sartography
/
cr-connect-workflow
mirror of https://github.com/sartography/cr-connect-workflow.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Fixes broken unit tests. But still broken.

This commit is contained in:
Aaron Louie 2020-06-11 11:29:58 -04:00
parent 1f5554d0d8
commit cccff9b856
7 changed files with 156 additions and 95 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
Pipfile.lock generated
View File

@ -104,17 +104,17 @@
},
"celery": {
"hashes": [
"sha256:9ae2e73b93cc7d6b48b56aaf49a68c91752d0ffd7dfdcc47f842ca79a6f13eae",
"sha256:c2037b6a8463da43b19969a0fc13f9023ceca6352b4dd51be01c66fbbb13647e"
"sha256:c3f4173f83ceb5a5c986c5fdaefb9456de3b0729a72a5776e46bd405fda7b647",
"sha256:d1762d6065522879f341c3d67c2b9fe4615eb79756d59acb1434601d4aca474b"
],
"version": "==4.4.4"
"version": "==4.4.5"
},
"certifi": {
"hashes": [
"sha256:1d987a998c75633c40847cc966fcf5904906c920a7f17ef374f5aa4282abd304",
"sha256:51fcb31174be6e6664c5f69e3e1691a2d72a1a12e90f872cbdb1567eb47b6519"
"sha256:5ad7e9a056d25ffa5082862e36f119f7f7cec6457fa07ee2f8c339814b80c9b1",
"sha256:9cd41137dc19af6a5e03b630eefe7d1f458d964d406342dd3edf625839b944cc"
],
"version": "==2020.4.5.1"
"version": "==2020.4.5.2"
},
"cffi": {
"hashes": [
@ -285,11 +285,11 @@
},
"flask-marshmallow": {
"hashes": [
"sha256:6e6aec171b8e092e0eafaf035ff5b8637bf3a58ab46f568c4c1bab02f2a3c196",
"sha256:a1685536e7ab5abdc712bbc1ac1a6b0b50951a368502f7985e7d1c27b3c21e59"
"sha256:1da1e6454a56a3e15107b987121729f152325bdef23f3df2f9b52bbd074af38e",
"sha256:aefc1f1d96256c430a409f08241bab75ffe97e5d14ac5d1f000764e39bf4873a"
],
"index": "pypi",
"version": "==0.12.0"
"version": "==0.13.0"
},
"flask-migrate": {
"hashes": [
@ -359,10 +359,10 @@
},
"inflection": {
"hashes": [
"sha256:32a5c3341d9583ec319548b9015b7fbdf8c429cbcb575d326c33ae3a0e90d52c",
"sha256:9a15d3598f01220e93f2207c432cfede50daff53137ce660fb8be838ef1ca6cc"
"sha256:88b101b2668a1d81d6d72d4c2018e53bc6c7fc544c987849da1c7f77545c3bc9",
"sha256:f576e85132d34f5bf7df5183c2c6f94cfb32e528f53065345cf71329ba0b8924"
],
"version": "==0.4.0"
"version": "==0.5.0"
},
"itsdangerous": {
"hashes": [
@ -751,11 +751,11 @@
},
"sphinx": {
"hashes": [
"sha256:779a519adbd3a70fc7c468af08c5e74829868b0a5b34587b33340e010291856c",
"sha256:ea64df287958ee5aac46be7ac2b7277305b0381d213728c3a49d8bb9b8415807"
"sha256:1c445320a3310baa5ccb8d957267ef4a0fc930dc1234db5098b3d7af14fbb242",
"sha256:7d3d5087e39ab5a031b75588e9859f011de70e213cd0080ccbc28079fb0786d1"
],
"index": "pypi",
"version": "==3.0.4"
"version": "==3.1.0"
},
"sphinxcontrib-applehelp": {
"hashes": [
@ -990,10 +990,10 @@
},
"wcwidth": {
"hashes": [
"sha256:980fbf4f3c196c0f329cdcd1e84c554d6a211f18e252e525a0cf4223154a41d6",
"sha256:edbc2b718b4db6cdf393eefe3a420183947d6aa312505ce6754516f458ff8830"
"sha256:79375666b9954d4a1a10739315816324c3e73110af9d0e102d906fdb0aec009f",
"sha256:8c6b5b6ee1360b842645f336d9e5d68c55817c26d3050f46b235ef2bc650e48f"
],
"version": "==0.2.3"
"version": "==0.2.4"
},
"zipp": {
"hashes": [

2
config/default.py
View File

@ -29,7 +29,7 @@ SQLALCHEMY_DATABASE_URI = environ.get(
'SQLALCHEMY_DATABASE_URI',
default="postgresql://%s:%s@%s:%s/%s" % (DB_USER, DB_PASSWORD, DB_HOST, DB_PORT, DB_NAME)
)
TOKEN_AUTH_TTL_HOURS = int(environ.get('TOKEN_AUTH_TTL_HOURS', default=4))
TOKEN_AUTH_TTL_HOURS = float(environ.get('TOKEN_AUTH_TTL_HOURS', default=24))
TOKEN_AUTH_SECRET_KEY = environ.get('TOKEN_AUTH_SECRET_KEY', default="Shhhh!!! This is secret! And better darn well not show up in prod.")
FRONTEND_AUTH_CALLBACK = environ.get('FRONTEND_AUTH_CALLBACK', default="http://localhost:4200/session")
SWAGGER_AUTH_KEY = environ.get('SWAGGER_AUTH_KEY', default="SWAGGER")

18
crc/api.yml
View File

@ -115,7 +115,7 @@ paths:
delete:
operationId: crc.api.study.delete_study
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Removes the given study completely.
tags:
- Studies
@ -218,7 +218,7 @@ paths:
put:
operationId: crc.api.workflow.update_workflow_specification
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Modifies an existing workflow specification with the given parameters.
tags:
- Workflow Specifications
@ -237,7 +237,7 @@ paths:
delete:
operationId: crc.api.workflow.delete_workflow_specification
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Removes an existing workflow specification
tags:
- Workflow Specifications
@ -284,7 +284,7 @@ paths:
post:
operationId: crc.api.workflow.add_workflow_spec_category
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Creates a new workflow spec category with the given parameters.
tags:
- Workflow Specification Category
@ -323,7 +323,7 @@ paths:
put:
operationId: crc.api.workflow.update_workflow_spec_category
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Modifies an existing workflow spec category with the given parameters.
tags:
- Workflow Specification Category
@ -342,7 +342,7 @@ paths:
delete:
operationId: crc.api.workflow.delete_workflow_spec_category
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Removes an existing workflow spec category
tags:
- Workflow Specification Category
@ -543,7 +543,7 @@ paths:
put:
operationId: crc.api.file.set_reference_file
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Update the contents of a named reference file.
tags:
- Files
@ -603,7 +603,7 @@ paths:
delete:
operationId: crc.api.workflow.delete_workflow
security:
- jwt_admin: ['secret']
- auth_admin: ['secret']
summary: Removes an existing workflow
tags:
- Workflows and Tasks
@ -924,7 +924,7 @@ components:
scheme: bearer
bearerFormat: JWT
x-bearerInfoFunc: crc.api.user.verify_token
jwt_admin:
auth_admin:
type: http
scheme: bearer
bearerFormat: JWT

52
crc/api/user.py
View File

@ -4,8 +4,7 @@ from flask import g, request
from crc import app, db
from crc.api.common import ApiError
from crc.models.user import UserModel, UserModelSchema
from crc.services.ldap_service import LdapService, LdapModel, LdapUserInfo
from crc.services.approval_service import ApprovalService
from crc.services.ldap_service import LdapService, LdapModel
"""
.. module:: crc.api.user
@ -31,7 +30,8 @@ def verify_token(token=None):
print('=== verify_token ===')
print('_is_production()', _is_production())
failure_error = ApiError("invalid_token", "Unable to decode the token you provided. Please re-authenticate", status_code=403)
failure_error = ApiError("invalid_token", "Unable to decode the token you provided. Please re-authenticate",
status_code=403)
if not _is_production():
g.user = UserModel.query.first()
@ -62,7 +62,8 @@ def verify_token(token=None):
return token_info
else:
ApiError("no_user", "User not found. Please login via the frontend app before accessing this feature.", status_code=403)
ApiError("no_user", "User not found. Please login via the frontend app before accessing this feature.",
status_code=403)
raise failure_error
@ -81,7 +82,6 @@ def verify_token_admin(token=None):
print('=== verify_token_admin ===')
print('_is_production()', _is_production())
# If this is production, check that the user is in the list of admins
if _is_production():
uid = _get_request_uid(request)
@ -175,7 +175,7 @@ def sso():
return response
def _handle_login(user_info: LdapUserInfo, redirect_url=None):
def _handle_login(user_info: LdapModel, redirect_url=None):
"""
On successful login, adds user to database if the user is not already in the system,
then returns the frontend auth callback URL, with auth token appended.
@ -187,22 +187,10 @@ def _handle_login(user_info: LdapUserInfo, redirect_url=None):
Returns:
Response. 302 - Redirects to the frontend auth callback URL, with auth token appended.
"""
print('=== _handle_login ===')
print('user_info', user_info)
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
if user is None:
# Add new user
user = UserModel()
user.uid = user_info.uid
user.display_name = user_info.display_name
user.email_address = user_info.email_address
user.affiliation = user_info.affiliation
user.title = user_info.title
db.session.add(user)
db.session.commit()
user = _upsert_user(user_info)
# Return the frontend auth callback URL, with auth token appended.
auth_token = user.encode_auth_token().decode()
@ -217,11 +205,35 @@ def _handle_login(user_info: LdapUserInfo, redirect_url=None):
return auth_token
def _upsert_user(user_info):
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).first()
if user is None:
# Add new user
user = UserModel()
else:
user = db.session.query(UserModel).filter(UserModel.uid == user_info.uid).with_for_update().first()
user.uid = user_info.uid
user.display_name = user_info.display_name
user.email_address = user_info.email_address
user.affiliation = user_info.affiliation
user.title = user_info.title
db.session.add(user)
db.session.commit()
return user
def _get_request_uid(req):
uid = None
if _is_production():
if 'user' in g and g.user is not None:
print('g.user.uid', g.user.uid)
return g.user.uid
print('req.headers', req.headers)
uid = req.headers.get("Uid")
if not uid:

8
crc/models/user.py
View File

@ -27,7 +27,7 @@ class UserModel(db.Model):
Generates the Auth Token
:return: string
"""
hours = int(app.config['TOKEN_AUTH_TTL_HOURS'])
hours = float(app.config['TOKEN_AUTH_TTL_HOURS'])
payload = {
'exp': datetime.datetime.utcnow() + datetime.timedelta(hours=hours, minutes=0, seconds=0),
'iat': datetime.datetime.utcnow(),
@ -36,7 +36,7 @@ class UserModel(db.Model):
return jwt.encode(
payload,
app.config.get('TOKEN_AUTH_SECRET_KEY'),
algorithm='HS256'
algorithm='HS256',
)
@staticmethod
@ -50,9 +50,9 @@ class UserModel(db.Model):
payload = jwt.decode(auth_token, app.config.get('TOKEN_AUTH_SECRET_KEY'), algorithms='HS256')
return payload
except jwt.ExpiredSignatureError:
raise ApiError('token_expired', 'The Authentication token you provided expired, and must be renewed.')
raise ApiError('token_expired', 'The Authentication token you provided expired and must be renewed.')
except jwt.InvalidTokenError:
raise ApiError('token_invalid', 'The Authentication token you provided. You need a new token. ')
raise ApiError('token_invalid', 'The Authentication token you provided is invalid. You need a new token. ')
class UserModelSchema(SQLAlchemyAutoSchema):

1
tests/base_test.py
View File

@ -95,7 +95,6 @@ class BaseTest(unittest.TestCase):
def tearDown(self):
ExampleDataLoader.clean_db()
session.flush()
self.auths = {}
def logged_in_headers(self, user=None, redirect_url='http://some/frontend/url'):

110
tests/test_authentication.py
View File

@ -1,9 +1,10 @@
import json
from datetime import timezone, datetime
from calendar import timegm
from datetime import timezone, datetime, timedelta
from tests.base_test import BaseTest
from crc import db, app
from crc.models.study import StudySchema
from crc.models.study import StudySchema, StudyModel
from crc.models.user import UserModel
from crc.models.protocol_builder import ProtocolBuilderStatus
@ -16,11 +17,29 @@ class TestAuthentication(BaseTest):
super().tearDown()
def test_auth_token(self):
# Save the orginal timeout setting
orig_ttl = float(app.config['TOKEN_AUTH_TTL_HOURS'])
self.load_example_data()
# Set the timeout to something else
new_ttl = 4.0
app.config['TOKEN_AUTH_TTL_HOURS'] = new_ttl
user = UserModel(uid="dhf8r")
auth_token = user.encode_auth_token()
self.assertTrue(isinstance(auth_token, bytes))
self.assertEqual("dhf8r", user.decode_auth_token(auth_token).get("sub"))
expected_exp_1 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple())
auth_token_1 = user.encode_auth_token()
self.assertTrue(isinstance(auth_token_1, bytes))
self.assertEqual("dhf8r", user.decode_auth_token(auth_token_1).get("sub"))
actual_exp_1 = user.decode_auth_token(auth_token_1).get("exp")
self.assertTrue(expected_exp_1 - 1000 <= actual_exp_1 <= expected_exp_1 + 1000)
# Set the timeout back to where it was
app.config['TOKEN_AUTH_TTL_HOURS'] = orig_ttl
expected_exp_2 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple())
auth_token_2 = user.encode_auth_token()
self.assertTrue(isinstance(auth_token_2, bytes))
actual_exp_2 = user.decode_auth_token(auth_token_1).get("exp")
self.assertTrue(expected_exp_2 - 1000 <= actual_exp_2 <= expected_exp_2 + 1000)
def test_non_production_auth_creates_user(self):
new_uid = 'lb3dp' ## Assure this user id is in the fake responses from ldap.
@ -48,12 +67,14 @@ class TestAuthentication(BaseTest):
self.assertTrue(str.startswith(rv_2.location, redirect_url))
def test_production_auth_creates_user(self):
# Switch production mode on
app.config['PRODUCTION'] = True
new_uid = 'lb3dp' # This user is in the test ldap system.
self.load_example_data()
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
new_uid = 'lb3dp' # This user is in the test ldap system.
user = db.session.query(UserModel).filter_by(uid=new_uid).first()
self.assertIsNone(user)
redirect_url = 'http://worlds.best.website/admin'
headers = dict(Uid=new_uid)
@ -61,7 +82,7 @@ class TestAuthentication(BaseTest):
rv = self.app.get('v1.0/login', follow_redirects=False, headers=headers)
self.assert_success(rv)
user = db.session.query(UserModel).filter(UserModel.uid == new_uid).first()
user = db.session.query(UserModel).filter_by(uid=new_uid).first()
self.assertIsNotNone(user)
self.assertEqual(new_uid, user.uid)
self.assertEqual("Laura Barnes", user.display_name)
@ -70,6 +91,14 @@ class TestAuthentication(BaseTest):
# Switch production mode back off
app.config['PRODUCTION'] = False
db.session.flush()
db.session.flush()
db.session.flush()
db.session.flush()
db.session.flush()
db.session.flush()
db.session.flush()
db.session.flush()
def test_current_user_status(self):
self.load_example_data()
@ -84,49 +113,65 @@ class TestAuthentication(BaseTest):
rv = self.app.get('/v1.0/user', headers=self.logged_in_headers(user, redirect_url='http://omg.edu/lolwut'))
self.assert_success(rv)
def test_admin_only_endpoints(self):
def test_admin_can_access_admin_only_endpoints(self):
# Switch production mode on
app.config['PRODUCTION'] = True
self.load_example_data()
admin_uids = app.config['ADMIN_UIDS']
self.assertGreater(len(admin_uids), 0)
admin_uid = admin_uids[0]
self.assertEqual(admin_uid, 'dhf8r') # This user is in the test ldap system.
admin_headers = dict(Uid=admin_uid)
for uid in admin_uids:
admin_headers = dict(Uid=uid)
rv = self.app.get(
'v1.0/login',
follow_redirects=False,
headers=admin_headers
)
rv = self.app.get('v1.0/login', follow_redirects=False, headers=admin_headers)
self.assert_success(rv)
admin_user = db.session.query(UserModel).filter_by(uid=uid).first()
admin_user = db.session.query(UserModel).filter(UserModel.uid == admin_uid).first()
self.assertIsNotNone(admin_user)
self.assertEqual(admin_uid, admin_user.uid)
admin_study = self._make_fake_study(uid)
admin_study = self._make_fake_study(admin_uid)
admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
rv_add_study = self.app.post(
'/v1.0/study',
content_type="application/json",
headers=admin_headers,
data=json.dumps(StudySchema().dump(admin_study))
headers=admin_token_headers,
data=json.dumps(StudySchema().dump(admin_study)),
follow_redirects=False
)
self.assert_success(rv_add_study, 'Admin user should be able to add a study')
new_study = json.loads(rv.get_data(as_text=True))
new_admin_study = json.loads(rv_add_study.get_data(as_text=True))
db_admin_study = db.session.query(StudyModel).filter_by(id=new_admin_study['id']).first()
self.assertIsNotNone(db_admin_study)
rv_del_study = self.app.delete(
'/v1.0/study/%i' % new_study.id,
'/v1.0/study/%i' % db_admin_study.id,
follow_redirects=False,
headers=admin_headers
headers=admin_token_headers
)
self.assert_success(rv_del_study, 'Admin user should be able to delete a study')
# Switch production mode back off
app.config['PRODUCTION'] = False
def test_nonadmin_cannot_access_admin_only_endpoints(self):
# Switch production mode on
app.config['PRODUCTION'] = True
self.load_example_data()
# Non-admin user should not be able to delete a study
non_admin_uid = 'lb3dp'
admin_uids = app.config['ADMIN_UIDS']
self.assertGreater(len(admin_uids), 0)
self.assertNotIn(non_admin_uid, admin_uids)
non_admin_headers = dict(Uid=non_admin_uid)
rv = self.app.get(
@ -138,24 +183,29 @@ class TestAuthentication(BaseTest):
non_admin_user = db.session.query(UserModel).filter_by(uid=non_admin_uid).first()
self.assertIsNotNone(non_admin_user)
non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode())
non_admin_study = self._make_fake_study(non_admin_uid)
rv_add_study = self.app.post(
'/v1.0/study',
content_type="application/json",
headers=non_admin_headers,
headers=non_admin_token_headers,
data=json.dumps(StudySchema().dump(non_admin_study))
)
self.assert_success(rv_add_study, 'Non-admin user should be able to add a study')
new_study = json.loads(rv.get_data(as_text=True))
new_non_admin_study = json.loads(rv_add_study.get_data(as_text=True))
db_non_admin_study = db.session.query(StudyModel).filter_by(id=new_non_admin_study['id']).first()
self.assertIsNotNone(db_non_admin_study)
rv_del_study = self.app.delete(
'/v1.0/study/%i' % new_study.id,
rv_non_admin_del_study = self.app.delete(
'/v1.0/study/%i' % db_non_admin_study.id,
follow_redirects=False,
headers=non_admin_headers
headers=non_admin_token_headers
)
self.assert_failure(rv_del_study, 'Non-admin user should not be able to delete a study')
self.assert_failure(rv_non_admin_del_study, 401)
# Switch production mode back off
app.config['PRODUCTION'] = False