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)
suffix = '_srg'
if not output.endswith('.xgmml'):
output = '{0}{1}.xgmml'.format(output, suffix)
else:
base_name = output.split('.xgmml')[0]
output = "{0}{1}.{2}".format(base_name, suffix, 'xgmml')
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 reaction species graph output...')
reg_system = SpeciesReactionGraph(rxncon_system)
graph = reg_system.to_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 reaction species graph file [{}] ...'.format(
graph_filename))
with open(graph_filename, "w") as graph_handle:
graph_handle.write(graph)
else:
print('Writing reaction species graph file [{}] ...'.format(
graph_filename))
gml_system = XGMML(graph, "{}".format(output))
gml_system.to_file(graph_filename)
def test_file_exists() -> None:
graph = DiGraph()
graph.add_node('A', str_value='A', int_value=1, float_value=1.0)
gml_system = XGMML(graph, "name")
with pytest.raises(FileExistsError):
gml_system.to_file(EXISTING_FILE)
with pytest.raises(NotADirectoryError):
gml_system.to_file(NOT_A_DIRECTORY)
def test_write_output() -> None:
digraph = _digraph_from_quick_str('''A_[b]_ppi+_B_[a]; ! A_[(x)]-{p}
C_p+_A_[(x)]''')
name = "test{0}".format(time.time())
gml_system = XGMML(digraph, "name")
path = "{0}/{1}.xgmml".format(tempfile.gettempdir(), name)
gml_system.to_file(path)
file_exists = os.path.exists(path)
file_size = os.stat(path).st_size
os.remove(path)
assert file_exists and file_size > 0
