def validate(id):
order = Order.query.get(id)
data_xls = pd.read_excel(order.file_url)
for index, row in data_xls.iterrows():
# one patient have samples that have results
# check patient number first if exist in db per row
patient = Patient()
patient_count = Patient.query.filter_by(code=row[0]).count()
if patient_count > 0:
sample_count = Sample.query.filter_by(code=row[7]).count()
if sample_count > 0:
# add new resltuts
print(row[0] + ' ' + str(index))
else:
sample = Sample()
sample.origin_id = 1
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature_id = sample_nature.id
print(row[14])
sample_type = SampleType.query.filter_by(name=row[9]).first()
sample.sample_type_id = sample_type.id
support = Support.query.filter_by(name=row[13]).first()
sample.support_id = support.id
jonc_type = JoncType.query.filter_by(name=row[14]).first()
if jonc_type is not None:
sample.jonc_type_id = jonc_type.id
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
patient.samples.append(sample)
order.patients.append(patient)
db.session.commit()
generateCode(sample, index + 1)
else:
# add new patient and samples and result of sample
patient.code = row[0]
patient.origin_id = 1
patient.bio_code = get_bio_code('HU')
patient.age = row[1]
patient.sexe = row[2]
patient.birthday = str(row[3])
patient.city = row[4]
patient.job = row[5]
patient.clinical_data = row[6]
# samples implementation
for r in range(int(row[15])):
sample = Sample()
sample.origin_id = 1
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature = sample_nature
sample_type = SampleType.query.filter_by(name=row[9]).first()
sample.sample_type = sample_type
support = Support.query.filter_by(name=row[13]).first()
sample.support = support
jonc_type = JoncType.query.filter_by(name=row[14]).first()
sample.jonc_type = jonc_type
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
sample.number = int(row[15])
patient.samples.append(sample)
generateCode(sample, r + 1)
print(str(sample.bio_code))
order.patients.append(patient)
db.session.commit()
order.status = 1
db.session.commit()
# and check sample id if already in db
flash(_('Traitement effectué avec succes!'))
return redirect(url_for('order.detail', id=order.id))
def do_import(id):
order = Order.query.get(id)
if request.method == 'POST':
file = request.files['file']
filename = documents.save(file)
data_xls = pd.read_excel(file)
for index, row in data_xls.iterrows():
# one patient have samples that have results
# check patient number first if exist in db per row
patient = Patient()
patient_count = Patient.query.filter_by(code=row[0]).count()
if patient_count > 0:
sample_count = Sample.query.filter_by(code=row[7]).count()
if sample_count > 0:
# add new resltuts
print(row[0] + ' ' + str(index))
else:
sample = Sample()
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature_id = sample_nature.id
sample_type = SampleType.query.filter_by(
name=row[9]).first()
sample.sample_type_id = sample_type.id
support = Support.query.filter_by(name=row[13]).first()
sample.support_id = support.id
jonc_type = JoncType.query.filter_by(name=row[14]).first()
sample.jonc_type_id = jonc_type.id
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
patient.samples.append(sample)
order.patients.append(patient)
db.session.commit()
generateCode(sample, r + 1)
else:
# add new patient and samples and result of sample
print(row[4] + ' ' + str(index))
patient.code = row[0]
patient.origin_id = 1
patient.bio_code = get_bio_code('HU')
patient.age = row[1]
patient.sexe = row[2]
patient.birthday = str(row[3])
patient.city = row[4]
patient.job = row[5]
patient.clinical_data = row[6]
# samples implementation
for r in range(int(row[15])):
sample = Sample()
sample.bio_code = patient.bio_code
sample.volume = row[16]
sample_nature = SampleNature.query.filter_by(
name=row[8]).first()
sample.sample_nature_id = sample_nature.id
sample_type = SampleType.query.filter_by(
name=row[9]).first()
sample.sample_type_id = sample_type.id
support = Support.query.filter_by(name=row[13]).first()
sample.support_id = support.id
jonc_type = JoncType.query.filter_by(name=row[14]).first()
sample.jonc_type_id = jonc_type.id
mesure = Mesure.query.filter_by(name=row[17]).first()
sample.mesure_id = mesure.id
sample.code = row[7]
sample.date = str(row[10])
sample.technique = row[11]
sample.site = row[12]
sample.status = 0
patient.samples.append(sample)
generateCode(sample, r + 1)
print(str(sample.bio_code))
order.patients.append(patient)
db.session.commit()
# and check sample id if already in db
url = documents.url(filename)
document = Document(name=filename, url=url)
order.documents.append(document)
db.session.add(document)
db.session.commit()
flash(_('Fichier importé avec succes!'))
return redirect(url_for('order.detail', id=order.id))
return render_template('order/import.html', order=order)
