def get_self_citations_count(recids, algorithm='simple',
precompute=CFG_BIBRANK_SELFCITES_PRECOMPUTE):
"""Depending on our site we config, we either:
* compute self-citations (using a simple algorithm)
* or fetch self-citations from pre-computed table"""
total_cites = 0
if not precompute:
tags = get_authors_tags()
selfcites_fun = ALL_ALGORITHMS[algorithm]
for recid in recids:
citers = get_cited_by(recid)
self_cites = selfcites_fun(recid, tags)
total_cites += len(citers) - len(self_cites)
else:
results = get_precomputed_self_cites_list(recids)
results_dict = {}
for r in results:
results_dict[r[0]] = r[1]
for r in recids:
citers = get_cited_by(r)
self_cites = results_dict.get(r, 0)
total_cites += len(citers) - self_cites
return total_cites
def get_self_citations_count(recids,
algorithm='simple',
precompute=CFG_BIBRANK_SELFCITES_PRECOMPUTE):
"""Depending on our site we config, we either:
* compute self-citations (using a simple algorithm)
* or fetch self-citations from pre-computed table"""
total_cites = 0
if not precompute:
tags = get_authors_tags()
selfcites_fun = ALL_ALGORITHMS[algorithm]
for recid in recids:
citers = get_cited_by(recid)
self_cites = selfcites_fun(recid, tags)
total_cites += len(citers) - len(self_cites)
else:
results = get_precomputed_self_cites_list(recids)
results_dict = {}
for r in results:
results_dict[r[0]] = r[1]
for r in recids:
citers = get_cited_by(r)
self_cites = results_dict.get(r, 0)
total_cites += len(citers) - self_cites
return total_cites
def find_citations(rank_method_code, recID, hitset, verbose):
"""Rank by the amount of citations."""
#calculate the cited-by values for all the members of the hitset
#returns: ((recordid,weight),prefix,postfix,message)
global voutput
voutput = ""
#If the recID is numeric, return only stuff that cites it. Otherwise return
#stuff that cites hitset
#try to convert to int
recisint = True
recidint = 0
try:
recidint = int(recID)
except:
recisint = False
ret = []
if recisint:
myrecords = get_cited_by(recidint) #this is a simple list
ret = get_cited_by_weight(myrecords)
else:
ret = get_cited_by_weight(hitset)
ret.sort(lambda x,y:cmp(x[1],y[1])) #ascending by the second member of the tuples
if verbose > 0:
voutput = voutput+"\nrecID "+str(recID)+" is int: "+str(recisint)+" hitset "+str(hitset)+"\n"+"find_citations retlist "+str(ret)
#voutput = voutput + str(ret)
if ret:
return (ret,"(", ")", "")
else:
return ((),"", "", "")
def related_records(recids, recids_processed):
if fmt == "HDREF" and recids:
# HDREF represents the references tab
# the tab needs to be recomputed not only when the record changes
# but also when one of the citations changes
sql = """SELECT id, modification_date FROM bibrec
WHERE id in (%s)""" % ','.join(str(r) for r in recids)
def check_date(mod_date):
return mod_date.strftime(
"%Y-%m-%d %H:%M:%S") < latest_bibrank_run
rel_recids = intbitset([
recid for recid, mod_date in run_sql(sql)
if check_date(mod_date)
])
for r in rel_recids:
recids |= intbitset(get_cited_by(r))
# To not process recids twice
recids -= recids_processed
# Adds to the set of processed recids
recids_processed += recids
return recids
def calculate_citation_history_coordinates(recid):
"""Return a list of citation graph coordinates for RECID, sorted by year."""
result = {}
for year in calculate_citation_graphe_x_coordinates(recid):
result[year] = 0
if len(result) < CFG_BIBRANK_CITATION_HISTORY_MIN_X_POINTS:
# do not generate graphs that have less than X points
return []
for recid in get_cited_by(recid):
rec_date = get_record_year(recid)
# Some records simlpy do not have these fields
if rec_date:
# Maybe rec_date[0][0:4] has a typo and cannot
# be converted to an int
try:
d = strptime(rec_date[0][:4], '%Y')
except ValueError:
pass
else:
if d.year in result:
result[d.year] += 1
return sorted(result.iteritems())
def compute_self_citations(recid, tags, authors_fun):
"""Compute the self-citations
We return the total numbers of citations minus the number of self-citations
Args:
- recid: record id
- lciters: list of record ids citing this record
- authors_cache: the authors cache which will be used to store an author
friends (to not compute friends twice)
- tags: the tag number for author, coauthors, collaborations,
required since it depends on how the marc was defined
"""
citers = get_cited_by(recid)
if not citers:
return set()
self_citations = set()
authors = frozenset(get_authors_from_record(recid, tags))
collaborations = None
if not authors or len(authors) > 20:
collaborations = frozenset(
get_collaborations_from_record(recid, tags))
if collaborations:
# Use collaborations names
for cit in citers:
cit_collaborations = frozenset(
get_collaborations_from_record(cit, tags))
if collaborations.intersection(cit_collaborations):
self_citations.add(cit)
else:
# Use authors names
for cit in citers:
cit_authors = get_authors_from_record(cit, tags)
if (not authors or len(cit_authors) > 20) and \
get_collaborations_from_record(cit, tags):
# Record from a collaboration that cites
# a record from an author, it's fine
pass
else:
cit_coauthors = frozenset(authors_fun(cit, tags))
if authors.intersection(cit_coauthors):
self_citations.add(cit)
return self_citations
def compute_self_citations(recid, tags, authors_fun):
"""Compute the self-citations
We return the total numbers of citations minus the number of self-citations
Args:
- recid: record id
- lciters: list of record ids citing this record
- authors_cache: the authors cache which will be used to store an author
friends (to not compute friends twice)
- tags: the tag number for author, coauthors, collaborations,
required since it depends on how the marc was defined
"""
citers = get_cited_by(recid)
if not citers:
return set()
self_citations = set()
authors = frozenset(get_authors_from_record(recid, tags))
collaborations = None
if not authors or len(authors) > 20:
collaborations = frozenset(get_collaborations_from_record(recid, tags))
if collaborations:
# Use collaborations names
for cit in citers:
cit_collaborations = frozenset(
get_collaborations_from_record(cit, tags))
if collaborations.intersection(cit_collaborations):
self_citations.add(cit)
else:
# Use authors names
for cit in citers:
cit_authors = get_authors_from_record(cit, tags)
if (not authors or len(cit_authors) > 20) and \
get_collaborations_from_record(cit, tags):
# Record from a collaboration that cites
# a record from an author, it's fine
pass
else:
cit_coauthors = frozenset(authors_fun(cit, tags))
if authors.intersection(cit_coauthors):
self_citations.add(cit)
return self_citations
def citations_nb_counts():
"""Get number of citations for the record `recid`."""
recid = request.view_args.get('recid')
if recid is None:
return
from intbitset import intbitset
from invenio.legacy.bibrank.citation_searcher import (get_cited_by,
get_cited_by_count)
if CFG_BIBRANK_SHOW_CITATION_LINKS:
if CFG_INSPIRE_SITE:
from invenio.legacy.search_engine import search_unit
citers_recids = intbitset(get_cited_by(recid))
citeable_recids = search_unit(p='citeable', f='collection')
return len(citers_recids & citeable_recids)
else:
return get_cited_by_count(recid)
return 0
def citations_nb_counts():
"""Get number of citations for the record `recid`."""
recid = request.view_args.get("recid")
if recid is None:
return
from intbitset import intbitset
from invenio.legacy.bibrank.citation_searcher import get_cited_by, get_cited_by_count
if CFG_BIBRANK_SHOW_CITATION_LINKS:
if CFG_INSPIRE_SITE:
from invenio.legacy.search_engine import search_unit
citers_recids = intbitset(get_cited_by(recid))
citeable_recids = search_unit(p="citeable", f="collection")
return len(citers_recids & citeable_recids)
else:
return get_cited_by_count(recid)
return 0
def related_records(recids, recids_processed):
if fmt == "HDREF" and recids:
# HDREF represents the references tab
# the tab needs to be recomputed not only when the record changes
# but also when one of the citations changes
sql = """SELECT id, modification_date FROM bibrec
WHERE id in (%s)""" % ','.join(str(r) for r in recids)
def check_date(mod_date):
return mod_date.strftime(
"%Y-%m-%d %H:%M:%S") < latest_bibrank_run
rel_recids = intbitset([recid for recid, mod_date in run_sql(sql)
if check_date(mod_date)])
for r in rel_recids:
recids |= intbitset(get_cited_by(r))
# To not process recids twice
recids -= recids_processed
# Adds to the set of processed recids
recids_processed += recids
return recids
def bibreformat_task(fmt, sql, sql_queries, cds_query, process_format, process, recids):
"""
BibReformat main task
@param fmt: output format to use
@param sql: dictionary with pre-created sql queries for various cases (for selecting records). Some of these queries will be picked depending on the case
@param sql_queries: a list of sql queries to be executed to select records to reformat.
@param cds_query: a search query to be executed to select records to reformat
@param process_format:
@param process:
@param recids: a list of record IDs to reformat
@return: None
"""
write_message("Processing format %s" % fmt)
t1 = os.times()[4]
start_date = datetime.now()
### Query the database
###
task_update_progress('Fetching records to process')
if process_format: # '-without' parameter
write_message("Querying database for records without cache...")
without_format = without_fmt(sql)
recIDs = intbitset(recids)
if cds_query['field'] != "" or \
cds_query['collection'] != "" or \
cds_query['pattern'] != "":
write_message("Querying database (CDS query)...")
if cds_query['collection'] == "":
# use search_pattern() whenever possible, as it can search
# even in private collections
res = search_pattern(p=cds_query['pattern'],
f=cds_query['field'],
m=cds_query['matching'])
else:
# use perform_request_search when '-c' argument has been
# defined, as it is not supported by search_pattern()
res = intbitset(perform_request_search(req=None, of='id',
c=cds_query['collection'],
p=cds_query['pattern'],
f=cds_query['field']))
recIDs |= res
for sql_query in sql_queries:
write_message("Querying database (%s) ..." % sql_query, verbose=2)
recIDs |= intbitset(run_sql(sql_query))
if fmt == "HDREF" and recIDs:
# HDREF represents the references tab
# the tab needs to be recomputed not only when the record changes
# but also when one of the citations changes
latest_bibrank_run = get_bibrankmethod_lastupdate('citation')
start_date = latest_bibrank_run
sql = """SELECT id, modification_date FROM bibrec
WHERE id in (%s)""" % ','.join(str(r) for r in recIDs)
def check_date(mod_date):
return mod_date < latest_bibrank_run
recIDs = intbitset([recid for recid, mod_date in run_sql(sql) \
if check_date(mod_date)])
for r in recIDs:
recIDs |= intbitset(get_cited_by(r))
### list of corresponding record IDs was retrieved
### now format the selected records
if process_format:
write_message("Records to be processed: %d" % (len(recIDs) \
+ len(without_format)))
write_message("Out of it records without existing cache: %d" % len(without_format))
else:
write_message("Records to be processed: %d" % (len(recIDs)))
### Initialize main loop
total_rec = 0 # Total number of records
tbibformat = 0 # time taken up by external call
tbibupload = 0 # time taken up by external call
### Iterate over all records prepared in lists I (option)
if process:
if CFG_BIBFORMAT_USE_OLD_BIBFORMAT: # FIXME: remove this
# when migration from php to
# python bibformat is done
(total_rec_1, tbibformat_1, tbibupload_1) = iterate_over_old(recIDs,
fmt)
else:
(total_rec_1, tbibformat_1, tbibupload_1) = iterate_over_new(recIDs,
fmt)
total_rec += total_rec_1
tbibformat += tbibformat_1
tbibupload += tbibupload_1
### Iterate over all records prepared in list II (no_format)
if process_format and process:
if CFG_BIBFORMAT_USE_OLD_BIBFORMAT: # FIXME: remove this
# when migration from php to
# python bibformat is done
(total_rec_2, tbibformat_2, tbibupload_2) = iterate_over_old(without_format,
fmt)
else:
(total_rec_2, tbibformat_2, tbibupload_2) = iterate_over_new(without_format,
fmt)
total_rec += total_rec_2
tbibformat += tbibformat_2
tbibupload += tbibupload_2
### Store last run time
if task_has_option("last"):
write_message("storing run date to %s" % start_date)
store_last_updated(fmt, start_date)
### Final statistics
t2 = os.times()[4]
elapsed = t2 - t1
message = "total records processed: %d" % total_rec
write_message(message)
message = "total processing time: %2f sec" % elapsed
write_message(message)
message = "Time spent on external call (os.system):"
write_message(message)
message = " bibformat: %2f sec" % tbibformat
write_message(message)
message = " bibupload: %2f sec" % tbibupload
write_message(message)