def update_virtualauthor_record(va_id, tag, value):
'''
Change the value associated to the given tag for a certain virtual author
@param va_id: ID of the virtual author
@type va_id: int
@param tag: tag to be updated
@type tag: string
@param value: value to be written for the tag
@type value: string
'''
current_tag_value = [row for row in dat.VIRTUALAUTHOR_DATA
if ((row['virtualauthorid'] == va_id)
and (row['tag'] == tag))]
if len(current_tag_value) > 0:
for tagupdate in [row for row in dat.VIRTUALAUTHOR_DATA
if ((row['virtualauthorid'] == va_id)
and (row['tag'] == tag))]:
tagupdate['tag'] = tag
tagupdate['value'] = value
dat.update_log("touched_vas", va_id)
else:
add_virtualauthor_record(va_id, tag, value)
def delete_virtual_author(va_id):
'''
This will delete a virtual author while cascading the change through the
different storages and instances: ra_data, ras, va_data and vas
@param va_id: the virtual author to be deleted
@type va_id: int
@return: success or failure of the process
@rtype: boolean
'''
if not isinstance(va_id, int):
try:
va_id = int(va_id)
except (ValueError, TypeError):
raise ValueError("Expecting the va id to be an int.")
tags = get_virtualauthor_record_tags()
for tag in tags:
delete_virtualauthor_record(va_id, tag)
for deletion_candidate in list([row for row in dat.VIRTUALAUTHORS
if row['virtualauthorid'] == va_id]):
dat.VIRTUALAUTHORS.remove(deletion_candidate)
dat.update_log("deleted_vas", va_id)
return True
def update_virtualauthor_record(va_id, tag, value):
'''
Change the value associated to the given tag for a certain virtual author
@param va_id: ID of the virtual author
@type va_id: int
@param tag: tag to be updated
@type tag: string
@param value: value to be written for the tag
@type value: string
'''
current_tag_value = [
row for row in dat.VIRTUALAUTHOR_DATA
if ((row['virtualauthorid'] == va_id) and (row['tag'] == tag))
]
if len(current_tag_value) > 0:
for tagupdate in [
row for row in dat.VIRTUALAUTHOR_DATA
if ((row['virtualauthorid'] == va_id) and (row['tag'] == tag))
]:
tagupdate['tag'] = tag
tagupdate['value'] = value
dat.update_log("touched_vas", va_id)
else:
add_virtualauthor_record(va_id, tag, value)
def delete_virtual_author(va_id):
'''
This will delete a virtual author while cascading the change through the
different storages and instances: ra_data, ras, va_data and vas
@param va_id: the virtual author to be deleted
@type va_id: int
@return: success or failure of the process
@rtype: boolean
'''
if not isinstance(va_id, int):
try:
va_id = int(va_id)
except (ValueError, TypeError):
raise ValueError("Expecting the va id to be an int.")
tags = get_virtualauthor_record_tags()
for tag in tags:
delete_virtualauthor_record(va_id, tag)
for deletion_candidate in list(
[row for row in dat.VIRTUALAUTHORS
if row['virtualauthorid'] == va_id]):
dat.VIRTUALAUTHORS.remove(deletion_candidate)
dat.update_log("deleted_vas", va_id)
return True
def delete_virtualauthor_record(va_id, tag):
'''
Remove a tag field from the virtualauthor_data table
@param va_id: ID of the virtual author
@type va_id: int
@param tag: tag of the record to be deleted
@type tag: string
'''
for tagupdate in list([row for row in dat.VIRTUALAUTHOR_DATA
if ((row['virtualauthorid'] == va_id)
and (row['tag'] == tag))]):
dat.VIRTUALAUTHOR_DATA.remove(tagupdate)
dat.update_log("touched_vas", va_id)
def delete_virtualauthor_record(va_id, tag):
'''
Remove a tag field from the virtualauthor_data table
@param va_id: ID of the virtual author
@type va_id: int
@param tag: tag of the record to be deleted
@type tag: string
'''
for tagupdate in list([
row for row in dat.VIRTUALAUTHOR_DATA
if ((row['virtualauthorid'] == va_id) and (row['tag'] == tag))
]):
dat.VIRTUALAUTHOR_DATA.remove(tagupdate)
dat.update_log("touched_vas", va_id)
def create_new_realauthor(va_id):
"""
Create a new real author connected to the given virtual author; the trust
value for the virtual author is obviously 1 because this virtual author is
incompatible with every other real author and is the first
one in this new real author.
RETURNS: the newly created realauthorid
"""
current_ra_id = dat.increment_tracker("raid_counter")
dat.REALAUTHORS.append({"realauthorid": current_ra_id, "virtualauthorid": va_id, "p": 1})
dat.update_log("new_ras", current_ra_id)
update_realauthor_data_by_vid(current_ra_id, va_id)
# update_realauthor_names(current_ra_id)
return current_ra_id
def create_new_realauthor(va_id):
"""
Create a new real author connected to the given virtual author; the trust
value for the virtual author is obviously 1 because this virtual author is
incompatible with every other real author and is the first
one in this new real author.
RETURNS: the newly created realauthorid
"""
current_ra_id = dat.increment_tracker("raid_counter")
dat.REALAUTHORS.append({'realauthorid': current_ra_id,
'virtualauthorid': va_id,
'p': 1})
dat.update_log("new_ras", current_ra_id)
update_realauthor_data_by_vid(current_ra_id, va_id)
# update_realauthor_names(current_ra_id)
return current_ra_id
def add_virtualauthor_record(va_id, tag, value):
'''
Adds a record to the virtualauthor_data table
@param va_id: id of the virtual author to attach the attribute to
@type va_id: int
@param tag: tag to alter the value of
@type tag: string
@param value: the new value of the tag
@type value: string
'''
dat.VIRTUALAUTHOR_DATA.append({'virtualauthorid': va_id,
'tag': tag,
'value': value})
if not tag == "updated":
update_virtualauthor_record(va_id, 'updated', 'True')
dat.update_log("touched_vas", va_id)
def add_virtualauthor_record(va_id, tag, value):
'''
Adds a record to the virtualauthor_data table
@param va_id: id of the virtual author to attach the attribute to
@type va_id: int
@param tag: tag to alter the value of
@type tag: string
@param value: the new value of the tag
@type value: string
'''
dat.VIRTUALAUTHOR_DATA.append({
'virtualauthorid': va_id,
'tag': tag,
'value': value
})
if not tag == "updated":
update_virtualauthor_record(va_id, 'updated', 'True')
dat.update_log("touched_vas", va_id)
def add_minimum_virtualauthor(orig_authornames_id,
orig_name_string,
bibrec_id,
author_index,
authorname_p_list,
refrec=""):
'''
Adds a complete virtual author to the virtual authors table.
@param orig_authornames_id: ID of the name in authornames table
@type orig_authornames_id: int
@param orig_name_string: String of the author name
@type orig_name_string: string
@param bibrec_id: ID of the record
@type bibrec_id: int
@param author_index: number of the author
@type author_index: int
@param authorname_p_list: list of authornamesID with confidence index
associated [[id1,p], [id2,p], .., [idn,p]]
@type authorname_p_list: list of lists
@param refrec: The bibref-bibrec pair of this author on a paper in format
"100:14424,12441"
@type refrec: string
'''
if authorname_p_list:
pass
current_va = create_new_virtualauthor(orig_authornames_id,
orig_name_string)
add_virtualauthor_record(current_va, 'bibrec_id', bibrec_id)
add_virtualauthor_record(current_va, 'author_index', author_index)
if refrec:
pair = "%s,%s" % (refrec, bibrec_id)
add_virtualauthor_record(current_va, 'bibrefrecpair', pair)
dat.update_log("new_vas", current_va)
update_virtualauthor_cluster(current_va)
def add_minimum_virtualauthor(orig_authornames_id,
orig_name_string,
bibrec_id,
author_index,
authorname_p_list,
refrec=""):
'''
Adds a complete virtual author to the virtual authors table.
@param orig_authornames_id: ID of the name in authornames table
@type orig_authornames_id: int
@param orig_name_string: String of the author name
@type orig_name_string: string
@param bibrec_id: ID of the record
@type bibrec_id: int
@param author_index: number of the author
@type author_index: int
@param authorname_p_list: list of authornamesID with confidence index
associated [[id1,p], [id2,p], .., [idn,p]]
@type authorname_p_list: list of lists
@param refrec: The bibref-bibrec pair of this author on a paper in format
"100:14424,12441"
@type refrec: string
'''
if authorname_p_list:
pass
current_va = create_new_virtualauthor(orig_authornames_id,
orig_name_string)
add_virtualauthor_record(current_va, 'bibrec_id', bibrec_id)
add_virtualauthor_record(current_va, 'author_index', author_index)
if refrec:
pair = "%s,%s" % (refrec, bibrec_id)
add_virtualauthor_record(current_va, 'bibrefrecpair', pair)
dat.update_log("new_vas", current_va)
update_virtualauthor_cluster(current_va)
def _update_authorid_universe():
'''
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:
print "SCREEEEEEWWWWWWED!!! Several bibrefs on one paper?!"
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 = get_user_log(userinfo='daemon',
action='update_aid',
only_most_recent=True)
updated_records = []
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
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):
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.")
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)
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')
update_personID_from_algorithm(personid_ra_format)
bconfig.LOGGER.log(25, "Done updating everything. Thanks for flying "
"with bibauthorid!")
def _update_authorid_universe():
'''
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:
print "SCREEEEEEWWWWWWED!!! Several bibrefs on one paper?!"
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 = get_user_log(userinfo='daemon',
action='update_aid',
only_most_recent=True)
updated_records = []
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
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):
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.")
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)
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')
update_personID_from_algorithm(personid_ra_format)
bconfig.LOGGER.log(
25, "Done updating everything. Thanks for flying "
"with bibauthorid!")