def parameters(cls):
parameters = [
ParameterFactory.file_uuid(PROBES, PROBES_COLLECTION),
ParameterFactory.file_uuid(TARGETS, TARGETS_COLLECTION),
ParameterFactory.boolean("absorb", "Check for absorbed probes."),
ParameterFactory.integer("num",
"Minimum number of probes for a target.",
default=3,
minimum=1),
ParameterFactory.lc_string(JOB_NAME,
"Unique name to give this job.")
]
return parameters
def process_request(cls, params_dict):
probes_file_uuid = params_dict[ParameterFactory.file_uuid(
"probes", PROBES_COLLECTION)][0]
targets_file_uuid = params_dict[ParameterFactory.file_uuid(
"targets", TARGETS_COLLECTION)][0]
absorb = params_dict[ParameterFactory.boolean(
"absorb", "Check for absorbed probes.")][0]
num = params_dict[ParameterFactory.integer(
"num",
"Minimum number of probes for a target.",
default=3,
minimum=1)][0]
job_name = params_dict[ParameterFactory.lc_string(
JOB_NAME, "Unique name to give this job.")][0]
json_response = {
PROBES: probes_file_uuid,
TARGETS: targets_file_uuid,
ABSORB: absorb,
NUM: num,
UUID: str(uuid4()),
STATUS: JOB_STATUS.submitted, # @UndefinedVariable
JOB_NAME: job_name,
DATESTAMP: datetime.today(),
}
http_status_code = 200
if job_name in cls._DB_CONNECTOR.distinct(VALIDATION_COLLECTION,
JOB_NAME):
http_status_code = 403
else:
try:
probes_path = cls._DB_CONNECTOR.find_one(
PROBES_COLLECTION, UUID, probes_file_uuid)[FILEPATH]
targets_path = cls._DB_CONNECTOR.find_one(
TARGETS_COLLECTION, UUID, targets_file_uuid)[FILEPATH]
#ADD VALIDATOR JOB TO QUEUE
cls._DB_CONNECTOR.insert(VALIDATION_COLLECTION,
[json_response])
del json_response[ID]
except:
APP_LOGGER.exception(traceback.format_exc())
json_response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
return make_clean_response(json_response, http_status_code)
def parameters(cls):
cls._probes_param = ParameterFactory.file_uuid(PROBES,
PROBES_COLLECTION)
cls._targets_param = ParameterFactory.file_uuid(
TARGETS, TARGETS_COLLECTION)
cls._strict_param = ParameterFactory.integer(STRICT, "Restrict " \
"each probe to this number of bases from the 3' end of its " \
"sequence (0 to use entire probe)", default=0, minimum=0)
cls._job_name_param = ParameterFactory.cs_string(JOB_NAME,
"Unique name to " \
"give this job.")
parameters = [
cls._probes_param,
cls._targets_param,
cls._strict_param,
cls._job_name_param,
]
return parameters