def parse_args(self, raw_args):
'''
Convert input strings to their appropriate types.
'''
if len(raw_args) > 1 and not self.allow_multiple:
APP_LOGGER.warning(
"Multiple parameter values for %s are not permitted. Only using the first value: %s."
% (self.name, raw_args[0]))
raw_args = raw_args[:1]
if len(raw_args) < 1:
if self.default is not None:
raw_args = [self.default]
elif self.required:
raise Exception("Required argument %s not provided." %
self.name)
converted_args = self._convert_args(raw_args)
if self.enum:
valid_args = set(self.enum)
if not set(converted_args).issubset(valid_args):
invalid_args = set(converted_args).difference(valid_args)
raise Exception(
"Provided arguments %s not a subset of valid arguments: %s"
% (invalid_args, valid_args))
return converted_args
def process_request(cls, params_dict):
users = params_dict[cls._users_param]
date = params_dict[cls._date_param][0]
archive_name = params_dict[cls._archive_param][0]
beta = params_dict[cls._beta_param][0]
device = params_dict[cls._device_param][0]
dye_prof_metrics = params_dict[cls._dye_profile_metrics_param]
surfactant = params_dict[cls._surfactant_param][0]
json_response = {}
# Ensure archive directory is valid
try:
archives = get_archive_dirs(archive_name)
except:
APP_LOGGER.exception(traceback.format_exc())
json_response[ERROR] = str(sys.exc_info()[1])
return make_clean_response(json_response, 500)
# Ensure only one valid archive is found
if len(archives) != 1:
APP_LOGGER.warning("Expected 1 archive, found %d" % len(archives))
return make_clean_response(json_response, 404)
response = {
USERS: users,
DATE: date,
ARCHIVE: archives[0],
BETA: beta,
DEVICE: device,
DYE_PROFILE_METRICS: dye_prof_metrics,
SURFACTANT: surfactant,
STATUS: JOB_STATUS.submitted, # @UndefinedVariable
JOB_TYPE_NAME: JOB_TYPE.dye_profile_images, # @UndefinedVariable
SUBMIT_DATESTAMP: datetime.today(),
}
status_code = 200
try:
# # Create helper functions
# callable = PaProcessCallable(archive, dyes, device,
# major, minor,
# offset, use_iid,
# outfile_path,
# config_path,
# response[UUID],
# cls._DB_CONNECTOR)
# callback = make_process_callback(response[UUID],
# outfile_path,
# config_path,
# cls._DB_CONNECTOR)
#
# # Add to queue and update DB
# cls._DB_CONNECTOR.insert(PA_PROCESS_COLLECTION, [response])
# cls._EXECUTION_MANAGER.add_job(response[UUID],
# abs_callable, callback)
except:
APP_LOGGER.exception(traceback.format_exc())
response[ERROR] = str(sys.exc_info()[1])
status_code = 500
finally:
if ID in response:
del response[ID]
http_status_code = 200
uuid = str(uuid4())
tmp_archive_path = os.path.join(TMP_PATH, uuid + ".tar.gz")
archive_path = os.path.join(RESULTS_PATH, uuid + ".tar.gz")
json_response = {
FILENAME: image_stack_tgz.filename,
UUID: uuid,
DATESTAMP: datetime.today(),
}
try:
# check tar file
image_stack_tgz.save(tmp_archive_path)
image_stack_tgz.close()
tar_error, nimgs = check_ham_tar_structure(tmp_archive_path, HAM)
# check for existing image stacks
existing_stacks = cls._DB_CONNECTOR.find(IMAGES_COLLECTION,
{NAME: img_stack_name, STACK_TYPE: HAM},
[NAME])
# check for exp def
exp_defs = ExperimentDefinitions()
exp_def_uuid = exp_defs.get_experiment_uuid(exp_def_name)
if existing_stacks:
http_status_code = 403
json_response[ERROR] = "Image stack with given name already " \
"exists."
elif not exp_def_uuid:
http_status_code = 404
json_response[ERROR] = "Couldn't locate UUID for " \
"experiment definition."
elif tar_error:
APP_LOGGER.error(tar_error)
http_status_code = 415
json_response[ERROR] = tar_error
else:
url = "http://%s/results/%s/%s" % (HOSTNAME, PORT,
os.path.basename(archive_path))
shutil.copy(tmp_archive_path, archive_path)
json_response[RESULT] = archive_path
json_response[URL] = url
json_response[NAME] = img_stack_name
json_response[DESCRIPTION] = short_desc
json_response[EXP_DEF_NAME] = exp_def_name
json_response[EXP_DEF_UUID] = exp_def_uuid
json_response[NUM_IMAGES] = nimgs
json_response[STACK_TYPE] = HAM
cls._DB_CONNECTOR.insert(IMAGES_COLLECTION,
[json_response])
except IOError:
APP_LOGGER.exception(traceback.format_exc())
http_status_code = 415
json_response[ERROR] = str(sys.exc_info()[1])
except:
APP_LOGGER.exception(traceback.format_exc())
http_status_code = 500
json_response[ERROR] = str(sys.exc_info()[1])
finally:
if ID in json_response:
del json_response[ID]
silently_remove_file(tmp_archive_path)
return make_clean_response(json_response, http_status_code)