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bibauthorid_bib_matrix.py
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Fri, Mar 21, 01:23

bibauthorid_bib_matrix.py
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import invenio.bibauthorid_config as bconfig
import os
import shutil
from cPickle import dump, load, UnpicklingError
from invenio.bibauthorid_dbinterface import get_db_time
import h5py
class Bib_matrix(object):
'''
Contains the sparse matrix and encapsulates it.
'''
# please increment this value every time you
# change the output of the comparison functions
current_comparison_version = 0
__special_items = ((None, -3.), ('+', -2.), ('-', -1.))
special_symbols = dict((x[0], x[1]) for x in __special_items)
special_numbers = dict((x[1], x[0]) for x in __special_items)
def __init__(self, name, cluster_set=None, storage_dir_override=None):
self.name = name
self._f = None
self._matrix = None
self._use_temporary_file = True
self._size = None
self._storage_dir_override = storage_dir_override
if cluster_set:
self._bibmap = dict((b[1], b[0]) for b in enumerate(cluster_set.all_bibs()))
width = len(self._bibmap)
self._size = ((width + 1) * width) / 2
else:
self._bibmap = dict()
self._matrix = None
self.creation_time = get_db_time()
def _initialize_matrix(self):
self.open_h5py_file()
self._matrix = self._f.create_dataset("array", (self._size, 2), 'f')
self._matrix[...] = self.special_symbols[None]
def _resolve_entry(self, bibs):
first, second = bibs
first, second = self._bibmap[first], self._bibmap[second]
if first > second:
first, second = second, first
return first + (second * second + second) / 2
def __setitem__(self, bibs, val):
entry = self._resolve_entry(bibs)
try:
self._matrix[entry] = Bib_matrix.special_symbols.get(val, val)
except TypeError:
self._initialize_matrix()
self._matrix[entry] = Bib_matrix.special_symbols.get(val, val)
def __getitem__(self, bibs):
entry = self._resolve_entry(bibs)
try:
ret = self._matrix[entry]
except TypeError:
self._initialize_matrix()
ret = self._matrix[entry]
return Bib_matrix.special_numbers.get(ret[0], ret)
def getitem_numeric(self, bibs):
return self._matrix[self._resolve_entry(bibs)]
def __contains__(self, bib):
return bib in self._bibmap
def get_keys(self):
return self._bibmap.keys()
def get_file_dir(self):
if self._storage_dir_override:
return self._storage_dir_override
sub_dir = self.name[:2]
if not sub_dir:
sub_dir = "empty_last_name"
return "%s%s/" % (bconfig.TORTOISE_FILES_PATH, sub_dir)
def get_map_path(self):
return "%s%s-bibmap.pickle" % (self.get_file_dir(), self.name)
def get_matrix_path(self):
path = "%s%s.hdf5" % (self.get_file_dir(), self.name)
if self._use_temporary_file:
path = path + '.tmp'
return path
def open_h5py_file(self, create_empty_on_failure=True):
self._prepare_destination_directory()
path = self.get_matrix_path()
try:
self._f = h5py.File(path)
except IOError, e:
#If the file is corrupted h5py fails with IOErorr.
#Give it a second try with an empty file before raising.
if create_empty_on_failure:
os.remove(path)
self._f = h5py.File(path)
else:
raise e
def load(self):
self._use_temporary_file = False
files_dir = self.get_file_dir()
if not os.path.isdir(files_dir):
self._bibmap = dict()
self._matrix = None
return False
try:
with open(self.get_map_path(), 'r') as fp:
bibmap_v = load(fp)
rec_v, self.creation_time, self._bibmap = bibmap_v # pylint: disable=W0612
# if (rec_v != Bib_matrix.current_comparison_version or
# # you can use negative version to recalculate
# Bib_matrix.current_comparison_version < 0):
# self._bibmap = dict()
self._use_temporary_file = False
if self._f:
self._f.close()
self.open_h5py_file(create_empty_on_failure=False)
self._matrix = self._f['array']
except (IOError, UnpicklingError, KeyError, OSError), e:
print 'Bib_matrix: error occurred while loading bibmap, cleaning... ', str(type(e)), str(e)
self._bibmap = dict()
self._matrix = None
try:
os.remove(self.get_map_path())
except OSError:
pass
try:
os.remove(self.get_matrix_path())
except OSError:
pass
self._use_temporary_file = True
try:
os.remove(self.get_matrix_path())
except OSError:
pass
self._bibmap = dict()
self._matrix = None
self._use_temporary_file = True
return False
return True
def _prepare_destination_directory(self):
files_dir = self.get_file_dir()
if not os.path.isdir(files_dir):
try:
os.mkdir(files_dir)
except OSError, e:
if e.errno == 17 or 'file exists' in str(e.strerror).lower():
pass
else:
raise e
def store(self):
#save only if we are not completey empty:
if self._bibmap:
self._prepare_destination_directory()
bibmap_v = (Bib_matrix.current_comparison_version, self.creation_time, self._bibmap)
with open(self.get_map_path(), 'w') as fp:
dump(bibmap_v, fp)
if not self._matrix:
self._initialize_matrix()
if self._f:
self._f.close()
if self._use_temporary_file:
curpath = self.get_matrix_path()
self._use_temporary_file = False
finalpath = self.get_matrix_path()
try:
os.rename(curpath, finalpath)
except OSError, e:
raise e
def duplicate_existing(self, name, newname):
'''
Make sure the original Bib_matrix have been store()-ed before calling this!
'''
self._use_temporary_file = False
self.name = name
srcmap = self.get_map_path()
srcmat = self.get_matrix_path()
self.name = newname
dstmap = self.get_map_path()
dstmat = self.get_matrix_path()
shutil.copy(srcmap, dstmap)
shutil.copy(srcmat, dstmat)
def destroy(self):
if self._f:
self._f.close()
try:
os.remove(self.get_map_path())
except OSError:
pass
try:
os.remove(self.get_matrix_path())
except OSError:
pass
self._use_temporary_file = True
try:
os.remove(self.get_matrix_path())
except OSError:
pass
self._bibmap = dict()
self._matrix = None

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