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merge.py
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# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## Invenio is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
from operator import itemgetter
from itertools import groupby, chain, imap, izip
from invenio.bibauthorid_general_utils import update_status \
, update_status_final
from invenio.bibauthorid_matrix_optimization import maximized_mapping
from invenio.bibauthorid_backinterface import update_personID_canonical_names
from invenio.bibauthorid_backinterface import get_existing_result_clusters
from invenio.bibauthorid_backinterface import get_lastname_results
from invenio.bibauthorid_backinterface import personid_name_from_signature
from invenio.bibauthorid_backinterface import personid_from_signature
from invenio.bibauthorid_backinterface import move_signature
from invenio.bibauthorid_backinterface import get_claimed_papers
from invenio.bibauthorid_backinterface import get_new_personid
from invenio.bibauthorid_backinterface import find_conflicts
from invenio.bibauthorid_backinterface import get_free_pids as backinterface_get_free_pids
from invenio.bibauthorid_backinterface import get_signature_info
from invenio.bibauthorid_backinterface import delete_empty_persons
from invenio.bibauthorid_backinterface import get_bibrefrec_to_pid_flag_mapping
def merge_static_classy():
'''
This function merges aidPERSONIDPAPERS with aidRESULTS.
Use it after tortoise.
This function is static: if aid* tables are changed while it's running,
probably everything will crash and a black hole will open, eating all your data.
NOTE: this is more elegant that merge_static but much slower. Will have to be improved
before it can replace it.
'''
class Sig(object):
def __init__(self, bibrefrec, pid_flag):
self.rejected = dict(filter(lambda p: p[1] <= -2, pid_flag))
self.assigned = filter(lambda p:-2 < p[1] and p[1] < 2, pid_flag)
self.claimed = filter(lambda p: 2 <= p[1], pid_flag)
self.bibrefrec = bibrefrec
assert self.invariant()
def invariant(self):
return len(self.assigned) + len(self.claimed) <= 1
def empty(self):
return not self.isclaimed and not self.isassigned
def isclaimed(self):
return len(self.claimed) == 1
def get_claimed(self):
return self.claimed[0][0]
def get_assigned(self):
return self.assigned[0][0]
def isassigned(self):
return len(self.assigned) == 1
def isrejected(self, pid):
return pid in self.rejected
def change_pid(self, pid):
assert self.invariant()
assert self.isassigned()
self.assigned = [(pid, 0)]
move_signature(self.bibrefrec, pid)
class Cluster(object):
def __init__(self, pid, sigs):
self.pid = pid
self.sigs = dict((sig.bibrefrec[2], sig) for sig in sigs if not sig.empty())
def send_sig(self, other, sig):
paper = sig.bibrefrec[2]
assert paper in self.sigs and paper not in other.sigs
del self.sigs[paper]
other.sigs[paper] = sig
if sig.isassigned():
sig.change_pid(other.pid)
last_names = frozenset(name[0].split('.')[0] for name in get_existing_result_clusters())
personid = get_bibrefrec_to_pid_flag_mapping()
free_pids = backinterface_get_free_pids()
for idx, last in enumerate(last_names):
update_status(float(idx) / len(last_names), "Merging, %d/%d current: %s" % (idx, len(last_names), last))
results = ((int(row[0].split(".")[1]), row[1:4]) for row in get_lastname_results(last))
# [(last name number, [bibrefrecs])]
results = [(k, map(itemgetter(1), d)) for k, d in groupby(sorted(results, key=itemgetter(0)), key=itemgetter(0))]
# List of dictionaries.
# [{new_pid -> N}]
matr = []
# Set of all old pids.
old_pids = set()
for k, ds in results:
pids = []
for d in ds:
pid_flag = filter(lambda x: x[1] > -2, personid.get(d, []))
if pid_flag:
assert len(pid_flag) == 1
pid = pid_flag[0][0]
pids.append(pid)
old_pids.add(pid)
matr.append(dict((k, len(list(d))) for k, d in groupby(sorted(pids))))
old_pids = list(old_pids)
best_match = maximized_mapping([[row.get(old, 0) for old in old_pids] for row in matr])
# [[bibrefrecs] -> pid]
matched_clusters = [(results[new_idx][1], old_pids[old_idx]) for new_idx, old_idx, _ in best_match]
not_matched_clusters = frozenset(xrange(len(results))) - frozenset(imap(itemgetter(0), best_match))
not_matched_clusters = izip((results[i][1] for i in not_matched_clusters), free_pids)
# pid -> Cluster
clusters = dict((pid, Cluster(pid, [Sig(bib, personid.get(bib, [])) for bib in sigs]))
for sigs, pid in chain(matched_clusters, not_matched_clusters))
todo = clusters.items()
for pid, clus in todo:
assert clus.pid == pid
for paper, sig in clus.sigs.items():
if sig.isclaimed():
if sig.get_claimed() != pid:
target_clus = clusters[sig.get_claimed()]
if paper in target_clus.sigs:
new_clus = Cluster(free_pids.next(), [])
target_clus.send_sig(new_clus, target_clus[paper])
todo.append(new_clus)
clusters[new_clus.pid] = new_clus
assert paper not in target_clus.sigs
clus.send_sig(target_clus, sig)
elif sig.get_assigned() != pid:
if not sig.isrejected(pid):
move_signature(sig.bibrefrec, pid)
else:
move_signature(sig.bibrefrec, free_pids.next())
else:
assert not sig.isrejected(pid)
update_status_final("Merging done.")
update_status_final()
delete_empty_persons()
update_personID_canonical_names()
def merge_static():
'''
This function merges aidPERSONIDPAPERS with aidRESULTS.
Use it after tortoise.
This function is static: if aid* tables are changed while it's running,
probably everything will crash and a black hole will open, eating all your data.
'''
last_names = frozenset(name[0].split('.')[0] for name in get_existing_result_clusters())
def get_free_pids():
while True:
yield get_new_personid()
free_pids = get_free_pids()
current_mapping = get_bibrefrec_to_pid_flag_mapping()
def move_sig_and_update_mapping(sig, old_pid_flag, new_pid_flag):
move_signature(sig, new_pid_flag[0])
current_mapping[sig].remove(old_pid_flag)
current_mapping[sig].append(new_pid_flag)
def try_move_signature(sig, target_pid):
"""
"""
paps = current_mapping[sig]
rejected = filter(lambda p: p[1] <= -2, paps)
assigned = filter(lambda p:-2 < p[1] and p[1] < 2, paps)
claimed = filter(lambda p: 2 <= p[1] and p[0] == target_pid, paps)
if claimed or not assigned or assigned[0] == target_pid:
return
assert len(assigned) == 1
if rejected:
newpid = free_pids.next()
move_sig_and_update_mapping(sig, assigned[0], (newpid, assigned[0][1]))
else:
conflicts = find_conflicts(sig, target_pid)
if not conflicts:
move_sig_and_update_mapping(sig, assigned[0], (target_pid, assigned[0][1]))
else:
assert len(conflicts) == 1
if conflicts[0][3] == 2:
newpid = free_pids.next()
move_sig_and_update_mapping(sig, assigned[0], (newpid, assigned[0][1]))
else:
newpid = free_pids.next()
csig = tuple(conflicts[0][:3])
move_sig_and_update_mapping(csig, (target_pid, conflicts[0][3]), (newpid, conflicts[0][3]))
move_sig_and_update_mapping(sig, assigned[0], (target_pid, assigned[0][1]))
for idx, last in enumerate(last_names):
update_status(float(idx) / len(last_names), "%d/%d current: %s" % (idx, len(last_names), last))
results = ((int(row[0].split(".")[1]), row[1:4]) for row in get_lastname_results(last))
# [(last name number, [bibrefrecs])]
results = [(k, map(itemgetter(1), d)) for k, d in groupby(sorted(results, key=itemgetter(0)), key=itemgetter(0))]
# List of dictionaries.
# [{new_pid -> N}]
matr = []
# Set of all old pids.
old_pids = set()
for k, ds in results:
pids = []
claim = []
for d in ds:
pid_flag = current_mapping.get(d, [])
if pid_flag:
pid, flag = pid_flag[0]
pids.append(pid)
old_pids.add(pid)
if flag > 1:
claim.append((d, pid))
matr.append(dict((k, len(list(d))) for k, d in groupby(sorted(pids))))
# We cast it to list in order to ensure the order persistence.
old_pids = list(old_pids)
best_match = maximized_mapping([[row.get(old, 0) for old in old_pids] for row in matr])
matched_clusters = [(results[new_idx][1], old_pids[old_idx]) for new_idx, old_idx, _ in best_match]
not_matched_clusters = frozenset(xrange(len(results))) - frozenset(imap(itemgetter(0), best_match))
not_matched_clusters = izip((results[i][1] for i in not_matched_clusters), free_pids)
for sigs, pid in chain(matched_clusters, not_matched_clusters):
for sig in sigs:
if sig in current_mapping:
if not pid in map(itemgetter(0), filter(lambda x: x[1] > -2, current_mapping[sig])):
try_move_signature(sig, pid)
update_status_final()
delete_empty_persons()
update_personID_canonical_names()
def merge_dynamic():
'''
This function merges aidPERSONIDPAPERS with aidRESULTS.
Use it after tortoise.
This function is dynamic: it allows aid* tables to be changed while it is still running,
hence the claiming faciity for example can stay online during the merge. This comfort
however is paid off in term of speed.
'''
last_names = frozenset(name[0].split('.')[0] for name in get_existing_result_clusters())
def get_free_pids():
while True:
yield get_new_personid()
free_pids = get_free_pids()
def try_move_signature(sig, target_pid):
"""
"""
paps = get_signature_info(sig)
rejected = filter(lambda p: p[1] <= -2, paps)
assigned = filter(lambda p:-2 < p[1] and p[1] < 2, paps)
claimed = filter(lambda p: 2 <= p[1] and p[0] == target_pid, paps)
if claimed or not assigned or assigned[0] == target_pid:
return
assert len(assigned) == 1
if rejected:
move_signature(sig, free_pids.next())
else:
conflicts = find_conflicts(sig, target_pid)
if not conflicts:
move_signature(sig, target_pid)
else:
assert len(conflicts) == 1
if conflicts[0][3] == 2:
move_signature(sig, free_pids.next())
else:
move_signature(conflicts[0][:3], free_pids.next())
move_signature(sig, target_pid)
for idx, last in enumerate(last_names):
update_status(float(idx) / len(last_names), "%d/%d current: %s" % (idx, len(last_names), last))
results = ((int(row[0].split(".")[1]), row[1:4]) for row in get_lastname_results(last))
# [(last name number, [bibrefrecs])]
results = [(k, map(itemgetter(1), d)) for k, d in groupby(sorted(results, key=itemgetter(0)), key=itemgetter(0))]
# List of dictionaries.
# [{new_pid -> N}]
matr = []
# Set of all old pids.
old_pids = set()
for k, ds in results:
pids = []
claim = []
for d in ds:
pid_flag = personid_from_signature(d)
if pid_flag:
pid, flag = pid_flag[0]
pids.append(pid)
old_pids.add(pid)
if flag > 1:
claim.append((d, pid))
matr.append(dict((k, len(list(d))) for k, d in groupby(sorted(pids))))
# We cast it to list in order to ensure the order persistence.
old_pids = list(old_pids)
best_match = maximized_mapping([[row.get(old, 0) for old in old_pids] for row in matr])
matched_clusters = [(results[new_idx][1], old_pids[old_idx]) for new_idx, old_idx, _ in best_match]
not_matched_clusters = frozenset(xrange(len(results))) - frozenset(imap(itemgetter(0), best_match))
not_matched_clusters = izip((results[i][1] for i in not_matched_clusters), free_pids)
for sigs, pid in chain(matched_clusters, not_matched_clusters):
for sig in sigs:
try_move_signature(sig, pid)
update_status_final()
delete_empty_persons()
update_personID_canonical_names()
def matched_claims(inspect=None):
'''
Checks how many claims are violated in aidRESULTS.
Returs the number of preserved and the total number of claims.
'''
last_names = frozenset(name[0].split('.')[0] for name in get_existing_result_clusters())
r_match = 0
r_total = 0
for lname in last_names:
if inspect and lname != inspect:
continue
results_dict = dict(((row[1], row[2], row[3]), int(row[0].split(".")[1]))
for row in get_lastname_results(lname))
results_clusters = max(results_dict.values()) + 1
assert frozenset(results_dict.values()) == frozenset(range(results_clusters))
pids = frozenset(x[0] for x in chain.from_iterable(personid_name_from_signature(r) for r in results_dict.keys()))
matr = ((results_dict[x] for x in get_claimed_papers(pid) if x in results_dict) for pid in pids)
matr = (dict((k, len(list(d))) for k, d in groupby(sorted(row))) for row in matr)
matr = [[row.get(i, 0) for i in xrange(results_clusters)] for row in matr]
r_match += sum(m[2] for m in maximized_mapping(matr))
r_total += sum(sum(row) for row in matr)
return r_match, r_total

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