def get_db_connection():
global connection
global fb
if not connection:
connection = psycopg2.connect(dbname='fhirbase',
user='******',
host='fhirbase',
port='5432')
fb = fhirbase.FHIRBase(connection)
return fb
def get_resource():
connection = psycopg2.connect(
database='fhirbase',
user='******',
host='fhirbasedb-service.globalhivteam30.svc.cluster.local',
port='5432',
password='******')
fb = fhirbase.FHIRBase(connection)
#patientData = fb.read(resource_type='Patient', id='patientId')
with fb.execute('SELECT * FROM patient') as cursor:
respons = (cursor.fetchall())
return jsonify(respons)
def get_patient_resource(id):
connection = psycopg2.connect(database='fhirbase',
user='******',
host='172.17.0.3',
port='5432',
password='******')
fb = fhirbase.FHIRBase(connection)
#patientData = fb.read(resource_type='Patient', id='patientId')
#with fb.execute('SELECT * FROM patient WHERE id=%s', [id]) as cursor:
#return(cursor.fetchall())
print('\nID of Patient: ', [id])
getPatient = fb.read({'resourceType': 'Patient', 'id': [id]})
print('\nGot Patient: ', getPatient)
def save_in_fhirbase(instances):
"""
Save instances of FHIR resources in the fhirbase
:param instances: list of instances
"""
config = Config("fhirbase")
with psycopg2.connect(dbname=config.database,
user=config.user,
host=config.host,
port=config.port) as connection:
fb = fhirbase.FHIRBase(connection)
for instance in instances:
fb.create(instance)
def fb(db):
instance = fhirbase.FHIRBase(db)
instance.execute_without_result('TRUNCATE TABLE transaction')
instance.execute_without_result('TRUNCATE TABLE patient')
return instance
def POST_resource():
#have new test
connection = psycopg2.connect(database='fhirbase',
user='******',
host='172.17.0.3',
port='5432',
password='******')
fb = fhirbase.FHIRBase(connection)
input_form = request.get_json()
#transform
#form_obj = json.loads(input_form, object_hook=testFormDecoder)
#return some sample values for display
testForm = input_form['testForm']
print('\nfirst name : ', testForm['name']['firstName'])
fb = fhirbase.FHIRBase(connection)
resultOfPatientCreation = fb.create({
'resourceType':
'Patient',
'name': [{
'use':
'official',
'family':
testForm['name']['lastName'],
'given':
[testForm['name']['firstName'], testForm['name']['middleName']]
}],
'gender':
testForm['sex'],
'birthDate':
testForm['dob'],
})
print('\nresult of create : ', resultOfPatientCreation)
mapOfTests = {}
for i in testForm['testData']['tests']:
print("\n loping over map: ", i)
if i['testNumber'] == 1:
mapOfTests[0] = i
elif i['testNumber'] == 2:
mapOfTests[1] = i
elif i['testNumber'] == 3:
mapOfTests[2] = i
print("\nwhat is in the map of tests: ", len(mapOfTests))
firstTest = returnTestTypeData(
testForm['testData']['tests'][0]['testAssay'])
secondTest = returnTestTypeData(
testForm['testData']['tests'][1]['testAssay'])
thirdTest = returnTestTypeData(
testForm['testData']['tests'][2]['testAssay'])
idOfPatient = resultOfPatientCreation['id']
print("\nID of patient: ", idOfPatient)
resultOfHIVObservationCreation = fb.create({
'resourceType':
'Observation',
'code': {
'coding': [{
'system': 'http://loinc.org',
'code': '69668-2',
'display': 'HIV 1 and 2 Ab IA.rapid Nom'
}]
},
'subject': {
'reference': 'Patient/' + str(idOfPatient)
},
'effectiveDateTime':
testForm['testData']['testDate'],
'valueString':
testForm['resultReceived'],
'component': [{
'code': {
'coding': [{
'system': firstTest.system,
'code': firstTest.code,
'display': firstTest.display
}]
},
'valueString': mapOfTests[0]['testResult']
}, {
'code': {
'coding': [{
'system': secondTest.system,
'code': secondTest.code,
'display': secondTest.display
}]
},
'valueString': mapOfTests[1]['testResult']
}, {
'code': {
'coding': [{
'system': thirdTest.system,
'code': thirdTest.code,
'display': thirdTest.display
}]
},
'valueString': mapOfTests[2]['testResult']
}]
})
print('\nresult of create : ', resultOfHIVObservationCreation)
sampleAns = str(resultOfPatientCreation) + "\n" + str(
resultOfHIVObservationCreation)
return sampleAns
)
with open("benchmark/examples.zip", "wb") as f:
for data in r.iter_content(block_size):
t.update(len(data))
f.write(data)
t.close()
else:
print("Using cached resources")
download_resources()
connection = psycopg2.connect(dbname="fb",
user="******",
host="localhost",
port="5432")
fb = fhirbase.FHIRBase(connection)
examples = tqdm(iter_examples(),
total=count_examples(),
desc="Running write benchmark")
stats = {}
inserted = []
for example, data in examples:
if not data.get("id"):
data["id"] = str(uuid4())
start = timer()
res = fb.create(data)
end = timer()
stats[example] = end - start
inserted.append(res)
def db_connect():
pguser = os.getenv('PGUSER', 'postgres')
pgpassword = os.getenv('PGPASSWORD', 'postgres')
pghost = os.getenv('PGHOST', 'localhost')
pgport = os.getenv('PGPORT', '5432')
dbname = os.getenv('PGDATABASE', 'fhirbase')
return psycopg2.connect(dbname=dbname, user=pguser,
password=pgpassword, host=pghost, port=pgport)
if __name__ == '__main__':
conn = db_connect()
try:
fb = fhirbase.FHIRBase(conn)
print('Create patient')
patient = fb.create({'resourceType': 'Patient'})
print(patient)
print()
print('Update patient')
patient.update({'name': [{'text': 'John'}]})
updated_patient = fb.update(patient)
print(updated_patient)
print()
print('List of patients')