def test_days_taking(self):
patient = Patient(prescriptions=[Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=2), days_supply=2),
Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=3), days_supply=2)])
assert patient.days_taking("Paracetamol") == set([date.today() - timedelta(days=3),
date.today() - timedelta(days=2),
date.today() - timedelta(days=1)])
def initData(): """Load data and mappings from Raw data files and mapping files""" Patient.load() Med.load() Problem.load() Lab.load() Refill.load()
def add_patient_clicked(self):
text, ok = QtGui.QInputDialog.getText(self, '', 'Enter patient name:')
if ok:
new_file_name = os.path.join(PATIENT_DIR, str(text) + '.pkl')
if os.path.exists(new_file_name):
QtGui.QMessageBox.about(self, 'Error', 'Name already exists!')
else:
new_patient = Patient(str(text))
else:
return
text, ok = QtGui.QInputDialog.getInt(self, '', 'Enter patient age:')
if ok:
new_patient.age = int(text)
else:
return
text, ok = QtGui.QInputDialog.getText(self, '', 'Enter patient diagnosis:')
if ok:
new_patient.diagnosis = str(text)
else:
return
text, ok = QtGui.QInputDialog.getItem(self, '', 'Enter patient gender:', ['Female', 'Male', 'Other'])
if ok:
new_patient.gender = str(text)
else:
return
pickle.dump(new_patient, open(new_file_name, 'wb'))
self.update_patient_list()
def test_clash_with_two_different_prescriptions(self):
patient = Patient(
prescriptions=[
Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=2),
Prescription("Prozac", dispense_date=days_ago(days=2), days_supply=2),
]
)
assert patient.clash(["Codeine", "Prozac"]) == {days_ago(days=2), days_ago(days=1)}
def test_clash_with_two_prescriptions_for_same_medication(self):
patient = Patient(
prescriptions=[
Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=2),
Prescription("Codeine", dispense_date=days_ago(days=3), days_supply=2),
]
)
assert patient.clash(["Codeine"]) == {days_ago(days=3), days_ago(days=2), days_ago(days=1)}
def test_days_taking(self):
patient = Patient(
prescriptions=[
Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=2),
Prescription("Codeine", dispense_date=days_ago(days=3), days_supply=2),
]
)
assert patient.days_taking("Codeine") == {days_ago(days=3), days_ago(days=2), days_ago(days=1)}
def test_clash_overlapping_today(self):
patient = Patient(
prescriptions=[
Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=3),
Prescription("Prozac", dispense_date=days_ago(days=2), days_supply=3),
]
)
assert patient.clash(["Codeine", "Prozac"]) == {days_ago(days=2), days_ago(days=1)}
def index():
form = MyForm()
results = None
resultsPrint = None
if form.validate_on_submit():
'''Try biomarker: estrogen receptor'''
patient_file = Patient(form.age.data,form.age_unit.data,form.gender.data,form.biomarker.data)
results = searcher.search(patient_file._get_query_string())
resultsPrint = searcher.print_results(results,form.biomarker.data)
return render_template('search.html', form=form, results = resultsPrint)
def script(patient_filename, hpo_filename, disease_phenotype_filename,
orphanet_lookup_filename=None, orphanet_prevalence_filename=None, proto=None,
use_disease_prevalence=False, use_phenotype_frequency=False,
use_patient_phenotypes=False, distribute_ic_to_leaves=False,
use_aoo=False, scores=None):
hpo = HPO(hpo_filename, new_root='HP:0000118')
diseases = Diseases(disease_phenotype_filename)
orphanet = None
if orphanet_lookup_filename and orphanet_prevalence_filename:
orphanet = Orphanet(orphanet_prevalence_filename, lookup_filename=orphanet_lookup_filename)
patients = [patient
for patient in Patient.iter_from_file(patient_filename, hpo)
if patient.hp_terms]
if proto:
proto = [patient
for patient in Patient.iter_from_file(proto, hpo)
if patient.hp_terms]
if use_patient_phenotypes:
use_patient_phenotypes = patients
hpoic = HPOIC(hpo, diseases, orphanet=orphanet, patients=use_patient_phenotypes,
use_disease_prevalence=use_disease_prevalence,
use_phenotype_frequency=use_phenotype_frequency,
distribute_ic_to_leaves=distribute_ic_to_leaves)
total_patient_logprob = 0
for patient in patients:
total_patient_logprob += hpoic.information_content(patient.hp_terms)
logging.info('Total patient logprob: {:.1f}'.format(-total_patient_logprob))
header = None
for i in range(len(patients)):
patient = patients[i]
id1 = patient.external_id if patient.external_id else patient.id
compare_against = [patients[j] for j in range(i+1, len(patients))]
if proto:
compare_against.extend(proto)
for o in compare_against:
id2 = o.external_id if o.external_id else o.id
sims = compare_patients(hpoic, patient, o, scores=scores, use_aoo=use_aoo)
if header is None:
header = sorted(sims)
print('\t'.join(['A', 'B'] + header))
sim_strs = ['{:.6f}'.format(sims[sim]) for sim in header]
for sim, sim_str in zip(header, sim_strs):
logging.debug('{}: {}'.format(sim, sim_str))
print('\t'.join([id1, id2] + sim_strs))
def initData(): """Load data and mappings from Raw data files and mapping files""" Patient.load() Med.load() Problem.load() Lab.load() Refill.load() VitalSigns.load() Immunization.load() Procedure.load() SocialHistory.load() FamilyHistory.load() Allergy.load()
def script(patient_hpo_filename, hpo_filename, disease_phenotype_filename,
**kwargs):
hpo = HPO(hpo_filename, new_root='HP:0000118')
diseases = Diseases(disease_phenotype_filename)
hpoic = HPOIC(hpo, diseases)
print('\t'.join(['Patient ID', 'External ID', 'IC']))
for patient in Patient.iter_from_file(patient_hpo_filename, hpo):
print('\t'.join(map(str, [patient.id, patient.external_id, hpoic.information_content(patient.hp_terms)])))
def test_clash_with_two_different_prescriptions(self):
patient = Patient(prescriptions=[Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=2), days_supply=2),
Prescription("Aspirin", dispense_date = date.today() - timedelta(days=2), days_supply=2)])
assert patient.clash(["Paracetamol", "Aspirin"]) == set([date.today() - timedelta(days=2), date.today() - timedelta(days=1)])
def apply(self, param):
param.name = '{}:{}'.format(param.name, self.value)
# announce all handlers
FHIRSearchParamHandler.announce_handler(FHIRSearchParamModifierHandler)
FHIRSearchParamHandler.announce_handler(FHIRSearchParamOperatorHandler)
FHIRSearchParamHandler.announce_handler(FHIRSearchParamMultiHandler)
FHIRSearchParamHandler.announce_handler(FHIRSearchParamTypeHandler)
if '__main__' == __name__:
from patient import Patient
print('1 '+FHIRSearch(Patient, {'name': 'Willis'}).construct())
print('1 '+Patient.where({'name': 'Willis'}).construct())
print('1 '+Patient.where().name('Willis').construct())
print('= Patient?name=Willis')
print('')
print('2 '+FHIRSearch(Patient, {'name': {'$exact': 'Willis'}}).construct())
print('= Patient?name:exact=Willis')
print('')
print('3 '+FHIRSearch(Patient, {'name': {'$or': ['Willis', 'Wayne', 'Bruce']}}).construct())
print('= Patient?name=Willis,Wayne,Bruce')
print('')
print('4 '+FHIRSearch(Patient, {'name': {'$and': ['Willis', {'$exact': 'Bruce'}]}}).construct())
print('= Patient?name=Willis&name:exact=Bruce')
print('')
print('5 '+FHIRSearch(Patient, {'birthDate': {'$gt': '1950', '$lte': '1970'}}).construct())
print('= Patient?birthDate=>1950&birthDate=<=1970')
print('')
# Show progress with '.' characters
print ".",
sys.stdout.flush()
parser.exit(0,"\nDone writing %d patient RDF files!"%len(Patient.mpi))
# Write all patient RDF files out to a directory
if args.writeIndivo:
print "Writing files to %s:"%args.writeIndivo
initData()
path = args.writeIndivo
if not os.path.exists(path):
parser.error("Invalid path: '%s'.Path must already exist."%path)
if not path.endswith('/'): path = path+'/' # Works with DOS? Who cares??
import indivo
for pid in Patient.mpi:
f = open(path+"p%s.py"%pid,'w')
indivo.writePatientFile(f, pid)
f.close()
# Show progress with '.' characters
print ".",
sys.stdout.flush()
parser.exit(0,"\nDone writing %d patient RDF files!"%len(Patient.mpi))
# Generate a new patients data file, re-randomizing old names, dob, etc:
Patient.generate()
parser.exit(0,"Patient data written to: %s\n"%PATIENTS_FILE)
parser.error("No arguments given")
# A small function to strip input down to the first phrase or sentence, to
# remove punctuation and captialization, and to replace superfluous whitespace.
# It returns the input as tokenized, capitalized, puctuation devoid words.
def input_tenderizer(input_str):
# Begin by tokenizing the sentence into individual, whitespace separated
# components.
temp = input_str.lower().translate(None, ',.?!:;\'\"').split()
# Translate second person to first person pronouns.
# Remove any punctuation from the tokens in temp.
#for x in temp:
# x = x.translate(None, ',.?!:;\'\"').upper()
# We might be able to terminate the sentence with str.find
# Return the list.
return ' '.join(temp)
patient = Patient()
patient.otherPersonName = 'individual'
#var = "Hello, cruel world!"
#print(var)
#while (var != "Die"):
print "Hello " + patient.otherPersonName
while True:
print '<' + patient.name + '> ' + patient.get_response(input_tenderizer(raw_input('<' + patient.otherPersonName + '> '))).lower().capitalize();
print("Goodbye, cruel world!")
def add_patient(self):
name = input("Enter patient name:\n")
info = input("Enter patient condition:\n")
self.new_pat_list.append(Patient(name, info))
print(f"{name} has been added to the patient list.")
print("")
def test_clash_with_one_prescription(self):
patient = Patient(prescriptions=[Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=2)])
assert patient.clash(["Codeine"]) == {days_ago(days=2), days_ago(days=1)}
from config import pid_noConcussion, pid_3stepProtocol, pid_testRetest, pid_concussion, feature_functions, epoch_size, \
channels
from patient import Patient
# go through each list of ids
for lst in [
pid_noConcussion, pid_3stepProtocol, pid_testRetest, pid_concussion
]:
# for each id...
for pid in lst:
print("Processing pid: {}".format(pid))
p = Patient(pid, load_session_examples=False, load_session_raw=True)
# generate file for pre_test
if p.pre_test is not None:
p.pre_test.remove_artifacts()
p.pre_test.get_examples(feature_functions,
epoch_size=epoch_size,
channels=channels)
p.pre_test.save_examples()
if p.post_test is not None:
# generate file for post_test
p.post_test.remove_artifacts()
p.post_test.get_examples(feature_functions,
epoch_size=epoch_size,
channels=channels)
p.post_test.save_examples()
delimiter=',')
seis1 = np.loadtxt('seis1_' + save_file_name + '.csv',
delimiter=',')
seis2 = np.loadtxt('seis2_' + save_file_name + '.csv',
delimiter=',')
phono1 = np.loadtxt('phono1_' + save_file_name + '.csv',
delimiter=',')
phono2 = np.loadtxt('phono2_' + save_file_name + '.csv',
delimiter=',')
else:
# Change directory
wd = 'data/' + folder_name + '/files_of_interest'
# Load TDMS file into Patient object
patient = Patient(wd, file_name)
# Declare time and signal
if use_intervals and files[folder_name][dosage][1][
"intervals"] != ["None"]:
start = (start_time -
np.min(patient.times)) * patient.frequency
end = patient.total_time * patient.frequency if end_time == "end" else (
end_time - np.min(patient.times)) * patient.frequency
interval = range(int(start), int(end))
time, signal, seis1, seis2, phono1, phono2 = patient.get_interval(
interval)
else:
time = patient.times
signal = patient.ecg
seis1 = patient.seis1
for i in range(d):
Q[i, i] = -np.sum(Q[i, :])
Q_true = Q
pi0 = np.array([0.5, 0.25, 0.25])
globalParams = {}
rate1 = np.random.uniform(0, 2)
rate2 = np.random.uniform(0, 2)
rate3 = np.random.uniform(0, 2)
Q = np.array([[-rate1, rate1 / 2, rate1 / 2],
[rate2 / 3, -rate2, 2 * rate2 / 3],
[2 * rate3 / 4, 2 * rate3 / 4, -rate3]])
globalParams['Q'] = Q
globalParams['numStates'] = 3
T_max = 5000
N = 2
patients = []
for n in range(N):
patient = Patient()
patient.initialize_randomly(Q_true, globalParams, T_max, pi0)
patients.append(patient)
for i in range(50):
globalParams['Q'] = EM_step(globalParams['Q'], patients, globalParams,
pi0)
print(Q_true)
print(globalParams['Q'])
def __get_patient_object(self, user_id):
self.__validate_patient_id(user_id)
self.cursor.execute(PATIENT_DATA, (user_id, ))
data = self.cursor.fetchone()
return Patient(data[0], data[1], data[2], data[3])
if self.beds[key] == 0:
self.beds[key] = patients[x]
patients[x].bedNum = key
break #this breaks so that once it assigns the patient being appended a bed number it doesnt keep looping
else:
print 'Hospital is full!!'
return self
def discharge(self, patient):
self.patients.remove(patient)
self.beds[patient.bedNum] = 0
patient.bedNum = None
return self
patient1 = Patient('Faith', ('kindess', 'goofy', 'caring'))
patient2 = Patient('Tiwa', ('cute', 'ratchet', 'loving'))
patient3 = Patient('Yako', ('ratchet', 'tall', 'pseudo english'))
patient4 = Patient('Wura', ('ratchet', 'tall', 'pseudo english'))
patient5 = Patient('Vitali', ('kindess', 'goofy', 'caring'))
patient6 = Patient('Matt', ('cute', 'ratchet', 'loving'))
patient7 = Patient('John', ('ratchet', 'tall', 'pseudo english'))
patient8 = Patient('Ryan', ('ratchet', 'tall', 'pseudo english'))
hospital1 = Hospital('Premier', 5)
hospital1.admit(
patient1, patient2, patient3
) #when a patient is admitted he gets a bed and the bedkey become his bed number
hospital1.admit(patient7)
print len(hospital1.patients)
def test_days_taking_for_irrelevant_prescription(self):
patient = Patient(prescriptions=[
Prescription(
"Codeine", dispense_date=days_ago(days=2), days_supply=2)
])
assert patient.days_taking("Prozak") == set()
def test_clash_with_one_irrelevant_prescription(self):
patient = Patient(prescriptions=[
Prescription(
"Codeine", dispense_date=days_ago(days=2), days_supply=2)
])
assert patient.clash(["Prozac"]) == set()
def test_days_taking_for_irrelevant_prescription(self):
patient = Patient(prescriptions=[Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=2), days_supply=2)])
assert patient.days_taking("Aspirin") == set()
def test_clash_with_no_prescriptions(self):
patient = Patient(prescriptions=[])
assert patient.clash([]) == set()
def load(cls, path):
# General
try:
with zipfile.ZipFile(path, "r") as zip:
namelist = zip.namelist()
# Load Settings
settings_path = next(name for name in namelist
if str.endswith(name, ".settings"))
settings = None
try:
settings = ProjectPreferences.from_json_file(
zip.extract(settings_path))
except OSError:
print("[1/1] Loading of the settings file %s failed" %
settings_path)
else:
print("[1/1] Successfully loaded the settings file %s" %
settings_path)
# Load Patients
patients_path = [
name for name in namelist
if str.endswith(name, ".patient")
]
patients = []
for i, patient_path in enumerate(patients_path):
try:
patients.append(
Patient.from_json_file(zip.extract(patient_path)))
except OSError:
print(
"[{0}/{1}] Loading of the patient file {2} failed".
format(i + 1, len(patients_path), patient_path))
else:
print(
"[{0}/{1}] Successfully loaded the patient file {2}"
.format(i + 1, len(patients_path), patient_path))
patients = [
Patient.from_json_file(zip.extract(patient))
for patient in patients_path
]
# Load Groups
groups_path = [
name for name in namelist if str.endswith(name, ".group")
]
groups = []
for i, group_path in enumerate(groups_path):
try:
groups.append(
Group.from_json_file(zip.extract(group_path),
patients))
except OSError:
print("[{0}/{1}] Loading of the group file {2} failed".
format(i + 1, len(groups_path), group_path))
else:
print(
"[{0}/{1}] Successfully loaded the group file {2}".
format(i + 1, len(groups_path), group_path))
# Load Protocols
protocols_path = [
name for name in namelist if str.endswith(name, ".prov")
]
protocols = []
for i, protocol_path in enumerate(protocols_path):
try:
protocols.append(
Protocol.from_json_file(
zip.extract(protocol_path)))
except OSError:
print(
"[{0}/{1}] Loading of the protocol file {2} failed"
.format(i + 1, len(protocols_path), protocol_path))
else:
print(
"[{0}/{1}] Successfully loaded the protocol file {2}"
.format(i + 1, len(protocols_path), protocol_path))
# Load Datasets
datasets_path = [
name for name in namelist
if str.endswith(name, ".dataset")
]
datasets = []
for i, dataset_path in enumerate(datasets_path):
try:
datasets.append(
Dataset.from_json_file(zip.extract(dataset_path),
protocols, patients))
except OSError:
print(
"[{0}/{1}] Loading of the dataset file {2} failed".
format(i + 1, len(datasets_path), dataset_path))
else:
print(
"[{0}/{1}] Successfully loaded the dataset file {2}"
.format(i + 1, len(datasets_path), dataset_path))
# Load Visualizations
visualizations_path = [
name for name in namelist
if str.endswith(name, ".visualization")
]
visualizations = []
for i, visualization_path in enumerate(visualizations_path):
try:
visualizations.append(
Visualization.from_json_file(
zip.extract(visualization_path), patients,
datasets))
except OSError:
print(
"[{0}/{1}] Loading of the visualization file {2} failed"
.format(i + 1, len(visualizations_path),
visualization_path))
else:
print(
"[{0}/{1}] Successfully loaded the visualization file {2}"
.format(i + 1, len(visualizations_path),
visualization_path))
print("Successfully loaded the project %s " % path)
return cls(settings, patients, groups, protocols, datasets,
visualizations)
except OSError:
print("Loading of the project %s failed" % path)
# It has a Queue which is set through the constructor.
# It has a method to add a Patient to the queue.
# It has a method to treat the next patient in the queue.
from patient import Patient
from my_queue import My_Queue
class Hospital:
def __init__(self, my_queue):
self.my_queue = my_queue
def add_a_patient(self, patient):
self.my_queue.addPatients(patient)
def treat_next_patient(self):
next_person = self.my_queue.get_next_person()
for patient in self.my_queue:
if patient == next_person:
patient.treat()
my_queue = My_Queue()
patient1 = Patient('Lucy', 38, 'female')
patient2 = Patient('Nicy', 56, 'female')
my_queue.addPatients(patient1)
hospital = Hospital(my_queue)
hospital.add_a_patient(patient2)
hospital.treat_next_patient()
class TestPatient(unittest.TestCase):
def setUp(self):
from datetime import date
self.day = date(2018, 2, 1)
self.appt_fields = ['Date', 'Appt Time', 'Type']
self.patient_fields = [
'MRN', 'Patient', 'Pref Language', 'Mobile #', 'Pt. E-mail Address'
]
self.patient = Patient(self.patient_fields, [
1445578838, 'patient_name', 'English', '333-333-3333',
'*****@*****.**'
])
def reset_appts(self):
self.patient.appts = {}
def test_non_english_speaking_patient(self):
self.patient.language = 'French'
assert not self.patient.enrolled(self.day)
assert self.patient.care_tour == None
self.patient.language = 'English'
def test_patient_with_past_appt(self):
self.patient.add_appt(self.appt_fields,
['1/20/18', '9:00 AM', 'THORACENTESIS'])
assert not self.patient.enrolled(self.day)
assert self.patient.care_tour == None
def test_patient_with_appt_tmrw(self):
self.patient.add_appt(self.appt_fields,
['2/2/18', '10:00 AM', 'PLEURX'])
assert not self.patient.enrolled(self.day)
assert self.patient.care_tour == None
self.reset_appts()
def test_patient_with_appt(self):
self.patient.add_appt(self.appt_fields,
['2/3/18', '10:00 AM', 'FLEX BRONCH WITH BAL'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 1
self.reset_appts()
self.patient.add_appt(self.appt_fields,
['2/3/18', '11:00 AM', 'TRANS BRONCH BX'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 1
self.reset_appts()
self.patient.add_appt(self.appt_fields,
['2/3/18', '12:00 PM', 'THORACENTESIS'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 3
self.reset_appts()
self.patient.add_appt(self.appt_fields,
['2/3/18', '1:00 PM', 'PLEURX'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 4
self.reset_appts()
def test_patient_with_same_day_appts(self):
self.patient.add_appt(self.appt_fields,
['2/3/18', '9:00 AM', 'THORACENTESIS'])
self.patient.add_appt(self.appt_fields,
['2/3/18', '10:00 AM', 'FLEX BRONCH WITH BAL'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 1
self.reset_appts()
self.patient.add_appt(self.appt_fields,
['2/3/18', '9:00 AM', 'TRANS BRONCH BX'])
self.patient.add_appt(self.appt_fields,
['2/3/18', '10:00 AM', 'PLEURX'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 1
self.reset_appts()
self.patient.add_appt(self.appt_fields,
['2/3/18', '9:00 AM', 'THORACENTESIS'])
self.patient.add_appt(self.appt_fields,
['2/3/18', '10:00 AM', 'PLEURX'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 3
self.reset_appts()
self.patient.add_appt(self.appt_fields,
['2/3/18', '9:00 AM', 'PLEURX'])
self.patient.add_appt(self.appt_fields,
['2/3/18', '10:00 AM', 'FLEX BRONCH WITH BAL'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 4
self.reset_appts()
def test_patient_with_diff_day_appts(self):
self.patient.add_appt(self.appt_fields,
['2/3/18', '9:00 AM', 'THORACENTESIS'])
self.patient.add_appt(self.appt_fields,
['2/4/18', '8:00 AM', 'FLEX BRONCH WITH BAL'])
assert self.patient.enrolled(self.day)
assert self.patient.care_tour == 3
self.reset_appts()
def test_clash_with_no_prescription(self):
patient = Patient(prescriptions=[])
assert patient.clash([]) == set()
def patients():
st.header('PATIENTS')
option_list = ['', 'Add patient', 'Update patient', 'Delete patient', 'Show complete patient record', 'Search patient']
option = st.sidebar.selectbox('Select function', option_list)
p = Patient()
if (option == option_list[1] or option == option_list[2] or option == option_list[3]) and verify_edit_mode_password():
if option == option_list[1]:
st.subheader('ADD PATIENT')
p.add_patient()
elif option == option_list[2]:
st.subheader('UPDATE PATIENT')
p.update_patient()
elif option == option_list[3]:
st.subheader('DELETE PATIENT')
try:
p.delete_patient()
except sql.IntegrityError: # handles foreign key constraint failure issue (due to integrity error)
st.error('This entry cannot be deleted as other records are using it.')
elif option == option_list[4]:
st.subheader('COMPLETE PATIENT RECORD')
p.show_all_patients()
elif option == option_list[5]:
st.subheader('SEARCH PATIENT')
p.search_patient()
centroids = vertices[:,:3]
positions = np.repeat(centroids, centroids.shape[0],axis=0) - np.vstack([centroids]*centroids.shape[0])
#contrasts = np.repeat(intensities, intensities.shape[0],axis=0) / np.vstack([intensities]*intensities.shape[0])
#ratios = np.repeat(sizes, sizes.shape[0],axis=0) / np.vstack([sizes]*sizes.shape[0])
# Assemble relational attributes as the edges matrix
edges = positions#np.concatenate([positions, contrasts, ratios],axis=-1)
# Initializing and returning the SRG
return SRG(vertices, edges, ["centroid_x", "centroid_y", "centroid_z", "intensity", "size"], ["position"])#, "contrast", "ratio"])
#if __name__ == '__main__':
# Step 1: Loading data
# -----------------------
print("# Step 1: Loading data")
model_patient = Patient.build_from_folder("data/4")
model_volume, model_labelmap = model_patient.volumes['t2'], model_patient.labelmaps['t2']
# Reconfiguring model_labelmap with extra backgrounds and unified liver
model_labelmap.data += 2 # Adding space for the extra labels at the start
model_labelmap.data[np.logical_and(model_volume.data < 10, model_labelmap.data == 2)] = 0 # posterior background is 0
model_labelmap.data[model_labelmap.data.shape[1]//2:,:,:][model_labelmap.data[model_labelmap.data.shape[1]//2:,:,:] == 0] = 1 # anterior background is 1
model_labelmap.data[model_labelmap.data >= 4] = 4
model_labelmap.header["num_labels"] = 5
display_overlayed_volume(model_volume.data, model_labelmap.data, label_colors=[(0,0,0),(0.5,0.5,0.5),(1,1,1),(0,0,1),(1,0,0)], title="Model")
observation_volume = deepcopy(model_volume)
# Step 2: Generating model graph
# -----------------------
print("# Step 2: Generating model graph")
model_graph = build_graph(model_volume, model_labelmap)
def add_patient(self):
self._canvas.destroy()
self.heading.destroy()
Patient(self.root)
ax = fig.add_subplot(111)
for i, medicine_name in enumerate(medicine_names):
prescriptions = filter(lambda p: p.name == medicine_name, patient.prescriptions)
days_to_plot = [(p.dispense_date.toordinal() - day_zero, p.days_supply) for p in prescriptions]
ax.broken_barh(days_to_plot, (10 * (i + 1), 9), facecolors=["red", "yellow", "green", "blue", "orange"][i])
days_taking_all = []
days_taking_all = sorted([(day.toordinal() - day_zero, 1) for day in patient.clash(medicine_names)])
ax.broken_barh(days_taking_all, (0, 9), facecolors="black")
medicine_count = len(medicine_names)
ax.set_ylim(-5, 10 * (medicine_count + 1) + 5)
ax.set_xlim(-110, 0)
ax.set_xlabel("relative to today")
ax.set_yticks([i * 10 + 5 for i in range(medicine_count + 2)])
ax.set_yticklabels(["Clash"] + medicine_names)
ax.grid(True)
fig.savefig(filename)
if __name__ == "__main__":
patient = Patient()
patient.add_prescription(Prescription("Fluoxetine", dispense_date=date.today() - timedelta(100), days_supply=20))
patient.add_prescription(Prescription("Fluoxetine", dispense_date=date.today() - timedelta(50), days_supply=50))
patient.add_prescription(Prescription("Codeine", dispense_date=date.today() - timedelta(15), days_supply=3))
patient.add_prescription(Prescription("Codeine", dispense_date=date.today() - timedelta(60), days_supply=3))
patient.add_prescription(Prescription("Codeine", dispense_date=date.today() - timedelta(30), days_supply=3))
plot(patient, ["Fluoxetine", "Codeine"], "graph.png")
from patient import Patient patient = Patient() patient.fill() patient.show() patient.diagnose()
def setUp(self):
config = {
"host": "localhost",
"user": "******",
"passwd": "MyNewPassword",
"database": "test",
"auth_plugin": "mysql_native_password"
}
self.connection = mysql.connector.connect(**config)
self.cursor = self.connection.cursor()
stmt_p = "SHOW TABLES LIKE 'patients'"
self.cursor.execute(stmt_p)
result = self.cursor.fetchone()
if not result:
self.cursor.execute("""CREATE TABLE `patients` (
`id` int NOT NULL AUTO_INCREMENT,
`name` varchar(250) NOT NULL,
`clinical_area` varchar(100) DEFAULT NULL,
`bed_num` int DEFAULT NULL,
`acuity` int DEFAULT NULL,
`a_trained` tinyint(1) DEFAULT NULL,
`transfer` tinyint(1) DEFAULT NULL,
`iv` tinyint(1) DEFAULT NULL,
`one_to_one` tinyint(1) DEFAULT NULL,
`previous_nurses` varchar(250) DEFAULT NULL,
`admission_date` varchar(250) DEFAULT NULL,
`discharged_date` varchar(250) DEFAULT '-',
`comments` varchar(250) DEFAULT NULL,
`twin` int DEFAULT NULL,
PRIMARY KEY (`id`))""")
stmt_n = "SHOW TABLES LIKE 'nurses'"
self.cursor.execute(stmt_n)
result = self.cursor.fetchone()
if not result:
self.cursor.execute("""CREATE TABLE `nurses` (
`id` int NOT NULL AUTO_INCREMENT,
`name` varchar(250) DEFAULT '',
`clinical_area` varchar(250) DEFAULT NULL,
`bed_num` int DEFAULT NULL,
`rotation` varchar(250) DEFAULT NULL,
`group_num` int DEFAULT NULL,
`fte` decimal(3,2) DEFAULT NULL,
`skill_level` int DEFAULT NULL,
`a_trained` tinyint(1) DEFAULT NULL,
`transfer` tinyint(1) DEFAULT NULL,
`iv` int DEFAULT NULL,
`advanced_role` varchar(250) DEFAULT NULL,
`previous_patients` varchar(250) DEFAULT NULL,
`dta` varchar(250) DEFAULT '',
`comments` varchar(250) DEFAULT '',
`priority` int DEFAULT NULL,
`current_shift` tinyint(1) DEFAULT NULL,
PRIMARY KEY (`id`)) """)
self.cursor.execute("""INSERT INTO patients VALUES
(1,'not discharged','F',3,5,1,0,0,0,'[2,5]','2020-11-18','-','',0),
(2,'patient discharged','F',6,3,1,0,1,1,'[]','2020-11-18','2020-11-20','',1)"""
)
self.cursor.execute("""INSERT INTO nurses VALUES
(1,'Rebecca Smith','B',1,'A01',1,0.50,
5,0,0,3,'None','[27]','','',2,1),
(2,'Holly Baker','D',3,'3',1,1.00,4,1,1,2,'Charge','[1, 2, 21]','1','1',2,0)"""
)
self.assignments = {}
self.patients = []
self.nurses = []
self.twins = []
self.patient_1 = Patient(1, 'not discharged', 'F', 3, 5, 1, 0, 0, 0,
'[2,5]', '2020-11-18', '-', '', 0)
self.patient_1.assigned = 0
self.patient_2 = Patient(2, 'patient discharged', 'F', 6, 3, 1, 0, 1,
1, '[]', '2020-11-18', '2020-11-20', '', 1)
self.patient_2.assigned = 1
self.current_n = Nurse(1, 'Rebecca Smith', 'B', 1, 'A01', 1, 0.50, 5,
0, 0, 3, 'None', '[27]', '', '', 2, 1)
def main():
parser = argparse.ArgumentParser(description='Infers the evolution of cancer.')
parser.add_argument("-m", "--mode", help="running mode: 1...run Treeomics and explore full solution space, "
"2...fast (one mutation pattern per variant).",
type=int, default=1)
group = parser.add_mutually_exclusive_group()
group.add_argument("--csv_file", help="path to the CSV file", type=str)
group.add_argument("-v", "--vcf_file", help="path to the VCF file", type=str)
group.add_argument("-d", "--directory", help="directory with multiple VCF files", type=str)
parser.add_argument("-n", "--normal", help="names of normal samples (excluded from analysis)", type=str, nargs='*',
default=None)
parser.add_argument("--suffix", help="suffix for output files", type=str, default=None)
parser.add_argument("-x", "--exclude", help="names of samples to exclude of analysis", type=str, nargs='*',
default=None)
parser.add_argument("--include", help="names of samples to include in analysis", type=str, nargs='*',
default=None)
parser.add_argument("--purities", help="provide estimated purities for samples given by '--include <SAMPLES>'",
type=float, nargs='*', default=None)
parser.add_argument("-r", "--mut_reads", help="path table with the number of reads with a mutation", type=str)
parser.add_argument("-s", "--coverage", help="path to table with read coverage at the mutated positions", type=str)
# specify output directory
parser.add_argument("-o", "--output", help="output directory", type=str, default=settings.OUTPUT_FOLDER)
# read in parameter value
parser.add_argument("-e", "--error_rate", help="sequencing error rate for bayesian inference",
type=float, default=settings.BI_E)
parser.add_argument("-z", "--prob_zero", help="prior probability of being absent",
type=float, default=settings.BI_C0)
parser.add_argument("-a", "--max_absent_vaf", help="maximal absent vaf before considering purity",
type=float, default=settings.MAX_ABSENT_VAF)
parser.add_argument("-c", "--min_median_coverage",
help="minimum median coverage of a sample",
type=int, default=settings.SAMPLE_COVERAGE_THRESHOLD)
parser.add_argument("-f", "--min_median_vaf",
help="minimum median mutant allele frequency of a sample",
type=float, default=settings.MAF_THRESHOLD)
parser.add_argument('-g', "--ref_genome",
help="to which reference genome was the sequencing data aligned",
type=str, default=settings.REF_GENOME)
parser.add_argument('--wes_filtering', action='store_true', help="Remove intronic and intergenic variants?")
# settings for filtering potential germline variants
parser.add_argument(
"--mut_reads_normal_th", type=float, default=settings.MUT_READS_NORMAL_TH,
help="variants are excluded if they reach this number of mutant reads with a given VAF in the normal sample")
parser.add_argument(
"--vaf_normal_th", type=float, default=settings.VAF_NORMAL_TH,
help="variants are excluded if they reach this VAF with a given number of mutant reads in the normal sample")
parser.add_argument('--driver_genes', type=str, default=settings.DRIVER_PATH,
help='path to CSV file with names of putative driver genes highlighted in inferred phylogeny')
parser.add_argument('--common_vars_file', type=str, default=settings.COMMON_VARS_FILE,
help='path to CSV file with common variants present in normal samples '
'and hence excl as artifacts')
# DEPRECATED FROM VERSION 1.7.0 ONWARD
parser.add_argument("-p", "--false_positive_rate",
help="false positive rate for the statistical test",
type=float, default=settings.FPR)
parser.add_argument("-i", "--false_discovery_rate",
help="false discovery rate for the statistical test",
type=float, default=settings.FDR)
parser.add_argument("-y", "--min_absent_coverage",
help="minimum coverage for a true negative (negative threshold)",
type=int, default=settings.MIN_ABSENT_COVERAGE)
parser.add_argument('--verbose', action='store_true', help="Run Treeomics in DEBUG logging level.")
plots_parser = parser.add_mutually_exclusive_group(required=False)
plots_parser.add_argument('--plots', dest='plots', action='store_true', help="Is plot generation enabled?")
plots_parser.add_argument('--no_plots', dest='plots', action='store_false', help="Is plot detection disabled?")
parser.set_defaults(plots=True)
plots_parser = parser.add_mutually_exclusive_group(required=False)
plots_parser.add_argument('--tikztrees', dest='tikztrees', action='store_true', help='Generate Tikz trees?')
plots_parser.add_argument('--no_tikztrees', dest='tikztrees', action='store_false', help='Generate Tikz trees?')
parser.set_defaults(tikztrees=True)
parser.add_argument('--benchmarking', action='store_true', help="Generate mutation matrix for benchmarking.")
parser.add_argument('-b', '--boot', help='Number of bootstrapping samples', type=int,
default=settings.NO_BOOTSTRAP_SAMPLES)
parser.add_argument('--pool_size', help='number of best solutions explored by ILP solver', type=int,
default=settings.POOL_SIZE)
# limit search space exploration to decrease the run time
parser.add_argument("-t", "--time_limit",
help="maximum running time for CPLEX to solve the MILP",
type=int, default=settings.TIME_LIMIT)
parser.add_argument('--threads', help='maximal number of parallel threads that will be invoked by CPLEX',
type=int, default=0)
parser.add_argument("-l", "--max_no_mps", help="limit the solution space size by the maximal number of " +
"explored mutation patterns per variant",
type=int, default=settings.MAX_NO_MPS)
feature_parser = parser.add_mutually_exclusive_group(required=False)
feature_parser.add_argument('-u', '--subclone_detection', dest='subclone_detection', action='store_true',
help="Is subclone detection enabled?")
feature_parser.add_argument('--no_subclone_detection', dest='subclone_detection', action='store_false',
help="Is subclone detection disabled?")
parser.set_defaults(subclone_detection=settings.SUBCLONE_DETECTION)
args = parser.parse_args()
if args.verbose:
logger.setLevel(logging.DEBUG)
logger.info('Run Treeomics in verbose mode.')
# disable plot generation if the script is called from another script (benchmarking)
# set log level to info
if not os.getcwd().endswith('treeomics') and not os.getcwd().endswith('src'):
# logger.setLevel(logging.INFO)
fh.setLevel(logging.INFO)
ch.setLevel(logging.INFO)
if args.subclone_detection:
logger.info('Subclone detection is enabled.')
else:
logger.info('Subclone detection is disabled.')
if args.plots:
logger.info('Plot generation is enabled.')
else:
logger.info('Plot generation is disabled.')
plots_report = args.plots # for debugging set to False
plots_paper = logger.isEnabledFor(logging.DEBUG)
# plots_report = False # for debugging set to False
# plots_paper = False
if args.normal:
normal_sample_name = args.normal[0]
excluded_samples = set(args.normal[1:]) if len(args.normal) > 1 else set()
logger.info('Exclude normal sample with name: ' + ', '.join(sa for sa in args.normal))
else:
normal_sample_name = None
excluded_samples = set()
# exclude given sample names from analysis
if args.exclude is not None:
for sample_name in args.exclude:
logger.info('Exclude sample from analysis: {}'.format(sample_name))
excluded_samples.add(sample_name)
# exclude given sample names from analysis
if args.include is not None:
included_samples = list()
for sample_name in args.include:
included_samples.append(sample_name)
logger.info('Only the following samples are included in the analysis: {}'.format(
', '.join(sa_name for sa_name in included_samples)))
else:
included_samples = None
if args.purities is not None:
if included_samples is None or len(included_samples) != len(args.purities):
raise ValueError('If externally estimated purity values are provided, the same number of samples must be '
'given by "--input <SAMPLE NAMES>"')
purities = dict()
for sample_name, purity in zip(included_samples, args.purities):
purities[sample_name] = purity
else:
purities = None
if args.min_median_coverage > 0:
logger.info('Minimum sample median coverage (otherwise discarded): {}'.format(
args.min_median_coverage))
if args.min_median_vaf > 0:
logger.info('Minimum sample median mutant allele frequency (otherwise discarded): {}'.format(
args.min_median_vaf))
if args.boot is not None:
if args.boot < 0:
raise AttributeError('Number of bootstrapping samples can not be negative!')
if args.time_limit is not None:
if args.time_limit <= 0:
raise AttributeError('Time limit for the MILP solver needs to be positive!')
logger.info('MILP solver running time is limited to {} seconds. Obtained solution may not be optimal.'.format(
args.time_limit))
if args.max_no_mps is not None:
if args.max_no_mps <= 0:
raise AttributeError('Solution space can only be limited to a positive number of mutation patterns!')
logger.info('Solution space is limited to the {} most likely mutation patterns per variant.'.format(
args.max_no_mps))
if args.max_absent_vaf < args.error_rate:
raise AttributeError('The maximal absent VAF has to be larger than the error rate in the Bayesian model!')
if args.pool_size < 1:
raise AttributeError('Solution pool size of ILP solver has to be at least 1!')
# DEPRECATED FROM VERSION 1.7.0 ONWARD
fpr = args.false_positive_rate
logger.debug('False positive rate for the statistical test: {}.'.format(fpr))
fdr = args.false_discovery_rate
logger.debug('False discovery rate for the statistical test: {}.'.format(fdr))
min_absent_cov = args.min_absent_coverage
logger.debug('Minimum coverage for an absent variant: {} (otherwise unknown)'.format(min_absent_cov))
ref_genome = args.ref_genome.lower() if args.ref_genome is not None else None
logger.info('Sequencing data was aligned to reference genome: {}'.format(ref_genome))
if args.boot > 0:
logger.info('Number of samples for bootstrapping analysis: {}'.format(args.boot))
if args.threads > 0:
logger.info('The maximal number of parallel threads that will be invoked by CPLEX has been set to {}.'.format(
args.threads))
if args.subclone_detection and args.max_no_mps is not None:
logger.error('Subclone and partial solution space search are not supported to be performed at the same time! ')
usage()
if os.getcwd().endswith('treeomics'):
# application has been started from this directory
input_directory = os.path.join('..')
else:
input_directory = os.path.join('.')
if args.wes_filtering:
logger.info('All intronic or intergenic variants will be excluded (WES filtering).')
if args.common_vars_file:
common_vars_filepath = os.path.join(input_directory, args.common_vars_file)
if os.path.isfile(common_vars_filepath):
common_vars = read_table(common_vars_filepath, ['Chromosome', 'Position', 'RefAllele', 'AltAllele'],
['__', '__', '>', ''], ['AlleleFrequency', 'Gene_Symbol'])
logger.info('Read common variants file with {:.2e} variants that are excluded as artifacts.'.format(
len(common_vars)))
else:
logger.error('Given path to common variants file {} could not be found!'.format(args.common_vars_file))
common_vars = None
else:
common_vars = None
# ##########################################################################################################
# ############################################### LOAD DATA ################################################
# ##########################################################################################################
# take mutant read and coverage tables to calculate positives, negatives, and unknowns
if args.mut_reads and args.coverage:
patient_name = get_patients_name(args.mut_reads)
if patient_name.find('_') != -1:
patient_name = patient_name[:patient_name.find('_')]
logger.debug('Patient name: {}'.format(patient_name))
patient = Patient(error_rate=args.error_rate, c0=args.prob_zero, max_absent_vaf=args.max_absent_vaf,
pat_name=patient_name, min_absent_cov=min_absent_cov, reference_genome=ref_genome,
purities=purities)
read_no_samples = patient.process_raw_data(
fpr, fdr, min_absent_cov, args.min_median_coverage, args.min_median_vaf,
mut_reads_normal_th=args.mut_reads_normal_th, vaf_normal_th=args.vaf_normal_th, var_table=args.mut_reads,
cov_table=args.coverage, normal_sample=normal_sample_name, excluded_columns=excluded_samples,
considered_samples=included_samples, wes_filtering=args.wes_filtering, artifacts=common_vars)
elif args.csv_file:
patient_name = get_patients_name(args.csv_file)
if patient_name.find('_') != -1:
patient_name = patient_name[:patient_name.find('_')]
logger.debug('Patient name: {}'.format(patient_name))
patient = Patient(error_rate=args.error_rate, c0=args.prob_zero, max_absent_vaf=args.max_absent_vaf,
pat_name=patient_name, min_absent_cov=min_absent_cov, reference_genome=ref_genome,
purities=purities)
read_no_samples = patient.process_raw_data(
fpr, fdr, min_absent_cov, args.min_median_coverage, args.min_median_vaf,
mut_reads_normal_th=args.mut_reads_normal_th, vaf_normal_th=args.vaf_normal_th, csv_file=args.csv_file,
normal_sample=normal_sample_name, excluded_columns=excluded_samples, considered_samples=included_samples)
elif args.vcf_file: # take path to the input VCF file
vcf_file = args.vcf_file
if not os.path.isfile(vcf_file):
logger.error("Provided VCF file {} does not exist.".format(vcf_file))
usage()
patient_name = get_patients_name(vcf_file)
if patient_name.find('_') != -1:
patient_name = patient_name[:patient_name.find('_')]
patient = Patient(error_rate=args.error_rate, c0=args.prob_zero, max_absent_vaf=args.max_absent_vaf,
pat_name=patient_name, reference_genome=ref_genome, purities=purities)
read_no_samples = patient.read_vcf_file(
vcf_file, fpr, fdr, min_sa_cov=args.min_median_coverage, min_sa_maf=args.min_median_vaf,
min_absent_cov=args.min_absent_coverage, normal_sample_name=normal_sample_name,
excluded_samples=excluded_samples, considered_samples=included_samples, wes_filtering=args.wes_filtering,
artifacts=common_vars)
elif args.directory: # take path to the directory with all VCF files
vcf_directory = args.directory
if not os.path.isdir(vcf_directory):
logger.error("Directory named {} does not exist ({}).".format(
args.directory, os.path.abspath(vcf_directory)))
usage()
patient_name = get_patients_name(
vcf_directory[:-1] if vcf_directory.endswith('/') else vcf_directory)
patient = Patient(error_rate=args.error_rate, c0=args.prob_zero, max_absent_vaf=args.max_absent_vaf,
pat_name=patient_name, reference_genome=ref_genome, purities=purities)
read_no_samples = patient.read_vcf_directory(
vcf_directory, args.min_median_coverage, args.min_median_vaf, fpr, fdr, min_absent_cov,
normal_sample_name=normal_sample_name, excluded_samples=excluded_samples,
considered_samples=included_samples, wes_filtering=args.wes_filtering, artifacts=common_vars)
else:
raise RuntimeError('No input files were provided!')
output_directory = init_output(patient_name=patient_name,
output_dir=args.output if args.output is not settings.OUTPUT_FOLDER else None)
# find and characterize all possible driver gene mutations
# if settings.DRIVER_PATH is not None:
# driver_filepath = os.path.join(input_directory, settings.DRIVER_PATH)
# else:
# driver_filepath = None
if args.driver_genes:
driver_filepath = args.driver_genes
if not os.path.isfile(driver_filepath):
driver_filepath = os.path.join(input_directory, args.driver_genes)
if not os.path.isfile(driver_filepath):
logger.warning('CSV-file with driver gene names for annotation was not found: {}'.format(
os.path.abspath(args.driver_genes)))
driver_filepath = None
if settings.CGC_PATH is not None:
cgc_filepath = os.path.join(input_directory, settings.CGC_PATH)
else:
cgc_filepath = None
put_driver_genes, put_driver_vars, unlikely_driver_mut_effects = characterize_drivers(
patient, ref_genome, driver_filepath, cgc_filepath,
output_filepath=os.path.join(
output_directory, get_output_fn_template(patient.name, read_no_samples, suffix=args.suffix))
+ '_putativedrivers')
# create output filename pattern
fn_pattern = get_output_fn_template(
patient.name, read_no_samples, mode=args.mode, min_sa_coverage=args.min_median_coverage,
min_sa_vaf=args.min_median_vaf, bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0,
max_absent_vaf=patient.max_absent_vaf, suffix=args.suffix)
# do basic analysis on provided input data
# create output file path for present posterior probabilities of the variants
post_filepath = os.path.join(output_directory, get_output_fn_template(
patient.name, read_no_samples, min_sa_coverage=args.min_median_coverage, min_sa_vaf=args.min_median_vaf,
bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0, max_absent_vaf=patient.max_absent_vaf, suffix=args.suffix)
+ '_posterior.txt')
# output file path to write all variants in a format acceptable to Ensembl VEP and CHASM/CRAVAT
vep_filepath = (os.path.join(
output_directory, get_output_fn_template(patient.name, read_no_samples, suffix=args.suffix))
+ '_func_variants_vep.tsv')
cravat_filepath = (os.path.join(
output_directory, get_output_fn_template(patient.name, read_no_samples, suffix=args.suffix))
+ '_func_variants_cravat.tsv')
analyze_data(patient, post_table_filepath=post_filepath,
vep_filepath=vep_filepath, cravat_filepath=cravat_filepath)
# write matrix with Jaccard similarity coefficients in CSV format
fp_jsc = os.path.join(
output_directory,
get_output_fn_template(patient.name, read_no_samples,
min_sa_coverage=args.min_median_coverage, min_sa_vaf=args.min_median_vaf,
bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0, max_absent_vaf=patient.max_absent_vaf,
suffix=args.suffix)) + '_jsc.csv'
with open(fp_jsc, 'w') as f_jsc:
jsc_title = \
('# {}: Probabilistic Jaccard similarity coefficient between'.format(patient.name)
+ ' all pairs of samples (median: {:.2f}; mean: {:.2f}; classification threshold: {:.0%}).\n'.format(
np.nanmedian(patient.df_bi_sim_coeff), np.nanmean(patient.df_bi_sim_coeff), def_sets.CLA_CONFID_TH))
f_jsc.write(jsc_title)
patient.df_bi_sim_coeff.to_csv(fp_jsc, index=True, mode='a')
# write matrix with genetic distances in CSV format
fp_gen_dist = os.path.join(
output_directory,
get_output_fn_template(patient.name, read_no_samples,
min_sa_coverage=args.min_median_coverage, min_sa_vaf=args.min_median_vaf,
bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0, max_absent_vaf=patient.max_absent_vaf,
suffix=args.suffix)) + '_gendist.csv'
with open(fp_gen_dist, 'w') as f_gen_dist:
gen_dist_title = \
('# {}: Probabilistic genetic distance between'.format(patient.name)
+ ' all pairs of samples (median: {:.2f}; mean: {:.2f}; classification threshold: {:.0%}).\n'.format(
np.nanmedian(patient.df_bi_gen_dist), np.nanmean(patient.df_bi_gen_dist), def_sets.CLA_CONFID_TH))
f_gen_dist.write(gen_dist_title)
patient.df_bi_gen_dist.to_csv(fp_gen_dist, index=True, mode='a')
if plots_report: # deactivate plot generation for debugging and benchmarking
# generate mutation table plot
# show only mutations which are present in at least one sample
if patient.gene_names is not None:
col_labels = patient.gene_names
else:
col_labels = patient.mut_keys
if len(col_labels) < def_sets.MAX_MUTS_TABLE_PLOT and plots_report:
mut_table_name = \
(get_output_fn_template(
patient.name, read_no_samples, min_sa_coverage=args.min_median_coverage,
min_sa_vaf=args.min_median_vaf, bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0,
max_absent_vaf=patient.max_absent_vaf, suffix=args.suffix)+'_bayesian_data_table')
plts.bayesian_hinton(patient.log_p01, output_directory, mut_table_name,
row_labels=patient.sample_names, column_labels=col_labels,
displayed_mutations=patient.present_mutations, put_driver_vars=put_driver_vars)
else:
logger.warning('Too many reported variants for a detailed mutation table plot: {}'.format(len(col_labels)))
mut_table_name = None
else:
mut_table_name = None
col_labels = None
if plots_paper: # deactivate plot generation for regular analysis
# generate violin coverage distribution plot
plts.coverage_plot(os.path.join(output_directory, patient.name+'_coverage_distr.pdf'), patient)
# generate box plots with MAFs per sample
# plts.boxplot(os.path.join(output_directory, 'fig_mafs_'+patient.name+'.pdf'), patient)
# generate violin VAF distribution plot
plts.vaf_distribution_plot(os.path.join(output_directory, patient.name+'_vaf_distr.pdf'), patient)
# create raw data analysis file
analysis.create_data_analysis_file(patient, os.path.join(output_directory, fn_pattern+'_data.txt'))
# utils.analysis.print_genetic_distance_table(patient)
# create output filename pattern
fn_pattern = get_output_fn_template(
patient.name, read_no_samples, mode=args.mode, min_sa_coverage=args.min_median_coverage,
min_sa_vaf=args.min_median_vaf, bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0,
max_absent_vaf=patient.max_absent_vaf, max_no_mps=args.max_no_mps, suffix=args.suffix)
# create HTML analysis report
html_report = HTMLReport(os.path.join(output_directory, fn_pattern+'_report.html'), patient_name)
html_report.start_report()
html_report.add_sequencing_information(
patient, mut_table_path=mut_table_name+'.png' if mut_table_name is not None else None,
put_driver_vars=put_driver_vars, unlikely_driver_mut_effects=unlikely_driver_mut_effects,
put_driver_genes=put_driver_genes)
html_report.add_similarity_information(patient)
# ############################################################################################
# infer evolutionary compatible mutation patterns and subsequently evolutionary trees based on
# different principles divided into three modes
# ############################################################################################
if args.mode == 1 or args.mode == 2:
phylogeny = None
# comp_node_frequencies = None
# ### RUN TREEOMICS ###
if args.mode == 1: # find likely sequencing artifacts based on a bayesian inference model
# generate filename for tree
fn_tree = get_output_fn_template(
patient.name, read_no_samples, subclone_detection=args.subclone_detection,
min_sa_coverage=args.min_median_coverage, min_sa_vaf=args.min_median_vaf, no_boot=args.boot,
max_no_mps=args.max_no_mps, bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0,
max_absent_vaf=patient.max_absent_vaf, mode=args.mode, suffix=args.suffix)
fn_matrix = get_output_fn_template(
patient.name, read_no_samples, subclone_detection=args.subclone_detection,
min_sa_coverage=args.min_median_coverage, min_sa_vaf=args.min_median_vaf, max_no_mps=args.max_no_mps,
bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0, max_absent_vaf=patient.max_absent_vaf, mode=args.mode,
suffix=args.suffix)
# create mutation matrix and mutation patterns output file for automatic benchmarking
if args.benchmarking:
mm_filepath = os.path.join(output_directory, fn_matrix+'_treeomics_mm.csv')
mp_filepath = os.path.join(output_directory, fn_matrix+'_treeomics_mps.tsv')
else:
mm_filepath = None
mp_filepath = None
# infer maximum likelihood tree
phylogeny = ti.create_max_lh_tree(
patient, tree_filepath=os.path.join(output_directory, fn_tree+'_mlhtree'),
mm_filepath=mm_filepath, mp_filepath=mp_filepath,
subclone_detection=args.subclone_detection, loh_frequency=settings.LOH_FREQUENCY,
driver_vars=put_driver_vars, pool_size=args.pool_size,
no_plotted_solutions=settings.NO_PLOTTED_SOLUTIONS, no_bootstrap_samples=args.boot,
max_no_mps=args.max_no_mps, time_limit=args.time_limit, n_max_threads=args.threads, plots=plots_report,
tikztrees=args.tikztrees, variant_filepath=os.path.join(output_directory, fn_tree+'_variants.csv'))
# previously used for benchmarking
# if plots_paper: # generate Java Script D3 trees
# json_file = 'mlhtree_'+fn_tree+'.json'
# Phylogeny.save_json_tree(os.path.join(output_directory, json_file), phylogeny.mlh_tree)
# Phylogeny.write_html_file(os.path.join(output_directory, 'mlhtree_'+fn_tree+'.html'), json_file)
# determine mutation patterns and generate an overview graph
if plots_report:
if phylogeny.tree_plot is not None: # add generated tree plot to HTML report
html_report.add_tree_plot(patient, phylogeny)
# create mutation pattern overview plot
# show only the different patterns and not the individual variants
# (convenient for large numbers of variants)
fn_mp_plot = get_output_fn_template(
patient.name, read_no_samples, min_sa_coverage=args.min_median_coverage, max_no_mps=args.max_no_mps,
min_sa_vaf=args.min_median_vaf, bi_e=patient.bi_error_rate, bi_c0=patient.bi_c0,
max_absent_vaf=patient.max_absent_vaf, mode=args.mode, suffix=args.suffix)
if args.subclone_detection:
pg = ti.create_max_lh_tree(
patient, tree_filepath=None, mm_filepath=None, mp_filepath=None, subclone_detection=False,
loh_frequency=settings.LOH_FREQUENCY, driver_vars=put_driver_vars, pool_size=args.pool_size,
no_plotted_solutions=settings.NO_PLOTTED_SOLUTIONS, no_bootstrap_samples=0,
max_no_mps=args.max_no_mps, time_limit=args.time_limit, plots=False, tikztrees=False)
else:
pg = phylogeny
mp_graph_name = mp_graph.create_mp_graph(
fn_mp_plot, pg, pg.node_scores.keys(), pg.node_scores,
output_directory=output_directory, min_node_weight=settings.MIN_MP_SCORE,
circos_max_no_mps=settings.CIRCOS_MAX_NO_MPS)
if mp_graph_name is not None:
html_report.add_conflict_graph(patient, mp_graph_name, phylogeny=pg)
opt_sol = phylogeny.solutions[0] # optimal solution
# create plot only if there is enough space for all the incompatible mutations
if (0 < len(opt_sol.false_positives) + len(opt_sol.false_negatives) +
len(opt_sol.false_negative_unknowns) < def_sets.MAX_MUTS_TABLE_PLOT):
# illustrative mutation table plot of incompatible mutation patterns and their putative artifacts
x_length, y_length = plts.create_incompatible_mp_table(
patient, os.path.join(output_directory, fn_pattern+settings.artifacts_plot_suffix),
phylogeny, row_labels=patient.sample_names, column_labels=col_labels)
if x_length > 0 and y_length > 0:
# add information about putative false-positives and false-negatives to the HTML report
html_report.add_artifacts_information(
phylogeny, artifacts_plot_filepath=fn_pattern+settings.artifacts_plot_suffix+'.png',
plot_width=x_length*7)
else:
html_report.add_artifacts_information(phylogeny)
# find evolutionary incompatible mutation patterns based on standard binary classification
elif args.mode == 2:
phylogeny = ti.infer_max_compatible_tree(os.path.join(output_directory, fn_pattern+'_btree.tex'),
patient, drivers=put_driver_genes)
if plots_report:
# create mutation pattern overview plot
# show only the different patterns and not the individual variants
# (convenient for large numbers of variants)
mp_graph_name = mp_graph.create_mp_graph(
fn_pattern, phylogeny, phylogeny.nodes, phylogeny.node_scores,
output_directory=output_directory, min_node_weight=settings.MIN_MP_SCORE,
circos_max_no_mps=settings.CIRCOS_MAX_NO_MPS)
if mp_graph_name is not None:
html_report.add_conflict_graph(patient, mp_graph_name)
# create plot only if there is enough space for all the incompatible mutations
if len(phylogeny.conflicting_mutations) < def_sets.MAX_MUTS_TABLE_PLOT:
# illustrative mutation table plot of incompatible mutation patterns
x_length, y_length = plts.create_incompatible_mp_table(
patient, os.path.join(output_directory, fn_pattern+settings.incomp_mps_plot_suffix),
phylogeny, row_labels=patient.sample_names, column_labels=col_labels)
if x_length > 0 and y_length > 0:
# add information about evolutionarily incompatible mutation patterns to the HTML report
html_report.add_inc_mp_information(
phylogeny, incomp_mps_plot_filepath=fn_pattern+settings.incomp_mps_plot_suffix + '.png',
plot_width=x_length*7)
else:
# too many evolutionarily incompatible mutation to create mutation table plot
# add information about evolutionarily incompatible mutation patterns to the HTML report
html_report.add_inc_mp_information(phylogeny)
# generate analysis file to provide an overview about the derived results
analysis.create_analysis_file(patient, args.min_median_coverage,
os.path.join(output_directory, fn_pattern+'_analysis.txt'), phylogeny)
# create input data file for circos conflict graph plots
if plots_report:
circos.create_raw_data_file(os.path.join(output_directory, 'fig_data_'+fn_pattern+'_mutdata.txt'),
patient.mutations, patient.mut_positions, data=patient.data,
sample_names=patient.sample_names)
# create labels file if gene names are available
# typically not available in VCF files
if patient.gene_names is not None and len(patient.gene_names):
circos.create_mutation_labels_file(
os.path.join(output_directory, 'fig_data_'+fn_pattern+'_mutlabels.txt'),
patient.mutations, patient.gene_names, patient.mut_positions, patient.driver_pathways)
if args.mode == 1 and len(patient.data) < 500:
# create input data files for circular plots with circos: conflict graph
circos.create_mlh_graph_files(
os.path.join(output_directory, 'mlh_nodes_'+fn_pattern+'.txt'),
os.path.join(output_directory, 'mlh_mutnode_labels_'+fn_pattern+'.txt'),
os.path.join(output_directory, 'mlh_mutnode_data_'+fn_pattern+'.txt'),
patient.data, phylogeny, patient.gene_names, patient.driver_pathways)
# if there are less than 10000 edges in the conflict graph
elif args.mode == 2:
if phylogeny.cf_graph.size() < 50000:
circos.create_mutation_links_file(
os.path.join(output_directory, 'fig_data_'+fn_pattern+'_conflicts.txt'),
phylogeny, patient.mut_positions)
else:
logger.warn('Circos mutation conflicts data has not been created as there '
'are {} edges in the graph.'.format(phylogeny.cf_graph.size()))
# create input data files for circular plots with circos: conflict graph
circos.create_conflict_graph_files(
os.path.join(output_directory, 'cfg_nodes_'+fn_pattern+'.txt'),
os.path.join(output_directory, 'cfg_mutnode_labels_'+fn_pattern+'.txt'),
os.path.join(output_directory, 'cfg_mutnode_data_'+fn_pattern+'.txt'),
os.path.join(output_directory, 'cfg_links_'+fn_pattern+'.txt'),
phylogeny, patient.gene_names, patient.driver_pathways, data=patient.data,
min_node_weight=settings.MIN_MP_SCORE, max_no_mps=settings.CIRCOS_MAX_NO_MPS)
else:
raise RuntimeError("No mode was provided (e.g. -m 1) to infer the phylogenetic tree.")
# finalize HTML report
html_report.end_report(patient.bi_error_rate, patient.bi_c0, patient.max_absent_vaf, settings.LOH_FREQUENCY,
fpr, fdr, min_absent_cov, args.min_median_coverage, args.min_median_vaf,
max_no_mps=args.max_no_mps)
logger.info('Treeomics finished evolutionary analysis.')
def test_clash_with_one_irrelevant_prescription(self):
patient = Patient(prescriptions=[Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=2), days_supply=2)])
assert patient.clash(["Aspirin"]) == set()
def search_database(self):
'''
A function to allow the user to search the patient's appointment
Parameters
----------
None
'''
patients = [] # empty list
self.input = self.nameupd.get()
# Used to choose appointment information from database
sql = "Select * FROM Appointments WHERE name LIKE ?"
self.result = c.execute(sql, (self.input, ))
for self.row in self.result:
patients.append(
Patient(self.row[6], self.row[1], self.row[2], self.row[3],
self.row[4], self.row[5], self.row[7]))
self.name = self.row[1]
self.age = self.row[2]
self.gender = self.row[3]
self.phone = self.row[4]
self.residence = self.row[5]
self.reason = self.row[6]
self.time = self.row[7]
if len(patients) == 0:
messagebox.showerror("Error", "Information is missing")
return
self.updname = Label(self.master,
text="Patient's Name",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updname.place(x=150, y=275)
self.entname = Entry(self.master, width=30)
self.entname.place(x=130, y=325)
self.entname.insert(END, str(patients[0].name))
self.updage = Label(self.master,
text="Age",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updage.place(x=570, y=275)
self.entage = Entry(self.master, width=30)
self.entage.place(x=506, y=325)
self.entage.insert(END, str(patients[0].age))
self.updgender = Label(self.master,
text="Gender",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updgender.place(x=940, y=275)
self.entgender = Entry(self.master, width=30)
self.entgender.place(x=882, y=325)
self.entgender.insert(END, str(patients[0].gender))
self.updphone = Label(self.master,
text="Phone",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updphone.place(x=184, y=375)
self.entphone = Entry(self.master, width=30)
self.entphone.place(x=130, y=425)
self.entphone.insert(END, str(patients[0].phone))
self.updresidence = Label(self.master,
text="Residence",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updresidence.place(x=550, y=375)
self.entresidence = Entry(self.master, width=30)
self.entresidence.place(x=506, y=425)
self.entresidence.insert(END, str(patients[0].residence))
self.updreason = Label(self.master,
text="Reason",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updreason.place(x=940, y=375)
self.entreason = Entry(self.master, width=30)
self.entreason.place(x=882, y=425)
self.entreason.insert(END, str(patients[0].reason))
self.updtime = Label(self.master,
text="Time",
bg='navajowhite',
font=('Times', 16, 'bold'))
self.updtime.place(x=570, y=475)
self.enttime = Entry(self.master, width=30)
self.enttime.place(x=506, y=525)
self.enttime.insert(END, str(patients[0].time))
# This button is used to update the appointment
self.update = Button(self.master,
text="Update",
width=15,
height=2,
bg='yellowgreen',
command=self.update_database)
self.update.place(x=630, y=575)
# This button is used to update the appointment
self.delete = Button(self.master,
text="Delete",
width=15,
height=2,
bg='orangered',
command=self.delete_appointment)
self.delete.place(x=450, y=575)
def test_clash_with_two_prescriptions_for_same_medication(self):
patient = Patient(prescriptions=[Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=2), days_supply=2),
Prescription("Paracetamol", dispense_date = date.today() - timedelta(days=3), days_supply=2)])
assert patient.clash(["Paracetamol"]) == set([date.today() - timedelta(days=3),
date.today() - timedelta(days=2),
date.today() - timedelta(days=1)])
def loadFromFile(filename, dataset, verbose=False, run_pca=True, explain_rat=4., ret_var=False):
# TODO: arg check
tissue_name = os.path.basename(filename).split('.')[0]
tissue = Tissue(tissue_name, dataset)
tissue_file = open(filename, 'r')
patient_ids = tissue_file.readline().strip().split('\t')[4:]
for patient_id in patient_ids:
if patient_id not in dataset.patients:
patient = Patient(patient_id)
dataset.addPatient(patient)
patient = dataset.patients[patient_id]
patient.addTissue(tissue)
tissue._rows[patient_id] = tissue.numPatients
tissue._patients[patient_id] = patient
# print 'got patients'
raw_t = [[float(val_str)
for val_str in line.strip().split('\t')[4:]]
for line in tissue_file]
# print 'got data'
val = np.array(raw_t).T
var_exp = 0.
if run_pca:
pca_model = PCA(n_components=50, copy=False)
pca_model.fit_transform(val)
#cov = val.T.dot(val)/(len(raw_t))
#U, W, _ = np.linalg.svd(cov)
#cum_var = np.cumsum(W**2)
#cum_var = cum_var/cum_var[-1]
cum_var = np.cumsum(pca_model.explained_variance_ratio_)
explained_ratio = [float(cum_var[i])/float(i+1)
for i in range(len(cum_var))]
best_dim = 0
for dim in range(len(cum_var)):
if explained_ratio[dim]*len(patient_ids) > explain_rat:
best_dim = dim
n_components = best_dim+1
n_components = max(n_components, 8)
#val = val.dot(U[:,:n_components])
val = val[:,:n_components]
var_exp = cum_var[n_components-1]
if verbose:
print tissue_name + ' has {} components to explain {}% variance for {} patients'.format(n_components, 100.*var_exp, len(patient_ids))
elif verbose:
print tissue_name + ' parsed'
tissue._value = val
if ret_var:
return tissue, var_exp
else:
return tissue
def insert_new_Patient():
"""
this allows you to append a Patient into the memory
"""
# A try and except Block to cheack errors
try:
# this request for the agumet to initiate new Petient
name = input("Enter Name: ")
age = input("Enter Age: ")
strand = input("Enter DNA strand: ")
name.strip()
strand.strip()
# local var
diabetes = ""
blue_eyes = ""
three_eyes = ""
# check for input !== ""
if len(name) == 0 or len(age) == 0:
raise Exception("pls check your input and try agen")
else:
# check for alphabet
if re.search('[a-zA-Z]', age) == True:
raise Exception("Sorry Age must be an integer")
# check for strand length
if len(strand) == MAX_STRAND:
# for three_eyes
if "AAA" in strand:
three_eyes = "True"
else:
three_eyes = "False"
# for blue_eyes
if "GGA" in strand:
blue_eyes = "True"
else:
blue_eyes = "False"
# diabete
if "CTA" in strand:
diabetes = "True"
else:
diabetes = "False"
# insert
init_storage.append(
Patient(name, age, strand, diabetes, blue_eyes, three_eyes))
return "Succesfull"
else:
raise Exception("Bad input! -length must be 20")
# this append a new initiated Patient into the init_storage
# this block catches any error that occurs
except Exception as err:
if err:
return err
for day in patient.clash(medicine_names)])
ax.broken_barh(days_taking_all, (0, 9), facecolors='black')
medicine_count = len(medicine_names)
ax.set_ylim(-5, 10 * (medicine_count + 1) + 5)
ax.set_xlim(-110, 0)
ax.set_xlabel('relative to today')
ax.set_yticks([i * 10 + 5 for i in range(medicine_count + 2)])
ax.set_yticklabels(["Clash"] + medicine_names)
ax.grid(True)
fig.savefig(filename)
if __name__ == "__main__":
patient = Patient()
patient.add_prescription(
Prescription("Fluoxetine",
dispense_date=date.today() - timedelta(100),
days_supply=20))
patient.add_prescription(
Prescription("Fluoxetine",
dispense_date=date.today() - timedelta(50),
days_supply=50))
patient.add_prescription(
Prescription("Codeine",
dispense_date=date.today() - timedelta(15),
days_supply=3))
patient.add_prescription(
Prescription("Codeine",
dispense_date=date.today() - timedelta(60),
def test_clash_with_one_irrelevant_prescription(self):
patient = Patient(prescriptions=[Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=2)])
assert patient.clash(["Prozac"]) == set()
availableFrom = calculateTime(availableFrom)
availableTo = input("\tEnter Available To Time(00:00): ")
availableTo = calculateTime(availableTo)
doctorObject = Doctor(name, doctorSpec, availableDay,
availableFrom, availableTo)
system1.addDoctor(doctorObject)
elif choice == 2:
name = input("\n\tEnter Name: ")
#Print Specializations
print("\n\t\t1. Pediatrician\n\t\t2. ENT\n\t\t3. GP")
patientSpec = int(input("\tEnter Specialization Required: "))
#Print Days
print(
"\n\t\t1. Monday\n\t\t2. Tuesday\n\t\t3. Wednesday\n\t\t4. Thursday\n\t\t5. Friday\n\t\t6. Saturday\n\t\t7. Sunday"
)
day = int(input("\tEnter Required Day: "))
fromTime = input("\tEnter From Time(00:00): ")
fromTime = calculateTime(fromTime)
toTime = input("\tEnter To Time(00:00): ")
toTime = calculateTime(toTime)
patientObject = Patient(name, patientSpec, day, fromTime, toTime)
system1.assignDoctor(patientObject)
elif choice == 3:
print("\n\t\tThank You!")
break
else:
print("\n\t\tInvalid Choice!")
continue
else:
diabetes = "False"
# assigning values with keys to the dictionary
final_res['strand'] = strans
final_res['diabetes'] = diabetes
final_res['blue'] = blue_eyes
final_res['three'] = three_eyes
return final_res
# Storage for each initiation
init_storage = [
Patient("Andrea", 37,
random_strand()['strand'],
random_strand()['diabetes'],
random_strand()['blue'],
random_strand()['three']),
Patient("Bob", 28,
random_strand()['strand'],
random_strand()['diabetes'],
random_strand()['blue'],
random_strand()['three']),
Patient("Brooke", 34,
random_strand()['strand'],
random_strand()['diabetes'],
random_strand()['blue'],
random_strand()['three']),
Patient("Connor", 27,
random_strand()['strand'],
random_strand()['diabetes'],
class TestDepartment(TestCase):
"""This is a test class to test the Department class"""
def setUp(self) -> None:
"""Initialize setup object"""
self.department = Department("Emergency")
self.department1 = Department("Surgery")
self.read_mock = Mock()
self.department._write_to_file = self.read_mock
self.doctor1 = Doctor("George", "Bush", "1982-2-28",
"97334 Oak Bridge , Vancouver, Vancouver, BC", 2,
False, 125, 190000)
self.patient1 = Patient("Jose", "McDonald", "1970-12-12",
"3432 Newtons, Richmond, BC", 1, False, 590)
self.doctor2 = Doctor("Johnny", "Kenedy", "1984-1-30",
"1444 Oakway, North Vancouver, Vancouver, BC", 1,
False, 123, 150000)
self.patient2 = Patient("Bill", "Stark", "1970-12-12",
"1111 Columbia, New Westminster, BC", 2, False,
589, 10000)
self.patient3 = Patient("Tony", "Stark", "1960-9-2",
"1111 Columbia, New Westminster, BC", 12,
False, 589)
def test_valid_constructor(self):
"""Test an object is created correctly"""
self.assertIsNotNone(self.department)
self.assertIsInstance(self.department, Department)
def test_invalid_constructor(self):
"""Test an object with invalid parameters"""
with self.assertRaises(TypeError):
department_1 = Department(1)
def test_add_person(self):
"""Test to add an object (person) to the department"""
with self.assertRaises(ValueError):
self.department.add_person(self.patient1)
self.assertTrue(self.read_mock.called)
# This is to test how many patient objects are added to the self.department
test_case = self.department.get_statistics()
self.assertEqual(test_case.get_not_released_patient_num(), 1)
def test_remove_person(self):
"""Test to remove an object (person) out of the department"""
test_id = self.patient1.get_id()
self.department.remove_person_by_id(test_id)
self.assertTrue(self.read_mock.called)
# This is to test how many patient objects left in the self.department
test_case = self.department.get_statistics()
self.assertEqual(test_case.get_not_released_patient_num(), 0)
# This is to test exception value error of remove method
with self.assertRaises(ValueError):
self.department.remove_person_by_id(100000)
def test_check_existing_person(self):
"""Test to check if an object (person) is in the department"""
test_id = self.patient3.get_id()
self.assertEqual(self.department.person_exist(test_id), False)
test_id_1 = self.doctor2.get_id()
self.assertEqual(self.department.person_exist(test_id_1), True)
def test_get_person_by_type(self):
"""Test to get all people with a given type"""
obj = self.department.get_person_by_type("Teacher")
self.assertEqual(len(obj), 0)
self.department.get_all_current_people()
obj1 = self.department.get_person_by_type("Patient")
self.assertEqual(len(obj1), 2)
def test_get_all_people(self):
"""Test to get all people in a department"""
self.department.get_all_current_people()
def test_get_existing_person_by_id(self):
"""Test to get an object (person) from the department"""
test_id = self.patient1.get_id()
obj1 = self.department.get_person_by_id(test_id)
D1 = obj1.to_dict()
self.assertEqual(D1, self.patient1.to_dict())
obj2 = self.department.get_person_by_id(10000)
self.assertEqual(obj2, None)
def test_get_department_name(self):
"""Test to get the name of the department"""
self.assertEqual(self.department.get_name(), "Emergency")
def test_get_get_statistics(self):
"""Test to get statistics of the department"""
test_case = self.department.get_statistics()
self.assertEqual(test_case.get_not_released_patient_num(), 1)
self.assertEqual(test_case.get_released_patient_num(), 1)
self.assertEqual(test_case.get_total_bill_amount_released_patients(),
10000)
def test_write_data_to_file(self):
"""Test to see if a file is opened and gotten data"""
self.department._write_to_file()
self.assertTrue(self.read_mock.called)
@mock.patch('department.Department._read_from_file')
def test_read_data_to_file(self, mock_read_func):
"""Test to see if a file is opened and data is written on"""
self.department._read_from_file()
self.assertTrue(mock_read_func.called)
def test_get_created_entities(self):
"""Test to check a valid object is created correctly"""
person1 = [{
'first_name': 'George',
'last_name': 'Bush',
'date_of_birth': "1970-12-12 00:00:00",
'address': '97334 Oak Bridge , Vancouver, Vancouver, BC',
'id': 2,
'is_released': False,
'office_num': 125,
'income': 190000
}]
person2 = [{
'first_name': 'Jose',
'last_name': 'McDonald',
'date_of_birth': "1970-12-12 00:00:00",
'address': '3432 Newtons, Richmond, BC',
'is_released': False,
'id': 1,
'room_num': 589,
'bill': 0.0
}]
self.department1.create_entities(person2, "Patient")
self.department1.create_entities(person1, "Doctor")
obj1 = self.department1.get_person_by_id(1)
self.assertIsNotNone(obj1)
self.assertIsInstance(obj1, (Doctor, Patient))
obj2 = self.department1.get_person_by_id(2)
self.assertIsNotNone(obj2)
self.assertIsInstance(obj2, (Doctor, Patient))
def test_update_person(self):
"""Test update information of a person"""
with self.assertRaises(ValueError):
self.department.update_person(4, "Uy", "Tran", 600, 10000)
self.department.update_person(1, "Uy", "Tran", 600, 10000)
self.assertTrue(self.read_mock.called)
def test_to_dict(self):
"""Test to check to_dict() return an expected value"""
self.D1 = self.department1.to_dict()
self.D2 = {
'name':
'Surgery',
'Patient': [{
'first_name': 'Jose',
'last_name': 'McDonald',
'date_of_birth': datetime(1970, 12, 12, 0, 0),
'address': '3432 Newtons, Richmond, BC',
'is_released': False,
'id': 1,
'room_num': 590,
'bill': 0
}, {
'first_name': 'Bill',
'last_name': 'Stark',
'date_of_birth': datetime(1960, 9, 2, 0, 0),
'address': '1111 Columbia, New Westminster, BC',
'is_released': True,
'id': 2,
'room_num': 589,
'bill': 10000
}],
'Doctor': [{
'first_name': 'George',
'last_name': 'Bush',
'date_of_birth': datetime(1982, 2, 28, 0, 0),
'address': '97334 Oak Bridge , Vancouver, Vancouver, BC',
'id': 2,
'is_released': False,
'office_num': 125,
'income': 190000
}]
}
self.assertDictEqual(self.D1, self.D2)
def test_days_taking_for_irrelevant_prescription(self):
patient = Patient(prescriptions=[Prescription("Codeine", dispense_date=days_ago(days=2), days_supply=2)])
assert patient.days_taking("Prozac") == set()
def patient(self):
self._canvas.destroy()
Patient(self.root)
import sqlite3
from patient import Patient
from datetime import date
zero = Patient('Surname', 'Name', str(date(2019, 11, 4)), 'Street', 185, 80)
first = Patient('Surname1', 'Name1', str(date(2019, 11, 4)), 'Street1', 171,
81)
conn = sqlite3.connect('hospital.db')
cursor = conn.cursor()
try:
cursor.execute(
"""insert into Patients values
(:surname, :name, :birthDate, :address,
:height, :weight, 1)""", {
"surname": zero.surname,
"name": zero.name,
"birthDate": zero.birth_date,
"address": zero.address,
"height": zero.height,
"weight": zero.weight
})
cursor.execute(
"""insert into Patients values
(:surname, :name, :birthDate, :address,
:height, :weight, 2)""", {
"surname": first.surname,
"name": first.name,
"birthDate": first.birth_date,
"address": first.address,
from student import Student
from patient import Patient
new_student = Student()
new_student.first_name = "John"
new_student.last_name = "Doe"
new_student.cohort_number = 36
new_student.age = 42
# new_student.full_name = "Happy Days"
print(new_student)
cashew = Patient(
"097-23-1003", "08/13/92", "7001294103",
"Daniela", "Agnoletti", "500 Infinity Way")
# This should not change the state of the object
# cashew.social_security_number = "838-31-2256"
# Neither should this
# cashew.date_of_birth = "01-30-90"
# But printing either of them should work
print(cashew.social_security_number)
# "097-23-1003"
# # These two statements should output nothing
# print(cashew.first_name)
# print(cashew.last_name)
# # But this should output the full name
def _schedule(self):
"""Obtains patient info and schedules patient."""
name = input("\nEnter the patient's name:")
condition = self._getCondition()
self._model.schedule(Patient(name, condition))
print(name, "is added to the", condition, "list\n")
# get training data from un-concussed individuals
n_keep = 1000
train_lists = [pid_concussion, pid_noConcussion]
train_bools = [True, False]
examples_lists = [[], []]
train_examples = []
labels = ["concussion", "noconcussion"]
# for lst, pat_list in zip([pid_noConcussion, pid_3stepProtocol, pid_testRetest, pid_concussion], [noCon_pats, step_pats, retest_pats, con_pats]):
# for lst, pat_list in zip([pid_noConcussion], [noCon_pats]):
i = 0
for pid_list, train_bool in zip(train_lists, train_bools):
for pid in pid_list:
print("Processing pid: {}".format(pid))
p = Patient(pid, subfolder, load_session_raw=False, load_session_examples=True)
# get examples from pre_test
pre = post = None
if p.pre_test is not None:
pre = p.pre_test.load_examples(subfolder)
if pre is not None:
np.random.shuffle(pre)
if (p.n_concussions == 0):
# get examples from post_test
if p.post_test is not None:
post = p.post_test.load_examples(subfolder)
if post is not None:
np.random.shuffle(post)
else:
if p.intermediate_tests[0] is not None: