def store_python_code(self, path, code):
self.assert_is_open()
if not isstring(code):
raise TypeError("Python code must be a string")
ds = self.code_group.require_dataset(path,
dtype=h5vstring, shape = ())
ds[...] = code
ds.attrs['ACTIVE_PAPER_LANGUAGE'] = "python"
return ds
def store_python_code(self, path, code):
self.assert_is_open()
if not isstring(code):
raise TypeError("Python code must be a string (is %s)" %
str(type(code)))
ds = self.code_group.require_dataset(path, dtype=h5vstring, shape=())
ds[...] = code.encode('utf-8')
ds.attrs['ACTIVE_PAPER_LANGUAGE'] = "python"
return ds
def __getitem__(self, path_or_ref):
if isstring(path_or_ref):
path = codepath(path_or_ref)
else:
path = self._node[path_or_ref].name
assert path.startswith('/code')
node = self._node[path]
if isinstance(node, h5py.Group):
return CodeGroup(self._paper, node)
else:
return CodeFile(self._paper, node)
def __getitem__(self, path_or_ref):
if isstring(path_or_ref):
path = datapath(path_or_ref)
else:
path = self._node[path_or_ref].name
assert path.startswith('/data')
path = path.split('/')
if path[0] == '':
# datapath() ensures that path must start with
# ['', 'data'] in this case. Move up the parent
# chain to the root of the /data hierarchy.
path = path[2:]
node = self
while node is not node.parent:
node = node.parent
else:
node = self
for element in path:
node = node._wrap_and_track_dependencies(node._node[element])
return node
def __init__(self, filename, mode="r", dependencies=None):
self.filename = filename
self.file = h5py.File(filename, mode)
self.open = True
self.writable = False
if mode[0] == 'r':
assert dependencies is None
if ascii(self.file.attrs['DATA_MODEL']) != 'active-papers-py':
raise ValueError("File %s is not an ActivePaper" % filename)
self.code_group = self.file["code"]
self.data_group = self.file["data"]
self.documentation_group = self.file["documentation"]
self.writable = '+' in mode
self.history = self.file['history']
deps = self.file.get('external-dependencies/'
'python-packages', None)
if deps is None:
self.dependencies = []
else:
self.dependencies = [ascii(n) for n in deps]
for module_name in self.dependencies:
importlib.import_module(module_name)
elif mode[0] == 'w':
self.file.attrs['DATA_MODEL'] = ascii('active-papers-py')
self.file.attrs['DATA_MODEL_MAJOR_VERSION'] = 0
self.file.attrs['DATA_MODEL_MINOR_VERSION'] = 1
self.code_group = self.file.create_group("code")
self.data_group = self.file.create_group("data")
self.documentation_group = self.file.create_group("documentation")
deps = self.file.create_group('external-dependencies')
if dependencies is None:
self.dependencies = []
else:
for module_name in dependencies:
assert isstring(module_name)
importlib.import_module(module_name)
self.dependencies = dependencies
deps.create_dataset('python-packages',
data = dependencies)
htype = np.dtype([('opened', np.int64),
('closed', np.int64),
('platform', h5vstring),
('hostname', h5vstring),
('username', h5vstring)]
+ [(name+"_version", h5vstring)
for name in ['activepapers','python',
'numpy', 'h5py', 'hdf5']
+ self.dependencies])
self.history = self.file.create_dataset("history", shape=(0,),
dtype=htype,
chunks=(1,),
maxshape=(None,))
readme = self.file.create_dataset("README",
dtype=h5vstring, shape = ())
readme[...] = readme_text
self.writable = True
if self.writable:
self.update_history(close=False)
import activepapers.utility
self.data = DataGroup(self, None, self.data_group, ExternalCode(self))
self.imported_modules = {}
self._local_modules = {}
paper_id = hex(id(self))[2:]
paper_registry[paper_id] = self
def forbidden(cls, key):
return isstring(key) and key.startswith('ACTIVE_PAPER')
def __init__(self, filename, mode="r", dependencies=None):
self.filename = filename
self.file = h5py.File(filename, mode)
self.open = True
self.writable = False
if mode[0] == 'r':
assert dependencies is None
if ascii(self.file.attrs['DATA_MODEL']) != 'active-papers-py':
raise ValueError("File %s is not an ActivePaper" % filename)
self.code_group = self.file["code"]
self.data_group = self.file["data"]
self.documentation_group = self.file["documentation"]
self.writable = '+' in mode
self.history = self.file['history']
deps = self.file.get('external-dependencies/'
'python-packages', None)
if deps is None:
self.dependencies = []
else:
self.dependencies = [ascii(n) for n in deps]
for module_name in self.dependencies:
importlib.import_module(module_name)
elif mode[0] == 'w':
self.file.attrs['DATA_MODEL'] = ascii('active-papers-py')
self.file.attrs['DATA_MODEL_MAJOR_VERSION'] = 0
self.file.attrs['DATA_MODEL_MINOR_VERSION'] = 1
self.code_group = self.file.create_group("code")
self.data_group = self.file.create_group("data")
self.documentation_group = self.file.create_group("documentation")
deps = self.file.create_group('external-dependencies')
if dependencies is None:
self.dependencies = []
else:
for module_name in dependencies:
assert isstring(module_name)
importlib.import_module(module_name)
self.dependencies = dependencies
ds = deps.create_dataset('python-packages',
dtype=h5vstring,
shape=(len(dependencies), ))
ds[:] = dependencies
htype = np.dtype(
[('opened', np.int64), ('closed',
np.int64), ('platform', h5vstring),
('hostname', h5vstring), ('username', h5vstring)] +
[(name + "_version", h5vstring) for name in
['activepapers', 'python', 'numpy', 'h5py', 'hdf5'] +
self.dependencies])
self.history = self.file.create_dataset("history",
shape=(0, ),
dtype=htype,
chunks=(1, ),
maxshape=(None, ))
readme = self.file.create_dataset("README",
dtype=h5vstring,
shape=())
readme[...] = readme_text
self.writable = True
if self.writable:
self.update_history(close=False)
import activepapers.utility
self.data = DataGroup(self, None, self.data_group, ExternalCode(self))
self.imported_modules = {}
self._local_modules = {}
paper_registry[self._id()] = self
