def crossref_normalize_name(record):
"""
Changes the format of author's name (often with initials) to the proper,
unified one, using bibauthor_name_utils tools
@return: changed record
"""
# pattern for removing the spaces between two initials
pattern_initials = '([A-Z]\\.)\\s([A-Z]\\.)'
# first, change the main author
for field in record_get_field_instances(record, '100'):
main_author = field[0][0][1]
new_author = create_normalized_name(split_name_parts(main_author))
# remove spaces between initials
# two iterations are required
for _ in range(2):
new_author = re.sub(pattern_initials, '\g<1>\g<2>', new_author)
position = field[4]
record_modify_subfield(rec=record, tag='100', subfield_code='a', \
value=new_author, subfield_position=0, field_position_global=position)
# then, change additional authors
for field in record_get_field_instances(record, '700'):
author = field[0][0][1]
new_author = create_normalized_name(split_name_parts(author))
for _ in range(2):
new_author = re.sub(pattern_initials, '\g<1>\g<2>', new_author)
position = field[4]
record_modify_subfield(rec=record, tag='700', subfield_code='a', \
value=new_author, subfield_position=0, field_position_global=position)
def crossref_normalize_name(record):
"""
Changes the format of author's name (often with initials) to the proper,
unified one, using bibauthor_name_utils tools
@return: changed record
"""
# pattern for removing the spaces between two initials
pattern_initials = '([A-Z]\\.)\\s([A-Z]\\.)'
# first, change the main author
for field in record_get_field_instances(record, '100'):
main_author = field[0][0][1]
new_author = create_normalized_name(split_name_parts(main_author))
# remove spaces between initials
# two iterations are required
for _ in range(2):
new_author = re.sub(pattern_initials, r'\g<1>\g<2>', new_author)
position = field[4]
record_modify_subfield(rec=record, tag='100', subfield_code='a',
value=new_author, subfield_position=0, field_position_global=position)
# then, change additional authors
for field in record_get_field_instances(record, '700'):
author = field[0][0][1]
new_author = create_normalized_name(split_name_parts(author))
for _ in range(2):
new_author = re.sub(pattern_initials, r'\g<1>\g<2>', new_author)
position = field[4]
record_modify_subfield(rec=record, tag='700', subfield_code='a',
value=new_author, subfield_position=0, field_position_global=position)
def convert_personid():
from invenio.dbquery import run_sql # oh come on, the whole function will be removed soon
from itertools import repeat
chunk = 1000
old_personid = run_sql("SELECT `personid`, `tag`, `data`, `flag`, `lcul` FROM `aidPERSONID`")
def flush_papers(args):
run_sql("INSERT INTO `aidPERSONIDPAPERS` "
"(`personid`, "
" `bibref_table`, "
" `bibref_value`, "
" `bibrec`, "
" `name`, "
" `flag`, "
" `lcul`) "
"VALUES " + " , ".join(repeat("(%s, %s, %s, %s, %s, %s, %s)", len(args) / 7))
, tuple(args))
def flush_data(args):
run_sql("INSERT INTO `aidPERSONIDDATA` "
"(`personid`, "
" `tag`, "
" `data`, "
" `opt1`, "
" `opt2`) "
"VALUES " + " , ".join(repeat("(%s, %s, %s, %s, %s)", len(args) / 5))
, tuple(args))
paper_args = []
data_args = []
for row in old_personid:
if row[1] == 'paper':
bibref, rec = row[2].split(',')
tab, ref = bibref.split(':')
try:
name = get_name_by_bibref((int(tab), int(ref), int(rec)))
except:
continue
name = split_name_parts(name)
name = create_normalized_name(name)
paper_args += [row[0], tab, ref, rec, name, row[3], row[4]]
if len(paper_args) > chunk:
flush_papers(paper_args)
paper_args = []
elif row[1] == 'gathered_name':
continue
else:
data_args += list(row)
if len(data_args) > chunk:
flush_data(data_args)
data_args = []
if paper_args:
flush_papers(paper_args)
if data_args:
flush_data(data_args)
def convert_personid():
from dbquery import run_sql # oh come on, the whole function will be removed soon
from itertools import repeat
chunk = 1000
old_personid = run_sql("SELECT `personid`, `tag`, `data`, `flag`, `lcul` FROM `aidPERSONID`")
def flush_papers(args):
run_sql("INSERT INTO `aidPERSONIDPAPERS` "
"(`personid`, "
" `bibref_table`, "
" `bibref_value`, "
" `bibrec`, "
" `name`, "
" `flag`, "
" `lcul`) "
"VALUES " + " , ".join(repeat("(%s, %s, %s, %s, %s, %s, %s)", len(args) / 7))
, tuple(args))
def flush_data(args):
run_sql("INSERT INTO `aidPERSONIDDATA` "
"(`personid`, "
" `tag`, "
" `data`, "
" `opt1`, "
" `opt2`) "
"VALUES " + " , ".join(repeat("(%s, %s, %s, %s, %s)", len(args) / 5))
, tuple(args))
paper_args = []
data_args = []
for row in old_personid:
if row[1] == 'paper':
bibref, rec = row[2].split(',')
tab, ref = bibref.split(':')
try:
name = get_name_by_bibrecref((int(tab), int(ref), int(rec)))
except:
continue
name = split_name_parts(name)
name = create_normalized_name(name)
paper_args += [row[0], tab, ref, rec, name, row[3], row[4]]
if len(paper_args) > chunk:
flush_papers(paper_args)
paper_args = []
elif row[1] == 'gathered_name':
continue
else:
data_args += list(row)
if len(data_args) > chunk:
flush_data(data_args)
data_args = []
if paper_args:
flush_papers(paper_args)
if data_args:
flush_data(data_args)
def rabbit(bibrecs,
check_invalid_papers=False,
personids_to_update_extids=None,
verbose=False):
'''
@param bibrecs: an iterable full of bibrecs
@type bibrecs: an iterable of ints
@return: none
'''
logfile = open('/tmp/RABBITLOG-%s' % str(now()).replace(" ", "_"), 'w')
logfile.write("RABBIT %s running on %s \n" % (str(now()), str(bibrecs)))
def logwrite(msg, is_error):
verb = 9
if is_error or verbose:
verb = 1
write_message(msg, verbose=verb)
if bconfig.RABBIT_USE_CACHED_PID:
PID_NAMES_CACHE = get_name_to_authors_mapping()
def find_pids_by_exact_names_cache(name):
try:
return zip(PID_NAMES_CACHE[name])
except KeyError:
return []
def add_signature_using_names_cache(sig, name, pid):
try:
PID_NAMES_CACHE[name].add(pid)
except KeyError:
PID_NAMES_CACHE[name] = set([pid])
_add_signature(sig, name, pid)
def new_person_from_signature_using_names_cache(sig, name):
pid = get_free_author_id()
add_signature_using_names_cache(sig, name, pid)
return pid
add_signature = add_signature_using_names_cache
new_person_from_signature = new_person_from_signature_using_names_cache
find_pids_by_exact_name = find_pids_by_exact_names_cache
else:
add_signature = _add_signature
new_person_from_signature = _new_person_from_signature
find_pids_by_exact_name = _find_pids_by_exact_name
compare_names = cached_sym(lambda x: x)(comp_names)
# fast assign threshold
threshold = 0.80
if not bibrecs or check_invalid_papers:
all_bibrecs = get_all_valid_papers()
if not bibrecs:
bibrecs = all_bibrecs
if check_invalid_papers:
filter_bibrecs_outside(all_bibrecs)
if (bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS and len(bibrecs) >
bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS_THRESHOLD):
populate_partial_marc_caches()
SWAPPED_GET_GROUPED_RECORDS = True
else:
SWAPPED_GET_GROUPED_RECORDS = False
updated_pids = set()
deleted = frozenset(p[0] for p in get_deleted_papers())
for idx, rec in enumerate(bibrecs):
logwrite("\nConsidering %s" % str(rec), False)
if idx % 200 == 0:
task_sleep_now_if_required(True)
update_status(
float(idx) / len(bibrecs),
"%d/%d current: %d" % (idx, len(bibrecs), rec))
task_update_progress("%d/%d current: %d" %
(idx, len(bibrecs), rec))
if rec in deleted:
logwrite(
" - Record was deleted, removing from pid and continuing with next record",
True)
remove_papers([rec])
continue
markrefs = frozenset(
chain(
izip(cycle([100]),
imap(itemgetter(0), get_author_refs_of_paper(rec))),
izip(cycle([700]),
imap(itemgetter(0), get_coauthor_refs_of_paper(rec)))))
personid_rows = [
map(int, row[:3]) + [row[4]]
for row in get_signatures_of_paper(rec)
]
personidrefs_names = dict(
((row[1], row[2]), row[3]) for row in personid_rows)
personidrefs = frozenset(personidrefs_names.keys())
new_signatures = list(markrefs - personidrefs)
old_signatures = list(personidrefs - markrefs)
new_signatures_names = dict(
(new,
create_normalized_name(split_name_parts(get_name_by_bibref(new))))
for new in new_signatures)
# matrix |new_signatures| X |old_signatures|
matrix = [[
compare_names(new_signatures_names[new], personidrefs_names[old])
for old in old_signatures
] for new in new_signatures]
logwrite(" - Old signatures: %s" % str(old_signatures),
bool(old_signatures))
logwrite(" - New signatures: %s" % str(new_signatures),
bool(new_signatures))
logwrite(" - Matrix: %s" % str(matrix), bool(matrix))
# [(new_signatures, old_signatures)]
best_match = [(new_signatures[new], old_signatures[old])
for new, old, score in maximized_mapping(matrix)
if score > threshold]
logwrite(" - Best match: %s " % str(best_match), bool(best_match))
for new, old in best_match:
logwrite(
" - - Moving signature: %s on %s to %s as %s" %
(old, rec, new, new_signatures_names[new]), True)
modify_signature(old, rec, new, new_signatures_names[new])
remove_signatures(tuple(list(old) + [rec]) for old in old_signatures)
not_matched = frozenset(new_signatures) - frozenset(
map(itemgetter(0), best_match))
pids_having_rec = set(
[int(row[0]) for row in get_signatures_of_paper(rec)])
logwrite(" - Not matched: %s" % str(not_matched), bool(not_matched))
if not_matched:
used_pids = set(r[0] for r in personid_rows)
for sig in not_matched:
name = new_signatures_names[sig]
matched_pids = list()
if USE_EXT_IDS:
if USE_INSPIREID:
inspire_id = get_inspire_id_of_signature(sig + (rec, ))
if inspire_id:
matched_pids = list(
get_author_by_external_id(inspire_id[0]))
if matched_pids and int(
matched_pids[0][0]) in pids_having_rec:
matched_pids = list()
if matched_pids:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
pids_having_rec.add(matched_pids[0][0])
continue
matched_pids = find_pids_by_exact_name(name)
matched_pids = [
p for p in matched_pids if int(p[0]) not in used_pids
]
if not matched_pids or int(matched_pids[0][0]) in pids_having_rec:
new_pid = new_person_from_signature(list(sig) + [rec], name)
used_pids.add(new_pid)
updated_pids.add(new_pid)
else:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
used_pids.add(matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
pids_having_rec.add(matched_pids[0][0])
logwrite('Finished with %s' % str(rec), False)
update_status_final()
if personids_to_update_extids:
updated_pids |= personids_to_update_extids
if updated_pids: # an empty set will update all canonical_names
update_canonical_names_of_authors(updated_pids)
update_external_ids_of_authors(
updated_pids,
limit_to_claimed_papers=bconfig.
LIMIT_EXTERNAL_IDS_COLLECTION_TO_CLAIMED_PAPERS)
if SWAPPED_GET_GROUPED_RECORDS:
destroy_partial_marc_caches()
remove_empty_authors()
def rabbit(bibrecs, check_invalid_papers=False, personids_to_update_extids=None):
'''
@param bibrecs: an iterable full of bibrecs
@type bibrecs: an iterable of ints
@return: none
'''
if bconfig.RABBIT_USE_CACHED_PID:
PID_NAMES_CACHE = get_name_string_to_pid_dictionary()
def find_pids_by_exact_names_cache(name):
try:
return zip(PID_NAMES_CACHE[name])
except KeyError:
return []
def add_signature_using_names_cache(sig, name, pid):
try:
PID_NAMES_CACHE[name].add(pid)
except KeyError:
PID_NAMES_CACHE[name] = set([pid])
_add_signature(sig, name, pid)
def new_person_from_signature_using_names_cache(sig, name):
pid = get_new_personid()
add_signature_using_names_cache(sig, name, pid)
return pid
add_signature = add_signature_using_names_cache
new_person_from_signature = new_person_from_signature_using_names_cache
find_pids_by_exact_name = find_pids_by_exact_names_cache
else:
add_signature = _add_signature
new_person_from_signature = _new_person_from_signature
find_pids_by_exact_name = _find_pids_by_exact_name
compare_names = cached_sym(lambda x: x)(comp_names)
# fast assign threshold
threshold = 0.80
if not bibrecs or check_invalid_papers:
all_bibrecs = get_all_valid_bibrecs()
if not bibrecs:
bibrecs = all_bibrecs
if check_invalid_papers:
filter_bibrecs_outside(all_bibrecs)
if (bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS and
len(bibrecs) > bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS_THRESHOLD):
populate_partial_marc_caches()
SWAPPED_GET_GROUPED_RECORDS = True
else:
SWAPPED_GET_GROUPED_RECORDS = False
updated_pids = set()
deleted = frozenset(p[0] for p in get_deleted_papers())
for idx, rec in enumerate(bibrecs):
task_sleep_now_if_required(True)
update_status(float(idx) / len(bibrecs), "%d/%d current: %d" % (idx, len(bibrecs), rec))
if rec in deleted:
delete_paper_from_personid(rec)
continue
markrefs = frozenset(chain(izip(cycle([100]), imap(itemgetter(0), get_authors_from_paper(rec))),
izip(cycle([700]), imap(itemgetter(0), get_coauthors_from_paper(rec)))))
personid_rows = [map(int, row[:3]) + [row[4]] for row in get_signatures_from_rec(rec)]
personidrefs_names = dict(((row[1], row[2]), row[3]) for row in personid_rows)
personidrefs = frozenset(personidrefs_names.keys())
new_signatures = list(markrefs - personidrefs)
old_signatures = list(personidrefs - markrefs)
new_signatures_names = dict((new, create_normalized_name(split_name_parts(get_name_by_bibrecref(new))))
for new in new_signatures)
# matrix |new_signatures| X |old_signatures|
matrix = [[compare_names(new_signatures_names[new], personidrefs_names[old])
for old in old_signatures] for new in new_signatures]
# [(new_signatures, old_signatures)]
best_match = [(new_signatures[new], old_signatures[old])
for new, old, score in maximized_mapping(matrix) if score > threshold]
for new, old in best_match:
modify_signature(old, rec, new, new_signatures_names[new])
remove_sigs(tuple(list(old) + [rec]) for old in old_signatures)
not_matched = frozenset(new_signatures) - frozenset(map(itemgetter(0), best_match))
if not_matched:
used_pids = set(r[0] for r in personid_rows)
for sig in not_matched:
name = new_signatures_names[sig]
matched_pids = []
if USE_EXT_IDS:
if USE_INSPIREID:
inspire_id = get_inspire_id(sig + (rec,))
if inspire_id:
matched_pids = list(get_person_with_extid(inspire_id[0]))
if matched_pids:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
continue
matched_pids = find_pids_by_exact_name(name)
matched_pids = [p for p in matched_pids if int(p[0]) not in used_pids]
if not matched_pids:
new_pid = new_person_from_signature(list(sig) + [rec], name)
used_pids.add(new_pid)
updated_pids.add(new_pid)
else:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
used_pids.add(matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
update_status_final()
if personids_to_update_extids:
updated_pids |= personids_to_update_extids
if updated_pids: # an empty set will update all canonical_names
update_personID_canonical_names(updated_pids)
update_personID_external_ids(updated_pids, limit_to_claimed_papers=bconfig.LIMIT_EXTERNAL_IDS_COLLECTION_TO_CLAIMED_PAPERS)
if SWAPPED_GET_GROUPED_RECORDS:
destroy_partial_marc_caches()
def arxiv_login(req, picked_profile=None):
'''
Log in through arxive. If user already associated to a personid, returns the personid.
If user has no pid, try to guess which personid to associate based on surname and papers
from arxiv. If no compatible person is found, creates a new person.
At the end of the process opens a ticket for the user claiming the papers from arxiv.
!!! the user will find the open ticket, which will require him to go through the
final review before getting committed.
@param req: Apache request object
@type req: Apache request object
@return: Returns the pid resulting in the process
@rtype: int
'''
def session_bareinit(req):
session = get_session(req)
try:
pinfo = session["personinfo"]
if 'ticket' not in pinfo:
pinfo["ticket"] = []
except KeyError:
pinfo = dict()
session['personinfo'] = pinfo
pinfo["ticket"] = []
session.dirty = True
session_bareinit(req)
session = get_session(req)
pinfo = session['personinfo']
ticket = session['personinfo']['ticket']
uinfo = collect_user_info(req)
pinfo['external_first_entry'] = False
try:
name = uinfo['external_firstname']
except KeyError:
name = ''
try:
surname = uinfo['external_familyname']
except KeyError:
surname = ''
if surname:
session['personinfo']['arxiv_name'] = nameapi.create_normalized_name(
nameapi.split_name_parts(surname + ', ' + name))
else:
session['personinfo']['arxiv_name'] = ''
session.dirty = True
try:
arxiv_p_ids = uinfo['external_arxivids'].split(';')
except KeyError:
arxiv_p_ids = []
#'external_arxivids': 'hep-th/0112017;hep-th/0112020',
#'external_familyname': 'Weiler',
#'external_firstname': 'Henning',
try:
found_bibrecs = set(reduce(add, [perform_request_search(p='037:' + str(arx), of='id', rg=0)for arx in arxiv_p_ids]))
except (IndexError, TypeError):
found_bibrecs = set()
#found_bibrecs = [567700, 567744]
uid = getUid(req)
pid, pid_found = dbapi.get_personid_from_uid([[uid]])
if pid_found:
pid = pid[0]
else:
if picked_profile == None:
top5_list = dbapi.find_top5_personid_for_new_arXiv_user(found_bibrecs,
nameapi.create_normalized_name(nameapi.split_name_parts(surname + ', ' + name)))
return ("top5_list", top5_list)
else:
pid = dbapi.check_personids_availability(picked_profile, uid)
pid_bibrecs = set([i[0] for i in dbapi.get_all_personids_recs(pid, claimed_only=True)])
missing_bibrecs = found_bibrecs - pid_bibrecs
#present_bibrecs = found_bibrecs.intersection(pid_bibrecs)
#assert len(found_bibrecs) == len(missing_bibrecs) + len(present_bibrecs)
tempticket = []
#now we have to open the tickets...
#person_papers contains the papers which are already assigned to the person and came from arxive,
#they can be claimed regardless
for bibrec in missing_bibrecs:
tempticket.append({'pid':pid, 'bibref':str(bibrec), 'action':'confirm'})
#check if ticket targets (bibref for pid) are already in ticket
for t in list(tempticket):
for e in list(ticket):
if e['pid'] == t['pid'] and e['bibref'] == t['bibref']:
ticket.remove(e)
ticket.append(t)
session.dirty = True
if picked_profile != None and picked_profile != pid and picked_profile != -1:
return ("chosen pid not available", pid)
elif picked_profile != None and picked_profile == pid and picked_profile != -1:
return ("pid assigned by user", pid)
else:
return ("pid", pid)
def arxiv_login(req, picked_profile=None):
'''
Log in through arxive. If user already associated to a personid, returns the personid.
If user has no pid, try to guess which personid to associate based on surname and papers
from arxiv. If no compatible person is found, creates a new person.
At the end of the process opens a ticket for the user claiming the papers from arxiv.
!!! the user will find the open ticket, which will require him to go through the
final review before getting committed.
@param req: Apache request object
@type req: Apache request object
@return: Returns the pid resulting in the process
@rtype: int
'''
def session_bareinit(req):
session = get_session(req)
try:
pinfo = session["personinfo"]
if 'ticket' not in pinfo:
pinfo["ticket"] = []
except KeyError:
pinfo = dict()
session['personinfo'] = pinfo
pinfo["ticket"] = []
session.dirty = True
session_bareinit(req)
session = get_session(req)
pinfo = session['personinfo']
ticket = session['personinfo']['ticket']
uinfo = collect_user_info(req)
pinfo['external_first_entry'] = False
try:
name = uinfo['external_firstname']
except KeyError:
name = ''
try:
surname = uinfo['external_familyname']
except KeyError:
surname = ''
if surname:
session['personinfo']['arxiv_name'] = nameapi.create_normalized_name(
nameapi.split_name_parts(surname + ', ' + name))
else:
session['personinfo']['arxiv_name'] = ''
session.dirty = True
try:
arxiv_p_ids = uinfo['external_arxivids'].split(';')
except KeyError:
arxiv_p_ids = []
#'external_arxivids': 'hep-th/0112017;hep-th/0112020',
#'external_familyname': 'Weiler',
#'external_firstname': 'Henning',
try:
found_bibrecs = set(reduce(add, [perform_request_search(p='037:' + str(arx), of='id', rg=0)for arx in arxiv_p_ids]))
except (IndexError, TypeError):
found_bibrecs = set()
#found_bibrecs = [567700, 567744]
uid = getUid(req)
pid, pid_found = dbapi.get_personid_from_uid([[uid]])
if pid_found:
pid = pid[0]
else:
if picked_profile == None:
top5_list = dbapi.find_top5_personid_for_new_arXiv_user(found_bibrecs,
nameapi.create_normalized_name(nameapi.split_name_parts(surname + ', ' + name)))
return ("top5_list", top5_list)
else:
pid = dbapi.check_personids_availability(picked_profile, uid)
pid_bibrecs = set([i[0] for i in dbapi.get_all_personids_recs(pid, claimed_only=True)])
missing_bibrecs = found_bibrecs - pid_bibrecs
#present_bibrecs = found_bibrecs.intersection(pid_bibrecs)
#assert len(found_bibrecs) == len(missing_bibrecs) + len(present_bibrecs)
tempticket = []
#now we have to open the tickets...
#person_papers contains the papers which are already assigned to the person and came from arxive,
#they can be claimed regardless
for bibrec in missing_bibrecs:
tempticket.append({'pid':pid, 'bibref':str(bibrec), 'action':'confirm'})
#check if ticket targets (bibref for pid) are already in ticket
for t in list(tempticket):
for e in list(ticket):
if e['pid'] == t['pid'] and e['bibref'] == t['bibref']:
ticket.remove(e)
ticket.append(t)
session.dirty = True
if picked_profile != None and picked_profile != pid and picked_profile != -1:
return ("chosen pid not available", pid)
elif picked_profile != None and picked_profile == pid and picked_profile != -1:
return ("pid assigned by user", pid)
else:
return ("pid", pid)
def rabbit(bibrecs, check_invalid_papers=False, personids_to_update_extids=None, verbose=False):
'''
@param bibrecs: an iterable full of bibrecs
@type bibrecs: an iterable of ints
@return: none
'''
logfile = open('/tmp/RABBITLOG-%s' % str(now()).replace(" ", "_"), 'w')
logfile.write("RABBIT %s running on %s \n" % (str(now()), str(bibrecs)))
def logwrite(msg, is_error):
verb = 9
if is_error or verbose:
verb = 1
write_message(msg, verbose=verb)
if bconfig.RABBIT_USE_CACHED_PID:
PID_NAMES_CACHE = get_name_to_authors_mapping()
def find_pids_by_exact_names_cache(name):
try:
return zip(PID_NAMES_CACHE[name])
except KeyError:
return []
def add_signature_using_names_cache(sig, name, pid):
try:
PID_NAMES_CACHE[name].add(pid)
except KeyError:
PID_NAMES_CACHE[name] = set([pid])
_add_signature(sig, name, pid)
def new_person_from_signature_using_names_cache(sig, name):
pid = get_free_author_id()
add_signature_using_names_cache(sig, name, pid)
return pid
add_signature = add_signature_using_names_cache
new_person_from_signature = new_person_from_signature_using_names_cache
find_pids_by_exact_name = find_pids_by_exact_names_cache
else:
add_signature = _add_signature
new_person_from_signature = _new_person_from_signature
find_pids_by_exact_name = _find_pids_by_exact_name
compare_names = cached_sym(lambda x: x)(comp_names)
# fast assign threshold
threshold = 0.80
if not bibrecs or check_invalid_papers:
all_bibrecs = get_all_valid_papers()
if not bibrecs:
bibrecs = all_bibrecs
if check_invalid_papers:
filter_bibrecs_outside(all_bibrecs)
if (bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS and
len(bibrecs) > bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS_THRESHOLD):
populate_partial_marc_caches()
SWAPPED_GET_GROUPED_RECORDS = True
else:
SWAPPED_GET_GROUPED_RECORDS = False
updated_pids = set()
deleted = frozenset(p[0] for p in get_deleted_papers())
for idx, rec in enumerate(bibrecs):
logwrite("\nConsidering %s" % str(rec), False)
if idx%200 == 0:
task_sleep_now_if_required(True)
update_status(float(idx) / len(bibrecs), "%d/%d current: %d" % (idx, len(bibrecs), rec))
task_update_progress("%d/%d current: %d" % (idx, len(bibrecs), rec))
if rec in deleted:
logwrite(" - Record was deleted, removing from pid and continuing with next record", True)
remove_papers([rec])
continue
markrefs = frozenset(chain(izip(cycle([100]), imap(itemgetter(0), get_author_refs_of_paper(rec))),
izip(cycle([700]), imap(itemgetter(0), get_coauthor_refs_of_paper(rec)))))
personid_rows = [map(int, row[:3]) + [row[4]] for row in get_signatures_of_paper(rec)]
personidrefs_names = dict(((row[1], row[2]), row[3]) for row in personid_rows)
personidrefs = frozenset(personidrefs_names.keys())
new_signatures = list(markrefs - personidrefs)
old_signatures = list(personidrefs - markrefs)
new_signatures_names = dict((new, create_normalized_name(split_name_parts(get_name_by_bibref(new))))
for new in new_signatures)
# matrix |new_signatures| X |old_signatures|
matrix = [[compare_names(new_signatures_names[new], personidrefs_names[old])
for old in old_signatures] for new in new_signatures]
logwrite(" - Old signatures: %s" % str(old_signatures), bool(old_signatures))
logwrite(" - New signatures: %s" % str(new_signatures), bool(new_signatures))
logwrite(" - Matrix: %s" % str(matrix), bool(matrix))
# [(new_signatures, old_signatures)]
best_match = [(new_signatures[new], old_signatures[old])
for new, old, score in maximized_mapping(matrix) if score > threshold]
logwrite(" - Best match: %s " % str(best_match), bool(best_match))
for new, old in best_match:
logwrite(" - - Moving signature: %s on %s to %s as %s" % (old, rec, new, new_signatures_names[new]), True)
modify_signature(old, rec, new, new_signatures_names[new])
remove_signatures(tuple(list(old) + [rec]) for old in old_signatures)
not_matched = frozenset(new_signatures) - frozenset(map(itemgetter(0), best_match))
pids_having_rec = set([int(row[0]) for row in get_signatures_of_paper(rec)])
logwrite(" - Not matched: %s" % str(not_matched), bool(not_matched))
if not_matched:
used_pids = set(r[0] for r in personid_rows)
for sig in not_matched:
name = new_signatures_names[sig]
matched_pids = list()
if USE_EXT_IDS:
if USE_INSPIREID:
inspire_id = get_inspire_id_of_signature(sig + (rec,))
if inspire_id:
matched_pids = list(get_author_by_external_id(inspire_id[0]))
if matched_pids and int(matched_pids[0][0]) in pids_having_rec:
matched_pids = list()
if matched_pids:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
pids_having_rec.add(matched_pids[0][0])
continue
matched_pids = find_pids_by_exact_name(name)
matched_pids = [p for p in matched_pids if int(p[0]) not in used_pids]
if not matched_pids or int(matched_pids[0][0]) in pids_having_rec:
new_pid = new_person_from_signature(list(sig) + [rec], name)
used_pids.add(new_pid)
updated_pids.add(new_pid)
else:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
used_pids.add(matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
pids_having_rec.add(matched_pids[0][0])
logwrite('Finished with %s' % str(rec), False)
update_status_final()
if personids_to_update_extids:
updated_pids |= personids_to_update_extids
if updated_pids: # an empty set will update all canonical_names
update_canonical_names_of_authors(updated_pids)
update_external_ids_of_authors(updated_pids, limit_to_claimed_papers=bconfig.LIMIT_EXTERNAL_IDS_COLLECTION_TO_CLAIMED_PAPERS)
if SWAPPED_GET_GROUPED_RECORDS:
destroy_partial_marc_caches()
remove_empty_authors()
def rabbit(bibrecs,
check_invalid_papers=False,
personids_to_update_extids=None):
'''
@param bibrecs: an iterable full of bibrecs
@type bibrecs: an iterable of ints
@return: none
'''
if bconfig.RABBIT_USE_CACHED_PID:
PID_NAMES_CACHE = get_name_string_to_pid_dictionary()
def find_pids_by_exact_names_cache(name):
try:
return zip(PID_NAMES_CACHE[name])
except KeyError:
return []
def add_signature_using_names_cache(sig, name, pid):
try:
PID_NAMES_CACHE[name].add(pid)
except KeyError:
PID_NAMES_CACHE[name] = set([pid])
_add_signature(sig, name, pid)
def new_person_from_signature_using_names_cache(sig, name):
pid = get_new_personid()
add_signature_using_names_cache(sig, name, pid)
return pid
add_signature = add_signature_using_names_cache
new_person_from_signature = new_person_from_signature_using_names_cache
find_pids_by_exact_name = find_pids_by_exact_names_cache
else:
add_signature = _add_signature
new_person_from_signature = _new_person_from_signature
find_pids_by_exact_name = _find_pids_by_exact_name
compare_names = cached_sym(lambda x: x)(comp_names)
# fast assign threshold
threshold = 0.80
if not bibrecs or check_invalid_papers:
all_bibrecs = get_all_valid_bibrecs()
if not bibrecs:
bibrecs = all_bibrecs
if check_invalid_papers:
filter_bibrecs_outside(all_bibrecs)
if (bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS and len(bibrecs) >
bconfig.RABBIT_USE_CACHED_GET_GROUPED_RECORDS_THRESHOLD):
populate_partial_marc_caches()
SWAPPED_GET_GROUPED_RECORDS = True
else:
SWAPPED_GET_GROUPED_RECORDS = False
updated_pids = set()
deleted = frozenset(p[0] for p in get_deleted_papers())
for idx, rec in enumerate(bibrecs):
task_sleep_now_if_required(True)
update_status(
float(idx) / len(bibrecs),
"%d/%d current: %d" % (idx, len(bibrecs), rec))
if rec in deleted:
delete_paper_from_personid(rec)
continue
markrefs = frozenset(
chain(
izip(cycle([100]),
imap(itemgetter(0), get_authors_from_paper(rec))),
izip(cycle([700]),
imap(itemgetter(0), get_coauthors_from_paper(rec)))))
personid_rows = [
map(int, row[:3]) + [row[4]]
for row in get_signatures_from_rec(rec)
]
personidrefs_names = dict(
((row[1], row[2]), row[3]) for row in personid_rows)
personidrefs = frozenset(personidrefs_names.keys())
new_signatures = list(markrefs - personidrefs)
old_signatures = list(personidrefs - markrefs)
new_signatures_names = dict(
(new,
create_normalized_name(
split_name_parts(get_name_by_bibrecref(new))))
for new in new_signatures)
# matrix |new_signatures| X |old_signatures|
matrix = [[
compare_names(new_signatures_names[new], personidrefs_names[old])
for old in old_signatures
] for new in new_signatures]
# [(new_signatures, old_signatures)]
best_match = [(new_signatures[new], old_signatures[old])
for new, old, score in maximized_mapping(matrix)
if score > threshold]
for new, old in best_match:
modify_signature(old, rec, new, new_signatures_names[new])
remove_sigs(tuple(list(old) + [rec]) for old in old_signatures)
not_matched = frozenset(new_signatures) - frozenset(
map(itemgetter(0), best_match))
if not_matched:
used_pids = set(r[0] for r in personid_rows)
for sig in not_matched:
name = new_signatures_names[sig]
matched_pids = []
if USE_EXT_IDS:
if USE_INSPIREID:
inspire_id = get_inspire_id(sig + (rec, ))
if inspire_id:
matched_pids = list(
get_person_with_extid(inspire_id[0]))
if matched_pids:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
continue
matched_pids = find_pids_by_exact_name(name)
matched_pids = [
p for p in matched_pids if int(p[0]) not in used_pids
]
if not matched_pids:
new_pid = new_person_from_signature(list(sig) + [rec], name)
used_pids.add(new_pid)
updated_pids.add(new_pid)
else:
add_signature(list(sig) + [rec], name, matched_pids[0][0])
used_pids.add(matched_pids[0][0])
updated_pids.add(matched_pids[0][0])
update_status_final()
if personids_to_update_extids:
updated_pids |= personids_to_update_extids
if updated_pids: # an empty set will update all canonical_names
update_personID_canonical_names(updated_pids)
update_personID_external_ids(
updated_pids,
limit_to_claimed_papers=bconfig.
LIMIT_EXTERNAL_IDS_COLLECTION_TO_CLAIMED_PAPERS)
if SWAPPED_GET_GROUPED_RECORDS:
destroy_partial_marc_caches()
def main():
"""
Reads import file and verfies the md5 hash.
For each line in the import file:
find new record from bibcode, find new ref from name on record
find old row in personid tables
copy row with new authorref (tab:bibref,rec) to temp table
overwrite personid tables w/ temp table
"""
## create temporary tables...
print "Creating temporary tables..."
create_temp_pid_sql_table()
create_temp_piddata_sql_table()
create_temp_user_input_log_sql_table()
## fill temp tables w/ static values...
print "Filling temporary tables with static, unchanged content"
copy_unaltered_piddata_rows_to_temp()
copy_unaltered_user_input_log_table_rows_to_temp()
## compile regexp for line break removal
nlr = re.compile('[\n\r]+')
#verify file integrity
print ("Verifying file integrity of %s with"
" MD5 checksum from %s" % (IMPORT_FILE_NAME, IMPORT_MD5_FILE_NAME))
fp = open(IMPORT_FILE_NAME, "rb")
fmd5 = md5_for_file(fp)
fp.close()
fp = open(IMPORT_MD5_FILE_NAME, "r")
vmd5 = fp.read()
fp.close()
if not fmd5 == vmd5:
print "WARNING: Detected a disturbance in the file. Will exit here."
return
total_lines = file_len()
fp = open(IMPORT_FILE_NAME, "r")
print "Processing file %s..." % IMPORT_FILE_NAME
for index, line in enumerate(fp.readlines()):
# if index == 100:
# break
if index % 5000 == 0:
percent = float(index) / float(total_lines)
update_status(percent, "%s of %s lines processed in %s" % (index, total_lines, IMPORT_FILE_NAME))
new_ref = None
tab1, old_ref, old_rec, tab2, enname, bibcode = line.split(" ")
assert tab1 == tab2
if tab1 == "table":
continue
name = base64.b64decode(enname)
# name = nq.sub("", name)
bibcode = nlr.sub("", bibcode)
new_rec = get_bibrec_from_bibcode(bibcode)
for ref in get_authorrefs_and_names_from_bibrec(new_rec):
# refname = create_normalized_name(split_name_parts(ref[2]))
refname = ref[2]
if refname == name and str(ref[0]) == tab1:
#MySQL equivalent: col_name COLLATE utf8_bin = 'Case SenSitive name'
new_ref = ref[1]
if not new_ref:
print "WARN: Authorref not found for name %s on new record %s?!" % (name, new_rec)
continue
# get personid, flag, lcul and last_updated from old aidPERSONIDPAPERS
old_data = find_old_pidtable_row(tab1, old_ref, old_rec)
if old_data:
## prepare data in temporary tables...
pid, flag, lcul, lupdate = old_data
old_authorref = "%s:%s,%s" % (tab1, old_ref, old_rec)
new_authorref = "%s:%s,%s" % (tab1, new_ref, new_rec)
## Transform the name into a more consistent form
inname = create_normalized_name(split_name_parts(name))
## Insert transformed data into temp tables...
insert_into_temp_table(pid, tab1, new_ref, new_rec, inname, flag, lcul, lupdate)
update_temp_piddata_table(old_authorref, new_authorref)
update_temp_user_input_log_table(old_authorref, new_authorref)
else:
print "WARN: %s does not exist in db!" % ([tab1, old_ref, old_rec])
# The following is true only if applied on the same data set
# Commented out by default. For testing/debug uses only
try:
if RUN_IN_TEST_MODE:
assert str(old_rec) == str(new_rec)
assert str(old_ref) == str(new_ref)
pass
except AssertionError, e:
print "ERROR: ", e
print "%s:%s,%s vs. %s:%s,%s on %s:%s" % (tab1, old_ref, old_rec, tab1, new_ref, new_rec, bibcode, name)
def test_create_normalized_name(self):
for tn in self.tc.keys():
self.assertEqual(create_normalized_name(split_name_parts(tn)),
self.tc[tn])
def test_create_normalized_name(self):
for tn in self.tc.keys():
self.assertEqual(create_normalized_name(split_name_parts(tn)), self.tc[tn])
