diff --git a/core/lcsb/rems.py b/core/lcsb/rems.py index 24a6f508..8c3c28b0 100644 --- a/core/lcsb/rems.py +++ b/core/lcsb/rems.py @@ -4,38 +4,60 @@ from datetime import datetime, date, timedelta from dateutil.parser import isoparse -from typing import Dict, Union +from typing import Dict, Union, Tuple from django.conf import settings from django.core.exceptions import ImproperlyConfigured from django.http import HttpRequest from core.synchronizers import DummyAccountSynchronizer -from core.lcsb.oidc import get_keycloak_config_from_settings, KeycloakSynchronizationMethod, CachedKeycloakAccountSynchronizer +from core.lcsb.oidc import ( + get_keycloak_config_from_settings, + KeycloakSynchronizationMethod, + CachedKeycloakAccountSynchronizer, +) from core.models.access import Access, StatusChoices from core.models.contact import Contact from core.models.dataset import Dataset from core.models.user import User from core.utils import DaisyLogger - +from django.db.models import Q logger = DaisyLogger(__name__) - -if getattr(settings, 'KEYCLOAK_INTEGRATION', False) == True: +if getattr(settings, "KEYCLOAK_INTEGRATION", False) == True: urllib3.disable_warnings() keycloak_config = get_keycloak_config_from_settings() try: keycloak_backend = KeycloakSynchronizationMethod(keycloak_config) synchronizer = CachedKeycloakAccountSynchronizer(keycloak_backend) except Exception as ex: - logger.error(f'Keycloak integration failed to initialize! {ex}') - logger.error('Falling back to the dummy synchronizer...') - synchronizer = DummyAccountSynchronizer() + logger.error(f"Keycloak integration failed to initialize! {ex}") + logger.error("Falling back to the dummy synchronizer...") + synchronizer = DummyAccountSynchronizer() else: synchronizer = DummyAccountSynchronizer() +def check_existence_automatic(item: Dict[str, str]) -> bool: + """ + Checks if an active access automatically created for the same received data already exists + """ + application, resource, user_oidc_id, email, expiration_date = extract_rems_data( + item + ) + filter_oidc = Q(user__oidc_id=user_oidc_id) | Q(contact__oidc_id=user_oidc_id) + filter_resource_and_status = Q( + dataset__elu_accession=resource, + grant_expires_on=expiration_date, + status=StatusChoices.active, + ) + existing_accesses = Access.objects.filter( + filter_resource_and_status & filter_oidc + ).all() + return any([a.was_generated_automatically for a in existing_accesses]) + + def handle_rems_callback(request: HttpRequest) -> bool: """ Handles an entitlements request coming from REMS @@ -46,57 +68,98 @@ def handle_rems_callback(request: HttpRequest) -> bool: :returns: True if everything was processed, False if not """ - # Ensure the most recent account inforrmation by pulling it from Keycloak - logger.debug('REMS :: Requesting refreshing the account information from Keycloak Synchronizer...') - synchronizer.synchronize() - logger.debug('REMS :: ...assuming that the OIDC account information has been synchronized') - - logger.debug('REMS :: Unpacking the data received from REMS...') - body_unicode = request.body.decode('utf-8') + logger.debug("REMS :: Unpacking the data received from REMS...") + body_unicode = request.body.decode("utf-8") try: request_post_data = json.loads(body_unicode) except: - message = f'REMS :: Received data in wrong format, because deserializing request''s POST body failed!)!' + message = ( + f"REMS :: Received data in wrong format, because deserializing request" + "s POST body failed!)!" + ) raise ValueError(message) if not isinstance(request_post_data, list): the_type = type(request_post_data) message = f'REMS :: Received data with wrong format (it is not a list, but "{the_type}" instead)!' raise TypeError(message) - - statuses = [handle_rems_entitlement(item) for item in request_post_data] + # check if accesses already exist for the received data and eventually update them + # if all accesses already exist, return True and stop processing to avoid triggering again the synchronizer + logger.debug( + "REMS :: check if accesses automatically created already exists for the received data..." + ) + already_existing_accesses = { + index + for index, item in enumerate(request_post_data) + if check_existence_automatic(item) + } + if len(already_existing_accesses) == len(request_post_data): + # all accesses already exist, stopping processing + logger.debug("REMS :: all accesses already exists, noop, stopping processing.") + return True + + logger.debug("REMS :: some accesses do not exist yet") + # Ensure the most recent account information by pulling it from Keycloak + logger.debug( + "REMS :: requesting refreshing the account information from Keycloak Synchronizer..." + ) + synchronizer.synchronize() + logger.debug( + "REMS :: ...assuming that the OIDC account information has been synchronized" + ) + statuses = [ + handle_rems_entitlement(item) + for index, item in enumerate(request_post_data) + if index not in already_existing_accesses + ] return all(statuses) -def handle_rems_entitlement(data: Dict[str, str]) -> bool: - """ - Handles a single information about the entitlement from REMS. - :returns: True if the user was found and the entitlement processed, False if not +def extract_rems_data(data: Dict[str, str]) -> Tuple[str, str, str, str, date]: + """ + Extracts the data from the REMS request """ - application = data.get('application') - resource = data.get('resource') - user_oidc_id = data.get('user') - email = data.get('mail') - expiration_date = data.get('end') + application = data.get("application") + resource = data.get("resource") + user_oidc_id = data.get("user") + email = data.get("mail") + expiration_date = data.get("end") if expiration_date is None: - expiration_date = date.today() + timedelta( - days=getattr(settings, 'ACCESS_DEFAULT_EXPIRATION_DAYS', 90) - ) + expiration_date = build_default_expiration_date() else: expiration_date = isoparse(expiration_date).date() - logger.debug(f'REMS :: * data access request id: {application}, user_oidc_id: {user_oidc_id}, user_email: {email}, resource: {resource}') + logger.debug( + f"REMS :: * data access request id: {application}, user_oidc_id: {user_oidc_id}, user_email: {email}, resource: {resource}" + ) + return application, resource, user_oidc_id, email, expiration_date + +def build_default_expiration_date(): + return date.today() + timedelta( + days=getattr(settings, "ACCESS_DEFAULT_EXPIRATION_DAYS", 90) + ) + + +def handle_rems_entitlement(data: Dict[str, str]) -> bool: + """ + Handles a single piece of information about the entitlement from REMS. + + :returns: True if the user was found and the entitlement processed, False if not + """ + application, resource, user_oidc_id, email, expiration_date = extract_rems_data( + data + ) try: Dataset.objects.get(elu_accession=resource) except Dataset.DoesNotExist: - message = f'REMS :: Dataset with such `elu_accession` ({resource}) does not exist! Quitting' - logger.error(f' * {message}') + message = f"REMS :: Dataset with such `elu_accession` ({resource}) does not exist! Quitting" + logger.error(f" * {message}") # TODO: E2E: Save and display a notification to DataStewards raise ValueError(message) - + # First, tries to find a user with given OIDC ID # Then, it tries to find a contact with given OIDC ID # Then, it tries to find a user with given email address @@ -108,45 +171,58 @@ def handle_rems_entitlement(data: Dict[str, str]) -> bool: users_by_email = User.objects.filter(email=email) contacts_by_email = Contact.objects.filter(email=email) - logger.debug(f'REMS :: Locating the User/Contact for the given Access information...') - + logger.debug( + f"REMS :: Locating the User/Contact for the given Access information..." + ) if users_by_oidc.count() + contacts_by_oidc.count() > 1: - logger.error(f'REMS :: error, found multiple users or contacts with given OIDC_ID: {user_oidc_id}!') + logger.error( + f"REMS :: error, found multiple users or contacts with given OIDC_ID: {user_oidc_id}!" + ) # Something is wrong - there are multiple users or contacts with given OIDC ID # TODO: E2E: Save and display a notification to DataStewards return False if users_by_oidc.count() == 1: - logger.debug(f'REMS :: OK, found a user with given OIDC_ID') + logger.debug(f"REMS :: OK, found a user with given OIDC_ID") user = users_by_oidc.first() - return create_rems_entitlement(user, application, resource, user_oidc_id, email, expiration_date) - logger.debug(f'REMS :: no users with given OIDC_ID') + return create_rems_entitlement( + user, application, resource, user_oidc_id, email, expiration_date + ) + logger.debug(f"REMS :: no users with given OIDC_ID") if contacts_by_oidc.count() == 1: contact = contacts_by_oidc.first() - logger.debug(f'REMS :: OK, found a contact with given OIDC_ID') - return create_rems_entitlement(contact, application, resource, user_oidc_id, email, expiration_date) - logger.debug(f'REMS :: no contacts with given OIDC_ID') + logger.debug(f"REMS :: OK, found a contact with given OIDC_ID") + return create_rems_entitlement( + contact, application, resource, user_oidc_id, email, expiration_date + ) + logger.debug(f"REMS :: no contacts with given OIDC_ID") if users_by_email.count() + contacts_by_email.count() > 1: - logger.error(f'REMS :: error, found multiple users or contacts with given email: {email}!') + logger.error( + f"REMS :: error, found multiple users or contacts with given email: {email}!" + ) # Something is wrong - there are multiple users or contacts with given OIDC ID # TODO: E2E: Save and display a notification to DataStewards return False if users_by_email.count() == 1: - logger.debug(f'REMS :: OK, found a user with given email') + logger.debug(f"REMS :: OK, found a user with given email") user = users_by_email.first() - return create_rems_entitlement(user, application, resource, user_oidc_id, email, expiration_date) - logger.debug(f'REMS :: no users with given email') + return create_rems_entitlement( + user, application, resource, user_oidc_id, email, expiration_date + ) + logger.debug(f"REMS :: no users with given email") if contacts_by_email.count() == 1: contact = contacts_by_email.first() - logger.debug(f'REMS :: OK, found a contact with given email') - return create_rems_entitlement(contact, application, resource, user_oidc_id, email, expiration_date) - logger.debug(f'REMS :: no contacts with given email') - + logger.debug(f"REMS :: OK, found a contact with given email") + return create_rems_entitlement( + contact, application, resource, user_oidc_id, email, expiration_date + ) + logger.debug(f"REMS :: no contacts with given email") + # At this moment, we didn't find any User nor Contact with given OIDC_ID nor email # Will attempt to create a new contact then Contact.get_or_create_from_rems(email, user_oidc_id) @@ -155,37 +231,22 @@ def handle_rems_entitlement(data: Dict[str, str]) -> bool: return True -def create_rems_entitlement(obj: Union[Access, User], - application: str, - dataset_id: str, - user_oidc_id: str, - email: str, - expiration_date: date) -> bool: +def create_rems_entitlement( + obj: Union[Access, User], + application: str, + dataset_id: str, + user_oidc_id: str, + email: str, + expiration_date: date, +) -> bool: """ Tries to find a dataset with `elu_accession` equal to `dataset_id`. If it exists, it will add a new logbook entry (Access object) set to the current user/contact Assumes that the Dataset exists, otherwise will throw an exception. """ - notes = f'Set automatically by REMS data access request #{application}' - dataset = Dataset.objects.get(elu_accession=dataset_id) - - system_rems_user = User.objects.filter( - username='system::REMS' - ) - - # The password is not a hash, therefore it is - # not possible to log into this account - if system_rems_user.count() == 0: - system_rems_user = User.objects.create( - username='system::REMS', - first_name=':REMS:', - last_name=':System Account:', - password='this is an invalid hash', - email='lcsb-sysadmins+REMS@uni.lu' - ) - else: - system_rems_user = system_rems_user.first() + notes = build_access_notes_rems(application) + system_rems_user = get_or_create_rems_user() if type(obj) == User: new_logbook_entry = Access( @@ -211,7 +272,36 @@ def create_rems_entitlement(obj: Union[Access, User], ) else: klass = obj.__class__.__name__ - raise TypeError(f'Wrong type of the object - should be Contact or User, is: {klass} instead') - + raise TypeError( + f"Wrong type of the object - should be Contact or User, is: {klass} instead" + ) + new_logbook_entry.save() return True + + +def build_access_notes_rems(application: str) -> str: + """ + Build and return note to be attached to the access created from a REMS application + """ + return f"Set automatically by REMS data access request #{application}" + + +def get_or_create_rems_user() -> User: + """ + Check if rems system user already exists and either return it directly or create it and return it + """ + system_rems_user = User.objects.filter(username="system::REMS") + # The password is not a hash, therefore it is + # not possible to log into this account + if system_rems_user.count() == 0: + system_rems_user = User.objects.create( + username="system::REMS", + first_name=":REMS:", + last_name=":System Account:", + password="this is an invalid hash", + email="lcsb-sysadmins+REMS@uni.lu", + ) + else: + system_rems_user = system_rems_user.first() + return system_rems_user diff --git a/core/models/access.py b/core/models/access.py index 8611c763..f48f4195 100644 --- a/core/models/access.py +++ b/core/models/access.py @@ -1,9 +1,11 @@ -from datetime import datetime +import logging + +from datetime import datetime, date from typing import List from django.core.exceptions import ValidationError from django.db import models -from django.db.models import Q, ObjectDoesNotExist, Count +from django.db.models import Q, ObjectDoesNotExist, Count, signals from enumchoicefield import EnumChoiceField, ChoiceEnum @@ -13,6 +15,9 @@ from auditlog.models import AuditlogHistoryField +logger = logging.getLogger(__name__) + + class StatusChoices(ChoiceEnum): precreated = "Pre-created" active = "Active" @@ -38,6 +43,35 @@ class Meta: ) ] + @classmethod + def expire_accesses(cls, upper_date: date) -> None: + """ + Set the status of Access objects with an expiration date lower than given `upper_date` + to terminated + + @param upper_date: Date threshold. + """ + accesses_to_expire = cls.objects.filter( + grant_expires_on__lt=upper_date + ).exclude( + status=StatusChoices.terminated, + ).all() + for access in accesses_to_expire: + logger.debug(f"Expiring access {access.pk} because expiration date ({access.grant_expires_on}) is lower than {upper_date.strftime('%Y-%m-%d')}") + access.status = StatusChoices.terminated + access.access_notes = "Automatically terminated" + # Necessary to manually send the signal because bulk_update does not use object.save() + # Without this, auditlog cannot create a LogEntry for the change of status + signals.pre_save.send( + sender=cls, + instance=access, + created=False, + raw=True, + update_fields=("status", "access_notes") + ) + cls.objects.bulk_update(accesses_to_expire, ["status", "access_notes"]) + logger.debug("Accesses expired successfully") + def clean(self): if self.user and self.contact: raise ValidationError( diff --git a/core/models/document.py b/core/models/document.py index 0f1b57f1..1600eeb9 100644 --- a/core/models/document.py +++ b/core/models/document.py @@ -42,7 +42,8 @@ class Meta: object_id = models.PositiveIntegerField() content_object = GenericForeignKey('content_type', 'object_id') - content = models.FileField(upload_to=get_file_name) + content = models.FileField(upload_to=get_file_name, + blank=False) content_url = models.URLField(verbose_name='Document Url', null=True, blank=True) content_notes = models.TextField(verbose_name='Document Notes', blank=True, @@ -50,9 +51,9 @@ class Meta: domain_type = models.TextField(verbose_name='Domain Type', choices=type, default=type.not_specified) expiry_date = models.DateField(verbose_name='Expiry date', - blank=True, - help_text='If the document has a validity period, please specify the expiry date here.', - null=True) + blank=True, + help_text='If the document has a validity period, please specify the expiry date here.', + null=True) def __str__(self): return f"{self.content.name} ({self.content_object})" diff --git a/core/models/partner.py b/core/models/partner.py index 5f3cac1c..c92a2cfa 100644 --- a/core/models/partner.py +++ b/core/models/partner.py @@ -1,3 +1,4 @@ +from django.conf import settings from django.apps import apps from django.db import models from django_countries.fields import CountryField @@ -5,7 +6,6 @@ from model_utils import Choices from .utils import CoreTrackedDBModel, TextFieldWithInputWidget -from elixir_daisy import settings GEO_CATEGORY = Choices( ('EU', 'EU'), diff --git a/core/models/project.py b/core/models/project.py index bc5511e2..b5690952 100644 --- a/core/models/project.py +++ b/core/models/project.py @@ -10,7 +10,7 @@ from .utils import CoreTrackedModel, COMPANY from .partner import HomeOrganisation -from elixir_daisy import settings +from django.conf import settings class Project(CoreTrackedModel): diff --git a/core/tasks.py b/core/tasks.py new file mode 100644 index 00000000..3ad28280 --- /dev/null +++ b/core/tasks.py @@ -0,0 +1,12 @@ +from datetime import date +from celery import shared_task +from core.models.access import Access + + +@shared_task +def check_accesses_expiration(): + """ + Task to expire accesses with a passed `grant_expiration_date` value + """ + upper_date = date.today() + Access.expire_accesses(upper_date) \ No newline at end of file diff --git a/core/tests/models/test_access.py b/core/tests/models/test_access.py new file mode 100644 index 00000000..8dc8aa16 --- /dev/null +++ b/core/tests/models/test_access.py @@ -0,0 +1,41 @@ +from auditlog.models import LogEntry +from core.models.access import StatusChoices, Access +from datetime import date, timedelta +from test.factories import AccessFactory + + +def test_expire_accesses(): + """ + Tests that `expire_accesses` method correctly terminates Access with an expiration + date previous to the given date and that this creates a LogEntry in the db + """ + dates = [ + date.today() - timedelta(days=15), + date.today() - timedelta(days=365), + date.today() - timedelta(days=1), + date.today(), + date.today() + timedelta(days=1), + ] + accesses = [AccessFactory(status=StatusChoices.active, grant_expires_on=dates[i]) for i in range(5)] + + Access.expire_accesses(date.today()) + + for access in accesses: + access.refresh_from_db() + if access.status == StatusChoices.terminated: + assert "Automatically terminated" in access.access_notes + logs = LogEntry.objects.get_for_object(access) + assert len(logs) == 2 + + last_log = logs.order_by("-timestamp").first() + assert last_log.action == LogEntry.Action.UPDATE + assert "status" in last_log.changes + assert "access_notes" in last_log.changes + + + assert accesses[0].status == StatusChoices.terminated + assert accesses[1].status == StatusChoices.terminated + assert accesses[2].status == StatusChoices.terminated + assert accesses[3].status == StatusChoices.active + assert accesses[4].status == StatusChoices.active + diff --git a/core/tests/test_lcsb.py b/core/tests/test_lcsb.py index 6ee24265..fdc5fa95 100644 --- a/core/tests/test_lcsb.py +++ b/core/tests/test_lcsb.py @@ -7,10 +7,11 @@ from core.models import User from core.models.access import StatusChoices from core.lcsb.oidc import KeycloakAccountSynchronizer, KeycloakSynchronizationMethod -from core.lcsb.rems import create_rems_entitlement +from core.lcsb.rems import create_rems_entitlement, extract_rems_data, build_default_expiration_date, \ + check_existence_automatic from core.models.access import Access from core.models.contact import Contact -from test.factories import ContactFactory, DatasetFactory, UserFactory, ExposureFactory, EndpointFactory +from test.factories import ContactFactory, DatasetFactory, UserFactory, ExposureFactory, EndpointFactory, AccessFactory from web.views.utils import get_user_or_contact_by_oidc_id @@ -20,53 +21,53 @@ def well_know(self) -> bool: def get_users(self, query) -> List[Dict]: return [{ - "id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee", - "createdTimestamp": 1634231689999, - "username": "0000-0001-2222-3333", - "enabled": True, - "totp": False, - "emailVerified": True, - "firstName": "TESTY", - "lastName": "MCTesty", + "id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee", + "createdTimestamp": 1634231689999, + "username": "0000-0001-2222-3333", + "enabled": True, + "totp": False, + "emailVerified": True, + "firstName": "TESTY", + "lastName": "MCTesty", "email": "testy.mctesty@uni.lu", - "disableableCredentialTypes": [], - "requiredActions": [], + "disableableCredentialTypes": [], + "requiredActions": [], "notBefore": 0, "access": { - "manageGroupMembership": False, - "view": True, + "manageGroupMembership": False, + "view": True, "mapRoles": False, - "impersonate": False, + "impersonate": False, "manage": False } }, { - "id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeef", - "createdTimestamp": 1634231689998, - "username": "0000-0001-2222-3334", - "enabled": True, - "totp": False, - "emailVerified": True, - "firstName": "BOBBY", - "lastName": "FISCHER", + "id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeef", + "createdTimestamp": 1634231689998, + "username": "0000-0001-2222-3334", + "enabled": True, + "totp": False, + "emailVerified": True, + "firstName": "BOBBY", + "lastName": "FISCHER", "email": "bobby.fischer@gmail.com", - "disableableCredentialTypes": [], - "requiredActions": [], + "disableableCredentialTypes": [], + "requiredActions": [], "notBefore": 0, "access": { - "manageGroupMembership": False, - "view": True, + "manageGroupMembership": False, + "view": True, "mapRoles": False, - "impersonate": False, + "impersonate": False, "manage": False } }, { - "id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeeg", - "createdTimestamp": 1634231689997, - "username": "0000-0001-2222-3335", - "firstName": "Ann", - "lastName": "Bann", + "id": "aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeeg", + "createdTimestamp": 1634231689997, + "username": "0000-0001-2222-3335", + "firstName": "Ann", + "lastName": "Bann", }] - + class KeycloakSynchronizationMethodMock(KeycloakSynchronizationMethod): def test_connection(self) -> bool: @@ -83,19 +84,106 @@ def _validate_config(config: Dict) -> None: def get_keycloak_admin_connection(self) -> None: return KeycloakAdminConnectionMock() - def _create_connection(self, config:Dict=None) -> KeycloakAdminConnectionMock: + def _create_connection(self, config: Dict = None) -> KeycloakAdminConnectionMock: return KeycloakAdminConnectionMock() def test_keycloak_synchronization_config_validation(): with pytest.raises(KeyError): kc = KeycloakSynchronizationMethod({}) - + with pytest.raises(KeyError): kc = KeycloakSynchronizationMethod({}, False) kc._create_connection({}) +def test_extract_rems_data_empty_expiration(): + application_id = 4056 + resource_id = "TEST-2-5591E3-1" + user_oidc_id = "4ce4f280-8095-4a20-bf19-6426d2292134" + email = "john.doe@uni.lu" + data = {"application": application_id, "resource": resource_id, "user": user_oidc_id, + "mail": email, "end": None} + application, resource, user_oidc_id, email, expiration_date = extract_rems_data(data) + assert application == application_id + assert resource == resource_id + assert user_oidc_id == user_oidc_id + assert email == email + assert expiration_date == build_default_expiration_date() + + +def test_extract_rems_data_with_expiration(): + application_id = 4056 + resource_id = "TEST-2-5591E3-1" + user_oidc_id = "4ce4f280-8095-4a20-bf19-6426d2292134" + email = "john.doe@uni.lu" + data = {"application": application_id, "resource": resource_id, "user": user_oidc_id, + "mail": email, "end": "2023-08-03T23:59:59.000Z"} + application, resource, user_oidc_id, email, expiration_date = extract_rems_data(data) + assert application == application_id + assert resource == resource_id + assert user_oidc_id == user_oidc_id + assert email == email + assert expiration_date == datetime.date(2023, 8, 3) + + +def test_check_existence_automatic_positive(): + resource_id = "TEST-2-5591E3-1" + expiration_date = datetime.date.today() + datetime.timedelta(days=1) + user = UserFactory(oidc_id='12345', email='example@example.org') + user.save() + dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession=resource_id) + dataset.save() + create_rems_entitlement(user, 'Test Application', resource_id, user.oidc_id, user.email, expiration_date) + application_id = 4056 + email = "john.doe@uni.lu" + data = {"application": application_id, "resource": resource_id, "user": user.oidc_id, + "mail": email, "end": expiration_date.strftime('%Y-%m-%d') + "T23:59:59.000Z"} + assert check_existence_automatic(data) + + +def test_check_existence_automatic_negative_mismatch(): + resource_id = "TEST-2-5591E3-1" + expiration_date = datetime.date.today() + datetime.timedelta(days=1) + user = UserFactory(oidc_id='12345', email='example@example.org') + user.save() + dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession=resource_id) + dataset.save() + create_rems_entitlement(user, 'Test Application', resource_id, user.oidc_id, user.email, expiration_date) + application_id = 4056 + email = "john.doe@uni.lu" + # resource id is different + data = {"application": application_id, "resource": "TEST-2-5591E3-2", "user": user.oidc_id, + "mail": email, "end": expiration_date.strftime('%Y-%m-%d') + "T23:59:59.000Z"} + assert not check_existence_automatic(data) + # user id is different + data = {"application": application_id, "resource": resource_id, "user": "xxx", + "mail": email, "end": expiration_date.strftime('%Y-%m-%d') + "T23:59:59.000Z"} + assert not check_existence_automatic(data) + # expiration date is different + data = {"application": application_id, "resource": resource_id, "user": user.oidc_id, + "mail": email, "end": datetime.date.today().strftime('%Y-%m-%d') + "T23:59:59.000Z"} + assert not check_existence_automatic(data) + +def test_check_existence_automatic_negative_manually_created(): + resource_id = "TEST-2-5591E3-1" + expiration_date = datetime.date.today() + datetime.timedelta(days=1) + email = "john.doe@uni.lu" + user = UserFactory(oidc_id='12345', email=email) + user.save() + dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession=resource_id) + dataset.save() + access = AccessFactory(dataset=dataset, user=user) + access.grant_expires_on=expiration_date + access.was_generated_automatically = False + access.status = StatusChoices.active + access.save() + application_id = 4056 + data = {"application": application_id, "resource": resource_id, "user": user.oidc_id, + "mail": email, "end": expiration_date.strftime('%Y-%m-%d') + "T23:59:59.000Z"} + assert not check_existence_automatic(data) + + def test_add_rems_entitlements(): elu_accession = '12345678' expiration_date = datetime.date.today() + datetime.timedelta(days=1) @@ -130,11 +218,12 @@ def test_permissions(): access2 = Access(access_notes='Access user', user=user, dataset=dataset, status=StatusChoices.active) access2.save() - + assert '123' in user.get_access_permissions() assert '123' in contact.get_access_permissions() assert len(user2.get_access_permissions()) == 0 + def test_get_user_or_contact_by_oidc_id(): user_found, contact_found, user, contact = get_user_or_contact_by_oidc_id('0') assert not user_found @@ -152,4 +241,4 @@ def test_get_user_or_contact_by_oidc_id(): user_found, contact_found, user, contact = get_user_or_contact_by_oidc_id('98765') assert not user_found - assert contact_found \ No newline at end of file + assert contact_found diff --git a/docker/node/Dockerfile b/docker/node/Dockerfile index c0b909d2..257112d8 100644 --- a/docker/node/Dockerfile +++ b/docker/node/Dockerfile @@ -1,4 +1,4 @@ -FROM node:14 +FROM node:16 COPY web/static/css /static/css COPY web/static/js /static/js COPY web/static/vendor/bootstrap-material-datetimepicker /static/vendor/bootstrap-material-datetimepicker diff --git a/elixir_daisy/settings_ci.py b/elixir_daisy/settings_ci.py index 3f6199a8..23f0450b 100644 --- a/elixir_daisy/settings_ci.py +++ b/elixir_daisy/settings_ci.py @@ -60,4 +60,7 @@ # Speed-up setting new accounts PASSWORD_HASHERS = ['django.contrib.auth.hashers.MD5PasswordHasher'] -DEBUG = True \ No newline at end of file +DEBUG = True + +REMS_INTEGRATION_ENABLED = True +REMS_ALLOWED_IP_ADDRESSES = ['127.0.0.1'] diff --git a/elixir_daisy/settings_compose_ci.py b/elixir_daisy/settings_compose_ci.py index 8591a507..ccaa84d5 100644 --- a/elixir_daisy/settings_compose_ci.py +++ b/elixir_daisy/settings_compose_ci.py @@ -30,8 +30,10 @@ ## Result backend CELERY_RESULT_BACKEND = 'django-db' -TESTING = os.environ.get('TEST', False) +TESTING = True GLOBAL_API_KEY = os.environ.get('GLOBAL_API_KEY', 'default_global_api_key_in_settings_compose_ci.py') +REMS_INTEGRATION_ENABLED = True +REMS_ALLOWED_IP_ADDRESSES = ['*'] try: from .settings_ci import * diff --git a/elixir_daisy/settings_local.template.py b/elixir_daisy/settings_local.template.py index 484482f4..eb1d02fa 100644 --- a/elixir_daisy/settings_local.template.py +++ b/elixir_daisy/settings_local.template.py @@ -1,3 +1,5 @@ +from celery.schedules import crontab + #SECURITY WARNING: change the key used in production and keep it secret ! GLOBAL_API_KEY = None # Generate a global api key by e.g. django.core.management.utils.get_random_secret_key() if GLOBAL_API_KEY is None: raise NotImplementedError('You must specify GLOBAL_API_KEY in settings_local.py') @@ -74,4 +76,12 @@ # KEYCLOAK_URL = 'https://root-address-to-your-keycloak.com:443' # KEYCLOAK_REALM = 'master' # KEYCLOAK_USER = 'your service user for daisy' -# KEYCLOAK_PASS = 'the password for the service user' \ No newline at end of file +# KEYCLOAK_PASS = 'the password for the service user' + +# Celery beat setting to schedule tasks on docker creation +CELERY_BEAT_SCHEDULE = { + "clean-accesses-every-day": { + "task": "core.tasks.check_accesses_expiration", + "schedule": crontab(minute=0, hour=0), # Execute task at midnight + } +} diff --git a/elixir_daisy/settings_tests.py b/elixir_daisy/settings_tests.py index 18b6d6d0..27a63bb5 100644 --- a/elixir_daisy/settings_tests.py +++ b/elixir_daisy/settings_tests.py @@ -54,3 +54,6 @@ ## Result backend CELERY_RESULT_BACKEND = 'django-db' + +REMS_INTEGRATION_ENABLED = True +REMS_ALLOWED_IP_ADDRESSES = ['*'] diff --git a/web/static/js/daisy.js b/web/static/js/daisy.js index 942ba4a7..ef137f4c 100644 --- a/web/static/js/daisy.js +++ b/web/static/js/daisy.js @@ -155,7 +155,10 @@ $(document).ready(function () { url: url, type: 'post', dataType: 'json', - data: modalForm.serialize(), + data: new FormData(modalForm[0]), + contentType: false, + processData: false, + cache: false, success: function (results) { if (redirectURI !== undefined) { window.location.replace(redirectURI); diff --git a/web/static/vendor/package-lock.json b/web/static/vendor/package-lock.json index 309616fd..d7e51b6a 100644 --- a/web/static/vendor/package-lock.json +++ b/web/static/vendor/package-lock.json @@ -1,128 +1,322 @@ { "name": "elixir-daisy", "version": "1.1.0", - "lockfileVersion": 1, + "lockfileVersion": 3, "requires": true, - "dependencies": { - "@ds-wizard/integration-widget-sdk": { + "packages": { + "": { + "name": "elixir-daisy", + "version": "1.1.0", + "license": "Apache-2.0", + "dependencies": { + "@ds-wizard/integration-widget-sdk": "^0.3.0", + "bootstrap": "4.2.1", + "bootstrap-material-design": "4.1.1", + "datatables.net": "1.10.19", + "datatables.net-dt": "1.10.19", + "jquery": "3.4.1", + "jquery-ui-dist": "1.12.1", + "js-cookie": "2.2.0", + "jsrender": "0.9.90", + "moment": "2.22.1", + "npm": "6.13.7", + "popper.js": "1.15.0", + "select2": "4.0.6-rc.1", + "select2-bootstrap-theme": "0.1.0-beta.10" + }, + "devDependencies": { + "concurrently": "4.1.0", + "cssnano-cli": "1.0.5", + "js-yaml": "3.13.1", + "node-sass": "9.0.0", + "node-sass-tilde-importer": "1.0.2" + } + }, + "node_modules/@babel/code-frame": { + "version": "7.22.5", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.5.tgz", + "integrity": "sha512-Xmwn266vad+6DAqEB2A6V/CcZVp62BbwVmcOJc2RPuwih1kw02TjQvWVWlcKGbBPd+8/0V5DEkOcizRGYsspYQ==", + "dev": true, + "dependencies": { + "@babel/highlight": "^7.22.5" + }, + "engines": { + "node": ">=6.9.0" + } + }, + "node_modules/@babel/helper-validator-identifier": { + "version": "7.22.5", + "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.5.tgz", + "integrity": "sha512-aJXu+6lErq8ltp+JhkJUfk1MTGyuA4v7f3pA+BJ5HLfNC6nAQ0Cpi9uOquUj8Hehg0aUiHzWQbOVJGao6ztBAQ==", + "dev": true, + "engines": { + "node": ">=6.9.0" + } + }, + "node_modules/@babel/highlight": { + "version": "7.22.5", + "resolved": "https://registry.npmjs.org/@babel/highlight/-/highlight-7.22.5.tgz", + "integrity": "sha512-BSKlD1hgnedS5XRnGOljZawtag7H1yPfQp0tdNJCHoH6AZ+Pcm9VvkrK59/Yy593Ypg0zMxH2BxD1VPYUQ7UIw==", + "dev": true, + "dependencies": { + "@babel/helper-validator-identifier": "^7.22.5", + "chalk": "^2.0.0", + "js-tokens": "^4.0.0" + }, + "engines": { + "node": ">=6.9.0" + } + }, + "node_modules/@ds-wizard/integration-widget-sdk": { "version": "0.3.0", "resolved": "https://registry.npmjs.org/@ds-wizard/integration-widget-sdk/-/integration-widget-sdk-0.3.0.tgz", "integrity": "sha512-tvhPitKOVL/W73Z8gsvsFkyiUcT6PltBkmARIxUH5VQioVsPYMk1w3lkD0S1ZJU0kGuySfHvECLy9woh7AEYLQ==" }, - 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"yallist": { + "node_modules/yallist": { "version": "3.0.3", "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.0.3.tgz", "integrity": "sha512-S+Zk8DEWE6oKpV+vI3qWkaK+jSbIK86pCwe2IF/xwIpQ8jEuxpw9NyaGjmp9+BoJv5FV2piqCDcoCtStppiq2A==", "dev": true }, - "yargs": { + "node_modules/yargs": { "version": "12.0.5", "resolved": "https://registry.npmjs.org/yargs/-/yargs-12.0.5.tgz", "integrity": "sha512-Lhz8TLaYnxq/2ObqHDql8dX8CJi97oHxrjUcYtzKbbykPtVW9WB+poxI+NM2UIzsMgNCZTIf0AQwsjK5yMAqZw==", "dev": true, - "requires": { + "dependencies": { "cliui": "^4.0.0", "decamelize": "^1.2.0", "find-up": "^3.0.0", @@ -6119,12 +8403,12 @@ "yargs-parser": "^11.1.1" } }, - "yargs-parser": { + "node_modules/yargs-parser": { "version": "11.1.1", "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-11.1.1.tgz", "integrity": "sha512-C6kB/WJDiaxONLJQnF8ccx9SEeoTTLek8RVbaOIsrAUS8VrBEXfmeSnCZxygc+XC2sNMBIwOOnfcxiynjHsVSQ==", "dev": true, - "requires": { + "dependencies": { "camelcase": "^5.0.0", "decamelize": "^1.2.0" } diff --git a/web/static/vendor/package.json b/web/static/vendor/package.json index 0c102469..7731b058 100644 --- a/web/static/vendor/package.json +++ b/web/static/vendor/package.json @@ -37,7 +37,7 @@ "concurrently": "4.1.0", "cssnano-cli": "1.0.5", "js-yaml": "3.13.1", - "node-sass": "4.13.1", + "node-sass": "9.0.0", "node-sass-tilde-importer": "1.0.2" } } diff --git a/web/templates/_includes/documents_table.html b/web/templates/_includes/documents_table.html index a9bc1ef9..17170471 100644 --- a/web/templates/_includes/documents_table.html +++ b/web/templates/_includes/documents_table.html @@ -30,6 +30,8 @@

link Documents data-post-mode="true" {% if project %} data-ajax-redirect-uri="{% url 'project' pk=project.id %}" + {% elif contract %} + data-ajax-redirect-uri="{% url 'contract' pk=contract.id %}" {% endif %} data-ajax-url="{% url "document_edit" pk=file.id %}" title="Update document"> diff --git a/web/templates/contracts/contract.html b/web/templates/contracts/contract.html index 4a97dcdf..c545f358 100644 --- a/web/templates/contracts/contract.html +++ b/web/templates/contracts/contract.html @@ -128,6 +128,8 @@

Participants

data-target="#modal" data-modal-title="Add document to contract" data-ajax-url="{% url 'document_add' object_id=object_id content_type=content_type %}" + data-ajax-redirect-uri="{% url 'contract' pk=object_id %}" + data-post-mode="true" class="dropdown-item" type="button" title="Add document to contract"> Upload new document diff --git a/web/templates/projects/project.html b/web/templates/projects/project.html index c581b497..e839084f 100644 --- a/web/templates/projects/project.html +++ b/web/templates/projects/project.html @@ -284,8 +284,16 @@

link Contracts add
- -
diff --git a/web/tests/test_rems.py b/web/tests/test_rems.py new file mode 100644 index 00000000..174ba092 --- /dev/null +++ b/web/tests/test_rems.py @@ -0,0 +1,76 @@ +import json + +from core.models import Access +from core.utils import DaisyLogger + +from django.shortcuts import reverse + +import datetime + +from test.factories import UserFactory, DatasetFactory, AccessFactory + +log = DaisyLogger(__name__) + +def test_rems_handler_duplicate(client, user_vip, user_data_steward): + resource_id = "TEST-2-5591E3-1" + expiration_date = datetime.date.today() + datetime.timedelta(days=1) + email = "john.doe@uni.lu" + user = UserFactory(oidc_id='12345', email=email) + user.save() + dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession=resource_id) + dataset.save() + application_id = 4056 + data = [{"application": application_id, "resource": resource_id, "user": user.oidc_id, + "mail": email, "end": expiration_date.strftime('%Y-%m-%d') + "T23:59:59.000Z"}] + + response = client.post(reverse('api_rems_endpoint'), json.dumps(data), content_type="application/json") + assert response.status_code == 200, response.content + accesses = Access.objects.filter(dataset=dataset, user=user).all() + assert len(accesses) == 1 + response = client.post(reverse('api_rems_endpoint'), json.dumps(data), content_type="application/json") + assert response.status_code == 200 , response.content + accesses = Access.objects.filter(dataset=dataset, user=user).all() + assert len(accesses) == 1 + +def test_rems_handler_no_expiration(client, user_vip, user_data_steward): + resource_id = "TEST-2-5591E3-1" + email = "john.doe@uni.lu" + user = UserFactory(oidc_id='12345', email=email) + user.save() + dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession=resource_id) + dataset.save() + application_id = 4056 + data = [{"application": application_id, "resource": resource_id, "user": user.oidc_id, + "mail": email, "end": None}] + + response = client.post(reverse('api_rems_endpoint'), json.dumps(data), content_type="application/json") + assert response.status_code == 200, response.content + accesses = Access.objects.filter(dataset=dataset, user=user).all() + assert len(accesses) == 1 + response = client.post(reverse('api_rems_endpoint'), json.dumps(data), content_type="application/json") + assert response.status_code == 200, response.content + accesses = Access.objects.filter(dataset=dataset, user=user).all() + assert len(accesses) == 1 + +def test_rems_handler_different_expiration(client, user_vip, user_data_steward): + resource_id = "TEST-2-5591E3-1" + expiration_date_1 = datetime.date.today() + datetime.timedelta(days=1) + expiration_date_2 = datetime.date.today() + datetime.timedelta(days=2) + email = "john.doe@uni.lu" + user = UserFactory(oidc_id='12345', email=email) + user.save() + dataset = DatasetFactory(title='Test', local_custodians=[user], elu_accession=resource_id) + dataset.save() + application_id = 4056 + data = [{"application": application_id, "resource": resource_id, "user": user.oidc_id, + "mail": email, "end": expiration_date_1.strftime('%Y-%m-%d') + "T23:59:59.000Z"}] + + response = client.post(reverse('api_rems_endpoint'), json.dumps(data), content_type="application/json") + assert response.status_code == 200, response.content + accesses = Access.objects.filter(dataset=dataset, user=user).all() + assert len(accesses) == 1 + data[0]['end'] = expiration_date_2.strftime('%Y-%m-%d') + "T23:59:59.000Z" + response = client.post(reverse('api_rems_endpoint'), json.dumps(data), content_type="application/json") + assert response.status_code == 200, response.content + accesses = Access.objects.filter(dataset=dataset, user=user).all() + assert len(accesses) == 2 diff --git a/web/views/api.py b/web/views/api.py index fffc5781..35c05028 100644 --- a/web/views/api.py +++ b/web/views/api.py @@ -23,7 +23,6 @@ from core.models import User, Cohort, Dataset, Partner, Project, DiseaseTerm, Contact, Endpoint from core.models.term_model import TermCategory, PhenotypeTerm, StudyTerm, GeneTerm from core.utils import DaisyLogger -from elixir_daisy import settings from web.views.utils import get_client_ip, get_user_or_contact_by_oidc_id @@ -248,7 +247,7 @@ def rems_endpoint(request): message = f'REMS - something is wrong with the configuration!' more = str(ex) logger.debug(f'{message} ({more})') - return create_error_response(ex.message) + return create_error_response(message) except Exception as ex: message = f'REMS - something went wrong during the import!' more = str(ex) @@ -307,4 +306,3 @@ def permissions(request, user_oidc_id: str) -> JsonResponse: {'more': more}, status=404 ) - \ No newline at end of file diff --git a/web/views/documents.py b/web/views/documents.py index 62be2b16..f3758701 100644 --- a/web/views/documents.py +++ b/web/views/documents.py @@ -6,12 +6,14 @@ from django.utils.http import urlquote from django.views.decorators.http import require_http_methods from django.contrib import messages +from django.contrib.contenttypes.models import ContentType from core.constants import Permissions from core.forms import DocumentForm from core.models import Document from core.permissions import permission_required, permission_required_from_content_type from core.utils import DaisyLogger +from web.views.utils import is_ajax_request log = DaisyLogger(__name__) @@ -30,24 +32,24 @@ def rfc5987_content_disposition(file_name): @permission_required_from_content_type(Permissions.EDIT, content_type_attr='content_type', object_id_attr='object_id') def upload_document(request, object_id, content_type): log.debug('uploading document', post=request.POST, files=request.FILES) + content_type_object = ContentType.objects.get(pk=content_type) if request.method == 'POST': - print(object_id, content_type) - if not request.FILES: - log.error('Upload failed: no document found.') - return JsonResponse( - { - 'error': {'type': 'Upload error', 'messages': ['No document to upload.']} - }, status=405) form = DocumentForm(request.POST, request.FILES) if not form.is_valid(): - return JsonResponse( - { - 'error': {'type': 'Upload error', 'messages': [str(e) for e in form.errors]} - }, status=405) - document = form.save() - messages.add_message(request, messages.SUCCESS, "Document added") - redirecturl = document.content_type.name - return redirect(to=redirecturl, pk=document.object_id) + if not request.FILES: + log.error('Upload failed: no document found.') + else: + log.error([str(e) for e in form.errors]) + return JsonResponse(form.errors, status=400) if is_ajax_request(request) else redirect(to=content_type_object.name, pk=object_id) + + else: + document = form.save() + messages.add_message(request, messages.SUCCESS, "Document added") + redirecturl = document.content_type.name + if is_ajax_request(request): + return JsonResponse({"status_code": 200}) + else: + return redirect(to=redirecturl, pk=document.object_id) else: form = DocumentForm(initial={'content_type':content_type, 'object_id': object_id}) @@ -65,16 +67,20 @@ def document_edit(request, pk): if form.is_valid(): form.save() messages.add_message(request, messages.SUCCESS, "Document updated") - return JsonResponse({ - 'success': {}, - }) + if is_ajax_request(request): + return JsonResponse({ + 'success': {}, + }) + else: + redirecturl = document.content_type.name + return redirect(to=redirecturl, pk=document.object_id) else: return JsonResponse({ 'error': { 'type': 'Edit error', 'messages': form.errors, }, - }, status=405) + }, status=405) if is_ajax_request(request) else redirect(to=document.content_type.name, pk=document.object_id) else: form = DocumentForm(instance=document)