def parameters(cls):
cls._file_param = ParameterFactory.file("Probe metadata file.")
cls._app_param = ParameterFactory.lc_string(
APPLICATION, "Case-insensitive application (e.g. Oncopanel).")
parameters = [
cls._file_param,
cls._app_param,
]
return parameters
def parameters(cls):
cls._file_param = ParameterFactory.file("Experiment results file.")
cls._sid_param = ParameterFactory.lc_string(SAMPLE_ID,
"Genomic DNA Sample ID.")
cls._rid_param = ParameterFactory.lc_string(RUN_ID, "Run ID.")
cls._date_param = ParameterFactory.date()
parameters = [
cls._file_param,
cls._sid_param,
cls._rid_param,
cls._date_param,
]
return parameters
def parameters(cls):
cls._file_param = ParameterFactory.file("Image stack tgz file.")
cls._exp_defs_param = ParameterFactory.experiment_definition()
cls._name_param = ParameterFactory.cs_string(
NAME, "Unique name to give this image stack.")
cls._short_desc_param = ParameterFactory.cs_string(
DESCRIPTION, "Short description of image stack.")
parameters = [
cls._file_param,
cls._exp_defs_param,
cls._name_param,
cls._short_desc_param,
]
return parameters
def parameters(cls):
cls._file_param = ParameterFactory.file('Image stack tgz file.')
cls._stack_type_param = ParameterFactory.mon_camera_type(
STACK_TYPE, 'Monitor Camera Number')
cls._name_param = ParameterFactory.cs_string(
NAME, 'Unique name to give this image stack.')
cls._short_desc_param = ParameterFactory.cs_string(
DESCRIPTION, 'Short description of image stack.')
parameters = [
cls._file_param,
cls._stack_type_param,
cls._name_param,
cls._short_desc_param,
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.file("Raw plate reader data file."),
ParameterFactory.cs_string("probe_sequence", "Probe sequence."),
ParameterFactory.cs_string("probe_tm",
"Probe melting temperature."),
ParameterFactory.cs_string("probe_length",
"Probe melting temperature."),
ParameterFactory.cs_string("target_sequence", "Target sequence."),
ParameterFactory.cs_string("variant_location",
"Variant location."),
ParameterFactory.cs_string("variant_allele", "Variant allele."),
ParameterFactory.cs_string("reference_allele",
"Reference allele."),
ParameterFactory.cs_string(
"incubation_temp",
"Incubation temperature (degrees celsius)."),
ParameterFactory.cs_string("incubation_time",
"Incubation time (minutes)."),
]
return parameters
def process_request(cls, params_dict):
targets_file = params_dict[ParameterFactory.file(
"Targets FASTA file.")][0]
json_response = {FILENAME: targets_file.filename}
http_status_code = 200
file_uuid = str(uuid4())
path = os.path.join(TARGETS_UPLOAD_PATH, file_uuid)
existing_filenames = cls._DB_CONNECTOR.distinct(
TARGETS_COLLECTION, FILENAME)
if os.path.exists(path) or targets_file.filename in existing_filenames:
http_status_code = 403
elif validate_fasta(targets_file) == False:
http_status_code = 415
else:
try:
targets_file.save(path)
targets_file.close()
json_response[URL] = "http://%s/uploads/%s/targets/%s" % (
HOSTNAME, PORT, file_uuid)
json_response[FILEPATH] = path
json_response[UUID] = file_uuid
json_response[DATESTAMP] = datetime.today()
json_response[TYPE] = "targets"
if "." in targets_file.filename:
json_response[FORMAT] = targets_file.filename.split(
".")[-1]
else:
json_response[FORMAT] = "Unknown"
cls._DB_CONNECTOR.insert(TARGETS_COLLECTION, [json_response])
except:
APP_LOGGER.exception(traceback.format_exc())
json_response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
finally:
if ID in json_response:
del json_response[ID]
return make_clean_response(json_response, http_status_code)
def parameters(cls):
parameters = [ParameterFactory.file("Probes file.")]
return parameters
def process_request(cls, params_dict):
plate_file = params_dict[ParameterFactory.file(
"Raw plate reader data file.")][0]
probe_sequence = params_dict[ParameterFactory.cs_string(
"probe_sequence", "Probe sequence.")][0]
probe_tm = params_dict[ParameterFactory.float(
"probe_tm", "Probe melting temperature (degrees celsius).")][0]
probe_length = params_dict[ParameterFactory.integer(
"probe_length", "Probe length.")][0]
target_sequence = params_dict[ParameterFactory.cs_string(
"target_sequence", "Target sequence.")][0]
variant_location = params_dict[ParameterFactory.cs_string(
"variant_location", "Variant location.")][0]
variant_allele = params_dict[ParameterFactory.cs_string(
"variant_allele", "Variant allele.")][0]
reference_allele = params_dict[ParameterFactory.cs_string(
"reference_allele", "Reference allele.")][0]
incubation_temp = params_dict[ParameterFactory.float(
"incubation_temp", "Incubation temperature (degrees celsius).")][0]
incubation_time = params_dict[ParameterFactory.float(
"incubation_time", "Incubation time (minutes).")][0]
json_response = {
FILENAME: plate_file.filename,
"probe_sequence": probe_sequence,
"probe_tm": probe_tm,
"probe_length": probe_length,
"target_sequence": target_sequence,
"variant_location": variant_location,
"variant_allele": variant_allele,
"reference_allele": reference_allele,
"incubation_temp": incubation_temp,
"incubation_time": incubation_time,
}
http_status_code = 200
file_uuid = str(uuid4())
path = os.path.join(PLATES_UPLOAD_PATH, file_uuid)
existing_filenames = cls._DB_CONNECTOR.distinct(
PLATES_COLLECTION, FILENAME)
if os.path.exists(path) or plate_file.filename in existing_filenames:
http_status_code = 403
else:
try:
plate_file.save(path)
plate_file.close()
json_response[URL] = "http://%s/uploads/%s/plates/%s" % (
HOSTNAME, PORT, file_uuid)
json_response[FILEPATH] = path
json_response[UUID] = file_uuid
json_response[DATESTAMP] = datetime.today()
json_response[TYPE] = "plate"
cls._DB_CONNECTOR.insert(PLATES_COLLECTION, [json_response])
except:
APP_LOGGER.exception(traceback.format_exc())
json_response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
finally:
if ID in json_response:
del json_response[ID]
silently_remove_file(path)
return make_clean_response(json_response, http_status_code)
def parameters(cls):
parameters = [ParameterFactory.file("Targets FASTA file.")]
return parameters
