frprep 0.0.1.prealpha

data/lib/rosy/opt_parser.rb

@@ -0,0 +1,379 @@
+# -*- coding: utf-8 -*-
+
+require 'getoptlong'
+
+require 'rosy/RosyConfigData'
+
+module Rosy
+
+  class OptParser
+    def self.parse(cmd_args)
+      
+      ##############################
+      # main starts here
+      ##############################
+      
+      ##
+      # evaluate runtime arguments
+      
+      tasks = {
+        "featurize" => [ [ '--testID', '-i', GetoptLong::REQUIRED_ARGUMENT],             # test table ID, required for test, no default
+                         [ '--dataset', '-d', GetoptLong::REQUIRED_ARGUMENT],            # set to featurize: 'train' or 'test', no default
+                         ['--logID', '-l', GetoptLong::REQUIRED_ARGUMENT],               # splitlog ID: if given, featurize this split. Cannot use both this and -d
+                         ['--append', '-A', GetoptLong::NO_ARGUMENT]
+                       ],
+        "split" => [ ['--logID', '-l', GetoptLong::REQUIRED_ARGUMENT],   # splitlog ID, required, no default
+                     [ '--trainpercent', '-r', GetoptLong::REQUIRED_ARGUMENT]       # percentage training data, default: 90
+                   ],
+        "train" => [ ['--logID', '-l', GetoptLong::REQUIRED_ARGUMENT],   # splitlog ID; if given, will train on split rather than all of main table
+                     ['--step', '-s', GetoptLong::REQUIRED_ARGUMENT]                # classification step: 'argrec', 'arglab', 'both' (default) or 'onestep'
+                   ],
+        "test" => [ ['--step', '-s', GetoptLong::REQUIRED_ARGUMENT],     # classification step: 'argrec', 'arglab', 'both' (default) or 'onestep'
+                    [ '--testID', '-i', GetoptLong::REQUIRED_ARGUMENT],            # test table ID: if given, test on this table
+                    ['--logID', '-l', GetoptLong::REQUIRED_ARGUMENT],              # splitlog ID: if given, test on this split. Cannot use both this and -i
+                    [ '--nooutput', '-N', GetoptLong::NO_ARGUMENT]                # set this to prevent output of disambiguated test data
+                  ],
+        "eval" => [['--step', '-s', GetoptLong::REQUIRED_ARGUMENT],      # classification step: 'argrec', 'arglab', 'both' (default) or 'onestep' 
+                   [ '--testID', '-i', GetoptLong::REQUIRED_ARGUMENT],            # test table ID: if given, test on this table
+                   ['--logID', '-l', GetoptLong::REQUIRED_ARGUMENT]
+                  ],
+        "inspect" => [['--tables', GetoptLong::NO_ARGUMENT],             # describe all tables
+                      [ '--tablecont', GetoptLong::OPTIONAL_ARGUMENT],               # describe table contents for current experiment
+                      [ '--testID', '-i', GetoptLong::REQUIRED_ARGUMENT],            # test table ID: if given, describe contents of this table
+                      [ '--runs', GetoptLong::NO_ARGUMENT],                          # describe classification runs for current experiment
+                      [ '--split', GetoptLong::REQUIRED_ARGUMENT]                    # list sentence IDs for given splitlog 
+                     ],
+        "services" => [['--deltable', GetoptLong::REQUIRED_ARGUMENT],    # delete database table
+                       [ '--delexp', GetoptLong::NO_ARGUMENT],                        # delete experiment tables and files
+                       [ '--deltables', GetoptLong::NO_ARGUMENT],                     # delete tables interactively
+                       [ '--delruns', GetoptLong::NO_ARGUMENT],                       # delete runs
+                       [ '--delsplit', GetoptLong::REQUIRED_ARGUMENT],                # delete split
+                       [ '--dump', GetoptLong::OPTIONAL_ARGUMENT],                    # dump experiment to files
+                       [ '--load', GetoptLong::OPTIONAL_ARGUMENT],                    # load experiment from files
+                       [ '--writefeatures', GetoptLong::OPTIONAL_ARGUMENT],           # write feature files
+                       ['--step', '-s', GetoptLong::REQUIRED_ARGUMENT],     # classification step: 'argrec', 'arglab', 'both' (default) or 'onestep'
+                       [ '--testID', '-i', GetoptLong::REQUIRED_ARGUMENT],            # test table ID: if given, test on this table
+                       ['--logID', '-l', GetoptLong::REQUIRED_ARGUMENT]              # splitlog ID: if given, test on this split. Cannot use both this and -i
+                      ]
+      }
+      
+      optnames = [[ '--help', '-h', GetoptLong::NO_ARGUMENT],            # get help
+                  [ '--expfile', '-e', GetoptLong::REQUIRED_ARGUMENT],              # experiment file name (and path), no default
+                  [ '--task', '-t', GetoptLong::REQUIRED_ARGUMENT ]                # task to perform: one of task.keys, no default
+                 ]
+      
+      tasks.values.each { |more_optnames|
+        optnames.concat more_optnames
+      }
+      
+      optnames.uniq!
+      
+      # asterisk: "explode" array into individual parameters
+      begin
+        opts = options_hash(GetoptLong.new(*optnames))
+      rescue
+        $stderr.puts "Error: unknown command line option: " + $!
+        exit 1
+      end
+      
+      experiment_filename = nil
+      
+      ##
+      # are we being asked for help?
+      if opts['--help']
+        help()
+        exit(0)
+      end
+      
+      ##
+      # now find the task
+      task = opts['--task']
+      # sanity checks for task
+      if task.nil?
+        help()
+        exit(0)
+      end
+      unless tasks.keys.include? task
+        $stderr.puts "Sorry, I don't know the task '#{task}'. Do 'ruby rosy.rb -h' for a list of tasks."
+        exit 1
+      end
+      
+      ##
+      # now evaluate the rest of the options
+      opts.each_pair { |opt,arg|
+        case opt
+        when '--help', '--task'
+          # we already handled this
+        when '--expfile'
+          experiment_filename = arg
+        else
+          # do we know this option?
+          unless tasks[task].assoc(opt)
+            $stderr.puts "Sorry, I don't know the option " + opt + " for task " + task
+            $stderr.puts "Do 'ruby rosy.rb -h' for a list of tasks and options."
+            exit 1
+          end
+        end
+      }
+      
+      
+      if experiment_filename.nil?
+        $stderr.puts "I need an experiment file name, option --expfile|-e"
+        exit 1
+      end
+      
+      ##
+      # open config file
+      
+      exp = RosyConfigData.new(experiment_filename)
+      
+      # sanity checks
+      unless exp.get("experiment_ID") =~ /^[A-Za-z0-9_]+$/
+        $stderr.puts "Please choose an experiment ID consisting only of the letters A-Za-z0-9_."
+        exit 1
+      end
+      
+      # enduser mode?
+      $ENDUSER_MODE = exp.get("enduser_mode") 
+
+      [exp, opts]
+    end
+    
+    private
+    def self.help
+      $stderr.puts "
+ROSY: semantic ROle assignment SYstem Version 0.2
+
+Usage:
+
+ruby rosy.rb --help|-h
+
+  gets you this help text.
+
+ruby rosy.rb --task|-t featurize --expfile|-e <e> 
+             [--dataset|-d <d>]  [--testID|-i <i>] 
+             [--logID|-l <l> ] [--append|-A]
+  featurizes input data and stores it in a database.
+  Enduser mode: dataset has to be 'test' (preset as default),
+    no --append.
+
+  --expfile <e>   Use <e> as the experiment description and 
+                  configuration file
+
+  --dataset <d>   Set to featurize: <d> is either 'train' 
+                  (put data into main table) or 'test' (put data 
+                  into separate test table with ID given using --testID)
+                  Use at least one of --logID, --dataset.
+
+  --logID <l>     Re-featurize the split with ID <l>:
+                  Features that train on training instances are done
+                  separately for each split.
+                  Use at least one of --logID, --dataset.
+
+  --testID <i>    Use <i> as the ID for the table to store the test data.
+                  necessary only with '--dataset test'. default: #{default_test_ID()}.
+
+  --append        Do not overwrite previously computed features 
+                  for this experiment.
+                  Rather, append the new features 
+                  to the old featurization files.
+                  Default: overwrite
+
+ruby rosy.rb --task|-t split --expfile|-e <f> --logID|-l <l> 
+            [--trainpercent|-r <r>]
+  produces a new train/test split on the main table of the experiment.
+  Not available in enduser mode.
+
+  --expfile <f>   Use <f> as the experiment description and configuration file
+
+  --logID <l>     Use <l> as the ID for storing this new split
+
+  --trainpercent <r> Allocate <r> percent of the data as train, 
+                  and 100-<r> as test
+                  default: <r>=90
+
+
+ruby rosy.rb --task|-t train --expfile|-e <f> [--step|-s <s>] [--logID|-l <l>]
+  train classifier(s) on the main table data (or a split of it)
+  Not available in enduser mode.
+
+  --expfile <f>   Use <f> as the experiment description and configuration file
+
+  --step <s>      What kind of classifier(s) to train?
+                  <s>=argrec: argument recognition, 
+                                distinguish role from nonrole
+                  <s>=arglab: argument labeling, naming roles, 
+                                builds on argrec
+                  <s>=both:   first argrec, then arglab
+                  <s>=onestep: do argument labeling right away without
+                                prior filtering of non-arguments
+                  default: both
+
+  --logID <l>     If given, train on this split of the main table rather than 
+                  the whole main table
+
+
+ruby rosy.rb --task|-t test --expfile|-e <f> [--step|-s <s>] 
+             [--logID|-l <l> | --testID|-i <i>] [--nooutput|-N]
+  apply classifier(s) on data from a test table, or a main table split
+  Enduser mode: only -s both, -s onestep available. Cleanup: Database with
+                featurization data is removed after the run.
+
+  --expfile <f>   Use <f> as the experiment description and configuration file
+
+  --step <s>      What kind of classifier(s) to use for testing?
+                  <s>=argrec: argument recognition, 
+                                distinguish role from nonrole
+                  <s>=arglab: argument labeling, naming roles, 
+                                builds on argrec
+                  <s>=both:   first argrec, then arglab
+                  <s>=onestep: do argument labeling right away without 
+                                prior filtering of non-arguments
+                  default: both
+  --logID <l>     If given, test on this split of the main table
+
+  --testID <i>    If given, test on this test table.
+                  (Use either this option or -l)
+
+  --nooutput      Do not produce an output of the disambiguated test data 
+                  in SalsaTigerXML format. This is useful if you just want
+                  to evaluate the system.
+                  Default: output is produced.
+
+
+ruby rosy.rb --task|-t eval --expfile|-e <f> [--step|-s <s>] 
+             [--logID|-l <l> | --testID|-i <i> 
+  evaluate the classification results.
+  Not available in enduser mode.
+
+  --expfile <f>   Use <f> as the experiment description and configuration file
+
+  --step <s>      Evaluate results of which classification step?
+                  <s>=argrec: argument recognition, 
+                                distinguish role from nonrole
+                  <s>=arglab: argument labeling, naming roles, 
+                                builds on argrec
+                  <s>=both:   first argrec, then arglab
+                  <s>=onestep: do argument labeling right away without 
+                                prior filtering of non-arguments
+                  default: both
+                  Need not be given if --runID is given.
+
+  --logID <l>     If given, evaluate on the test data from this split of 
+                  the main table.
+                  (use either this option or -i or -R)
+
+  --testID <i>    If given, evaluate on this test table.
+                  (Use either this option or -l or -R)
+
+
+ruby rosy.rb --task|-t inspect --expfile|-e <f> [--tables] [--runs] 
+             [--tablecont [N]] [--testID|-i <i>] [--split <l>]
+  inspect system-internal data, both global and pertaining to the current 
+  experiment.
+  If no options are chosen, an overview of the current experiment 
+  is given.
+
+  --expfile <f>   Use <f> as the experiment description and 
+                  configuration file
+
+  --tables        Lists all tables of the DB: table name,column names
+
+  --tablecont [N|id:N] Lists the training instances (as feature vectors) 
+                  of the current experiment.
+                  If test ID is given, test instances are listed as well.
+                  The optional argument may have one of two forms:
+                  - It may be a number N. Then only the N first lines 
+                    of each set are listed.
+                  - It may be a pair id:N. Then only the N first lines of
+                    the DB table with ID id are listed. To list all lines
+                    of a single DB table, use id:
+
+  --testID <i>    If given, --tablecont also lists the feature vectors for 
+                  this test table
+
+  --runs          List all classification runs of the current experiment
+
+  --split <l>     List the split with the given ID
+
+ruby rosy.rb --task|-t services --expfile|-e <f> [--deltable <t>]
+             [--delexp] [--dump [<D>]] [--load [<D>]] [--delrun <R>]
+             [--delsplit <l>] [--writefeatures [<D>]]              
+             [--step|-s <s>]  [--testID|-i <i>] [--logID|-l <l> ] 
+  diverse services.
+  The --del* services are not available in enduser mode.
+
+  --dump [<D>]    Dump the database tables for the current experiment file.
+                  If a directory <D> is given, the tables are written there,
+                  otherwise they are written to 
+                  data_dir/<experiment_ID>/tables, where data_dir is the 
+                  data directory given in the experiment file.
+                  No existing files in the directory are removed.
+
+  --load [<D>]    Construct new database tables from the files in
+                  the directory <D>, if it is given, otherwise from 
+                  data_dir/<experiment_id>/tables, where data_dir 
+                  is the data directory given in the experiment file.
+                  Warning: Database tables are loaded into the 
+                  current experiment, the one described in the
+                  experiment file. Existing data in tables with
+                  the same names is overwritten!
+
+  --deltable <t>  Remove database table <t>
+ 
+  --deltables     Presents all tables in the database for interactive deletion
+
+  --delexp        Remove the experiment described in the given experiment file,
+                  all its database tables and files.
+
+  --delruns       Presents all classification runs for the current experiment
+                  for interactive deletion
+
+  --delsplit <l>  Remove the split with ID <l> from the experiment
+                  described in the given experiment file.
+
+  --writefeatures <D> Write feature files to directory <D>, such
+                  that you can use them with some external machine learning
+                  system. If <D> is not given, feature files are written
+                  to data_dir/<experiment_id>/your_feature_files/.
+
+                  Uses the parameters --step, --testID, --logID to 
+                  determine which feature files will be written.
+
+  --step <s>      Use with --writefeatures: task for which to write features.
+                  <s>=argrec: argument recognition, 
+                                distinguish role from nonrole
+                  <s>=arglab: argument labeling, naming roles
+                  <s>=onestep: do argument labeling right away without 
+                                prior filtering of non-arguments
+                  default: onestep.
+
+  --logID <l>     Use with --writefeatures: write features
+                  for the the split with ID <l>.
+
+  --testID <i>    Use with --writefeatures: write features
+                  for the test set with ID <i>. 
+                  default: #{default_test_ID()}.
+"
+
+    end
+
+    ###
+    # options_hash:
+    #
+    # GetoptLong only allows you to access options via each(),
+    # not individually, and it only allows you to cycle through the options once.
+    # So we re-code the options as a hash
+    def self.options_hash(opts_obj) # GetoptLong object
+      opt_hash = Hash.new
+      
+      opts_obj.each do |opt, arg|
+        opt_hash[opt] = arg
+      end
+      
+      return opt_hash
+    end
+    
+  end # class OptParser
+  
+end # module Rosy

data/lib/rosy/rosy.rb

@@ -0,0 +1,77 @@
+# AB: 2011-11-14
+# Initial import done, need to reimplement the whole interface.
+
+require 'common/DBInterface'
+require 'rosy/RosyFeaturize'
+require 'rosy/RosyTest'
+require 'rosy/RosyTrain'
+require 'rosy/RosyInspect'
+require 'rosy/RosyEval'
+require 'rosy/RosyServices'
+
+module Rosy
+  class Rosy
+
+    def initialize(options)
+      @exp, @opts = options
+      @task = @opts['--task']
+    end
+
+    def assign
+      
+      # make rosy directory pattern:
+      # main rosy directory name (data_dir) plus subdirectory
+      # named after the experiment ID
+      rosy_dir_pattern = File.new_dir(@exp.get("data_dir")) + "<exp_ID>/"
+      @exp.set_entry("rosy_dir",  rosy_dir_pattern)
+      
+      ##
+      # open database
+      
+      rosy_dir = File.new_dir(@exp.instantiate("rosy_dir",
+                                              "exp_ID" => @exp.get("experiment_ID")))
+      database = get_db_interface(@exp, rosy_dir, "features")
+      
+      table_obj = RosyTrainingTestTable.new(@exp, database)
+      
+      ##
+      # start the actual processing,
+      # according to given arguments
+      
+      # initialize task object
+      #begin
+      case @task
+      when "featurize"
+        task_obj = RosyFeaturize.new(@exp, @opts, table_obj)
+      when "split"
+        task_obj = RosySplit.new(@exp, @opts, table_obj)
+      when "train"
+        task_obj = RosyTrain.new(@exp, @opts, table_obj)
+      when "test"
+        task_obj = RosyTest.new(@exp, @opts, table_obj)
+      when "eval"
+        task_obj = RosyEvalTask.new(@exp, @opts, table_obj)
+      when "inspect"
+        task_obj = RosyInspect.new(@exp, @opts, table_obj)
+      when "services"
+        task_obj = RosyServices.new(@exp, @opts, table_obj)
+      else
+        raise "Shouldn't be here"
+      end
+      
+      
+      # execute task
+      begin
+        task_obj.perform
+      rescue => e
+        fail "Error during task execution: #{e.class}=>#{e.message}"
+      ensure
+        database.close
+      end
+      
+      
+      $stderr.puts "Rosy: done."      
+    end
+    
+  end # class Rosy
+end # module Rosy