persistence_update, :persistence_dir, :persistence_file, :filename
-
-    filename         ||= get_filename(file)
-    persistence_file ||= get_persistence_file(filename, prefix, o.merge(:persistence_dir => persistence_dir))
-
-    if persistence == :no_create
-      persistence = false if not File.exists? persistence_file
-    end
-
-    if not persistence
-      Log.low "Non Persistent Loading for #{filename}. Prefix: #{prefix}"
-      yield file, options, filename
-    else
-      Log.low "Persistent Loading for #{filename}. Prefix: #{prefix}. Type #{persistence_type.to_s}"
-      Misc.lock(persistence_file, file, prefix, options, block) do |persistence_file,file,prefix,options,block|
-        case persistence_type.to_sym
-        when :string
-          persist_string(file, prefix, options, &block)
-        when :marshal
-          persist_marshal(file, prefix, options, &block)
-        when :yaml
-          persist_yaml(file, prefix, options, &block)
-        when :tsv
-          persist_tsv(file, prefix, options, &block)
-        when :tsv_string
-          persist_tsv_string(file, prefix, options, &block)
-        when :tsv_extra
-          persist_tsv_extra(file, prefix, options, &block)
-        when :fwt
-          persist_fwt(file, prefix, options, &block)
-        end
-      end
-    end
-  end
-end
-
-module LocalPersist
-
-  attr_accessor :local_persistence_dir
-  def local_persist(name, prefix, type, options= {}, &block)
-    Persistence.persist(name, prefix, type, options.merge({:persistence_dir => @local_persistence_dir}), &block)
-  end
-
-end
-