diff --git a/modules/bibrank/lib/bibrank_citation_indexer.py b/modules/bibrank/lib/bibrank_citation_indexer.py index a5de33f19..1d5db433a 100644 --- a/modules/bibrank/lib/bibrank_citation_indexer.py +++ b/modules/bibrank/lib/bibrank_citation_indexer.py @@ -1,338 +1,341 @@ # -*- coding: utf-8 -*- ## ## $Id$ ## ## This file is part of CDS Invenio. ## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007 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 time import os import marshal from zlib import decompress, compress, error from invenio.dbquery import run_sql, escape_string, serialize_via_marshal, deserialize_via_marshal from invenio.search_engine import print_record, search_pattern from invenio.bibrecord import create_records, record_get_field_values from invenio.bibformat_utils import parse_tag 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 inforamtion """ begin_time = time.time() last_update_time = get_bibrankmethod_lastupdate(rank_method_code) last_modified_records = get_last_modified_rec(last_update_time) if last_modified_records: updated_recid_list = create_recordid_list(last_modified_records) result_intermediate = last_updated_result(rank_method_code, updated_recid_list) #result_intermed should be warranted to exists! citation_weight_dic_intermediate = result_intermediate[0] citation_list_intermediate = result_intermediate[1] reference_list_intermediate = result_intermediate[2] citation_informations = get_citation_informations(updated_recid_list, config) dic = ref_analyzer(citation_informations, citation_weight_dic_intermediate, citation_list_intermediate, reference_list_intermediate) #dic is docid-nuberofreferences like {1: 2, 2: 0, 3: 1} end_time = time.time() print "Total time of software: ", (end_time - begin_time) else: dic = {} print "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) - return last_update_time[0][0] + r = last_update_time[0][0] + if (r == 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 execution of bibrank method. The result is expected to have ascending numerical order. """ query = """SELECT id FROM bibrec WHERE modification_date>= '%s' """ % bibrank_method_lastupdate query += "order by id ASC" list = run_sql(query) return list 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(list): """Creates a tuple of record id from a list of id. The result is expected to have ascending numerical order. """ list_length = len(list) 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, recid_list): """ 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 = make_initial_result() query = """select relevance_data from rnkMETHOD, rnkMETHODDATA where rnkMETHOD.id = rnkMETHODDATA.id_rnkMETHOD and rnkMETHOD.Name = '%s'"""% rank_method_code dict = run_sql(query) if dict and dict[0] and dict[0][0]: #has to be prepared for corrupted data! try: dic = marshal.loads(decompress(dict[0][0])) except error: return result query = "select citation_data from rnkCITATIONDATA" cit_compressed = run_sql(query) cit = [] if cit_compressed and cit_compressed[0] and cit_compressed[0][0]: cit = marshal.loads(decompress(cit_compressed[0][0])) if cit: query = "select citation_data_reversed from rnkCITATIONDATA" ref_compressed = run_sql(query) if ref_compressed and ref_compressed[0] and ref_compressed[0][0]: ref = marshal.loads(decompress(ref_compressed[0][0])) result = get_initial_result(dic, cit, ref, recid_list) return result def get_initial_result(dic, cit, ref, recid_list): """initialieze the citation weights of the last updated record with zero for recalculating it later """ for recid in recid_list: dic[recid] = 0 cit[recid] = [] if ref.has_key(recid) and ref[recid]: for id in ref[recid]: if cit.has_key(id) and recid in cit[id]: cit[id].remove(recid) dic[id] -= 1 if cit.has_key(recid) and cit[recid]: for id in cit[recid]: if ref.has_key(id) and recid in ref[id]: ref[id].remove(recid) ref[recid] = [] return [dic, cit, ref] def make_initial_result(): """return an initial dictinary with recID as key and zero as value """ dic = {} cit = {} ref = {} query = "select id from bibrec" res = run_sql(query) for key in res: dic[key[0]] = 0 cit[key[0]] = [] ref[key[0]] = [] return [dic, cit, ref] def get_citation_informations(recid_list, config): """return une dictionary that contains the citation information of cds records """ begin_time = os.times()[4] d_reports_numbers = {} d_references_report_numbers = {} d_references_s = {} d_records_s = {} citation_informations = [] record_pri_number_tag = config.get(config.get("rank_method", "function"),"publication_primary_number_tag") record_add_number_tag = config.get(config.get("rank_method", "function"),"publication_aditional_number_tag") reference_number_tag = config.get(config.get("rank_method", "function"),"publication_reference_number_tag") reference_tag = config.get(config.get("rank_method", "function"),"publication_reference_tag") record_publication_info_tag = config.get(config.get("rank_method", "function"),"publication_info_tag") p_record_pri_number_tag = parse_tag(record_pri_number_tag) p_record_add_number_tag = parse_tag(record_add_number_tag) p_reference_number_tag = parse_tag(reference_number_tag) p_reference_tag = parse_tag(reference_tag) p_record_publication_info_tag = parse_tag(record_publication_info_tag) for recid in recid_list: xml = print_record(int(recid),'xm') rs = create_records(xml) recs = map((lambda x:x[0]), rs) l_report_numbers = [] for rec in recs: pri_report_number = record_get_field_values(rec, p_record_pri_number_tag[0], ind1=p_record_pri_number_tag[1], ind2=p_record_pri_number_tag[2], code=record_pri_number_tag[3]) add_report_numbers = record_get_field_values(rec, p_record_add_number_tag[0], ind1=p_record_add_number_tag[1], ind2=p_record_add_number_tag[2], code=record_add_number_tag[3]) if pri_report_number: l_report_numbers.extend(pri_report_number) if add_report_numbers: l_report_numbers.extend(add_report_numbers) d_reports_numbers[recid] = l_report_numbers reference_report_number = record_get_field_values(rec, p_reference_number_tag[0], ind1=p_reference_number_tag[1], ind2=p_reference_number_tag[2], code=p_reference_number_tag[3]) if reference_report_number: d_references_report_numbers[recid] = reference_report_number references_s = record_get_field_values(rec, p_reference_tag[0], ind1=p_reference_tag[1], ind2=p_reference_tag[2], code=p_reference_tag[3]) if references_s: d_references_s[recid] = references_s record_s = record_get_field_values(rec, p_record_publication_info_tag[0], ind1=p_record_publication_info_tag[1], ind2=p_record_publication_info_tag[2], code=p_record_publication_info_tag[3]) if record_s: d_records_s[recid] = record_s[0] 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] print "Execution time for generating citation inforamtions by parsing xml contents: ", (end_time - begin_time) return citation_informations def ref_analyzer(citation_informations, initialresult, initial_citationlist, initial_referencelist): """Analyze the citation informations and calculate the citation weight and cited by list dictionary """ citation_list = initial_citationlist reference_list = initial_referencelist result = initialresult d_reports_numbers = citation_informations[0] d_references_report_numbers = citation_informations[1] d_references_s = citation_informations[2] #of type: {77: ['Nucl. Phys. B 72 (1974) 461','blah blah'], 93: [' d_records_s = citation_informations[3] t1 = os.times()[4] for recid, refnumbers in d_references_report_numbers.iteritems(): for refnumber in refnumbers: p = refnumber f = 'reportnumber' rec_id = get_recids_matching_query(p, f) if rec_id: if result.has_key(rec_id[0]): result[rec_id[0]] += 1 citation_list[rec_id[0]].append(recid) reference_list[recid].append(rec_id[0]) t2 = os.times()[4] for recid, refss in d_references_s.iteritems(): for refs in refss: p = refs f = 'publref' rec_id = get_recids_matching_query(p, f) if rec_id and not recid in citation_list[rec_id[0]]: result[rec_id[0]] += 1 citation_list[rec_id[0]].append(recid) if rec_id and not rec_id[0] in reference_list[recid]: reference_list[recid].append(rec_id[0]) t3 = os.times()[4] for rec_id, recnumbers in d_reports_numbers.iteritems(): for recnumber in recnumbers: p = recnumber f = '999C5r' recid_list = get_recids_matching_query(p, f) if recid_list: for recid in recid_list: if not recid in citation_list[rec_id]: result[rec_id] += 1 citation_list[rec_id].append(recid) if not rec_id in reference_list[recid]: reference_list[recid].append(rec_id) t4 = os.times()[4] for recid, recs in d_records_s.iteritems(): tmp = recs.find("-") if tmp < 0: recs_modified = recs else: recs_modified = recs[:tmp] p = recs_modified f = '999C5s' rec_ids = get_recids_matching_query(p, f) if rec_ids: for rec_id in rec_ids: if not rec_id in citation_list[recid]: result[recid] += 1 citation_list[recid].append(rec_id) if not recid in reference_list[rec_id]: reference_list[rec_id].append(recid) t5 = os.times()[4] insert_cit_ref_list_intodb(citation_list, reference_list) print "\nExecution time for analizing the citation information generating the dictionary: " print "checking ref number: ", (t2-t1) print "checking ref ypvt: ", (t3-t2) print "checking rec number: ", (t4-t3) print "checking rec ypvt: ", (t5-t4) print "total time of refAnalize: ", (t5-t1) return result def get_decompressed_xml(xml): """return a decompressed content of xml into a xml content """ decompressed_xml = create_records(decompress(xml)) return decompressed_xml def insert_cit_ref_list_intodb(citation_dic, reference_dic): """Insert the reference and citation list into the database""" date = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime()) id = run_sql("SELECT * from rnkCITATIONDATA ") if id: run_sql("update rnkCITATIONDATA set citation_data_reversed = %s", (serialize_via_marshal(reference_dic), )) run_sql("update rnkCITATIONDATA set citation_data = %s", (serialize_via_marshal(citation_dic), )) else: run_sql("INSERT INTO rnkCITATIONDATA VALUES (%s, null)", (serialize_via_marshal(citation_dic), )) - run_sql("update rnkCITATIONDATA set citation_data_reversed = %s"% + run_sql("update rnkCITATIONDATA set citation_data_reversed = %s", (serialize_via_marshal(reference_dic), )) def get_compressed_dictionary(dic): """Serialize Python object vi a marshal into a compressed string.""" return escape_string(compress(marshal.dumps(dic)))