def write_xgmml(excel_filename: str, output=None, layout_template_file=None):
"""
creating the xgmml file from an excel input and writing it into a new file.
Args:
excel_filename: Name of the excel input file.
output: Name of the new output.
layout_template_file: Name of the layout template file.
Returns:
None
"""
if not output:
output = os.path.splitext(os.path.basename(excel_filename))[0]
base_path = os.path.dirname(excel_filename)
if not output.endswith('.xgmml'):
output = '{0}.xgmml'.format(output)
graph_filename = os.path.join(base_path, '{0}'.format(output))
print('graph_filename: ', graph_filename)
_file_path_existence(graph_filename)
print('Reading in Excel file [{}] ...'.format(excel_filename))
excel_book = ExcelBook(excel_filename)
rxncon_system = excel_book.rxncon_system
print('Constructed rxncon system: [{} reactions], [{} contingencies]'
.format(len(rxncon_system.reactions), len(rxncon_system.contingencies)))
print('Generating regulatory graph output...')
rxngraph_system = rxngraph_from_rxncon_system(rxncon_system)
graph = rxngraph_system.reaction_graph
if layout_template_file:
print('Writing layout information from [{0}] to graph file [{1}] ...'.format(layout_template_file, graph_filename))
gml_system = XGMML(graph, "{}".format(output))
graph = map_layout2xgmml(gml_system.to_string(), layout_template_file)
print('Writing regulatory graph file [{}] ...'.format(graph_filename))
with open(graph_filename, "w") as graph_handle:
graph_handle.write(graph)
else:
print('Writing regulatory graph file [{}] ...'.format(graph_filename))
gml_system = XGMML(graph, "{}".format(output))
gml_system.to_file(graph_filename)
def test_format_attributes() -> None:
"""
Testing attribute annotation in xgmml.
Returns:
None
Raises:
AssertionError if an expected attribute type is not within the node attributes.
"""
graph = DiGraph()
graph.add_node('A', str_value='A', int_value=1, float_value=1.0)
format_attribute_system_str = XGMML(graph, "graph").to_string()
expected_attribute_type = ['integer', 'double', 'string']
xmldoc_actual = minidom.parseString(format_attribute_system_str)
actual_node_attribute_types = [_get_node_att_type(xmldoc_actual.getElementsByTagName('node')[0], attribute_name=attribute)
for attribute in ['int_value', 'float_value', 'str_value']]
while expected_attribute_type:
attribute_type = expected_attribute_type.pop()
assert attribute_type in actual_node_attribute_types