def test_preprocess_task_for_model(self): task = FITBTask.from_gml_files(self.test_gml_files) task_filepath = os.path.join(self.output_dataset_dir, 'FITBTask.pkl') task.save(task_filepath) FITBClosedVocab.preprocess_task( task=task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder='new', data_encoder_kwargs=dict(), instance_to_datapoints_kwargs=dict(max_nodes_per_graph=100)) self.assertNotIn( 'jobs.txt', os.listdir(self.output_dataset_dir), "The jobs.txt file from process_graph_to_datapoints_with_xargs didn't get deleted" ) self.assertTrue( all(len(i) > 10 for i in os.listdir(self.output_dataset_dir)), "Hacky check for if pickled jobs didn't get deleted") reencoding_dir = os.path.join(self.output_dataset_dir, 're-encoding') os.mkdir(reencoding_dir) data_encoder = FITBClosedVocab.DataEncoder.load( os.path.join(self.output_dataset_dir, 'FITBClosedVocabDataEncoder.pkl')) self.assertCountEqual( data_encoder.all_edge_types, list(all_edge_types) + ['reverse_{}'.format(i) for i in all_edge_types], "DataEncoder found weird edge types") FITBClosedVocab.preprocess_task(task=task, output_dir=reencoding_dir, n_jobs=30, data_encoder=data_encoder) orig_datapoints = [] for file in os.listdir(self.output_dataset_dir): if file not in [ 'FITBClosedVocabDataEncoder.pkl', 'FITBTask.pkl', 're-encoding' ]: with open(os.path.join(self.output_dataset_dir, file), 'rb') as f: dp = pickle.load(f) self.assertCountEqual( dp.edges.keys(), list(all_edge_types) + ['reverse_{}'.format(i) for i in all_edge_types], 'We lost some edge types') orig_datapoints.append( (dp.node_types, dp.node_names, dp.label, dp.origin_file, dp.encoder_hash, dp.edges.keys())) reencoded_datapoints = [] for file in os.listdir(reencoding_dir): with open(os.path.join(reencoding_dir, file), 'rb') as f: dp = pickle.load(f) reencoded_datapoints.append( (dp.node_types, dp.node_names, dp.label, dp.origin_file, dp.encoder_hash, dp.edges.keys())) self.assertCountEqual(orig_datapoints, reencoded_datapoints)
def test_encode(self): de = FITBClosedVocabDataEncoder(self.task.graphs_and_instances, excluded_edge_types=frozenset(), instance_to_datapoints_kwargs=dict()) for graph, instances in self.task.graphs_and_instances: graph, instances = FITBClosedVocab.extra_graph_processing( graph, instances, de) for instance in tqdm(instances): dporig = FITBClosedVocab.instance_to_datapoint( graph, instance, de, max_nodes_per_graph=50) dp = deepcopy(dporig) de.encode(dp) self.assertEqual(list(dp.edges.keys()), sorted(list(de.all_edge_types)), "Not all adjacency matrices were created") for edge_type, adj_mat in dp.edges.items(): np.testing.assert_equal( adj_mat.todense(), dporig.subgraph.get_adjacency_matrix( edge_type).todense()) self.assertIsInstance( adj_mat, sp.sparse.coo_matrix, "Encoding produces adjacency matrix of wrong type") self.assertEqual( len(dporig.node_types), len(dp.node_types), "Type for some node got lost during encoding") self.assertEqual( [len(i) for i in dporig.node_types], [len(i) for i in dp.node_types], "Some type for some node got lost during encoding") for i in range(len(dp.node_types)): for j in range(len(dp.node_types[i])): self.assertEqual( dp.node_types[i][j], de.all_node_types[dporig.node_types[i][j]], "Some node type got encoded wrong") self.assertEqual( len(dporig.node_names), len(dp.node_names), "Name for some node got lost during encoding") self.assertEqual([len(i) for i in dporig.node_names], [ len(i) for i in dp.node_names ], "Some name subtoken for some node got lost during encoding") for i in range(len(dp.node_names)): for j in range(len(dp.node_names[i])): self.assertEqual( dp.node_names[i][j], de.all_node_name_subtokens[ dporig.node_names[i][j]], "Some node name got encoded wrong") self.assertEqual(tuple(dporig.label), dp.label)
def test_preprocess_task_existing_encoding_basic_functionality(self): FITBClosedVocab.preprocess_task( self.task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder='new', data_encoder_kwargs=dict(), instance_to_datapoints_kwargs=dict(max_nodes_per_graph=20)) de = FITBClosedVocabDataEncoder.load( os.path.join(self.output_dataset_dir, '{}.pkl'.format(FITBClosedVocabDataEncoder.__name__))) FITBClosedVocab.preprocess_task( self.task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder=de, instance_to_datapoints_kwargs=dict(max_nodes_per_graph=20)) with self.assertRaises(AssertionError): de = BaseDataEncoder(dict(), frozenset()) FITBClosedVocab.preprocess_task( self.task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder=de, instance_to_datapoints_kwargs=dict(max_nodes_per_graph=20))
def test_batchify_and_unbatchify_are_inverses(self): FITBClosedVocab.preprocess_task( self.task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder='new', data_encoder_kwargs=dict(), instance_to_datapoints_kwargs=dict(max_nodes_per_graph=20)) with open( os.path.join( self.output_dataset_dir, '{}.pkl'.format(FITBClosedVocab.DataEncoder.__name__)), 'rb') as f: de = pickle.load(f) model = FITBClosedVocabGGNN(data_encoder=de, hidden_size=17, type_emb_size=5, name_emb_size=7, n_msg_pass_iters=1) model.collect_params().initialize('Xavier', ctx=mx.cpu()) datapoints = [ os.path.join(self.output_dataset_dir, i) for i in os.listdir(self.output_dataset_dir) if 'Encoder.pkl' not in i ] batch_size = 64 for b in tqdm(range(int(math.ceil(len(datapoints) / batch_size)))): batchdpspaths = datapoints[batch_size * b:batch_size * (b + 1)] batchdps = [de.load_datapoint(b) for b in batchdpspaths] batchified = model.batchify(batchdpspaths, ctx=mx.cpu()) unbatchified = model.unbatchify(batchified, model(batchified.data)) self.assertEqual(len(batchdps), len(unbatchified), "We lost some datapoints somewhere") self.assertEqual(sum(len(dp.node_names) for dp in batchdps), sum(batchified.data.batch_sizes).asscalar()) self.assertEqual(sum(len(dp.node_types) for dp in batchdps), sum(batchified.data.batch_sizes).asscalar()) for adj_mat in batchified.data.edges.values(): self.assertEqual(adj_mat.shape, (sum(len(dp.node_names) for dp in batchdps), sum(len(dp.node_names) for dp in batchdps)), "Batchified adjacency matrix is wrong size") for i, (dp, (prediction, label)) in enumerate(zip(batchdps, unbatchified)): self.assertEqual( len(dp.node_types), len(dp.node_names), "node_types and node_names arrays are different lengths") self.assertEqual( len(dp.node_types), batchified.data.batch_sizes[i], "batch_sizes doesn't match datapoint's array size") self.assertEqual( prediction.shape, label.shape, "Prediction and one-hot label don't match size") self.assertEqual( sum(prediction), 1, "Made more than one prediction for this datapoint") for j in range(len(label)): if j in dp.label: self.assertEqual(label[j], 1, "Something didn't get one-hotted") else: self.assertEqual( label[j], 0, "Something got one-hotted that shouldn't have")
def test_instance_to_datapoint(self): for excluded_edge_types in [ syntax_only_excluded_edge_types, frozenset() ]: de = FITBClosedVocab.DataEncoder( self.task.graphs_and_instances, excluded_edge_types=excluded_edge_types, instance_to_datapoints_kwargs=dict()) for graph, instances in tqdm(self.task.graphs_and_instances): FITBClosedVocab.fix_up_edges(graph, instances, excluded_edge_types) FITBClosedVocab.extra_graph_processing(graph, instances, de) for instance in instances: dp = FITBClosedVocab.instance_to_datapoint( graph, instance, de, max_nodes_per_graph=100) self.assertEqual(type(dp), FITBClosedVocabDataPoint) self.assertEqual(len(dp.subgraph.nodes), len(dp.node_types)) self.assertEqual(len(dp.subgraph.nodes), len(dp.node_names)) fill_in_nodes = [ i for i in dp.subgraph.nodes_that_represent_variables if i[1]['identifier'] == de.fill_in_flag ] self.assertEqual( len(fill_in_nodes), 1, "Zero or more than one variable got flagged") fill_in_idx = fill_in_nodes[0][0] self.assertEqual(dp.node_names[fill_in_idx], [de.fill_in_flag], "Variable flagged wrong") self.assertEqual(dp.node_types[fill_in_idx], [de.fill_in_flag], "Variable flagged wrong") self.assertEqual( len([ i for i in dp.node_names if i == [de.fill_in_flag] ]), 1, "Zero or more than one variable got flagged") self.assertEqual( len([ i for i in dp.node_types if i == [de.fill_in_flag] ]), 1, "Zero of more than one variable got flagged") for et in too_useful_edge_types: self.assertNotIn(et, [ e[3]['type'] for e in dp.subgraph.all_adjacent_edges(fill_in_idx) ]) self.assertEqual( len(instance[1]), len([ n for n, d in dp.subgraph.nodes if 'other_use' in d.keys() and d['other_use'] == True ]), "Wrong number of other uses in label") for i, (names, types) in enumerate( zip(dp.node_names, dp.node_types)): self.assertEqual(type(names), list) self.assertGreaterEqual(len(names), 1) self.assertEqual(type(types), list) self.assertGreaterEqual(len(types), 1) if dp.subgraph.is_variable_node( i) and names != [de.fill_in_flag]: self.assertCountEqual( set( re.split(r'[,.]', dp.subgraph[i]['reference'])), types) for name in names: self.assertIn( name, dp.subgraph[i]['identifier'].lower()) else: self.assertEqual(len(names), 1) self.assertEqual(len(types), 1) for i in dp.label: del dp.subgraph[i]['other_use'] self.assertCountEqual([dp.subgraph[i] for i in dp.label], [graph[i] for i in instance[1]]) de.encode(dp) self.assertIn('AST', dp.edges.keys()) self.assertIn('NEXT_TOKEN', dp.edges.keys()) de.save_datapoint(dp, self.output_dataset_dir)
def test_preprocess_task_type_check_basic_functionality(self): task = Task with self.assertRaises(AssertionError): FITBClosedVocab.preprocess_task(task)