def __init__(self, path=None):
import punx.cache_manager
if path is None:
cm = punx.cache_manager.CacheManager()
if cm is None or cm.default_file_set is None:
raise ValueError('Could not get NXDL file set from the cache')
path = cm.default_file_set.path
schema_file = os.path.join(path, 'nxdl.xsd')
if not os.path.exists(schema_file):
raise punx.FileNotFound(schema_file)
self.schema_file = schema_file
if not os.path.exists(self.schema_file):
raise punx.FileNotFound('XML Schema file: ' + self.schema_file)
self.lxml_tree = lxml.etree.parse(self.schema_file)
self.lxml_schema = lxml.etree.XMLSchema(self.lxml_tree)
self.lxml_root = self.lxml_tree.getroot()
nodes = self.lxml_root.xpath('xs:element', namespaces=self.ns)
if len(nodes) != 1:
raise punx.InvalidNxdlFile(self.schema_file)
self.nxdl = Schema_Root(nodes[0],
ns_dict=self.ns,
schema_root=self.lxml_root,
schema_manager=self)
# cleanup these internal structures
del self.lxml_root
#del self.lxml_schema # needed for XML file validation
del self.lxml_tree
def __init__(self, filename):
'''store filename and test if file is NeXus HDF5'''
self.requested_filename = filename
self.filename = None
self.show_attributes = True
if os.path.exists(filename):
self.filename = filename
self.isNeXus = isNeXusFile(filename)
else:
raise punx.FileNotFound(filename)
def abs_NXDL_filename(file_name):
'''return absolute path to file_name, within NXDL directory'''
import punx.cache_manager
cm = punx.cache_manager.CacheManager()
punx.LOG_MESSAGE('file_name: ' + str(file_name), punx.DEBUG)
punx.LOG_MESSAGE('cm.default_file_set: ' + str(cm.default_file_set), punx.DEBUG)
if cm.default_file_set is None:
raise ValueError('no default file set')
absolute_name = os.path.abspath(os.path.join(cm.default_file_set.path, file_name))
if not os.path.exists(absolute_name):
msg = 'file does not exist: ' + absolute_name
raise punx.FileNotFound(msg)
punx.LOG_MESSAGE('user cache: ' + absolute_name, punx.DEBUG)
return absolute_name
def get_NXDL_file_list(nxdl_dir):
'''
return a list of all NXDL files in the ``nxdl_dir``
'''
if not os.path.exists(nxdl_dir):
raise punx.FileNotFound('NXDL directory: ' + nxdl_dir)
NXDL_categories = 'base_classes applications contributed_definitions'.split(
)
nxdl_file_list = []
for category in NXDL_categories:
path = os.path.join(nxdl_dir, category)
if not os.path.exists(path):
raise IOError('no definition available, cannot find ' + path)
for fname in sorted(os.listdir(path)):
if fname.endswith('.nxdl.xml'):
nxdl_file_list.append(os.path.join(path, fname))
return nxdl_file_list
def __init__(self, file_set):
import punx.cache_manager
assert (isinstance(file_set, punx.cache_manager.NXDL_File_Set))
if file_set.path is None or not os.path.exists(file_set.path):
raise punx.FileNotFound('NXDL directory: ' + str(file_set.path))
self.nxdl_file_set = file_set
self.classes = collections.OrderedDict()
# get_element = file_set.nxdl_element_factory.get_element
for nxdl_file_name in get_NXDL_file_list(file_set.path):
definition = NXDL_element__definition(file_set.path) # the default
obj = copy.deepcopy(definition) # ALWAYS make a copy of that
# TODO: adjust minOccurs defaults for application definition or contributed definition
obj.set_file(nxdl_file_name)
obj.parse()
self.classes[obj.title] = obj
def read_info_file(self, file_name=None):
if file_name is None and self.ref is None:
raise ValueError('NXDL_File_Set() does not refer to any files')
file_name = file_name or self.info
if not os.path.exists(file_name):
raise punx.FileNotFound('info file not found: ' + file_name)
self.info = file_name
self.path = os.path.abspath(os.path.dirname(file_name))
if self.path.find(os.path.join('punx', 'cache')) > 0:
self.cache = u'source'
else:
self.cache = u'user'
# read the NXDL file set's info file for GitHub information
obj = read_json_file(file_name)
for k in self.json_file_keys:
self.__setattr__(k, obj.get(k))
def report(self, show_attributes=True):
'''
return the structure of the HDF5 file in a list of strings
The work of parsing the datafile is done in this method.
'''
if self.filename is None: return None
if not os.path.exists(self.filename):
raise punx.FileNotFound(self.filename)
self.show_attributes = show_attributes
try:
f = h5py.File(self.filename, 'r')
except IOError:
raise punx.HDF5_Open_Error(self.filename)
txt = self.filename
if self.isNeXus:
txt += " : NeXus data file"
structure = self._renderGroup(f, txt, indentation="")
f.close()
return structure
def parse_nxdlTypes(self):
'''
get the allowed data types and unit types from nxdlTypes.xsd
'''
if os.path.exists(self.schema_file):
path = os.path.dirname(self.schema_file)
else:
import punx.cache_manager
cm = punx.cache_manager.CacheManager()
if cm is None or cm.default_file_set is None:
raise ValueError('Could not get NXDL file set from the cache')
path = cm.default_file_set.path
self.types_file = os.path.join(path, 'nxdlTypes.xsd')
if not os.path.exists(self.types_file):
raise punx.FileNotFound(self.types_file)
lxml_types_tree = lxml.etree.parse(self.types_file)
db = {}
root = lxml_types_tree.getroot()
for node in root:
if isinstance(node, lxml.etree._Comment):
pass
elif node.tag.endswith('}annotation'):
pass
else:
obj = Schema_nxdlType(node, ns_dict=self.ns, schema_root=root)
if obj.name is not None:
db[obj.name] = obj
# re-arrange
units = list(db['anyUnitsAttr'].values)
del db['anyUnitsAttr']
del db['primitiveType']
return db, units