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bibrank_word_indexer.py.wml
08ec71b289f2iugw2017

bibrank_word_indexer.py.wml
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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:
			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
			from cdsware.bibindex_engine_stemmer import stem_by_lang, lang_available
			from cdsware.bibindex_engine_stopwords import is_stopword_force
			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])

			#for (e, count) in list2.iteritems():
			# list1[e] = (list1.get(e, (0, 0))[0] + count[0], count[1])

			#return list1
			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)
			phrase = lower(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 options["remove_stopword"] == "True" and not is_stopword_force(word) and check_term(word, 0):
			if lang and lang !="none" and options["use_stemming"]:
			word = stem_by_lang(word, lang)
			if not words.has_key(word):
			words[word] = (0,0)
			words[word] = (words[word][0] + weight, 0)
			elif options["remove_stopword"] == "True" and not is_stopword_force(word):
			phrase = re.sub(chars_alphanumericseparators, ' ', word)
			for word_ in split(phrase):
			if lang and lang !="none" and options["use_stemming"]:
			word_ = stem_by_lang(word_, lang)
			if word_:
			if not words.has_key(word_):
			words[word_] = (0,0)
			words[word_] = (words[word_][0] + weight, 0)
			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
			rnkWORD 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:
			options["modified_words"][word] = 1
			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)
			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, languages

			# 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")
			options["use_stemming"] = config.get(config.get("rank_method","function"),"stemming")
			options["remove_stopword"] = config.get(config.get("rank_method","function"),"stopword")
			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
			function = config.get("rank_method","function")
			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"""
			tags = []
			function = config.get("rank_method","function")
			i = 1
			shown_error = 0

			#try:
			if 1:
			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])

			#check if stemmer for language is available
			if config.get(function,"stemming") and stem_by_lang("information", "en") != "inform":
			if shown_error == 0:
			write_message("Warning: PyStemmer not found. Please read INSTALL.")
			shown_error = 1
			elif tag[2] and tag[2] != "none" and config.get(function,"stemming") and not lang_available(tag[2]):
			write_message("Warning: Language '%s' not available in PyStemmer." % tag[2])
			tags.append(tag)
			i += 1
			#except Exception:
			# write_message("Could not read data from configuration file, please check for errors")
			# raise StandardError

			return 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 check_term(term, termlength):
			"""Check if term contains not allowed characters, or for any other reasons for not using this term."""
			try:
			if len(term) <= termlength:
			return False
			reg = re.compile(r"[1234567890\!\"\#\$\%\&\'\*\+\,\-\.\/\:\;\<\=\>\?\@\[\\\]\^\_\`\{\\|\}\~]")
			if re.search(reg, term):
			return False
			term = str.replace(term, "-", "")
			term = str.replace(term, ".", "")
			term = str.replace(term, ",", "")
			if int(term):
			return False
			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]

			write_message("Beginning post-processing of %s terms" % len(terms))
			if len(terms) == 0:
			write_message("No terms to process, ending...")
			return ""

			#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):
			terms_docs = get_from_forward_index(terms, i, (i+5000), table)
			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):
			docs_terms = get_from_reverse_index(records, i, (i + 5000), table)
			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):
			terms_docs = get_from_forward_index(terms, i, (i+5000), table)
			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):
			terms_docs = get_from_forward_index(terms, i, (i+5000), table)
			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.
			docs_terms = get_from_reverse_index(records, i, (i + 5000), table)
			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.
			terms_docs = get_from_forward_index(terms, i, (i+5000), table)
			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 get_from_forward_index(terms, start, stop, table):
			current_terms = ""
			for j in range(start, (stop < len(terms) and stop 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]))
			return terms_docs

			def get_from_reverse_index(records, start, stop, table):
			current_recs = "%s" % records[start:stop]
			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))
			return docs_terms

			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)

R3600/modules/bibrank/lib/bibrank_word_indexer.py.wml08ec71b289f2iugw2017

bibrank_word_indexer.py.wmlView Options

R3600/modules/bibrank/lib/bibrank_word_indexer.py.wml
08ec71b289f2iugw2017

bibrank_word_indexer.py.wml
View Options