mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
2cd95c48f6
- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports and py27-lint-imports-include-list tox envs - Fix most E201 and E202 errors reported by flake8-import-order v0.15, but pin flake8-import-order to v0.14.3 until https://github.com/PyCQA/flake8-import-order/issues/123 is fixed This let us drop 2 jobs on Travis per each job.
449 lines
22 KiB
Python
449 lines
22 KiB
Python
# -*- coding: utf-8 -*-
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"""
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"""
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import unittest
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import sqlalchemy
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from six import string_types
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from galaxy import (
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exceptions,
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model
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)
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from galaxy.managers import rbac_secured
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from galaxy.managers.base import SkipAttribute
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from galaxy.managers.datasets import (
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DatasetDeserializer,
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DatasetManager,
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DatasetSerializer
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)
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from galaxy.managers.roles import RoleManager
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from .base import BaseTestCase
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# =============================================================================
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default_password = '123456'
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user2_data = dict(email='user2@user2.user2', username='user2', password=default_password)
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user3_data = dict(email='user3@user3.user3', username='user3', password=default_password)
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# =============================================================================
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class DatasetManagerTestCase(BaseTestCase):
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def set_up_managers(self):
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super(DatasetManagerTestCase, self).set_up_managers()
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self.dataset_manager = DatasetManager(self.app)
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def test_create(self):
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self.log("should be able to create a new Dataset")
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dataset1 = self.dataset_manager.create()
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self.assertIsInstance(dataset1, model.Dataset)
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self.assertEqual(dataset1, self.trans.sa_session.query(model.Dataset).get(dataset1.id))
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def test_base(self):
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dataset1 = self.dataset_manager.create()
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dataset2 = self.dataset_manager.create()
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self.log("should be able to query")
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datasets = self.trans.sa_session.query(model.Dataset).all()
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self.assertEqual(self.dataset_manager.list(), datasets)
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self.assertEqual(self.dataset_manager.one(filters=(model.Dataset.id == dataset1.id)), dataset1)
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self.assertEqual(self.dataset_manager.by_id(dataset1.id), dataset1)
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self.assertEqual(self.dataset_manager.by_ids([dataset2.id, dataset1.id]), [dataset2, dataset1])
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self.log("should be able to limit and offset")
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self.assertEqual(self.dataset_manager.list(limit=1), datasets[0:1])
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self.assertEqual(self.dataset_manager.list(offset=1), datasets[1:])
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self.assertEqual(self.dataset_manager.list(limit=1, offset=1), datasets[1:2])
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self.assertEqual(self.dataset_manager.list(limit=0), [])
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self.assertEqual(self.dataset_manager.list(offset=3), [])
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self.log("should be able to order")
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self.assertEqual(self.dataset_manager.list(order_by=sqlalchemy.desc(model.Dataset.create_time)),
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[dataset2, dataset1])
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def test_delete(self):
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item1 = self.dataset_manager.create()
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self.log("should be able to delete and undelete a dataset")
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self.assertFalse(item1.deleted)
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self.assertEqual(self.dataset_manager.delete(item1), item1)
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self.assertTrue(item1.deleted)
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self.assertEqual(self.dataset_manager.undelete(item1), item1)
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self.assertFalse(item1.deleted)
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def test_purge_allowed(self):
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self.trans.app.config.allow_user_dataset_purge = True
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item1 = self.dataset_manager.create()
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self.log("should purge a dataset if config does allow")
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self.assertFalse(item1.purged)
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self.assertEqual(self.dataset_manager.purge(item1), item1)
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self.assertTrue(item1.purged)
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self.log("should delete a dataset when purging")
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self.assertTrue(item1.deleted)
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def test_purge_not_allowed(self):
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self.trans.app.config.allow_user_dataset_purge = False
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item1 = self.dataset_manager.create()
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self.log("should raise an error when purging a dataset if config does not allow")
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self.assertFalse(item1.purged)
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self.assertRaises(exceptions.ConfigDoesNotAllowException, self.dataset_manager.purge, item1)
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self.assertFalse(item1.purged)
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def test_create_with_no_permissions(self):
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self.log("should be able to create a new Dataset without any permissions")
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dataset = self.dataset_manager.create()
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permissions = self.dataset_manager.permissions.get(dataset)
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self.assertIsInstance(permissions, tuple)
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self.assertEqual(len(permissions), 2)
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manage_permissions, access_permissions = permissions
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self.assertEqual(manage_permissions, [])
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self.assertEqual(access_permissions, [])
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user3 = self.user_manager.create(**user3_data)
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self.log("a dataset without permissions shouldn't be manageable to just anyone")
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self.assertFalse(self.dataset_manager.permissions.manage.is_permitted(dataset, user3))
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self.log("a dataset without permissions should be accessible")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, user3))
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self.log("a dataset without permissions should be manageable by an admin")
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self.assertTrue(self.dataset_manager.permissions.manage.is_permitted(dataset, self.admin_user))
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self.log("a dataset without permissions should be accessible by an admin")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, self.admin_user))
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self.log("a dataset without permissions shouldn't be manageable by an anonymous user")
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self.assertFalse(self.dataset_manager.permissions.manage.is_permitted(dataset, None))
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self.log("a dataset without permissions should be accessible by an anonymous user")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, None))
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def test_create_public_dataset(self):
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self.log("should be able to create a new Dataset and give it some permissions that actually, you know, "
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"might work if there's any justice in this universe")
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owner = self.user_manager.create(**user2_data)
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owner_private_role = self.user_manager.private_role(owner)
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dataset = self.dataset_manager.create(manage_roles=[owner_private_role])
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permissions = self.dataset_manager.permissions.get(dataset)
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self.assertIsInstance(permissions, tuple)
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self.assertEqual(len(permissions), 2)
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manage_permissions, access_permissions = permissions
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self.assertIsInstance(manage_permissions, list)
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self.assertIsInstance(manage_permissions[0], model.DatasetPermissions)
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self.assertEqual(access_permissions, [])
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user3 = self.user_manager.create(**user3_data)
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self.log("a public dataset should be manageable to it's owner")
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self.assertTrue(self.dataset_manager.permissions.manage.is_permitted(dataset, owner))
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self.log("a public dataset shouldn't be manageable to just anyone")
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self.assertFalse(self.dataset_manager.permissions.manage.is_permitted(dataset, user3))
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self.log("a public dataset should be accessible")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, user3))
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self.log("a public dataset should be manageable by an admin")
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self.assertTrue(self.dataset_manager.permissions.manage.is_permitted(dataset, self.admin_user))
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self.log("a public dataset should be accessible by an admin")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, self.admin_user))
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self.log("a public dataset shouldn't be manageable by an anonymous user")
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self.assertFalse(self.dataset_manager.permissions.manage.is_permitted(dataset, None))
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self.log("a public dataset should be accessible by an anonymous user")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, None))
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def test_create_private_dataset(self):
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self.log("should be able to create a new Dataset and give it private permissions")
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owner = self.user_manager.create(**user2_data)
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owner_private_role = self.user_manager.private_role(owner)
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dataset = self.dataset_manager.create(
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manage_roles=[owner_private_role], access_roles=[owner_private_role])
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permissions = self.dataset_manager.permissions.get(dataset)
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self.assertIsInstance(permissions, tuple)
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self.assertEqual(len(permissions), 2)
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manage_permissions, access_permissions = permissions
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self.assertIsInstance(manage_permissions, list)
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self.assertIsInstance(manage_permissions[0], model.DatasetPermissions)
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self.assertIsInstance(access_permissions, list)
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self.assertIsInstance(access_permissions[0], model.DatasetPermissions)
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self.log("a private dataset should be manageable by it's owner")
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self.assertTrue(self.dataset_manager.permissions.manage.is_permitted(dataset, owner))
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self.log("a private dataset should be accessible to it's owner")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, owner))
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user3 = self.user_manager.create(**user3_data)
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self.log("a private dataset shouldn't be manageable to just anyone")
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self.assertFalse(self.dataset_manager.permissions.manage.is_permitted(dataset, user3))
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self.log("a private dataset shouldn't be accessible to just anyone")
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self.assertFalse(self.dataset_manager.permissions.access.is_permitted(dataset, user3))
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self.log("a private dataset should be manageable by an admin")
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self.assertTrue(self.dataset_manager.permissions.manage.is_permitted(dataset, self.admin_user))
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self.log("a private dataset should be accessible by an admin")
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self.assertTrue(self.dataset_manager.permissions.access.is_permitted(dataset, self.admin_user))
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self.log("a private dataset shouldn't be manageable by an anonymous user")
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self.assertFalse(self.dataset_manager.permissions.manage.is_permitted(dataset, None))
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self.log("a private dataset shouldn't be accessible by an anonymous user")
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self.assertFalse(self.dataset_manager.permissions.access.is_permitted(dataset, None))
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# =============================================================================
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class DatasetRBACPermissionsTestCase(BaseTestCase):
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def set_up_managers(self):
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super(DatasetRBACPermissionsTestCase, self).set_up_managers()
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self.dataset_manager = DatasetManager(self.app)
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# def test_manage( self ):
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# self.log( "should be able to create a new Dataset" )
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# dataset1 = self.dataset_manager.create()
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# self.assertIsInstance( dataset1, model.Dataset )
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# self.assertEqual( dataset1, self.app.model.context.query( model.Dataset ).get( dataset1.id ) )
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#
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# =============================================================================
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# web.url_for doesn't work well in the framework
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def testable_url_for(*a, **k):
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return '(fake url): %s, %s' % (a, k)
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DatasetSerializer.url_for = staticmethod(testable_url_for)
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class DatasetSerializerTestCase(BaseTestCase):
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def set_up_managers(self):
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super(DatasetSerializerTestCase, self).set_up_managers()
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self.dataset_manager = DatasetManager(self.app)
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self.dataset_serializer = DatasetSerializer(self.app)
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self.role_manager = RoleManager(self.app)
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def test_views(self):
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dataset = self.dataset_manager.create()
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self.log('should have a summary view')
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summary_view = self.dataset_serializer.serialize_to_view(dataset, view='summary')
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self.assertKeys(summary_view, self.dataset_serializer.views['summary'])
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self.log('should have the summary view as default view')
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self.dataset_serializer.serialize_to_view(dataset, default_view='summary')
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self.assertKeys(summary_view, self.dataset_serializer.views['summary'])
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self.log('should have a serializer for all serializable keys')
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for key in self.dataset_serializer.serializable_keyset:
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instantiated_attribute = getattr(dataset, key, None)
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if not ((key in self.dataset_serializer.serializers) or
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(isinstance(instantiated_attribute, self.TYPES_NEEDING_NO_SERIALIZERS))):
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self.fail('no serializer for: %s (%s)' % (key, instantiated_attribute))
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else:
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self.assertTrue(True, 'all serializable keys have a serializer')
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def test_views_and_keys(self):
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dataset = self.dataset_manager.create()
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self.log('should be able to use keys with views')
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serialized = self.dataset_serializer.serialize_to_view(dataset,
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# file_name is exposed using app.config.expose_dataset_path = True
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view='summary', keys=['file_name'])
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self.assertKeys(serialized,
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self.dataset_serializer.views['summary'] + ['file_name'])
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self.log('should be able to use keys on their own')
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serialized = self.dataset_serializer.serialize_to_view(dataset,
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keys=['purgable', 'file_size'])
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self.assertKeys(serialized, ['purgable', 'file_size'])
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def test_serialize_permissions(self):
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dataset = self.dataset_manager.create()
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who_manages = self.user_manager.create(**user2_data)
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self.dataset_manager.permissions.manage.grant(dataset, who_manages)
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self.log('serialized permissions should be returned for the user who can manage and be well formed')
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permissions = self.dataset_serializer.serialize_permissions(dataset, 'perms', user=who_manages)
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self.assertIsInstance(permissions, dict)
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self.assertKeys(permissions, ['manage', 'access'])
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self.assertIsInstance(permissions['manage'], list)
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self.assertIsInstance(permissions['access'], list)
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manage_perms = permissions['manage']
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self.assertTrue(len(manage_perms) == 1)
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role_id = manage_perms[0]
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self.assertEncodedId(role_id)
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role_id = self.app.security.decode_id(role_id)
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role = self.role_manager.get(self.trans, role_id)
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self.assertTrue(who_manages in [user_role.user for user_role in role.users])
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self.log('permissions should be not returned for non-managing users')
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not_my_supervisor = self.user_manager.create(**user3_data)
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self.assertRaises(SkipAttribute, self.dataset_serializer.serialize_permissions,
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dataset, 'perms', user=not_my_supervisor)
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self.log('permissions should not be returned for anon users')
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self.assertRaises(SkipAttribute, self.dataset_serializer.serialize_permissions,
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dataset, 'perms', user=None)
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self.log('permissions should be returned for admin users')
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permissions = self.dataset_serializer.serialize_permissions(dataset, 'perms', user=self.admin_user)
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self.assertIsInstance(permissions, dict)
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self.assertKeys(permissions, ['manage', 'access'])
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def test_serializers(self):
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# self.user_manager.create( **user2_data )
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dataset = self.dataset_manager.create()
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all_keys = list(self.dataset_serializer.serializable_keyset)
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serialized = self.dataset_serializer.serialize(dataset, all_keys)
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self.log('everything serialized should be of the proper type')
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self.assertEncodedId(serialized['id'])
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self.assertDate(serialized['create_time'])
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self.assertDate(serialized['update_time'])
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self.assertUUID(serialized['uuid'])
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self.assertIsInstance(serialized['state'], string_types)
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self.assertIsInstance(serialized['deleted'], bool)
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self.assertIsInstance(serialized['purged'], bool)
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self.assertIsInstance(serialized['purgable'], bool)
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# # TODO: no great way to do these with mocked dataset
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# self.assertIsInstance( serialized[ 'file_size' ], int )
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# self.assertIsInstance( serialized[ 'total_size' ], int )
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self.log('serialized should jsonify well')
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self.assertIsJsonifyable(serialized)
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# =============================================================================
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class DatasetDeserializerTestCase(BaseTestCase):
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def set_up_managers(self):
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super(DatasetDeserializerTestCase, self).set_up_managers()
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self.dataset_manager = DatasetManager(self.app)
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self.dataset_serializer = DatasetSerializer(self.app)
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self.dataset_deserializer = DatasetDeserializer(self.app)
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self.role_manager = RoleManager(self.app)
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def test_deserialize_delete(self):
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dataset = self.dataset_manager.create()
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self.log('should raise when deserializing deleted from non-bool')
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self.assertFalse(dataset.deleted)
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self.assertRaises(exceptions.RequestParameterInvalidException,
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self.dataset_deserializer.deserialize, dataset, data={'deleted': None})
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self.assertFalse(dataset.deleted)
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self.log('should be able to deserialize deleted from True')
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self.dataset_deserializer.deserialize(dataset, data={'deleted': True})
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self.assertTrue(dataset.deleted)
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self.log('should be able to reverse by deserializing deleted from False')
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self.dataset_deserializer.deserialize(dataset, data={'deleted': False})
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self.assertFalse(dataset.deleted)
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def test_deserialize_purge(self):
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dataset = self.dataset_manager.create()
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self.log('should raise when deserializing purged from non-bool')
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self.assertRaises(exceptions.RequestParameterInvalidException,
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self.dataset_deserializer.deserialize, dataset, data={'purged': None})
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self.assertFalse(dataset.purged)
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self.log('should be able to deserialize purged from True')
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self.dataset_deserializer.deserialize(dataset, data={'purged': True})
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self.assertTrue(dataset.purged)
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# TODO: should this raise an error?
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self.log('should NOT be able to deserialize purged from False (will remain True)')
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self.dataset_deserializer.deserialize(dataset, data={'purged': False})
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self.assertTrue(dataset.purged)
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def test_deserialize_permissions(self):
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dataset = self.dataset_manager.create()
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who_manages = self.user_manager.create(**user2_data)
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self.dataset_manager.permissions.manage.grant(dataset, who_manages)
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existing_permissions = self.dataset_serializer.serialize_permissions(dataset, 'permissions', user=who_manages)
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existing_manage_permissions = existing_permissions['manage']
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user3 = self.user_manager.create(**user3_data)
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self.log('deserializing permissions from a non-dictionary should error')
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not_a_dict = []
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self.assertRaises(exceptions.RequestParameterInvalidException, self.dataset_deserializer.deserialize,
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dataset, user=who_manages, data={'permissions': not_a_dict})
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self.log('deserializing permissions from a malformed dictionary should error')
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self.assertRaises(exceptions.RequestParameterInvalidException, self.dataset_deserializer.deserialize,
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dataset, user=who_manages, data={'permissions': dict(nope=[], access=[])})
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self.log('deserializing permissions with no manage roles should error')
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self.assertRaises(exceptions.RequestParameterInvalidException, self.dataset_deserializer.deserialize,
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dataset, user=who_manages, data={'permissions': dict(manage=[], access=[])})
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self.log('deserializing permissions using a non-managing user should error')
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self.assertRaises(rbac_secured.DatasetManagePermissionFailedException, self.dataset_deserializer.deserialize,
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dataset, user=user3, data={'permissions': existing_permissions})
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self.log('deserializing permissions using an anon user should error')
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self.assertRaises(rbac_secured.DatasetManagePermissionFailedException, self.dataset_deserializer.deserialize,
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dataset, user=None, data={'permissions': existing_permissions})
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self.log('deserializing permissions with a single access should make the dataset private')
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private_role = self.user_manager.private_role(who_manages)
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private_role = private_role.to_dict(value_mapper={'id': self.app.security.encode_id})
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permissions = dict(manage=existing_manage_permissions, access=[private_role['id']])
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self.dataset_deserializer.deserialize(dataset, user=who_manages, data={
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'permissions': permissions
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})
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self.assertFalse(self.dataset_manager.is_accessible(dataset, user=user3))
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self.log('deserializing permissions manage should make the permissions available')
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self.assertRaises(SkipAttribute, self.dataset_serializer.serialize_permissions,
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dataset, 'perms', user=user3)
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# now, have who_manages give a manage permission to user3
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private_role = self.user_manager.private_role(user3)
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new_manage_permissions = existing_manage_permissions + [self.app.security.encode_id(private_role.id)]
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permissions = dict(manage=new_manage_permissions, access=[])
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|
self.dataset_deserializer.deserialize(dataset, user=who_manages, data={
|
|
'permissions': permissions
|
|
})
|
|
|
|
# deserializing for user3 shouldn't throw a skip bc they can manage
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|
permissions = self.dataset_serializer.serialize_permissions(dataset, 'perms', user=who_manages)
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|
self.assertEqual(new_manage_permissions, permissions['manage'])
|
|
|
|
def test_deserialize_permissions_with_admin(self):
|
|
dataset = self.dataset_manager.create()
|
|
who_manages = self.user_manager.create(**user2_data)
|
|
self.dataset_manager.permissions.manage.grant(dataset, who_manages)
|
|
existing_permissions = self.dataset_serializer.serialize_permissions(dataset, 'permissions', user=who_manages)
|
|
existing_manage_permissions = existing_permissions['manage']
|
|
|
|
user3 = self.user_manager.create(**user3_data)
|
|
self.assertRaises(rbac_secured.DatasetManagePermissionFailedException, self.dataset_deserializer.deserialize,
|
|
dataset, user=user3, data={'permissions': existing_permissions})
|
|
|
|
self.log('deserializing permissions using an admin user should not error')
|
|
private_role = self.user_manager.private_role(who_manages)
|
|
private_role = private_role.to_dict(value_mapper={'id' : self.app.security.encode_id})
|
|
permissions = dict(manage=existing_manage_permissions, access=[private_role['id']])
|
|
self.dataset_deserializer.deserialize(dataset, user=who_manages, data={
|
|
'permissions': permissions
|
|
})
|
|
|
|
self.assertRaises(rbac_secured.DatasetManagePermissionFailedException, self.dataset_deserializer.deserialize,
|
|
dataset, user=user3, data={'permissions': existing_permissions})
|
|
|
|
|
|
# =============================================================================
|
|
# NOTE: that we test the DatasetAssociation* classes in either test_HDAManager or test_LDAManager
|
|
# (as part of those subclasses):
|
|
# DatasetAssociationManager,
|
|
# DatasetAssociationSerializer,
|
|
# DatasetAssociationDeserializer,
|
|
# DatasetAssociationFilterParser
|
|
|
|
# =============================================================================
|
|
if __name__ == '__main__':
|
|
# or more generally, nosetests test_resourcemanagers.py -s -v
|
|
unittest.main()
|