示例#1
0
文件: tasks.py 项目: msauria/galaxy
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)
示例#2
0
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)
示例#3
0
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 )
示例#4
0
文件: tasks.py 项目: mvdbeek/galaxy
def purge_hda(hda_manager: HDAManager, hda_id):
    hda = hda_manager.by_id(hda_id)
    hda_manager._purge(hda)