frprep 0.0.1.prealpha

data/lib/frprep/frprep.rb

@@ -0,0 +1,686 @@
+require 'frprep/do_parses'
+require 'frprep/FrprepHelper'
+require 'frprep/FixSynSemMapping'
+
+##############################
+# The class that does all the work
+module FrPrep
+class FrPrep
+
+  def initialize(exp)   # FrprepConfigData object
+    @exp = exp
+
+    # AB: move to FRprepOptionParser    
+    # remove previous contents of frprep internal data directory
+    unless exp.get("frprep_directory")
+      raise "Please set 'frprep_directory', the frprep internal data directory,\n" +
+            "in the experiment file."
+    end
+
+    # experiment directory: 
+    # frprep internal data directory, subdir according to experiment ID
+     exp_dir = File.new_dir(@exp.get("frprep_directory"),
+                            @exp.get("prep_experiment_ID"))
+    # %x{rm -rf #{exp_dir}}
+
+    # suffixes for different types of output files
+    @file_suffixes = {"lemma" => ".lemma",
+      "pos" => ".pos",
+      "tab" => ".tab",
+      "stxml" => ".xml"}
+  end
+  
+  def transform()
+
+    # AB: Debugging.
+    debugger if $DEBUG
+    
+    current_format = @exp.get("format")
+
+    # AB: move to FRprepOptionParser
+    unless @exp.get("directory_input")
+      $stderr.puts "Please specify 'directory_input' in the experiment file."
+      exit 1
+    end
+    # AB: move to FRprepOptionParser    
+    unless @exp.get("directory_preprocessed")
+      $stderr.puts "Please specify 'directory_preprocessed' in the experiment file."
+      exit 1
+    end
+
+    ##
+    # input and output directories.
+    #
+    # sanity check: output in tab format will not work
+    # if we also do a parse
+    if @exp.get("tabformat_output") and @exp.get("do_parse")
+      $stderr.puts "Error: Cannot do Tab format output"
+      $stderr.puts "when the input text is being parsed."
+      $stderr.puts "Please set either 'tabformat_output' or 'do_parse' to false."
+      exit 1
+    end
+    input_dir = File.existing_dir(@exp.get("directory_input"))
+    output_dir = File.new_dir(@exp.get("directory_preprocessed"))
+    if @exp.get("tabformat_output")
+      split_dir = output_dir
+    else
+      split_dir = frprep_dirname("split", "new")
+    end
+
+    ####
+    # transform data to UTF-8
+
+    if ["iso", "hex"].include? @exp.get("encoding")
+      # transform ISO -> UTF-8 or Hex -> UTF-8
+      # write result to encoding_dir, 
+      # then set encoding_dir to be the new input_dir
+
+      encoding_dir = frprep_dirname("encoding", "new")
+      $stderr.puts "Frprep: Transforming  to UTF-8."
+      Dir[input_dir + "*"].each { |filename|
+        unless File.file? filename
+          # not a file? then skip
+          next
+        end
+        outfilename = encoding_dir + File.basename(filename)
+        FrprepHelper.to_utf8_file(filename, outfilename, @exp.get("encoding"))
+      }
+      
+      input_dir = encoding_dir
+    end
+
+    
+    ####
+    # transform data all the way to the output format,
+    # which is SalsaTigerXML by default,
+    # except when tabformat_output has been set, in which case it's 
+    # Tab format.
+    current_dir = input_dir
+
+    if @exp.get("tabformat_output")
+      done_format = "SalsaTabWithPos"
+    else
+      done_format = "Done"
+    end
+
+    while not(current_format == done_format)
+      case current_format
+
+      when "BNC"
+        # basically plain, plus some tags to be removed
+        plain_dir = frprep_dirname("plain", "new")
+        
+        $stderr.puts "Frprep: Transforming BNC format text in #{current_dir} to plain format."
+        $stderr.puts "Storing the result in #{plain_dir}."
+        $stderr.puts "Expecting one sentence per line."
+        
+	transform_bncformat_dir(current_dir, plain_dir)
+        
+	current_dir = plain_dir
+	current_format = "Plain"
+
+      when "Plain" 
+	# transform to tab format
+        
+        tab_dir = frprep_dirname("tab", "new")
+
+        $stderr.puts "Frprep: Transforming plain text in #{current_dir} to SalsaTab format."
+        $stderr.puts "Storing the result in #{tab_dir}."
+        $stderr.puts "Expecting one sentence per line."
+        
+	transform_plain_dir(current_dir, tab_dir)
+        
+	current_dir = tab_dir
+	current_format = "SalsaTab"
+
+      when "FNXml"
+	# transform to tab format
+
+        tab_dir = frprep_dirname("tab", "new")
+
+	$stderr.puts "Frprep: Transforming FN data in #{current_dir} to tabular format."
+	$stderr.puts "Storing the result in " + tab_dir
+
+	fndata = FNDatabase.new(current_dir)
+	fndata.extract_everything(tab_dir)
+	Kernel.system("chmod -R g+rx #{tab_dir}")
+
+	current_dir = tab_dir
+	current_format = "SalsaTab"
+
+      when "FNCorpusXml"
+        # transform to tab format
+        tab_dir = frprep_dirname("tab", "new")
+
+	$stderr.puts "Frprep: Transforming FN data in #{current_dir} to tabular format."
+	$stderr.puts "Storing the result in " + tab_dir
+        # assuming that all XML files in the current directory are FN Corpus XML files
+        Dir[current_dir + "*.xml"].each { |fncorpusfilename|
+          corpus = FNCorpusXMLFile.new(fncorpusfilename)
+          outfile = File.new(tab_dir + File.basename(fncorpusfilename, ".xml") + ".tab", 
+                             "w")
+          corpus.print_conll_style(outfile)
+          outfile.close()
+        }
+
+	Kernel.system("chmod -R g+rx #{tab_dir}")
+	current_dir = tab_dir
+	current_format = "SalsaTab"
+
+      when "SalsaTab"
+	# lemmatize and POStag
+
+        $stderr.puts "Frprep: Lemmatizing and parsing text in #{current_dir}."
+        $stderr.puts "Storing the result in #{split_dir}."
+        transform_pos_and_lemmatize(current_dir, split_dir)
+
+        current_dir = split_dir
+	current_format = "SalsaTabWithPos"
+
+      when "SalsaTabWithPos"
+        # parse
+
+        parse_dir = frprep_dirname("parse", "new")
+
+        $stderr.puts "Frprep: Transforming tabular format text in #{current_dir} to SalsaTigerXML format."
+        $stderr.puts "Storing the result in #{parse_dir}."
+
+        transform_salsatab_dir(current_dir, parse_dir, output_dir)
+
+        current_dir = output_dir
+	current_format = "Done"
+
+      when "SalsaTigerXML"
+        
+        parse_dir = frprep_dirname("parse", "new")
+	print "Transform parser output into stxml\n"	
+        transform_stxml_dir(parse_dir, split_dir, input_dir, output_dir, @exp)
+        current_dir = output_dir
+        current_format = "Done"
+
+      else
+	$stderr.puts "Unknown data format #{current_format}"
+        $stderr.puts "Please check the 'format' entry in your experiment file."
+        raise "Experiment file problem"
+      end
+    end
+
+    $stderr.puts "Frprep: Done preprocessing."
+  end
+  
+  ############################################################################3
+  private
+  ############################################################################3
+
+  ###############
+  # frprep_dirname:
+  # make directory name for frprep-internal data
+  # of a certain kind described in <subdir>
+  #
+  # frprep_directory has one subdirectory for each experiment ID,
+  # and below that there is one subdir per subtask
+  #
+  # If this is a new directory, it is constructed,
+  # if it should be an existing directory, its existence is  checked.
+  def frprep_dirname(subdir,     # string: designator of subdirectory
+                     new = nil)  # non-nil: this may be a new directory
+
+    dirname = File.new_dir(@exp.get("frprep_directory"),
+                           @exp.get("prep_experiment_ID"),
+                           subdir)
+
+
+    if new
+      return File.new_dir(dirname)
+    else
+      return File.existing_dir(dirname)
+    end
+  end
+  
+
+
+  ###############
+  # transform_plain:
+  #
+  # transformation for BNC format:
+  #
+  # transform to plain format, removing <> elements
+  def transform_bncformat_dir(input_dir,  # string: input directory
+                              output_dir) # string: output directory
+
+    Dir[input_dir + "*"].each { |bncfilename|
+      
+      # open input and output file
+      # end output file name in "tab" because that is, at the moment, required
+      outfilename = output_dir + File.basename(bncfilename)
+      FrprepHelper.bnc_to_plain_file(bncfilename, outfilename)
+    }
+  end
+
+
+  ###############
+  # transform_plain:
+  #
+  # transformation for plaintext:
+  #
+  # transform to Tab format, separating punctuation from adjacent words
+  def transform_plain_dir(input_dir,  # string: input directory
+                          output_dir) # string: output directory
+
+    Dir[input_dir + "*"].each { |plainfilename|
+      
+      # open input and output file
+      # end output file name in "tab" because that is, at the moment, required
+      outfilename = output_dir + File.basename(plainfilename) + @file_suffixes["tab"]
+      FrprepHelper.plain_to_tab_file(plainfilename, outfilename)
+    }
+  end
+
+  ###############
+  # transform_pos_and_lemmatize
+  #
+  # transformation for Tab format files:
+  #
+  # - Split into parser-size chunks
+  # - POS-tag, lemmatize
+  def transform_pos_and_lemmatize(input_dir, # string: input directory
+                                  output_dir) # string: output directory
+    ##
+    # split the TabFormatFile into chunks of max_sent_num size
+    FrprepHelper.split_dir(input_dir, output_dir,@file_suffixes["tab"],
+			   @exp.get("parser_max_sent_num"), 
+			   @exp.get("parser_max_sent_len"))
+    
+    ##
+    # POS-Tagging
+    if @exp.get("do_postag")
+      $stderr.puts "Frprep: Tagging."
+      unless @exp.get("pos_tagger_path") and @exp.get("pos_tagger")
+	raise "POS-tagging: I need 'pos_tagger' and 'pos_tagger_path' in the experiment file."
+      end
+      
+      sys_class = SynInterfaces.get_interface("pos_tagger", 
+					      @exp.get("pos_tagger"))
+      print "pos tagger interface: ", sys_class, "\n" 
+      unless sys_class
+        raise "Shouldn't be here"
+      end
+      sys = sys_class.new(@exp.get("pos_tagger_path"),
+			  @file_suffixes["tab"],
+			  @file_suffixes["pos"])
+      sys.process_dir(output_dir, output_dir)
+    end
+      
+    
+    ## 
+    # Lemmatization
+    if @exp.get("do_lemmatize")
+      $stderr.puts "Frprep: Lemmatizing."
+      unless @exp.get("lemmatizer_path") and @exp.get("lemmatizer")
+	raise "Lemmatization: I need 'lemmatizer' and 'lemmatizer_path' in the experiment file."
+      end
+
+      sys_class = SynInterfaces.get_interface("lemmatizer", 
+					      @exp.get("lemmatizer"))
+      # AB: make this exception explicit.
+      unless sys_class
+        raise 'I got a empty interface class for the lemmatizer!'
+      end
+      sys = sys_class.new(@exp.get("lemmatizer_path"),
+			  @file_suffixes["tab"],
+			  @file_suffixes["lemma"])
+      sys.process_dir(output_dir, output_dir)
+    end
+  end
+
+  ###############
+  # transform_salsatab
+  #
+  # transformation for Tab format files:
+  #
+  # - parse
+  # - Transform parser output to SalsaTigerXML
+  #   If no parsing, make flat syntactic structure.
+  def transform_salsatab_dir(input_dir,        # string: input directory
+                             parse_dir,     # string: output directory for parses 
+                             output_dir)       # string: global output directory
+    
+    ##
+    # (Parse and) transform to SalsaTigerXML 
+
+    # get interpretation class for this 
+    # parser/lemmatizer/POS tagger combination
+    interpreter_class = SynInterfaces.get_interpreter_according_to_exp(@exp)
+    unless interpreter_class
+      raise "Shouldn't be here"
+    end
+    
+    parse_obj = DoParses.new(@exp, @file_suffixes,
+			     parse_dir, 
+			     "tab_dir" => input_dir)
+    parse_obj.each_parsed_file { |parsed_file_obj|
+
+      outfilename = output_dir + parsed_file_obj.filename + ".xml"
+      $stderr.puts "Writing #{outfilename}"
+      begin
+        outfile = File.new(outfilename, "w")
+      rescue
+        raise "Cannot write to SalsaTigerXML output file #{outfilename}"
+      end
+
+      outfile.puts SalsaTigerXMLHelper.get_header()
+      # work with triples
+      # SalsaTigerSentence, FNTabSentence,
+      # hash: tab sentence index(integer) -> array:SynNode
+      parsed_file_obj.each_sentence { |st_sent, tabformat_sent, mapping|
+
+        # parsed: add headwords using parse tree
+        if @exp.get("do_parse")
+          FrprepHelper.add_head_attributes(st_sent, interpreter_class)
+        end
+
+        # add lemmas, if they are there. If they are not, don't print out a warning.
+        if @exp.get("do_lemmatize")
+          FrprepHelper.add_lemmas_from_tab(st_sent, tabformat_sent, mapping)
+        end
+        
+        # add semantics
+	# we can use the method in SalsaTigerXMLHelper
+	# that reads semantic information from the tab file
+	# and combines all targets of a sentence into one frame
+	FrprepHelper.add_semantics_from_tab(st_sent, tabformat_sent, mapping, 
+					    interpreter_class, @exp)
+
+        # remove pseudo-frames from FrameNet data
+        FrprepHelper.remove_deprecated_frames(st_sent, @exp)
+
+        # handle multiword targets
+        FrprepHelper.handle_multiword_targets(st_sent, 
+					      interpreter_class, @exp.get("language"))
+
+        # handle Unknown frame names
+        FrprepHelper.handle_unknown_framenames(st_sent, interpreter_class)	       
+	
+        outfile.puts st_sent.get()
+      }
+      outfile.puts SalsaTigerXMLHelper.get_footer()
+    }
+  end
+
+  #############################################
+  # transform_stxml
+  # 
+  # transformation for SalsaTigerXML data
+  #
+  # - If the input format was SalsaTigerXML:
+  #   - Tag, lemmatize and parse, if the experiment file tells you so
+  #
+  # - If the origin is the Salsa corpus: 
+  #   Change frame names from Unknown\d+ to lemma_Unknown\d+
+  #
+  # - fix multiword lemmas, or at least try
+  # - transform to UTF 8
+  def transform_stxml_dir(parse_dir,  # string: name of directory for parse data
+                          tab_dir,    # string: name of directory for split/tab data
+                          input_dir,  # string: name of input directory
+                          output_dir, # string: name of final output directory
+                          exp)        # FrprepConfigData
+
+    ####
+    # Data preparation
+    
+    # Data with Salsa as origin:
+    # remember the target lemma as an attribute on the 
+    # <target> elements
+    #
+    # currently deactivated: encoding problems
+    #     if @exp.get("origin") == "SalsaTiger"
+    #       $stderr.puts "Frprep: noting target lemmas"
+    #       changed_input_dir = frprep_dirname("salsalemma", "new") 
+    #       FrprepHelper.note_salsa_targetlemmas(input_dir, changed_input_dir)     
+    
+    #       # remember changed input dir as input dir
+    #       input_dir = changed_input_dir
+    #     end
+    
+    #  If data is to be parsed, split and tabify input files
+    #    else copy data to stxml_indir.
+    
+    # stxml_dir: directory where SalsaTiger data is situated
+    if @exp.get("do_parse")
+      # split data
+      stxml_splitdir = frprep_dirname("stxml_split", "new")
+      stxml_dir = stxml_splitdir
+
+      $stderr.puts "Frprep: splitting data"
+      FrprepHelper.stxml_split_dir(input_dir, stxml_splitdir, 
+				   @exp.get("parser_max_sent_num"), 
+				   @exp.get("parser_max_sent_len"))
+    else
+      # no parsing: copy data to split dir
+      stxml_dir = parse_dir
+      $stderr.puts "Frprep: Copying data to #{stxml_dir}"
+      Dir[input_dir + "*.xml"].each { |filename|
+        `cp #{filename} #{stxml_dir}#{File.basename(filename)}`
+      }
+    end
+
+    # Some syntactic processing will take place:
+    # tabify data
+    if @exp.get("do_parse") or @exp.get("do_lemmatize") or @exp.get("do_postag")      
+      $stderr.puts "Frprep: making input for syn. processing" 
+      
+      Dir[stxml_dir+"*"+@file_suffixes["stxml"]].each { |stxmlfilename|
+        
+        tabfilename = tab_dir + File.basename(stxmlfilename,@file_suffixes["stxml"]) + @file_suffixes["tab"]
+        FrprepHelper.stxml_to_tab_file(stxmlfilename, tabfilename, exp)
+      }
+    end
+    
+    ###
+    # POS-tagging
+    if @exp.get("do_postag")
+      $stderr.puts "Frprep: Tagging."
+      unless @exp.get("pos_tagger_path") and @exp.get("pos_tagger")
+	raise "POS-tagging: I need 'pos_tagger' and 'pos_tagger_path' in the experiment file."
+      end
+
+      sys_class = SynInterfaces.get_interface("pos_tagger", 
+					      @exp.get("pos_tagger"))
+      unless sys_class
+        raise "Shouldn't be here"
+      end
+      sys = sys_class.new(@exp.get("pos_tagger_path"),
+			  @file_suffixes["tab"],
+			  @file_suffixes["pos"])
+      sys.process_dir(tab_dir, tab_dir)
+    end
+
+    ###
+    # Lemmatization
+    if @exp.get("do_lemmatize")
+      $stderr.puts "Frprep: Lemmatizing."
+      unless @exp.get("lemmatizer_path") and @exp.get("lemmatizer")
+	raise "Lemmatization: I need 'lemmatizer' and 'lemmatizer_path' in the experiment file."
+      end
+
+      sys_class = SynInterfaces.get_interface("lemmatizer", 
+					      @exp.get("lemmatizer"))
+      unless sys_class
+        raise "Shouldn't be here"
+      end
+      sys = sys_class.new(@exp.get("lemmatizer_path"),
+			  @file_suffixes["tab"],
+			  @file_suffixes["lemma"])
+      sys.process_dir(tab_dir, tab_dir)
+    end
+
+    ###
+    # Parsing, production of SalsaTigerXML output
+
+    # get interpretation class for this 
+    # parser/lemmatizer/POS tagger combination
+    sys_class_names = Hash.new
+    [["do_postag", "pos_tagger"],
+      ["do_lemmatize", "lemmatizer"],
+      ["do_parse", "parser"]].each { |service, system_name|
+      if @exp.get(service)  # yes, perform this service
+	sys_class_names[system_name] = @exp.get(system_name)
+      end
+    }
+    interpreter_class = SynInterfaces.get_interpreter(sys_class_names)
+    unless interpreter_class
+      raise "Shouldn't be here"
+    end
+
+    parse_obj = DoParses.new(@exp, @file_suffixes,
+			     parse_dir, 
+			     "tab_dir" => tab_dir,
+                             "stxml_dir" => stxml_dir)
+    parse_obj.each_parsed_file { |parsed_file_obj|
+      outfilename = output_dir + parsed_file_obj.filename + ".xml"
+      $stderr.puts "Writing #{outfilename}"
+      begin
+        outfile = File.new(outfilename, "w")
+      rescue
+        raise "Cannot write to SalsaTigerXML output file #{outfilename}"
+      end
+
+
+      if @exp.get("do_parse")
+        # read old SalsaTigerXML file
+        # so we can integrate the old file's semantics later
+        oldxml = Array.new # array of sentence strings
+        # we assume that the old and the new file have the same name,
+        # ending in .xml.
+        oldxmlfile = FilePartsParser.new(stxml_dir + parsed_file_obj.filename + ".xml")
+        oldxmlfile.scan_s { |sent_string|
+          # remember this sentence by its ID
+          oldxml << sent_string
+        }
+      end       
+
+      outfile.puts SalsaTigerXMLHelper.get_header()
+      index = 0
+      # work with triples
+      # SalsaTigerSentence, FNTabSentence,
+      # hash: tab sentence index(integer) -> array:SynNode
+      parsed_file_obj.each_sentence { |st_sent, tabformat_sent, mapping|
+
+        # parsed? then integrate semantics and lemmas from old file
+        if @exp.get("do_parse")
+          oldsent_string = oldxml[index]
+          index += 1
+          if oldsent_string
+
+            # modified by ines, 27/08/08
+            # for Berkeley => substitute ( ) for *LRB* *RRB*
+            if exp.get("parser") == "berkeley"
+              oldsent_string.gsub!(/word='\('/, "word='*LRB*'")
+              oldsent_string.gsub!(/word='\)'/, "word='*RRB*'")
+              oldsent_string.gsub!(/word=\"\(\"/, "word='*LRB*'")
+              oldsent_string.gsub!(/word=\"\)\"/, "word='*RRB*'")
+            end
+
+            # we have both an old and a new sentence, so integrate semantics
+            oldsent = SalsaTigerSentence.new(oldsent_string)
+	if st_sent.nil?
+		next
+	end
+          if ( FrprepHelper.integrate_stxml_semantics_and_lemmas(oldsent, st_sent, interpreter_class, @exp) == false)
+		#print "FALSE \n";
+		#print oldsent, "\n", st_sent, "\n\n";
+
+      	    	oldsent_string = oldxml[index]
+        	index += 1
+          	if oldsent_string
+
+            	# modified by ines, 27/08/08
+            	# for Berkeley => substitute ( ) for *LRB* *RRB*
+            	if exp.get("parser") == "berkeley"
+            	  oldsent_string.gsub!(/word='\('/, "word='*LRB*'")
+            	  oldsent_string.gsub!(/word='\)'/, "word='*RRB*'")
+            	  oldsent_string.gsub!(/word=\"\(\"/, "word='*LRB*'")
+            	  oldsent_string.gsub!(/word=\"\)\"/, "word='*RRB*'")
+            	end
+
+            	# we have both an old and a new sentence, so integrate semantics
+            	oldsent = SalsaTigerSentence.new(oldsent_string)
+                #print oldsent, "\n", st_sent, "\n\n";
+		FrprepHelper.integrate_stxml_semantics_and_lemmas(oldsent, st_sent, interpreter_class, @exp) 
+	
+		end
+	  #else
+			#print "TRUE\n";
+			#print oldsent, "\n", st_sent, "\n\n";
+ 	  end
+        else
+            # no corresponding old sentence for this new sentence
+            $stderr.puts "Warning: transporting semantics -- missing source sentence, skipping"
+          end
+        end
+
+        # remove pseudo-frames from FrameNet data
+        FrprepHelper.remove_deprecated_frames(st_sent, @exp)
+
+        # repair syn/sem mapping problems?
+        if @exp.get("fe_syn_repair") or @exp.get("fe_rel_repair")
+          FixSynSemMapping.fixit(st_sent, @exp, interpreter_class)
+        end
+
+        outfile.puts st_sent.get()
+      } # each ST sentence
+      outfile.puts SalsaTigerXMLHelper.get_footer()
+    } # each file parsed
+  end
+
+
+  ###################################
+  # general file iterators
+
+  # yields pairs of [infile name, outfile stream]
+  def change_each_file_in_dir(dir,                 # string: directory name
+                              suffix)    # string: filename pattern, e.g. "*.xml"
+    Dir[dir + "*#{suffix}"].each { |filename|
+      tempfile = Tempfile.new("FrprepHelper")
+      yield [filename, tempfile]
+      
+      # move temp file to original file location
+      tempfile.close()
+      `cp #{filename} #{filename}.bak`
+      `mv #{tempfile.path()} #{filename}`
+      tempfile.close(true)
+    } # each file
+  end
+
+  #######
+  # change_each_stxml_file_in_dir
+  #
+  # use change_each_file_in_dir, but assume that the files
+  # are SalsaTigerXML files: Keep file headers and footers,
+  # and just offer individual sentences for changing
+  #
+  # Yields SalsaTigerSentence objects, each sentence to be changed
+  def change_each_stxml_file_in_dir(dir)            # string: directory name
+
+    change_each_file_in_dir(dir, "*.xml") { |stfilename, tf|
+      infile = FilePartsParser.new(stfilename)
+
+      # write header
+      tf.puts infile.head()
+
+      # iterate through sentences, yield as SalsaTigerSentence objects
+      infile.scan_s() { |sent_string|
+        sent = SalsaTigerSentence.new(sent_string)
+        yield sent
+        # write changed sentence
+        tf.puts sent.get()
+      } # each sentence
+      
+      # write footer
+      tf.puts infile.tail()
+      infile.close()
+    }
+  end
+end
+end