def test_invalid_columns(self):
sifFilename = tempfile.NamedTemporaryFile(suffix='.sif', delete=False)
try:
# Write the network file
write_valid_graph(sifFilename)
# Add another line with an extra column
sifFilename.write('A\tdd\tF\t0.85\n')
finally:
sifFilename.close()
# Load the DiGraph and expect an Exception for the extra column
with pytest.raises(Exception):
loadGraph(sifFilename.name)
# Remove because delete=False above
os.remove(sifFilename.name)
def test_valid_graph(self):
sifFilename = tempfile.NamedTemporaryFile(suffix='.sif', delete=False)
try:
# Write the network file
write_valid_graph(sifFilename)
finally:
sifFilename.close()
# Load the DiGraph
graph = loadGraph(sifFilename.name)
# Check that the DiGraph has the expected properties
assert graph.order() == 5, "Unexpected number of nodes"
assert graph.size() == 7, "Unexpected number of edges"
# Check that the DiGraph has the expected edges
assert graph.has_edge('A', 'B')
assert graph.has_edge('B', 'A')
assert graph.has_edge('B', 'C')
assert graph.has_edge('C', 'D')
assert graph.has_edge('D', 'C')
assert graph.has_edge('A', 'E')
assert graph.has_edge('E', 'A')
# Remove because delete=False above
os.remove(sifFilename.name)
def test_invalid_columns(self):
sifFilename= tempfile.NamedTemporaryFile(suffix='.sif', delete=False)
try:
# Write the network file
write_valid_graph(sifFilename)
# Add another line with an extra column
sifFilename.write('A\tdd\tF\t0.85\n')
finally:
sifFilename.close()
# Load the DiGraph and expect an Exception for the extra column
with pytest.raises(Exception):
loadGraph(sifFilename.name)
# Remove because delete=False above
os.remove(sifFilename.name)
def test_valid_graph(self):
sifFilename= tempfile.NamedTemporaryFile(suffix='.sif', delete=False)
try:
# Write the network file
write_valid_graph(sifFilename)
finally:
sifFilename.close()
# Load the DiGraph
graph = loadGraph(sifFilename.name)
# Check that the DiGraph has the expected properties
assert graph.order() == 5, "Unexpected number of nodes"
assert graph.size() == 7, "Unexpected number of edges"
# Check that the DiGraph has the expected edges
assert graph.has_edge('A','B')
assert graph.has_edge('B','A')
assert graph.has_edge('B','C')
assert graph.has_edge('C','D')
assert graph.has_edge('D','C')
assert graph.has_edge('A','E')
assert graph.has_edge('E','A')
# Remove because delete=False above
os.remove(sifFilename.name)
def run_forest(msgsteiner, conf_params, forest_opts):
'''
Run Forest on the test network
INPUT:
msgsteiner - the path to msgsteiner
conf_params - dictionary, see write_conf
forest_opts - dictionary with long form option names for forest.py as keys
OUTPUT:
graph - the DiGraph object for the optimal Steiner forest
objective - the objective function value of the optimal Steiner forest (float)
'''
assert msgsteiner is not None, 'Please provide path to msgsteiner using --msgpath option'
forest_opts = copy.deepcopy(forest_opts)
forest_opts['msgpath'] = msgsteiner
# For reproducibility, though it is likely not needed for this
# small test case
forest_opts['seed'] = 2016
# Write the configuration file with the specified parameters
conf_filename= tempfile.NamedTemporaryFile(suffix='.txt', delete=False)
try:
write_conf(conf_filename, conf_params)
finally:
conf_filename.close()
forest_opts['conf'] = conf_filename.name
default_outpath = True
if 'outpath' in forest_opts:
default_outpath = False
else:
# Create a tmp directory for output unless one is provided
forest_opts['outpath'] = tempfile.mkdtemp()
try:
cur_dir = os.path.dirname(__file__)
forest_opts['forest'] = os.path.join(cur_dir, '..', 'scripts', 'forest.py')
forest_cmd = 'python {forest} --prize={prize} --edge={edge} --conf={conf} --dummyMode={dummyMode} --outpath={outpath} --msgpath={msgpath} --seed={seed}'.format(**forest_opts)
subprocess.call(shlex.split(forest_cmd), shell=False)
# Test the optimal Forest to see if parameter value has the intended effect
opt_forest = os.path.join(forest_opts['outpath'], 'result_optimalForest.sif')
assert os.path.isfile(opt_forest), 'Forest did not generate the optimal forest file'
graph = loadGraph(opt_forest)
# Parse the objective function value of the optimal forest
# This cannot be recovered from the forest file because it depends on w
info_filename = os.path.join(forest_opts['outpath'], 'result_info.txt')
assert os.path.isfile(info_filename), 'Forest did not generate the info file'
objective = parse_obj(info_filename)
finally:
# Remove here because delete=False above
os.remove(conf_filename.name)
# Remove the Forest output directory and all files
# Leave the output directory intact if it was manually set
if default_outpath:
shutil.rmtree(forest_opts['outpath'])
return (graph, objective)