def get(self):
open_humans = self.get_secure_cookie('open-humans')
# If the user isn't authenticated render the page to allow them to
# authenticate
if not open_humans:
ag_login_id = ag_data.get_user_for_kit(self.current_user)
human_participants = ag_data.getHumanParticipants(ag_login_id)
survey_ids = {}
for participant_name in human_participants:
survey_id = ag_data.get_survey_id(ag_login_id,
participant_name)
if survey_id:
survey_ids[participant_name] = survey_id
self.render('open-humans.html',
skid=self.current_user,
survey_ids=survey_ids,
access_token=None,
origin=self.coerce_origin(),
open_humans_home_url=self._HOME_URL,
open_humans_research_url=self._RESEARCH_URL,
open_humans_api_url=self._API_URL)
return
open_humans = escape.json_decode(open_humans)
self.open_humans_request(
'/american-gut/user-data/',
self._on_user_data_cb,
access_token=open_humans['access_token'])
def get(self):
open_humans = self.get_secure_cookie('open-humans')
# If the user isn't authenticated render the page to allow them to
# authenticate
if not open_humans:
ag_login_id = ag_data.get_user_for_kit(self.current_user)
human_participants = ag_data.getHumanParticipants(ag_login_id)
survey_ids = {}
for participant_name in human_participants:
# Get survey ID 1, the main human survey
survey_id = ag_data.get_survey_ids(ag_login_id,
participant_name)[1]
if survey_id:
survey_ids[participant_name] = survey_id
self.render('open-humans.html',
skid=self.current_user,
survey_ids=survey_ids,
access_token=None,
origin=self.coerce_origin(),
open_humans_home_url=self._HOME_URL,
open_humans_research_url=self._RESEARCH_URL,
open_humans_api_url=self._API_URL)
return
open_humans = escape.json_decode(open_humans)
self.open_humans_request('/american-gut/user-data/',
self._on_user_data_cb,
access_token=open_humans['access_token'])
def post(self):
# Required vars
participant_name = self.get_argument('participant_name',
'environmental')
form = self.build_form()
args = {k: v[0] for k, v in viewitems(self.request.arguments)}
form.process(data=args)
if not form.validate():
self.render('add_sample.html', skid=self.current_user,
participant_name=participant_name,
form=self.build_form(), page_type=self.page_type,
message='Invalid form submission, please try again')
return
barcode = form.barcode.data
sample_site = form.sample_site.data
sample_date = form.sample_date.data
sample_time = form.sample_time.data
notes = form.notes.data
if participant_name == 'environmental':
# environmental sample
env_sampled = sample_site
sample_site = None
else:
env_sampled = None
ag_login_id = ag_data.get_user_for_kit(self.current_user)
ag_data.logParticipantSample(ag_login_id, barcode, sample_site,
env_sampled, sample_date,
sample_time, participant_name, notes)
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
def post(self, participant_name):
text = text_locale['participant_overview.html']
participant_name = participant_name.strip('/') # for nginx
skid = self.current_user
ag_login_id = ag_data.get_user_for_kit(skid)
barcodes = ag_data.getParticipantSamples(ag_login_id, participant_name)
if barcodes:
ebi_submitted = any(ag_data.is_deposited_ebi(b['barcode'])
for b in barcodes)
else:
ebi_submitted = False
# Check if we have to remove the participant
participant_to_remove = self.get_argument("remove", None)
if participant_to_remove and not ebi_submitted:
barcodes = ag_data.getParticipantSamples(
ag_login_id, participant_to_remove)
# Remove all the samples attached to the participant
for bc in barcodes:
ag_data.deleteSample(bc['barcode'], ag_login_id)
# Remove the participant
ag_data.deleteAGParticipantSurvey(
ag_login_id, participant_to_remove)
# Redirect to portal
self.redirect(media_locale['SITEBASE'] + "/authed/portal/")
return
participant_type = self.get_argument('participant_type')
internal_surveys = ag_data.get_participants_surveys(ag_login_id,
participant_name)
vioscreens = []
if internal_surveys is None:
raise HTTPError(404, "Could not retrieve survey details for "
"participant '%s'" % participant_name)
else:
for survey_group, survey_id, survey_name in internal_surveys:
if survey_group == -1:
# Magic number 3 is the vioscreen code for complete survey
status = ag_data.get_vioscreen_status(survey_id)
url = (("https://vioscreen.com/remotelogin.aspx?Key=%s"
"&RegCode=KLUCB") %
url_escape(encrypt_key(survey_id)))
if status is not None and status != 3:
vioscreens.append(text['VIOSCREEN_CONTINUE'] % url)
elif status is not None:
vioscreens.append(text['VIOSCREEN_COMPLETE'])
else:
vioscreens.append(text['VIOSCREEN_START'] % url)
# Get the list of samples for this participant
samples = ag_data.getParticipantSamples(ag_login_id,
participant_name)
self.render('participant_overview.html', skid=skid,
participant_name=participant_name,
internal_surveys=internal_surveys,
participant_type=participant_type, samples=samples,
vioscreens=vioscreens, ebi_submitted=ebi_submitted)
def post(self):
bc_to_remove = self.get_argument("remove", None)
if bc_to_remove:
ag_login_id = ag_data.get_user_for_kit(self.current_user)
ag_data.deleteSample(bc_to_remove, ag_login_id)
self.redirect(media_locale['SITEBASE'] + "/authed/portal/")
return
self._sample_overview_renderer()
def post(self):
bc_to_remove = self.get_argument("remove", None)
if bc_to_remove:
ag_login_id = ag_data.get_user_for_kit(self.current_user)
ag_data.deleteSample(bc_to_remove, ag_login_id)
self.redirect(media_locale['SITEBASE'] + "/authed/portal/")
return
self._sample_overview_renderer()
def build_form(self):
kit_id = self.current_user
ag_login_id = ag_data.get_user_for_kit(kit_id)
kit_barcodes = ag_data.getAvailableBarcodes(ag_login_id)
form = LogSample()
form.barcode.choices = [(v, v) for v in kit_barcodes]
form.sample_site.choices = self._get_sample_sites()
return form
def build_form(self):
kit_id = self.current_user
ag_login_id = ag_data.get_user_for_kit(kit_id)
kit_barcodes = ag_data.getAvailableBarcodes(ag_login_id)
form = LogSample()
form.barcode.choices = [(v, v) for v in kit_barcodes]
form.sample_site.choices = self._get_sample_sites()
return form
def post(self):
skid = self.current_user
tl = text_locale['handlers']
ag_login_id = ag_data.get_user_for_kit(skid)
ag_login_info = ag_data.get_login_info(ag_login_id)[0]
animal_survey_id = self.get_argument('survey_id', None)
sitebase = media_locale['SITEBASE']
if not animal_survey_id:
animal_survey_id = binascii.hexlify(os.urandom(8))
new_survey = True
else:
new_survey = False
form = self.animal_survey()
form.process(data=self.request.arguments)
data = {'questions': form.data}
participant_name = form['Pet_Information_127_0'].data[0]
# If the participant already exists, stop them outright
if new_survey and \
ag_data.check_if_consent_exists(ag_login_id, participant_name):
errmsg = url_escape(tl['PARTICIPANT_EXISTS'] % participant_name)
url = sitebase + "/authed/portal/?errmsg=%s" % errmsg
self.redirect(url)
return
consent = {
'login_id': ag_login_id,
'participant_name': participant_name,
'participant_email': ag_login_info['email'],
'assent_obtainer': 'ANIMAL_SURVEY',
'parent_1_name': 'ANIMAL_SURVEY',
'parent_2_name': 'ANIMAL_SURVEY',
'survey_id': animal_survey_id,
'is_juvenile': True,
'deceased_parent': False,
'obtainer_name': 'ANIMAL_SURVEY',
'age_range': 'ANIMAL_SURVEY'
}
redis.hset(animal_survey_id, 'consent', dumps(consent))
redis.hset(animal_survey_id, 0, dumps(data))
redis.expire(animal_survey_id, 86400)
store_survey(primary_animal_survey, animal_survey_id)
if not new_survey:
message = urlencode([('errmsg', tl['SUCCESSFULLY_EDITED'] %
participant_name)])
else:
message = urlencode([('errmsg', tl['SUCCESSFULLY_ADDED'] %
participant_name)])
url = sitebase + '/authed/portal/?%s' % message
self.redirect(url)
def post(self):
# Required vars
participant_name = self.get_argument('participant_name',
'environmental')
form = self.build_form()
args = {a: v[0] for a, v in viewitems(self.request.arguments)}
form.process(data=args)
# Validate input
invalid = False
if not form.validate():
invalid = True
else:
try:
datetime.strptime(form.sample_date.data, '%m/%d/%Y').date()
except ValueError:
invalid = True
form.sample_date.errors = ['Invalid date format']
try:
datetime.strptime(form.sample_time.data, '%I:%M %p').time()
except ValueError:
invalid = True
form.sample_time.errors = ['Invalid time format']
if invalid:
self.render('add_sample.html',
skid=self.current_user,
participant_name=participant_name,
form=self.build_form(),
page_type=self.page_type,
message='Invalid form submission, please try again')
return
barcode = form.barcode.data
sample_site = form.sample_site.data
sample_date = form.sample_date.data
sample_time = form.sample_time.data
notes = form.notes.data
if participant_name == 'environmental':
# environmental sample
env_sampled = sample_site
sample_site = None
else:
env_sampled = None
ag_login_id = ag_data.get_user_for_kit(self.current_user)
ag_data.logParticipantSample(ag_login_id, barcode, sample_site,
env_sampled, sample_date, sample_time,
participant_name, notes)
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
def post(self, participant_name):
text = text_locale['participant_overview.html']
participant_name = participant_name.strip('/') # for nginx
skid = self.current_user
ag_login_id = ag_data.get_user_for_kit(skid)
# Check if we have to remove the participant
participant_to_remove = self.get_argument("remove", None)
if participant_to_remove:
barcodes = ag_data.getParticipantSamples(
ag_login_id, participant_to_remove)
# Remove all the samples attached to the participant
for bc in barcodes:
ag_data.deleteSample(bc['barcode'], ag_login_id)
# Remove the participant
ag_data.deleteAGParticipantSurvey(
ag_login_id, participant_to_remove)
# Redirect to portal
self.redirect(media_locale['SITEBASE'] + "/authed/portal/")
return
participant_type = self.get_argument('participant_type')
vioscreen_status = None
vioscreen_text = ''
survey_id = ag_data.get_survey_id(ag_login_id, participant_name)
if survey_id is None:
raise HTTPError(404, "Could not retrieve survey details for "
"participant '%s'" % participant_name)
else:
vioscreen_status = ag_data.get_vioscreen_status(survey_id)
url = ("https://vioscreen.com/remotelogin.aspx?Key=%s"
"&RegCode=KLUCB" % url_escape(encrypt_key(survey_id)))
# Magic number 3 is the vioscreen code for complete survey
if vioscreen_status is not None and vioscreen_status != 3:
vioscreen_text = text['VIOSCREEN_CONTINUE'] % url
elif vioscreen_status is not None:
vioscreen_text = text['VIOSCREEN_COMPLETE']
else:
vioscreen_text = text['VIOSCREEN_START'] % url
# Get the list of samples for this participant
samples = ag_data.getParticipantSamples(ag_login_id,
participant_name)
self.render('participant_overview.html', skid=skid,
participant_name=participant_name, survey_id=survey_id,
participant_type=participant_type, samples=samples,
vioscreen_text=vioscreen_text)
def post(self):
# Required vars
participant_name = self.get_argument('participant_name',
'environmental')
form = self.build_form()
args = {a: v[0] for a, v in viewitems(self.request.arguments)}
form.process(data=args)
# Validate input
invalid = False
if not form.validate():
invalid = True
else:
try:
datetime.strptime(form.sample_date.data, '%m/%d/%Y').date()
except ValueError:
invalid = True
form.sample_date.errors = ['Invalid date format']
try:
datetime.strptime(form.sample_time.data, '%I:%M %p').time()
except ValueError:
invalid = True
form.sample_time.errors = ['Invalid time format']
if invalid:
self.render('add_sample.html', skid=self.current_user,
participant_name=participant_name,
form=self.build_form(), page_type=self.page_type,
message='Invalid form submission, please try again')
return
barcode = form.barcode.data
sample_site = form.sample_site.data
sample_date = form.sample_date.data
sample_time = form.sample_time.data
notes = form.notes.data
if participant_name == 'environmental':
# environmental sample
env_sampled = sample_site
sample_site = None
else:
env_sampled = None
ag_login_id = ag_data.get_user_for_kit(self.current_user)
ag_data.logParticipantSample(ag_login_id, barcode, sample_site,
env_sampled, sample_date,
sample_time, participant_name, notes)
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
def get(self):
kit_id = self.current_user
ag_login_id = ag_data.get_user_for_kit(kit_id)
kit_barcodes = ag_data.getAvailableBarcodes(ag_login_id)
participant_name = self.get_argument('participant_name',
'environmental')
form = LogSample()
form.barcode.choices = [(v, v) for v in kit_barcodes]
form.sample_site.choices = self._get_sample_sites()
self.render('add_sample.html', skid=kit_id,
kit_barcodes=kit_barcodes,
participant_name=participant_name,
form=form)
def test_post(self):
# test reaction to invalid kit IDs
response = self.post(
'/auth/register/', {
'kit_id': 'wrong_kit_id',
'password': '******',
'email': 'e@mail',
'email2': 'e@mail',
'participantname': 'joe',
'address': 'street',
'city': 'metropolis',
'state': 'XX',
'zip': '12345',
'country': 'Afghanistan'
})
port = self.get_http_port()
self.assertEqual(response.effective_url,
'http://*****:*****@mail',
'email2': 'e@mail',
'participantname': 'joe',
'address': 'street',
'city': 'metropolis',
'state': 'XX',
'zip': '12345',
'country': 'Afghanistan'
})
port = self.get_http_port()
self.assertEqual(response.code, 200)
self.assertEqual(
response.effective_url, 'http://localhost:%d/?next=%s' %
(port, url_escape('/authed/portal/')))
# Check that registration changed the DB. A proxy to test that no
# ValueError is raised.
self.assertNotEqual(ag_data.get_user_for_kit(unregistered_kits[0]),
'something')
def on_message(self, msg):
tl = text_locale['handlers']
skid = self.current_user
participant_name = msg
ag_login_id = ag_data.get_user_for_kit(skid)
human_participants = ag_data.getHumanParticipants(ag_login_id)
animal_participants = ag_data.getAnimalParticipants(ag_login_id)
if participant_name in (human_participants + animal_participants):
# if the participant already exists in the system, fail nicely
output_message = (tl['PARTICIPANT_EXISTS'] % participant_name)
else:
# otherwise, success!
output_message = 'success'
self.write_message(output_message)
def test_post(self):
# test reaction to invalid kit IDs
response = self.post('/auth/register/',
{'kit_id': 'wrong_kit_id',
'password': '******',
'email': 'e@mail',
'email2': 'e@mail',
'participantname': 'joe',
'address': 'street',
'city': 'metropolis',
'state': 'XX',
'zip': '12345',
'country': 'Afghanistan'})
port = self.get_http_port()
self.assertEqual(
response.effective_url,
'http://*****:*****@mail',
'email2': 'e@mail',
'participantname': 'joe',
'address': 'street',
'city': 'metropolis',
'state': 'XX',
'zip': '12345',
'country': 'Afghanistan'})
port = self.get_http_port()
self.assertEqual(response.code, 200)
self.assertEqual(
response.effective_url,
'http://localhost:%d/?next=%s' %
(port, url_escape('/authed/portal/')))
# Check that registration changed the DB. A proxy to test that no
# ValueError is raised.
self.assertNotEqual(ag_data.get_user_for_kit(unregistered_kits[0]),
'something')
def post(self):
tl = text_locale['handlers']
participant_name = self.get_argument("participant_name").strip()
participant_email = self.get_argument("participant_email").strip()
age_range = self.get_argument("age_range")
parent_1_name = self.get_argument("parent_1_name", None)
parent_2_name = self.get_argument("parent_2_name", None)
obtainer_name = self.get_argument("obtainer_name", None)
deceased_parent = self.get_argument("deceased_parent", 'No')
sitebase = media_locale['SITEBASE']
if not participant_name or not participant_email:
self.render("new_participant.html",
skid=self.current_user,
message=tl['MISSING_NAME_EMAIL'])
return
ag_login_id = ag_data.get_user_for_kit(self.current_user)
# If the participant already exists, stop them outright
if ag_data.check_if_consent_exists(ag_login_id, participant_name):
errmsg = url_escape(tl['PARTICIPANT_EXISTS'] % participant_name)
url = sitebase + "/authed/portal/?errmsg=%s" % errmsg
self.redirect(url)
return
human_survey_id = binascii.hexlify(os.urandom(8))
consent = {
'participant_name': participant_name,
'participant_email': participant_email,
'parent_1_name': parent_1_name,
'parent_2_name': parent_2_name,
'is_juvenile': True if age_range != '18-plus' else False,
'deceased_parent': deceased_parent,
'obtainer_name': obtainer_name,
'age_range': age_range,
'login_id': ag_login_id,
'survey_id': human_survey_id
}
redis.hset(human_survey_id, 'consent', dumps(consent))
redis.expire(human_survey_id, 86400)
self.set_secure_cookie('human_survey_id', human_survey_id)
self.redirect(sitebase + "/authed/survey_main/")
def on_message(self, msg):
tl = text_locale['handlers']
skid = self.current_user
participant_name = msg
ag_login_id = ag_data.get_user_for_kit(skid)
human_participants = ag_data.getHumanParticipants(ag_login_id)
animal_participants = ag_data.getAnimalParticipants(ag_login_id)
if participant_name in (human_participants + animal_participants):
# if the participant already exists in the system, fail nicely
output_message = (tl['PARTICIPANT_EXISTS'] % participant_name)
else:
# otherwise, success!
output_message = 'success'
self.write_message(output_message)
def post(self):
tl = text_locale['handlers']
participant_name = self.get_argument("participant_name").strip()
participant_email = self.get_argument("participant_email").strip()
age_range = self.get_argument("age_range")
parent_1_name = self.get_argument("parent_1_name", None)
parent_2_name = self.get_argument("parent_2_name", None)
obtainer_name = self.get_argument("obtainer_name", None)
deceased_parent = self.get_argument("deceased_parent", 'No')
sitebase = media_locale['SITEBASE']
if not participant_name or not participant_email:
self.render("new_participant.html", skid=self.current_user,
message=tl['MISSING_NAME_EMAIL'])
return
ag_login_id = ag_data.get_user_for_kit(self.current_user)
# If the participant already exists, stop them outright
if ag_data.check_if_consent_exists(ag_login_id, participant_name):
errmsg = url_escape(tl['PARTICIPANT_EXISTS'] % participant_name)
url = sitebase + "/authed/portal/?errmsg=%s" % errmsg
self.redirect(url)
return
human_survey_id = binascii.hexlify(os.urandom(8))
consent = {'participant_name': participant_name,
'participant_email': participant_email,
'parent_1_name': parent_1_name,
'parent_2_name': parent_2_name,
'is_juvenile': True if age_range != '18-plus' else False,
'deceased_parent': deceased_parent,
'obtainer_name': obtainer_name,
'age_range': age_range,
'login_id': ag_login_id,
'survey_id': human_survey_id}
redis.hset(human_survey_id, 'consent', dumps(consent))
redis.expire(human_survey_id, 86400)
self.set_secure_cookie('human_survey_id', human_survey_id)
self.redirect(sitebase + "/authed/survey_main/")
def post(self):
skid = self.current_user
tl = text_locale['handlers']
ag_login_id = ag_data.get_user_for_kit(skid)
survey_id = self.get_argument('survey_id', None)
survey_type = self.get_argument('type')
participant_name = url_unescape(self.get_argument('participant_name'))
sitebase = media_locale['SITEBASE']
if not survey_id:
survey_id = binascii.hexlify(os.urandom(8))
sec_survey = self.sec_surveys[survey_type]
survey_class = make_survey_class(sec_survey.groups[0],
survey_type='SecondarySurvey')
form = survey_class()
form.process(data=self.request.arguments)
data = {'questions': form.data}
consent = {
'login_id': ag_login_id,
'participant_name': participant_name,
'survey_id': survey_id,
'secondary': True
}
redis.hset(survey_id, 'consent', dumps(consent))
redis.hset(survey_id, 0, dumps(data))
redis.expire(survey_id, 86400)
store_survey(sec_survey, survey_id)
if survey_id:
message = urlencode([
('errmsg', tl['SUCCESSFULLY_EDITED'] % participant_name)
])
else:
message = urlencode([
('errmsg', tl['SUCCESSFULLY_ADDED'] % participant_name)
])
url = '%s/authed/portal/?%s' % (sitebase, message)
self.redirect(url)
def _on_user_data_cb(self, user_data):
open_humans = escape.json_decode(self.get_secure_cookie('open-humans'))
try:
link_survey_id = escape.json_decode(
base64.b64decode(self.get_cookie('link-survey-id')))
except (AttributeError, ValueError, TypeError):
link_survey_id = None
if link_survey_id:
self.open_humans_request(
'/american-gut/user-data/',
self._on_post_user_data_cb,
method='PATCH',
body={'data': {
'surveyIds': link_survey_id
}},
access_token=open_humans['access_token'])
return
survey_ids = {}
ag_login_id = ag_data.get_user_for_kit(self.current_user)
human_participants = ag_data.getHumanParticipants(ag_login_id)
for participant_name in human_participants:
# Get survey ID 1, the main human survey
survey_id = ag_data.get_survey_ids(ag_login_id,
participant_name)[1]
if survey_id:
survey_ids[participant_name] = survey_id
self.render('open-humans.html',
skid=self.current_user,
survey_ids=survey_ids,
access_token=open_humans['access_token'],
origin=self.coerce_origin(),
open_humans_home_url=self._HOME_URL,
open_humans_research_url=self._RESEARCH_URL,
open_humans_api_url=self._API_URL)
def post(self):
skid = self.current_user
tl = text_locale['handlers']
ag_login_id = ag_data.get_user_for_kit(skid)
survey_id = self.get_argument('survey_id', None)
survey_type = self.get_argument('type')
participant_name = self.get_argument('participant_name')
sitebase = media_locale['SITEBASE']
if not survey_id:
survey_id = binascii.hexlify(os.urandom(8))
sec_survey = self.sec_surveys[survey_type]
survey_class = make_survey_class(sec_survey.groups[0],
survey_type='SecondarySurvey')
form = survey_class()
form.process(data=self.request.arguments)
data = {'questions': form.data}
consent = {
'login_id': ag_login_id,
'participant_name': participant_name,
'survey_id': survey_id,
'secondary': True
}
redis.hset(survey_id, 'consent', dumps(consent))
redis.hset(survey_id, 0, dumps(data))
redis.expire(survey_id, 86400)
store_survey(sec_survey, survey_id)
if survey_id:
message = urlencode([('errmsg', tl['SUCCESSFULLY_EDITED'] %
participant_name)])
else:
message = urlencode([('errmsg', tl['SUCCESSFULLY_ADDED'] %
participant_name)])
url = '%s/authed/portal/?%s' % (sitebase, message)
self.redirect(url)
def _on_user_data_cb(self, user_data):
open_humans = escape.json_decode(self.get_secure_cookie('open-humans'))
try:
link_survey_id = escape.json_decode(
base64.b64decode(self.get_cookie('link-survey-id')))
except (AttributeError, ValueError, TypeError):
link_survey_id = None
if link_survey_id:
self.open_humans_request(
'/american-gut/user-data/',
self._on_post_user_data_cb,
method='PATCH',
body={'data': {'surveyIds': link_survey_id}},
access_token=open_humans['access_token'])
return
survey_ids = {}
ag_login_id = ag_data.get_user_for_kit(self.current_user)
human_participants = ag_data.getHumanParticipants(ag_login_id)
for participant_name in human_participants:
# Get survey ID 1, the main human survey
survey_id = ag_data.get_survey_ids(ag_login_id,
participant_name)[1]
if survey_id:
survey_ids[participant_name] = survey_id
self.render('open-humans.html',
skid=self.current_user,
survey_ids=survey_ids,
access_token=open_humans['access_token'],
origin=self.coerce_origin(),
open_humans_home_url=self._HOME_URL,
open_humans_research_url=self._RESEARCH_URL,
open_humans_api_url=self._API_URL)
def post(self):
# Required vars
barcode = self.get_argument('barcode')
sample_date = self.get_argument('sample_date')
sample_time = self.get_argument('sample_time')
notes = self.get_argument('notes')
participant_name = self.get_argument('participant_name')
sample_site = self.get_argument('sample_site', '')
if participant_name == 'environmental':
# environmental sample
env_sampled = sample_site
sample_site = None
else:
env_sampled = None
ag_login_id = ag_data.get_user_for_kit(self.current_user)
ag_data.logParticipantSample(ag_login_id, barcode, sample_site,
env_sampled, sample_date,
sample_time, participant_name, notes)
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
def post(self):
tl = text_locale['handlers']
deceased_parent = self.get_argument("deceased_parent", None)
participant_name = self.get_argument("participant_name")
participant_email = self.get_argument("participant_email")
is_juvenile = self.get_argument("is_juvenile", 'off')
parent_1_name = self.get_argument("parent_1_name", None)
parent_2_name = self.get_argument("parent_2_name", None)
ag_login_id = ag_data.get_user_for_kit(self.current_user)
kit_email = ag_data.get_user_info(self.current_user)['email']
# Check if the participant is on the exceptions list
is_exception = (
participant_name
in ag_data.getParticipantExceptions(ag_login_id))
# If the participant already exists, stop them outright
if ag_data.check_if_consent_exists(ag_login_id, participant_name):
errmsg = url_escape(tl['PARTICIPANT_EXISTS'] % participant_name)
self.redirect(media_locale['SITEBASE'] + "/authed/portal/?errmsg=%s" % errmsg)
return
if is_juvenile == 'off' and is_exception:
errmsg = url_escape(tl["JUVENILE_CONSENT_EXPECTED"] %
participant_name)
self.redirect(media_locale['SITEBASE'] + "/authed/portal/?errmsg=%s" % errmsg)
return
if is_juvenile == 'on':
# If they aren't already an exception, we need to verify them
if not is_exception:
alert_message = tl['MINOR_PARENTAL_BODY']
subject = ("AGJUVENILE: %s (ag_login_id: %s) is a child"
% (participant_name, ag_login_id))
message = MESSAGE_TEMPLATE % (participant_name,
parent_1_name, parent_2_name,
deceased_parent,
self.current_user, kit_email)
try:
send_email(message, subject, sender=kit_email)
alert_message = tl['MESSAGE_SENT']
except:
alert_message = media_locale['EMAIL_ERROR']
self.redirect(media_locale['SITEBASE'] + "/authed/portal/?errmsg=%s" % alert_message)
return
human_survey_id = binascii.hexlify(os.urandom(8))
consent= {'participant_name': participant_name,
'participant_email': participant_email,
'parent_1_name': parent_1_name,
'parent_2_name': parent_2_name,
'is_juvenile': True if is_juvenile == 'on' else False,
'deceased_parent': deceased_parent,
'login_id': ag_login_id,
'survey_id': human_survey_id}
redis.hset(human_survey_id, 'consent', dumps(consent))
redis.expire(human_survey_id, 86400)
self.set_secure_cookie('human_survey_id', human_survey_id)
self.redirect(media_locale['SITEBASE'] + "/authed/survey_main/")
def post(self, participant_name):
text = text_locale['participant_overview.html']
participant_name = participant_name.strip('/') # for nginx
skid = self.current_user
ag_login_id = ag_data.get_user_for_kit(skid)
barcodes = ag_data.getParticipantSamples(ag_login_id, participant_name)
if barcodes:
ebi_submitted = any(
ag_data.is_deposited_ebi(b['barcode']) for b in barcodes)
else:
ebi_submitted = False
# Check if we have to remove the participant
participant_to_remove = self.get_argument("remove", None)
if participant_to_remove and not ebi_submitted:
barcodes = ag_data.getParticipantSamples(ag_login_id,
participant_to_remove)
# Remove all the samples attached to the participant
for bc in barcodes:
ag_data.deleteSample(bc['barcode'], ag_login_id)
# Remove the participant
ag_data.deleteAGParticipantSurvey(ag_login_id,
participant_to_remove)
# Redirect to portal
self.redirect(media_locale['SITEBASE'] + "/authed/portal/")
return
participant_type = self.get_argument('participant_type')
internal_surveys = ag_data.get_participants_surveys(
ag_login_id, participant_name)
vioscreens = []
if internal_surveys is None:
raise HTTPError(
404, "Could not retrieve survey details for "
"participant '%s'" % participant_name)
else:
for survey_group, survey_id, survey_name in internal_surveys:
if survey_group == -1:
# Magic number 3 is the vioscreen code for complete survey
status = ag_data.get_vioscreen_status(survey_id)
url = (("https://vioscreen.com/remotelogin.aspx?Key=%s"
"&RegCode=KLUCB") %
url_escape(encrypt_key(survey_id)))
if status is not None and status != 3:
vioscreens.append(text['VIOSCREEN_CONTINUE'] % url)
elif status is not None:
vioscreens.append(text['VIOSCREEN_COMPLETE'])
else:
vioscreens.append(text['VIOSCREEN_START'] % url)
# Get the list of samples for this participant
samples = ag_data.getParticipantSamples(ag_login_id, participant_name)
self.render('participant_overview.html',
skid=skid,
participant_name=participant_name,
internal_surveys=internal_surveys,
participant_type=participant_type,
samples=samples,
vioscreens=vioscreens,
ebi_submitted=ebi_submitted)
