def test_neurolucida_format_convert():
with open("test/neurolucida.asc", "rt") as fp:
data = fp.read()
out, err = command.run_lmeasure(data, *lm_metrics)
command.check_errors(err)
swc = command.run_convert(data)
out, err = command.run_lmeasure(swc, *lm_metrics)
command.check_errors(err)
def lmeasure():
if request.method == "OPTIONS":
resp = jsonify(measure_options)
resp.headers['Allow'] = "POST,OPTIONS"
return resp
elif request.method == "POST":
if request.is_json:
d = request.get_json()
else:
d = request.form
if "data" not in d:
return jsonify({"error": "no 'data' field in request"}), 400
if "metrics" not in d:
metrics = command.lm_function_names
elif isinstance(d["metrics"], str):
metrics = (d["metrics"], )
elif isinstance(d["metrics"], list):
metrics = d["metrics"]
app.logger.debug('requested metrics: %s', metrics)
try:
out, err = command.run_lmeasure(d["data"], *metrics)
app.logger.debug('stdout: %s', out)
app.logger.debug('stderr: %s', err)
command.check_errors(err)
measures = [d for d in command.parse_results(out)]
except KeyError as e:
return jsonify({"error":
"bad metric '{}' requested".format(e)}), 400
except RuntimeError as e:
return jsonify({"error": "l-measure failed: {!s}".format(e)}), 400
else:
return jsonify({"error": None, "measures": measures})
def test_metric_names_match_list():
with open("test/neuron.swc", "rt") as fp:
data = fp.read()
out, err = command.run_lmeasure(data, *lm_metrics)
command.check_errors(err)
result = tuple(command.parse_results(out))
assert_sequence_equal([x['metric'] for x in result], lm_metrics)
def test_neurolucida_format_ok():
with open("test/neurolucida.asc", "rt") as fp:
data = fp.read()
out, err = command.run_lmeasure(data, lm_metrics[0])
command.check_errors(err)
tuple(command.parse_results(out))
def test_bad_metric_raises_error():
data = "blah blah blah"
out, err = command.run_lmeasure(data, "amazingness")
def test_no_metrics_raises_error():
data = "blah blah blah"
out, err = command.run_lmeasure(data)
def test_garbage_input_raises_error():
data = "blah blah blah"
out, err = command.run_lmeasure(data, lm_metrics[0])
command.check_errors(err)
def test_blank_file_rasies_error():
with open("test/blank.swc", "rt") as fp:
data = fp.read()
out, err = command.run_lmeasure(data, lm_metrics[0])
command.check_errors(err)