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implementation.py
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implementation.py
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import json
import os
import flask
import flask_babel
from flask_babel import gettext
from flask import render_template, session, redirect, make_response, request, \
jsonify
import jwt
import requests
from requests.auth import AuthBase
from urllib.parse import quote
from os import path
from datetime import datetime
import base64
import functools
import re
from string import ascii_lowercase
from microsetta_interface.model_i18n import translate_source, \
translate_sample, translate_survey_template, EN_US_KEY, LANGUAGES, \
ES_MX_KEY, ES_ES_KEY, JA_JP_KEY, PARTIAL_TO_FULL_LOCALES
# Authrocket uses RS256 public keys, so you can validate anywhere and safely
# store the key in code. Obviously using this mechanism, we'd have to push code
# to roll the keys, which is not ideal, but you can instead hold this in a
# config somewhere and reload
# Python is dumb, don't put spaces anywhere in this string.
from werkzeug.exceptions import BadRequest, Unauthorized
from microsetta_interface.config_manager import SERVER_CONFIG
import importlib.resources as pkg_resources
from microsetta_interface.redis_cache import RedisCache
from microsetta_interface.util import has_non_keyword_arguments, \
parse_request_csv_col, parse_request_csv, dict_to_csv
from collections import defaultdict
# TODO: source from a microsetta_private_api endpoint
class Source:
SOURCE_TYPE_HUMAN = "human"
SOURCE_TYPE_ANIMAL = "animal"
SOURCE_TYPE_ENVIRONMENT = "environmental"
PUBKEY_ENVVAR = 'MICROSETTA_INTERFACE_DEBUG_JWT_PUB'
if os.environ.get(PUBKEY_ENVVAR, False):
PUB_KEY = open(os.environ[PUBKEY_ENVVAR]).read()
else:
PUB_KEY = pkg_resources.read_text(
'microsetta_interface',
"authrocket.pubkey")
TOKEN_KEY_NAME = 'token'
ADMIN_MODE_KEY = 'admin_mode'
LOGIN_INFO_KEY = 'login_info'
LANG_KEY = "language"
RECONSENT_DECLINED_KEY = "reconsent_declined"
SOURCE_ID = "source_id"
HOME_URL = "/home"
HELP_EMAIL = "microsetta@ucsd.edu"
REROUTE_KEY = "reroute"
ACTIVATION_CODE_KEY = "code"
KIT_NAME_KEY = "kit_name"
EMAIL_CHECK_KEY = "email_checked"
ACCT_FNAME_KEY = "first_name"
ACCT_LNAME_KEY = "last_name"
ACCT_EMAIL_KEY = "email"
ACCT_ADDR_KEY = "address"
ACCT_ADDR_STREET_KEY = "street"
ACCT_ADDR_STREET2_KEY = "street2"
ACCT_ADDR_CITY_KEY = "city"
ACCT_ADDR_STATE_KEY = "state"
ACCT_ADDR_POST_CODE_KEY = "post_code"
ACCT_ADDR_COUNTRY_CODE_KEY = "country_code"
ACCT_LANG_KEY = "language"
ACCT_TERMS_KEY = "consent_privacy_terms"
ACCT_WRITEABLE_KEYS = [ACCT_FNAME_KEY, ACCT_LNAME_KEY, ACCT_EMAIL_KEY,
ACCT_ADDR_KEY, ACCT_LANG_KEY, ACCT_TERMS_KEY]
# Age groups for consent purposes, in order. Order is key as this will be
# used to govern progression. E.g., a child may move to teen, but a teen may
# not move to child.
HUMAN_CONSENT_TODDLER = "0-6"
HUMAN_CONSENT_CHILD = "7-12"
HUMAN_CONSENT_ADOLESCENT = "13-17"
HUMAN_CONSENT_ADULT = "18-plus"
HUMAN_CONSENT_AGE_GROUPS = (
HUMAN_CONSENT_TODDLER,
HUMAN_CONSENT_CHILD,
HUMAN_CONSENT_ADOLESCENT,
HUMAN_CONSENT_ADULT
)
# States
NEEDS_REROUTE = "NeedsReroute"
NEEDS_LOGIN = "NeedsLogin"
NEEDS_ACCOUNT = "NeedsAccount"
NEEDS_EMAIL_CHECK = "NeedsEmailCheck"
NEEDS_PRIMARY_SURVEYS = "NeedsPrimarySurveys"
HOME_PREREQS_MET = "TokenPrereqsMet"
ACCT_PREREQS_MET = "AcctPrereqsMet"
SOURCE_PREREQS_MET = "SourcePrereqsMet"
NEEDS_BIOSPECIMEN_CONSENT = "NeedsBiospecimenConsent"
BIOSPECIMEN_PREREQS_MET = "BiospecimenPrereqsMet"
# TODO FIXME HACK: VIOSCREEN_ID is just hardcoded. Api does not specify what
# special handling is required. API must specify per-sample survey templates
# in some way, as well as any special handling for external surveys.
BASIC_INFO_ID = 10
AT_HOME_ID = 11
LIFESTYLE_ID = 12
GUT_ID = 13
GENERAL_HEALTH_ID = 14
HEALTH_DIAG_ID = 15
ALLERGIES_ID = 16
DIET_ID = 17
DETAILED_DIET_ID = 18
MIGRAINE_ID = 19
SURFERS_ID = 20
COVID19_ID = 21
OTHER_ID = 22
VIOSCREEN_ID = 10001
MYFOODREPO_ID = 10002
POLYPHENOL_FFQ_ID = 10003
SPAIN_FFQ_ID = 10004
SYSTEM_MSG_DICTIONARY = {
"going_down": {
EN_US_KEY: "The system is going down at ",
ES_MX_KEY: "El sistema se apaga a las ",
ES_ES_KEY: "El sistema se apaga a las ",
JA_JP_KEY: "システムは にダウンしています "
},
"test_mode": {
EN_US_KEY: 'The system is currently undergoing maintenance and '
'testing. Please refrain from using the site and check '
'back later, or <a href="mailto:microsetta@ucsd.edu">'
'contact us</a> with any questions.',
ES_MX_KEY: 'Por el momento, el sistema se encuentra en mantenimiento '
'y pruebas. Por favor no use el sitio web y vuelva a '
'consultar más tarde, o '
'<a href="mailto:microsetta@ucsd.edu">contáctenos</a> si '
'tiene alguna pregunta.',
ES_MX_KEY: 'Por el momento, el sistema se encuentra en mantenimiento '
'y pruebas. Por favor no use el sitio web y vuelva a '
'consultar más tarde, o '
'<a href="mailto:microsetta@ucsd.edu">contáctenos</a> si '
'tiene alguna pregunta.',
JA_JP_KEY: 'The system is currently undergoing maintenance and '
'testing. Please refrain from using the site and check '
'back later, or <a href="mailto:microsetta@ucsd.edu">'
'contact us</a> with any questions.'
'-- REAL TRANSLATION PENDING --',
}
}
client_state = RedisCache()
# Countries allowed to view the contents of the My Kits tab
KITS_TAB_WHITELIST = {'US', 'ES', 'JP', 'MX', 'GB'}
# Countries allowed to view the contents of the My Nutrition tab
NUTRITION_TAB_WHITELIST = {'US'}
# Description of MelissaData error codes to use on the /update_address path.
# https://wiki.melissadata.com/?title=Result_Code_Details#Global_Address_Ver\
# ification
ADDRESS_ERRORS = {
EN_US_KEY: {
'AE01': 'The address could not be verified at least up to the postal '
'code level.',
'AE02': 'Could not match the input street to a unique street name. '
'Either no matches or too many matches found.',
'AE03': 'The combination of directionals (N, E, SW, etc) and the '
'suffix (AVE, ST, BLVD) is not correct and produced multiple '
'possible matches.',
'AE05': 'The address was matched to multiple records. There is not '
'enough information available in the address to break the tie '
'between multiple records.',
'AE08': 'An address element after the house number, in most cases the '
'sub-premise, was not valid.',
'AE09': 'An address element after the house number, in most cases the '
'sub-premise, was missing.',
'AE10': 'The premise (house or building) number for the address is '
'not valid.',
'AE11': 'The premise (house or building) number for the address is '
'missing.',
'AE12': 'The PO (Post Office Box), RR (Rural Route), or HC (Highway '
'Contract) Box number is invalid.',
'AE13': 'The PO (Post Office Box), RR (Rural Route), or HC (Highway '
'Contract) Box number is missing.',
'AE14': 'US Only. The address is a Commercial Mail Receiving Agency '
'(CMRA) and the Private Mail Box (PMB or #) number is '
'missing.',
'AEPOBOX': 'PO Boxes are not permitted. Please enter a physical '
'address.'
},
ES_MX_KEY: {
'AE01': 'La dirección no se pudo verificar al menos hasta el nivel '
'del código postal.',
'AE02': 'La dirección ingresada no coincide con una dirección única.'
' Ya sea porque no se encontró una dirección coincidente o '
'se encontraron varias coincidencias.',
'AE03': 'La combinación de la direccional (N, E, SW, etc.) y el '
'sufijo (AVE, ST, BLVD) no es correcta y produce múltiples '
'coincidencias.',
'AE05': 'La dirección coincidió con múltiples registros. No hay '
'suficientes datos disponibles en la dirección para '
'diferenciarla entre los múltiples registros.',
'AE08': 'Un dato de la dirección después del número de la casa, en '
'la mayoría de los casos el sublocal (por ejemplo Unit A, '
'#10), no era válido.',
'AE09': 'Un dato de la dirección después del número de la casa, en '
'la mayoría de los casos el sublocal (por ejemplo Unit A, '
'#10), faltaba.',
'AE10': 'El número del local (casa o edificio) para la dirección no '
'es válido.',
'AE11': 'Falta el número del local (casa o edificio) para la '
'dirección.',
'AE12': 'El número de apartado PO (Apartado postal), RR (Ruta rural) '
'o HC (Contrato de carretera) no es válido.',
'AE13': 'Falta el número del apartado PO (Apartado postal), RR (Ruta '
'rural) o HC (Contrato de carretera).',
'AE14': 'La dirección es una Agencia receptora de correo comercial '
'(CMRA) y falta el número del buzón de correo privado (PMB '
'o #).',
'AEPOBOX': 'No se permiten PO Boxes. Por favor ingrese una dirección '
'física.'
},
ES_ES_KEY: {
'AE01': 'La dirección no se pudo verificar al menos hasta el nivel '
'del código postal.',
'AE02': 'La dirección ingresada no coincide con una dirección única.'
' Ya sea porque no se encontró una dirección coincidente o '
'se encontraron varias coincidencias.',
'AE03': 'La combinación de la direccional (N, E, SW, etc.) y el '
'sufijo (AVE, ST, BLVD) no es correcta y produce múltiples '
'coincidencias.',
'AE05': 'La dirección coincidió con múltiples registros. No hay '
'suficientes datos disponibles en la dirección para '
'diferenciarla entre los múltiples registros.',
'AE08': 'Un dato de la dirección después del número de la casa, en '
'la mayoría de los casos el sublocal (por ejemplo Unit A, '
'#10), no era válido.',
'AE09': 'Un dato de la dirección después del número de la casa, en '
'la mayoría de los casos el sublocal (por ejemplo Unit A, '
'#10), faltaba.',
'AE10': 'El número del local (casa o edificio) para la dirección no '
'es válido.',
'AE11': 'Falta el número del local (casa o edificio) para la '
'dirección.',
'AE12': 'El número de apartado PO (Apartado postal), RR (Ruta rural) '
'o HC (Contrato de carretera) no es válido.',
'AE13': 'Falta el número del apartado PO (Apartado postal), RR (Ruta '
'rural) o HC (Contrato de carretera).',
'AE14': 'La dirección es una Agencia receptora de correo comercial '
'(CMRA) y falta el número del buzón de correo privado (PMB '
'o #).',
'AEPOBOX': 'No se permiten PO Boxes. Por favor ingrese una dirección '
'física.'
},
JA_JP_KEY: {
'AE01': 'The address could not be verified at least up to the postal '
'code level.',
'AE02': 'Could not match the input street to a unique street name. '
'Either no matches or too many matches found.',
'AE03': 'The combination of directionals (N, E, SW, etc) and the '
'suffix (AVE, ST, BLVD) is not correct and produced multiple '
'possible matches.',
'AE05': 'The address was matched to multiple records. There is not '
'enough information available in the address to break the tie '
'between multiple records.',
'AE08': 'An address element after the house number, in most cases the '
'sub-premise, was not valid.',
'AE09': 'An address element after the house number, in most cases the '
'sub-premise, was missing.',
'AE10': 'The premise (house or building) number for the address is '
'not valid.',
'AE11': 'The premise (house or building) number for the address is '
'missing.',
'AE12': 'The PO (Post Office Box), RR (Rural Route), or HC (Highway '
'Contract) Box number is invalid.',
'AE13': 'The PO (Post Office Box), RR (Rural Route), or HC (Highway '
'Contract) Box number is missing.',
'AE14': 'US Only. The address is a Commercial Mail Receiving Agency '
'(CMRA) and the Private Mail Box (PMB or #) number is '
'missing.',
'AEPOBOX': 'PO Boxes are not permitted. Please enter a physical '
'address.'
},
}
# TODO: Move this sort of survey info ino the database
SURVEY_INFO = {
BASIC_INFO_ID: {
'description': '',
'est_minutes': '2',
'icon': 'survey_basic_information.svg'
},
AT_HOME_ID: {
'description': '',
'est_minutes': '2',
'icon': 'survey_at_home.svg'
},
LIFESTYLE_ID: {
'description': '',
'est_minutes': '8',
'icon': 'survey_lifestyle.svg'
},
GUT_ID: {
'description': '',
'est_minutes': '4',
'icon': 'survey_gut.svg'
},
GENERAL_HEALTH_ID: {
'description': '',
'est_minutes': '8',
'icon': 'survey_general_health.svg'
},
HEALTH_DIAG_ID: {
'description': '',
'est_minutes': '8',
'icon': 'survey_health_diagnosis.svg'
},
ALLERGIES_ID: {
'description': '',
'est_minutes': '2',
'icon': 'survey_allergies.svg'
},
DIET_ID: {
'description': '',
'est_minutes': '5',
'icon': 'survey_diet.svg'
},
DETAILED_DIET_ID: {
'description': '',
'est_minutes': '18',
'icon': 'survey_detailed_diet.svg'
},
COVID19_ID: {
'description': '',
'est_minutes': '8',
'icon': 'survey_covid_19.svg'
},
OTHER_ID: {
'description': '',
'est_minutes': '2',
'icon': 'survey_other.svg'
},
VIOSCREEN_ID: {
'description': 'Our standard food frequency questionnaire',
'est_minutes': '30',
'icon': 'survey_external.svg'
},
MYFOODREPO_ID: {
'description': '<strong>Only for US Participants:</strong><br />'
'By sharing photos of all the food you eat via a '
'mobile app for <strong>seven days</strong>, you '
'will help us learn more about the microbes in the '
'gut.<br /><br />'
'<font color="red"><strong>Important!</strong></font> '
'Before taking part, please read more from the '
'following link: '
'<a href="https://microsetta.ucsd.edu/myfoodrepo/" '
'target="_blank">How to complete participation</a>.'
'<br /><br /><strong>Availability is limited</strong>: '
'Once you click on the "Start" button, you will be '
'directed to a site containing a unique code for you '
'to use to activate the app on your phone. <strong>'
'Please note</strong> - The code will only be '
'available to view once, so please keep a record of it '
'if you are not able to use it immediately. You will '
'have <strong>two weeks</strong> to use the app before '
'your access expires.',
'est_minutes': 'N/A',
'icon': 'survey_external.svg'
},
POLYPHENOL_FFQ_ID: {
'description': 'Polyphenols are chemical compounds naturally found in '
'plants that have been shown to provide many beneficial'
' properties. They are antioxidants, fighting aging and'
' protecting your heart, but they may also provide'
' benefits by interacting with the microbes in your '
'gut. This survey will allow us to better quantify '
'your consumption of polyphenols through your diet.',
'est_minutes': '30',
'icon': 'survey_external.svg'
},
SPAIN_FFQ_ID: {
'description': '<strong>Only for participants in Spain:</strong><br />'
'The Food Frequency Questionnaire (FFQ) will ask you '
'about your usual frequency of consumption of a list '
'of foods and beverages. The questionnaire consists of '
'28 questions, and will allow us to find out what your '
'usual diet is like.',
'est_minutes': '30',
'icon': 'survey_external.svg'
},
}
LOCAL_SURVEY_SEQUENCE = [
BASIC_INFO_ID,
AT_HOME_ID,
LIFESTYLE_ID,
GUT_ID,
GENERAL_HEALTH_ID,
HEALTH_DIAG_ID,
ALLERGIES_ID,
DIET_ID,
DETAILED_DIET_ID,
OTHER_ID
]
DAKLAPACK_KIT_RE = re.compile(r"DMK[234689ACDEFHJKMNPRTVWXY]{6}")
def _render_with_defaults(template_name, **context):
defaults = {}
admin_mode = session.get(ADMIN_MODE_KEY, False)
defaults["login_info"] = session.get(LOGIN_INFO_KEY, None)
defaults["admin_mode"] = admin_mode
msg, style, hours, minutes = client_state.get(RedisCache.SYSTEM_BANNER,
(None, None, None, None))
today = datetime.today()
if hours is None:
sys_msg_dt = datetime(today.year, today.month, today.day)
else:
sys_msg_dt = datetime(today.year, today.month, today.day, int(hours),
int(minutes))
defaults["system_msg_text"] = msg
defaults["system_msg_style"] = style
defaults["system_msg_time"] = flask_babel.format_datetime(sys_msg_dt,
'h:mm a')
defaults["system_msg_dictionary"] = SYSTEM_MSG_DICTIONARY
endpoint = SERVER_CONFIG["endpoint"]
public_endpoint = SERVER_CONFIG["public_api_endpoint"]
authrocket_url = SERVER_CONFIG["authrocket_url"]
defaults["endpoint"] = endpoint
defaults["authrocket_url"] = authrocket_url
defaults["public_endpoint"] = public_endpoint
defaults["EN_US_KEY"] = EN_US_KEY
defaults["languages"] = LANGUAGES
defaults.update(context)
return render_template(template_name, **defaults)
def _get_req_survey_templates_by_source_type(source_type):
if source_type == Source.SOURCE_TYPE_HUMAN:
return []
elif source_type == Source.SOURCE_TYPE_ANIMAL:
return []
elif source_type == Source.SOURCE_TYPE_ENVIRONMENT:
return []
else:
raise ValueError("Unknown source type: '%s'" % source_type)
def _get_opt_survey_templates_by_source_type(source_type):
if source_type == Source.SOURCE_TYPE_HUMAN:
return [3, 4, 5, 7, MYFOODREPO_ID, POLYPHENOL_FFQ_ID, SPAIN_FFQ_ID]
elif source_type == Source.SOURCE_TYPE_ANIMAL:
return []
elif source_type == Source.SOURCE_TYPE_ENVIRONMENT:
return []
else:
raise ValueError("Unknown source type: '%s'" % source_type)
def _make_path(account_id=None, source_id=None, suffix=None):
result = "/accounts"
if account_id is not None:
result = path.join(result, account_id)
if source_id is not None:
result = path.join(result, "sources", source_id)
if suffix is not None:
result = path.join(result, suffix)
return result
def _make_acct_path(account_id, suffix=None):
return _make_path(account_id=account_id, suffix=suffix)
def _make_source_path(account_id, source_id, suffix=None):
return _make_path(account_id=account_id, source_id=source_id,
suffix=suffix)
def _check_home_prereqs():
current_state = {}
if TOKEN_KEY_NAME not in session:
return NEEDS_LOGIN, current_state
if not session.get(ADMIN_MODE_KEY, False):
# Do they need to make an account? YES-> account_details.html
needs_reroute, accts_output, _ = ApiRequest.get("/accounts")
# if there's an error, reroute to error page
if needs_reroute:
current_state[REROUTE_KEY] = accts_output
return NEEDS_REROUTE, current_state
if len(accts_output) == 0:
# NB: Overwriting outputs from get call above
needs_reroute, accts_output, _ = ApiRequest.post(
"/accounts/legacies")
if needs_reroute:
current_state[REROUTE_KEY] = accts_output
return NEEDS_REROUTE, current_state
# if no legacy account found, need new account
if len(accts_output) == 0:
return NEEDS_ACCOUNT, current_state
# If you got here, you have a token and you have (at least one) account
# (True even of admins who skipped the above account check, as you can't
# be an admin unless you have a microsetta account that says you are)
return HOME_PREREQS_MET, current_state
def _check_acct_prereqs(account_id, current_state=None):
current_state = {} if current_state is None else current_state
current_state['account_id'] = account_id
# If we haven't yet checked for email mismatches and gotten user decision,
# and the user isn't an admin (who could be looking at another person's
# account and thus have that email not match their login one):
if not session.get(EMAIL_CHECK_KEY, False) and \
not session.get(ADMIN_MODE_KEY, False):
# Does email in our accounts table match email in authrocket?
needs_reroute, email_match, _ = ApiRequest.get(
'/accounts/{0}/email_match'.format(account_id))
if needs_reroute:
current_state[REROUTE_KEY] = email_match
return NEEDS_REROUTE, current_state
# if they don't match AND the user hasn't already refused update
if not email_match["email_match"]:
return NEEDS_EMAIL_CHECK, current_state
# IF we decide that every acct needs at least one source,
# this is where that check would go
return ACCT_PREREQS_MET, current_state
def _check_source_prereqs(acct_id, source_id, current_state=None):
SURVEY_TEMPLATE_ID_KEY = "survey_template_id"
current_state = {} if current_state is None else current_state
current_state[SOURCE_ID] = source_id
if not session.get(ADMIN_MODE_KEY, False):
# Get the input source
needs_reroute, source_output, _ = ApiRequest.get(
'/accounts/%s/sources/%s' %
(acct_id, source_id))
if needs_reroute:
current_state[REROUTE_KEY] = source_output
return NEEDS_REROUTE, current_state
# Get all required survey template ids for this source type
req_survey_template_ids = _get_req_survey_templates_by_source_type(
source_output["source_type"])
# Get all the current answered surveys for this source
needs_reroute, surveys_output, _ = ApiRequest.get(
'/accounts/{0}/sources/{1}/surveys'.format(acct_id, source_id))
if needs_reroute:
current_state[REROUTE_KEY] = surveys_output
return NEEDS_REROUTE, current_state
template_ids_of_answered_surveys = [x[SURVEY_TEMPLATE_ID_KEY] for x
in surveys_output]
# Get next required survey
# NOTE: current_state is updated *inplace*
needs_reroute = _update_needed_survey(req_survey_template_ids,
template_ids_of_answered_surveys,
current_state)
if needs_reroute is not None:
return needs_reroute, current_state
return SOURCE_PREREQS_MET, current_state
def _check_biospecimen_prereqs(acct_id, source_id, current_state=None):
current_state = {} if current_state is None else current_state
current_state[SOURCE_ID] = source_id
if not session.get(ADMIN_MODE_KEY, False):
# Get the input source
needs_reroute, source_output, _ = ApiRequest.get(
'/accounts/%s/sources/%s' %
(acct_id, source_id))
if needs_reroute:
current_state[REROUTE_KEY] = source_output
return NEEDS_REROUTE, current_state
# Test if biospecimen consent is required! If Required,
# route user to biospecimen consent
needs_reroute, consent_output, _ = ApiRequest.get(
'/accounts/%s/sources/%s/consent/%s' %
(acct_id, source_id, 'biospecimen'))
if needs_reroute:
current_state[REROUTE_KEY] = consent_output
return NEEDS_REROUTE, current_state
if consent_output["result"]:
session[SOURCE_ID] = source_id
return NEEDS_BIOSPECIMEN_CONSENT, current_state
return BIOSPECIMEN_PREREQS_MET, current_state
def _update_needed_survey(survey_template_ids, ids_of_answered, current_state):
# For each required survey template id for this source type
for curr_survey_template_id in survey_template_ids:
# Does this source LACK an answered survey with this template id?
if curr_survey_template_id not in ids_of_answered:
current_state["needed_survey_template_id"] = \
curr_survey_template_id
return NEEDS_PRIMARY_SURVEYS
return None
def _check_relevant_prereqs(acct_id=None, source_id=None):
# Check home prereqs
prereq_step, current_state = _check_home_prereqs()
if prereq_step != HOME_PREREQS_MET:
return prereq_step, current_state
# Check acct prereqs
if acct_id is None:
return prereq_step, current_state
prereq_step, current_state = _check_acct_prereqs(acct_id, current_state)
if prereq_step != ACCT_PREREQS_MET:
return prereq_step, current_state
# Check source prereqs
if source_id is None:
return prereq_step, current_state
prereq_step, current_state = _check_source_prereqs(
acct_id, source_id, current_state
)
if prereq_step != SOURCE_PREREQS_MET:
return prereq_step, current_state
prereq_step, current_state = _check_biospecimen_prereqs(
acct_id, source_id, current_state
)
if prereq_step != BIOSPECIMEN_PREREQS_MET:
return SOURCE_PREREQS_MET, current_state
else:
return prereq_step, current_state
# To send arguments to a decorator, you define a factory method with those args
# that returns a decorator. The decorator then takes a function and returns
# a wrapper that you want to call instead. Thus there should be three layers.
def prerequisite(allowed_states: list, **parameter_overrides):
"""
Usage
@prerequisite([NEEDS_EMAIL_CHECK])
def get_update_email(account_id):
# If client is not in the NEEDS_EMAIL_CHECK state, they will be
# redirected rather than reaching get_update_email.
@prerequisite([State1, State2, State3])
def crazy_function(account_id, source_id):
# If client is not in one of State1, State2, State3 stats, they will
# be redirected.
@prerequisite([State1, State2], survey_template_id=VIOSCREEN_ID)
def vioscreen_callback(account_id, source_id, key):
# If client is not in one of State1, State2, they will be redirected
# Further, if they are determined to be in NEEDS_PRIMARY_SURVEYS, but
# their required survey template id is not VIOSCREEN_ID, they will be
# redirected. Note that this makes use of the parameter_overrides to
# set a specific parameter (survey_template_id) when the wrapped
# function knows what would be sent, but does not expose it within its
# method signature. (You might encounter this when the wrapped function
# is a callback function that must match some defined signature)
:param allowed_states: A list of states that are valid for
entry to the decorated function
:param parameter_overrides: A set of keyword arguments added or replacing
the wrapped function's input args for the purpose of determining prereqs
The wrapped function itself will never see these overridden values.
"""
if not isinstance(allowed_states, list):
raise TypeError("allowed_states must be a list")
allowed_states = set(allowed_states)
def decorator(func):
if has_non_keyword_arguments(func):
raise TypeError("Only functions with solely keyword arguments are "
"supported by this decorator. "
"Example: f(*, a=1, b=2, c=3)")
# Calling functools.wraps preserves information about the wrapped func
# so introspection/reflection can pull the original documentation even
# when passed the wrapper function.
@functools.wraps(func)
def wrapper(**kwargs):
kwargs_copy = dict(kwargs)
kwargs_copy.update(parameter_overrides)
# Check relevant prereqs from those arguments
prereqs_step, curr_state = _check_relevant_prereqs(
kwargs_copy.get('account_id'),
kwargs_copy.get(SOURCE_ID)
)
# Route to closest sink if state doesn't match a required state
if prereqs_step not in allowed_states:
return _route_to_closest_sink(prereqs_step, curr_state)
# For any states that require checking additional parameters, we do
# so here. (Remember to lookup from kwargs_copy)
# TODO: Ensure state specific checks don't grow unwieldy
if prereqs_step == NEEDS_PRIMARY_SURVEYS:
passed_id = kwargs_copy.get('survey_template_id')
needed_id = curr_state.get("needed_survey_template_id")
if passed_id != needed_id:
return _route_to_closest_sink(prereqs_step, curr_state)
# Add new state specific checks here
# if prereqs_state == XXX:
# if something's not right, reroute.
return func(**kwargs)
return wrapper
return decorator
# Client might not technically care who the user is, but if they do, they
# get the token, validate it, and pull email out of it.
def _parse_jwt(token):
decoded = jwt.decode(token, PUB_KEY, algorithms=['RS256'], verify=True)
email_verified = decoded.get('email_verified', False)
return decoded["email"], email_verified
def _route_to_closest_sink(prereqs_step, current_state):
# print("Current Prereq Step:", prereqs_step)
acct_id = current_state.get("account_id", None)
source_id = current_state.get(SOURCE_ID, None)
if prereqs_step == NEEDS_REROUTE:
# where you get rerouted to depends on why you need
# rerouting: api authorization errors go back to home page,
# all other api errors go to error page
return current_state[REROUTE_KEY]
elif prereqs_step == NEEDS_LOGIN or prereqs_step == HOME_PREREQS_MET:
return redirect(HOME_URL)
elif prereqs_step == NEEDS_ACCOUNT:
return redirect("/create_account")
elif prereqs_step == NEEDS_EMAIL_CHECK:
return redirect(_make_acct_path(acct_id, suffix="update_email"))
elif prereqs_step == NEEDS_PRIMARY_SURVEYS:
needed_survey_template_id = current_state["needed_survey_template_id"]
return redirect(_make_source_path(
acct_id, source_id, suffix="take_survey?survey_template_id=%s"
% needed_survey_template_id))
elif prereqs_step == ACCT_PREREQS_MET:
# redirect to the account details page (showing all the sources)
return redirect(_make_acct_path(acct_id))
elif prereqs_step == SOURCE_PREREQS_MET:
# redirect to the source details page (showing all samples)
return redirect(_make_source_path(acct_id, source_id))
elif prereqs_step == NEEDS_BIOSPECIMEN_CONSENT:
return render_consent_page(acct_id, source_id, "biospecimen")
elif prereqs_step == BIOSPECIMEN_PREREQS_MET:
return redirect(_make_source_path(acct_id, source_id, suffix="kits"))
else:
return get_show_error_page(
"Unknown prereq_step: '{0}'".format(prereqs_step))
def _refresh_state_and_route_to_sink(account_id=None, source_id=None):
prereqs_step, curr_state = _check_relevant_prereqs(account_id, source_id)
return _route_to_closest_sink(prereqs_step, curr_state)
def _get_kit(kit_name):
unable_to_validate_msg = gettext(
"The provided Kit ID is not in our system or has already been used."
)
error_msg = None
response = None
try:
# call api and find out if kit name has unclaimed samples.
# NOT doing this through ApiRequest.get bc in this case
# DON'T want the automated error-handling
response = requests.get(
ApiRequest.API_URL + '/kits/', # appending slash saves a 308 redir
auth=BearerAuth(session[TOKEN_KEY_NAME]),
verify=ApiRequest.CAfile,
params=ApiRequest.build_params({KIT_NAME_KEY: kit_name}))
if response.status_code == 404:
error_msg = unable_to_validate_msg
elif response.status_code > 200:
error_msg = unable_to_validate_msg
except: # noqa
error_msg = unable_to_validate_msg
if error_msg is not None:
if response is None:
return None, error_msg, 500
else:
return None, error_msg, response.status_code
return response.json(), None, response.status_code
def get_ajax_check_ffq_code(ffq_code):
try:
response = requests.get(
ApiRequest.API_URL + '/check_ffq_code',
auth=BearerAuth(session[TOKEN_KEY_NAME]),
verify=ApiRequest.CAfile,
params=ApiRequest.build_params({'ffq_code': ffq_code})
)
if response.status_code == 200:
return_val = True
else:
return_val = False
except: # noqa
return_val = False
return return_val
def _associate_sample_to_survey(account_id, source_id, sample_id, survey_id):
# Associate the input answered surveys with this sample.
has_error, sample_survey_output, _ = ApiRequest.post(
'/accounts/{0}/sources/{1}/samples/{2}/surveys'.format(
account_id, source_id, sample_id
), json={"survey_id": survey_id}
)
if has_error:
return sample_survey_output
return None
# Error display does not require any prereqs, so this method doesn't check any
def get_show_error_page(error_msg):
# output is general error page
error_txt = quote(error_msg)
mailto_url = "mailto:{0}?subject={1}&body={2}".format(
HELP_EMAIL, quote("minimal interface error"), error_txt)
output = _render_with_defaults('error.jinja2',
mailto_url=mailto_url,
error_msg=error_msg)
return output
def get_home():
email_verified = False
accts_output = None
has_session = TOKEN_KEY_NAME in session
if has_session:
try:
# If user leaves the page open, the token can expire before the
# session, so if our token goes back we need to force them to login
# again.
email, email_verified = _parse_jwt(session[TOKEN_KEY_NAME])
except jwt.exceptions.ExpiredSignatureError:
return redirect('/logout')
if email_verified:
home_step, curr_state = _check_home_prereqs()
if home_step == NEEDS_REROUTE:
return curr_state[REROUTE_KEY]
has_error, accts_output, _ = ApiRequest.get("/accounts")
# if there's an error, reroute to error page
if has_error:
return accts_output
else:
return _render_with_defaults('email_confirmation.jinja2')
else:
return _render_with_defaults('home.jinja2')
# Switch out home page in administrator mode
if session.get(ADMIN_MODE_KEY, False):
return _render_with_defaults('admin_home.jinja2',
accounts=[])
if accts_output is not None and len(accts_output) > 0:
account_id = accts_output[0]['account_id']
# If an account has exactly one source, we're going to redirect to
# that profile page. Otherwise, we go to the Account Dashboard
has_error, sources, _ = ApiRequest.get(
'/accounts/%s/sources' % account_id
)
if has_error:
return sources
if len(sources) == 1:
return redirect(
f'/accounts/{account_id}/sources/{sources[0][SOURCE_ID]}'
)
else:
return redirect(f'/accounts/{account_id}')
else:
# Note: account_details.jinja2 sends the user directly to authrocket
# to complete the login if they aren't logged in yet.
return redirect('/create_account')
def get_rootpath():
return redirect(HOME_URL)
def get_authrocket_callback(token=None, redirect_uri=None):
if token is None:
return redirect('/home')
session[TOKEN_KEY_NAME] = token
email, _ = _parse_jwt(token)
session[LOGIN_INFO_KEY] = {
"email": email
}
do_return, accts_output, _ = ApiRequest.get('/accounts')
if do_return:
return accts_output
# new authrocket logins do not have an account yet
if len(accts_output) > 0:
primary = accts_output[0]
session[ADMIN_MODE_KEY] = primary['account_type'] == 'admin'
session[LOGIN_INFO_KEY] = {
"account_id": primary['account_id'],
"email": primary['email']
}
session[LANG_KEY] = primary["language"]
else:
session[ADMIN_MODE_KEY] = False
session[LOGIN_INFO_KEY] = {
"account_id": None,
"email": email
}
if redirect_uri:
uri = base64.urlsafe_b64decode(redirect_uri).decode()
return redirect(uri)
return redirect(HOME_URL)
def get_logout():
session.clear()
return redirect(HOME_URL)
@prerequisite([NEEDS_ACCOUNT])
def get_create_account():
email, _ = _parse_jwt(session[TOKEN_KEY_NAME])
browser_lang = session_locale()
# TODO: Need to support other countries
# and not default to US and California
default_account_values = {
ACCT_EMAIL_KEY: email,
ACCT_FNAME_KEY: '',
ACCT_LNAME_KEY: '',
ACCT_ADDR_KEY: {
ACCT_ADDR_STREET_KEY: '',
ACCT_ADDR_STREET2_KEY: '',
ACCT_ADDR_CITY_KEY: '',
ACCT_ADDR_STATE_KEY: 'CA',
ACCT_ADDR_POST_CODE_KEY: '',
ACCT_ADDR_COUNTRY_CODE_KEY: 'US'
},
ACCT_LANG_KEY: browser_lang
}
return _render_with_defaults('account_details.jinja2',
CREATE_ACCT=True,