diff --git a/Pipfile.lock b/Pipfile.lock index 4064fec4..099e141e 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -25,19 +25,11 @@ }, "alembic": { "hashes": [ - "sha256:8a259f0a4c8b350b03579d77ce9e810b19c65bf0af05f84efb69af13ad50801e", - "sha256:e27fd67732c97a1c370c33169ef4578cf96436fa0e7dcfaeeef4a917d0737d56" + "sha256:3ff4f90d23dd283d7822d78ffbc07cb256344ae1d60500b933378bc13407efcc", + "sha256:d7f6d4dc6abed18e1591932a85349a7d621298ef0daa40021609cdca54a6047c" ], "index": "pypi", - "version": "==1.5.8" - }, - "amqp": { - "hashes": [ - "sha256:03e16e94f2b34c31f8bf1206d8ddd3ccaa4c315f7f6a1879b7b1210d229568c2", - "sha256:493a2ac6788ce270a2f6a765b017299f60c1998f5a8617908ee9be082f7300fb" - ], - "markers": "python_version >= '3.6'", - "version": "==5.0.6" + "version": "==1.6.0" }, "aniso8601": { "hashes": [ @@ -51,16 +43,14 @@ "sha256:31b2eced602aa8423c2aea9c76a724617ed67cf9513173fd3a4f03e3a929c7e6", "sha256:832aa3cde19744e49938b91fea06d69ecb9e649c93ba974535d08ad92164f700" ], - "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", "version": "==20.3.0" }, "babel": { "hashes": [ - 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study = StudyService().get_study(study_model.id) + study = StudyService().get_study(study_model.id, do_status=True) study_data = StudySchema().dump(study) study_data["errors"] = ApiErrorSchema(many=True).dump(errors) return study_data diff --git a/crc/api/user.py b/crc/api/user.py index bbd51130..8cdbbf47 100644 --- a/crc/api/user.py +++ b/crc/api/user.py @@ -214,7 +214,7 @@ def _handle_login(user_info: LdapModel, redirect_url=None): g.user = user # Return the frontend auth callback URL, with auth token appended. - auth_token = user.encode_auth_token().decode() + auth_token = user.encode_auth_token() g.token = auth_token if redirect_url is not None: diff --git a/migrations/versions/665624ac29f1_.py b/migrations/versions/665624ac29f1_.py index c9053a57..30171d03 100644 --- a/migrations/versions/665624ac29f1_.py +++ b/migrations/versions/665624ac29f1_.py @@ -19,12 +19,11 @@ depends_on = None def upgrade(): # ### commands auto generated by Alembic - please adjust! ### op.add_column('data_store', sa.Column('file_id', sa.Integer(), nullable=True)) - op.create_foreign_key(None, 'data_store', 'file', ['file_id'], ['id']) + op.create_foreign_key('file_id_key', 'data_store', 'file', ['file_id'], ['id']) # ### end Alembic commands ### - def downgrade(): # ### commands auto generated by Alembic - please adjust! ### - op.drop_constraint(None, 'data_store', type_='foreignkey') + op.drop_constraint('file_id_key', 'data_store', type_='foreignkey') op.drop_column('data_store', 'file_id') # ### end Alembic commands ### diff --git a/migrations/versions/c1449d1d1681_.py b/migrations/versions/c1449d1d1681_.py new file mode 100644 index 00000000..e23055ce --- /dev/null +++ b/migrations/versions/c1449d1d1681_.py @@ -0,0 +1,24 @@ +"""empty message + +Revision ID: c1449d1d1681 +Revises: abeffe547305, 8b976945a54e, 62910318009f +Create Date: 2021-05-04 13:20:55.447143 + +""" +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision = 'c1449d1d1681' +down_revision = ('abeffe547305', '8b976945a54e', '62910318009f') +branch_labels = None +depends_on = None + + +def upgrade(): + pass + + +def downgrade(): + pass diff --git a/tests/base_test.py b/tests/base_test.py index b19f3e06..5876e503 100644 --- a/tests/base_test.py +++ b/tests/base_test.py @@ -131,7 +131,7 @@ class BaseTest(unittest.TestCase): user = UserService.current_user(allow_admin_impersonate=True) self.assertEqual(uid, user.uid, 'Logged in user should match given user uid') - return dict(Authorization='Bearer ' + user_model.encode_auth_token().decode()) + return dict(Authorization='Bearer ' + user_model.encode_auth_token()) def delete_example_data(self, use_crc_data=False, use_rrt_data=False): """ diff --git a/tests/files/test_file_service.py b/tests/files/test_file_service.py index 53a644a0..94f5945f 100644 --- a/tests/files/test_file_service.py +++ b/tests/files/test_file_service.py @@ -15,7 +15,7 @@ class FakeGithubCreates(Mock): def get_repo(var, name): class FakeRepo(Mock): def get_contents(var, filename, ref): - raise UnknownObjectException(status='Failure', data='Failed data') + raise UnknownObjectException(status='Failure', data='Failed data', headers=[]) def update_file(var, path, message, content, sha, branch): pass return FakeRepo() diff --git a/tests/study/test_study_api.py b/tests/study/test_study_api.py index 409cc5c5..f3ef1aff 100644 --- a/tests/study/test_study_api.py +++ b/tests/study/test_study_api.py @@ -1,8 +1,8 @@ import json from profile import Profile +from tests.base_test import BaseTest from crc.services.ldap_service import LdapService -from tests.base_test import BaseTest from datetime import datetime, timezone from unittest.mock import patch @@ -113,10 +113,9 @@ class TestStudyApi(BaseTest): self.assertEqual(study["ind_number"], db_study.ind_number) self.assertEqual(study["user_uid"], db_study.user_uid) - workflow_spec_count =session.query(WorkflowSpecModel).filter(WorkflowSpecModel.is_master_spec == False).count() + workflow_spec_count =session.query(WorkflowSpecModel).count() workflow_count = session.query(WorkflowModel).filter(WorkflowModel.study_id == study['id']).count() - error_count = len(study["errors"]) - self.assertEqual(workflow_spec_count, workflow_count + error_count) + self.assertEqual(workflow_spec_count, workflow_count) study_event = session.query(StudyEvent).first() self.assertIsNotNone(study_event) diff --git a/tests/test_authentication.py b/tests/test_authentication.py index 23cfe55e..c2199624 100644 --- a/tests/test_authentication.py +++ b/tests/test_authentication.py @@ -33,7 +33,7 @@ class TestAuthentication(BaseTest): user_1 = UserModel(uid="dhf8r") expected_exp_1 = timegm((datetime.utcnow() + timedelta(hours=new_ttl)).utctimetuple()) auth_token_1 = user_1.encode_auth_token() - self.assertTrue(isinstance(auth_token_1, bytes)) + self.assertTrue(isinstance(auth_token_1, str)) self.assertEqual("dhf8r", user_1.decode_auth_token(auth_token_1).get("sub")) #actual_exp_1 = user_1.decode_auth_token(auth_token_1).get("exp") #self.assertTrue(expected_exp_1 - 1000 <= actual_exp_1 <= expected_exp_1 + 1000) @@ -131,7 +131,7 @@ class TestAuthentication(BaseTest): admin_user = self._login_as_admin() admin_study = self._make_fake_study(admin_user.uid) - admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode()) + admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token()) rv_add_study = self.app.post( '/v1.0/study', @@ -164,7 +164,7 @@ class TestAuthentication(BaseTest): # Non-admin user should not be able to delete a study non_admin_user = self._login_as_non_admin() - non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode()) + non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token()) non_admin_study = self._make_fake_study(non_admin_user.uid) rv_add_study = self.app.post( @@ -211,7 +211,7 @@ class TestAuthentication(BaseTest): self.load_example_data() admin_user = self._login_as_admin() - admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token().decode()) + admin_token_headers = dict(Authorization='Bearer ' + admin_user.encode_auth_token()) # User should not be in the system yet. non_admin_user = session.query(UserModel).filter(UserModel.uid == self.non_admin_uid).first() @@ -230,7 +230,7 @@ class TestAuthentication(BaseTest): self.logout() non_admin_user = self._login_as_non_admin() self.assertEqual(non_admin_user.uid, self.non_admin_uid) - non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token().decode()) + non_admin_token_headers = dict(Authorization='Bearer ' + non_admin_user.encode_auth_token()) # Add a study for the non-admin user non_admin_study = self._make_fake_study(self.non_admin_uid)