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GraphCodeBERT.py
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GraphCodeBERT.py
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import argparse
import logging
import os
import pdb
# os.environ['CUDA_VISIBLE_DEVICES'] = "1"
import pickle
import random
import torch
import json
import numpy as np
from torch.nn import CrossEntropyLoss, MSELoss
from torch.utils.data import DataLoader, Dataset, SequentialSampler, RandomSampler, TensorDataset
from transformers import (WEIGHTS_NAME, AdamW, get_linear_schedule_with_warmup,
RobertaConfig, RobertaModel, RobertaTokenizer)
from tqdm import tqdm, trange
import multiprocessing
from parser_graphCodeBert import DFG_python, DFG_java, DFG_ruby, DFG_go, DFG_php, DFG_javascript
from parser_graphCodeBert import (remove_comments_and_docstrings,
tree_to_token_index, tree_to_root_index,
index_to_code_token,
tree_to_variable_index)
from tree_sitter import Language, Parser
from two_stage_utils import sliding_window
import evaluation
import time
logger = logging.getLogger(__name__)
cpu_cont = 16
dfg_function = {
'python': DFG_python,
'java': DFG_java,
'ruby': DFG_ruby,
'go': DFG_go,
'php': DFG_php,
'javascript': DFG_javascript
}
# load parsers
parsers = {}
for lang in dfg_function:
LANGUAGE = Language('parser_graphCodeBert/my-languages.so', lang)
parser = Parser()
parser.set_language(LANGUAGE)
parser = [parser, dfg_function[lang]]
parsers[lang] = parser
def extract_ast_subcode(raw_code, parser, lang, max_depth=4, min_line=5, remove_comments=True):
"""
按照 AST 解析来抽取 subcode
"""
# remove comments
try:
if remove_comments:
raw_code = remove_comments_and_docstrings(raw_code, lang)
except:
pass
# obtain dataflow
if lang == "php":
raw_code = "<?php" + raw_code + "?>"
try:
tree = parser[0].parse(bytes(raw_code, 'utf8'))
root_node = tree.root_node
code = raw_code.split('\n')
start_index = tree_to_root_index(root_node, 0, max_depth=max_depth, min_line=min_line)
subcode_list = []
if len(start_index) > 1:
for i in range(1, len(start_index)):
subcode_list.append("\n".join(code[start_index[i-1][0]:start_index[i][0]])
+ code[start_index[i][0]][0:start_index[i][1]])
else:
subcode_list = [raw_code]
except Exception as e:
print(e)
subcode_list = [raw_code]
return subcode_list
# remove comments, tokenize code and extract dataflow
def extract_dataflow(code, parser, lang, remove_comments=True):
# remove comments
try:
if remove_comments:
code = remove_comments_and_docstrings(code, lang)
except:
pass
# obtain dataflow
if lang == "php":
code = "<?php" + code + "?>"
try:
tree = parser[0].parse(bytes(code, 'utf8'))
root_node = tree.root_node
tokens_index = tree_to_token_index(root_node)
code = code.split('\n')
code_tokens = [index_to_code_token(x, code) for x in tokens_index]
# tokens_index = tree_to_root_index(root_node, 0)
index_to_code = {}
for idx, (index, code) in enumerate(zip(tokens_index, code_tokens)):
index_to_code[index] = (idx, code)
try:
DFG, _ = parser[1](root_node, index_to_code, {})
except:
DFG = []
DFG = sorted(DFG, key=lambda x: x[1])
indexs = set()
for d in DFG:
if len(d[-1]) != 0:
indexs.add(d[1])
for x in d[-1]:
indexs.add(x)
new_DFG = []
for d in DFG:
if d[1] in indexs:
new_DFG.append(d)
dfg = new_DFG
except:
dfg = []
print(code)
raise Exception("Code error")
return code_tokens, dfg
class InputFeatures(object):
"""A single training/test features for a example."""
def __init__(self,
code_tokens,
code_ids,
position_idx,
dfg_to_code,
dfg_to_dfg,
nl_tokens,
nl_ids,
url,
):
self.code_tokens = code_tokens
self.code_ids = code_ids
self.position_idx = position_idx
self.dfg_to_code = dfg_to_code
self.dfg_to_dfg = dfg_to_dfg
self.nl_tokens = nl_tokens
self.nl_ids = nl_ids
self.url = url
def convert_examples_to_features(item):
js, tokenizer, args = item
# *********************萌萌哒***********************
# code
parser = parsers[args.lang]
# extract data flow
code_tokens, dfg = extract_dataflow(js['original_string'], parser, args.lang)
code_tokens = [tokenizer.tokenize('@ ' + x)[1:] if idx != 0 else tokenizer.tokenize(x) for idx, x in
enumerate(code_tokens)]
ori2cur_pos = {}
ori2cur_pos[-1] = (0, 0)
for i in range(len(code_tokens)):
ori2cur_pos[i] = (ori2cur_pos[i - 1][1], ori2cur_pos[i - 1][1] + len(code_tokens[i]))
code_tokens = [y for x in code_tokens for y in x]
# truncating
code_tokens = code_tokens[:args.code_length + args.data_flow_length - 2 - min(len(dfg), args.data_flow_length)]
code_tokens = [tokenizer.cls_token] + code_tokens + [tokenizer.sep_token]
code_ids = tokenizer.convert_tokens_to_ids(code_tokens)
position_idx = [i + tokenizer.pad_token_id + 1 for i in range(len(code_tokens))]
dfg = dfg[:args.code_length + args.data_flow_length - len(code_tokens)]
code_tokens += [x[0] for x in dfg]
position_idx += [0 for x in dfg]
code_ids += [tokenizer.unk_token_id for x in dfg]
padding_length = args.code_length + args.data_flow_length - len(code_ids)
position_idx += [tokenizer.pad_token_id] * padding_length
code_ids += [tokenizer.pad_token_id] * padding_length
# reindex
reverse_index = {}
for idx, x in enumerate(dfg):
reverse_index[x[1]] = idx
for idx, x in enumerate(dfg):
dfg[idx] = x[:-1] + ([reverse_index[i] for i in x[-1] if i in reverse_index],)
dfg_to_dfg = [x[-1] for x in dfg]
dfg_to_code = [ori2cur_pos[x[1]] for x in dfg]
length = len([tokenizer.cls_token])
dfg_to_code = [(x[0] + length, x[1] + length) for x in dfg_to_code]
# *********************萌萌哒***********************
# nl
nl = ' '.join(js['docstring_tokens'])
nl_tokens = tokenizer.tokenize(nl)[:args.nl_length - 2]
nl_tokens = [tokenizer.cls_token] + nl_tokens + [tokenizer.sep_token]
nl_ids = tokenizer.convert_tokens_to_ids(nl_tokens)
padding_length = args.nl_length - len(nl_ids)
nl_ids += [tokenizer.pad_token_id] * padding_length
return InputFeatures(code_tokens, code_ids, position_idx, dfg_to_code, dfg_to_dfg, nl_tokens, nl_ids, js['url'])
class TextDataset(Dataset):
def __init__(self, tokenizer, args, file_path=None, pool=None):
self.args = args
if not hasattr(args, "output_dir"):
args.output_dir = os.path.join(
args.root_path, "TwoStageModels", 'GraphCodeBERT', 'models', '%s' % (args.lang))
args.data_flow_length = 64
pass
prefix = file_path.split('/')[-1][:-6]
if self.args.code_length != 256:
prefix = prefix + "-code_length_%d" % self.args.code_length
if self.args.nl_length != 128:
prefix = prefix + "-nl_length_%d" % self.args.nl_length
cache_file = args.output_dir + '/' + prefix + '.pkl'
if os.path.exists(cache_file):
# if os.path.exists(cache_file):
self.examples = pickle.load(open(cache_file, 'rb'))
else:
self.examples = []
data = []
with open(file_path) as f:
for line in f:
line = line.strip()
js = json.loads(line)
data.append((js, tokenizer, args))
self.examples = pool.map(convert_examples_to_features, tqdm(data, total=len(data)))
pickle.dump(self.examples, open(cache_file, 'wb'))
if 'train' in file_path:
for idx, example in enumerate(self.examples[:3]):
logger.info("*** Example ***")
logger.info("idx: {}".format(idx))
logger.info("code_tokens: {}".format([x.replace('\u0120', '_') for x in example.code_tokens]))
logger.info("code_ids: {}".format(' '.join(map(str, example.code_ids))))
logger.info("position_idx: {}".format(example.position_idx))
logger.info("dfg_to_code: {}".format(' '.join(map(str, example.dfg_to_code))))
logger.info("dfg_to_dfg: {}".format(' '.join(map(str, example.dfg_to_dfg))))
logger.info("nl_tokens: {}".format([x.replace('\u0120', '_') for x in example.nl_tokens]))
logger.info("nl_ids: {}".format(' '.join(map(str, example.nl_ids))))
def __len__(self):
return len(self.examples)
def __getitem__(self, item):
# calculate graph-guided masked function
attn_mask = np.zeros((self.args.code_length + self.args.data_flow_length,
self.args.code_length + self.args.data_flow_length), dtype=bool)
# calculate begin index of node and max length of input
node_index = sum([i > 1 for i in self.examples[item].position_idx])
max_length = sum([i != 1 for i in self.examples[item].position_idx])
# sequence can attend to sequence
attn_mask[:node_index, :node_index] = True
# special tokens attend to all tokens
for idx, i in enumerate(self.examples[item].code_ids):
if i in [0, 2]:
attn_mask[idx, :max_length] = True
# nodes attend to code tokens that are identified from
for idx, (a, b) in enumerate(self.examples[item].dfg_to_code):
if a < node_index and b < node_index:
attn_mask[idx + node_index, a:b] = True
attn_mask[a:b, idx + node_index] = True
# nodes attend to adjacent nodes
for idx, nodes in enumerate(self.examples[item].dfg_to_dfg):
for a in nodes:
if a + node_index < len(self.examples[item].position_idx):
attn_mask[idx + node_index, a + node_index] = True
return (torch.tensor(self.examples[item].code_ids),
torch.tensor(attn_mask),
torch.tensor(self.examples[item].position_idx),
torch.tensor(self.examples[item].nl_ids))
class TextDatasetSplit(Dataset):
"""
- 把 nl 和 code 分开编码
- 加入划分窗口代码
"""
def __init__(self, tokenizer, args, file_path=None, pool=None):
self.args = args
if not hasattr(args, "output_dir"):
args.output_dir = os.path.join(
args.root_path, "TwoStageModels", 'GraphCodeBERT', 'models', '%s' % (args.lang))
pass
if not hasattr(args, "data_flow_length"):
args.data_flow_length = 64
prefix = file_path.split('/')[-1][:-6]
if self.args.code_length != 256:
prefix = prefix + "-code_length_%d" % self.args.code_length
if self.args.nl_length != 128:
prefix = prefix + "-nl_length_%d" % self.args.nl_length
cache_file = args.output_dir + '/' + prefix + '.pkl'
if os.path.exists(cache_file) and (not args.do_debug):
# if os.path.exists(cache_file):
self.examples = pickle.load(open(cache_file, 'rb'))
else:
self.examples = []
data = []
with open(file_path) as f:
for line in f:
line = line.strip()
js = json.loads(line)
data.append((js, tokenizer, args))
# ***********************萌萌哒**************************
# cdsaaae===- =-= --095304 003535
window_size, step = self.args.window_size, self.args.step
if window_size > 0:
# 仅仅给要检索的 query 得 gt 划分 multi-passages
new_query_ids = [[each] for each in self.query_ids]
data_len = len(data)
for data_index in range(len(data_len)):
code = data[data_index][0]['code']
code_list = code.split(" ")
code_subset_list = [" ".join(each[1]) for each in sliding_window(code_list, window_size, step)]
data[data_index][0]['code'] = code_subset_list[0]
data[data_index][0]['code'] = code_subset_list[0]
pass
# ***********************萌萌哒**************************
self.examples = pool.map(convert_examples_to_features, tqdm(data, total=len(data)))
pickle.dump(self.examples, open(cache_file, 'wb'))
if 'train' in file_path:
for idx, example in enumerate(self.examples[:3]):
logger.info("*** Example ***")
logger.info("idx: {}".format(idx))
logger.info("code_tokens: {}".format([x.replace('\u0120', '_') for x in example.code_tokens]))
logger.info("code_ids: {}".format(' '.join(map(str, example.code_ids))))
logger.info("position_idx: {}".format(example.position_idx))
logger.info("dfg_to_code: {}".format(' '.join(map(str, example.dfg_to_code))))
logger.info("dfg_to_dfg: {}".format(' '.join(map(str, example.dfg_to_dfg))))
logger.info("nl_tokens: {}".format([x.replace('\u0120', '_') for x in example.nl_tokens]))
logger.info("nl_ids: {}".format(' '.join(map(str, example.nl_ids))))
def __len__(self):
return len(self.examples)
def __getitem__(self, item):
# calculate graph-guided masked function
attn_mask = np.zeros((self.args.code_length + self.args.data_flow_length,
self.args.code_length + self.args.data_flow_length), dtype=bool)
# calculate begin index of node and max length of input
node_index = sum([i > 1 for i in self.examples[item].position_idx])
max_length = sum([i != 1 for i in self.examples[item].position_idx])
# sequence can attend to sequence
attn_mask[:node_index, :node_index] = True
# special tokens attend to all tokens
for idx, i in enumerate(self.examples[item].code_ids):
if i in [0, 2]:
attn_mask[idx, :max_length] = True
# nodes attend to code tokens that are identified from
for idx, (a, b) in enumerate(self.examples[item].dfg_to_code):
if a < node_index and b < node_index:
attn_mask[idx + node_index, a:b] = True
attn_mask[a:b, idx + node_index] = True
# nodes attend to adjacent nodes
for idx, nodes in enumerate(self.examples[item].dfg_to_dfg):
for a in nodes:
if a + node_index < len(self.examples[item].position_idx):
attn_mask[idx + node_index, a + node_index] = True
return (torch.tensor(self.examples[item].code_ids),
torch.tensor(attn_mask),
torch.tensor(self.examples[item].position_idx),
torch.tensor(self.examples[item].nl_ids))
class Model(torch.nn.Module):
def __init__(self, encoder):
super(Model, self).__init__()
self.encoder = encoder
def forward(self, code_inputs=None, attn_mask=None, position_idx=None, nl_inputs=None):
if code_inputs is not None:
nodes_mask = position_idx.eq(0)
token_mask = position_idx.ge(2)
inputs_embeddings = self.encoder.embeddings.word_embeddings(code_inputs)
nodes_to_token_mask = nodes_mask[:, :, None] & token_mask[:, None, :] & attn_mask
nodes_to_token_mask = nodes_to_token_mask / (nodes_to_token_mask.sum(-1) + 1e-10)[:, :, None]
avg_embeddings = torch.einsum("abc,acd->abd", nodes_to_token_mask, inputs_embeddings)
inputs_embeddings = inputs_embeddings * (~nodes_mask)[:, :, None] + avg_embeddings * nodes_mask[:, :, None]
# import pdb; pdb.set_trace()
return self.encoder(inputs_embeds=inputs_embeddings, attention_mask=attn_mask, position_ids=position_idx)[1]
else:
return self.encoder(nl_inputs, attention_mask=nl_inputs.ne(1))[1]
class GraphCodeBert(object):
def __init__(self, model_suffix="", lang="python", root_path=None, input_args=None, dataset="GraphCodeBERT_python"):
super(GraphCodeBert, self).__init__()
self.dataset = dataset
if root_path is None:
root_path = "~/VisualSearch".replace('~', os.path.expanduser('~'))
store_root_path = os.path.join(root_path, "TwoStageModels", self.dataset)
model_dir = os.path.join(
root_path, "TwoStageModels", 'GraphCodeBERT', 'models', '%s%s' % (lang, model_suffix))
if "valid" in dataset:
eval_data_file = os.path.join(root_path, "GraphCodeBERT_dataset", lang, 'valid.jsonl')
else:
eval_data_file = os.path.join(root_path, "GraphCodeBERT_dataset", lang, 'test.jsonl')
codebase_file = os.path.join(root_path, "GraphCodeBERT_dataset", lang, 'codebase.jsonl')
logger.info("eval_data_file: %s" % eval_data_file)
self.test_query = []
self.query_ids = []
self.retrieval_code_base = []
self.retrieval_raw_code_base = []
self.code_ids = []
if input_args is None:
input_args = argparse.Namespace()
input_args.code_length = 256
input_args.nl_length = 128
input_args.n_gpu = torch.cuda.device_count()
if input_args.n_gpu >= 1:
input_args.device = torch.device("cuda")
else:
input_args.device = torch.device("cpu")
args = argparse.Namespace(code_length=input_args.code_length,
codebase_file=codebase_file,
config_name='microsoft/graphcodebert-base', data_flow_length=64,
eval_batch_size=256, eval_data_file=eval_data_file,
lang=lang, n_gpu=input_args.n_gpu, device=input_args.device,
model_name_or_path='microsoft/graphcodebert-base',
nl_length=input_args.nl_length,
output_dir=model_dir,
store_root_path=store_root_path,
do_debug=input_args.do_debug,
tokenizer_name='microsoft/graphcodebert-base')
self.args = args
tokenizer = RobertaTokenizer.from_pretrained(args.tokenizer_name)
pool = multiprocessing.Pool(cpu_cont)
query_dataset = TextDataset(tokenizer, args, args.eval_data_file, pool)
query_sampler = SequentialSampler(query_dataset)
self.query_dataloader = DataLoader(query_dataset, sampler=query_sampler, batch_size=args.eval_batch_size,
num_workers=1, shuffle=False)
code_dataset = TextDataset(tokenizer, args, args.codebase_file, pool)
code_sampler = SequentialSampler(code_dataset)
self.code_dataloader = DataLoader(code_dataset, sampler=code_sampler, batch_size=args.eval_batch_size,
num_workers=1, shuffle=False)
self.tokenizer = RobertaTokenizer.from_pretrained(args.model_name_or_path)
pretrained_path = os.path.join(model_dir, "checkpoint-best-mrr/model.bin")
self.model = Model(RobertaModel.from_pretrained(args.model_name_or_path))
logger.info("Read %s" % pretrained_path)
self.model.load_state_dict(torch.load(pretrained_path, map_location=torch.device('cpu')), strict=True)
self.model.to(args.device)
def encode_text_and_code(self, read_scores=True, neg_candidate=-1):
args = self.args
# store_score_path = os.path.join(self.args.output_dir, os.path.basename(self.args.eval_data_file)+".scores.pkl")
# if read_scores and os.path.exists(store_score_path):
# logger.info("Read "+store_score_path)
# return pickle.load(open(store_score_path, 'rb'))
feature_data_path = os.path.join(
args.store_root_path, "FeatureData",
"CSN-"+args.lang)
if read_scores and os.path.exists(os.path.join(feature_data_path, "GraphCodeBERT.pkl")):
logger.info("Read "+feature_data_path)
feature_data_path_name = os.path.join(feature_data_path, "GraphCodeBERT.pkl")
feature_dict = pickle.load(open(feature_data_path_name, 'rb'))
nl_vecs, code_vecs = feature_dict["query"].float(), feature_dict["database"].float()
if torch.cuda.device_count() >= 1:
time_path1 = feature_data_path_name.replace(".pkl", "") + "-time_gpu.pkl"
else:
time_path1 = feature_data_path_name.replace(".pkl", "") + "-time.pkl"
time_dict1 = pickle.load(open(time_path1, 'rb'))
cal_query_time = time_dict1["all_query_time"]
start_time = time.time()
scores = nl_vecs.mm(code_vecs.T)
end_time = time.time()
stage_time = end_time - start_time
graphcodebert_time = cal_query_time + stage_time
if neg_candidate != -1:
graphcodebert_time = cal_query_time + neg_candidate/len(code_vecs)*stage_time
return scores, graphcodebert_time
model = self.model
query_dataloader = self.query_dataloader
code_dataloader = self.code_dataloader
if args.n_gpu > 1:
model = torch.nn.DataParallel(model)
# Eval!
logger.info("***** Running GraphCodeBERT evaluation *****")
logger.info(" Num queries = %d", len(query_dataloader.dataset))
logger.info(" Num codes = %d", len(code_dataloader.dataset))
logger.info(" Batch size = %d", args.eval_batch_size)
model.eval()
# Encode raw query and query ids
code_vecs = []
nl_vecs = []
with tqdm(total=len(query_dataloader.dataset)) as pbar:
start_time = time.time()
for i_q, batch in enumerate(query_dataloader):
if i_q == 0:
start_time = time.time()
pbar.update(len(batch[0]))
nl_inputs = batch[3].to(args.device)
with torch.no_grad():
nl_vec = model(nl_inputs=nl_inputs)
nl_vecs.append(nl_vec.cpu())
# break
all_query_time = time.time()-start_time
start_time = time.time()
with torch.no_grad():
nl_vec = model(nl_inputs=nl_inputs[[0]])
one_query_time = time.time()-start_time
with tqdm(total=len(code_dataloader.dataset)) as pbar:
for batch in code_dataloader:
pbar.update(len(batch[0]))
code_inputs = batch[0].to(args.device)
attn_mask = batch[1].to(args.device)
position_idx = batch[2].to(args.device)
with torch.no_grad():
code_vec = model(code_inputs=code_inputs, attn_mask=attn_mask, position_idx=position_idx)
code_vecs.append(code_vec.cpu())
# break
code_vecs = torch.cat(code_vecs, 0)
nl_vecs = torch.cat(nl_vecs, 0)
start_time = time.time()
scores = nl_vecs.mm(code_vecs.T)
end_time = time.time()
stage_time = end_time-start_time
# pdb.set_trace()
# *****************************萌萌哒*******************************
# 保存特征文件,以及 query 计算时间
if not os.path.exists(feature_data_path):
os.makedirs(feature_data_path)
feature_data_path_name = os.path.join(feature_data_path, "GraphCodeBERT.pkl")
logger.info("Restore to %s" % feature_data_path_name)
feature_dict = {
"query": nl_vecs, "database": code_vecs
}
if read_scores:
pickle.dump(feature_dict, open(feature_data_path_name, 'wb'))
if args.n_gpu >= 1:
feature_time_path_name = os.path.join(feature_data_path, "GraphCodeBERT-time_gpu.pkl")
one_query_time = args.n_gpu*one_query_time
all_query_time = args.n_gpu*all_query_time
else:
feature_time_path_name = os.path.join(feature_data_path, "GraphCodeBERT-time.pkl")
time_dict = {"all_query_time": all_query_time,
"one_query_time": one_query_time}
if read_scores:
pickle.dump(time_dict, open(feature_time_path_name, 'wb'))
# *****************************萌萌哒*******************************
# self.code_ids = list(np.arange(0, len(self.retrieval_code_base)))
# self.query_ids = []
# codeurl_to_int = {}
# for i, each in enumerate(code_dataloader.dataset.examples):
# if each.url in codeurl_to_int:
# print("存在重复: ", each['url'])
# codeurl_to_int[each['url']] = i
# query_urls = []
# for example in query_dataloader.dataset.examples:
# query_urls.append(example.url)
# for each in query_urls:
# self.query_ids.append(codeurl_to_int[each])
# *****************************萌萌哒*******************************
# sort_ids = np.argsort(scores.numpy(), axis=-1, order=None)[:, ::-1]
# nl_urls = []
# code_urls = []
# for example in query_dataloader.dataset.examples:
# nl_urls.append(example.url)
#
# for example in code_dataloader.dataset.examples:
# code_urls.append(example.url)
# ranks = []
# for url, sort_id in zip(nl_urls, sort_ids):
# rank = 0
# find = False
# for idx in sort_id[:1000]:
# if find is False:
# rank += 1
# if code_urls[idx] == url:
# find = True
# if find:
# ranks.append(1 / rank)
# else:
# ranks.append(0)
# print("eval_mrr", float(np.mean(ranks)))
# ****************************萌萌哒********************************
return scores, all_query_time+stage_time
if __name__ == "__main__":
a = GraphCodeBert(model_suffix="")
a.encode_text_and_code(read_scores=True)