def load_from_dynetml(self, mn_text, properties_to_include=None, properties_to_ignore=None,
nodeclasses_to_include=None, nodeclasses_to_ignore=None, networks_to_include=None,
networks_to_ignore=None):
"""
Parses XML containing a Meta-Network and loads the contents
:param mn_text: XML containing a Meta-Network
:param properties_to_include: a list of nodeclass properties that should be included
:param properties_to_ignore: a list of nodeclass properties that should be ignored
:param nodeclasses_to_include: a list of nodeclasses that should be included
:param nodeclasses_to_ignore: a list of nodeclasses that should be ignored
:param networks_to_include: a list of networks that should be included
:param networks_to_ignore: a list of networks that should be ignored
:param mn_text: str or unicode
:param properties_to_include: lists
:param properties_to_ignore: lists
:param nodeclasses_to_include: lists
:param nodeclasses_to_ignore: lists
:param networks_to_include: lists
:param networks_to_ignore: lists
:raise TypeError: if mn_text isn't a str or unicode
"""
dmlpu.check_type(mn_text, 'mn_text', (unicode, str))
mn_tag = etree.XML(mn_text)
if mn_tag.tag != 'MetaNetwork':
return
for attrib_key in mn_tag.attrib:
self.attributes[attrib_key] = dmlpu.format_prop(mn_tag.attrib[attrib_key])
self.load_from_tag(mn_tag, properties_to_include, properties_to_ignore, nodeclasses_to_include,
nodeclasses_to_ignore, networks_to_include, networks_to_ignore)
def create_nodeset_property(self, nodeclass_name, nodeset_name, property_name, type_str, singlevalued_bool):
"""
Create a new nodeset property
:param nodeclass_name: the name of the parent of nodeset_name
:param nodeset_name: the name of the nodeset that should get the new property
:param property_name: the name of the property to be added
:param type_str: the type of the parameter
:param singlevalued_bool: whether or not the parameter should be single-valued
:type nodeclass_name: str or unicode
:type nodeset_name: str or unicode
:type property_name: str or unicode
:type type_str: str or unicode
:type singlevalued_bool: bool
:raise KeyError: If a property named property_name already exists.
:raise TypeError: If type_str isn't a str or unicode
:raise ValueError: If type_str isn't "number", "date", "text", "categoryText", or "URI"
:raise TypeError: If singlevalued_bool isn't a bool
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name)
dmlpu.check_key(property_name, self.__node_tree[nodeclass_name][nodeset_name],
'property {0} already exists for nodeset {1}'.format(property_name, nodeset_name), False)
dmlpu.check_type(type_str, 'type_str', (str, unicode))
if type_str not in ['number', 'date', 'text', 'categoryText', 'URI']:
raise ValueError('type_str must be "number", "date" "text", "categoryText", or "URI"; got {0}'.
format(type_str))
dmlpu.check_type(singlevalued_bool, 'singlevalued_bool', bool)
self.__node_tree[nodeclass_name][nodeset_name][0][property_name] = type_str, singlevalued_bool
def union_nodesets(self, nodeclass_name, *args):
"""
Takes two nodesets and combines them in a new nodeset. Properties and entries from the first nodeset override
those from the second nodeset.
:param nodeclass_name: The name of the parent nodeclass of nodeset_one_name and nodeset_two_name
:param nodeset_one_name: The name of the first nodeset in the union.
:param nodset_two_name: The name of the second ndeset in the union.
:param other_nodesets: union_nodesets takes a *args argument, so any number of nodesets is acceptable
:param new_nodeset_name: The name of the new nodeset to be created
:type nodeset_one_name: str or unicode
:type nodeset_two_name: str or unicode
:type new_nodeset_name: str or unicode
"""
if len(args) < 3:
raise ValueError('Need at least 3 argumets; got {0}'.format(len(args)))
for nodeset_name in args[:-1]:
self.__validate_tree_branch(nodeclass_name, nodeset_name)
dmlpu.check_type(args[-1], 'new_nodeset_name', (str, unicode))
dmlpu.check_key(args[-1], 'union_nodeset', self.__node_tree[nodeclass_name], nodeclass_name,
False)
merge_nodeset = self.__node_tree[nodeclass_name][args[-2]]
for i in range(len(args)-3, -1, -1):
for entry in self.__node_tree[nodeclass_name][args[i]][1]:
merge_nodeset[1][entry] = self.__node_tree[nodeclass_name][args[i]][1][entry]
for entry in self.__node_tree[nodeclass_name][args[i]][0]:
merge_nodeset[0][entry] = self.__node_tree[nodeclass_name][args[i]][0][entry]
self.__node_tree[nodeclass_name][args[-1]] = merge_nodeset
def write_dynetml(self, out_file_path):
""":param str|unicode out_file_path: Write the meta-network to this path."""
dmlpu.check_type(out_file_path, 'out_file_path', (str, unicode))
if os.path.exists(out_file_path) and os.path.isdir(out_file_path):
raise IOError('out_file_path cannot be a directory')
# bs = self.convert_to_dynetml(True)
#
# with codecs.open(out_file_path, 'w', 'utf8') as outfile:
# outfile.write(bs.prettify())
xml_root = self.convert_to_dynetml()
with codecs.open(out_file_path, 'w', 'utf8') as outfile:
outfile.write('<?xml version="1.0" standalone="yes"?>\n\n')
outfile.write(etree.tostring(xml_root, pretty_print=True))
def set_node_property(self, nodeclass_name, nodeset_name, node_name, property_name, value):
"""
Set the value of a node property
:param str|unicode nodeclass_name: the name of the parent of nodeset_name
:param str|unicode nodeset_name: the name of the parent of node_name
:param str|unicode node_name: the name of the node whose property is being set
:param str|unicode property_name: the name of the property to be set
:param str|unicode|bool|float|datetime.datetime value: the value of the parameter
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name, node_name)
dmlpu.check_type(property_name, 'property_name', (str, unicode))
dmlpu.check_key(property_name, 'property_name', self.__node_tree[nodeclass_name][nodeset_name][0], nodeset_name)
self.__node_tree[nodeclass_name][nodeset_name][1][node_name][property_name] = \
dmlpu.format_prop(value, self.__node_tree[nodeclass_name][nodeset_name][0][property_name][0])
def convert_to_dynetml(self, is_entire_file=False):
"""
Converts the graph to dynetml and returns a BeautifulSoup tag
:param is_entire_file: if True, wraps value as a soup. If False, returns the top tag
:type is_entire_file: bool
:return: bs4.element.Tag
:raise TypeError: if is_entire_file isn't a bool
"""
dmlpu.check_type(is_entire_file, 'is_entire_file', bool)
bs = BeautifulSoup(features='xml')
bs.append(bs.new_tag('MetaNetwork'))
for attr in self.attributes:
bs.MetaNetwork[attr] = dmlpu.unformat_prop(self.attributes[attr])
bs.MetaNetwork.append(dmlpu.get_property_identities_tag(self.propertyIdentities))
bs.MetaNetwork.append(bs.new_tag('properties'))
for key in self.properties:
prop_tag = bs.new_tag('property')
prop_tag['id'] = key
prop_tag['value'] = dmlpu.unformat_prop(self.properties[key])
bs.MetaNetwork.properties.append(prop_tag)
bs.MetaNetwork.append(bs.new_tag('nodes'))
for class_type in self.__node_tree:
for class_id in self.__node_tree[class_type]:
nodeclass_tag = bs.new_tag('nodeclass', type=class_type, id=class_id)
nodeclass_tag.append(dmlpu.get_property_identities_tag(self.__node_tree[class_type][class_id][0]))
for key in self.__node_tree[class_type][class_id][1]:
node_tag = bs.new_tag('node', id=key)
for attr in self.__node_tree[class_type][class_id][1][key][0]:
node_tag[attr] = dmlpu.unformat_prop(self.__node_tree[class_type][class_id][1][key][0][attr])
node_tag.append(dmlpu.get_properties_tag(self.__node_tree[class_type][class_id][1][key][1]))
nodeclass_tag.append(node_tag)
bs.MetaNetwork.nodes.append(nodeclass_tag)
networks_tag = self._get_networks_tag()
bs.MetaNetwork.networks.append(networks_tag)
if not is_entire_file:
bs = bs.MetaNetwork
return bs
def create_node(self, nodeclass_name, nodeset_name, node_name, property_dict=None):
"""
Create a node in a give nodeset in a give nodeclass. If a set of properties are specified, add the properties.
:param str|unicode nodeclass_name: name of the parent of nodeset_name
:param str|unicode nodeset_name: name of the parent of node_name
:param str|unicode node_name: name of the node to be created
:param dict|None property_dict: A dictionary of properties to assign the new node.
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name)
dmlpu.check_type(node_name, 'node_name', (str, unicode))
dmlpu.check_key(node_name, 'node_name', self.__node_tree[nodeclass_name][nodeset_name][1], nodeset_name, False)
dmlpu.check_type(property_dict, 'property_dict', (dict, None))
for property_name in property_dict.keys():
dmlpu.check_key(
property_name, 'property_name',
self.__node_tree[nodeclass_name][nodeset_name][0], '{0} properties'.format(nodeset_name))
self.__node_tree[nodeclass_name][nodeset_name][1][node_name] = property_dict
def create_nodeset_property(self, nodeclass_name, nodeset_name, property_name, type_str, singlevalued_bool):
"""
Create a new nodeset property
:param str|unicode nodeclass_name: the name of the parent of nodeset_name
:param str|unicode nodeset_name: the name of the nodeset that should get the new property
:param str|unicode property_name: the name of the property to be added
:param str|unicode type_str: the type of the parameter
:param bool singlevalued_bool: whether or not the parameter should be single-valued
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name)
dmlpu.check_key(property_name, 'property_name',
self.__node_tree[nodeclass_name][nodeset_name][0], nodeset_name, False)
dmlpu.check_type(type_str, 'type_str', (str, unicode))
if type_str not in ['number', 'date', 'text', 'categoryText', 'URI']:
raise ValueError('type_str must be "number", "date" "text", "categoryText", or "URI"; got {0}'.
format(type_str))
dmlpu.check_type(singlevalued_bool, 'singlevalued_bool', bool)
self.__node_tree[nodeclass_name][nodeset_name][0][property_name] = type_str, singlevalued_bool
def add_node(self, nodeclass_name, nodeset_name, node_name, property_dict=None):
"""
Add a node to a give nodeset in a give nodeclass. If a set of properties are specified, add the properties.
:param nodeclass_name: name of the parent of nodeset_name
:param nodeset_name: name of the parent of node_name
:param node_name: name of the node to be created
:param property_dict: A dictionary of properties to assign the new node.
:type nodeclass_name: str or unicode
:type nodeset_name: str or unicode
:type node_name: str or unicode
:type property_dict: dict or None
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name)
dmlpu.check_type(node_name, 'node_name', (str, unicode))
dmlpu.check_key(node_name, 'node_name', self.__node_tree[nodeclass_name][nodeset_name][1], nodeset_name, False)
dmlpu.check_type(property_dict, 'property_dict', (dict, None))
for property_name in property_dict.keys():
dmlpu.check_key(property_name, 'property_name', self.__node_tree[nodeclass_name][nodeset_name][0],
'{0} properties'.format(nodeset_name))
self.__node_tree[nodeclass_name][nodeset_name][1][node_name] = property_dict
def set_node_property(self, nodeclass_name, nodeset_name, node_name, property_name, value):
"""
Set the value of a node property
:param nodeclass_name: the name of the parent of nodeset_name
:param nodeset_name: the name of the parent of node_name
:param node_name: the name of the node whose property is being set
:param property_name: the name of the property to be set
:param value: the value of the parameter
:type nodeclass_name: str or unicode
:type nodeset_name: str or unicode
:type node_name: str or unicode
:type property_name: str or unicode
:type value: str, unicode, or the appropriate type specified in dmlpu.format_prop
:raise TypeError: if property_name isn't a str or unicode
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name, node_name)
dmlpu.check_type(property_name, 'property_name', (str, unicode))
dmlpu.check_key(property_name, 'property_name', self.__node_tree[nodeclass_name][nodeset_name][0], nodeset_name)
self.__node_tree[nodeclass_name][nodeset_name][1][node_name][property_name] = \
dmlpu.format_prop(value, self.__node_tree[nodeclass_name][nodeset_name][0][property_name][0])
def rename_node(self, nodeclass_name, nodeset_name, node_name, new_node_name):
"""
Rename a particular node, both in the node tree and in the networks containing it.
:param str|unicode nodeclass_name: name of the parent of nodeset_name
:param str|unicode nodeset_name: name of the parent of node_name
:param str|unicode node_name: current node name
:param str|unicode new_node_name: new name for the node
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name, node_name)
dmlpu.check_type(new_node_name, 'new_node_name', (str, unicode))
dmlpu.check_key(new_node_name, 'new_node_name',
self.__node_tree[nodeclass_name][nodeset_name][1], nodeset_name, False)
self.__node_tree[nodeclass_name][nodeset_name][1][new_node_name] = \
self.__node_tree[nodeclass_name][nodeset_name][1][node_name]
del self.__node_tree[nodeclass_name][nodeset_name][1][node_name]
# We assume 'id' exists. If it doesn't, the data has bigger problems.
self.__node_tree[nodeclass_name][nodeset_name][new_node_name]['id'] = new_node_name
self._rename_network_nodes(nodeclass_name, nodeset_name, node_name, new_node_name)
def rename_node(self, nodeclass_name, nodeset_name, node_name, new_node_name):
"""
Rename a particular node, both in the node tree and in the networks containing it.
:param nodeclass_name: name of the parent of nodeset_name
:param nodeset_name: name of the parent of node_name
:param node_name: current node name
:param new_node_name: new name for the node
:type nodeclass_name: str or unicode
:type nodeset_name: str or unicode
:type node_name: str or unicode
:type new_node_name: str or unicode
:raise TypeError: if new_node_name is not a str or unicode
:raise KeyError: if new_node_name is already a node in the node class
"""
self.__validate_tree_branch(nodeclass_name, nodeset_name, node_name)
dmlpu.check_type(new_node_name, 'new_node_name', (str, unicode))
dmlpu.check_key(new_node_name, self.__node_tree[nodeclass_name][nodeset_name],
'{0} is already a key in nodeset {1}'.format(new_node_name, nodeset_name), False)
self.__node_tree[nodeclass_name][nodeset_name][new_node_name] = \
self.__node_tree[nodeclass_name][nodeset_name][node_name]
del self.__node_tree[nodeclass_name][nodeset_name][node_name]
self._rename_network_nodes(nodeclass_name, nodeset_name, node_name, new_node_name)
def __validate_tree_branch(self, nodeclass_name, nodeset_name=None, node_name=None):
"""
Verify that a particular nodeclass, nodeset, or node exists in __node_tree
:param unicde|str nodeclass_name: The name of a nodeclass
:param unicode|str|None nodeset_name: The name of a nodeset
:param unicode|str|None node_name: The name of a node
"""
dmlpu.check_type(nodeclass_name, 'nodeclass_name', (str, unicode))
dmlpu.check_type(nodeset_name, 'nodeset_name', (str, unicode, None))
dmlpu.check_type(node_name, 'node_name', (str, unicode, None))
dmlpu.check_key(nodeclass_name, 'nodeclass_name', self.__node_tree, 'self.__node_tree')
if nodeset_name is not None:
dmlpu.check_key(nodeset_name, 'nodeset_name', self.__node_tree[nodeclass_name], nodeclass_name)
if node_name is not None:
dmlpu.check_key(node_name, 'node_name', self.__node_tree[nodeclass_name][nodeset_name][1], 'nodeset_name')
def __validate_tree_branch(self, nodeclass_name, nodeset_name=None, node_name=None):
"""
Verify that a particular nodeclass, nodeset, or node exists in the node tree
:param nodeclass_name: The name of a nodeclass
:param nodeset_name: The name of a nodeset
:param node_name: The name of a node
:type nodeclass_name: unicode or str
:type nodeset_name: unicode, str, or None
:type node_name: unicode, str, or None
:raise TypeError: if nodeclass_name, nodeset_name, or node_name is not a str, unicode or None
:raise KeyError: if nodeclass_name, nodeset_name, or node_name cannot be found in self.__node_tree
"""
dmlpu.check_type(nodeclass_name, 'nodeclass_name', (str, unicode))
dmlpu.check_type(nodeset_name, 'nodeset_name', (str, unicode, None))
dmlpu.check_type(node_name, 'node_name', (str, unicode, None))
dmlpu.check_key(nodeclass_name, 'nodeclass_name', self.__node_tree, 'self.__node_tree')
if nodeset_name is not None:
dmlpu.check_key(nodeset_name, 'nodeset_name', self.__node_tree[nodeclass_name], nodeclass_name)
if node_name is not None:
dmlpu.check_key(node_name, 'node_name', self.__node_tree[nodeclass_name][nodeset_name][1], 'nodeset_name')