def user_info():
"""List participant details"""
barcode = request.args.get('barcode')
user = User.query.filter_by(sample_id=barcode.split("_")[0]).first()
info = UserInfo.query.filter_by(user_id=user.id).first()
if not info:
UserInfo.create(user_id=user.id)
info = UserInfo.query.filter_by(user_id=user.id).first()
form = userInfoForm(request.form)
else:
form = userInfoForm(request.form)
# form.sex = info.sex
# form.race = info.race
# form.ethnicity = info.ethnicity
# form.process()
if current_user.is_admin:
if form.validate_on_submit():
if user.gtid != form.gtid.data:
user.gtid = form.gtid.data
user.save()
today = dt.date.today()
dob = form.dob.data
info.update(
commit=True,
age=today.year - dob.year,
# sex=form.sex.data,
dob=dob
# race=form.race.data,
# ethnicity=form.ethnicity.data,
# address=form.address.data,
# zipcode=form.zipcode.data,
# county=form.county.data
)
result = Results.query.filter_by(result_id=barcode).first()
result.result_text = "Sample received, awaiting processing"
result.result = None
result.updated_time = roundSeconds(dt.datetime.now())
result.save()
AuditLog.create(
user_id=user.id,
result_id=result.id,
status=f"Specimen received, in tube {result.tube_id}")
flash('Added sample for processing', 'success')
return redirect(url_for('manage.sample'))
else:
flash_errors(form)
return render_template("manage/user_info.html",
form=form,
barcode=barcode,
user=user,
info=info)
def update_results():
"""Home page."""
if current_user.is_admin:
if request.method == 'POST':
if 'resultsfile' not in request.form or not allowed_file(
request.form.get('resultsfile')):
flash('Selected file not in list of allowed files')
return redirect(url_for('manage.home'))
else:
flash(
f"Updating consent data with: {request.form.get('resultsfile')}"
)
return redirect(url_for('manage.home'))
return redirect(url_for('manage.home'))
def upload():
"""Home page."""
if current_user.is_admin:
if request.method == 'POST':
if 'kind' not in request.form:
flash('No upload type chosen')
return redirect(request.url)
if 'file' not in request.files:
flash('No file part')
return redirect(request.url)
file = request.files['file']
# if user does not select file, browser also
# submit an empty part without filename
if file.filename == '':
flash('No selected file')
return redirect(request.url)
if file and allowed_file(file.filename):
filename = secure_filename(file.filename)
file.save(
os.path.join(current_app.config['UPLOAD_FOLDER'],
request.form['kind'], filename))
return redirect(url_for('manage.home'))
return render_template("manage/home.html",
files=os.listdir(
os.path.join(
current_app.config['UPLOAD_FOLDER'],
'consent')))
def update_consents():
"""Home page."""
if current_user.is_admin:
if request.method == 'POST':
if 'consentfile' not in request.form or not allowed_file(
request.form.get('consentfile')):
flash('Selected file not in list of allowed files')
return redirect(url_for('manage.home'))
else:
flash(
f"Updating consent data with: {request.form.get('consentfile')}"
)
fname = os.path.join(current_app.config['UPLOAD_FOLDER'],
"consent",
request.form.get('consentfile'))
with open(fname, encoding='utf8') as fh:
fh.readline()
for l in fh:
l = l.rstrip().split(",")
add_consent(l[0], l[4])
return redirect(url_for('manage.home'))
return redirect(url_for('manage.home'))
def details():
"""List participant details"""
form = detailsForm(request.form)
barcode = request.args.get('barcode')
user = User.query.filter_by(sample_id=barcode.split("_")[0]).first()
consent_id = ''
consent = Consent.query.filter_by(user_id=user.id).first()
result = Results.query.filter_by(result_id=barcode).first()
if consent and consent.consent_id != "No consent id available":
consent_id = consent.consent_id
if current_user.is_admin:
if form.validate_on_submit():
result.tube_id = form.tubeid.data
result.save()
if form.consent_id.data != consent_id:
if consent:
if consent.consent_id == "No consent id available" or consent.consent_id == None:
consent.consent_id = form.consent_id.data
consent.save()
else:
flash('You cannot replace an existing consent ID',
'danger')
return redirect(
url_for('manage.details', barcode=barcode))
else:
Consent.create(user_id=user.id,
consented=True,
consent_id=form.consent_id.data,
unverified=False)
return redirect(url_for('manage.user_info', barcode=barcode))
return render_template("manage/details.html",
form=form,
barcode=barcode,
consent_id=consent_id,
tubeid=result.tube_id,
user=user)
def home():
"""Home page."""
roles = Role.query.filter_by(user_id=current_user.id).all()
if not roles or all([role.name != "stamps" for role in roles]):
flash("You don't have permission to view this page")
abort(404)
# to_report = Results.query.filter_by(reported=False).join(User).join(UserInfo).all()
to_report = db.session.query(Results, User, UserInfo)
# to_report = to_report.filter(Results.reported == False).filter(Results.user_id == User.id).all()
to_report = to_report.filter(Results.user_id == User.id).filter(Results.user_id == UserInfo.user_id).all()
results = []
columns = [
{
"field" : "Result ID",
"title" : "Result ID",
"sortable" : True,
},
{
"field" : "First name",
"title" : "First name",
"sortable" : True,
},
{
"field" : "Last name",
"title" : "Last name",
"sortable" : True,
},
{
"field" : "Phone",
"title" : "Phone",
"sortable" : False,
},
{
"field" : "GTID",
"title" : "GTID",
"sortable" : True,
},
{
"field" : "Result",
"title" : "Result",
"sortable" : True,
},
{
"field" : "Patient age",
"title" : "Patient age",
"sortable" : True,
},
{
"field" : "Patient sex",
"title" : "Patient sex",
"sortable" : True,
},
{
"field" : "Patient race",
"title" : "Patient race",
"sortable" : True,
},
{
"field" : "Patient ethnicity",
"title" : "Patient ethnicity",
"sortable" : True,
},
{
"field" : "Patient address",
"title" : "Patient address",
"sortable" : True,
},
{
"field" : "Patient zip",
"title" : "Patient zip",
"sortable" : True,
},
{
"field" : "Patient county",
"title" : "Patient county",
"sortable" : True,
},
]
for report in to_report:
results.append( {
"Result ID": report.Results.result_id,
"First name": report.User.first_name,
"Last name": report.User.last_name,
"Phone": report.User.phone,
"GTID": report.User.gtid,
"result": str(report.Results.result),
"Patient age": report.UserInfo.age,
"Patient sex": report.UserInfo.sex,
"Patient race": report.UserInfo.race,
"Patient ethnicity": report.UserInfo.ethnicity,
"Patient address": report.UserInfo.address,
"Patient zip": report.UserInfo.zipcode,
"Patient county": report.UserInfo.county,
})
return render_template('stamps/home.html',
data=results,
columns=columns)