bibrank_citation_indexer.py
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bibrank_citation_indexer.py
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	# -- coding: utf-8 --
	##
	## This file is part of CDS Invenio.
	## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
	##
	## CDS Invenio 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.
	##
	## CDS Invenio 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 CDS Invenio; if not, write to the Free Software Foundation, Inc.,
	## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.

	__revision__ = "$Id$"

	import re
	import time
	import sys
	import os
	import zlib

	if sys.hexversion < 0x2040000:
	# pylint: disable=W0622
	from sets import Set as set
	# pylint: enable=W0622

	from invenio.dbquery import run_sql, serialize_via_marshal, \
	deserialize_via_marshal
	from invenio.search_engine import search_pattern, get_fieldvalues, \
	search_unit
	from invenio.bibformat_utils import parse_tag
	from invenio.bibtask import write_message, task_get_option, \
	task_update_progress, task_sleep_now_if_required, \
	task_get_task_param
	from invenio.errorlib import register_exception

	class memoise:
	def __init__(self, function):
	self.memo = {}
	self.function = function
	def __call__(self, *args):
	if self.memo.has_key(args):
	return self.memo[args]
	else:
	object = self.memo[args] = self.function(*args)
	return object

	def get_recids_matching_query(pvalue, fvalue):
	"""Return list of recIDs matching query for PVALUE and FVALUE."""
	rec_id = list(search_pattern(p=pvalue, f=fvalue, m='e'))
	return rec_id
	get_recids_matching_query = memoise(get_recids_matching_query)

	def get_citation_weight(rank_method_code, config):
	"""return a dictionary which is used by bibrank daemon for generating
	the index of sorted research results by citation information
	"""
	begin_time = time.time()
	last_update_time = get_bibrankmethod_lastupdate(rank_method_code)

	if task_get_option("quick") == "no":
	last_update_time = "0000-00-00 00:00:00"
	write_message("running thorough indexing since quick option not used", verbose=3)

	last_modified_records = get_last_modified_rec(last_update_time)
	#id option forces re-indexing a certain range even if there are no new recs
	if last_modified_records or task_get_option("id"):
	if task_get_option("id"):
	#construct a range of records to index
	taskid = task_get_option("id")
	first = taskid[0][0]
	last = taskid[0][1]
	#make range, last+1 so that e.g. -i 1-2 really means [1,2] not [1]
	updated_recid_list = range(first, last+1)
	else:
	updated_recid_list = create_recordid_list(last_modified_records)

	write_message("Last update "+str(last_update_time)+" records: "+ \
	str(len(last_modified_records))+" updates: "+ \
	str(len(updated_recid_list)))

	#write_message("updated_recid_list: "+str(updated_recid_list))
	result_intermediate = last_updated_result(rank_method_code)

	#result_intermed should be warranted to exists!
	#but if the user entered a "-R" (do all) option, we need to
	#make an empty start set
	if task_get_option("quick") == "no":
	result_intermediate = [{}, {}, {}]

	citation_weight_dic_intermediate = result_intermediate[0]
	citation_list_intermediate = result_intermediate[1]
	reference_list_intermediate = result_intermediate[2]

	#call the procedure that does the hard work by reading fields of
	#citations and references in the updated_recid's (but nothing else)!
	if task_get_task_param('verbose') >= 9:
	write_message("Entering get_citation_informations")
	citation_informations = get_citation_informations(updated_recid_list,
	config)
	#write_message("citation_informations: "+str(citation_informations))
	#create_analysis_tables() #temporary..
	#test how much faster in-mem indexing is
	write_message("Entering ref_analyzer", verbose=9)
	#call the analyser that uses the citation_informations to really
	#search x-cites-y in the coll..
	dic = ref_analyzer(citation_informations,
	citation_weight_dic_intermediate,
	citation_list_intermediate,
	reference_list_intermediate,
	config,updated_recid_list)
	#dic is docid-numberofreferences like {1: 2, 2: 0, 3: 1}
	#write_message("Docid-number of known references "+str(dic))
	end_time = time.time()
	write_message("Total time of get_citation_weight(): %.2f sec" % (end_time - begin_time))
	task_update_progress("citation analysis done")
	else:
	dic = {}
	write_message("No new records added since last time this rank method was executed")
	return dic

	def get_bibrankmethod_lastupdate(rank_method_code):
	"""return the last excution date of bibrank method
	"""
	query = """select last_updated from rnkMETHOD where name ='%s'""" % rank_method_code
	last_update_time = run_sql(query)
	r = last_update_time[0][0]
	if r is None:
	return "0000-00-00 00:00:00"
	return r

	def get_last_modified_rec(bibrank_method_lastupdate):
	""" return the list of recods which have been modified after the last exec
	of bibrank method. The result is expected to have ascending num order.
	"""
	query = """SELECT id FROM bibrec
	WHERE modification_date >= '%s' """ % bibrank_method_lastupdate
	query += "order by id ASC"
	ilist = run_sql(query)
	return ilist

	def create_recordid_list(rec_ids):
	"""Create a list of record ids out of RECIDS.
	The result is expected to have ascending numerical order.
	"""
	rec_list = []
	for row in rec_ids:
	rec_list.append(row[0])
	return rec_list

	def create_record_tuple(ilist):
	"""Creates a tuple of record id from a list of id.
	The result is expected to have ascending numerical order.
	"""
	list_length = len(ilist)
	if list_length:
	rec_tuple = '('
	for row in list[0:list_length-1]:
	rec_tuple += str(row)
	rec_tuple += ','
	rec_tuple += str(list[list_length-1])
	rec_tuple += ')'
	else: rec_tuple = '()'
	return rec_tuple

	def last_updated_result(rank_method_code):
	""" return the last value of dictionary in rnkMETHODDATA table if it exists and
	initialize the value of last updated records by zero,
	otherwise an initial dictionary with zero as value for all recids
	"""
	result = [{}, {}, {}]
	query = """select relevance_data from rnkMETHOD, rnkMETHODDATA where
	rnkMETHOD.id = rnkMETHODDATA.id_rnkMETHOD
	and rnkMETHOD.Name = '%s'"""% rank_method_code
	rdict = run_sql(query)
	if rdict and rdict[0] and rdict[0][0]:
	#has to be prepared for corrupted data!
	try:
	dic = deserialize_via_marshal(rdict[0][0])
	except zlib.error:
	return [{}, {}, {}]
	query = "select object_value from rnkCITATIONDATA where object_name='citationdict'"
	cit_compressed = run_sql(query)
	cit = []
	if cit_compressed and cit_compressed[0] and cit_compressed[0][0]:
	cit = deserialize_via_marshal(cit_compressed[0][0])
	if cit:
	query = """select object_value from rnkCITATIONDATA
	where object_name='reversedict'"""
	ref_compressed = run_sql(query)
	if ref_compressed and ref_compressed[0] and ref_compressed[0][0]:
	ref = deserialize_via_marshal(ref_compressed[0][0])
	result = (dic, cit, ref)
	return result

	def get_citation_informations(recid_list, config):
	"""scans the collections searching references (999C5x -fields) and
	citations for items in the recid_list
	returns a 4 list of dictionaries that contains the citation information
	of cds records
	examples: [ {} {} {} {} ]
	[ {5: 'SUT-DP-92-70-5'},
	{ 93: ['astro-ph/9812088']},
	{ 93: ['Phys. Rev. Lett. 96 (2006) 081301'] }, {} ]
	NB: stuff here is for analysing new or changed records.
	see "ref_analyzer" for more.
	"""
	begin_time = os.times()[4]
	d_reports_numbers = {} #dict of recid -> institute-given-report-code
	d_references_report_numbers = {} #dict of recid -> ['astro-ph/xyz']
	d_references_s = {} #dict of recid -> list_of_the_entries_of_this_recs_bibliography
	d_records_s = {} #dict of recid -> this_records_publication_info
	citation_informations = []

	write_message("config function "+config.get("rank_method", "function"), verbose=9)
	function = ""
	try:
	function = config.get("rank_method", "function")
	except:
	register_exception(prefix="cfg section [rank_method] has no attribute called function", alert_admin=True)
	#we cannot continue
	return [ {}, {}, {}, {} ]
	record_pri_number_tag = ""
	try:
	record_pri_number_tag = config.get(function, "primary_report_number")
	except:
	register_exception(prefix="cfg section "+function+" has no attribute primary_report_number", alert_admin=True)
	return [ {}, {}, {}, {} ]
	record_add_number_tag = ""
	try:
	record_add_number_tag = config.get(config.get("rank_method", "function"),
	"additional_report_number")
	except:
	register_exception(prefix="config error. cfg section "+function+" has no attribute additional_report_number", alert_admin=True)
	return [ {}, {}, {}, {} ]

	reference_number_tag = ""
	try:
	reference_number_tag = config.get(config.get("rank_method", "function"),
	"reference_via_report_number")
	except:
	register_exception(prefix="config error. cfg section "+function+" has no attribute reference_via_report_number", alert_admin=True)
	return [ {}, {}, {}, {} ]

	reference_tag = ""
	try:
	reference_tag = config.get(config.get("rank_method", "function"),
	"reference_via_pubinfo")
	except:
	register_exception(prefix="config error. cfg section "+function+" has no attribute reference_via_pubinfo", alert_admin=True)
	return [ {}, {}, {}, {} ]

	p_record_pri_number_tag = tagify(parse_tag(record_pri_number_tag))
	#037a: contains (often) the "hep-ph/0501084" tag of THIS record
	p_record_add_number_tag = tagify(parse_tag(record_add_number_tag))
	#088a: additional short identifier for the record
	p_reference_number_tag = tagify(parse_tag(reference_number_tag))
	#999C5r. this is in the reference list, refers to other records. Looks like: hep-ph/0408002
	p_reference_tag = tagify(parse_tag(reference_tag))
	#999C5s. A standardized way of writing a reference in the reference list. Like: Nucl. Phys. B 710 (2000) 371
	#fields needed to construct the pubinfo for this record
	publication_pages_tag = ""
	publication_year_tag = ""
	publication_journal_tag = ""
	publication_volume_tag = ""
	publication_format_string = "p v (y) c"
	try:
	tag = config.get(function, "pubinfo_journal_page")
	publication_pages_tag = tagify(parse_tag(tag))
	tag = config.get(function, "pubinfo_journal_year")
	publication_year_tag = tagify(parse_tag(tag))
	tag = config.get(function, "pubinfo_journal_title")
	publication_journal_tag = tagify(parse_tag(tag))
	tag = config.get(function, "pubinfo_journal_volume")
	publication_volume_tag = tagify(parse_tag(tag))
	publication_format_string = config.get(function, "pubinfo_journal_format")
	except:
	pass

	#print values for tags for debugging
	if task_get_task_param('verbose') >= 9:
	write_message("tag values")
	write_message("p_record_pri_number_tag "+str(p_record_pri_number_tag))
	write_message("p_reference_tag "+str(p_reference_tag))
	write_message("publication_journal_tag "+str(publication_journal_tag))
	write_message("publication_format_string is "+publication_format_string)
	done = 0 #for status reporting
	numrecs = len(recid_list)

	# perform quick check to see if there are some records with
	# reference tags, because otherwise get.cit.inf would be slow even
	# if there is nothing to index:
	if run_sql("SELECT value FROM bib%sx WHERE tag=%%s LIMIT 1" % p_reference_tag[0:2],
	(p_reference_tag,)) or \
	run_sql("SELECT value FROM bib%sx WHERE tag=%%s LIMIT 1" % p_reference_number_tag[0:2],
	(p_reference_number_tag,)):
	for recid in recid_list:
	if (done % 10 == 0):
	task_sleep_now_if_required()
	#in fact we can sleep any time here

	if (done % 1000 == 0):
	mesg = "get cit.inf done "+str(done)+" of "+str(numrecs)
	write_message(mesg)
	task_update_progress(mesg)
	done = done+1

	pri_report_numbers = get_fieldvalues(recid, p_record_pri_number_tag)
	add_report_numbers = get_fieldvalues(recid, p_record_add_number_tag)
	reference_report_numbers = get_fieldvalues(recid, p_reference_number_tag)
	references_s = get_fieldvalues(recid, p_reference_tag)

	l_report_numbers = pri_report_numbers
	l_report_numbers.extend(add_report_numbers)
	d_reports_numbers[recid] = l_report_numbers

	if reference_report_numbers:
	d_references_report_numbers[recid] = reference_report_numbers

	references_s = get_fieldvalues(recid, p_reference_tag)
	write_message(str(recid)+"'s "+str(p_reference_tag)+" values "+str(references_s), verbose=9)
	if references_s:
	d_references_s[recid] = references_s

	#get a combination of
	#journal vol (year) pages
	if publication_pages_tag and publication_journal_tag and \
	publication_volume_tag and publication_year_tag and publication_format_string:
	tagsvalues = {} #we store the tags and their values here
	#like c->444 y->1999 p->"journal of foo",v->20
	tagsvalues["p"] = ""
	tagsvalues["y"] = ""
	tagsvalues["c"] = ""
	tagsvalues["v"] = ""
	tmp = get_fieldvalues(recid, publication_journal_tag)
	if tmp:
	tagsvalues["p"] = tmp[0]
	tmp = get_fieldvalues(recid, publication_volume_tag)
	if tmp:
	tagsvalues["v"] = tmp[0]
	tmp = get_fieldvalues(recid, publication_year_tag)
	if tmp:
	tagsvalues["y"] = tmp[0]
	tmp = get_fieldvalues(recid, publication_pages_tag)
	if tmp:
	#if the page numbers have "x-y" take just x
	pages = tmp[0]
	hpos = pages.find("-")
	if hpos > 0:
	pages = pages[:hpos]
	tagsvalues["c"] = pages
	#format the publ infostring according to the format
	publ = ""
	ok = 1
	for i in range (0, len(publication_format_string)):
	current = publication_format_string[i]
	#these are supported
	if current == "p" or current == "c" or current == "v" \
	or current == "y":
	if tagsvalues[current]:
	#add the value in the string
	publ += tagsvalues[current]
	else:
	ok = 0
	break #it was needed and not found
	else:
	publ += current #just add the character in the format string
	if ok:
	write_message("d_records_s (publication info) for "+str(recid)+" is "+publ, verbose=9)
	d_records_s[recid] = publ
	else:
	mesg = "Warning: there are no records with tag values for "
	mesg += p_reference_number_tag+" or "+p_reference_tag+". Nothing to do."
	write_message(mesg)

	mesg = "get cit.inf done fully"
	write_message(mesg)
	task_update_progress(mesg)

	citation_informations.append(d_reports_numbers)
	citation_informations.append(d_references_report_numbers)
	citation_informations.append(d_references_s)
	citation_informations.append(d_records_s)
	end_time = os.times()[4]
	write_message("Execution time for generating citation info from record: %.2f sec" % \
	(end_time - begin_time))
	return citation_informations

	def get_self_citations(new_record_list, citationdic, initial_selfcitdict, config):
	"""Check which items have been cited by one of the authors of the
	citing item: go through id's in new_record_list, use citationdic to get citations,
	update "selfcites". Selfcites is originally initial_selfcitdict. Return selfcites.
	"""
	i = 0 #just for debugging ..
	#get the tags for main author, coauthors, ext authors from config
	tags = ['first_author', 'additional_author', 'alternative_author_name']
	for t in tags:
	try:
	dummy = config.get(config.get("rank_method", "function"), t)
	except:
	register_exception(prefix="attribute "+t+" missing in config", alert_admin=True)
	return initial_selfcitdict

	r_mainauthortag = config.get(config.get("rank_method", "function"), "first_author")
	r_coauthortag = config.get(config.get("rank_method", "function"), "additional_author")
	r_extauthortag = config.get(config.get("rank_method", "function"), "alternative_author_name")
	#parse the tags
	mainauthortag = tagify(parse_tag(r_mainauthortag))
	coauthortag = tagify(parse_tag(r_coauthortag))
	extauthortag = tagify(parse_tag(r_extauthortag))

	selfcites = initial_selfcitdict
	for k in new_record_list:
	if (i % 1000 == 0):
	mesg = "Selfcites done "+str(i)+" of "+str(len(new_record_list))+" records"
	write_message(mesg)
	task_update_progress(mesg)
	i = i+1
	#get the author of k
	authorlist = get_fieldvalues(k, mainauthortag)
	coauthl = get_fieldvalues(k, coauthortag)
	extauthl = get_fieldvalues(k, extauthortag)
	authorlist.append(coauthl)
	authorlist.append(extauthl)
	#author tag
	#print "record "+str(k)+" by "+str(authorlist)
	#print "is cited by"
	#get the "x-cites-this" list
	if citationdic.has_key(k):
	xct = citationdic[k]
	for c in xct:
	#get authors of c
	cauthorlist = get_fieldvalues(c, mainauthortag)
	coauthl = get_fieldvalues(c, coauthortag)
	extauthl = get_fieldvalues(c, extauthortag)
	cauthorlist.extend(coauthl)
	cauthorlist.extend(extauthl)
	#print str(c)+" by "+str(cauthorlist)
	for ca in cauthorlist:
	if (ca in authorlist):
	#found!
	if selfcites.has_key(k):
	val = selfcites[k]
	#add only if not there already
	if val:
	if not c in val:
	val.append(c)
	selfcites[k] = val
	else:
	#new key for selfcites
	selfcites[k] = [c]

	mesg = "Selfcites done fully"
	write_message(mesg)
	task_update_progress(mesg)

	return selfcites

	def get_author_citations(updated_redic_list, citedbydict, initial_author_dict, config):
	"""Traverses citedbydict in order to build "which author is quoted where" dict.
	The keys of this are author names. An entry like "Apollinaire"->[1,2,3] means
	Apollinaire is cited in records 1,2 and 3.
	Input: citedbydict, updated_redic_list = records to be searched, initial_author_dict:
	the dicts from the database.
	Output: authorciteddict. It is initially set to initial_author_dict
	"""

	#sorry bout repeated code to get the tags
	tags = ['first_author', 'additional_author', 'alternative_author_name']
	tagvals = {}
	for t in tags:
	try:
	x = config.get(config.get("rank_method", "function"), t)
	tagvals[t] = x
	except:
	register_exception(prefix="attribute "+t+" missing in config", alert_admin=True)
	return initial_author_dict

	#parse the tags
	mainauthortag = tagify(parse_tag(tagvals['first_author']))
	coauthortag = tagify(parse_tag(tagvals['additional_author']))
	extauthortag = tagify(parse_tag(tagvals['alternative_author_name']))
	if task_get_task_param('verbose') >= 9:
	write_message("mainauthortag "+mainauthortag)
	write_message("coauthortag "+coauthortag)
	write_message("extauthortag "+extauthortag)

	author_cited_in = initial_author_dict
	if citedbydict:
	i = 0 #just a counter for debug
	write_message("Checking records referred to in new records")
	for u in updated_redic_list:
	if (i % 1000 == 0):
	mesg = "Author ref done "+str(i)+" of "+str(len(updated_redic_list))+" records"
	write_message(mesg)
	task_update_progress(mesg)
	i = i + 1

	if citedbydict.has_key(u):
	these_cite_k = citedbydict[u]
	if (these_cite_k is None):
	these_cite_k = [] #verify it is an empty list, not None
	authors = get_fieldvalues(u, mainauthortag)
	coauthl = get_fieldvalues(u, coauthortag)
	extauthl = get_fieldvalues(u, extauthortag)
	authors.extend(coauthl)
	authors.extend(extauthl)
	for a in authors:
	if a and author_cited_in.has_key(a):
	#add all elements in these_cite_k
	#that are not there already
	for citer in these_cite_k:
	tmplist = author_cited_in[a]
	if (tmplist.count(citer) == 0):
	tmplist.append(citer)
	author_cited_in[a] = tmplist
	else:
	author_cited_in[a] = these_cite_k

	mesg = "Author ref done fully"
	write_message(mesg)
	task_update_progress(mesg)

	#go through the dictionary again: all keys but search only if new records are cited
	write_message("Checking authors in new records")
	i = 0
	for k in citedbydict.keys():
	if (i % 1000 == 0):
	mesg = "Author cit done "+str(i)+" of "+str(len(citedbydict.keys()))+" records"
	write_message(mesg)
	task_update_progress(mesg)
	i = i + 1

	these_cite_k = citedbydict[k]
	if (these_cite_k is None):
	these_cite_k = [] #verify it is an empty list, not None
	#do things only if these_cite_k contains any new stuff
	intersec_list = list(set(these_cite_k)&set(updated_redic_list))
	if intersec_list:
	authors = get_fieldvalues(k, mainauthortag)
	coauthl = get_fieldvalues(k, coauthortag)
	extauthl = get_fieldvalues(k, extauthortag)
	authors.extend(coauthl)
	authors.extend(extauthl)
	for a in authors:
	if a and author_cited_in.has_key(a):
	#add all elements in these_cite_k
	#that are not there already
	for citer in these_cite_k:
	tmplist = author_cited_in[a]
	if (tmplist.count(citer) == 0):
	tmplist.append(citer)
	author_cited_in[a] = tmplist
	else:
	author_cited_in[a] = these_cite_k

	mesg = "Author cit done fully"
	write_message(mesg)
	task_update_progress(mesg)

	return author_cited_in


	def ref_analyzer(citation_informations, initialresult, initial_citationlist,
	initial_referencelist,config, updated_rec_list ):
	"""Analyze the citation informations and calculate the citation weight
	and cited by list dictionary.
	"""
	function = ""
	try:
	function = config.get("rank_method", "function")
	except:
	register_exception(prefix="cfg section [rank_method] has no attr function", alert_admin=True)
	return {}

	pubrefntag = ""
	try:
	pubrefntag = config.get(function, "reference_via_report_number")
	except:
	register_exception(prefix="cfg section "+function+" has no attr reference_via_report_number", alert_admin=True)
	return {}

	pubreftag = ""
	try:
	pubreftag = config.get(function, "reference_via_pubinfo")
	except:
	register_exception(prefix="cfg section "+function+" has no attr reference_via_pubinfo", alert_admin=True)
	return {}

	#pubrefntag is often 999C5r, pubreftag 999C5s
	if task_get_task_param('verbose') >= 9:
	write_message("pubrefntag "+pubrefntag)
	write_message("pubreftag "+pubreftag)

	citation_list = initial_citationlist
	reference_list = initial_referencelist
	result = initialresult
	d_reports_numbers = citation_informations[0] #dict of recid -> institute_give_publ_id
	d_references_report_numbers = citation_informations[1] #dict of recid -> ['astro-ph/xyz'..]
	d_references_s = citation_informations[2]
	#dict of recid -> publication_infos_in_its_bibliography
	d_records_s = citation_informations[3] #recid -> its publication inf
	t1 = os.times()[4]

	write_message("Phase 1: d_references_report_numbers")
	#d_references_report_numbers: e.g 8 -> ([astro-ph/9889],[hep-ph/768])
	#meaning: rec 8 contains these in bibliography

	done = 0
	numrecs = len(d_references_report_numbers)
	for thisrecid, refnumbers in d_references_report_numbers.iteritems():
	if (done % 1000 == 0):
	mesg = "d_references_report_numbers done "+str(done)+" of "+str(numrecs)
	write_message(mesg)
	task_update_progress(mesg)
	#write to db!
	insert_into_cit_db(reference_list, "reversedict")
	insert_into_cit_db(citation_list, "citationdict")
	#it's ok to sleep too, we got something done
	task_sleep_now_if_required()
	done = done+1

	for refnumber in refnumbers:
	if refnumber:
	p = refnumber
	f = 'reportnumber'
	#sanitise p
	p.replace("\n",'')
	#search for "hep-th/5644654 or such" in existing records
	rec_ids = get_recids_matching_query(p, f)
	if rec_ids and rec_ids[0]:
	write_citer_cited(thisrecid, rec_ids[0])
	remove_from_missing(p)
	if not result.has_key(rec_ids[0]):
	result[rec_ids[0]] = 0
	# Citation list should have rec_ids[0] but check anyway
	if not citation_list.has_key(rec_ids[0]):
	citation_list[rec_ids[0]] = []
	#append unless this key already has the item
	if not thisrecid in citation_list[rec_ids[0]]:
	citation_list[rec_ids[0]].append(thisrecid)
	#and update result
	result[rec_ids[0]] += 1

	if not reference_list.has_key(thisrecid):
	reference_list[thisrecid] = []
	if not rec_ids[0] in reference_list[thisrecid]:
	reference_list[thisrecid].append(rec_ids[0])
	else:
	#the reference we wanted was not found among our records.
	#put the reference in the "missing".. however, it will look
	#bad.. gfhgf/1254312, so get the corresponding 999C5s (full ref) too
	#This should really be done in the next loop d_references_s
	#but the 999C5s fields are not yet normalized

	#rectext = print_record(thisrecid, format='hm', ot=pubreftag[:-1])
	rectext = "" # print_record() call disabled to speed things up
	lines = rectext.split("\n")
	rpart = p #to be used..
	for l in lines:
	if (l.find(p) > 0): #the gfhgf/1254312 was found.. get the s-part of it
	st = l.find('$s')
	if (st > 0):
	end = l.find('$', st)
	if (end == st):
	end = len(l)
	rpart = l[st+2:end]
	insert_into_missing(thisrecid, rpart)

	mesg = "d_references_report_numbers done fully"
	write_message(mesg)
	task_update_progress(mesg)

	t2 = os.times()[4]

	#try to find references based on 999C5s, like Phys.Rev.Lett. 53 (1986) 2285
	write_message("Phase 2: d_references_s")
	done = 0
	numrecs = len(d_references_s)
	for thisrecid, refss in d_references_s.iteritems():
	if (done % 1000 == 0):
	mesg = "d_references_s done "+str(done)+" of "+str(numrecs)
	write_message(mesg)
	task_update_progress(mesg)
	#write to db!
	insert_into_cit_db(reference_list, "reversedict")
	insert_into_cit_db(citation_list, "citationdict")
	task_sleep_now_if_required()

	done = done+1

	for refs in refss:
	if refs:
	p = refs
	#remove the latter page number if it is like 67-74
	matches = re.compile("(.*)(-\d+$)").findall(p)
	if matches and matches[0]:
	p = matches[0][0]
	rec_id = None
	try:
	rec_ids = list(search_unit(p, 'journal'))
	except:
	rec_ids = None
	write_message("These match searching "+p+" in journal: "+str(rec_id), verbose=9)
	if rec_ids and rec_ids[0]:
	#the refered publication is in our collection, remove
	#from missing
	remove_from_missing(p)
	else:
	#it was not found so add in missing
	insert_into_missing(thisrecid, p)
	#check citation and reference for this..
	if rec_ids and rec_ids[0]:
	#the above should always hold
	if not result.has_key(rec_ids[0]):
	result[rec_ids[0]] = 0
	if not citation_list.has_key(rec_ids[0]):
	citation_list[rec_ids[0]] = []
	if not thisrecid in citation_list[rec_ids[0]]:
	citation_list[rec_ids[0]].append(thisrecid) #append actual list
	result[rec_ids[0]] += 1 #add count for this..

	#update reference_list accordingly
	if not reference_list.has_key(thisrecid):
	reference_list[thisrecid] = []
	if not rec_ids[0] in reference_list[thisrecid]:
	reference_list[thisrecid].append(rec_ids[0])
	mesg = "d_references_s done fully"
	write_message(mesg)
	task_update_progress(mesg)

	t3 = os.times()[4]
	done = 0
	numrecs = len(d_reports_numbers)
	write_message("Phase 3: d_reports_numbers")

	#search for stuff like CERN-TH-4859/87 in list of refs
	for thisrecid, reportcodes in d_reports_numbers.iteritems():
	if (done % 1000 == 0):
	mesg = "d_report_numbers done "+str(done)+" of "+str(numrecs)
	write_message(mesg)
	task_update_progress(mesg)
	done = done+1

	for reportcode in reportcodes:
	if reportcode:
	rec_ids = []
	try:
	rec_ids = get_recids_matching_query(reportcode, pubrefntag)
	except:
	rec_ids = []

	if rec_ids:
	for recid in rec_ids:
	#normal checks..
	if not citation_list.has_key(thisrecid):
	citation_list[thisrecid] = []
	if not reference_list.has_key(recid):
	reference_list[recid] = []
	if not result.has_key(thisrecid):
	result[thisrecid] = 0

	#normal updates
	if not recid in citation_list[thisrecid]:
	result[thisrecid] += 1
	citation_list[thisrecid].append(recid)
	if not thisrecid in reference_list[recid]:
	reference_list[recid].append(thisrecid)

	mesg = "d_report_numbers done fully"
	write_message(mesg)
	task_update_progress(mesg)

	#find this record's pubinfo in other records' bibliography
	write_message("Phase 4: d_records_s")
	done = 0
	numrecs = len(d_records_s)
	t4 = os.times()[4]
	for thisrecid, recs in d_records_s.iteritems():
	if (done % 1000 == 0):
	mesg = "d_records_s done "+str(done)+" of "+str(numrecs)
	write_message(mesg)
	task_update_progress(mesg)
	done = done+1
	p = recs.replace("\"","")
	#search the publication string like Phys. Lett., B 482 (2000) 417 in 999C5s
	rec_ids = list(search_unit(f=pubreftag, p=p, m='a'))
	write_message("These records match "+p+" in "+pubreftag+" : "+str(rec_ids), verbose=9)
	if rec_ids:
	for rec_id in rec_ids:
	#normal checks
	if not result.has_key(thisrecid):
	result[thisrecid] = 0
	if not citation_list.has_key(thisrecid):
	citation_list[thisrecid] = []
	if not reference_list.has_key(rec_id):
	reference_list[rec_id] = []

	if not rec_id in citation_list[thisrecid]:
	result[thisrecid] += 1
	citation_list[thisrecid].append(rec_id)
	if not thisrecid in reference_list[rec_id]:
	reference_list[rec_id].append(thisrecid)

	mesg = "d_records_s done fully"
	write_message(mesg)
	task_update_progress(mesg)

	write_message("Phase 5: reverse lists")

	#remove empty lists in citation and reference
	keys = citation_list.keys()
	for k in keys:
	if not citation_list[k]:
	del citation_list[k]

	keys = reference_list.keys()
	for k in keys:
	if not reference_list[k]:
	del reference_list[k]

	write_message("Phase 6: self-citations")
	selfdic = {}
	#get the initial self citation dict
	initial_self_dict = get_cit_dict("selfcitdict")
	selfdic = initial_self_dict
	#add new records to selfdic
	acit = task_get_option("author-citations")
	if not acit:
	write_message("Self cite processing disabled. Use -A option to enable it.")
	else:
	write_message("self cite and author citations enabled")
	selfdic = get_self_citations(updated_rec_list, citation_list,
	initial_self_dict, config)
	#selfdic consists of
	#key k -> list of values [v1,v2,..]
	#where k is a record with author A and k cites v1,v2.. and A appears in v1,v2..

	#create a reverse "x cited by y" self cit dict
	selfcitedbydic = {}
	for k in selfdic.keys():
	vlist = selfdic[k]
	for v in vlist:
	if selfcitedbydic.has_key(v):
	tmplist = selfcitedbydic[v]
	if not k in tmplist:
	tmplist.append(k)
	else:
	tmplist = [k]
	selfcitedbydic[v] = tmplist

	write_message("Getting author citations")

	#get author citations for records in updated_rec_list
	initial_author_dict = get_initial_author_dict()
	authorcitdic = initial_author_dict
	acit = task_get_option("author-citations")
	if not acit:
	print "Author cites disabled. Use -A option to enable it."
	else:
	write_message("author citations enabled")
	authorcitdic = get_author_citations(updated_rec_list, citation_list,
	initial_author_dict, config)


	if task_get_task_param('verbose') >= 3:
	#print only X first to prevent flood
	tmpdict = {}
	tmp = citation_list.keys()[0:10]
	for t in tmp:
	tmpdict[t] = citation_list[t]
	write_message("citation_list (x is cited by y): "+str(tmpdict))
	write_message("size: "+str(len(citation_list.keys())))
	tmp = reference_list.keys()[0:10]
	tmpdict = {}
	for t in tmp:
	tmpdict[t] = reference_list[t]
	write_message("reference_list (x cites y): "+str(tmpdict))
	write_message("size: "+str(len(reference_list.keys())))
	tmp = selfcitedbydic.keys()[0:10]
	tmpdict = {}
	for t in tmp:
	tmpdict[t] = selfcitedbydic[t]
	mesg = "selfcitedbydic (x is cited by y and one of the authors of x same as y's):"
	mesg += str(tmpdict)
	write_message(mesg)
	write_message("size: "+str(len(selfcitedbydic.keys())))
	tmp = selfdic.keys()[0:100]
	tmpdict = {}
	for t in tmp:
	tmpdict[t] = selfdic[t]
	mesg = "selfdic (x cites y and one of the authors of x same as y's): "+str(tmpdict)
	write_message(mesg)
	write_message("size: "+str(len(selfdic.keys())))
	tmp = authorcitdic.keys()[0:10]
	tmpdict = {}
	for t in tmp:
	tmpdict[t] = authorcitdic[t]
	write_message("authorcitdic (author is cited in recs): "+str(tmpdict))
	write_message("size: "+str(len(authorcitdic.keys())))
	insert_cit_ref_list_intodb(citation_list, reference_list,
	selfcitedbydic, selfdic, authorcitdic)

	t5 = os.times()[4]

	write_message("Execution time for analyzing the citation information generating the dictionary:")
	write_message("... checking ref number: %.2f sec" % (t2-t1))
	write_message("... checking ref ypvt: %.2f sec" % (t3-t2))
	write_message("... checking rec number: %.2f sec" % (t4-t3))
	write_message("... checking rec ypvt: %.2f sec" % (t5-t4))
	write_message("... total time of ref_analyze: %.2f sec" % (t5-t1))

	return result

	def insert_cit_ref_list_intodb(citation_dic, reference_dic, selfcbdic,
	selfdic, authorcitdic):
	"""Insert the reference and citation list into the database"""
	insert_into_cit_db(reference_dic,"reversedict")
	insert_into_cit_db(citation_dic,"citationdict")
	insert_into_cit_db(selfcbdic,"selfcitedbydict")
	insert_into_cit_db(selfdic,"selfcitdict")

	for a in authorcitdic.keys():
	lserarr = (serialize_via_marshal(authorcitdic[a]))
	#author name: replace " with something else
	a.replace('"', '\'')
	a = unicode(a, 'utf-8')
	try:
	ablob = run_sql("select hitlist from rnkAUTHORDATA where aterm = %s", (a,))
	if not (ablob):
	#print "insert into rnkAUTHORDATA(aterm,hitlist) values (%s,%s)" , (a,lserarr)
	run_sql("insert into rnkAUTHORDATA(aterm,hitlist) values (%s,%s)",
	(a,lserarr))
	else:
	#print "UPDATE rnkAUTHORDATA SET hitlist = %s where aterm=%s""" , (lserarr,a)
	run_sql("UPDATE rnkAUTHORDATA SET hitlist = %s where aterm=%s",
	(lserarr,a))
	except:
	register_exception(prefix="could not read/write rnkAUTHORDATA aterm="+a+" hitlist="+str(lserarr), alert_admin=True)

	def insert_into_cit_db(dic, name):
	"""an aux thing to avoid repeating code"""
	ndate = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
	try:
	s = serialize_via_marshal(dic)
	write_message("size of "+name+" "+str(len(s)))
	#check that this column really exists
	testres = run_sql("select object_name from rnkCITATIONDATA where object_name = %s",
	(name,))
	if testres:
	run_sql("UPDATE rnkCITATIONDATA SET object_value = %s where object_name = %s",
	(s, name))
	else:
	#there was no entry for name, let's force..
	run_sql("INSERT INTO rnkCITATIONDATA(object_name,object_value) values (%s,%s)",
	(name,s))
	run_sql("UPDATE rnkCITATIONDATA SET last_updated = %s where object_name = %s",
	(ndate,name))
	except:
	register_exception(prefix="could not write "+name+" into db", alert_admin=True)


	def get_cit_dict(name):
	"""get a named citation dict from the db"""
	cdict = {}
	try:
	cdict = run_sql("select object_value from rnkCITATIONDATA where object_name = %s",
	(name,))
	if cdict and cdict[0] and cdict[0][0]:
	dict_from_db = deserialize_via_marshal(cdict[0][0])
	return dict_from_db
	else:
	return {}
	except:
	register_exception(prefix="could not read "+name+" from db", alert_admin=True)
	return dict

	def get_initial_author_dict():
	"""read author->citedinlist dict from the db"""
	adict = {}
	try:
	ah = run_sql("select aterm,hitlist from rnkAUTHORDATA")
	for (a, h) in ah:
	adict[a] = deserialize_via_marshal(h)
	return adict
	except:
	register_exception(prefix="could not read rnkAUTHORDATA", alert_admin=True)
	return {}


	def insert_into_missing(recid, report):
	"""put the referingrecordnum-publicationstring into
	the "we are missing these" table"""
	report.replace('"','\'')
	try:
	srecid = str(recid)
	wasalready = run_sql("select id_bibrec from rnkCITATIONDATAEXT where id_bibrec = %s and extcitepubinfo = %s",
	(srecid,report))
	if not wasalready:
	run_sql("insert into rnkCITATIONDATAEXT(id_bibrec, extcitepubinfo) values (%s,%s)",
	(srecid, report))
	except:
	#we should complain but it can result to million lines of warnings so just pass..
	pass

	def remove_from_missing(report):
	"""remove the recid-ref -pairs from the "missing" table for report x: prob
	in the case ref got in our library collection"""
	report.replace('"','\'')
	try:
	run_sql("delete from rnkCITATIONDATAEXT where extcitepubinfo= %s", (report,))
	except:
	#we should complain but it can result to million lines of warnings so just pass..
	pass


	def create_analysis_tables():
	"""temporary simple table + index"""
	sql1 = "CREATE TABLE IF NOT EXISTS tmpcit (citer mediumint(10), cited mediumint(10)) TYPE=MyISAM"
	sql2 = "CREATE UNIQUE INDEX citercited on tmpcit(citer, cited)"
	sql3 = "CREATE INDEX citer on tmpcit(citer)"
	sql4 = "CREATE INDEX cited on tmpcit(cited)"
	try:
	run_sql(sql1)
	run_sql(sql2)
	run_sql(sql3)
	run_sql(sql4)
	except:
	pass

	def write_citer_cited(citer, cited):
	"""write an entry to tmp table"""
	sciter = str(citer)
	scited = str(cited)
	try:
	run_sql("insert into tmpcit(citer, cited) values (%s,%s)", (sciter, scited))
	except:
	pass

	def print_missing(num):
	"""
	Print the contents of rnkCITATIONDATAEXT table containing external
	records that were cited by NUM or more internal records.

	NUM is by default taken from the -E command line option.
	"""
	if not num:
	num = task_get_option("print-extcites")

	write_message("Listing external papers cited by %i or more internal records:" % num)

	res = run_sql("SELECT COUNT(id_bibrec), extcitepubinfo FROM rnkCITATIONDATAEXT \
	GROUP BY extcitepubinfo HAVING COUNT(id_bibrec) >= %s \
	ORDER BY COUNT(id_bibrec) DESC", (num,))
	for (cnt, brec) in res:
	print str(cnt)+"\t"+brec

	write_message("Listing done.")

	def tagify(parsedtag):
	"""aux auf to make '100__a' out of ['100','','','a']"""
	tag = ""
	for t in parsedtag:
	if t == '':
	t = '_'
	tag = tag+t
	return tag

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