def get(self, biometric_id):
"""Get a biometric record by ID from the database
Example **GET http://hrsdb/biometric/1** ::
{
"response": {
"id": 1,
"patient_id": 1,
"timestamp": "2015/05/19" 12:04:59,
"type_id": 1,
"value": "167"
}
}
"""
record = None
with open_session() as session:
try:
record = session.query(Biometric) \
.filter(Biometric.id == biometric_id).one()
except NoResultFound:
logger.warn("No record found")
resp = gen_response("No record found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
logger.debug(record)
return gen_response(to_dict(record))
def get(self):
"""Get all biometric types from the database
Example **GET http://hrsdb/biometric_types** ::
{
"response": [
{
"id": 1,
"name": "height",
"units" "cm"
}
{
"id": 2,
"name": "weight",
"units": "kg"
}
...
]
}
"""
records = None
with open_session() as session:
try:
records = session.query(BiometricType).all()
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
logger.debug(records)
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def get(self):
"""Get all biometric types from the database
Example **GET http://hrsdb/biometric_types** ::
{
"response": [
{
"id": 1,
"name": "height",
"units" "cm"
}
{
"id": 2,
"name": "weight",
"units": "kg"
}
...
]
}
"""
records = None
with open_session() as session:
try:
records = session.query(BiometricType).all()
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
logger.debug(records)
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def put(self):
""" Upload an ECG datafile to the server.
The file should be labled as "data" when uploaded
Example URL **PUT http://hrsdb/ecgdata**
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.put_parser.parse_args(strict=True)
ecgfile = args.data
# Save the file on disk using a uuid
filename = "%s%s.dat" % (self.file_prefix, uuid())
ecgfile.save(
os.path.join(current_app.config['UPLOAD_FOLDER'], filename))
# Create a new database record for this file
with open_session() as session:
ecgdata = ECGData(filename)
session.add(ecgdata)
session.flush()
session.commit()
print(ecgdata.id)
return gen_response({"id": ecgdata.id})
def put(self):
""" Upload an ECG datafile to the server.
The file should be labled as "data" when uploaded
Example URL **PUT http://hrsdb/ecgdata**
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.put_parser.parse_args(strict=True)
ecgfile = args.data
# Save the file on disk using a uuid
filename = "%s%s.dat" % (self.file_prefix, uuid())
ecgfile.save(os.path.join(current_app.config['UPLOAD_FOLDER'], filename))
# Create a new database record for this file
with open_session() as session:
ecgdata = ECGData(filename)
session.add(ecgdata)
session.flush()
session.commit()
print(ecgdata.id)
return gen_response({"id": ecgdata.id})
def get(self, patient_id):
"""Get a patient record by ID from the database
Example **GET http://hrsdb/patient/1** ::
{
"response": {
"id": 1,
"first_name": "Bob",
"last_name": "Smith",
"gender": 0,
"date_of_birth": "1997/04/12"
}
}
"""
with open_session() as session:
try:
record = session.query(Patient) \
.filter(Patient.id == patient_id).one()
except NoResultFound:
logger.info("No record found")
resp = gen_response("No record found")
resp.status_code = 404
return resp
except Exception as error:
print("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
return gen_response(to_dict(record))
def get(self):
"""
Fetchs the ECG data for a specific entry from disk
Example **GET http://hrsdb/ecgdata?id=1**
.. code-block:: javascript
{
"response": [
0,0,0,0,10,40...
]
}
"""
args = self.get_parser.parse_args(strict=True)
with open_session() as session:
try:
db_record = query = session.query(ECGData) \
.filter(ECGData.id == args.id).one()
except NoResultFound:
logger.info("No record found") # TODO: remove debugging
resp = gen_response("No result found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
data_file_path = os.path.join(current_app.config['UPLOAD_FOLDER'],
db_record.path)
with open(data_file_path) as data_file:
csv_reader = csv.reader(data_file)
data = list(csv_reader)[0]
return gen_response(data)
def get(self):
"""
Fetchs the ECG data for a specific entry from disk
Example **GET http://hrsdb/ecgdata?id=1**
.. code-block:: javascript
{
"response": [
0,0,0,0,10,40...
]
}
"""
args = self.get_parser.parse_args(strict=True)
with open_session() as session:
try:
db_record = query = session.query(ECGData) \
.filter(ECGData.id == args.id).one()
except NoResultFound:
logger.info("No record found") # TODO: remove debugging
resp = gen_response("No result found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
data_file_path = os.path.join(current_app.config['UPLOAD_FOLDER'], db_record.path)
with open(data_file_path) as data_file:
csv_reader = csv.reader(data_file)
data = list(csv_reader)[0]
return gen_response(data)
def get(self, biometric_id):
"""Get a biometric record by ID from the database
Example **GET http://hrsdb/biometric/1** ::
{
"response": {
"id": 1,
"patient_id": 1,
"timestamp": "2015/05/19" 12:04:59,
"type_id": 1,
"value": "167"
}
}
"""
record = None
with open_session() as session:
try:
record = session.query(Biometric) \
.filter(Biometric.id == biometric_id).one()
except NoResultFound:
logger.warn("No record found")
resp = gen_response("No record found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
logger.debug(record)
return gen_response(to_dict(record))
def get(self, patient_id):
"""Get a patient record by ID from the database
Example **GET http://hrsdb/patient/1** ::
{
"response": {
"id": 1,
"first_name": "Bob",
"last_name": "Smith",
"gender": 0,
"date_of_birth": "1997/04/12"
}
}
"""
with open_session() as session:
try:
record = session.query(Patient) \
.filter(Patient.id == patient_id).one()
except NoResultFound:
logger.info("No record found")
resp = gen_response("No record found")
resp.status_code = 404
return resp
except Exception as error:
print("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
return gen_response(to_dict(record))
def put(self):
"""Put a new ECG record into the database
Example JSON Body **PUT http://hrsdb/ecg** ::
{
"id": 1,
"patient_id": 1,
"sampling_freq": 1000.0
"timestamp": "2015/05/19" 12:04:59,
"data_id": 1,
}
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.put_parser.parse_args()
# Convert data_time and validate
timestamp = utils.str2date(args.timestamp)
if timestamp is None:
abort(500)
return_id = None
with open_session() as session:
try:
patient = session.query(Patient) \
.filter(Patient.id == args.patient_id).one()
ecgdata = session.query(ECGData) \
.filter(ECGData.id == args.data_id).one()
except NoResultFound:
logger.warn("PUT: No Patient matching id for biometric")
return gen_response("No matching Patient")
except Exception as error:
logger.exception("Exception: %s" % (str(error)))
return gen_response("Internal server error")
# Add ecg record
ecg = patient.add_ecg(
session,
args.sampling_freq,
ecgdata,
timestamp
)
session.commit()
return gen_response({"id": ecg.id})
def put(self, biometric_id):
"""Put a new biometric record into the database
Example JSON Body **PUT http://hrsdb/biometric/0** ::
{
"patient_id": 1,
"timestamp": "2015/05/19" 12:04:59,
"type_id": 1,
"value": "167"
}
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.parser.parse_args()
# Convert data_time and validate
timestamp = utils.str2date(args.timestamp)
if timestamp is None:
abort(500)
return_id = None
with open_session() as session:
try:
patient = session.query(Patient) \
.filter(Patient.id == args.patient_id).one()
except NoResultFound:
logger.warn("PUT: No Patient matching id for biometric")
return gen_response("No matching Patient")
except Exception as error:
logger.exception("Exception: %s" % (str(error)))
return gen_response("Internal server error")
# Add biometric record
biometric = patient.add_biometric(session,
args.biometric_type_id,
args.value,
timestamp
)
if biometric is None:
logger.warn("PUT: No Patient matching id for biometric")
return gen_response("No matching Biometric type")
session.commit()
return gen_response({"id": biometric.id})
def get(self):
"""
Fetchs the list of biometric records from the database for this patient
The list can optionally be filtered using a biometric_type id.
Example **GET http://hrsdb/biometrics?patient_id=1&biometric_type_id=1**
.. code-block:: javascript
{
"response": [
{
"id": 1,
"patient_id": 1,
"timestamp": "2015/05/19" 12:04:59,
"type_id": 1,
"value": "167"
}
{
"id":2,
...
}
]
}
"""
args = self.parser.parse_args(strict=True)
with open_session() as session:
try:
query = session.query(Biometric) \
.filter(Biometric.patient_id == args.patient_id)
# Optional filter by type_id
if (args.biometric_type_id):
query = query.filter(
Biometric.type_id == args.biometric_type_id)
records = query.all()
except NoResultFound:
logger.info("No record found")
resp = gen_response("No result found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
# Build the response list
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def get(self):
"""
Fetchs the list of biometric records from the database for this patient
The list can optionally be filtered using a biometric_type id.
Example **GET http://hrsdb/biometrics?patient_id=1&biometric_type_id=1**
.. code-block:: javascript
{
"response": [
{
"id": 1,
"patient_id": 1,
"timestamp": "2015/05/19" 12:04:59,
"type_id": 1,
"value": "167"
}
{
"id":2,
...
}
]
}
"""
args = self.parser.parse_args(strict=True)
with open_session() as session:
try:
query = session.query(Biometric) \
.filter(Biometric.patient_id == args.patient_id)
# Optional filter by type_id
if(args.biometric_type_id):
query = query.filter(Biometric.type_id == args.biometric_type_id)
records = query.all()
except NoResultFound:
logger.info("No record found")
resp = gen_response("No result found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
# Build the response list
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def put(self):
"""Put a new ECG record into the database
Example JSON Body **PUT http://hrsdb/ecg** ::
{
"id": 1,
"patient_id": 1,
"sampling_freq": 1000.0
"timestamp": "2015/05/19" 12:04:59,
"data_id": 1,
}
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.put_parser.parse_args()
# Convert data_time and validate
timestamp = utils.str2date(args.timestamp)
if timestamp is None:
abort(500)
return_id = None
with open_session() as session:
try:
patient = session.query(Patient) \
.filter(Patient.id == args.patient_id).one()
ecgdata = session.query(ECGData) \
.filter(ECGData.id == args.data_id).one()
except NoResultFound:
logger.warn("PUT: No Patient matching id for biometric")
return gen_response("No matching Patient")
except Exception as error:
logger.exception("Exception: %s" % (str(error)))
return gen_response("Internal server error")
# Add ecg record
ecg = patient.add_ecg(session, args.sampling_freq, ecgdata,
timestamp)
session.commit()
return gen_response({"id": ecg.id})
def put(self, biometric_id):
"""Put a new biometric record into the database
Example JSON Body **PUT http://hrsdb/biometric/0** ::
{
"patient_id": 1,
"timestamp": "2015/05/19" 12:04:59,
"type_id": 1,
"value": "167"
}
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.parser.parse_args()
# Convert data_time and validate
timestamp = utils.str2date(args.timestamp)
if timestamp is None:
abort(500)
return_id = None
with open_session() as session:
try:
patient = session.query(Patient) \
.filter(Patient.id == args.patient_id).one()
except NoResultFound:
logger.warn("PUT: No Patient matching id for biometric")
return gen_response("No matching Patient")
except Exception as error:
logger.exception("Exception: %s" % (str(error)))
return gen_response("Internal server error")
# Add biometric record
biometric = patient.add_biometric(session, args.biometric_type_id,
args.value, timestamp)
if biometric is None:
logger.warn("PUT: No Patient matching id for biometric")
return gen_response("No matching Biometric type")
session.commit()
return gen_response({"id": biometric.id})
def put(self, patient_id):
"""PUT a new record into the database
Example JSON Body **PUT http://hrsdb/patient/0** ::
{
"first_name": "Bob",
"last_name": "Smith",
"gender": 0,
"date_of_birth": "1997/04/12"
}
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.parser.parse_args()
# Convert data_time and validate
date_of_birth = utils.str2date(args.date_of_birth)
if date_of_birth is None:
abort()
return_id = None
with open_session() as session:
record = Patient(args.first_name,
args.last_name,
args.gender,
date_of_birth)
session.add(record)
session.flush()
session.commit()
return_id = record.id
# Check for error handling
if return_id is None:
return gen_response("internal server error")
else:
return gen_response({"id": return_id})
def get(self):
"""
Fetchs a list of ecgc records from the database for a specific patient.
Example **GET http://hrsdb/ecg?patient_id=1**
.. code-block:: javascript
{
"response": [
{
"id": 1,
"patient_id": 1,
"sampling_freq": 1000.0
"timestamp": "2015/05/19" 12:04:59,
"data_id": 1,
}
{
"id":2,
...
}
]
}
"""
args = self.get_parser.parse_args(strict=True)
with open_session() as session:
try:
records = session.query(ECG) \
.filter(ECG.patient_id == args.patient_id) \
.all()
except NoResultFound:
logger.info("No record found")
resp = gen_response("No result found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
# Build the response list
print(records)
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def get(self):
"""
Fetchs a list of ecgc records from the database for a specific patient.
Example **GET http://hrsdb/ecg?patient_id=1**
.. code-block:: javascript
{
"response": [
{
"id": 1,
"patient_id": 1,
"sampling_freq": 1000.0
"timestamp": "2015/05/19" 12:04:59,
"data_id": 1,
}
{
"id":2,
...
}
]
}
"""
args = self.get_parser.parse_args(strict=True)
with open_session() as session:
try:
records = session.query(ECG) \
.filter(ECG.patient_id == args.patient_id) \
.all()
except NoResultFound:
logger.info("No record found")
resp = gen_response("No result found")
resp.status_code = 404
return resp
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
# Build the response list
print(records)
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def put(self, patient_id):
"""PUT a new record into the database
Example JSON Body **PUT http://hrsdb/patient/0** ::
{
"first_name": "Bob",
"last_name": "Smith",
"gender": 0,
"date_of_birth": "1997/04/12"
}
Example response::
{
"response": {
"id": 1
}
}
"""
args = self.parser.parse_args()
# Convert data_time and validate
date_of_birth = utils.str2date(args.date_of_birth)
if date_of_birth is None:
abort()
return_id = None
with open_session() as session:
record = Patient(args.first_name, args.last_name, args.gender,
date_of_birth)
session.add(record)
session.flush()
session.commit()
return_id = record.id
# Check for error handling
if return_id is None:
return gen_response("internal server error")
else:
return gen_response({"id": return_id})
def get(self):
"""Gets all patient records from the database
Example **GET http://hrsdb/patients**
.. code-block:: javascript
{
"response": [
{
"id": 1,
"first_name": "Bob",
"last_name": "Smith",
"gender": 0,
"date_of_birth": "1997/04/12"
}
{
"id": 2
...
}
]
}
"""
with open_session() as session:
try:
records = session.query(Patient).all()
except NoResultFound:
logger.info("No record found") # TODO: remove debugging
return gen_response("No result found")
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
# Build the response list
rlist = [to_dict(record) for record in records]
return gen_response(rlist)
def get(self):
"""Gets all patient records from the database
Example **GET http://hrsdb/patients**
.. code-block:: javascript
{
"response": [
{
"id": 1,
"first_name": "Bob",
"last_name": "Smith",
"gender": 0,
"date_of_birth": "1997/04/12"
}
{
"id": 2
...
}
]
}
"""
with open_session() as session:
try:
records = session.query(Patient).all()
except NoResultFound:
logger.info("No record found") # TODO: remove debugging
return gen_response("No result found")
except Exception as error:
logger.exception("Exeption: %s" % (str(error)))
return gen_response("Internal server error")
# Build the response list
rlist = [to_dict(record) for record in records]
return gen_response(rlist)