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Merge pull request #116 from biocore/email_verification
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Email verification
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@AmandaBirmingham
AmandaBirmingham committed Apr 23, 2020
2 parents caf422a + e297f3c commit 17d5c8d
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Showing 6 changed files with 310 additions and 69 deletions.
99 changes: 62 additions & 37 deletions microsetta_private_api/api/implementation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
from microsetta_private_api.model.source import Source, info_from_api
from microsetta_private_api.model.source import human_info_from_api

from werkzeug.exceptions import BadRequest, Unauthorized, NotFound
from werkzeug.exceptions import BadRequest, Unauthorized, Forbidden, NotFound

from microsetta_private_api.util import vue_adapter
from microsetta_private_api.util.util import fromisotime
Expand All @@ -51,8 +51,10 @@
"authrocket.pubkey")
JWT_ISS_CLAIM_KEY = 'iss'
JWT_SUB_CLAIM_KEY = 'sub'
JWT_EMAIL_CLAIM_KEY = 'email'

ACCT_NOT_FOUND_MSG = "Account not found"
INVALID_TOKEN_MSG = "Invalid token"


def find_accounts_for_login(token_info):
Expand All @@ -77,7 +79,7 @@ def claim_legacy_acct(token_info):
# 404 code. This function can also trigger a 422 from the repo layer in the
# case of inconsistent account data.

email = token_info['email']
email = token_info[JWT_EMAIL_CLAIM_KEY]
auth_iss = token_info[JWT_ISS_CLAIM_KEY]
auth_sub = token_info[JWT_SUB_CLAIM_KEY]

Expand Down Expand Up @@ -117,12 +119,29 @@ def register_account(body, token_info):


def read_account(account_id, token_info):
acc = validate_access(token_info, account_id)
acc = _validate_account_access(token_info, account_id)
return jsonify(acc.to_api()), 200


def check_email_match(account_id, token_info):
acc = _validate_account_access(token_info, account_id)

match_status = acc.account_matches_auth(
token_info[JWT_EMAIL_CLAIM_KEY], token_info[JWT_ISS_CLAIM_KEY],
token_info[JWT_SUB_CLAIM_KEY])

if match_status == AuthorizationMatch.AUTH_ONLY_MATCH:
result = {'email_match': False}
elif match_status == AuthorizationMatch.FULL_MATCH:
result = {'email_match': True}
else:
raise ValueError("Unexpected authorization match value")

return jsonify(result), 200


def update_account(account_id, body, token_info):
acc = validate_access(token_info, account_id)
acc = _validate_account_access(token_info, account_id)

with Transaction() as t:
acct_repo = AccountRepo(t)
Expand All @@ -145,7 +164,7 @@ def update_account(account_id, body, token_info):


def read_sources(account_id, token_info, source_type=None):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
source_repo = SourceRepo(t)
Expand All @@ -156,7 +175,7 @@ def read_sources(account_id, token_info, source_type=None):


def create_source(account_id, body, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
source_repo = SourceRepo(t)
Expand Down Expand Up @@ -192,7 +211,7 @@ def create_source(account_id, body, token_info):


def read_source(account_id, source_id, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
source_repo = SourceRepo(t)
Expand All @@ -203,7 +222,7 @@ def read_source(account_id, source_id, token_info):


def update_source(account_id, source_id, body, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
source_repo = SourceRepo(t)
Expand All @@ -220,7 +239,7 @@ def update_source(account_id, source_id, body, token_info):


def delete_source(account_id, source_id, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
source_repo = SourceRepo(t)
Expand All @@ -232,7 +251,7 @@ def delete_source(account_id, source_id, token_info):


def read_survey_templates(account_id, source_id, language_tag, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

# TODO: I don't think surveys have names... only survey groups have names.
# So what can I pass down to the user that will make any sense here?
Expand Down Expand Up @@ -261,7 +280,7 @@ def read_survey_templates(account_id, source_id, language_tag, token_info):

def read_survey_template(account_id, source_id, survey_template_id,
language_tag, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

# TODO: can we get rid of source_id? I don't have anything useful to do
# with it... I guess I could check if the source is a dog before giving
Expand Down Expand Up @@ -302,7 +321,7 @@ def read_survey_template(account_id, source_id, survey_template_id,


def read_answered_surveys(account_id, source_id, language_tag, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
survey_answers_repo = SurveyAnswersRepo(t)
Expand All @@ -320,7 +339,7 @@ def read_answered_surveys(account_id, source_id, language_tag, token_info):

def read_answered_survey(account_id, source_id, survey_id, language_tag,
token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
survey_answers_repo = SurveyAnswersRepo(t)
Expand All @@ -342,7 +361,7 @@ def read_answered_survey(account_id, source_id, survey_id, language_tag,

def submit_answered_survey(account_id, source_id, language_tag, body,
token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

# TODO: Is this supposed to return new survey id?
# TODO: Rename survey_text to survey_model/model to match Vue's naming?
Expand All @@ -369,7 +388,7 @@ def submit_answered_survey(account_id, source_id, language_tag, body,


def read_sample_associations(account_id, source_id, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
sample_repo = SampleRepo(t)
Expand All @@ -380,7 +399,7 @@ def read_sample_associations(account_id, source_id, token_info):


def associate_sample(account_id, source_id, body, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
sample_repo = SampleRepo(t)
Expand All @@ -396,7 +415,7 @@ def associate_sample(account_id, source_id, body, token_info):


def read_sample_association(account_id, source_id, sample_id, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
sample_repo = SampleRepo(t)
Expand All @@ -409,7 +428,7 @@ def read_sample_association(account_id, source_id, sample_id, token_info):

def update_sample_association(account_id, source_id, sample_id, body,
token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

# TODO: API layer doesn't understand that BadRequest can be thrown,
# but that looks to be the right result if sample_site bad.
Expand Down Expand Up @@ -458,7 +477,7 @@ def update_sample_association(account_id, source_id, sample_id, body,


def dissociate_sample(account_id, source_id, sample_id, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
sample_repo = SampleRepo(t)
Expand All @@ -469,7 +488,7 @@ def dissociate_sample(account_id, source_id, sample_id, token_info):

def read_answered_survey_associations(account_id, source_id, sample_id,
token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
answers_repo = SurveyAnswersRepo(t)
Expand All @@ -491,7 +510,7 @@ def read_answered_survey_associations(account_id, source_id, sample_id,

def associate_answered_survey(account_id, source_id, sample_id, body,
token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
answers_repo = SurveyAnswersRepo(t)
Expand All @@ -513,7 +532,7 @@ def associate_answered_survey(account_id, source_id, sample_id, body,

def dissociate_answered_survey(account_id, source_id, sample_id, survey_id,
token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

with Transaction() as t:
answers_repo = SurveyAnswersRepo(t)
Expand All @@ -525,8 +544,8 @@ def dissociate_answered_survey(account_id, source_id, sample_id, survey_id,

def read_kit(kit_name):
# NOTE: Nothing in this route requires a particular user to be logged in,
# so long as the user has -an- account. Thus there is nothing to validate
# a particular token_info against.
# so long as the user has -an- account.

with Transaction() as t:
kit_repo = KitRepo(t)
kit = kit_repo.get_kit_unused_samples(kit_name)
Expand All @@ -536,7 +555,7 @@ def read_kit(kit_name):


def render_consent_doc(account_id, language_tag, consent_post_url, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

# return render_template("new_participant.jinja2",
# message=MockJinja("message"),
Expand All @@ -558,7 +577,7 @@ def render_consent_doc(account_id, language_tag, consent_post_url, token_info):


def create_human_source_from_consent(account_id, body, token_info):
validate_access(token_info, account_id)
_validate_account_access(token_info, account_id)

# Must convert consent form body into object processable by create_source.

Expand Down Expand Up @@ -591,29 +610,34 @@ def create_human_source_from_consent(account_id, body, token_info):


def verify_authrocket(token):
email_verification_key = 'email_verification'

try:
token_info = jwt.decode(token,
AUTHROCKET_PUB_KEY,
algorithms=["RS256"],
verify=True,
issuer="https://authrocket.com")

# TODO: Ensure that decode checks every field that we care about

return token_info
except InvalidTokenError as e:
raise(Unauthorized("Invalid Token", e))
raise(Unauthorized(INVALID_TOKEN_MSG, e))


def validate_access(token_info, account_id):
if JWT_ISS_CLAIM_KEY not in token_info or \
JWT_SUB_CLAIM_KEY not in token_info or \
'email' not in token_info:
JWT_EMAIL_CLAIM_KEY not in token_info:
# token is malformed--no soup for you
return Unauthorized()
raise Unauthorized(INVALID_TOKEN_MSG)

# if the user's email is not yet verified, they are forbidden to
# access their account even regardless of whether they have
# authenticated with authrocket
if email_verification_key not in token_info or \
token_info[email_verification_key] is not True:
raise Forbidden("Email is not verified")

return token_info

# TODO: Put email verification check here

def _validate_account_access(token_info, account_id):
with Transaction() as t:
account_repo = AccountRepo(t)
account = account_repo.get_account(account_id)
Expand All @@ -622,7 +646,8 @@ def validate_access(token_info, account_id):
raise NotFound(ACCT_NOT_FOUND_MSG)
else:
auth_match = account.account_matches_auth(
token_info['email'], token_info[JWT_ISS_CLAIM_KEY],
token_info[JWT_EMAIL_CLAIM_KEY],
token_info[JWT_ISS_CLAIM_KEY],
token_info[JWT_SUB_CLAIM_KEY])
if auth_match == AuthorizationMatch.NO_MATCH:
raise Unauthorized()
Expand Down

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