def set_metadata(hda_manager: HDAManager,
ldda_manager: LDDAManager,
dataset_id,
model_class='HistoryDatasetAssociation'):
if model_class == 'HistoryDatasetAssociation':
dataset = hda_manager.by_id(dataset_id)
elif model_class == 'LibraryDatasetDatasetAssociation':
dataset = ldda_manager.by_id(dataset_id)
dataset.datatype.set_meta(dataset)
class HDAManagerTestCase(BaseTestCase):
def set_up_managers(self):
super(HDAManagerTestCase, self).set_up_managers()
self.history_mgr = HistoryManager(self.app)
self.dataset_mgr = DatasetManager(self.app)
self.hda_mgr = HDAManager(self.app)
def test_base(self):
hda_model = model.HistoryDatasetAssociation
owner = self.user_mgr.create(self.trans, **user2_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
hda1 = self.hda_mgr.create(self.trans, history=history1, hid=1)
hda2 = self.hda_mgr.create(self.trans, history=history1, hid=2)
hda3 = self.hda_mgr.create(self.trans, history=history1, hid=3)
self.log("should be able to query")
hdas = self.trans.sa_session.query(hda_model).all()
self.assertEqual(self.hda_mgr.list(self.trans), hdas)
self.assertEqual(
self.hda_mgr.one(self.trans, filters=(hda_model.id == hda1.id)),
hda1)
self.assertEqual(self.hda_mgr.by_id(self.trans, hda1.id), hda1)
self.assertEqual(self.hda_mgr.by_ids(self.trans, [hda2.id, hda1.id]),
[hda2, hda1])
self.log("should be able to limit and offset")
self.assertEqual(self.hda_mgr.list(self.trans, limit=1), hdas[0:1])
self.assertEqual(self.hda_mgr.list(self.trans, offset=1), hdas[1:])
self.assertEqual(self.hda_mgr.list(self.trans, limit=1, offset=1),
hdas[1:2])
self.assertEqual(self.hda_mgr.list(self.trans, limit=0), [])
self.assertEqual(self.hda_mgr.list(self.trans, offset=3), [])
self.log("should be able to order")
self.assertEqual(
self.hda_mgr.list(self.trans,
order_by=sqlalchemy.desc(hda_model.create_time)),
[hda3, hda2, hda1])
def test_create(self):
owner = self.user_mgr.create(self.trans, **user2_data)
non_owner = self.user_mgr.create(self.trans, **user3_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
self.log(
"should be able to create a new HDA with a specified history and dataset"
)
hda1 = self.hda_mgr.create(self.trans,
history=history1,
dataset=dataset1)
self.assertIsInstance(hda1, model.HistoryDatasetAssociation)
self.assertEqual(
hda1,
self.trans.sa_session.query(model.HistoryDatasetAssociation).get(
hda1.id))
self.assertEqual(hda1.history, history1)
self.assertEqual(hda1.dataset, dataset1)
self.assertEqual(hda1.hid, 1)
self.log(
"should be able to create a new HDA with only a specified history and no dataset"
)
hda2 = self.hda_mgr.create(self.trans, history=history1)
self.assertIsInstance(hda2, model.HistoryDatasetAssociation)
self.assertIsInstance(hda2.dataset, model.Dataset)
self.assertEqual(hda2.history, history1)
self.assertEqual(hda2.hid, 2)
self.log(
"should be able to create a new HDA with no history and no dataset"
)
hda3 = self.hda_mgr.create(self.trans, hid=None)
self.assertIsInstance(hda3, model.HistoryDatasetAssociation)
self.assertIsInstance(hda3.dataset,
model.Dataset,
msg="dataset will be auto created")
self.assertIsNone(hda3.history, msg="history will be None")
self.assertEqual(
hda3.hid,
None,
msg="should allow setting hid to None (or any other value)")
def test_copy_from_hda(self):
owner = self.user_mgr.create(self.trans, **user2_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
hda1 = self.hda_mgr.create(self.trans,
history=history1,
dataset=dataset1)
self.log("should be able to copy an HDA")
hda2 = self.hda_mgr.copy(self.trans, hda1, history=history1)
self.assertIsInstance(hda2, model.HistoryDatasetAssociation)
self.assertEqual(
hda2,
self.trans.sa_session.query(model.HistoryDatasetAssociation).get(
hda2.id))
self.assertEqual(hda2.name, hda1.name)
self.assertEqual(hda2.history, hda1.history)
self.assertEqual(hda2.dataset, hda1.dataset)
self.assertNotEqual(hda2, hda1)
#def test_copy_from_ldda( self ):
# owner = self.user_mgr.create( self.trans, **user2_data )
# history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
#
# self.log( "should be able to copy an HDA" )
# hda2 = self.hda_mgr.copy_ldda( self.trans, history1, hda1 )
def test_delete(self):
owner = self.user_mgr.create(self.trans, **user2_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
item1 = self.hda_mgr.create(self.trans,
history=history1,
dataset=dataset1)
self.log("should be able to delete and undelete an hda")
self.assertFalse(item1.deleted)
self.assertEqual(self.hda_mgr.delete(self.trans, item1), item1)
self.assertTrue(item1.deleted)
self.assertEqual(self.hda_mgr.undelete(self.trans, item1), item1)
self.assertFalse(item1.deleted)
def test_purge_allowed(self):
self.trans.app.config.allow_user_dataset_purge = True
owner = self.user_mgr.create(self.trans, **user2_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
item1 = self.hda_mgr.create(self.trans,
history=history1,
dataset=dataset1)
self.log("should purge an hda if config does allow")
self.assertFalse(item1.purged)
self.assertEqual(self.hda_mgr.purge(self.trans, item1), item1)
self.assertTrue(item1.purged)
def test_purge_not_allowed(self):
self.trans.app.config.allow_user_dataset_purge = False
owner = self.user_mgr.create(self.trans, **user2_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
item1 = self.hda_mgr.create(self.trans,
history=history1,
dataset=dataset1)
self.log(
"should raise an error when purging an hda if config does not allow"
)
self.assertFalse(item1.purged)
self.assertRaises(exceptions.ConfigDoesNotAllowException,
self.hda_mgr.purge, self.trans, item1)
self.assertFalse(item1.purged)
def test_ownable(self):
owner = self.user_mgr.create(self.trans, **user2_data)
non_owner = self.user_mgr.create(self.trans, **user3_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
item1 = self.hda_mgr.create(self.trans, history1, dataset1)
self.log("should be able to poll whether a given user owns an item")
self.assertTrue(self.hda_mgr.is_owner(self.trans, item1, owner))
self.assertFalse(self.hda_mgr.is_owner(self.trans, item1, non_owner))
self.log(
"should raise an error when checking ownership with non-owner")
self.assertRaises(exceptions.ItemOwnershipException,
self.hda_mgr.error_unless_owner, self.trans, item1,
non_owner)
self.log(
"should raise an error when checking ownership with anonymous")
self.assertRaises(exceptions.ItemOwnershipException,
self.hda_mgr.error_unless_owner, self.trans, item1,
None)
self.log(
"should not raise an error when checking ownership with owner")
self.assertEqual(
self.hda_mgr.error_unless_owner(self.trans, item1, owner), item1)
self.log(
"should not raise an error when checking ownership with admin")
self.assertEqual(
self.hda_mgr.error_unless_owner(self.trans, item1,
self.admin_user), item1)
def test_accessible(self):
owner = self.user_mgr.create(self.trans, **user2_data)
non_owner = self.user_mgr.create(self.trans, **user3_data)
history1 = self.history_mgr.create(self.trans,
name='history1',
user=owner)
dataset1 = self.dataset_mgr.create(self.trans)
item1 = self.hda_mgr.create(self.trans, history1, dataset1)
self.log(
"(by default, dataset permissions are lax) should be accessible to all"
)
for user in self.user_mgr.list(self.trans):
self.assertTrue(self.hda_mgr.is_accessible(self.trans, item1,
user))
#TODO: set perms on underlying dataset and then test accessible
def test_anon(self):
anon_user = None
self.trans.set_user(anon_user)
history1 = self.history_mgr.create(self.trans,
name='anon_history',
user=anon_user)
self.trans.set_history(history1)
dataset1 = self.dataset_mgr.create(self.trans)
item1 = self.hda_mgr.create(self.trans, history1, dataset1)
self.log(
"should not raise an error when checking ownership/access on anonymous' own dataset"
)
self.assertTrue(
self.hda_mgr.is_accessible(self.trans, item1, anon_user))
self.assertEqual(
self.hda_mgr.error_unless_owner(self.trans, item1, anon_user),
item1)
self.log(
"should raise an error when checking ownership on anonymous' dataset with other user"
)
non_owner = self.user_mgr.create(self.trans, **user3_data)
self.assertRaises(exceptions.ItemOwnershipException,
self.hda_mgr.error_unless_owner, self.trans, item1,
non_owner)
class HDAManagerTestCase( BaseTestCase ):
def set_up_managers( self ):
super( HDAManagerTestCase, self ).set_up_managers()
self.history_mgr = HistoryManager( self.app )
self.dataset_mgr = DatasetManager( self.app )
self.hda_mgr = HDAManager( self.app )
def test_base( self ):
hda_model = model.HistoryDatasetAssociation
owner = self.user_mgr.create( self.trans, **user2_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
hda1 = self.hda_mgr.create( self.trans, history=history1, hid=1 )
hda2 = self.hda_mgr.create( self.trans, history=history1, hid=2 )
hda3 = self.hda_mgr.create( self.trans, history=history1, hid=3 )
self.log( "should be able to query" )
hdas = self.trans.sa_session.query( hda_model ).all()
self.assertEqual( self.hda_mgr.list( self.trans ), hdas )
self.assertEqual( self.hda_mgr.one( self.trans, filters=( hda_model.id == hda1.id ) ), hda1 )
self.assertEqual( self.hda_mgr.by_id( self.trans, hda1.id ), hda1 )
self.assertEqual( self.hda_mgr.by_ids( self.trans, [ hda2.id, hda1.id ] ), [ hda2, hda1 ] )
self.log( "should be able to limit and offset" )
self.assertEqual( self.hda_mgr.list( self.trans, limit=1 ), hdas[0:1] )
self.assertEqual( self.hda_mgr.list( self.trans, offset=1 ), hdas[1:] )
self.assertEqual( self.hda_mgr.list( self.trans, limit=1, offset=1 ), hdas[1:2] )
self.assertEqual( self.hda_mgr.list( self.trans, limit=0 ), [] )
self.assertEqual( self.hda_mgr.list( self.trans, offset=3 ), [] )
self.log( "should be able to order" )
self.assertEqual( self.hda_mgr.list( self.trans, order_by=sqlalchemy.desc( hda_model.create_time ) ),
[ hda3, hda2, hda1 ] )
def test_create( self ):
owner = self.user_mgr.create( self.trans, **user2_data )
non_owner = self.user_mgr.create( self.trans, **user3_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
self.log( "should be able to create a new HDA with a specified history and dataset" )
hda1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
self.assertIsInstance( hda1, model.HistoryDatasetAssociation )
self.assertEqual( hda1, self.trans.sa_session.query( model.HistoryDatasetAssociation ).get( hda1.id ) )
self.assertEqual( hda1.history, history1 )
self.assertEqual( hda1.dataset, dataset1 )
self.assertEqual( hda1.hid, 1 )
self.log( "should be able to create a new HDA with only a specified history and no dataset" )
hda2 = self.hda_mgr.create( self.trans, history=history1 )
self.assertIsInstance( hda2, model.HistoryDatasetAssociation )
self.assertIsInstance( hda2.dataset, model.Dataset )
self.assertEqual( hda2.history, history1 )
self.assertEqual( hda2.hid, 2 )
self.log( "should be able to create a new HDA with no history and no dataset" )
hda3 = self.hda_mgr.create( self.trans, hid=None )
self.assertIsInstance( hda3, model.HistoryDatasetAssociation )
self.assertIsInstance( hda3.dataset, model.Dataset, msg="dataset will be auto created" )
self.assertIsNone( hda3.history, msg="history will be None" )
self.assertEqual( hda3.hid, None, msg="should allow setting hid to None (or any other value)" )
def test_copy_from_hda( self ):
owner = self.user_mgr.create( self.trans, **user2_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
hda1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
self.log( "should be able to copy an HDA" )
hda2 = self.hda_mgr.copy( self.trans, hda1, history=history1 )
self.assertIsInstance( hda2, model.HistoryDatasetAssociation )
self.assertEqual( hda2, self.trans.sa_session.query( model.HistoryDatasetAssociation ).get( hda2.id ) )
self.assertEqual( hda2.name, hda1.name )
self.assertEqual( hda2.history, hda1.history )
self.assertEqual( hda2.dataset, hda1.dataset )
self.assertNotEqual( hda2, hda1 )
#def test_copy_from_ldda( self ):
# owner = self.user_mgr.create( self.trans, **user2_data )
# history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
#
# self.log( "should be able to copy an HDA" )
# hda2 = self.hda_mgr.copy_ldda( self.trans, history1, hda1 )
def test_delete( self ):
owner = self.user_mgr.create( self.trans, **user2_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
item1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
self.log( "should be able to delete and undelete an hda" )
self.assertFalse( item1.deleted )
self.assertEqual( self.hda_mgr.delete( self.trans, item1 ), item1 )
self.assertTrue( item1.deleted )
self.assertEqual( self.hda_mgr.undelete( self.trans, item1 ), item1 )
self.assertFalse( item1.deleted )
def test_purge_allowed( self ):
self.trans.app.config.allow_user_dataset_purge = True
owner = self.user_mgr.create( self.trans, **user2_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
item1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
self.log( "should purge an hda if config does allow" )
self.assertFalse( item1.purged )
self.assertEqual( self.hda_mgr.purge( self.trans, item1 ), item1 )
self.assertTrue( item1.purged )
def test_purge_not_allowed( self ):
self.trans.app.config.allow_user_dataset_purge = False
owner = self.user_mgr.create( self.trans, **user2_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
item1 = self.hda_mgr.create( self.trans, history=history1, dataset=dataset1 )
self.log( "should raise an error when purging an hda if config does not allow" )
self.assertFalse( item1.purged )
self.assertRaises( exceptions.ConfigDoesNotAllowException, self.hda_mgr.purge, self.trans, item1 )
self.assertFalse( item1.purged )
def test_ownable( self ):
owner = self.user_mgr.create( self.trans, **user2_data )
non_owner = self.user_mgr.create( self.trans, **user3_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
item1 = self.hda_mgr.create( self.trans, history1, dataset1 )
self.log( "should be able to poll whether a given user owns an item" )
self.assertTrue( self.hda_mgr.is_owner( self.trans, item1, owner ) )
self.assertFalse( self.hda_mgr.is_owner( self.trans, item1, non_owner ) )
self.log( "should raise an error when checking ownership with non-owner" )
self.assertRaises( exceptions.ItemOwnershipException,
self.hda_mgr.error_unless_owner, self.trans, item1, non_owner )
self.log( "should raise an error when checking ownership with anonymous" )
self.assertRaises( exceptions.ItemOwnershipException,
self.hda_mgr.error_unless_owner, self.trans, item1, None )
self.log( "should not raise an error when checking ownership with owner" )
self.assertEqual( self.hda_mgr.error_unless_owner( self.trans, item1, owner ), item1 )
self.log( "should not raise an error when checking ownership with admin" )
self.assertEqual( self.hda_mgr.error_unless_owner( self.trans, item1, self.admin_user ), item1 )
def test_accessible( self ):
owner = self.user_mgr.create( self.trans, **user2_data )
non_owner = self.user_mgr.create( self.trans, **user3_data )
history1 = self.history_mgr.create( self.trans, name='history1', user=owner )
dataset1 = self.dataset_mgr.create( self.trans )
item1 = self.hda_mgr.create( self.trans, history1, dataset1 )
self.log( "(by default, dataset permissions are lax) should be accessible to all" )
for user in self.user_mgr.list( self.trans ):
self.assertTrue( self.hda_mgr.is_accessible( self.trans, item1, user ) )
#TODO: set perms on underlying dataset and then test accessible
def test_anon( self ):
anon_user = None
self.trans.set_user( anon_user )
history1 = self.history_mgr.create( self.trans, name='anon_history', user=anon_user )
self.trans.set_history( history1 )
dataset1 = self.dataset_mgr.create( self.trans )
item1 = self.hda_mgr.create( self.trans, history1, dataset1 )
self.log( "should not raise an error when checking ownership/access on anonymous' own dataset" )
self.assertTrue( self.hda_mgr.is_accessible( self.trans, item1, anon_user ) )
self.assertEqual( self.hda_mgr.error_unless_owner( self.trans, item1, anon_user ), item1 )
self.log( "should raise an error when checking ownership on anonymous' dataset with other user" )
non_owner = self.user_mgr.create( self.trans, **user3_data )
self.assertRaises( exceptions.ItemOwnershipException,
self.hda_mgr.error_unless_owner, self.trans, item1, non_owner )
def purge_hda(hda_manager: HDAManager, hda_id):
hda = hda_manager.by_id(hda_id)
hda_manager._purge(hda)