def __delitem__(self, path):
test = self._node[datapath(path)]
if owner(test) == self._codelet.path:
del self._node[datapath(path)]
else:
raise ValueError("%s trying to remove data created by %s"
% (str(self._codelet.path), str(owner(test))))
def open_internal_file(self, path, mode='r', creator=None):
# path is always relative to the root group
if path.startswith('/'):
path = path[1:]
if not path.startswith('data/') \
and not path.startswith('documentation/'):
raise IOError((13, "Permission denied: '%s'" % path))
if creator is None:
creator = ExternalCode(self)
if mode[0] in ['r', 'a']:
ds = self.file[path]
elif mode[0] == 'w':
test = self.file.get(path, None)
if test is not None:
if not creator.owns(test):
raise ValueError("%s trying to overwrite data"
" created by %s"
% (creator.path, owner(test)))
del self.file[path]
ds = self.file.create_dataset(
path, shape = (0,), dtype = np.uint8,
chunks = (100,), maxshape = (None,))
else:
raise ValueError("unknown file mode %s" % mode)
return InternalFile(ds, mode)
def _wrap_and_track_dependencies(self, node):
ap_type = datatype(node)
if ap_type == 'reference':
from activepapers.storage import dereference
paper, node = dereference(node)
if isinstance(node, h5py.Group):
node = DataGroup(paper, None, node, None, None)
else:
node = DatasetWrapper(None, node, None)
else:
if self._codelet is not None:
if ap_type is not None and ap_type != "group":
self._codelet.add_dependency(node.name
if self._data_item is None
else self._data_item.name)
codelet = owner(node)
if codelet is not None \
and datatype(self._node[codelet]) == "calclet":
self._codelet.add_dependency(codelet)
if isinstance(node, h5py.Group):
node = DataGroup(self._paper, self, node,
self._codelet, self._data_item)
else:
node = DatasetWrapper(self, node, self._codelet)
return node
def open_internal_file(self, path, mode='r', encoding=None, creator=None):
# path is always relative to the root group
if path.startswith('/'):
path = path[1:]
if not path.startswith('data/') \
and not path.startswith('documentation/'):
raise IOError((13, "Permission denied: '%s'" % path))
if creator is None:
creator = ExternalCode(self)
if mode[0] in ['r', 'a']:
ds = self.file[path]
elif mode[0] == 'w':
test = self.file.get(path, None)
if test is not None:
if not creator.owns(test):
raise ValueError("%s trying to overwrite data"
" created by %s" %
(creator.path, owner(test)))
del self.file[path]
ds = self.file.create_dataset(path,
shape=(0, ),
dtype=np.uint8,
chunks=(100, ),
maxshape=(None, ))
else:
raise ValueError("unknown file mode %s" % mode)
return InternalFile(ds, mode, encoding)
def owned(group):
nodes = []
for node in group.values():
if owner(node) == codelet:
nodes.append(node.name)
elif isinstance(node, h5py.Group) \
and datatype(node) != 'data':
nodes.extend(owned(node))
return nodes
def owned(group):
nodes = []
for node in group.values():
if owner(node) == codelet:
nodes.append(node.name)
elif isinstance(node, h5py.Group) \
and datatype(node) != 'data':
nodes.extend(owned(node))
return nodes
def __repr__(self):
codelet = owner(self._node)
if codelet is None:
owned = ""
else:
owned = " generated by %s" % codelet
items = list(self._node)
if not items:
lines = ["Empty group %s%s" % (self._node.name, owned)]
else:
lines = ["Group %s%s containing" % (self._node.name, owned)]
lines.extend(" "+i for i in items)
return "\n".join(lines)
def __repr__(self):
codelet = owner(self._node)
if codelet is None:
owned = ""
else:
owned = " generated by %s" % codelet
lines = ["Dataset %s%s" % (self._node.name, owned)]
nelems = np.product(self._node.shape)
if nelems < 100:
lines.append(str(self._node[...]))
else:
lines.append("shape %s, dtype %s"
% (repr(self._node.shape), str(self._node.dtype)))
return "\n".join(lines)
def replace_by_dummy(self, item_name):
item = self.file[item_name]
codelet = owner(item)
assert codelet is not None
dtype = datatype(item)
mtime = mod_time(item)
deps = item.attrs.get('ACTIVE_PAPER_DEPENDENCIES')
del self.file[item_name]
ds = self.file.create_dataset(item_name,
data=np.zeros((), dtype=np.int))
stamp(ds, dtype,
dict(ACTIVE_PAPER_GENERATING_CODELET=codelet,
ACTIVE_PAPER_DEPENDENCIES=list(deps)))
timestamp(ds, mtime)
ds.attrs['ACTIVE_PAPER_DUMMY_DATASET'] = True
def replace_by_dummy(self, item_name):
item = self.file[item_name]
codelet = owner(item)
assert codelet is not None
dtype = datatype(item)
mtime = mod_time(item)
deps = item.attrs.get('ACTIVE_PAPER_DEPENDENCIES')
del self.file[item_name]
ds = self.file.create_dataset(item_name,
data=np.zeros((), dtype=np.int))
stamp(ds, dtype,
dict(ACTIVE_PAPER_GENERATING_CODELET=codelet,
ACTIVE_PAPER_DEPENDENCIES=list(deps)))
timestamp(ds, mtime)
ds.attrs['ACTIVE_PAPER_DUMMY_DATASET'] = True
def owns(self, node):
return owner(node) == self.path