def is_digraph_to_xgmml_correct(digraph: DiGraph, expected_xgmml: str) -> bool:
"""
Args:
test_case_quick:
expected_xgmml: expected xgmml content.
Returns:
bool: True if the created xgmml is the same as the expected, False otherwise.
"""
gml_system = XGMML(digraph, "test_graph")
expected_xgmml_lines = [
line.strip() for line in expected_xgmml.split("\n") if line.strip()
]
produced_xgmml_lines = [
line.strip() for line in gml_system.to_string().split("\n")
if line.strip()
]
if not sorted(produced_xgmml_lines) == sorted(expected_xgmml_lines):
for i, line in enumerate(produced_xgmml_lines):
if line not in expected_xgmml_lines:
print("generated line: {}".format(line))
print("expected line: {}".format(expected_xgmml_lines[i]))
return sorted(produced_xgmml_lines) == sorted(expected_xgmml_lines)
def test_layout_remains_correct_when_adding_node() -> None:
"""
Testing if the new graph gets the correct layout of the old graph if we add an additional node.
Returns:
None
Raises:
AssertionError: If the node coordinates of the new graph differ from expected coordinates.
"""
test_case = Quick("""A_[b]_ppi+_B_[a]; ! A_[(c)]-{p}
C_p+_A_[(c)]; ! C_[d]--D_[c]
C_[d]_ppi+_D_[c]""")
reg_graph = RegulatoryGraph(test_case.rxncon_system)
gml_system = XGMML(reg_graph.to_graph(), "add_node")
mapped_layout = map_layout2xgmml(gml_system.to_string(), NODE_LAYOUT_MANIPULATION)
xmldoc_no_layout = minidom.parseString(mapped_layout)
xmldoc_no_layout_info = _get_labels_and_coordinates_dict(xmldoc_no_layout)
xmldoc_expected_layout = minidom.parse(NODE_LAYOUT_MANIPULATION)
xmldoc_expected_layout_info = _get_labels_and_coordinates_dict(xmldoc_expected_layout)
assert all(xmldoc_no_layout_info[no_layout_node] == xmldoc_expected_layout_info[no_layout_node]
for no_layout_node in xmldoc_no_layout_info)
assert all(xmldoc_no_layout_info[expected_layout_node] == xmldoc_expected_layout_info[expected_layout_node]
for expected_layout_node in xmldoc_expected_layout_info)
def test_layout_remains_correct_when_removing_node() -> None:
"""
Testing if the new graph gets tie correct layout of the old graph if we remove a node.
Returns:
None
Raises:
AssertionError: If the node coordinates of the new graph differ from expected coordinates.
"""
test_case = Quick("""A_[b]_ppi+_B_[a]""")
reg_graph = SpeciesReactionGraph(test_case.rxncon_system)
gml_system = XGMML(reg_graph.to_graph(), "remove_node")
mapped_layout = map_layout2xgmml(gml_system.to_string(),
NODE_LAYOUT_MANIPULATION)
xmldoc_no_layout = minidom.parseString(mapped_layout)
xmldoc_no_layout_info = _get_labels_and_coordinates_dict(xmldoc_no_layout)
xmldoc_expected_layout = minidom.parse(NODE_LAYOUT_MANIPULATION)
xmldoc_expected_layout_info = _get_labels_and_coordinates_dict(
xmldoc_expected_layout)
assert all(xmldoc_no_layout_info[no_layout_node] ==
xmldoc_expected_layout_info[no_layout_node]
for no_layout_node in xmldoc_no_layout_info)
def test_regulatory_graph_layout_remains() -> None:
"""
Testing if the new graph gets the correct layout of the old graph.
Returns:
None
Raises:
AssertionError: If the node coordinates of the new graph differ from expected coordinates.
"""
book = ExcelBook(PHEROMONE_XLS)
reg_graph = RegulatoryGraph(book.rxncon_system)
gml_system = XGMML(reg_graph.to_graph(), "pheromone_layout")
mapped_layout = map_layout2xgmml(gml_system.to_string(), PHEROMONE_XGMML)
xmldoc_no_layout = minidom.parseString(mapped_layout)
xmldoc_no_layout_info = _get_labels_and_coordinates_dict(xmldoc_no_layout)
xmldoc_expected_layout = minidom.parse(PHEROMONE_XGMML)
xmldoc_expected_layout_info = _get_labels_and_coordinates_dict(
xmldoc_expected_layout)
assert all(xmldoc_no_layout_info[no_layout_node] ==
xmldoc_expected_layout_info[no_layout_node]
for no_layout_node in xmldoc_no_layout_info)
assert all(xmldoc_no_layout_info[expected_layout_node] ==
xmldoc_expected_layout_info[expected_layout_node]
for expected_layout_node in xmldoc_expected_layout_info)
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)