def test_console(self):
"""
Console command for end to end test, run by passing the output of
`program_executable [JSON_STRING]` from module to module, essentially simulating
>>> collate | validate | structure | featurize | run_model
"""
rename_output = subprocess.check_output("collate", shell=True).decode('utf-8')
# Validation console test
rename_output = json.loads(rename_output)
validation_input = {
"mode": self.events_mode, # mode run|test|events_off
"file_list": rename_output['file_list'], # list of file paths ['path/test1.csv', 'path/test2.csv']
'run_list': list(range(len(rename_output['file_list']))) # list of run_ids [0, 1]
}
validation_input = os_format(json.dumps(validation_input))
validation_output = subprocess.check_output("validate {}".format(validation_input),
shell=True).decode('utf-8')
# Structure console test
validation_output = json.loads(validation_output)
structure_input = {
"mode": self.events_mode, # mode run|test|events_off
"file_list": validation_output['file_list'], # list of file paths ['path/test1.json', 'path/test2.json']
'run_list': list(range(len(validation_output['file_list']))), # list of run_ids [0, 1]
"validity": validation_output['validity'] # list of validities ['valid', 'invalid']
}
structure_input = os_format(json.dumps(structure_input))
structure_output = subprocess.check_output("structure {}".format(structure_input),
shell=True).decode('utf-8')
# Featurizing console test
structure_output = json.loads(structure_output)
feature_input = {
"mode": self.events_mode, # mode run|test|events_off
"file_list": structure_output['file_list'], # list of file paths ['path/test1.json', 'path/test2.json']
'run_list': list(range(len(structure_output['file_list']))) # list of run_ids [0, 1]
}
feature_input = os_format(json.dumps(feature_input))
feature_output = subprocess.check_output("featurize {}".format(feature_input),
shell=True).decode('utf-8')
# Fitting console test
# feature_output = json.loads(feature_output)
# fitting_input = {
# "mode": self.events_mode, # mode run|test|events_off
# "file_list": feature_output['file_list'], # list of file paths ['path/test1.json', 'path/test2.json']
# 'run_list': list(range(len(feature_output['file_list']))) # list of run_ids [0, 1]
# }
# fitting_input = os_format(json.dumps(fitting_input))
# model_output = subprocess.check_output("run_model {}".format(fitting_input),
# shell=True).decode('utf-8')
# Validate output files
self._check_result_file_validity()
def test_simple_conversion(self):
with ScratchDir('.'):
# Set root env
os.environ['BEEP_PROCESSING_DIR'] = os.getcwd()
# Make necessary directories
os.mkdir("data-share")
os.mkdir(os.path.join("data-share", "structure"))
# Create dummy json obj
json_obj = {
"mode": self.events_mode,
"file_list": [self.arbin_file],
'run_list': [0],
"validity": ['valid']
}
json_string = json.dumps(json_obj)
command = "structure {}".format(os_format(json_string))
result = subprocess.check_call(command, shell=True)
self.assertEqual(result, 0)
print(os.listdir(os.path.join("data-share", "structure")))
processed = loadfn(
os.path.join("data-share", "structure",
"2017-12-04_4_65C-69per_6C_CH29_structure.json"))
self.assertIsInstance(processed, ProcessedCyclerRun)
def test_console_script(self):
csv_file = os.path.join(TEST_FILE_DIR, "parameter_test.csv")
# Test script functionality
with ScratchDir('.') as scratch_dir:
# Set BEEP_ROOT directory to scratch_dir
os.environ['BEEP_ROOT'] = os.getcwd()
procedures_path = os.path.join("data-share", "protocols", "procedures")
names_path = os.path.join("data-share", "protocols", "names")
makedirs_p(procedures_path)
makedirs_p(names_path)
# Test the script
json_input = json.dumps(
{"file_list": [csv_file],
"mode": self.events_mode})
os.system("generate_protocol {}".format(os_format(json_input)))
self.assertEqual(len(os.listdir(procedures_path)), 3)
