def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.sequence_names(required=True),
ParameterFactory.sequences(required=True),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.sequence_names(required=True),
ParameterFactory.sequences(required=True),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.snpsearch_name(required=True),
ParameterFactory.chromosome_num(required=True),
ParameterFactory.chromosome_start(required=True),
ParameterFactory.chromosome_stop(required=True),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.probes(required=True),
ParameterFactory.boolean("absorb", "Check for absorbed probes."),
ParameterFactory.integer("num", "Minimum number of probes for a target.",
default=3, minimum=1),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.probes(required=True),
ParameterFactory.boolean("absorb", "Check for absorbed probes."),
ParameterFactory.integer("num",
"Minimum number of probes for a target.",
default=3,
minimum=1),
]
return parameters
def process_request(cls, params_dict):
sequences = params_dict[ParameterFactory.sequences(required=True)]
sequence_names = params_dict[ParameterFactory.sequence_names(required=True)]
# Every sequence must have an accompanying name
if len(sequences) != len(sequence_names):
return (None, None, None)
data = list()
for i, sequence in enumerate(sequences):
melting_temp = cls._IDT_CLIENT.get_melting_temp(sequence)
data.append({"Name": sequence_names[i],
"Sequence": sequence,
"Tm": melting_temp.tm})
columns = ["Name", "Sequence", "Tm"]
return (data, columns, None)
def _parse_query_params(cls, query_params):
'''
Valid query_params are defined by parameters(). However, a user can
supply parameters not contained in this list. Therefore, invalid
parameters are discarded and a params_dict is populated only with those
parameters that are valid. Since format is a special required input
parameter for every API function, it is parsed and returned separately.
Note that each parameter parses its own arguments. This allows it to
set a default when the parameter isn't included in the API call, as well
as format the input appropriately (string, float, int, date, etc.).
'''
params_dict = dict()
_format = FORMATS.json # @UndefinedVariable
parameters = cls.parameters()
for parameter in parameters:
# Path parameters are parsed in _handle_path_fields()
if not parameter.is_path():
# query_params is a default_dict(list), so it returns an empty
# list if this parameter was not provided - parse_args must
# be called on every parameter to set its default value if one
# exists.
args = parameter.parse_args(query_params[parameter.alias.lower()])
if args:
if parameter == ParameterFactory.format():
_format = args[0]
else:
params_dict[parameter] = args
return (params_dict, _format)
def process_request(cls, params_dict):
response = {}
http_status_code = 200
targets_uuids = params_dict[ParameterFactory.uuid()]
criteria = {UUID: {"$in": targets_uuids}}
try:
records = cls._DB_CONNECTOR.find(TARGETS_COLLECTION, criteria,
{ID: 0})
response["deleted"] = {}
if len(records) > 0:
# Record records
for record in records:
response["deleted"][record[UUID]] = record
# Delete records from database
result = cls._DB_CONNECTOR.remove(TARGETS_COLLECTION, criteria)
# Delete files from disk only if removal from DB was successful
if result and result['n'] == len(response["deleted"]):
for _, record in response["deleted"].iteritems():
os.remove(record[FILEPATH])
else:
del response["deleted"]
raise Exception(
"Error deleting records from the database: %s" %
result)
else:
http_status_code = 404
except:
response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
return make_response(jsonify(response), http_status_code)
def _parse_query_params(cls, query_params):
'''
Valid query_params are defined by parameters(). However, a user can
supply parameters not contained in this list. Therefore, invalid
parameters are discarded and a params_dict is populated only with those
parameters that are valid. Since format is a special required input
parameter for every API function, it is parsed and returned separately.
Note that each parameter parses its own arguments. This allows it to
set a default when the parameter isn't included in the API call, as well
as format the input appropriately (string, float, int, date, etc.).
'''
params_dict = dict()
_format = FORMATS.json # @UndefinedVariable
parameters = cls.parameters()
for parameter in parameters:
# Path parameters are parsed in _handle_path_fields()
if not parameter.is_path():
# query_params is a default_dict(list), so it returns an empty
# list if this parameter was not provided - parse_args must
# be called on every parameter to set its default value if one
# exists.
args = parameter.parse_args(
query_params[parameter.alias.lower()])
if args:
if parameter == ParameterFactory.format():
_format = args[0]
else:
params_dict[parameter] = args
return (params_dict, _format)
def process_request(cls, params_dict):
response = {}
http_status_code = 200
targets_uuids = params_dict[ParameterFactory.uuid()]
criteria = {UUID: {"$in": targets_uuids}}
try:
records = cls._DB_CONNECTOR.find(TARGETS_COLLECTION, criteria, {ID:0})
response["deleted"] = {}
if len(records) > 0:
# Record records
for record in records:
response["deleted"][record[UUID]] = record
# Delete records from database
result = cls._DB_CONNECTOR.remove(TARGETS_COLLECTION, criteria)
# Delete files from disk only if removal from DB was successful
if result and result['n'] == len(response["deleted"]):
for _,record in response["deleted"].iteritems():
os.remove(record[FILEPATH])
else:
del response["deleted"]
raise Exception("Error deleting records from the database: %s" % result)
else:
http_status_code = 404
except:
response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
return make_response(jsonify(response), http_status_code)
def process_request(cls, params_dict):
snp_search_name = params_dict[ParameterFactory.snpsearch_name(
required=True)]
chromosome_num = params_dict[ParameterFactory.chromosome_num(
required=True)]
start_pos = params_dict[ParameterFactory.chromosome_start(
required=True)]
stop_pos = params_dict[ParameterFactory.chromosome_stop(required=True)]
data = list()
ncbi_snps = snps_in_interval_multiple(snp_search_name, chromosome_num,
start_pos, stop_pos)
for snp in ncbi_snps:
data.append(snp)
columns = [
'search_name', 'rs', 'chromosome', 'loc', 'ref', 'alt', 'validated'
]
return data, columns, None
def process_request(cls, params_dict):
sequences = params_dict[ParameterFactory.sequences(required=True)]
sequence_names = params_dict[ParameterFactory.sequence_names(
required=True)]
# Every sequence must have an accompanying name
if len(sequences) != len(sequence_names):
return (None, None, None)
data = list()
for i, sequence in enumerate(sequences):
melting_temp = cls._IDT_CLIENT.get_melting_temp(sequence)
data.append({
"Name": sequence_names[i],
"Sequence": sequence,
"Tm": melting_temp.tm
})
columns = ["Name", "Sequence", "Tm"]
return (data, columns, None)
def process_request(cls, params_dict):
probes_file = params_dict[ParameterFactory.file("Probes file.")][0]
json_response = {
FILENAME: probes_file.filename,
ERROR: "",
}
http_status_code = 200
file_uuid = str(uuid4())
path = os.path.join(PROBES_UPLOAD_FOLDER, file_uuid)
existing_filenames = cls._DB_CONNECTOR.distinct(
PROBES_COLLECTION, FILENAME)
if os.path.exists(path) or probes_file.filename in existing_filenames:
http_status_code = 403
elif validate_fasta(probes_file) == False:
http_status_code = 415
else:
try:
probes_file.save(path)
probes_file.close()
json_response[URL] = "http://%s/probes/%s" % (HOSTNAME,
file_uuid)
json_response[FILEPATH] = path
json_response[UUID] = file_uuid
json_response[DATESTAMP] = datetime.today().strftime(
TIME_FORMAT)
json_response[TYPE] = "probes"
if "." in probes_file.filename:
json_response[FORMAT] = probes_file.filename.split(".")[-1]
else:
json_response[FORMAT] = "Unknown"
cls._DB_CONNECTOR.insert(PROBES_COLLECTION, [json_response])
del json_response[ID]
except:
json_response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
return make_response(jsonify(json_response), http_status_code)
def process_request(cls, params_dict):
probes_file = params_dict[ParameterFactory.file("Probes file.")][0]
json_response = {
FILENAME: probes_file.filename,
ERROR: "",
}
http_status_code = 200
file_uuid = str(uuid4())
path = os.path.join(PROBES_UPLOAD_FOLDER, file_uuid)
existing_filenames = cls._DB_CONNECTOR.distinct(PROBES_COLLECTION, FILENAME)
if os.path.exists(path) or probes_file.filename in existing_filenames:
http_status_code = 403
elif validate_fasta(probes_file) == False:
http_status_code = 415
else:
try:
probes_file.save(path)
probes_file.close()
json_response[URL] = "http://%s/probes/%s" % (HOSTNAME, file_uuid)
json_response[FILEPATH] = path
json_response[UUID] = file_uuid
json_response[DATESTAMP] = datetime.today().strftime(TIME_FORMAT)
json_response[TYPE] = "probes"
if "." in probes_file.filename:
json_response[FORMAT] = probes_file.filename.split(".")[-1]
else:
json_response[FORMAT] = "Unknown"
cls._DB_CONNECTOR.insert(PROBES_COLLECTION, [json_response])
del json_response[ID]
except:
json_response[ERROR] = str(sys.exc_info()[1])
http_status_code = 500
return make_response(jsonify(json_response), http_status_code)
def parameters(cls):
parameters = [ParameterFactory.file("Probes file.")]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.uuid(),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.file("Probes file.")
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.uuid(),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.file("Targets FASTA file.")
]
return parameters