def compute_cache(pids):
bibtask.write_message("WebAuthorProfile: %s persons to go" % len(pids),
stream=sys.stdout, verbose=0)
for i, p in enumerate(pids):
bibtask.write_message("WebAuthorProfile: doing %s out of %s" % (pids.index(p) + 1, len(pids)))
bibtask.task_update_progress("WebAuthorProfile: doing %s out of %s" % (pids.index(p) + 1, len(pids)))
_compute_cache_for_person(p)
bibtask.task_sleep_now_if_required(can_stop_too=True)
def compute_cache(pids):
bibtask.write_message("WebAuthorProfile: %s persons to go" % len(pids),
stream=stdout, verbose=0)
for _, p in enumerate(pids):
bibtask.write_message("WebAuthorProfile: doing %s out of %s (personid: %s)" % (pids.index(p) + 1, len(pids), p))
bibtask.task_update_progress("WebAuthorProfile: doing %s out of %s (personid: %s)" % (pids.index(p) + 1, len(pids), p))
_compute_cache_for_person(p)
bibtask.task_sleep_now_if_required(can_stop_too=True)
def compute_cache_mp(pids):
from multiprocessing import Pool
p = Pool()
bibtask.write_message("WebAuthorProfileMP: %s persons to go" % len(pids),
stream=sys.stdout, verbose=0)
sl = 100
ss = [pids[i: i + sl] for i in range(0, len(pids), sl)]
for i, bunch in enumerate(ss):
bibtask.write_message("WebAuthorProfileMP: doing bunch %s out of %s" % (str(i + 1), len(ss)))
bibtask.task_update_progress("WebAuthorProfileMP: doing bunch %s out of %s" % (str(i + 1), len(ss)))
p.map(_compute_cache_for_person, bunch)
bibtask.task_sleep_now_if_required(can_stop_too=True)
def compute_cache_mp(pids):
from multiprocessing import Pool
p = Pool()
bibtask.write_message("WebAuthorProfileMP: %s persons to go" % len(pids),
stream=stdout, verbose=0)
sl = 100
ss = [pids[i: i + sl] for i in range(0, len(pids), sl)]
for i, bunch in enumerate(ss):
bibtask.write_message("WebAuthorProfileMP: doing bunch %s out of %s" % (str(i + 1), len(ss)))
bibtask.task_update_progress("WebAuthorProfileMP: doing bunch %s out of %s" % (str(i + 1), len(ss)))
p.map(_compute_cache_for_person, bunch)
bibtask.task_sleep_now_if_required(can_stop_too=True)
def _task_run_core():
"""
Runs the requested task in the bibsched environment.
"""
repair_pid = bibtask.task_get_option('repair_pid')
fast_update_personid = bibtask.task_get_option('fast_update_personid')
personid_gc = bibtask.task_get_option('personid_gc')
record_ids = bibtask.task_get_option('record_ids')
all_records = bibtask.task_get_option('all_records')
if record_ids:
record_ids_nested = [[p] for p in record_ids]
else:
record_ids_nested = None
if repair_pid:
bibtask.task_update_progress('Updating names cache...')
_run_update_authornames_tables_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Removing person entities not touched by '
'humans...')
personid_remove_automatically_assigned_papers()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Updating person entities...')
update_personID_from_algorithm()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Cleaning person tables...')
_run_update_personID_table_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('All repairs done.')
if fast_update_personid:
bibtask.task_update_progress('Updating personid...')
_run_personid_fast_assign_papers(record_ids_nested, all_records)
bibtask.task_update_progress('PersonID update finished!')
if personid_gc:
bibtask.task_update_progress('Updating personid (GC)...')
_run_personid_gc(record_ids_nested, all_records)
bibtask.task_update_progress('PersonID update finished (GC)!')
return 1
def _task_run_core():
"""
Runs the requested task in the bibsched environment.
"""
lastname = bibtask.task_get_option("lastname")
process_all = bibtask.task_get_option("process_all")
prepare_grid = bibtask.task_get_option("prepare_grid")
load_grid = bibtask.task_get_option("load_grid_results")
data_dir = bibtask.task_get_option("data_dir")
prefix = bibtask.task_get_option("prefix")
max_records_option = bibtask.task_get_option("max_records")
update = bibtask.task_get_option("update")
clean_cache = bibtask.task_get_option("clean_cache")
update_cache = bibtask.task_get_option("update_cache")
record_ids = bibtask.task_get_option("record_ids")
record_ids_nested = None
all_records = bibtask.task_get_option("all_records")
repair_pid = bibtask.task_get_option("repair_pid")
fast_update_personid = bibtask.task_get_option("fast_update_personid")
if record_ids:
record_ids_nested = [[p] for p in record_ids]
if fast_update_personid:
fast_update_personid = [[p] for p in fast_update_personid]
# automated_daemon_mode_p = True
if lastname:
bibtask.write_message("Processing last name %s" % (lastname), stream=sys.stdout, verbose=0)
if process_all:
if bconfig.STANDALONE:
bibtask.write_message("Processing not possible in standalone!", stream=sys.stdout, verbose=0)
return 0
bibtask.write_message("Processing all names...", stream=sys.stdout, verbose=0)
lengths = get_len_authornames_bibrefs()
if not check_and_create_aid_tables():
bibtask.write_message("Failed to create database tables!", stream=sys.stdout, verbose=0)
return 0
if lengths["names"] < 1:
bibtask.write_message("Populating Authornames table. It's Empty.", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("Populating Authornames table.")
populate_authornames()
insert_user_log(
"daemon",
"-1",
"UATFP",
"bibsched",
"status",
comment="bibauthorid_daemon, " "update_authornames_tables_from_paper",
)
if lengths["bibrefs"] < 1:
bibtask.write_message("Populating Bibrefs lookup. It's Empty.", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("Populating Bibrefs lookup table.")
populate_authornames_bibrefs_from_authornames()
bibtask.task_update_progress("Processing all authors.")
start_full_disambiguation(
last_names="all", process_orphans=True, db_exists=False, populate_doclist=True, write_to_db=True
)
update_personID_from_algorithm()
insert_user_log(
"daemon", "-1", "update_aid", "bibsched", "status", comment="bibauthorid_daemon, update_authorid_universe"
)
if prepare_grid:
bibtask.write_message("Preparing Grid Job", stream=sys.stdout, verbose=0)
data_dir_name = "grid_data"
workdir_prefix = "job"
max_records = 4000
if data_dir:
data_dir_name = data_dir
if prefix:
workdir_prefix = prefix
if max_records_option:
max_records = max_records_option
_prepare_data_files_from_db(data_dir_name, workdir_prefix, max_records)
if load_grid:
bibtask.write_message(
"Reading Grid Job results and will write" " them to the database.", stream=sys.stdout, verbose=0
)
_write_data_files_to_db(data_dir)
if update or update_cache:
bibtask.write_message("update-cache: Processing recently updated" " papers", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("update-cache: Processing recently" " updated papers")
_run_update_authornames_tables_from_paper(record_ids_nested, all_records)
bibtask.write_message("update-cache: Finished processing papers", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("update-cache: DONE")
if update:
bibtask.write_message("updating authorid universe", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("updating authorid universe")
_update_authorid_universe(record_ids, all_records)
bibtask.write_message("done updating authorid universe", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("done updating authorid universe")
if clean_cache:
bibtask.write_message("clean-cache: Processing recently updated" " papers", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("clean-cache: Processing recently updated" " papers for names")
_run_authornames_tables_gc()
bibtask.write_message("update-cache: Finished cleaning authornames " "tables", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("clean-cache: Processing recently updated" " papers for persons")
_run_update_personID_table_from_paper(record_ids_nested, all_records)
bibtask.write_message("update-cache: Finished cleaning PersonID" " table", stream=sys.stdout, verbose=0)
bibtask.task_update_progress("clean-cache: DONE")
if repair_pid:
bibtask.task_update_progress("Updating names cache...")
_run_update_authornames_tables_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress("Removing person entities not touched by " "humans...")
personid_remove_automatically_assigned_papers()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress("Updating person entities...")
update_personID_from_algorithm()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress("Cleaning person tables...")
_run_update_personID_table_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress("All repairs done.")
if fast_update_personid:
bibtask.task_update_progress("Updating personid...")
_run_personid_fast_assign_papers(fast_update_personid)
bibtask.task_update_progress("Update finished...")
# TODO: remember to pass the papers list!
return 1
def personid_fast_assign_papers(paperslist=None, use_threading_not_multiprocessing=True):
'''
Assign papers to the most compatible person.
Compares only the name to find the right person to assign to. If nobody seems compatible,
create a new person.
'''
class Worker(Thread):
def __init__(self, i, p_q, atul, personid_new_id_lock, checker):
Thread.__init__(self)
self.i = i
self.checker = checker
self.p_q = p_q
self.atul = atul
self.personid_new_id_lock = personid_new_id_lock
def run(self):
while True:
if checker.should_stop():
break
try:
bibrec = self.p_q.get_nowait()
except Empty:
break
close_connection()
pfap_assign_paper_iteration(self.i, bibrec, self.atul, self.personid_new_id_lock)
def _pfap_assign_paper(i, p_q, atul, personid_new_id_lock, checker):
while True:
# check bibsched
if checker.should_stop():
break
try:
bibrec = p_q.get_nowait()
except Empty:
break
pfap_assign_paper_iteration(i, bibrec, atul, personid_new_id_lock)
_pfap_printmsg('starter', 'Started')
if not paperslist:
#paperslist = run_sql('select id from bibrec where 1')
paperslist = [[x] for x in perform_request_search(p="")]
paperslist = [k[0] for k in paperslist]
_pfap_printmsg('starter', 'Starting on %s papers ' % len(paperslist))
if use_threading_not_multiprocessing:
authornames_table_update_lock = Lock()
personid_new_id_lock = Lock()
papers_q = Queue()
else:
authornames_table_update_lock = multiprocessing.Lock()
personid_new_id_lock = multiprocessing.Lock()
papers_q = multiprocessing.Queue()
for p in paperslist:
papers_q.put(p)
process_list = []
c = 0
if not use_threading_not_multiprocessing:
while not papers_q.empty():
checker = status_checker()
while len(process_list) <= bconfig.CFG_BIBAUTHORID_MAX_PROCESSES:
p = multiprocessing.Process(target=_pfap_assign_paper, args=(c, papers_q,
authornames_table_update_lock,
personid_new_id_lock, checker))
c += 1
process_list.append(p)
p.start()
for i, p in enumerate(tuple(process_list)):
if not p.is_alive():
p.join()
process_list.remove(p)
task_sleep_now_if_required(can_stop_too=False)
else:
max_processes = bconfig.CFG_BIBAUTHORID_PERSONID_SQL_MAX_THREADS
checker = status_checker()
workers = []
while not papers_q.empty():
i = 0
while len(workers) < max_processes:
w = Worker(i, papers_q, authornames_table_update_lock,
personid_new_id_lock, checker)
i += 1
w.start()
workers.append(w)
for c, p in enumerate(tuple(workers)):
if not p.is_alive():
p.join()
workers.remove(p)
task_sleep_now_if_required(can_stop_too=False)
def _task_run_core():
"""Runs analyse_documents for each ontology, collection, record ids
set."""
automated_daemon_mode_p = True
recids = bibtask.task_get_option('recids')
collections = bibtask.task_get_option('collections')
taxonomy = bibtask.task_get_option('taxonomy')
if recids or collections:
# We want to run some records/collection only, so we are not
# in the automated daemon mode; this will be useful later.
automated_daemon_mode_p = False
# Check if the user specified which documents to extract keywords from.
if recids:
onto_recids = _get_recids_foreach_ontology(recids=recids,
taxonomy=taxonomy)
elif collections:
onto_recids = _get_recids_foreach_ontology(collections=collections,
taxonomy=taxonomy)
else:
onto_recids = _get_recids_foreach_ontology()
if not onto_recids:
# Nothing to do.
if automated_daemon_mode_p:
_update_date_of_last_run(bibtask.task_get_task_param('task_starting_time'))
return 1
# We will write to a temporary file as we go, because we might be processing
# big collections with many docs
_rid = time.strftime("%Y%m%d%H%M%S", time.localtime())
abs_path = bibclassify_engine.get_tmp_file(_rid)
fo = open(abs_path, 'w')
fo.write('<?xml version="1.0" encoding="UTF-8"?>\n')
fo.write('<collection xmlns="http://www.loc.gov/MARC21/slim">\n')
# Count the total number of records in order to update the progression.
global _RECIDS_NUMBER
for onto_rec in onto_recids:
_RECIDS_NUMBER += len(onto_rec['recIDs'])
rec_added = False
for onto_rec in onto_recids:
bibtask.task_sleep_now_if_required(can_stop_too=False)
if onto_rec['collection'] is not None:
bibtask.write_message('INFO: Applying taxonomy %s to collection %s (%s '
'records)' % (onto_rec['ontology'], onto_rec['collection'],
len(onto_rec['recIDs'])), stream=sys.stderr, verbose=3)
else:
bibtask.write_message('INFO: Applying taxonomy %s to recIDs %s. ' %
(onto_rec['ontology'],
', '.join([str(recid) for recid in onto_rec['recIDs']])),
stream=sys.stderr, verbose=3)
if onto_rec['recIDs']:
xml = _analyze_documents(onto_rec['recIDs'],
onto_rec['ontology'], onto_rec['collection'])
if len(xml) > 5:
fo.write(xml)
rec_added = True
fo.write('</collection>\n')
fo.close()
# Apply the changes.
if rec_added:
if bconfig.CFG_DB_SAVE_KW:
bibclassify_webinterface.upload_keywords(abs_path)
else:
bibtask.write_message("INFO: CFG_DB_SAVE_KW is false, we don't save results",
stream=sys.stderr, verbose=0)
else:
bibtask.write_message("WARNING: No keywords found, recids: %s" % onto_recids,
stream=sys.stderr, verbose=0)
os.remove(abs_path)
# Update the date of last run in the clsMETHOD table, but only if
# we were running in an automated mode.
if automated_daemon_mode_p:
_update_date_of_last_run(bibtask.task_get_task_param('task_starting_time'))
return 1
def _analyze_documents(records, taxonomy_name, collection,
output_limit=bconfig.CFG_BIBCLASSIFY_DEFAULT_OUTPUT_NUMBER):
"""For each collection, parse the documents attached to the records
in collection with the corresponding taxonomy_name.
@var records: list of recids to process
@var taxonomy_name: str, name of the taxonomy, e.g. HEP
@var collection: str, collection name
@keyword output_limit: int, max number of keywords to extract [3]
@return: str, marcxml output format of results
"""
global _INDEX
if not records:
# No records could be found.
bibtask.write_message("WARNING: No records were found in collection %s." %
collection, stream=sys.stderr, verbose=2)
return False
# Process records:
output = []
for record in records:
bibdocfiles = BibRecDocs(record).list_latest_files() # TODO: why this doesn't call list_all_files() ?
keywords = {}
akws = {}
acro = {}
single_keywords = composite_keywords = author_keywords = acronyms = None
for doc in bibdocfiles:
# Get the keywords for all PDF documents contained in the record.
if bibclassify_text_extractor.is_pdf(doc.get_full_path()):
bibtask.write_message('INFO: Generating keywords for record %d.' %
record, stream=sys.stderr, verbose=3)
fulltext = doc.get_path()
single_keywords, composite_keywords, author_keywords, acronyms = \
bibclassify_engine.get_keywords_from_local_file(fulltext,
taxonomy_name, with_author_keywords=True, output_mode="raw",
output_limit=output_limit, match_mode='partial')
else:
bibtask.write_message('WARNING: BibClassify does not know how to process \
doc: %s (type: %s) -- ignoring it.' %
(doc.fullpath, doc.doctype), stream=sys.stderr, verbose=3)
if single_keywords or composite_keywords:
cleaned_single = bibclassify_engine.clean_before_output(single_keywords)
cleaned_composite = bibclassify_engine.clean_before_output(composite_keywords)
# merge the groups into one
keywords.update(cleaned_single)
keywords.update(cleaned_composite)
acro.update(acronyms)
akws.update(author_keywords)
if len(keywords):
output.append('<record>')
output.append('<controlfield tag="001">%s</controlfield>' % record)
output.append(bibclassify_engine._output_marc(keywords.items(), (), akws, acro,
spires=bconfig.CFG_SPIRES_FORMAT))
output.append('</record>')
else:
bibtask.write_message('WARNING: No keywords found for record %d.' %
record, stream=sys.stderr, verbose=0)
_INDEX += 1
bibtask.task_update_progress('Done %d out of %d.' % (_INDEX, _RECIDS_NUMBER))
bibtask.task_sleep_now_if_required(can_stop_too=False)
return '\n'.join(output)
deleted_recs = dbinter.get_deleted_papers()
deleted_recs = frozenset(x[0] for x in deleted_recs)
if bconfig.TABLES_UTILS_DEBUG:
print "%d total deleted papers" % (len(deleted_recs),)
if personid:
personid_q = dbinter.list_2_SQL_str(personid, lambda x: str(x[0]))
else:
personid_q = None
counter = 0
rows_limit = 10000000
end_loop = False
while not end_loop:
task_sleep_now_if_required(True)
papers_data = dbinter.collect_personid_papers(person=personid_q,
limit=(counter, rows_limit,))
if bconfig.TABLES_UTILS_DEBUG:
print "query with limit %d %d" % (counter, rows_limit)
if len(papers_data) == rows_limit:
counter += rows_limit
else:
end_loop = True
papers_data = tuple((extract_bibrec(p[3]), p) for p in papers_data)
to_remove = set()
jobs = dict()
for p in papers_data:
def personid_fast_assign_papers(paperslist=None, use_threading_not_multiprocessing=True):
'''
Assign papers to the most compatible person.
Compares only the name to find the right person to assign to. If nobody seems compatible,
create a new person.
'''
class Worker(Thread):
def __init__(self, i, p_q, atul, personid_new_id_lock, checker):
Thread.__init__(self)
self.i = i
self.checker = checker
self.p_q = p_q
self.atul = atul
self.personid_new_id_lock = personid_new_id_lock
def run(self):
while True:
if checker.should_stop():
break
try:
bibrec = self.p_q.get_nowait()
except Empty:
break
close_connection()
pfap_assign_paper_iteration(self.i, bibrec, self.atul, self.personid_new_id_lock)
def _pfap_assign_paper(i, p_q, atul, personid_new_id_lock, checker):
while True:
# check bibsched
if checker.should_stop():
break
try:
bibrec = p_q.get_nowait()
except Empty:
break
pfap_assign_paper_iteration(i, bibrec, atul, personid_new_id_lock)
_pfap_printmsg('starter', 'Started')
if not paperslist:
#paperslist = run_sql('select id from bibrec where 1')
paperslist = [[x] for x in perform_request_search(p="")]
paperslist = [k[0] for k in paperslist]
_pfap_printmsg('starter', 'Starting on %s papers ' % len(paperslist))
if use_threading_not_multiprocessing:
authornames_table_update_lock = Lock()
personid_new_id_lock = Lock()
papers_q = Queue()
else:
authornames_table_update_lock = multiprocessing.Lock()
personid_new_id_lock = multiprocessing.Lock()
papers_q = multiprocessing.Queue()
for p in paperslist:
papers_q.put(p)
process_list = []
c = 0
if not use_threading_not_multiprocessing:
while not papers_q.empty():
checker = status_checker()
while len(process_list) <= bconfig.CFG_BIBAUTHORID_MAX_PROCESSES:
p = multiprocessing.Process(target=_pfap_assign_paper, args=(c, papers_q,
authornames_table_update_lock,
personid_new_id_lock, checker))
c += 1
process_list.append(p)
p.start()
for i, p in enumerate(tuple(process_list)):
if not p.is_alive():
p.join()
process_list.remove(p)
task_sleep_now_if_required(True)
else:
max_processes = bconfig.CFG_BIBAUTHORID_PERSONID_SQL_MAX_THREADS
checker = status_checker()
workers = []
while not papers_q.empty():
i = 0
while len(workers) < max_processes:
w = Worker(i, papers_q, authornames_table_update_lock,
personid_new_id_lock, checker)
i += 1
w.start()
workers.append(w)
for c, p in enumerate(tuple(workers)):
if not p.is_alive():
p.join()
workers.remove(p)
task_sleep_now_if_required(True)
def _task_run_core():
"""Runs analyse_documents for each ontology, collection, record ids
set."""
automated_daemon_mode_p = True
recids = bibtask.task_get_option('recids')
collections = bibtask.task_get_option('collections')
taxonomy = bibtask.task_get_option('taxonomy')
if recids or collections:
# We want to run some records/collection only, so we are not
# in the automated daemon mode; this will be useful later.
automated_daemon_mode_p = False
# Check if the user specified which documents to extract keywords from.
if recids:
onto_recids = _get_recids_foreach_ontology(recids=recids,
taxonomy=taxonomy)
elif collections:
onto_recids = _get_recids_foreach_ontology(collections=collections,
taxonomy=taxonomy)
else:
onto_recids = _get_recids_foreach_ontology()
if not onto_recids:
# Nothing to do.
if automated_daemon_mode_p:
_update_date_of_last_run(
bibtask.task_get_task_param('task_starting_time'))
return 1
# We will write to a temporary file as we go, because we might be processing
# big collections with many docs
_rid = time.strftime("%Y%m%d%H%M%S", time.localtime())
abs_path = bibclassify_engine.get_tmp_file(_rid)
fo = open(abs_path, 'w')
fo.write('<?xml version="1.0" encoding="UTF-8"?>\n')
fo.write('<collection xmlns="http://www.loc.gov/MARC21/slim">\n')
# Count the total number of records in order to update the progression.
global _RECIDS_NUMBER
for onto_rec in onto_recids:
_RECIDS_NUMBER += len(onto_rec['recIDs'])
rec_added = False
for onto_rec in onto_recids:
bibtask.task_sleep_now_if_required(can_stop_too=False)
if onto_rec['collection'] is not None:
bibtask.write_message(
'INFO: Applying taxonomy %s to collection %s (%s '
'records)' % (onto_rec['ontology'], onto_rec['collection'],
len(onto_rec['recIDs'])),
stream=sys.stderr,
verbose=3)
else:
bibtask.write_message(
'INFO: Applying taxonomy %s to recIDs %s. ' %
(onto_rec['ontology'], ', '.join(
[str(recid) for recid in onto_rec['recIDs']])),
stream=sys.stderr,
verbose=3)
if onto_rec['recIDs']:
xml = _analyze_documents(onto_rec['recIDs'], onto_rec['ontology'],
onto_rec['collection'])
if len(xml) > 5:
fo.write(xml)
rec_added = True
fo.write('</collection>\n')
fo.close()
# Apply the changes.
if rec_added:
if bconfig.CFG_DB_SAVE_KW:
bibclassify_webinterface.upload_keywords(abs_path)
else:
bibtask.write_message(
"INFO: CFG_DB_SAVE_KW is false, we don't save results",
stream=sys.stderr,
verbose=0)
else:
bibtask.write_message("WARNING: No keywords found, recids: %s" %
onto_recids,
stream=sys.stderr,
verbose=0)
os.remove(abs_path)
# Update the date of last run in the clsMETHOD table, but only if
# we were running in an automated mode.
if automated_daemon_mode_p:
_update_date_of_last_run(
bibtask.task_get_task_param('task_starting_time'))
return 1
def _task_run_core():
"""
Runs the requested task in the bibsched environment.
"""
lastname = bibtask.task_get_option('lastname')
process_all = bibtask.task_get_option('process_all')
prepare_grid = bibtask.task_get_option('prepare_grid')
load_grid = bibtask.task_get_option('load_grid_results')
data_dir = bibtask.task_get_option('data_dir')
prefix = bibtask.task_get_option('prefix')
max_records_option = bibtask.task_get_option('max_records')
update = bibtask.task_get_option('update')
clean_cache = bibtask.task_get_option('clean_cache')
update_cache = bibtask.task_get_option('update_cache')
record_ids = bibtask.task_get_option('record_ids')
record_ids_nested = None
all_records = bibtask.task_get_option('all_records')
repair_pid = bibtask.task_get_option('repair_pid')
if record_ids:
record_ids_nested = [[p] for p in record_ids]
# automated_daemon_mode_p = True
if lastname:
bibtask.write_message("Processing last name %s" % (lastname),
stream=sys.stdout, verbose=0)
if process_all:
if bconfig.STANDALONE:
bibtask.write_message("Processing not possible in standalone!",
stream=sys.stdout, verbose=0)
return 0
bibtask.write_message("Processing all names...",
stream=sys.stdout, verbose=0)
lengths = get_len_authornames_bibrefs()
if not check_and_create_aid_tables():
bibtask.write_message("Failed to create database tables!",
stream=sys.stdout, verbose=0)
return 0
if lengths['names'] < 1:
bibtask.write_message("Populating Authornames table. It's Empty.",
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('Populating Authornames table.')
populate_authornames()
insert_user_log('daemon', '-1', 'UATFP', 'bibsched', 'status',
comment='bibauthorid_daemon, '
'update_authornames_tables_from_paper')
if lengths['bibrefs'] < 1:
bibtask.write_message("Populating Bibrefs lookup. It's Empty.",
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('Populating Bibrefs lookup table.')
populate_authornames_bibrefs_from_authornames()
bibtask.task_update_progress('Processing all authors.')
start_full_disambiguation(last_names="all",
process_orphans=True,
db_exists=False,
populate_doclist=True,
write_to_db=True)
update_personID_from_algorithm()
insert_user_log('daemon', '-1', 'update_aid', 'bibsched', 'status',
comment='bibauthorid_daemon, update_authorid_universe')
if prepare_grid:
bibtask.write_message("Preparing Grid Job",
stream=sys.stdout, verbose=0)
data_dir_name = "grid_data"
workdir_prefix = "job"
max_records = 4000
if data_dir:
data_dir_name = data_dir
if prefix:
workdir_prefix = prefix
if max_records_option:
max_records = max_records_option
_prepare_data_files_from_db(data_dir_name, workdir_prefix, max_records)
if load_grid:
bibtask.write_message("Reading Grid Job results and will write"
" them to the database.",
stream=sys.stdout, verbose=0)
_write_data_files_to_db(data_dir)
if update or update_cache:
bibtask.write_message("update-cache: Processing recently updated"
" papers", stream=sys.stdout, verbose=0)
bibtask.task_update_progress('update-cache: Processing recently'
' updated papers')
_run_update_authornames_tables_from_paper(record_ids_nested, all_records)
bibtask.write_message("update-cache: Finished processing papers",
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('update-cache: DONE')
if update:
bibtask.write_message("updating authorid universe",
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('updating authorid universe')
_update_authorid_universe(record_ids, all_records)
bibtask.write_message("done updating authorid universe",
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('done updating authorid universe')
if clean_cache:
bibtask.write_message("clean-cache: Processing recently updated"
" papers", stream=sys.stdout, verbose=0)
bibtask.task_update_progress('clean-cache: Processing recently updated'
' papers for names')
_run_authornames_tables_gc()
bibtask.write_message("update-cache: Finished cleaning authornames "
"tables", stream=sys.stdout, verbose=0)
bibtask.task_update_progress('clean-cache: Processing recently updated'
' papers for persons')
_run_update_personID_table_from_paper(record_ids_nested, all_records)
bibtask.write_message("update-cache: Finished cleaning PersonID"
" table", stream=sys.stdout, verbose=0)
bibtask.task_update_progress('clean-cache: DONE')
if repair_pid:
bibtask.task_update_progress('Updating names cache...')
_run_update_authornames_tables_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Removing person entities not touched by '
'humans...')
personid_remove_automatically_assigned_papers()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Updating person entities...')
update_personID_from_algorithm()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Cleaning person tables...')
_run_update_personID_table_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('All repairs done.')
return 1
def _prepare_data_files_from_db(data_dir_name="grid_data",
workdir_prefix="job",
max_records=4000):
'''
Prepares grid jobs. Is a task running in bibsched.
Meaning:
1. Find all last names in the database
2. For each last name:
- find all documents regarding this last name (ignore first names)
- if number of documents loaded into memory exceeds max_records,
write the memory cache into files (cf. Files section).
Each write back procedure will happen into a newly created
directory. The prefix for the respective job directory may
be specified as well as the name of the data directory where
these job directories will be created.
Files:
- authornames.dat
- virtual_authors.dat
- virtual_author_data.dat
- virtual_author_clusters.dat
- virtual_author_cluster_cache.dat
- realauthors.dat
- realauthor_data.dat
- doclist.dat
- records.dat
- ids.dat
- ra_va_cache.dat
@param data_dir_name: the name of the directory that will hold all the
sub directories for the jobs.
@type data_dir_name: string
@param workdir_prefix: prefix for the job sub directories.
@type workdir_prefix: string
@param max_records: maximum number of records after which the memory
cache is to be flushed to files.
@type max_records: int
'''
try:
max_records = int(max_records)
except ValueError:
max_records = 4000
bibtask.write_message("Loading last names", stream=sys.stdout, verbose=0)
bibtask.write_message("Limiting files to %s records" % (max_records, ),
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('Loading last names...')
last_names = find_all_last_names()
last_name_queue = Queue.Queue()
for last_name in sorted(last_names):
last_name_queue.put(last_name)
total = len(last_names)
status = 1
bibtask.write_message("Done. Loaded %s last names." % (total),
stream=sys.stdout,
verbose=0)
job_id = 0
data_dir = ""
if data_dir_name.startswith("/"):
data_dir = data_dir_name
else:
data_dir = "%s/%s/" % (bconfig.FILE_PATH, data_dir_name)
if not data_dir.endswith("/"):
data_dir = "%s/" % (data_dir, )
job_lnames = []
while True:
if last_name_queue.empty():
bibtask.write_message("Done with all names.",
stream=sys.stdout,
verbose=0)
break
bibtask.task_sleep_now_if_required(can_stop_too=False)
lname_list = last_name_queue.get()
lname = None
if lname_list:
lname = lname_list[0]
del (lname_list[0])
else:
bconfig.LOGGER.warning("Got an empty Queue element. "
"Queue seems corrupted.")
continue
job_lnames.append(lname)
bibtask.task_update_progress('Preparing job %d of %d: %s.' %
(status, total, lname))
bibtask.write_message(
("Processing: %s (%d/%d).") % (lname, status, total),
stream=sys.stdout,
verbose=0)
bibtask.task_sleep_now_if_required(can_stop_too=False)
populate_doclist_for_author_surname(lname)
post_remove_names = set()
for name in [
row['name'] for row in dat.AUTHOR_NAMES if not row['processed']
]:
potential_removal = "%s," % (name.split(',')[0], )
if not potential_removal == "%s" % (lname, ):
post_remove_names.add(potential_removal)
if len(post_remove_names) > 1:
removed = 0
removed_names = []
for post_remove_name in post_remove_names:
if post_remove_name in lname_list:
lname_list.remove(post_remove_name)
removed_names.append(post_remove_name)
removed += 1
bibtask.write_message(
("-> Removed %s entries from the " + "computation list: %s") %
(removed, removed_names),
stream=sys.stdout,
verbose=0)
total -= removed
if lname_list:
last_name_queue.put(lname_list)
if len(dat.RELEVANT_RECORDS) >= max_records:
if not os.path.exists(data_dir):
os.mkdir(data_dir)
work_dir = "%s%s%s" % (data_dir, workdir_prefix, job_id)
_write_to_files(work_dir, job_lnames)
bibtask.task_sleep_now_if_required(can_stop_too=True)
job_lnames = []
job_id += 1
status += 1
if dat.RELEVANT_RECORDS:
if not os.path.exists(data_dir):
os.mkdir(data_dir)
work_dir = "%s%s%s" % (data_dir, workdir_prefix, job_id)
_write_to_files(work_dir, job_lnames)
bibtask.task_sleep_now_if_required(can_stop_too=True)
return True
deleted_recs = dbinter.get_deleted_papers()
deleted_recs = frozenset(x[0] for x in deleted_recs)
if bconfig.TABLES_UTILS_DEBUG:
print "%d total deleted papers" % (len(deleted_recs),)
if personid:
personid_q = dbinter.list_2_SQL_str(personid, lambda x: str(x[0]))
else:
personid_q = None
counter = 0
rows_limit = 10000000
end_loop = False
while not end_loop:
task_sleep_now_if_required(True)
papers_data = dbinter.collect_personid_papers(person=personid_q, limit=(counter, rows_limit))
if bconfig.TABLES_UTILS_DEBUG:
print "query with limit %d %d" % (counter, rows_limit)
if len(papers_data) == rows_limit:
counter += rows_limit
else:
end_loop = True
papers_data = tuple((extract_bibrec(p[3]), p) for p in papers_data)
to_remove = set()
jobs = dict()
for p in papers_data:
if int(p[0]) in deleted_recs:
def _task_run_core():
"""
Runs the requested task in the bibsched environment.
"""
lastname = bibtask.task_get_option('lastname')
process_all = bibtask.task_get_option('process_all')
prepare_grid = bibtask.task_get_option('prepare_grid')
load_grid = bibtask.task_get_option('load_grid_results')
data_dir = bibtask.task_get_option('data_dir')
prefix = bibtask.task_get_option('prefix')
max_records_option = bibtask.task_get_option('max_records')
update = bibtask.task_get_option('update')
clean_cache = bibtask.task_get_option('clean_cache')
update_cache = bibtask.task_get_option('update_cache')
record_ids = bibtask.task_get_option('record_ids')
record_ids_nested = None
all_records = bibtask.task_get_option('all_records')
repair_pid = bibtask.task_get_option('repair_pid')
if record_ids:
record_ids_nested = [[p] for p in record_ids]
# automated_daemon_mode_p = True
if lastname:
bibtask.write_message("Processing last name %s" % (lastname),
stream=sys.stdout,
verbose=0)
if process_all:
if bconfig.STANDALONE:
bibtask.write_message("Processing not possible in standalone!",
stream=sys.stdout,
verbose=0)
return 0
bibtask.write_message("Processing all names...",
stream=sys.stdout,
verbose=0)
lengths = get_len_authornames_bibrefs()
if not check_and_create_aid_tables():
bibtask.write_message("Failed to create database tables!",
stream=sys.stdout,
verbose=0)
return 0
if lengths['names'] < 1:
bibtask.write_message("Populating Authornames table. It's Empty.",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('Populating Authornames table.')
populate_authornames()
insert_user_log('daemon',
'-1',
'UATFP',
'bibsched',
'status',
comment='bibauthorid_daemon, '
'update_authornames_tables_from_paper')
if lengths['bibrefs'] < 1:
bibtask.write_message("Populating Bibrefs lookup. It's Empty.",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('Populating Bibrefs lookup table.')
populate_authornames_bibrefs_from_authornames()
bibtask.task_update_progress('Processing all authors.')
start_full_disambiguation(last_names="all",
process_orphans=True,
db_exists=False,
populate_doclist=True,
write_to_db=True)
update_personID_from_algorithm()
insert_user_log('daemon',
'-1',
'update_aid',
'bibsched',
'status',
comment='bibauthorid_daemon, update_authorid_universe')
if prepare_grid:
bibtask.write_message("Preparing Grid Job",
stream=sys.stdout,
verbose=0)
data_dir_name = "grid_data"
workdir_prefix = "job"
max_records = 4000
if data_dir:
data_dir_name = data_dir
if prefix:
workdir_prefix = prefix
if max_records_option:
max_records = max_records_option
_prepare_data_files_from_db(data_dir_name, workdir_prefix, max_records)
if load_grid:
bibtask.write_message(
"Reading Grid Job results and will write"
" them to the database.",
stream=sys.stdout,
verbose=0)
_write_data_files_to_db(data_dir)
if update or update_cache:
bibtask.write_message(
"update-cache: Processing recently updated"
" papers",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('update-cache: Processing recently'
' updated papers')
_run_update_authornames_tables_from_paper(record_ids_nested,
all_records)
bibtask.write_message("update-cache: Finished processing papers",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('update-cache: DONE')
if update:
bibtask.write_message("updating authorid universe",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('updating authorid universe')
_update_authorid_universe(record_ids, all_records)
bibtask.write_message("done updating authorid universe",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('done updating authorid universe')
if clean_cache:
bibtask.write_message(
"clean-cache: Processing recently updated"
" papers",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('clean-cache: Processing recently updated'
' papers for names')
_run_authornames_tables_gc()
bibtask.write_message(
"update-cache: Finished cleaning authornames "
"tables",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('clean-cache: Processing recently updated'
' papers for persons')
_run_update_personID_table_from_paper(record_ids_nested, all_records)
bibtask.write_message(
"update-cache: Finished cleaning PersonID"
" table",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('clean-cache: DONE')
if repair_pid:
bibtask.task_update_progress('Updating names cache...')
_run_update_authornames_tables_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Removing person entities not touched by '
'humans...')
personid_remove_automatically_assigned_papers()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Updating person entities...')
update_personID_from_algorithm()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('Cleaning person tables...')
_run_update_personID_table_from_paper()
bibtask.task_sleep_now_if_required(can_stop_too=False)
bibtask.task_update_progress('All repairs done.')
return 1
def _update_authorid_universe(record_ids=None, all_records=False):
'''
Updates all data related to the authorid algorithm.
Sequence of operations:
- Get all recently updated papers and remember time in the log
- Get all authors on all papers
- Extract collection of last names
- For each last name:
- Populate mem cache with cluster data
- Delete updated records and their virtual authors from mem cache
- Create virtual authors for new and updated records
- Start matching algorithm
- Update tables with results of the computation
- Start personid update procedure
'''
def create_vas_from_specific_doclist(bibrec_ids):
'''
Processes the document list and creates a new minimal virtual author
for each author in each record specified in the given list.
@param bibrec_ids: Record IDs to concern in this update
@type bibrec_ids: list of int
'''
num_docs = len([row for row in dat.DOC_LIST
if row['bibrecid'] in bibrec_ids])
bconfig.LOGGER.log(25, "Creating minimal virtual authors for "
"all loaded docs (%s)"
% (num_docs))
for docs in [row for row in dat.DOC_LIST
if row['bibrecid'] in bibrec_ids]:
for author_id in docs['authornameids']:
author_name = [an['name'] for an in dat.AUTHOR_NAMES
if an['id'] == author_id]
refrecs = [ref[1] for ref in docs['authornameid_bibrefrec']
if ref[0] == author_id]
refrec = -1
if len(refrecs) > 1:
refrec = refrecs[0]
elif refrecs:
refrec = refrecs[0]
if refrec and author_name:
add_minimum_virtualauthor(author_id, author_name[0],
docs['bibrecid'], 0, [], refrec)
elif author_name:
add_minimum_virtualauthor(author_id, author_name[0],
docs['bibrecid'], 0, [])
dat.reset_mem_cache(True)
last_log = None
updated_records = []
if not record_ids and not all_records:
last_log = get_user_log(userinfo='daemon',
action='update_aid',
only_most_recent=True)
if last_log:
#select only the most recent papers
recently_modified, last_update_time = get_papers_recently_modified(
date=last_log[0][2])
insert_user_log('daemon', '-1', 'update_aid', 'bibsched', 'status',
comment='bibauthorid_daemon, update_authorid_universe',
timestamp=last_update_time[0][0])
bibtask.write_message("Update authorid will operate on %s records."
% (len(recently_modified)), stream=sys.stdout,
verbose=0)
if not recently_modified:
bibtask.write_message("Update authorid: Nothing to do",
stream=sys.stdout, verbose=0)
return
for rec in recently_modified:
updated_records.append(rec[0])
dat.update_log("rec_updates", rec[0])
else:
bibtask.write_message("Update authorid: Nothing to do",
stream=sys.stdout, verbose=0)
return
elif record_ids and not all_records:
updated_records = record_ids
elif not record_ids and all_records:
bibtask.write_message("Update is going to empty all aid tables...",
stream=sys.stdout, verbose=0)
empty_aid_tables()
bibtask.write_message("Update authorid will operate on all! records.",
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('Update is operating on all! records.')
start_full_disambiguation(process_orphans=True,
db_exists=False,
populate_doclist=True,
write_to_db=True)
bibtask.task_update_progress('Update is done.')
return
bibtask.task_sleep_now_if_required(can_stop_too=True)
authors = []
author_last_names = set()
bibtask.task_update_progress('Reading authors from updated records')
bibtask.write_message("Reading authors from updated records",
stream=sys.stdout, verbose=0)
updated_ras = set()
# get all authors from all updated records
for rec in updated_records:
rec_authors = get_field_values_on_condition(rec, ['100', '700'], "a",
source="API")
for rec_author in rec_authors:
if not rec_author:
bconfig.LOGGER.error("Invalid empty author string, which "
"will be skipped on record %s"
% (rec))
continue
author_in_list = [row for row in authors
if row['db_name'] == rec_author]
if author_in_list:
for upd in [row for row in authors
if row['db_name'] == rec_author]:
upd['records'].append(rec)
else:
last_name = split_name_parts(rec_author)[0]
author_last_names.add(last_name)
authors.append({'db_name': rec_author,
'records': [rec],
'last_name': last_name})
for status, author_last_name in enumerate(author_last_names):
bibtask.task_sleep_now_if_required(can_stop_too=False)
current_authors = [row for row in authors
if row['last_name'] == author_last_name]
total_lnames = len(author_last_names)
total_authors = len(current_authors)
bibtask.task_update_progress('Processing %s of %s cluster: "%s" '
'(%s authors)'
% (status + 1, total_lnames,
author_last_name, total_authors))
bibtask.write_message('Processing %s of %s cluster: "%s" '
'(%s authors)'
% (status + 1, total_lnames, author_last_name,
total_authors), stream=sys.stdout, verbose=0)
dat.reset_mem_cache(True)
init_authornames(author_last_name)
load_mem_cache_from_tables()
bconfig.LOGGER.log(25, "-- Relevant data successfully read into memory"
" to start processing")
for current_author in current_authors:
load_records_to_mem_cache(current_author['records'])
authornamesid = [row['id'] for row in dat.AUTHOR_NAMES
if row['db_name'] == current_author['db_name']]
if not authornamesid:
bconfig.LOGGER.error("The author '%s' rec '%s' is not in authornames "
"and will be skipped. You might want "
"to run authornames update before?"
% (current_author['db_name'], rec))
continue
else:
try:
authornamesid = int(authornamesid[0])
except (IndexError, TypeError, ValueError):
bconfig.LOGGER.error("Invalid authornames ID!")
continue
if not current_author['records']:
bconfig.LOGGER.error("The author '%s' is not associated to any"
" document and will be skipped."
% (current_author['db_name']))
continue
for rec in current_author['records']:
# remove VAs already existing for the record
va_ids = get_va_ids_by_recid_lname(rec,
current_author["last_name"])
if va_ids:
for va_id in va_ids:
ra_list = get_realauthors_by_virtuala_id(va_id)
for ra_id in ra_list:
remove_va_from_ra(ra_id, va_id)
del_ra_data_by_vaid(ra_id, va_id)
va_anames_id = get_virtualauthor_records(va_id,
"orig_authorname_id")
for an_list in [row['authornameids'] for row in
dat.DOC_LIST if row['bibrecid'] == rec]:
try:
an_list.remove(va_anames_id)
except (ValueError):
# This names id is not in the list...don't care
pass
delete_virtual_author(va_id)
# create new VAs for the record.
update_doclist(rec, authornamesid)
dat.update_log("rec_updates", rec)
create_vas_from_specific_doclist(current_author['records'])
bconfig.LOGGER.log(25, "-- Relevant data pre-processed successfully.")
bibtask.task_sleep_now_if_required(can_stop_too=False)
start_computation(process_doclist=False,
process_orphans=True,
print_stats=True)
bconfig.LOGGER.log(25, "-- Computation finished. Will write back to "
"the database now.")
update_db_result = update_tables_from_mem_cache(return_ra_updates=True)
bibtask.task_sleep_now_if_required(can_stop_too=True)
if not update_db_result[0]:
bconfig.LOGGER.log(25, "Writing to persistence layer failed.")
else:
if update_db_result[1]:
for updated_ra in update_db_result[1]:
if updated_ra:
updated_ras.add(updated_ra[0])
bconfig.LOGGER.log(25, "Done updating authorid universe.")
personid_ra_format = []
for ra_id in updated_ras:
personid_ra_format.append((ra_id,))
bconfig.LOGGER.log(25, "Will now run personid update to make the "
"changes visible also on the front end and to "
"create person IDs for %s newly created and changed "
"authors." % len(updated_ras))
bibtask.task_update_progress('Updating persistent Person IDs')
bibtask.task_sleep_now_if_required(can_stop_too=False)
update_personID_from_algorithm(personid_ra_format)
bconfig.LOGGER.log(25, "Done updating everything. Thanks for flying "
"with bibauthorid!")
def _prepare_data_files_from_db(data_dir_name="grid_data",
workdir_prefix="job",
max_records=4000):
'''
Prepares grid jobs. Is a task running in bibsched.
Meaning:
1. Find all last names in the database
2. For each last name:
- find all documents regarding this last name (ignore first names)
- if number of documents loaded into memory exceeds max_records,
write the memory cache into files (cf. Files section).
Each write back procedure will happen into a newly created
directory. The prefix for the respective job directory may
be specified as well as the name of the data directory where
these job directories will be created.
Files:
- authornames.dat
- virtual_authors.dat
- virtual_author_data.dat
- virtual_author_clusters.dat
- virtual_author_cluster_cache.dat
- realauthors.dat
- realauthor_data.dat
- doclist.dat
- records.dat
- ids.dat
- ra_va_cache.dat
@param data_dir_name: the name of the directory that will hold all the
sub directories for the jobs.
@type data_dir_name: string
@param workdir_prefix: prefix for the job sub directories.
@type workdir_prefix: string
@param max_records: maximum number of records after which the memory
cache is to be flushed to files.
@type max_records: int
'''
try:
max_records = int(max_records)
except ValueError:
max_records = 4000
bibtask.write_message("Loading last names", stream=sys.stdout, verbose=0)
bibtask.write_message("Limiting files to %s records" % (max_records,),
stream=sys.stdout, verbose=0)
bibtask.task_update_progress('Loading last names...')
last_names = find_all_last_names()
last_name_queue = Queue.Queue()
for last_name in sorted(last_names):
last_name_queue.put(last_name)
total = len(last_names)
status = 1
bibtask.write_message("Done. Loaded %s last names."
% (total), stream=sys.stdout, verbose=0)
job_id = 0
data_dir = ""
if data_dir_name.startswith("/"):
data_dir = data_dir_name
else:
data_dir = "%s/%s/" % (bconfig.FILE_PATH, data_dir_name)
if not data_dir.endswith("/"):
data_dir = "%s/" % (data_dir,)
job_lnames = []
while True:
if last_name_queue.empty():
bibtask.write_message("Done with all names.",
stream=sys.stdout, verbose=0)
break
bibtask.task_sleep_now_if_required(can_stop_too=False)
lname_list = last_name_queue.get()
lname = None
if lname_list:
lname = lname_list[0]
del(lname_list[0])
else:
bconfig.LOGGER.warning("Got an empty Queue element. "
"Queue seems corrupted.")
continue
job_lnames.append(lname)
bibtask.task_update_progress('Preparing job %d of %d: %s.'
% (status, total, lname))
bibtask.write_message(("Processing: %s (%d/%d).")
% (lname, status, total),
stream=sys.stdout, verbose=0)
bibtask.task_sleep_now_if_required(can_stop_too=False)
populate_doclist_for_author_surname(lname)
post_remove_names = set()
for name in [row['name'] for row in dat.AUTHOR_NAMES
if not row['processed']]:
potential_removal = "%s," % (name.split(',')[0],)
if not potential_removal == "%s" % (lname,):
post_remove_names.add(potential_removal)
if len(post_remove_names) > 1:
removed = 0
removed_names = []
for post_remove_name in post_remove_names:
if post_remove_name in lname_list:
lname_list.remove(post_remove_name)
removed_names.append(post_remove_name)
removed += 1
bibtask.write_message(("-> Removed %s entries from the "
+ "computation list: %s")
% (removed, removed_names),
stream=sys.stdout, verbose=0)
total -= removed
if lname_list:
last_name_queue.put(lname_list)
if len(dat.RELEVANT_RECORDS) >= max_records:
if not os.path.exists(data_dir):
os.mkdir(data_dir)
work_dir = "%s%s%s" % (data_dir, workdir_prefix, job_id)
_write_to_files(work_dir, job_lnames)
bibtask.task_sleep_now_if_required(can_stop_too=True)
job_lnames = []
job_id += 1
status += 1
if dat.RELEVANT_RECORDS:
if not os.path.exists(data_dir):
os.mkdir(data_dir)
work_dir = "%s%s%s" % (data_dir, workdir_prefix, job_id)
_write_to_files(work_dir, job_lnames)
bibtask.task_sleep_now_if_required(can_stop_too=True)
return True
deleted_recs = dbinter.get_deleted_papers()
deleted_recs = frozenset(x[0] for x in deleted_recs)
if bconfig.TABLES_UTILS_DEBUG:
print "%d total deleted papers" % (len(deleted_recs),)
if personid:
personid_q = dbinter.list_2_SQL_str(personid, lambda x: str(x[0]))
else:
personid_q = None
counter = 0
rows_limit = 10000000
end_loop = False
while not end_loop:
task_sleep_now_if_required(can_stop_too=False)
papers_data = dbinter.collect_personid_papers(person=personid_q,
limit=(counter, rows_limit,))
if bconfig.TABLES_UTILS_DEBUG:
print "query with limit %d %d" % (counter, rows_limit)
if len(papers_data) == rows_limit:
counter += rows_limit
else:
end_loop = True
papers_data = tuple((extract_bibrec(p[3]), p) for p in papers_data)
to_remove = set()
jobs = dict()
for p in papers_data:
def _analyze_documents(
records,
taxonomy_name,
collection,
output_limit=bconfig.CFG_BIBCLASSIFY_DEFAULT_OUTPUT_NUMBER):
"""For each collection, parse the documents attached to the records
in collection with the corresponding taxonomy_name.
@var records: list of recids to process
@var taxonomy_name: str, name of the taxonomy, e.g. HEP
@var collection: str, collection name
@keyword output_limit: int, max number of keywords to extract [3]
@return: str, marcxml output format of results
"""
global _INDEX
if not records:
# No records could be found.
bibtask.write_message(
"WARNING: No records were found in collection %s." % collection,
stream=sys.stderr,
verbose=2)
return False
# Process records:
output = []
for record in records:
bibdocfiles = BibRecDocs(record).list_latest_files(
) # TODO: why this doesn't call list_all_files() ?
keywords = {}
akws = {}
acro = {}
single_keywords = composite_keywords = author_keywords = acronyms = None
for doc in bibdocfiles:
# Get the keywords for all PDF documents contained in the record.
if bibclassify_text_extractor.is_pdf(doc.get_full_path()):
bibtask.write_message(
'INFO: Generating keywords for record %d.' % record,
stream=sys.stderr,
verbose=3)
fulltext = doc.get_path()
single_keywords, composite_keywords, author_keywords, acronyms = \
bibclassify_engine.get_keywords_from_local_file(fulltext,
taxonomy_name, with_author_keywords=True, output_mode="raw",
output_limit=output_limit, match_mode='partial')
else:
bibtask.write_message(
'WARNING: BibClassify does not know how to process \
doc: %s (type: %s) -- ignoring it.' %
(doc.fullpath, doc.doctype),
stream=sys.stderr,
verbose=3)
if single_keywords or composite_keywords:
cleaned_single = bibclassify_engine.clean_before_output(
single_keywords)
cleaned_composite = bibclassify_engine.clean_before_output(
composite_keywords)
# merge the groups into one
keywords.update(cleaned_single)
keywords.update(cleaned_composite)
acro.update(acronyms)
akws.update(author_keywords)
if len(keywords):
output.append('<record>')
output.append('<controlfield tag="001">%s</controlfield>' % record)
output.append(
bibclassify_engine._output_marc(
keywords.items(), (),
akws,
acro,
spires=bconfig.CFG_SPIRES_FORMAT))
output.append('</record>')
else:
bibtask.write_message('WARNING: No keywords found for record %d.' %
record,
stream=sys.stderr,
verbose=0)
_INDEX += 1
bibtask.task_update_progress('Done %d out of %d.' %
(_INDEX, _RECIDS_NUMBER))
bibtask.task_sleep_now_if_required(can_stop_too=False)
return '\n'.join(output)
def _update_authorid_universe(record_ids=None, all_records=False):
'''
Updates all data related to the authorid algorithm.
Sequence of operations:
- Get all recently updated papers and remember time in the log
- Get all authors on all papers
- Extract collection of last names
- For each last name:
- Populate mem cache with cluster data
- Delete updated records and their virtual authors from mem cache
- Create virtual authors for new and updated records
- Start matching algorithm
- Update tables with results of the computation
- Start personid update procedure
'''
def create_vas_from_specific_doclist(bibrec_ids):
'''
Processes the document list and creates a new minimal virtual author
for each author in each record specified in the given list.
@param bibrec_ids: Record IDs to concern in this update
@type bibrec_ids: list of int
'''
num_docs = len(
[row for row in dat.DOC_LIST if row['bibrecid'] in bibrec_ids])
bconfig.LOGGER.log(
25, "Creating minimal virtual authors for "
"all loaded docs (%s)" % (num_docs))
for docs in [
row for row in dat.DOC_LIST if row['bibrecid'] in bibrec_ids
]:
for author_id in docs['authornameids']:
author_name = [
an['name'] for an in dat.AUTHOR_NAMES
if an['id'] == author_id
]
refrecs = [
ref[1] for ref in docs['authornameid_bibrefrec']
if ref[0] == author_id
]
refrec = -1
if len(refrecs) > 1:
refrec = refrecs[0]
elif refrecs:
refrec = refrecs[0]
if refrec and author_name:
add_minimum_virtualauthor(author_id, author_name[0],
docs['bibrecid'], 0, [], refrec)
elif author_name:
add_minimum_virtualauthor(author_id, author_name[0],
docs['bibrecid'], 0, [])
dat.reset_mem_cache(True)
last_log = None
updated_records = []
if not record_ids and not all_records:
last_log = get_user_log(userinfo='daemon',
action='update_aid',
only_most_recent=True)
if last_log:
#select only the most recent papers
recently_modified, last_update_time = get_papers_recently_modified(
date=last_log[0][2])
insert_user_log(
'daemon',
'-1',
'update_aid',
'bibsched',
'status',
comment='bibauthorid_daemon, update_authorid_universe',
timestamp=last_update_time[0][0])
bibtask.write_message(
"Update authorid will operate on %s records." %
(len(recently_modified)),
stream=sys.stdout,
verbose=0)
if not recently_modified:
bibtask.write_message("Update authorid: Nothing to do",
stream=sys.stdout,
verbose=0)
return
for rec in recently_modified:
updated_records.append(rec[0])
dat.update_log("rec_updates", rec[0])
else:
bibtask.write_message("Update authorid: Nothing to do",
stream=sys.stdout,
verbose=0)
return
elif record_ids and not all_records:
updated_records = record_ids
elif not record_ids and all_records:
bibtask.write_message("Update is going to empty all aid tables...",
stream=sys.stdout,
verbose=0)
empty_aid_tables()
bibtask.write_message("Update authorid will operate on all! records.",
stream=sys.stdout,
verbose=0)
bibtask.task_update_progress('Update is operating on all! records.')
start_full_disambiguation(process_orphans=True,
db_exists=False,
populate_doclist=True,
write_to_db=True)
bibtask.task_update_progress('Update is done.')
return
bibtask.task_sleep_now_if_required(can_stop_too=True)
authors = []
author_last_names = set()
bibtask.task_update_progress('Reading authors from updated records')
bibtask.write_message("Reading authors from updated records",
stream=sys.stdout,
verbose=0)
updated_ras = set()
# get all authors from all updated records
for rec in updated_records:
rec_authors = get_field_values_on_condition(rec, ['100', '700'],
"a",
source="API")
for rec_author in rec_authors:
if not rec_author:
bconfig.LOGGER.error("Invalid empty author string, which "
"will be skipped on record %s" % (rec))
continue
author_in_list = [
row for row in authors if row['db_name'] == rec_author
]
if author_in_list:
for upd in [
row for row in authors if row['db_name'] == rec_author
]:
upd['records'].append(rec)
else:
last_name = split_name_parts(rec_author)[0]
author_last_names.add(last_name)
authors.append({
'db_name': rec_author,
'records': [rec],
'last_name': last_name
})
for status, author_last_name in enumerate(author_last_names):
bibtask.task_sleep_now_if_required(can_stop_too=False)
current_authors = [
row for row in authors if row['last_name'] == author_last_name
]
total_lnames = len(author_last_names)
total_authors = len(current_authors)
bibtask.task_update_progress(
'Processing %s of %s cluster: "%s" '
'(%s authors)' %
(status + 1, total_lnames, author_last_name, total_authors))
bibtask.write_message(
'Processing %s of %s cluster: "%s" '
'(%s authors)' %
(status + 1, total_lnames, author_last_name, total_authors),
stream=sys.stdout,
verbose=0)
dat.reset_mem_cache(True)
init_authornames(author_last_name)
load_mem_cache_from_tables()
bconfig.LOGGER.log(
25, "-- Relevant data successfully read into memory"
" to start processing")
for current_author in current_authors:
load_records_to_mem_cache(current_author['records'])
authornamesid = [
row['id'] for row in dat.AUTHOR_NAMES
if row['db_name'] == current_author['db_name']
]
if not authornamesid:
bconfig.LOGGER.error(
"The author '%s' rec '%s' is not in authornames "
"and will be skipped. You might want "
"to run authornames update before?" %
(current_author['db_name'], rec))
continue
else:
try:
authornamesid = int(authornamesid[0])
except (IndexError, TypeError, ValueError):
bconfig.LOGGER.error("Invalid authornames ID!")
continue
if not current_author['records']:
bconfig.LOGGER.error("The author '%s' is not associated to any"
" document and will be skipped." %
(current_author['db_name']))
continue
for rec in current_author['records']:
# remove VAs already existing for the record
va_ids = get_va_ids_by_recid_lname(rec,
current_author["last_name"])
if va_ids:
for va_id in va_ids:
ra_list = get_realauthors_by_virtuala_id(va_id)
for ra_id in ra_list:
remove_va_from_ra(ra_id, va_id)
del_ra_data_by_vaid(ra_id, va_id)
va_anames_id = get_virtualauthor_records(
va_id, "orig_authorname_id")
for an_list in [
row['authornameids'] for row in dat.DOC_LIST
if row['bibrecid'] == rec
]:
try:
an_list.remove(va_anames_id)
except (ValueError):
# This names id is not in the list...don't care
pass
delete_virtual_author(va_id)
# create new VAs for the record.
update_doclist(rec, authornamesid)
dat.update_log("rec_updates", rec)
create_vas_from_specific_doclist(current_author['records'])
bconfig.LOGGER.log(25, "-- Relevant data pre-processed successfully.")
bibtask.task_sleep_now_if_required(can_stop_too=False)
start_computation(process_doclist=False,
process_orphans=True,
print_stats=True)
bconfig.LOGGER.log(
25, "-- Computation finished. Will write back to "
"the database now.")
update_db_result = update_tables_from_mem_cache(return_ra_updates=True)
bibtask.task_sleep_now_if_required(can_stop_too=True)
if not update_db_result[0]:
bconfig.LOGGER.log(25, "Writing to persistence layer failed.")
else:
if update_db_result[1]:
for updated_ra in update_db_result[1]:
if updated_ra:
updated_ras.add(updated_ra[0])
bconfig.LOGGER.log(25, "Done updating authorid universe.")
personid_ra_format = []
for ra_id in updated_ras:
personid_ra_format.append((ra_id, ))
bconfig.LOGGER.log(
25, "Will now run personid update to make the "
"changes visible also on the front end and to "
"create person IDs for %s newly created and changed "
"authors." % len(updated_ras))
bibtask.task_update_progress('Updating persistent Person IDs')
bibtask.task_sleep_now_if_required(can_stop_too=False)
update_personID_from_algorithm(personid_ra_format)
bconfig.LOGGER.log(
25, "Done updating everything. Thanks for flying "
"with bibauthorid!")
def rabbit(bibrecs, check_invalid_papers=False):
'''
@param bibrecs: an iterable full of bibrecs
@type bibrecs: an iterable of ints
@return: none
'''
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)
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 = 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 updated_pids: # an empty set will update all canonical_names
update_personID_canonical_names(updated_pids)