bibrank_word_indexer.py
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Created: Sat, May 18, 13:23

bibrank_word_indexer.py
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	# $Id$
	## BibRank word frequency indexer utility.

	## This file is part of the CERN Document Server Software (CDSware).
	## Copyright (C) 2002 CERN.
	##
	## The CDSware is free software; you can redistribute it and/or
	## modify it under the terms of the GNU General Public License as
	## published by the Free Software Foundation; either version 2 of the
	## License, or (at your option) any later version.
	##
	## The CDSware is distributed in the hope that it will be useful, but
	## WITHOUT ANY WARRANTY; without even the implied warranty of
	## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
	## General Public License for more details.
	##
	## You should have received a copy of the GNU General Public License
	## along with CDSware; if not, write to the Free Software Foundation, Inc.,
	## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.

	## read config variables:
	#include "config.wml"
	#include "configbis.wml"
	#include "cdswmllib.wml"

	## start Python:
	<protect>#!</protect><PYTHON>
	<protect># -- coding: utf-8 --</protect>
	<protect>## $Id$</protect>
	<protect>## DO NOT EDIT THIS FILE! IT WAS AUTOMATICALLY GENERATED FROM CDSware WML SOURCES.</protect>

	__version__ = "<: print generate_pretty_version_string('$Id$'); :>"

	## fill config variables:
	pylibdir = "<LIBDIR>/python"

	## programs used to convert fulltext files to text:
	conv_programs = {#"ps": ["<PSTOTEXT>","<PSTOASCII>"], # switched off at the moment, since PDF is faster
	#"ps.gz": ["<PSTOTEXT>","<PSTOASCII>"],
	"pdf": ["<PDFTOTEXT>","<PSTOTEXT>","<PSTOASCII>"],
	"doc": ["<ANTIWORD>","<CATDOC>","<WVTEXT>"],
	"ppt": ["<PPTHTML>"],
	"xls": ["<XLHTML>"]
	}
	## helper programs used if the above programs convert only to html or other intermediate file formats:
	conv_programs_helpers = {"html": "<HTMLTOTEXT>",
	"gz": "<GZIP>" }

	## okay, rest of the Python code goes below
	#######

	## import interesting modules:
	try:
	from zlib import compress,decompress
	from string import split,translate,lower,upper
	import marshal
	import getopt
	import getpass
	import string
	import os
	import sre
	import sys
	import time
	import MySQLdb
	import Numeric
	import urllib
	import signal
	import tempfile
	import unicodedata
	import traceback
	import cStringIO
	import math
	import re
	import ConfigParser
	except ImportError, e:
	import sys

	try:
	import Stemmer
	except ImportError, e:
	pass

	try:
	sys.path.append('%s' % pylibdir)
	from cdsware.config import *
	from cdsware.search_engine_config import cfg_max_recID
	from cdsware.search_engine import perform_request_search, strip_accents, HitSet
	from cdsware.dbquery import run_sql
	except ImportError, e:
	import sys

	## safety parameters concerning MySQL thread-multiplication problem:
	cfg_check_mysql_threads = 0 # to check or not to check the problem?
	cfg_max_mysql_threads = 50 # how many threads (connections) we consider as still safe
	cfg_mysql_thread_timeout = 20 # we'll kill threads that were sleeping for more than X seconds

	## override urllib's default password-asking behaviour:
	class MyFancyURLopener(urllib.FancyURLopener):
	def prompt_user_passwd(self, host, realm):
	# supply some dummy credentials by default
	return ("mysuperuser", "mysuperpass")
	def http_error_401(self, url, fp, errcode, errmsg, headers):
	# do not bother with protected pages
	raise IOError, (999, 'unauthorized access')
	return None

	#urllib._urlopener = MyFancyURLopener()

	## precompile some often-used regexp for speed reasons:
	re_subfields = sre.compile('\$\$\w');

	nb_char_in_line = 50 # for verbose pretty printing
	chunksize = 1000 # default size of chunks that the records will be treated by
	wordTables = []
	base_process_size = 4500 # process base size

	## Dictionary merging functions
	def dict_union(list1, list2):
	"Returns union of the two dictionaries."
	union_dict = {}

	for (e, count) in list1.iteritems():
	union_dict[e] = count
	for (e, count) in list2.iteritems():
	if not union_dict.has_key(e):
	union_dict[e] = count
	else:
	union_dict[e] = (union_dict[e][0] + count[0], count[1])
	return union_dict

	## safety function for killing slow MySQL threads:
	def kill_sleepy_mysql_threads(max_threads=cfg_max_mysql_threads, thread_timeout=cfg_mysql_thread_timeout):
	"""Check the number of MySQL threads and if there are more than
	MAX_THREADS of them, lill all threads that are in a sleeping
	state for more than THREAD_TIMEOUT seconds. (This is useful
	for working around the the max_connection problem that appears
	during indexation in some not-yet-understood cases.) If some
	threads are to be killed, write info into the log file.
	"""
	res = run_sql("SHOW FULL PROCESSLIST")
	if len(res) > max_threads:
	for row in res:
	r_id,r_user,r_host,r_db,r_command,r_time,r_state,r_info = row
	if r_command == "Sleep" and int(r_time) > thread_timeout:
	run_sql("KILL %s", (r_id,))
	if options["verbose"] >= 1:
	write_message("WARNING: too many MySQL threads, killing thread %s" % r_id)
	return

	# tagToFunctions mapping. It offers an indirection level necesary for
	# indexing fulltext. The default is get_words_from_phrase
	tagToWordsFunctions = {}

	def get_words_from_phrase(phrase, weight, lang="",
	chars_punctuation=r"[\.\,\:\;\?\!\"]",
	chars_alphanumericseparators=r"[1234567890\!\"\#\$\%\&\'\*\+\,\-\.\/\:\;\<\=\>\?\@\[\\\]\^\_\`\{\\|\}\~]",
	split=string.split):
	"Returns list of words from phrase 'phrase'."
	words = {}
	#print phrase
	phrase = strip_accents(phrase)
	phrase = lower(phrase)
	#Getting rid of strange characters
	phrase = re.sub("é", 'e', phrase)
	phrase = re.sub("è", 'e', phrase)
	phrase = re.sub("à", 'a', phrase)
	phrase = re.sub(" ", ' ', phrase)
	phrase = re.sub("«", ' ', phrase)
	phrase = re.sub("»", ' ', phrase)
	phrase = re.sub("ê", ' ', phrase)
	phrase = re.sub("&", ' ', phrase)

	if string.find(phrase, "</") > -1:
	#Most likely html, remove html code
	phrase = re.sub("(?s)<[^>]*>\|&#?\w+;", ' ', phrase)
	phrase = re.sub(chars_punctuation, ' ', phrase)

	#By doing this like below, characters standing alone, like c a b is not added to the inedx, but when they are together with characters like c++ or c$ they are added.
	for word in split(phrase):
	if not stopwords.has_key(word) and check_term(word, 0):
	if lang and lang !="none" and stemmer.has_key(lang):
	word = stemmer[lang].stem(word)
	if not words.has_key(word):
	words[word] = (0,0)
	words[word] = (words[word][0] + weight, 0)
	elif not stopwords.has_key(word):
	phrase = re.sub(chars_alphanumericseparators, ' ', word)
	for word_ in split(phrase):
	if lang and lang !="none" and stemmer.has_key(lang):
	word_ = stemmer[lang].stem(word_)
	if word_:
	if not words.has_key(word_):
	words[word_] = (0,0)
	words[word_] = (words[word_][0] + weight, 0)
	#print words
	return words

	def split_ranges(parse_string):
	recIDs = []
	ranges = string.split(parse_string, ",")
	for range in ranges:
	tmp_recIDs = string.split(range, "-")

	if len(tmp_recIDs)==1:
	recIDs.append([int(tmp_recIDs[0]), int(tmp_recIDs[0])])
	else:
	if int(tmp_recIDs[0]) > int(tmp_recIDs[1]): # sanity check
	tmp = tmp_recIDs[0]
	tmp_recIDs[0] = tmp_recIDs[1]
	tmp_recIDs[1] = tmp
	recIDs.append([int(tmp_recIDs[0]), int(tmp_recIDs[1])])
	return recIDs

	def get_date_range(var):
	"Returns the two dates contained as a low,high tuple"
	limits = string.split(var, ",")
	if len(limits)==1:
	low = get_date(limits[0])
	return low,None
	if len(limits)==2:
	low = get_date(limits[0])
	high = get_date(limits[1])
	return low,high

	def get_datetime(var, format_string="%Y-%m-%d %H:%M:%S"):
	"""Returns a date string according to the format string.
	It can handle normal date strings and shifts with respect
	to now."""
	date = time.time()
	shift_re=sre.compile("([-\+]{0,1})([\d]+)([dhms])")
	factors = {"d":24*3600, "h":3600, "m":60, "s":1}
	m = shift_re.match(var)
	if m:
	sign = m.groups()[0] == "-" and -1 or 1
	factor = factors[m.groups()[2]]
	value = float(m.groups()[1])
	date = time.localtime(date + sign * factor * value)
	date = time.strftime(format_string, date)
	else:
	date = time.strptime(var, format_string)
	date = time.strftime(format_string, date)
	return date

	def create_range_list(res):
	"""Creates a range list from a recID select query result contained
	in res. The result is expected to have ascending numerical order."""
	if not res:
	return []
	row = res[0]
	if not row:
	return []
	else:
	range_list = [[row[0],row[0]]]
	for row in res[1:]:
	id = row[0]
	if id == range_list[-1][1] + 1:
	range_list[-1][1] = id
	else:
	range_list.append([id,id])
	return range_list

	def beautify_range_list(range_list):
	"""Returns a non overlapping, maximal range list"""
	ret_list = []
	for new in range_list:
	found = 0
	for old in ret_list:
	if new[0] <= old[0] <= new[1] + 1 or new[0] - 1 <= old[1] <= new[1]:
	old[0] = min(old[0], new[0])
	old[1] = max(old[1], new[1])
	found = 1
	break

	if not found:
	ret_list.append(new)

	return ret_list

	def serialize_via_numeric_array_dumps(arr):
	return Numeric.dumps(arr)

	def serialize_via_numeric_array_compr(str):
	return compress(str)

	def serialize_via_numeric_array(arr):
	"""Serialize Numeric array into a compressed string."""
	return serialize_via_numeric_array_compr(serialize_via_numeric_array_dumps(arr))

	def deserialize_via_numeric_array(string):
	"""Decompress and deserialize string into a Numeric array."""
	return Numeric.loads(decompress(string))

	def serialize_via_marshal(obj):
	"""Serialize Python object via marshal into a compressed string."""
	return MySQLdb.escape_string(compress(marshal.dumps(obj)))

	def deserialize_via_marshal(string):
	"""Decompress and deserialize string into a Python object via marshal."""
	return marshal.loads(decompress(string))

	class WordTable:
	"A class to hold the words table."

	def __init__(self, tablename, fields_to_index, separators="[^\s]"):
	"Creates words table instance."
	self.tablename = tablename
	self.recIDs_in_mem = []
	self.fields_to_index = fields_to_index
	self.separators = separators
	self.value = {}

	def get_field(self, recID, tag):
	"""Returns list of values of the MARC-21 'tag' fields for the
	record 'recID'."""

	out = []
	bibXXx = "bib" + tag[0] + tag[1] + "x"
	bibrec_bibXXx = "bibrec_" + bibXXx
	query = """SELECT value FROM %s AS b, %s AS bb
	WHERE bb.id_bibrec=%s AND bb.id_bibxxx=b.id
	AND tag LIKE '%s'""" % (bibXXx, bibrec_bibXXx, recID, tag);
	res = run_sql(query)
	for row in res:
	out.append(row[0])
	return out

	def clean(self):
	"Cleans the words table."
	self.value={}

	def put_into_db(self, mode="normal", split=string.split):
	"""Updates the current words table in the corresponding MySQL's
	idxFOO table. Mode 'normal' means normal execution,
	mode 'emergency' means words index reverting to old state.
	"""
	if options["verbose"]:
	write_message("%s %s wordtable flush started" % (self.tablename,mode))
	write_message('...updating %d words into %sR started' % \
	(len(self.value), self.tablename[:-1]))
	task_update_progress("%s flushed %d/%d words" % (self.tablename, 0, len(self.value)))

	self.recIDs_in_mem = beautify_range_list(self.recIDs_in_mem)

	if mode == "normal":
	for group in self.recIDs_in_mem:
	query = """UPDATE %sR SET type='TEMPORARY' WHERE id_bibrec
	BETWEEN '%d' AND '%d' AND type='CURRENT'""" % \
	(self.tablename[:-1], group[0], group[1])
	if options["verbose"] >= 9:
	write_message(query)
	run_sql(query)

	nb_words_total = len(self.value)
	nb_words_report = int(nb_words_total/10)
	nb_words_done = 0
	for word in self.value.keys():
	self.put_word_into_db(word, self.value[word])
	nb_words_done += 1
	if nb_words_report!=0 and ((nb_words_done % nb_words_report) == 0):
	if options["verbose"]:
	write_message('......processed %d/%d words' % (nb_words_done, nb_words_total))
	task_update_progress("%s flushed %d/%d words" % (self.tablename, nb_words_done, nb_words_total))
	if options["verbose"] >= 9:
	write_message('...updating %d words into %s ended' % \
	(nb_words_total, self.tablename))

	#if options["verbose"]:
	# write_message('...updating reverse table %sR started' % self.tablename[:-1])
	if mode == "normal":
	for group in self.recIDs_in_mem:
	query = """UPDATE %sR SET type='CURRENT' WHERE id_bibrec
	BETWEEN '%d' AND '%d' AND type='FUTURE'""" % \
	(self.tablename[:-1], group[0], group[1])
	if options["verbose"] >= 9:
	write_message(query)
	run_sql(query)
	query = """DELETE FROM %sR WHERE id_bibrec
	BETWEEN '%d' AND '%d' AND type='TEMPORARY'""" % \
	(self.tablename[:-1], group[0], group[1])
	if options["verbose"] >= 9:
	write_message(query)
	run_sql(query)
	if options["verbose"] >= 9:
	write_message('End of updating wordTable into %s' % self.tablename)
	elif mode == "emergency":
	write_message("emergency")
	for group in self.recIDs_in_mem:
	query = """UPDATE %sR SET type='CURRENT' WHERE id_bibrec
	BETWEEN '%d' AND '%d' AND type='TEMPORARY'""" % \
	(self.tablename[:-1], group[0], group[1])
	if options["verbose"] >= 9:
	write_message(query)
	run_sql(query)
	query = """DELETE FROM %sR WHERE id_bibrec
	BETWEEN '%d' AND '%d' AND type='FUTURE'""" % \
	(self.tablename[:-1], group[0], group[1])
	if options["verbose"] >= 9:
	write_message(query)
	run_sql(query)
	if options["verbose"] >= 9:
	write_message('End of emergency flushing wordTable into %s' % self.tablename)
	#if options["verbose"]:
	# write_message('...updating reverse table %sR ended' % self.tablename[:-1])

	self.clean()
	self.recIDs_in_mem = []
	if options["verbose"]:
	write_message("%s %s wordtable flush ended" % (self.tablename, mode))
	task_update_progress("%s flush ended" % (self.tablename))

	def load_old_recIDs(self,word):
	"""Load existing hitlist for the word from the database index files."""
	query = "SELECT hitlist FROM %s WHERE term=%%s" % self.tablename
	res = run_sql(query, (word,))
	if res:
	return deserialize_via_marshal(res[0][0])
	else:
	return None

	def merge_with_old_recIDs(self,word,recIDs, set):
	"""Merge the system numbers stored in memory (hash of recIDs with value[0] > 0 or -1
	according to whether to add/delete them) with those stored in the database index
	and received in set universe of recIDs for the given word.

	Return 0 in case no change was done to SET, return 1 in case SET was changed.
	"""

	set_changed_p = 0
	for recID,sign in recIDs.iteritems():
	if sign[0] == -1 and set.has_key(recID):
	# delete recID if existent in set and if marked as to be deleted
	del set[recID]
	set_changed_p = 1
	elif sign[0] > -1 and not set.has_key(recID):
	# add recID if not existent in set and if marked as to be added
	set[recID] = sign
	set_changed_p = 1
	elif sign[0] > -1 and sign[0] != set[recID][0]:
	set[recID] = sign
	set_changed_p = 1

	return set_changed_p

	def put_word_into_db(self, word, recIDs, split=string.split):
	"""Flush a single word to the database and delete it from memory"""
	set = self.load_old_recIDs(word)
	#write_message("%s %s" % (word, self.value[word]))

	if set: # merge the word recIDs found in memory:
	if self.merge_with_old_recIDs(word, recIDs, set) == 0:
	# nothing to update:
	if options["verbose"] >= 9:
	write_message("......... unchanged hitlist for ``%s''" % word)
	pass
	else:
	# yes there were some new words:
	if options["verbose"] >= 9:
	write_message("......... updating hitlist for ``%s''" % word)
	options["modified_words"][word] = 1
	run_sql("UPDATE %s SET hitlist='%s' WHERE term='%s'" % (self.tablename, serialize_via_marshal(set), MySQLdb.escape_string(word)))
	else: # the word is new, will create new set:
	if options["verbose"] >= 9:
	write_message("......... inserting hitlist for ``%s''" % word)
	set = self.value[word]
	if len(set) > 0:
	#new word, add to list
	options["modified_words"][word] = 1
	run_sql("INSERT INTO %s (term, hitlist) VALUES ('%s', '%s')" % (self.tablename, MySQLdb.escape_string(word), serialize_via_marshal(set)))
	if not set: # never store empty words
	run_sql("DELETE from %s WHERE term=%%s" % self.tablename,
	(word,))

	del self.value[word]

	def display(self):
	"Displays the word table."
	keys = self.value.keys()
	keys.sort()
	for k in keys:
	if options["verbose"]:
	write_message("%s: %s" % (k, self.value[k]))

	def count(self):
	"Returns the number of words in the table."
	return len(self.value)

	def info(self):
	"Prints some information on the words table."
	if options["verbose"]:
	write_message("The words table contains %d words." % self.count())

	def lookup_words(self, word=""):
	"Lookup word from the words table."

	if not word:
	done = 0
	while not done:
	try:
	word = raw_input("Enter word: ")
	done = 1
	except (EOFError, KeyboardInterrupt):
	return

	if self.value.has_key(word):
	if options["verbose"]:
	write_message("The word '%s' is found %d times." \
	% (word, len(self.value[word])))
	else:
	if options["verbose"]:
	write_message("The word '%s' does not exist in the word file."\
	% word)

	def update_last_updated(self, rank_method_code, starting_time=None):
	"""Update last_updated column of the index table in the database.
	Puts starting time there so that if the task was interrupted for record download,
	the records will be reindexed next time."""
	if starting_time is None:
	return None
	if options["verbose"] >= 9:
	write_message("updating last_updated to %s...", starting_time)
	return run_sql("UPDATE rnkMETHOD SET last_updated=%s WHERE name=%s",
	(starting_time, rank_method_code,))

	def add_recIDs(self, recIDs):
	"""Fetches records which id in the recIDs range list and adds
	them to the wordTable. The recIDs range list is of the form:
	[[i1_low,i1_high],[i2_low,i2_high], ..., [iN_low,iN_high]].
	"""
	global chunksize
	flush_count = 0
	records_done = 0
	records_to_go = 0

	for range in recIDs:
	records_to_go = records_to_go + range[1] - range[0] + 1

	time_started = time.time() # will measure profile time
	for range in recIDs:
	i_low = range[0]
	chunksize_count = 0
	while i_low <= range[1]:
	# calculate chunk group of recIDs and treat it:
	i_high = min(i_low+options["flush"]-flush_count-1,range[1])
	i_high = min(i_low+chunksize-chunksize_count-1, i_high)
	try:
	self.chk_recID_range(i_low, i_high)
	except StandardError, e:
	write_message("Exception caught: %s" % e, sys.stderr)
	if options["verbose"] >= 9:
	traceback.print_tb(sys.exc_info()[2])
	task_update_status("ERROR")
	task_sig_stop_commands()
	sys.exit(1)
	if options["verbose"]:
	write_message("%s adding records #%d-#%d started" % \
	(self.tablename, i_low, i_high))
	if cfg_check_mysql_threads:
	kill_sleepy_mysql_threads()
	task_update_progress("%s adding recs %d-%d" % (self.tablename, i_low, i_high))
	self.del_recID_range(i_low, i_high)
	just_processed = self.add_recID_range(i_low, i_high)
	flush_count = flush_count + i_high - i_low + 1
	chunksize_count = chunksize_count + i_high - i_low + 1
	records_done = records_done + just_processed
	if options["verbose"]:
	write_message("%s adding records #%d-#%d ended " % \
	(self.tablename, i_low, i_high))
	if chunksize_count >= chunksize:
	chunksize_count = 0
	# flush if necessary:
	if flush_count >= options["flush"]:
	self.put_into_db()
	self.clean()
	if options["verbose"]:
	write_message("%s backing up" % (self.tablename))
	flush_count = 0
	self.log_progress(time_started,records_done,records_to_go)
	# iterate:
	i_low = i_high + 1
	if flush_count > 0:
	self.put_into_db()
	self.log_progress(time_started,records_done,records_to_go)

	def add_date(self, date=""):
	# If date is not set, then retrieve it from the database.
	# Reindex all formats newer than the modification date
	if not date:
	write_message("Using the last update time for the rank method")
	id = self.tablename[len("bibindex"):]
	query = """SELECT last_updated FROM rnkMETHOD WHERE name='%s'
	""" % options["current_run"]
	res = run_sql(query)

	if not res:
	return
	if not res[0][0]:
	date = ("0000-00-00",'')
	else:
	date = (res[0][0],'')

	query = """SELECT b.id FROM bibrec AS b WHERE b.modification_date >=
	'%s'""" % date[0]
	if date[1]:
	query += "and b.modification_date <= '%s'" % date[1]
	query += "ORDER BY b.id ASC"""
	res = run_sql(query)

	list = create_range_list(res)
	if not list:
	if options["verbose"]:
	write_message( "No new records added. %s is up to date" % self.tablename)
	else:
	self.add_recIDs(list)
	return list


	def add_recID_range(self, recID1, recID2):
	empty_list_string = serialize_via_marshal([])
	wlist = {}
	normalize = {}

	self.recIDs_in_mem.append([recID1,recID2])
	# secondly fetch all needed tags:
	for (tag, weight, lang) in self.fields_to_index:
	if tag in tagToWordsFunctions.keys():
	get_words_function = tagToWordsFunctions[ tag ]
	else: get_words_function = get_words_from_phrase
	bibXXx = "bib" + tag[0] + tag[1] + "x"
	bibrec_bibXXx = "bibrec_" + bibXXx
	query = """SELECT bb.id_bibrec,b.value FROM %s AS b, %s AS bb
	WHERE bb.id_bibrec BETWEEN %d AND %d
	AND bb.id_bibxxx=b.id AND tag LIKE '%s'""" % (bibXXx, bibrec_bibXXx, recID1, recID2, tag)
	res = run_sql(query)
	nb_total_to_read = len(res)
	verbose_idx = 0 # for verbose pretty printing
	for row in res:
	recID, phrase = row
	if options["validset"].contains(recID):
	if not wlist.has_key(recID): wlist[recID] = {}
	new_words = get_words_function(phrase, weight, lang) # ,self.separators
	wlist[recID] = dict_union(new_words,wlist[recID])

	# were there some words for these recIDs found?
	if len(wlist) == 0: return 0
	recIDs = wlist.keys()
	for recID in recIDs:
	# was this record marked as deleted?
	if "DELETED" in self.get_field(recID, "980__c"):
	wlist[recID] = {}
	if options["verbose"] >= 9:
	write_message("... record %d was declared deleted, removing its word list" % recID)
	if options["verbose"] >= 9:
	write_message("... record %d, termlist: %s" % (recID, wlist[recID]))
	query_factory = cStringIO.StringIO()
	qwrite = query_factory.write
	qwrite( "INSERT INTO %sR (id_bibrec,termlist,type) VALUES" % self.tablename[:-1])
	qwrite( "('" )
	qwrite( str(recIDs[0]) )
	qwrite( "','" )
	qwrite( serialize_via_marshal(wlist[recIDs[0]]) )
	qwrite( "','FUTURE')" )
	for recID in recIDs[1:]:
	qwrite(",('")
	qwrite(str(recID))
	qwrite("','")
	qwrite(serialize_via_marshal(wlist[recID]))
	qwrite("','FUTURE')")

	query = query_factory.getvalue()
	query_factory.close()
	run_sql(query)
	query_factory = cStringIO.StringIO()
	qwrite = query_factory.write
	qwrite("INSERT INTO %sR (id_bibrec,termlist,type) VALUES" % self.tablename[:-1])
	qwrite("('")
	qwrite(str(recIDs[0]))
	qwrite("','")
	qwrite(serialize_via_marshal(wlist[recIDs[0]]))
	qwrite("','CURRENT')")
	for recID in recIDs[1:]:
	qwrite( ",('" )
	qwrite( str(recID) )
	qwrite( "','" )
	qwrite( empty_list_string )
	qwrite( "','CURRENT')" )
	query = query_factory.getvalue()
	query_factory.close()
	try:
	run_sql(query)
	except MySQLdb.DatabaseError:
	pass

	put = self.put
	for recID in recIDs:
	for (w, count) in wlist[recID].iteritems():
	put(recID, w, count)

	return len(recIDs)

	def log_progress(self, start, done, todo):
	"""Calculate progress and store it.
	start: start time,
	done: records processed,
	todo: total number of records"""
	time_elapsed = time.time() - start
	# consistency check
	if time_elapsed == 0 or done > todo:
	return

	time_recs_per_min = done/(time_elapsed/60.0)
	if options["verbose"]:
	write_message("%d records took %.1f seconds to complete.(%1.f recs/min)"\
	% (done, time_elapsed, time_recs_per_min))

	if time_recs_per_min:
	if options["verbose"]:
	write_message("Estimated runtime: %.1f minutes" % \
	((todo-done)/time_recs_per_min))

	def put(self, recID, word, sign):
	"Adds/deletes a word to the word list."
	try:
	word = lower(word[:50])
	if self.value.has_key(word):
	# the word 'word' exist already: update sign
	self.value[word][recID] = sign
	# PROBLEM ?
	else:
	self.value[word] = {recID: sign}
	except:
	write_message("Error: Cannot put word %s with sign %d for recID %s." % (word, sign, recID))


	def del_recIDs(self, recIDs):
	"""Fetches records which id in the recIDs range list and adds
	them to the wordTable. The recIDs range list is of the form:
	[[i1_low,i1_high],[i2_low,i2_high], ..., [iN_low,iN_high]].
	"""
	count = 0
	for range in recIDs:
	self.del_recID_range(range[0],range[1])
	count = count + range[1] - range[0]
	self.put_into_db()

	def del_recID_range(self, low, high):
	"""Deletes records with 'recID' system number between low
	and high from memory words index table."""
	if options["verbose"] > 2:
	write_message("%s fetching existing words for records #%d-#%d started" % \
	(self.tablename, low, high))
	self.recIDs_in_mem.append([low,high])
	query = """SELECT id_bibrec,termlist FROM %sR as bb WHERE bb.id_bibrec
	BETWEEN '%d' AND '%d'""" % (self.tablename[:-1], low, high)
	recID_rows = run_sql(query)
	for recID_row in recID_rows:
	recID = recID_row[0]
	wlist = deserialize_via_marshal(recID_row[1])
	for word in wlist:
	self.put(recID, word, (-1, 0))
	if options["verbose"] > 2:
	write_message("%s fetching existing words for records #%d-#%d ended" % \
	(self.tablename, low, high))

	def report_on_table_consistency(self):
	"""Check reverse words index tables (e.g. rnkWORD01R) for
	interesting states such as 'TEMPORARY' state.
	Prints small report (no of words, no of bad words).
	"""
	# find number of words:
	query = """SELECT COUNT(*) FROM %s""" % (self.tablename)
	res = run_sql(query, None, 1)
	if res:
	nb_words = res[0][0]
	else:
	nb_words = 0

	# find number of records:
	query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR""" % (self.tablename[:-1])
	res = run_sql(query, None, 1)
	if res:
	nb_records = res[0][0]
	else:
	nb_records = 0

	# report stats:
	if options["verbose"]:
	write_message("%s contains %d words from %d records" % (self.tablename, nb_words, nb_records))

	# find possible bad states in reverse tables:
	query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR WHERE type <> 'CURRENT'""" % (self.tablename[:-1])
	res = run_sql(query)
	if res:
	nb_bad_records = res[0][0]
	else:
	nb_bad_records = 999999999
	if nb_bad_records:
	write_message("EMERGENCY: %s needs to repair %d of %d records" % \
	(self.tablename, nb_bad_records, nb_records))
	else:
	if options["verbose"]:
	write_message("%s is in consistent state" % (self.tablename))

	return nb_bad_records

	def repair(self):
	"""Repair the whole table"""
	# find possible bad states in reverse tables:
	query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR WHERE type <> 'CURRENT'""" % (self.tablename[:-1])
	res = run_sql(query, None, 1)
	if res:
	nb_bad_records = res[0][0]
	else:
	nb_bad_records = 0

	# find number of records:
	query = """SELECT COUNT(DISTINCT(id_bibrec)) FROM %sR""" % (self.tablename[:-1])
	res = run_sql(query)
	if res:
	nb_records = res[0][0]
	else:
	nb_records = 0

	if nb_bad_records == 0:
	return
	query = """SELECT id_bibrec FROM %sR WHERE type <> 'CURRENT' ORDER BY id_bibrec""" \
	% (self.tablename[:-1])
	res = run_sql(query)
	recIDs = create_range_list(res)

	flush_count = 0
	records_done = 0
	records_to_go = 0

	for range in recIDs:
	records_to_go = records_to_go + range[1] - range[0] + 1

	time_started = time.time() # will measure profile time
	for range in recIDs:
	i_low = range[0]
	chunksize_count = 0
	while i_low <= range[1]:
	# calculate chunk group of recIDs and treat it:
	i_high = min(i_low+options["flush"]-flush_count-1,range[1])
	i_high = min(i_low+chunksize-chunksize_count-1, i_high)
	try:
	self.fix_recID_range(i_low, i_high)
	except StandardError, e:
	write_message("Exception caught: %s" % e, sys.stderr)
	if options["verbose"] >= 9:
	traceback.print_tb(sys.exc_info()[2])
	task_update_status("ERROR")
	task_sig_stop_commands()
	sys.exit(1)

	flush_count = flush_count + i_high - i_low + 1
	chunksize_count = chunksize_count + i_high - i_low + 1
	records_done = records_done + i_high - i_low + 1
	if chunksize_count >= chunksize:
	chunksize_count = 0
	# flush if necessary:
	if flush_count >= options["flush"]:
	self.put_into_db("emergency")
	self.clean()
	flush_count = 0
	self.log_progress(time_started,records_done,records_to_go)
	# iterate:
	i_low = i_high + 1
	if flush_count > 0:
	self.put_into_db("emergency")
	self.log_progress(time_started,records_done,records_to_go)
	write_message("%s inconsistencies repaired." % self.tablename)

	def chk_recID_range(self, low, high):
	"""Check if the reverse index table is in proper state"""
	## check db
	query = """SELECT COUNT(*) FROM %sR WHERE type <> 'CURRENT'
	AND id_bibrec BETWEEN '%d' AND '%d'""" % (self.tablename[:-1], low, high)
	res = run_sql(query, None, 1)
	if res[0][0]==0:
	if options["verbose"]:
	write_message("%s for %d-%d is in consistent state"%(self.tablename,low,high))
	return # okay, words table is consistent

	## inconsistency detected!
	write_message("EMERGENCY: %s inconsistencies detected..." % self.tablename)
	write_message("""EMERGENCY: Errors found. You should check consistency of the %s - %sR tables.\nRunning 'bibindex --repair' is recommended.""" \
	% (self.tablename, self.tablename[:-1]))
	raise StandardError

	def fix_recID_range(self, low, high):
	"""Try to fix reverse index database consistency (e.g. table rnkWORD01R) in the low,high doc-id range.

	Possible states for a recID follow:
	CUR TMP FUT: very bad things have happened: warn!
	CUR TMP : very bad things have happened: warn!
	CUR FUT: delete FUT (crash before flushing)
	CUR : database is ok
	TMP FUT: add TMP to memory and del FUT from memory
	flush (revert to old state)
	TMP : very bad things have happened: warn!
	FUT: very bad things have happended: warn!
	"""

	state = {}
	query = "SELECT id_bibrec,type FROM %sR WHERE id_bibrec BETWEEN '%d' AND '%d'"\
	% (self.tablename[:-1], low, high)
	res = run_sql(query)
	for row in res:
	if not state.has_key(row[0]):
	state[row[0]]=[]
	state[row[0]].append(row[1])

	ok = 1 # will hold info on whether we will be able to repair
	for recID in state.keys():
	if not 'TEMPORARY' in state[recID]:
	if 'FUTURE' in state[recID]:
	if 'CURRENT' not in state[recID]:
	write_message("EMERGENCY: Record %d is in inconsistent state. Can't repair it" % recID)
	ok = 0
	else:
	write_message("EMERGENCY: Inconsistency in record %d detected" % recID)
	query = """DELETE FROM %sR
	WHERE id_bibrec='%d'""" % (self.tablename[:-1], recID)
	run_sql(query)
	write_message("EMERGENCY: Inconsistency in record %d repaired." % recID)
	else:
	if 'FUTURE' in state[recID] and not 'CURRENT' in state[recID]:
	self.recIDs_in_mem.append([recID,recID])
	# Get the words file
	query = """SELECT type,termlist FROM %sR
	WHERE id_bibrec='%d'""" % (self.tablename[:-1], recID)
	if options["verbose"] >= 9:
	write_message(query)
	res = run_sql(query)
	for row in res:
	wlist = deserialize_via_marshal(row[1])
	if options["verbose"] >= 9:
	write_message("Words are %s " % wlist)
	if row[0] == 'TEMPORARY':
	sign = 1
	else:
	sign = -1
	for word in wlist:
	self.put(recID, word, wlist[word])

	else:
	write_message("EMERGENCY: %s for %d is in inconsistent state. Couldn't repair it." % (self.tablename, recID))
	ok = 0

	if not ok:
	write_message("""EMERGENCY: Unrepairable errors found. You should check consistency
	of the %s - %sR tables. Deleting affected records is
	recommended.""" % (self.tablename, self.tablename[:-1]))
	raise StandardError

	def word_index(row, run):
	"""Run the indexing task. The row argument is the BibSched task
	queue row, containing if, arguments, etc.
	Return 1 in case of success and 0 in case of failure.
	"""

	## import optional modules:
	try:
	import psyco
	psyco.bind(get_words_from_phrase)
	psyco.bind(WordTable.merge_with_old_recIDs)
	psyco.bind(serialize_via_numeric_array)
	psyco.bind(serialize_via_marshal)
	psyco.bind(deserialize_via_numeric_array)
	psyco.bind(deserialize_via_marshal)
	psyco.bind(update_rnkWORD)
	psyco.bind(check_rnkWORD)
	except StandardError,e:
	print "Warning: Psyco", e
	pass

	global options, task_id, wordTables, stopwords, stemmer, languages
	languages = {'fr': 'french', 'en': 'porter', 'no':'norwegian', 'se':'swedish', 'de': 'german', 'it':'italian', 'pt':'portugese'}

	stemmer = {}

	# read from SQL row:
	task_id = row[0]
	task_proc = row[1]
	options = marshal.loads(row[6])

	# install signal handlers
	signal.signal(signal.SIGUSR1, task_sig_sleep)
	signal.signal(signal.SIGTERM, task_sig_stop)
	signal.signal(signal.SIGABRT, task_sig_suicide)
	signal.signal(signal.SIGCONT, task_sig_wakeup)
	signal.signal(signal.SIGINT, task_sig_unknown)
	## go ahead and treat each table:

	options["run"] = []
	options["run"].append(run)
	for rank_method_code in options["run"]:
	method_starting_time = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
	write_message("Running rank method: %s" % getName(rank_method_code))
	try:
	file = etcdir + "/bibrank/" + rank_method_code + ".cfg"
	config = ConfigParser.ConfigParser()
	config.readfp(open(file))
	except StandardError, e:
	write_message("Cannot find configurationfile: %s" % file, sys.stderr)
	raise StandardError

	options["current_run"] = rank_method_code
	options["modified_words"] = {}
	options["table"] = config.get(config.get("rank_method", "function"), "table")
	(stopwords, tags) = get_tags(config) #get the tags to include
	options["validset"] = get_valid_range(rank_method_code) #get the records from the collections the method is enabled for

	wordTable = WordTable(options["table"], tags)
	wordTable.report_on_table_consistency()
	try:
	if options["cmd"] == "del":
	if options["id"]:
	wordTable.del_recIDs(options["id"])
	elif options["collection"]:
	l_of_colls = string.split(options["collection"], ",")
	recIDs = perform_request_search(c=l_of_colls)
	recIDs_range = []
	for recID in recIDs:
	recIDs_range.append([recID,recID])
	wordTable.del_recIDs(recIDs_range)
	else:
	write_message("Missing IDs of records to delete from index %s.", wordTable.tablename,
	sys.stderr)
	raise StandardError
	elif options["cmd"] == "add":
	if options["id"]:
	wordTable.add_recIDs(options["id"])
	elif options["collection"]:
	l_of_colls = string.split(options["collection"], ",")
	recIDs = perform_request_search(c=l_of_colls)
	recIDs_range = []
	for recID in recIDs:
	recIDs_range.append([recID,recID])
	wordTable.add_recIDs(recIDs_range)
	elif options["last_updated"]:
	wordTable.add_date("")
	wordTable.update_last_updated(rank_method_code, method_starting_time)
	else:
	wordTable.add_recIDs([[0,cfg_max_recID]])
	#wordTable.add_date(options["modified"])
	# only update last_updated if run via automatic mode:
	elif options["cmd"] == "repair":
	wordTable.repair()
	check_rnkWORD(options["table"])
	elif options["cmd"] == "check":
	check_rnkWORD(options["table"])
	options["modified_words"] = {}
	elif options["cmd"] == "stat":
	rank_method_code_statistics(options["table"])
	else:
	write_message("Invalid command found processing %s" % \
	wordTable.tablename, sys.stderr)
	raise StandardError
	update_rnkWORD(options["table"], options["modified_words"])
	except StandardError, e:
	write_message("Exception caught: %s" % e, sys.stderr)
	if options["verbose"] >= 9:
	traceback.print_tb(sys.exc_info()[2])
	sys.exit(1)
	wordTable.report_on_table_consistency()
	# We are done. State it in the database, close and quit

	return 1

	def get_tags(config):
	"""Get the tags that should be used creating the index and each tag's parameter, also get stemmer for language"""
	tags = []
	function = config.get("rank_method","function")
	i = 1
	shown_error = 0

	try:
	while config.has_option(function,"tag%s"% i):
	tag = config.get(function, "tag%s" % i)
	tag = string.split(tag, ",")
	tag[1] = int(string.strip(tag[1]))
	tag[2] = string.strip(tag[2])
	#get stopwordlist
	stopwords = get_stopwords("%s" % config.get(function, "stopword"))

	try:
	#get stemmer for language if possible
	if tag[2] and tag[2] != "none" and languages.has_key(tag[2]) and config.get(function,"stem_if_avail") == "yes" and not stemmer.has_key(tag[2]):
	stemmer[tag[2]] = Stemmer.Stemmer(languages[tag[2]])
	if options["verbose"] >=9:
	write_message("Stemmer for language '%s' initiated" % tag[2])
	elif tag[2] != "none" and config.get(function,"stem_if_avail") == "yes" and not stemmer.has_key(tag[2]):
	write_message("Warning: Language '%s' not available in PyStemmer." % tag[2])
	except NameError:
	if shown_error == 0:
	write_message("Warning: PyStemmer not found. Please read INSTALL.")
	shown_error = 1
	tags.append(tag)
	i += 1
	except Exception:
	write_message("Could not read data from configuration file, please check for errors")
	raise StandardError

	return (stopwords, tags)

	def get_valid_range(rank_method_code):
	"""Returns which records are valid for this rank method, according to which collections it is enabled for."""

	#if options["verbose"] >=9:
	# write_message("Getting records from collections enabled for rank method.")
	#res = run_sql("SELECT collection.name FROM collection,collection_rnkMETHOD,rnkMETHOD WHERE collection.id=id_collection and id_rnkMETHOD=rnkMETHOD.id and rnkMETHOD.name='%s'" % rank_method_code)
	#l_of_colls = []
	#for coll in res:
	# l_of_colls.append(coll[0])
	#if len(l_of_colls) > 0:
	# recIDs = perform_request_search(c=l_of_colls)
	#else:
	# recIDs = []

	valid = HitSet(Numeric.ones(cfg_max_recID+1, Numeric.Int0))
	#valid.addlist(recIDs)
	return valid

	def write_message(msg, stream=sys.stdout):
	"""Prints message and flush output stream (may be sys.stdout or sys.stderr)."""
	if stream == sys.stdout or stream == sys.stderr:
	stream.write(time.strftime("%Y-%m-%d %H:%M:%S --> ", time.localtime()))
	stream.write("%s\n" % msg)
	stream.flush()
	else:
	sys.stderr.write("Unknown stream %s. [must be sys.stdout or sys.stderr]\n" % stream)

	def get_stopwords(file='stopwords.txt'):
	"""Get stopword list"""
	stopwords = open(file, 'r')
	lines = stopwords.readlines()
	stopwords.close()
	stopwords = {}
	for line in lines:
	stopwords[string.rstrip(line)] = 1
	return stopwords

	def check_term(term, termlength):
	"""Check if term is a stopword, or for any other reasons for not using this term."""
	try:
	if stopwords.has_key(lower(term)) or (len(term) <= termlength):
	return ""
	reg = re.compile(r"[1234567890\!\"\#\$\%\&\'\*\+\,\-\.\/\:\;\<\=\>\?\@\[\\\]\^\_\`\{\\|\}\~]")
	if re.search(reg, term):
	return ""
	term = str.replace(term, "-", "")
	term = str.replace(term, ".", "")
	term = str.replace(term, ",", "")
	if int(term):
	return ""
	except StandardError, e:
	pass
	return "true"

	def check_rnkWORD(table):
	"""Checks for any problems in rnkWORD tables."""
	i = 0
	errors = {}
	termslist = run_sql("SELECT term FROM %s" % table)
	N = run_sql("select max(id_bibrec) from %sR" % table[:-1])[0][0]
	write_message("Checking integrity of rank values in %s" % table)
	terms = map(lambda x: x[0], termslist)

	while i < len(terms):
	current_terms = ""
	for j in range(i, ((i+5000)< len(terms) and (i+5000) or len(terms))):
	current_terms += "'%s'," % terms[j]
	terms_docs = run_sql("SELECT term, hitlist FROM %s WHERE term in (%s)" % (table, current_terms[:-1]))
	for (t, hitlist) in terms_docs:
	term_docs = deserialize_via_marshal(hitlist)
	if (term_docs.has_key("Gi") and term_docs["Gi"][1] == 0) or not term_docs.has_key("Gi"):
	write_message("ERROR: Missing value for term: %s (%s) in %s: %s" % (t, repr(t), table, len(term_docs)))
	errors[t] = 1
	i += 5000
	write_message("Checking integrity of rank values in %sR" % table[:-1])
	i = 0
	while i < N:
	docs_terms = run_sql("SELECT id_bibrec, termlist FROM %sR WHERE id_bibrec>=%s and id_bibrec<=%s" % (table[:-1], i, i+5000))
	for (j, termlist) in docs_terms:
	termlist = deserialize_via_marshal(termlist)
	for (t, tf) in termlist.iteritems():
	if tf[1] == 0 and not errors.has_key(t):
	errors[t] = 1
	write_message("ERROR: Gi missing for record %s and term: %s (%s) in %s" % (j,t,repr(t), table))
	terms_docs = run_sql("SELECT term, hitlist FROM %s WHERE term='%s'" % (table, t))
	termlist = deserialize_via_marshal(terms_docs[0][1])
	i += 5000

	if len(errors) == 0:
	write_message("No direct errors found, but nonconsistent data may exist.")
	else:
	write_message("%s errors found during integrity check, repair and rebalancing recommended." % len(errors))
	options["modified_words"] = errors

	def rank_method_code_statistics(table):
	"""Shows some statistics about this rank method."""

	maxID = run_sql("select max(id) from %s" % table)
	maxID = maxID[0][0]
	terms = {}
	Gi = {}

	write_message("Showing statistics of terms in index:")
	write_message("Important: For the 'Least used terms', the number of terms is shown first, and the number of occurences second.")
	write_message("Least used terms---Most important terms---Least important terms")
	i = 0
	while i < maxID:
	terms_docs=run_sql("SELECT term, hitlist FROM %s WHERE id>= %s and id < %s" % (table, i, i + 10000))
	for (t, hitlist) in terms_docs:
	term_docs=deserialize_via_marshal(hitlist)
	terms[len(term_docs)] = terms.get(len(term_docs), 0) + 1
	if term_docs.has_key("Gi"):
	Gi[t] = term_docs["Gi"]
	i=i + 10000
	terms=terms.items()
	terms.sort(lambda x, y: cmp(y[1], x[1]))
	Gi=Gi.items()
	Gi.sort(lambda x, y: cmp(y[1], x[1]))
	for i in range(0, 20):
	write_message("%s/%s---%s---%s" % (terms[i][0],terms[i][1], Gi[i][0],Gi[len(Gi) - i - 1][0]))

	def update_rnkWORD(table, terms):
	"""Updates rnkWORDF and rnkWORDR with Gi and Nj values. For each term in rnkWORDF, a Gi value for the term is added. And for each term in each document, the Nj value for that document is added. In rnkWORDR, the Gi value for each term in each document is added. For description on how things are computed, look in the hacking docs.
	table - name of forward index to update
	terms - modified terms"""

	stime = time.time()
	Gi = {}
	Nj = {}
	N = run_sql("select count(id_bibrec) from %sR" % table[:-1])[0][0]

	if len(terms) == 0:
	return ""

	write_message("Beginning post-processing of %s terms" % len(terms))

	#Locating all documents related to the modified/new/deleted terms, if fast update,
	#only take into account new/modified occurences
	write_message("Phase 1: Finding records containing modified terms")
	terms = terms.keys()
	i = 0
	while i < len(terms):
	current_terms = ""
	for j in range(i, ((i+5000)< len(terms) and (i+5000) or len(terms))):
	current_terms += "'%s'," % terms[j]
	terms_docs = run_sql("SELECT term, hitlist FROM %s WHERE term in (%s)" % (table,current_terms[:-1]))
	for (t, hitlist) in terms_docs:
	term_docs = deserialize_via_marshal(hitlist)
	if term_docs.has_key("Gi"):
	del term_docs["Gi"]
	for (j, tf) in term_docs.iteritems():
	if (options["quick"] == "yes" and tf[1] == 0) or options["quick"] == "no":
	Nj[j] = 0
	write_message("Phase 1: ......processed %s/%s terms" % ((i+5000>len(terms) and len(terms) or (i+5000)), len(terms)))
	i += 5000
	write_message("Phase 1: Finished finding records containing modified terms")

	#Find all terms in the records found in last phase
	write_message("Phase 2: Finding all terms in affected records")
	records = Nj.keys()
	i = 0
	while i < len(records):
	current_recs = "%s" % records[i:i+5000]
	docs_terms = run_sql("SELECT id_bibrec, termlist FROM %sR WHERE id_bibrec in (%s)" % (table[:-1],current_recs[1:-1]))
	for (j, termlist) in docs_terms:
	doc_terms = deserialize_via_marshal(termlist)
	for (t, tf) in doc_terms.iteritems():
	Gi[t] = 0
	write_message("Phase 2: ......processed %s/%s records " % ((i+5000>len(records) and len(records) or (i+5000)), len(records)))
	i += 5000
	write_message("Phase 2: Finished finding all terms in affected records")

	terms = Gi.keys()
	Gi = {}
	i = 0
	if options["quick"] == "no":
	#Calculating Fi and Gi value for each term
	write_message("Phase 3: Calculating importance of all affected terms")
	while i < len(terms):
	current_terms = ""
	for j in range(i, ((i+5000)< len(terms) and (i+5000) or len(terms))):
	current_terms += "'%s'," % terms[j]
	terms_docs = run_sql("SELECT term, hitlist FROM %s WHERE term in (%s)" % (table,current_terms[:-1]))
	for (t, hitlist) in terms_docs:
	term_docs = deserialize_via_marshal(hitlist)
	if term_docs.has_key("Gi"):
	del term_docs["Gi"]
	Fi = 0
	Gi[t] = 1
	for (j, tf) in term_docs.iteritems():
	Fi += tf[0]
	for (j, tf) in term_docs.iteritems():
	if tf[0] != Fi:
	Gi[t] = Gi[t] + ((float(tf[0]) / Fi) * math.log(float(tf[0]) / Fi) / math.log(2)) / math.log(N)
	write_message("Phase 3: ......processed %s/%s terms" % ((i+5000>len(terms) and len(terms) or (i+5000)), len(terms)))
	i += 5000
	write_message("Phase 3: Finished calculating importance of all affected terms")
	else:
	#Using existing Gi value instead of calculating a new one. Missing some accurancy.
	write_message("Phase 3: Getting approximate importance of all affected terms")
	while i < len(terms):
	current_terms = ""
	for j in range(i, ((i+5000)< len(terms) and (i+5000) or len(terms))):
	current_terms += "'%s'," % terms[j]
	terms_docs = run_sql("SELECT term, hitlist FROM %s WHERE term in (%s)" % (table,current_terms[:-1]))
	for (t, hitlist) in terms_docs:
	term_docs = deserialize_via_marshal(hitlist)
	if term_docs.has_key("Gi"):
	Gi[t] = term_docs["Gi"][1]
	else:
	write_message("Please rebalance these records,(may require deletion before adding again)")
	raise Exception("Rebalance")
	write_message("Phase 3: ......processed %s/%s terms" % ((i+5000>len(terms) and len(terms) or (i+5000)), len(terms)))
	i += 5000
	write_message("Phase 3: Finished getting approximate importance of all affected terms")

	write_message("Phase 4: Calculating normalization value for all affected records and updating %sR" % table[:-1])
	records = Nj.keys()
	i = 0
	while i < len(records):
	#Calculating the normalization value for each document, and adding the Gi value to each term in each document.
	current_recs = "%s" % records[i:i+5000]
	current_recs = current_recs[1:-1]
	docs_terms = run_sql("SELECT id_bibrec, termlist FROM %sR WHERE id_bibrec IN (%s)" % (table[:-1],current_recs))
	for (j, termlist) in docs_terms:
	doc_terms = deserialize_via_marshal(termlist)
	for (t, tf) in doc_terms.iteritems():
	if Gi.has_key(t):
	Nj[j] = Nj.get(j, 0) + math.pow(Gi[t] * (1 + math.log(tf[0])), 2)
	Git = int(math.floor(Gi[t]*100))
	if Git >= 0:
	Git += 1
	doc_terms[t] = (tf[0], Git)
	else:
	Nj[j] = Nj.get(j, 0) + math.pow(tf[1] * (1 + math.log(tf[0])), 2)
	Nj[j] = 1.0 / math.sqrt(Nj[j])
	Nj[j] = int(Nj[j] * 100)
	if Nj[j] >= 0:
	Nj[j] += 1
	run_sql("UPDATE %sR SET termlist='%s' WHERE id_bibrec=%s" % (table[:-1], serialize_via_marshal(doc_terms), j))
	write_message("Phase 4: ......processed %s/%s records" % ((i+5000>len(records) and len(records) or (i+5000)), len(records)))
	i += 5000
	write_message("Phase 4: Finished calculating normalization value for all affected records and updating %sR" % table[:-1])
	write_message("Phase 5: Updating %s with new normalization values" % table)
	i = 0
	terms = Gi.keys()
	while i < len(terms):
	#Adding the Gi value to each term, and adding the normalization value to each term in each document.
	current_terms = ""
	for j in range(i, ((i+5000)< len(terms) and (i+5000) or len(terms))):
	current_terms += "'%s'," % terms[j]
	terms_docs = run_sql("SELECT term, hitlist FROM %s WHERE term IN (%s)" % (table,current_terms[:-1]))
	for (t, hitlist) in terms_docs:
	term_docs = deserialize_via_marshal(hitlist)
	if term_docs.has_key("Gi"):
	del term_docs["Gi"]
	for (j, tf) in term_docs.iteritems():
	if Nj.has_key(j):
	term_docs[j] = (tf[0], Nj[j])
	Git = int(math.floor(Gi[t]*100))
	if Git >= 0:
	Git += 1
	term_docs["Gi"] = (0, Git)
	run_sql("UPDATE %s SET hitlist='%s' WHERE term='%s'" % (table, serialize_via_marshal(term_docs), MySQLdb.escape_string(t)))
	write_message("Phase 5: ......processed %s/%s terms" % ((i+5000>len(terms) and len(terms) or (i+5000)), len(terms)))
	i += 5000
	write_message("Phase 5: Finished updating %s with new normalization values" % table)
	write_message("Time used for post-processing: %.1fmin" % ((time.time() - stime) / 60))
	write_message("Finished post-processing")

	def test_word_separators(phrase="hep-th/0101001"):
	"""Tests word separating policy on various input."""
	print "%s:" % phrase
	gwfp = get_words_from_phrase(phrase)
	for (word, count) in gwfp.iteritems():
	print "\t-> %s - %s" % (word, count)

	def task_sig_sleep(sig, frame):
	"""Signal handler for the 'sleep' signal sent by BibSched."""
	if options["verbose"] >= 9:
	write_message("got signal %d" % sig)
	write_message("sleeping...")
	task_update_status("SLEEPING")
	signal.pause() # wait for wake-up signal

	def task_sig_wakeup(sig, frame):
	"""Signal handler for the 'wakeup' signal sent by BibSched."""
	if options["verbose"] >= 9:
	write_message("got signal %d" % sig)
	write_message("continuing...")
	task_update_status("CONTINUING")

	def task_sig_stop(sig, frame):
	"""Signal handler for the 'stop' signal sent by BibSched."""
	if options["verbose"] >= 9:
	write_message("got signal %d" % sig)
	write_message("stopping...")
	task_update_status("STOPPING")
	errcode = 0
	try:
	task_sig_stop_commands()
	write_message("stopped")
	task_update_status("STOPPED")
	except StandardError, err:
	write_message("Error during stopping! %e" % err)
	task_update_status("STOPPINGFAILED")
	errcode = 1
	sys.exit(errcode)

	def task_sig_stop_commands():
	"""Do all the commands necessary to stop the task before quitting.
	Useful for task_sig_stop() handler.
	"""
	write_message("stopping commands started")
	for table in wordTables:
	table.put_into_db()
	write_message("stopping commands ended")

	def task_sig_suicide(sig, frame):
	"""Signal handler for the 'suicide' signal sent by BibSched."""
	if options["verbose"] >= 9:
	write_message("got signal %d" % sig)
	write_message("suiciding myself now...")
	task_update_status("SUICIDING")
	write_message("suicided")
	task_update_status("SUICIDED")
	sys.exit(0)

	def task_sig_unknown(sig, frame):
	"""Signal handler for the other unknown signals sent by shell or user."""
	if options["verbose"] >= 9:
	write_message("got signal %d" % sig)
	write_message("unknown signal %d ignored" % sig) # do nothing for other signals

	def task_update_progress(msg):
	"""Updates progress information in the BibSched task table."""
	global task_id, options
	if options["verbose"] >= 9:
	write_message("Updating task progress to %s." % msg)
	return run_sql("UPDATE schTASK SET progress=%s where id=%s", (msg, task_id))

	def task_update_status(val):
	"""Updates state information in the BibSched task table."""
	global task_id, options
	if options["verbose"] >= 9:
	write_message("Updating task status to %s." % val)
	return run_sql("UPDATE schTASK SET status=%s where id=%s", (val, task_id))

	def getName(methname, ln=cdslang, type='ln'):
	"""Returns the name of the rank method, either in default language or given language.
	methname = short name of the method
	ln - the language to get the name in
	type - which name "type" to get."""

	try:
	rnkid = run_sql("SELECT id FROM rnkMETHOD where name='%s'" % methname)
	if rnkid:
	rnkid = str(rnkid[0][0])
	res = run_sql("SELECT value FROM rnkMETHODNAME where type='%s' and ln='%s' and id_rnkMETHOD=%s" % (type, ln, rnkid))
	if not res:
	res = run_sql("SELECT value FROM rnkMETHODNAME WHERE ln='%s' and id_rnkMETHOD=%s and type='%s'" % (cdslang, rnkid, type))
	if not res:
	return methname
	return res[0][0]
	else:
	raise Exception
	except Exception, e:
	write_message("Cannot run rank method, either given code for method is wrong, or it has not been added using the webinterface.")
	raise Exception

	def word_similarity(row, run):
	"""Call correct method"""
	return word_index(row, run)

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