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, 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')
vioscreen_status = None
vioscreen_text = ''
survey_id = ag_data.get_survey_ids(ag_login_id, participant_name)[1]
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, ebi_submitted=ebi_submitted)
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 _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 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'])
