def save_coverages(contigs, coverage_filename):
"""
:param contigs: A dict contig_name -> contig_id.
:param coverage_filename: The name of the dsv file.
"""
coverage_file = utils.parse_dsv(coverage_filename)
# Determine if the file has a header.
fields = next(coverage_file)
has_header = not utils.is_number(fields[1])
def add_coverages(contig_name, _coverages):
try:
contig_id = contigs.pop(contig_name)
except KeyError:
return
for i, cov in enumerate(_coverages):
db.session.add(Coverage(value=cov, name=header[i], contig_id=contig_id))
header = fields[1:]
if not has_header:
header = ['cov_{}'.format(i) for i, _ in enumerate(fields[1:], 1)]
contig_name, *_coverages = fields
add_coverages(contig_name, _coverages)
for contig_name, *_coverages in coverage_file:
add_coverages(contig_name, _coverages)
db.session.commit()
def save_coverages(contigs, coverage_filename):
"""
:param contigs: A dict contig_name -> contig_id.
:param coverage_filename: The name of the dsv file.
"""
coverage_file = utils.parse_dsv(coverage_filename)
# Determine if the file has a header.
fields = next(coverage_file)
has_header = not utils.is_number(fields[1])
def add_coverages(contig_name, _coverages):
try:
contig_id = contigs.pop(contig_name)
except KeyError:
return
for i, cov in enumerate(_coverages):
db.session.add(
Coverage(value=cov, name=header[i], contig_id=contig_id))
header = fields[1:]
if not has_header:
header = ['cov_{}'.format(i) for i, _ in enumerate(fields[1:], 1)]
contig_name, *_coverages = fields
add_coverages(contig_name, _coverages)
for contig_name, *_coverages in coverage_file:
add_coverages(contig_name, _coverages)
db.session.commit()
def handle_on_message(client, userdata, msg, app, db):
try:
msg.payload = bytes_to_json(msg.payload)
print("Received message '" + str(msg.payload) + "' on topic '" +
msg.topic + "' with QoS " + str(msg.qos),
flush=True)
except:
print("Received invalid message '" + str(msg.payload) +
"' on topic '" + msg.topic + "' with QoS " + str(msg.qos),
flush=True)
return
if msg.topic.endswith("/"):
msg.topic = msg.topic[:-1].encode()
topic = msg.topic.split("/")
if len(topic) >= 2 and topic[1] == "server":
t, sender_id = topic[0].split(":")
if t == "d" and is_number(sender_id):
if len(topic) == 2:
_save_device_pk(int(sender_id), msg, app, db)
elif len(topic) == 3:
if topic[2] in ["save_data", "remove_data"]:
_edit_device_data(int(sender_id), topic[2], msg, app, db)
else:
print(f"Invalid topic: {msg.topic}", flush=True)
else:
print(f"Invalid Device type or ID", flush=True)
def can_use_device(cls, user, device_id):
if not is_number(device_id):
return False
q = db.session.query(
db.session.query(User).
join(UserDevice).
filter(User.id == user.id).
filter(UserDevice.device_id == device_id).
exists()
)
return q.scalar()
def find_project_id_from_id(project_id):
"""Find the project in the database or return None"""
if is_number(project_id):
project_id = int(project_id)
project = Project.query.filter_by(id=project_id).first()
return project.id
else:
return None
def filter_contigs(attr, value):
_value = value
value = value.rstrip('e').rstrip('l').rstrip('g')
if not utils.is_number(value):
return
value = float(value)
if _value.endswith('l'):
filter = attr < value
elif _value.endswith('le'):
filter = attr <= value
elif _value.endswith('g'):
filter = attr > value
elif _value.endswith('ge'):
filter = attr >= value
else:
filter = attr == value
return filter
def read_coverages(filename):
coverage_file = utils.parse_dsv(filename)
coverages = {}
# Determine if the file has a header.
fields = next(coverage_file)
has_header = not utils.is_number(fields[1])
if has_header:
samples = fields[1:]
else:
samples = ['sample_{}'.format(i) for i, _ in enumerate(fields[1:], 1)]
contig_name, *_coverages = fields
coverages[contig_name] = {samples[i]: _coverages[i] for i, _ in enumerate(samples)}
for contig_name, *_coverages in coverage_file:
coverages[contig_name] = {samples[i]: _coverages[i] for i, _ in enumerate(samples)}
os.remove(filename)
return samples, coverages
def get_data_by_num_range():
lower_bound = request.args.get("lower", "")
upper_bound = request.args.get("upper", "")
device_name_bi = request.args.get("device_name_bi", None)
user = User.get_using_jwt_token(request.headers.get("Authorization", ""))
arg_check = check_missing_request_argument(
(device_name_bi, DEVICE_NAME_BI_MISSING_ERROR_MSG))
if arg_check is not True:
return arg_check
device = Device.get_by_name_bi(device_name_bi)
if device is None:
return http_json_response(
False, 400, **{"error": DEVICE_NAME_BI_INVALID_ERROR_MSG})
if not User.can_use_device(user, device.id):
return http_json_response(False, 400,
**{"error": UNAUTHORIZED_USER_ERROR_MSG})
if not is_number(lower_bound) and not is_number(upper_bound):
return http_json_response(False, 400,
**{"error": DATA_RANGE_MISSING_ERROR_MSG})
with suppress(ValueError):
lower_bound = int(lower_bound)
with suppress(ValueError):
upper_bound = int(upper_bound)
data = []
if isinstance(lower_bound, int) and isinstance(upper_bound, int):
if -214748364800 <= lower_bound < upper_bound <= 214748364700:
data = db.session.query(DeviceData).join(Device).filter(
and_(DeviceData.num_data > lower_bound,
DeviceData.num_data < upper_bound,
Device.name_bi == device_name_bi)).all()
else:
return http_json_response(
False, 400, **{"error": DATA_OUT_OF_OUTPUT_RANGE_ERROR_MSG})
elif not isinstance(upper_bound, int) and isinstance(lower_bound, int):
if -214748364800 <= lower_bound <= 214748364700:
data = db.session.query(DeviceData).join(Device).filter(
and_(DeviceData.num_data > lower_bound,
Device.name_bi == device_name_bi)).all()
else:
return http_json_response(
False, 400, **{"error": DATA_OUT_OF_OUTPUT_RANGE_ERROR_MSG})
elif not isinstance(lower_bound, int) and isinstance(upper_bound, int):
if -214748364800 <= upper_bound <= 214748364700:
data = db.session.query(DeviceData).join(Device).filter(
and_(DeviceData.num_data < upper_bound,
Device.name_bi == device_name_bi)).all()
else:
return http_json_response(
False, 400, **{"error": DATA_OUT_OF_OUTPUT_RANGE_ERROR_MSG})
result = []
for row in data:
r = row.as_dict()
for k, v in r.items():
if isinstance(v, bytes):
r[k] = v.decode()
result.append(r)
return http_json_response(**{'device_data': result})