def setUp(self):
"""
Set up an empty bibmatrix and one filled with ten clusters of 10 elements each.
"""
self.bm = Bib_matrix('testname', storage_dir_override='/tmp/')
self.css = ClusterSet()
self.css.clusters = [ClusterSet.Cluster(range(i*10,i*10+10)) for i in range(10)]
self.css.update_bibs()
self.bmcs0 = Bib_matrix('testname2', self.css, storage_dir_override='/tmp/')
def FIXME_1678_test_save_matrix(self):
'''
Matrix should save, be loadable, and stay equal to a newly loaded one on the same files
'''
self.bmcs0.store()
loaded = Bib_matrix('testname2', storage_dir_override='/tmp/')
self.assertTrue(loaded.load())
bmcs0 = self.bmcs0
for i in range(100):
for j in range(100):
self.assertTrue(bmcs0[i,j] == loaded[i,j])
def recalculate(self, cluster_set):
'''
Constructs probability matrix. If use_cache is true, it will
try to load old computations from the database. If save cache
is true it will save the current results into the database.
@param cluster_set: A cluster set object, used to initialize
the matrix.
'''
last_cleaned = 0
self._bib_matrix.store()
try:
old_matrix = Bib_matrix(self._bib_matrix.name + 'copy')
old_matrix.duplicate_existing(self._bib_matrix.name,
self._bib_matrix.name + 'copy')
old_matrix.load()
cached_bibs = self.__get_up_to_date_bibs(old_matrix)
have_cached_bibs = bool(cached_bibs)
except IOError:
old_matrix.destroy()
cached_bibs = None
have_cached_bibs = False
self._bib_matrix.destroy()
self._bib_matrix = Bib_matrix(cluster_set.last_name,
cluster_set=cluster_set)
ncl = cluster_set.num_all_bibs
expected = ((ncl * (ncl - 1)) / 2)
if expected == 0:
expected = 1
try:
cur_calc, opti, prints_counter = 0, 0, 0
for cl1 in cluster_set.clusters:
if cur_calc + opti - prints_counter > 100000 or cur_calc == 0:
update_status(
(float(opti) + cur_calc) / expected,
"Prob matrix: calc %d, opti %d." % (cur_calc, opti))
prints_counter = cur_calc + opti
# #clean caches
if cur_calc - last_cleaned > 20000000:
gc.collect()
# clear_comparison_caches()
last_cleaned = cur_calc
for cl2 in cluster_set.clusters:
if id(cl1) < id(cl2) and not cl1.hates(cl2):
for bib1 in cl1.bibs:
for bib2 in cl2.bibs:
if have_cached_bibs:
try:
val = old_matrix[bib1, bib2]
opti += 1
if bconfig.DEBUG_CHECKS:
assert _debug_is_eq_v(
val,
compare_bibrefrecs(bib1, bib2))
except KeyError:
cur_calc += 1
val = compare_bibrefrecs(bib1, bib2)
if not val:
cur_calc += 1
val = compare_bibrefrecs(bib1, bib2)
else:
cur_calc += 1
val = compare_bibrefrecs(bib1, bib2)
self._bib_matrix[bib1, bib2] = val
except Exception, e:
raise Exception("""Error happened in prob_matrix.recalculate with
val:%s
original_exception: %s
""" % (str(val), str(e)))
def __init__(self, name):
self._bib_matrix = Bib_matrix(name)
