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R3600/modules/bibrank/lib/bibrank_citation_indexer.py
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bibrank_citation_indexer.py
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# -*- Coding: utf-8 -*-
##
## $Id$
##
## 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, writeto 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 marshal
import traceback
from zlib import decompress, error
from invenio.dbquery import run_sql, serialize_via_marshal, \
deserialize_via_marshal
from invenio.search_engine import print_record, 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.bibrecord import create_records
NO_AUTHOR_CITES = 1
#a config param to turn off self citation searching
try:
Set = set
except NameError:
from sets import Set
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)
#addition: YOU DO NEED TO RUN WITH OPTION -R SOMETIMES. This is
#because among the new set (X) there can be records such that the old
#records Y cite them. But this kind of situation is not detected
#unless you go though all the records Y+X.
if task_get_option("quick") == "no":
last_update_time = "0000-00-00 00:00:00"
#if task_get_option('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
id = task_get_option("id")
first = id[0][0]
last = id[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,
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]
#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.. needed to test how much faster in-mem indexing is
#call the analyser that uses the citation_informations to really search x-cites-y in the coll..
if task_get_task_param('verbose') >= 9:
write_message("Entering ref_analyzer")
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 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 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 = marshal.loads(decompress(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 = 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):
"""initialize 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)
if dic.has_key(id):
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):
"""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 = {}
d_references_report_numbers = {}
d_references_s = {}
d_records_s = {}
citation_informations = []
if task_get_task_param('verbose') >= 9:
write_message("config function "+config.get("rank_method", "function") )
function = ""
try:
function = config.get("rank_method", "function")
except:
print "critical error. cfg section [rank_method] has no attr function"
raise "config error"
record_pri_number_tag = ""
try:
record_pri_number_tag = config.get(function,
"primary_report_number")
except:
print "critical error. primary_report_number not in cfg section "+function
raise "config error"
record_add_number_tag = ""
try:
record_add_number_tag = config.get(config.get("rank_method", "function"),
"additional_report_number")
except:
print "critical error. additional_report_number not in cfg section "+function
raise "config error"
reference_number_tag = ""
try:
reference_number_tag = config.get(config.get("rank_method", "function"),
"reference_via_report_number")
except:
print "critical error. reference_via_report_number not in cfg section "+function
raise "config error"
reference_tag = ""
try:
reference_tag = config.get(config.get("rank_method", "function"),
"reference_via_pubinfo")
except:
print "critical error. reference_via_pubinfo not in cfg section "+function
raise "config error"
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_pages")
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_vol")
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, verbose=9)
done = 0 #for status reporting
numrecs = len(recid_list)
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)
if task_get_task_param('verbose') >= 9:
write_message(str(recid)+"'s "+str(p_reference_tag)+" values "+str(references_s))
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
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
r_mainauthortag = config.get(config.get("rank_method", "function"), "first_author")
r_coauthortag = config.get(config.get("rank_method", "function"), "additiona_author")
r_extauthortag = config.get(config.get("rank_method", "function"), "extauthor")
#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
r_mainauthortag = config.get(config.get("rank_method", "function"), "main_author_tag")
r_coauthortag = config.get(config.get("rank_method", "function"), "coauthor_tag")
r_extauthortag = config.get(config.get("rank_method", "function"), "extauthor_tag")
#parse the tags
mainauthortag = tagify(parse_tag(r_mainauthortag))
coauthortag = tagify(parse_tag(r_coauthortag))
extauthortag = tagify(parse_tag(r_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:
print "critical error. cfg section [rank_method] has no attr function"
raise "config error"
pubrefntag = ""
try:
pubrefntag = config.get(function, "reference_via_report_number")
except:
print "critical error. cfg section "+function+" has no attr reference_via_report_number"
raise "cfg error"
pubreftag = ""
try:
pubreftag = config.get(function, "reference_via_pubinfo")
except:
print "critical error. cfg section "+function+" has no attr reference_via_pubinfo"
raise "cfg error"
#pubrefntag is prob 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]
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]
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 recid, 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_id = get_recids_matching_query(p, f)
if rec_id and rec_id[0]:
write_citer_cited(recid, rec_id[0])
remove_from_missing(p)
if result.has_key(rec_id[0]):
result[rec_id[0]] += 1
# Citation list should have rec_id[0] but check anyway
if citation_list.has_key(rec_id[0]):
citation_list[rec_id[0]].append(recid)
else:
citation_list[rec_id[0]] = [recid]
if reference_list.has_key(recid):
reference_list[recid].append(rec_id[0])
else:
reference_list[recid] = [rec_id[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(recid, 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(recid, 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 recid, 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 = list(search_unit(p, 'journal'))
write_message("These match searching "+p+" in journal: "+str(rec_id), verbose=9)
if rec_id and rec_id[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(recid, p)
#check citation and reference for this..
if rec_id and rec_id[0]:
#the above should always hold
if citation_list.has_key(rec_id[0]):
if not recid in citation_list[rec_id[0]]:
result[rec_id[0]] += 1 #add count for this..
citation_list[rec_id[0]].append(recid) #append actual list
else:
#it was not in the hash so this is the first for rec_id[0]
citation_list[rec_id[0]] = [recid]
result[rec_id[0]] = 1
#update reference_list accordingly
if reference_list.has_key(recid):
reference_list[recid].append(rec_id[0])
else:
reference_list[recid] = [rec_id[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 rec_id, recnumbers 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 recnumber in recnumbers:
if recnumber:
p = recnumber
recid_list = get_recids_matching_query(p, pubrefntag)
if recid_list:
for recid in recid_list:
if not citation_list.has_key(rec_id):
citation_list[rec_id] = []
if not recid in citation_list[rec_id]:
result[rec_id] += 1
citation_list[rec_id].append(recid)
if not reference_list.has_key(recid):
reference_list[recid] = []
if not rec_id in reference_list[recid]:
reference_list[recid].append(rec_id)
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 recid, 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:
if not citation_list.has_key(recid):
citation_list[recid] = []
result[recid] = 0
if not reference_list.has_key(rec_id):
reference_list[rec_id] = []
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)
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
if NO_AUTHOR_CITES:
print "Self cite processing disabled"
else:
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]
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
if NO_AUTHOR_CITES:
print "Author cites disabled"
else:
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]
write_message("selfcitedbydic (x is cited by y and one \
of the authors of x same as y's): "+str(tmpdict))
write_message("size: "+str(len(selfcitedbydic.keys())))
tmp = selfdic.keys()[0:100]
tmpdict = {}
for t in tmp:
tmpdict[t] = selfdic[t]
write_message("selfdic (x cites y and one of the authors \
of x same as y's): "+str(tmpdict))
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 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, 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 rnkAUTHORDATAR where aterm = %s", (a,))
if not (ablob):
#print "insert into rnkAUTHORDATAR(aterm,hitlist) values (%s,%s)" , (a,lserarr)
run_sql("insert into rnkAUTHORDATAR(aterm,hitlist) values (%s,%s)",
(a,lserarr))
else:
#print "UPDATE rnkAUTHORDATAR SET hitlist = %s where aterm=%s""" , (lserarr,a)
run_sql("UPDATE rnkAUTHORDATAR SET hitlist = %s where aterm=%s",
(lserarr,a))
except:
print "Critical error: could not read/write rnkAUTHORDATAR "
print "aterm="+a+" hitlist="+str(lserarr)+"\n"
traceback.print_tb(sys.exc_info()[2])
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:
print "Critical error: could not write "+name+" into db"
traceback.print_tb(sys.exc_info()[2])
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 = marshal.loads(decompress(cdict[0][0]))
return dict_from_db
else:
return {}
except:
print "Critical error: could not read "+name+" from db"
traceback.print_tb(sys.exc_info()[2])
return dict
def get_initial_author_dict():
"""read author->citedinlist dict from the db"""
dict = {}
try:
ah = run_sql("select aterm,hitlist from rnkAUTHORDATAR")
for (a, h) in ah:
dict[a] = deserialize_via_marshal(h)
return dict
except:
print "Critical error: could not read rnkAUTHORDATAR"
traceback.print_tb(sys.exc_info()[2])
dict = {}
return dict
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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