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)
FITBGSCVocab.preprocess_task(
task=task,
output_dir=self.output_dataset_dir,
n_jobs=30,
data_encoder='new',
data_encoder_kwargs=dict(
max_name_encoding_length=self.max_name_encoding_length),
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 = FITBGSCVocab.DataEncoder.load(
os.path.join(self.output_dataset_dir,
'FITBGSCVocabDataEncoder.pkl'))
self.assertCountEqual(
data_encoder.all_edge_types,
list(all_edge_types) +
['reverse_{}'.format(i) for i in all_edge_types] +
['SUBTOKEN_USE', 'reverse_SUBTOKEN_USE'],
"DataEncoder found weird edge types")
FITBGSCVocab.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 [
'FITBGSCVocabDataEncoder.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] +
['SUBTOKEN_USE', 'reverse_SUBTOKEN_USE'],
'We lost some edge types')
orig_datapoints.append(
(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.origin_file, dp.encoder_hash, dp.edges.keys()))
self.assertCountEqual(orig_datapoints, reencoded_datapoints)
def test_batchify_and_unbatchify_are_inverses(self):
FITBGSCVocab.preprocess_task(self.task,
output_dir=self.output_dataset_dir,
n_jobs=30,
data_encoder='new',
data_encoder_kwargs=dict(
max_name_encoding_length=self.max_name_encoding_length),
instance_to_datapoints_kwargs=dict(max_nodes_per_graph=20))
with open(os.path.join(self.output_dataset_dir, '{}.pkl'.format(FITBGSCVocab.DataEncoder.__name__)),
'rb') as f:
de = pickle.load(f)
model = FITBGSCVocabGGNN(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[i], 1, "Something didn't get one-hotted")
else:
self.assertEqual(label[i], 0, "Something got one-hotted that shouldn't have")
def test_encode(self):
de = FITBGSCVocabDataEncoder(self.task.graphs_and_instances,
excluded_edge_types=frozenset(),
instance_to_datapoints_kwargs=dict(),
max_name_encoding_length=self.max_name_encoding_length)
for graph, instances in self.task.graphs_and_instances:
FITBGSCVocab.fix_up_edges(graph, instances, frozenset())
FITBGSCVocab.extra_graph_processing(graph, instances, de)
for instance in tqdm(instances):
dporig = FITBGSCVocab.instance_to_datapoint(graph, instance, de, max_nodes_per_graph=50)
dp = deepcopy(dporig)
de.encode(dp)
self.assertCountEqual(list(all_edge_types) + [de.subtoken_edge_type, de.subtoken_reverse_edge_type],
dp.edges.keys())
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")
orig_subtoken_nodes = [i for i, data in dporig.subgraph.nodes if data['type'] == de.subtoken_flag]
dp_subtoken_nodes = [i for i in range(len(dp.node_types)) if
dp.node_types[i] == (de.all_node_types[de.subtoken_flag],)]
self.assertGreater(len(orig_subtoken_nodes), 0)
self.assertEqual(len(orig_subtoken_nodes), len(dp_subtoken_nodes), "Some subtoken nodes got lost")
for i in dp_subtoken_nodes:
self.assertEqual(dp.node_names[i], dporig.subgraph[i]['identifier'],
"Some subtoken node got the wrong name")
self.assertEqual(tuple(dporig.node_names), dp.node_names)
self.assertEqual(tuple(dporig.label), dp.label)
def test_preprocess_task_existing_encoding_basic_functionality(self):
FITBGSCVocab.preprocess_task(self.task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder='new',
data_encoder_kwargs=dict(
max_name_encoding_length=self.max_name_encoding_length),
instance_to_datapoints_kwargs=dict(max_nodes_per_graph=20))
de = FITBGSCVocabDataEncoder.load(
os.path.join(self.output_dataset_dir, '{}.pkl'.format(FITBGSCVocabDataEncoder.__name__)))
FITBGSCVocab.preprocess_task(self.task, output_dir=self.output_dataset_dir, n_jobs=30, data_encoder=de)
with self.assertRaises(AssertionError):
de = BaseDataEncoder(dict(), frozenset())
FITBGSCVocab.preprocess_task(self.task, output_dir=self.output_dataset_dir, n_jobs=30,
data_encoder=de)
def test_instance_to_datapoint(self):
for excluded_edge_types in [
syntax_only_excluded_edge_types,
frozenset()
]:
de = FITBGSCVocab.DataEncoder(
self.task.graphs_and_instances,
excluded_edge_types=excluded_edge_types,
instance_to_datapoints_kwargs=dict(),
max_name_encoding_length=self.max_name_encoding_length)
for graph, instances in tqdm(self.task.graphs_and_instances):
FITBGSCVocab.fix_up_edges(graph, instances,
excluded_edge_types)
FITBGSCVocab.extra_graph_processing(graph, instances, de)
node_names = []
for _, data in graph.nodes_that_represent_variables:
node_names += de.name_to_subtokens(data['identifier'])
node_names = set(node_names)
subtoken_nodes = [
i for i, data in graph.nodes
if data['type'] == de.subtoken_flag
]
self.assertCountEqual(
node_names,
set([graph[i]['identifier'] for i in subtoken_nodes]),
"There isn't a subtoken node for each word in the graph")
for node in subtoken_nodes:
self.assertFalse(
graph.is_variable_node(node),
"Subtoken node got flagged as a variable node")
self.assertEqual(graph[node]['type'], de.subtoken_flag,
"Subtoken node got the wrong type")
for node, data in graph.nodes:
if graph.is_variable_node(node):
node_names = de.name_to_subtokens(data['identifier'])
subtoken_nodes = graph.successors(
node, of_type=frozenset([de.subtoken_edge_type]))
back_subtoken_nodes = graph.predecessors(
node,
of_type=frozenset(
['reverse_' + de.subtoken_edge_type]))
self.assertCountEqual(
subtoken_nodes, back_subtoken_nodes,
"Same forward and reverse subtoken nodes aren't present"
)
self.assertCountEqual(
set(node_names), [
graph.nodes[d]['identifier']
for d in subtoken_nodes
],
"Node wasn't connected to all the right subtoken nodes"
)
for instance in instances:
dp = FITBGSCVocab.instance_to_datapoint(
graph, instance, de, max_nodes_per_graph=100)
self.assertEqual(type(dp), FITBGSCVocabDataPoint)
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, (name, types) in enumerate(
zip(dp.node_names, dp.node_types)):
self.assertEqual(type(name), str)
self.assertGreater(len(name), 0)
self.assertEqual(type(types), list)
self.assertGreaterEqual(len(types), 1)
if dp.subgraph.is_variable_node(i):
if name != de.fill_in_flag:
self.assertCountEqual(
set(
re.split(r'[,.]',
dp.subgraph[i]['reference'])),
types)
self.assertEqual(name,
dp.subgraph[i]['identifier'])
else:
self.assertEqual(name, de.fill_in_flag)
self.assertEqual(types, [de.fill_in_flag])
else:
if types == [de.subtoken_flag]:
self.assertEqual(dp.subgraph[i]['identifier'],
name)
else:
self.assertEqual(name, de.internal_node_flag)
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):
FITBGSCVocab.preprocess_task(task)