Fixes broken unit tests. But still broken.

Pipfile.lock

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

config/default.py

@@ -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")

crc/api.yml

@@ -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

crc/api/user.py

@@ -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.ldap_service import LdapService, LdapModel
-from crc.services.approval_service import ApprovalService
 
 """
 .. 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)
@@ -101,8 +101,8 @@ def get_current_user():
 
 
 def login(
-    uid=None,
+        uid=None,
-    redirect_url=None,
+        redirect_url=None,
 ):
     """
         In non-production environment, provides an endpoint for end-to-end system testing that allows the system
@@ -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()
+    user = _upsert_user(user_info)
-
-    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()
 
     # 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:

crc/models/user.py

@@ -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):

tests/base_test.py

@@ -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'):

tests/test_authentication.py

@@ -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()
+        expected_exp_1 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple())
-        self.assertTrue(isinstance(auth_token, bytes))
+        auth_token_1 = user.encode_auth_token()
-        self.assertEqual("dhf8r", user.decode_auth_token(auth_token).get("sub"))
+        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:
+        rv = self.app.get('v1.0/login', follow_redirects=False, headers=admin_headers)
-            admin_headers = dict(Uid=uid)
+        self.assert_success(rv)
 
-            rv = self.app.get(
+        admin_user = db.session.query(UserModel).filter(UserModel.uid == admin_uid).first()
-                'v1.0/login',
+        self.assertIsNotNone(admin_user)
-                follow_redirects=False,
+        self.assertEqual(admin_uid, admin_user.uid)
-                headers=admin_headers
-            )
-            self.assert_success(rv)
 
-            admin_user = db.session.query(UserModel).filter_by(uid=uid).first()
+        admin_study = self._make_fake_study(admin_uid)
-            self.assertIsNotNone(admin_user)
 
-            admin_study = self._make_fake_study(uid)
+        admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode())
 
-            rv_add_study = self.app.post(
+        rv_add_study = self.app.post(
-                '/v1.0/study',
+            '/v1.0/study',
-                content_type="application/json",
+            content_type="application/json",
-                headers=admin_headers,
+            headers=admin_token_headers,
-                data=json.dumps(StudySchema().dump(admin_study))
+            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')
+        )
+        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(
+        rv_del_study = self.app.delete(
-                '/v1.0/study/%i' % new_study.id,
+            '/v1.0/study/%i' % db_admin_study.id,
-                follow_redirects=False,
+            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')
+        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(
+        rv_non_admin_del_study = self.app.delete(
-            '/v1.0/study/%i' % new_study.id,
+            '/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