-
Notifications
You must be signed in to change notification settings - Fork 0
/
all_scripts_combined_together.py
1118 lines (993 loc) · 64 KB
/
all_scripts_combined_together.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
#!/usr/bin/env python
# coding: utf-8
# In[ ]:
import pandas as pd
from pydriller import Repository
import os
import subprocess
import json
import signal
import math
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib import rcParams
from matplotlib_venn import venn2, venn2_circles, venn3, venn3_circles
PATH_GITHUB = "path_github_dir"
PATH_DATASET_DIR = PATH_GITHUB + "/sub_137"
CHECKOUT_AND_VERIFY = False
VERIFY_ALL_CHECKOUTS_AGAIN = False
VERIFY_PATCHES = False
SEPARATE_OUT_FIXES_FOR_MUTATION_PURPOSE = False
EXECUTE_MUTANTS = False
ANALYZE_MUTANTS_SIMULATIONS = True
CREATE_ML_DATASET = False
ANALYSE_AT_HIGH_LEVEL = False
PATH_VUL4J_CSV = PATH_DATASET_DIR + "/dataset.csv"
PATH_PATCHES_DIR = PATH_DATASET_DIR + "/patches"
ALL_METHODS_CSV_NAME = "all_methods.csv"
CHANGED_METHODS_CSV_NAME = "changed_methods.csv"
PATH_CODE_DIR = PATH_DATASET_DIR + "/code"
PATH_FIXED_CODE_DIR = PATH_DATASET_DIR + "/fixed_code"
WASTE_CODE_DIR = PATH_DATASET_DIR + "/waste_code"
WASTE_PATCHES_DIR = PATH_DATASET_DIR + "/waste_patches"
WASTE_FIXED_PATCHES_DIR = PATH_DATASET_DIR + "/waste_fixed_patches"
PATH_FIXES_FOR_MUTATION_DIR = PATH_DATASET_DIR + "/fixes_for_mutation"
PATH_MUTANTS_DIR = PATH_DATASET_DIR + "/mutants_mbert"
PATH_MUTATED_CODE_DIR = PATH_DATASET_DIR + "/mutated_code"
PATH_MUTANTS_ANALYSIS_DIR = PATH_DATASET_DIR + "/mutants_mbert_analysis"
ALL_ANALYSIS_CSV_NAME = "all_analysis.csv"
TIMEOUT = 120
COMPLETED_VUL4J_IDS_CSV_NAME = "completed_vul4j_ids.csv"
PLOT_FILE_NAME = "plot_ochiai.pdf"
PATH_ML_DATASET_DIR = PATH_DATASET_DIR + "/ml_dataset"
PATH_SRC2ABS = PATH_GITHUB + "/src2abs/src2abs/target/src2abs-0.1-jar-with-dependencies.jar"
PATH_IDIOMS = PATH_ML_DATASET_DIR + "/idioms.txt"
ML_DATASET_CSV_NAME = "ml_dataset.csv"
HIGH_LEVEL_ANALYSIS_CSV_NAME = "high_level_analysis.csv"
PLOT_COUPLING_FILE_NAME = "plot_coupling.pdf"
PLOT_VENN_FILE_NAME = "plot_venn.pdf"
PLOT_VENN_INTERSECTION_FILE_NAME = "plot_venn_intersection.pdf"
keyword_strong_substitution = "\"SS\""
keyword_strong_substitution_with_add_tests_failed = "\"SS+ATF\""
keyword_test_substitution = "\"TS\""
keyword_test_substitution_with_add_tests_failed = "\"TS+ATF\""
keyword_partial_substitution = "\"PS\""
keyword_partial_substitution_with_add_tests_failed = "\"PS+ATF\""
keyword_partial_test_substitution = "\"PTS\""
keyword_partial_test_substitution_with_add_tests_failed = "\"PTS+ATF\""
keyword_no_substitution = "\"NS\""
keyword_mutant_not_killed = "\"MNK\""
keyword_compilation_error = "\"CE\""
def compare_between_and_get_methods_details(method_new, allmethods_old):
long_name = method_new.long_name
start_line_new = method_new.start_line
end_line_new = method_new.end_line
old_method_found = False
for method_old in allmethods_old:
if method_old.long_name == method_new.long_name:
start_line_old = method_old.start_line
end_line_old = method_old.end_line
old_method_found = True
break
if old_method_found is False:
print("method", method_new.name,", in new file, ranging from", method_new.start_line, "till", method_new.end_line,
"does not exists in old file!")
start_line_old = -1
end_line_old = -1
return "\"" + long_name + "\"", start_line_new, end_line_new, start_line_old, end_line_old
def get_details_from_modified_file(file, df_all_methods, df_changed_methods, path_vul_dir):
df_mod = pd.DataFrame(columns = ['line_num', 'mod_type', 'mod'])
df_changed_methods_without_change = pd.DataFrame(columns = ['file_path', 'long_name',
'start_line_new', 'end_line_new',
'start_line_old', 'end_line_old'])
file_path = file.old_path
if file_path is None:
return df_all_methods, df_changed_methods
file_path = "\"" + file_path + "\""
file_name = file.filename
for method in file.methods:
long_name, start_line_new, end_line_new, start_line_old, end_line_old = compare_between_and_get_methods_details(method, file.methods_before)
df_all_methods = df_all_methods.append({'file_path' : file_path, 'long_name' : long_name,
'start_line_new' : start_line_new, 'end_line_new' : end_line_new,
'start_line_old' : start_line_old, 'end_line_old' : end_line_old}, ignore_index = True)
for method in file.changed_methods:
long_name, start_line_new, end_line_new, start_line_old, end_line_old = compare_between_and_get_methods_details(method, file.methods_before)
df_changed_methods_without_change = df_changed_methods_without_change.append({
'file_path' : file_path, 'long_name' : long_name,
'start_line_new' : start_line_new, 'end_line_new' : end_line_new,
'start_line_old' : start_line_old, 'end_line_old' : end_line_old}, ignore_index = True)
for addition in file.diff_parsed.get("added"):
line_num = addition[0]
modification_type = "\"added\""
modification = "\"" + addition[1] + "\""
df_mod = df_mod.append({'line_num' : line_num, 'mod_type' : modification_type, 'mod' : modification},
ignore_index = True)
for deletion in file.diff_parsed.get("deleted"):
line_num = deletion[0]
modification_type = "\"deleted\""
modification = "\"" + deletion[1] + "\""
df_mod = df_mod.append({'line_num' : line_num, 'mod_type' : modification_type, 'mod' : modification},
ignore_index = True)
df_mod = df_mod.sort_values(['line_num', 'mod_type'], ascending = [True, False], ignore_index = True)
for df_mod_index in df_mod.index:
is_change_within_function = False
for df_changed_methods_without_change_index in df_changed_methods_without_change.index:
if is_change_within_function is False and \
df_mod['line_num'][df_mod_index] >= df_changed_methods_without_change['start_line_new'][df_changed_methods_without_change_index] and \
df_mod['line_num'][df_mod_index] <= df_changed_methods_without_change['end_line_new'][df_changed_methods_without_change_index]:
is_change_within_function = True
df_changed_methods = df_changed_methods.append({
'file_path' : df_changed_methods_without_change['file_path'][df_changed_methods_without_change_index],
'long_name' : df_changed_methods_without_change['long_name'][df_changed_methods_without_change_index],
'start_line_new' : df_changed_methods_without_change['start_line_new'][df_changed_methods_without_change_index],
'end_line_new' : df_changed_methods_without_change['end_line_new'][df_changed_methods_without_change_index],
'start_line_old' : df_changed_methods_without_change['start_line_old'][df_changed_methods_without_change_index],
'end_line_old' : df_changed_methods_without_change['end_line_old'][df_changed_methods_without_change_index],
'line_num' : df_mod['line_num'][df_mod_index], 'mod_type' : df_mod['mod_type'][df_mod_index],
'mod' : df_mod['mod'][df_mod_index]}, ignore_index = True)
if is_change_within_function is False:
df_changed_methods = df_changed_methods.append({
'file_path' : file_path,
'long_name' : "\"\"",
'start_line_new' : -1,
'end_line_new' : -1,
'start_line_old' : -1,
'end_line_old' : -1,
'line_num' : df_mod['line_num'][df_mod_index], 'mod_type' : df_mod['mod_type'][df_mod_index],
'mod' : df_mod['mod'][df_mod_index]}, ignore_index = True)
source_code_after = file.source_code
source_code_before = file.source_code_before
if df_changed_methods.empty is False:
os.makedirs(path_vul_dir, exist_ok=True)
after_file = open(path_vul_dir + "/" + file_name.split(".")[0] + "_after.java", "w")
after_file.write(source_code_after)
after_file.close()
if source_code_before is None:
print("source_code_before is not available, will require to get from the code dir!")
else:
before_file = open(path_vul_dir + "/" + file_name.split(".")[0] + "_before.java", "w")
before_file.write(source_code_before)
before_file.close()
return df_all_methods, df_changed_methods
def extract_patches_and_modifications_information_for_vulnerability (vul_id, patch_url):
bool_extraction_successful = False
path_vul_dir = PATH_PATCHES_DIR + "/" + vul_id
if os.path.exists(path_vul_dir + "/commit_date.txt"):
return True
print("processing", vul_id)
if "/commit/" in patch_url:
patch_arr = patch_url.split("/commit/")
else:
print("no commit found in URL!")
return False
repo = patch_arr[0]
commit_id = patch_arr[1].split(",")[0]
print("searching for commit:", commit_id, "in repo:", repo)
df_all_methods = pd.DataFrame(columns = ['file_path', 'long_name',
'start_line_new', 'end_line_new',
'start_line_old', 'end_line_old'])
df_changed_methods = pd.DataFrame(columns = ['file_path', 'long_name',
'start_line_new', 'end_line_new',
'start_line_old', 'end_line_old',
'line_num', "mod_type", "mod"])
for commit in Repository(repo, single=commit_id).traverse_commits():
commit_date = commit.committer_date
for modified_file in commit.modified_files:
df_all_methods, df_changed_methods = get_details_from_modified_file(
modified_file, df_all_methods, df_changed_methods, path_vul_dir)
if df_changed_methods.empty is False:
df_all_methods.to_csv(path_vul_dir + "/" + ALL_METHODS_CSV_NAME, index = False)
df_changed_methods.to_csv(path_vul_dir + "/" + CHANGED_METHODS_CSV_NAME, index = False)
commit_date_file = open(path_vul_dir + "/commit_date.txt", "w")
commit_date_file.write(str(commit_date))
commit_date_file.close()
bool_extraction_successful = True
return bool_extraction_successful
def get_changed_code_files_paths (vul_id):
path_patches_dir_for_vulnerability = PATH_PATCHES_DIR + "/" + vul_id
lst_changed_code_files_paths = []
if os.path.exists(path_patches_dir_for_vulnerability + "/" + CHANGED_METHODS_CSV_NAME):
df_changed_methods = pd.read_csv(path_patches_dir_for_vulnerability + "/" + CHANGED_METHODS_CSV_NAME)
for df_changed_methods_ind in df_changed_methods.index:
file_path = df_changed_methods["file_path"][df_changed_methods_ind].replace("\"","")
if ("/test/" not in file_path) and ("/tests/" not in file_path) and (".java" in file_path) and (file_path not in lst_changed_code_files_paths):
lst_changed_code_files_paths.append(file_path)
return lst_changed_code_files_paths
def get_compilation_results(path_dir, vul_id):
bool_compiled = None
path_compile_result_text_file = path_dir + "/" + vul_id + "/VUL4J/compile_result.txt"
if os.path.exists(path_compile_result_text_file):
compile_result_text_file = open(path_compile_result_text_file, "r")
content_compile_result_text_file = compile_result_text_file.read()
compile_result_text_file.close()
if content_compile_result_text_file == "1":
bool_compiled = True
else:
bool_compiled = False
return bool_compiled
def get_test_results(path_dir, vul_id):
test_passed = None
path_testing_results_json_file = path_dir + "/" + vul_id + "/VUL4J/testing_results.json"
if os.path.exists(path_testing_results_json_file):
file_testing_results_json = open(path_testing_results_json_file)
try:
content_testing_results_json_file = json.load(file_testing_results_json)
except:
print("error in loading json")
content_testing_results_json_file = ""
file_testing_results_json.close()
if content_testing_results_json_file != "":
overall_metrics = content_testing_results_json_file["tests"]["overall_metrics"]
number_error = overall_metrics["number_error"]
number_failing = overall_metrics["number_failing"]
if number_error == 0 and number_failing == 0:
test_passed = True
else:
test_passed = False
return test_passed
def execute_tests_and_get_results(path_dir, vul_id):
bool_compiled = get_compilation_results(path_dir, vul_id)
bool_test_passed = None
if bool_compiled is None:
print("compiled", vul_id, ", but coudn't find the compilation results!")
elif bool_compiled is True:
command_to_execute = ["vul4j","test","-d",path_dir + "/" + vul_id]
print("executing", command_to_execute)
try:
p = subprocess.Popen(command_to_execute, stdout=subprocess.DEVNULL, start_new_session=True)
p.wait(timeout=TIMEOUT)
except subprocess.TimeoutExpired:
print("timed out!")
print('Terminating the whole process group...')
os.killpg(os.getpgid(p.pid), signal.SIGTERM)
bool_test_passed = get_test_results(path_dir, vul_id)
if bool_test_passed is None:
print("tests executed for", vul_id, ", but coudn't find the test results!")
elif bool_test_passed is True:
print("all tests passed for", vul_id)
else:
print("tests failed for", vul_id)
else:
print(vul_id, "didn't compile!")
return bool_compiled, bool_test_passed
def execute_and_get_vul4j_results (path_dir, vul_id):
command_to_execute = ["vul4j","compile","-d",path_dir + "/" + vul_id]
print("executing", command_to_execute)
try:
p = subprocess.Popen(command_to_execute, stdout=subprocess.DEVNULL, start_new_session=True)
p.wait(timeout=TIMEOUT)
except subprocess.TimeoutExpired:
print("timed out!")
print('Terminating the whole process group...')
os.killpg(os.getpgid(p.pid), signal.SIGTERM)
return execute_tests_and_get_results(path_dir, vul_id)
def checkout_vulnerability(path_dir, vul_id):
if os.path.exists(path_dir + "/" + vul_id):
return False
else:
command_to_execute = ["vul4j", "checkout", "--id", vul_id, "-d", path_dir + "/" + vul_id]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
return True
def recheckout_vulnerability(path_dir, vul_id):
if os.path.exists(path_dir + "/" + vul_id):
command_to_execute = ["rm", "-r", path_dir + "/" + vul_id]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
checkout_vulnerability(path_dir, vul_id)
def verify_checkout_and_retry(vul_id):
bool_verified_ok = False
bool_compiled, bool_test_passed = execute_and_get_vul4j_results (PATH_CODE_DIR, vul_id)
if (bool_compiled is None) or (bool_compiled is False) or (bool_test_passed is True) :
recheckout_vulnerability(PATH_CODE_DIR, vul_id)
bool_compiled, bool_test_passed = execute_and_get_vul4j_results (PATH_CODE_DIR, vul_id)
if (bool_compiled is None) or (bool_compiled is False) or (bool_test_passed is True):
print("re-downloading", vul_id, "didn't solve the problem!")
if os.path.exists(PATH_CODE_DIR + "/" + vul_id):
command_to_execute = ["mv", PATH_CODE_DIR + "/" + vul_id, WASTE_CODE_DIR + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
return bool_verified_ok
command_to_execute = ["cp", "-r", PATH_CODE_DIR + "/" + vul_id, PATH_FIXED_CODE_DIR + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
return True
def verify_extracted_vulnerable_files(vul_id):
path_code_dir_for_vulnerability = PATH_CODE_DIR + "/" + vul_id
path_patches_dir_for_vulnerability = PATH_PATCHES_DIR + "/" + vul_id
if os.path.exists(path_patches_dir_for_vulnerability) is False:
print(path_patches_dir_for_vulnerability, "does not exist!")
return False
lst_changed_code_files_paths = get_changed_code_files_paths (vul_id)
for changed_code_file_path in lst_changed_code_files_paths:
arr_changed_code_file_path = changed_code_file_path.split("/")
changed_code_file_name = arr_changed_code_file_path[len(arr_changed_code_file_path) - 1]
original_vulnerable_file = open(path_code_dir_for_vulnerability + "/" + changed_code_file_path, "r")
content_original_vulnerable_file = original_vulnerable_file.read()
original_vulnerable_file.close()
extracted_vulnerable_file = open(path_patches_dir_for_vulnerability + "/" + changed_code_file_name.replace(".java", "_before.java"), "r")
content_extracted_vulnerable_file = extracted_vulnerable_file.read()
extracted_vulnerable_file.close()
if content_original_vulnerable_file.replace(" ","") != content_extracted_vulnerable_file.replace(" ",""):
print("File mismatch for", vul_id)
print(path_code_dir_for_vulnerability + "/" + changed_code_file_path,"does not match with", \
path_patches_dir_for_vulnerability + "/" + changed_code_file_name.replace(".java", "_before.java"))
command_to_execute = ["mv", PATH_PATCHES_DIR + "/" + vul_id, WASTE_PATCHES_DIR + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
return False
return True
def verify_extracted_fixed_files(vul_id):
path_fixed_code_dir_for_vulnerability = PATH_FIXED_CODE_DIR + "/" + vul_id
path_patches_dir_for_vulnerability = PATH_PATCHES_DIR + "/" + vul_id
if os.path.exists(path_patches_dir_for_vulnerability) is False:
print(path_patches_dir_for_vulnerability, "does not exist!")
return False
if os.path.exists(path_fixed_code_dir_for_vulnerability) is False:
command_to_execute = ["cp", "-r", PATH_CODE_DIR + "/" + vul_id, PATH_FIXED_CODE_DIR + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
lst_changed_code_files_paths = get_changed_code_files_paths (vul_id)
dict_vulnerable_files = {}
for changed_code_file_path in lst_changed_code_files_paths:
arr_changed_code_file_path = changed_code_file_path.split("/")
changed_code_file_name = arr_changed_code_file_path[len(arr_changed_code_file_path) - 1]
extracted_fixed_file = open(path_patches_dir_for_vulnerability + "/" + changed_code_file_name.replace(".java", "_after.java"), "r")
content_extracted_fixed_file = extracted_fixed_file.read()
extracted_fixed_file.close()
original_file = open(path_fixed_code_dir_for_vulnerability + "/" + changed_code_file_path, "w")
original_file.write(content_extracted_fixed_file)
original_file.close()
bool_compiled, test_passed = execute_and_get_vul4j_results (PATH_FIXED_CODE_DIR, vul_id)
if test_passed is not True:
print("Test suite didn't pass, restoring files...")
command_to_execute = ["rm", "-r", PATH_FIXED_CODE_DIR + "/" + vul_id]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
command_to_execute = ["mv", PATH_PATCHES_DIR + "/" + vul_id, WASTE_FIXED_PATCHES_DIR + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
return False
return True
def checkout_and_verify():
df_csv = pd.read_csv(PATH_VUL4J_CSV)
if os.path.exists(PATH_CODE_DIR) is False:
os.mkdir(PATH_CODE_DIR)
if os.path.exists(WASTE_CODE_DIR) is False:
os.mkdir(WASTE_CODE_DIR)
if os.path.exists(PATH_FIXED_CODE_DIR) is False:
os.mkdir(PATH_FIXED_CODE_DIR)
if os.path.exists(PATH_PATCHES_DIR) is False:
os.mkdir(PATH_PATCHES_DIR)
for df_csv_ind in df_csv.index:
vul_id = df_csv["vul_id"][df_csv_ind]
patch_url = df_csv["human_patch"][df_csv_ind]
# checkout vulnerability and return if it is new
bool_is_new = checkout_vulnerability(PATH_CODE_DIR, vul_id)
if VERIFY_ALL_CHECKOUTS_AGAIN is True:
bool_is_new = True
if bool_is_new is True:
#returns if verified ok or not
bool_verified_ok = verify_checkout_and_retry(vul_id)
if bool_verified_ok is not True:
continue
# extract patches for vulnerabilities using commit IDs and returns if successful or not
bool_extraction_successful = extract_patches_and_modifications_information_for_vulnerability (vul_id, patch_url)
def process_this_mutant(vul_id, mutant_id, mutant_file_name, mutant_desired_path):
dir_class_mutants = mutant_file_name.replace(".java","_mutants")
path_mutant = PATH_MUTANTS_DIR + "/" + vul_id + "/" + dir_class_mutants + "/" + mutant_id + "/" + mutant_file_name
file_mutant = open(path_mutant, "r")
content_mutant = file_mutant.read()
file_mutant.close()
path_fixed = PATH_MUTATED_CODE_DIR + "/" + vul_id + "/" + mutant_desired_path
file_fixed = open(path_fixed, "r")
content_fixed = file_fixed.read()
file_fixed.close()
file_to_change = open(path_fixed, "w")
file_to_change.write(content_mutant)
file_to_change.close()
bool_compiled, test_passed = execute_and_get_vul4j_results (PATH_MUTATED_CODE_DIR, vul_id)
command_to_execute = ["cp", "-r", PATH_MUTATED_CODE_DIR + "/" + vul_id + "/VUL4J", \
PATH_MUTANTS_DIR + "/" + vul_id + "/" + dir_class_mutants + "/" + mutant_id + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
file_to_change = open(path_fixed, "w")
file_to_change.write(content_fixed)
file_to_change.close()
def execute_mutants(vul_id):
print("\nexecuting mutants for", vul_id, "\n")
path_mutated_code_dir_for_vulnerability = PATH_MUTATED_CODE_DIR + "/" + vul_id
lst_changed_code_files_paths = get_changed_code_files_paths (vul_id)
dict_changed_files_with_path = {}
for changed_code_file_path in lst_changed_code_files_paths:
arr_changed_code_file_path = changed_code_file_path.split("/")
changed_code_file_name = arr_changed_code_file_path[len(arr_changed_code_file_path) - 1]
if changed_code_file_name not in dict_changed_files_with_path:
dict_changed_files_with_path[changed_code_file_name] = changed_code_file_path
if os.path.exists(path_mutated_code_dir_for_vulnerability) is True:
command_to_execute = ["rm", "-r", path_mutated_code_dir_for_vulnerability]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
path_fixed_code_dir_for_vulnerability = PATH_FIXED_CODE_DIR + "/" + vul_id
if os.path.exists(path_fixed_code_dir_for_vulnerability) is False:
print(path_fixed_code_dir_for_vulnerability, "does not exist!")
return
else:
command_to_execute = ["cp", "-r", path_fixed_code_dir_for_vulnerability, PATH_MUTATED_CODE_DIR + "/"]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
for changed_file in dict_changed_files_with_path:
dir_class_mutants = changed_file.replace(".java","_mutants")
path_mutants_dir_for_vulnerability = PATH_MUTANTS_DIR + "/" + vul_id + "/" + dir_class_mutants
if os.path.exists(path_mutants_dir_for_vulnerability) is False:
continue
for mutant_id in os.listdir(path_mutants_dir_for_vulnerability):
print("\nprocessing for mutant", mutant_id)
if os.path.isdir(path_mutants_dir_for_vulnerability + "/" + mutant_id) is False:
continue
if os.path.exists(path_mutants_dir_for_vulnerability + "/" + mutant_id + \
"/VUL4J") is True:
continue
path_looking_for = path_mutants_dir_for_vulnerability + "/" + mutant_id + "/" + changed_file
print("looking for", path_looking_for)
if os.path.exists(path_looking_for):
process_this_mutant(vul_id, mutant_id, changed_file, \
dict_changed_files_with_path[changed_file])
def get_cve_id_and_failed_test_details(path_dir, vul_id):
dict_failed_tests = {}
path_testing_results_json_file = path_dir + "/" + vul_id + "/VUL4J/testing_results.json"
cve_id = ""
print("looking for", path_testing_results_json_file)
if os.path.exists(path_testing_results_json_file):
file_testing_results_json = open(path_testing_results_json_file)
content_testing_results_json_file = json.load(file_testing_results_json)
file_testing_results_json.close()
cve_id = content_testing_results_json_file["cve_id"]
failures = content_testing_results_json_file["tests"]["failures"]
for failure in failures:
failed_test = failure["test_class"] + "#" + failure["test_method"]
failure_name = failure["failure_name"]
if failed_test not in dict_failed_tests:
dict_failed_tests[failed_test] = failure_name
return cve_id, dict_failed_tests
def get_intersection_and_ochiai (broken_tests_by_vuln, broken_tests_by_mutant):
if len(broken_tests_by_vuln) == 0 or len(broken_tests_by_mutant) == 0:
return "\"\"", 0
intersection = []
for broken_test_by_vuln in broken_tests_by_vuln:
if broken_test_by_vuln in broken_tests_by_mutant:
intersection.append(broken_test_by_vuln)
if len(intersection) == 0:
return "\"\"", 0
prod = len(broken_tests_by_vuln) * len(broken_tests_by_mutant)
ochiai = round((len(intersection) / math.sqrt(prod)), 4)
string_intersection = "\""
for interesection_test in intersection:
if string_intersection == "\"":
string_intersection = string_intersection + interesection_test
else:
string_intersection = string_intersection + "," + interesection_test
string_intersection = string_intersection + "\""
return string_intersection, ochiai
def traverse_dictionary_get_failed_tests_with_failures (dict_failed_tests):
failed_tests = ""
failures = ""
for failed_test in dict_failed_tests:
if failed_tests == "":
failed_tests = failed_test
failures = dict_failed_tests[failed_test]
else:
failed_tests = failed_tests + "," + failed_test
failures = failures + "," + dict_failed_tests[failed_test]
return failed_tests, failures
def get_vuln_coupling_analysis_results(dict_failed_tests_by_vuln, dict_failed_tests_by_mutant):
keys_failed_tests_by_vuln = set(dict_failed_tests_by_vuln.keys())
keys_failed_tests_by_mutant = set(dict_failed_tests_by_mutant.keys())
if len(keys_failed_tests_by_mutant) == 0:
return keyword_mutant_not_killed
if dict_failed_tests_by_vuln == dict_failed_tests_by_mutant:
return keyword_strong_substitution
if keys_failed_tests_by_vuln == keys_failed_tests_by_mutant:
return keyword_test_substitution
shared_keys_failed_tests = keys_failed_tests_by_vuln.intersection(keys_failed_tests_by_mutant)
if len(shared_keys_failed_tests) == 0:
return keyword_no_substitution
if len(keys_failed_tests_by_mutant) > len(shared_keys_failed_tests):
if len(shared_keys_failed_tests) == len(keys_failed_tests_by_vuln):
for key in shared_keys_failed_tests:
if dict_failed_tests_by_mutant[key] != dict_failed_tests_by_vuln[key]:
return keyword_test_substitution_with_add_tests_failed
return keyword_strong_substitution_with_add_tests_failed
else:
for key in shared_keys_failed_tests:
if dict_failed_tests_by_mutant[key] != dict_failed_tests_by_vuln[key]:
return keyword_partial_test_substitution_with_add_tests_failed
return keyword_partial_substitution_with_add_tests_failed
else:
for key in shared_keys_failed_tests:
if dict_failed_tests_by_mutant[key] != dict_failed_tests_by_vuln[key]:
return keyword_partial_test_substitution
return keyword_partial_substitution
def get_mutant_vulnerability_comparison_scores(vul_id, dir_class_mutants, mutant_id, dict_failed_tests_by_vuln):
did_mutant_compile = False
did_tests_fail = False
imitates_vuln = False
ochiai = 0
failed_tests_intersection = "\"\""
path_mutants_dir_for_vulnerability = PATH_MUTANTS_DIR + "/" + vul_id + "/" + dir_class_mutants
bool_compiled = get_compilation_results(path_mutants_dir_for_vulnerability, mutant_id)
bool_test_passed = get_test_results(path_mutants_dir_for_vulnerability, mutant_id)
failed_tests_vuln, failures_vuln = traverse_dictionary_get_failed_tests_with_failures (dict_failed_tests_by_vuln)
failed_tests_vuln = "\"" + failed_tests_vuln + "\""
failures_vuln = "\"" + failures_vuln + "\""
failed_tests_mutant = ""
failures_mutant = ""
vuln_coupling_result = keyword_compilation_error
if bool_compiled is True:
did_mutant_compile = True
if bool_test_passed is False:
did_tests_fail = True
cve_id, dict_failed_tests_by_mutant = get_cve_id_and_failed_test_details(path_mutants_dir_for_vulnerability, mutant_id)
if set(dict_failed_tests_by_mutant.keys()) == set(dict_failed_tests_by_vuln.keys()):
print(mutant_id, "triggers the same tests triggered by the vulnerability!")
imitates_vuln = True
failed_tests_intersection, ochiai = get_intersection_and_ochiai (set(dict_failed_tests_by_vuln.keys()), set(dict_failed_tests_by_mutant.keys()))
failed_tests_mutant, failures_mutant = traverse_dictionary_get_failed_tests_with_failures (dict_failed_tests_by_mutant)
# for failed_test in dict_failed_tests_by_mutant:
# if failed_tests == "":
# failed_tests = failed_test
# failures = dict_failed_tests_by_mutant[failed_test]
# else:
# failed_tests = failed_tests + "," + failed_test
# failures = failures + "," + dict_failed_tests_by_mutant[failed_test]
failed_tests_mutant = "\"" + failed_tests_mutant + "\""
failures_mutant = "\"" + failures_mutant + "\""
vuln_coupling_result = get_vuln_coupling_analysis_results(dict_failed_tests_by_vuln, dict_failed_tests_by_mutant)
else:
vuln_coupling_result = keyword_mutant_not_killed
return did_mutant_compile, did_tests_fail, imitates_vuln, ochiai, failed_tests_intersection, failed_tests_mutant, failures_mutant, failed_tests_vuln, failures_vuln, vuln_coupling_result
def separate_out_fixed_files(vul_id):
path_patches_dir_for_vulnerability = PATH_PATCHES_DIR + "/" + vul_id
dir_fixes_this_vuln = PATH_FIXES_FOR_MUTATION_DIR + "/" + vul_id
if os.path.exists(dir_fixes_this_vuln):
return
lst_changed_code_files_paths = get_changed_code_files_paths (vul_id)
if len(lst_changed_code_files_paths) > 0:
os.mkdir(dir_fixes_this_vuln)
print("created directory:", dir_fixes_this_vuln)
for changed_code_file_path in lst_changed_code_files_paths:
arr_changed_code_file_path = changed_code_file_path.split("/")
changed_code_file_name = arr_changed_code_file_path[len(arr_changed_code_file_path) - 1]
path_fixed_file = path_patches_dir_for_vulnerability + "/" + changed_code_file_name.replace(".java", "_after.java")
command_to_execute = ["cp", path_fixed_file, dir_fixes_this_vuln + "/" + changed_code_file_name]
print("executing", command_to_execute)
subprocess.run(command_to_execute, stdout=subprocess.DEVNULL)
def analyze_mutants_simulations_and_get_analysis():
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME):
df_analysis_csv = pd.read_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME)
return df_analysis_csv
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR) is False:
os.mkdir(PATH_MUTANTS_ANALYSIS_DIR)
df_analysis_csv = pd.DataFrame(columns = ['vul_id', 'cve_id', 'class', 'mut_id', 'did_mutant_compile', 'did_tests_fail', \
'imitates_vuln', 'ochiai', 'failed_tests_intersection', 'failed_tests', 'failures'])
for vul_id in os.listdir(PATH_MUTANTS_DIR):
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME.replace("all",vul_id)):
df_vul_id_analysis_csv = pd.read_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME.replace("all",vul_id))
df_analysis_csv = df_analysis_csv.append(df_vul_id_analysis_csv, ignore_index=True)
continue
df_vul_id_analysis_csv = pd.DataFrame(columns = ['vul_id', 'cve_id', 'class', 'mut_id', 'did_mutant_compile', 'did_tests_fail', \
'imitates_vuln', 'ochiai', 'failed_tests_intersection', 'failed_tests', 'failures'])
if os.path.isdir(PATH_MUTANTS_DIR + "/" + vul_id) is False:
continue
dict_changed_files_with_path = {}
lst_changed_code_files_paths = get_changed_code_files_paths (vul_id)
for changed_code_file_path in lst_changed_code_files_paths:
arr_changed_code_file_path = changed_code_file_path.split("/")
changed_code_file_name = arr_changed_code_file_path[len(arr_changed_code_file_path) - 1]
if changed_code_file_name not in dict_changed_files_with_path:
dict_changed_files_with_path[changed_code_file_name] = changed_code_file_path
for changed_file in dict_changed_files_with_path:
dir_class_mutants = changed_file.replace(".java","_mutants")
path_mutants_dir_for_vulnerability = PATH_MUTANTS_DIR + "/" + vul_id + "/" + dir_class_mutants
if os.path.exists(path_mutants_dir_for_vulnerability) is False:
continue
cve_id, dict_failed_tests_by_vuln = get_cve_id_and_failed_test_details(PATH_CODE_DIR, vul_id)
if len(dict_failed_tests_by_vuln) == 0:
continue
for mutant_id in os.listdir(path_mutants_dir_for_vulnerability):
if os.path.isdir(path_mutants_dir_for_vulnerability + "/" + mutant_id) is False:
continue
print("\nanalyzing vul_id:", vul_id, "| class:", changed_file, "| mut_id:", mutant_id)
did_mutant_compile, did_tests_fail, imitates_vuln, ochiai, failed_tests_intersection, failed_tests, failures, failed_tests_vuln, failures_vuln, vuln_coupling_result = \
get_mutant_vulnerability_comparison_scores(vul_id, dir_class_mutants, mutant_id, dict_failed_tests_by_vuln)
df_vul_id_analysis_csv = df_vul_id_analysis_csv.append({'vul_id' : "\"" + vul_id + "\"",
'cve_id' : "\"" + cve_id + "\"",
'class' : "\"" + changed_file + "\"",
'mut_id' : mutant_id,
'did_mutant_compile': did_mutant_compile,
'did_tests_fail' : did_tests_fail,
'imitates_vuln' : imitates_vuln,
'ochiai' : ochiai,
'failed_tests_intersection' : failed_tests_intersection,
'failed_tests' : failed_tests,
'failures' : failures,
'failed_tests_vuln' : failed_tests_vuln,
'failures_vuln' : failures_vuln,
'vuln_coupling_result' : vuln_coupling_result}, ignore_index = True)
df_analysis_csv = df_analysis_csv.append({'vul_id' : "\"" + vul_id + "\"",
'cve_id' : "\"" + cve_id + "\"",
'class' : "\"" + changed_file + "\"",
'mut_id' : mutant_id,
'did_mutant_compile': did_mutant_compile,
'did_tests_fail' : did_tests_fail,
'imitates_vuln' : imitates_vuln,
'ochiai' : ochiai,
'failed_tests_intersection' : failed_tests_intersection,
'failed_tests' : failed_tests,
'failures' : failures,
'failed_tests_vuln' : failed_tests_vuln,
'failures_vuln' : failures_vuln,
'vuln_coupling_result' : vuln_coupling_result}, ignore_index = True)
if len(df_vul_id_analysis_csv) > 0:
print("writing", ALL_ANALYSIS_CSV_NAME.replace("all",vul_id), "in", PATH_MUTANTS_ANALYSIS_DIR)
df_vul_id_analysis_csv.to_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME.replace("all",vul_id), index = False)
print("writing", ALL_ANALYSIS_CSV_NAME, "in", PATH_MUTANTS_ANALYSIS_DIR)
df_analysis_csv.to_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME, index = False)
return df_analysis_csv
def write_to_completed_vul4j_ids_file(file_path, vul_id):
print("writing to", file_path)
df_completed_vul4j_ids = pd.DataFrame(columns = ['vul_id'])
if os.path.exists(file_path):
df_completed_vul4j_ids = pd.read_csv(file_path)
df_completed_vul4j_ids = df_completed_vul4j_ids.append({'vul_id' : vul_id}, ignore_index = True)
df_completed_vul4j_ids.to_csv(file_path, index = False)
def execute_command_with_timeout(command_to_execute):
try:
print("executing", command_to_execute)
p = subprocess.Popen(command_to_execute, stdout=subprocess.DEVNULL, start_new_session=True)
p.wait(timeout=TIMEOUT)
except subprocess.TimeoutExpired:
print("timed out!")
print('Terminating the whole process group...')
os.killpg(os.getpgid(p.pid), signal.SIGTERM)
def iterate_over_analysis_csv ():
if os.path.exists(PATH_ML_DATASET_DIR + "/" + ML_DATASET_CSV_NAME):
print(PATH_ML_DATASET_DIR + "/" + ML_DATASET_CSV_NAME, "exists. Skipping...")
return
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME) is False:
print(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME, "does not exist!")
return
df_ml_dataset = pd.DataFrame(columns = ['vul_id', 'cve_id', 'class', 'mut_id', 'did_mutant_compile', 'did_tests_fail', \
'imitates_vuln', 'ochiai', 'failed_tests_intersection', 'failed_tests', 'failures', \
'abs_seq'])
df_analysis_csv = pd.read_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + ALL_ANALYSIS_CSV_NAME)
df_compilable_mutants = df_analysis_csv.loc[(df_analysis_csv['did_mutant_compile'] == True)]
dict_vuln_mapping_csv = {}
for df_compilable_mutants_index in df_compilable_mutants.index:
vul_id = df_compilable_mutants['vul_id'][df_compilable_mutants_index].replace("\"","")
class_name = df_compilable_mutants['class'][df_compilable_mutants_index].replace("\"","")
mut_id = df_compilable_mutants['mut_id'][df_compilable_mutants_index]
file_from_src2abs_name = vul_id + "_" + class_name.replace(".java","") + "_" + str(mut_id) + "_abs.txt"
if os.path.exists(PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name) is False:
class_mutants_dir_name = class_name.replace(".java","_mutants")
class_mutants_mapping_csv_name = class_name.replace(".java","-mapping.csv")
class_mutants_mapping_csv_path = PATH_MUTANTS_DIR + "/" + vul_id + "/" + class_mutants_dir_name + "/" + class_mutants_mapping_csv_name
if vul_id not in dict_vuln_mapping_csv:
print("searching for", class_mutants_mapping_csv_path)
if os.path.exists(class_mutants_mapping_csv_path) is False:
continue
df_class_mutants_mapping_csv = pd.read_csv(class_mutants_mapping_csv_path)
dict_vuln_mapping_csv[vul_id] = df_class_mutants_mapping_csv
df_class_mutants_mapping_csv = dict_vuln_mapping_csv[vul_id]
df_selected_mapping = df_class_mutants_mapping_csv.loc[(df_class_mutants_mapping_csv['id'] == mut_id)]
for df_selected_mapping_index in df_selected_mapping.index:
mut_operator = df_selected_mapping["mut_operator"][df_selected_mapping_index]
orig_token = df_selected_mapping["orig_token"][df_selected_mapping_index]
orig_token = str(orig_token)
masked_expr = df_selected_mapping["masked_expr"][df_selected_mapping_index]
masked_seq = df_selected_mapping["masked_seq"][df_selected_mapping_index]
break
original_seq_with_mutation_operator = masked_seq.replace("<mask>", " " + orig_token + " [MUTATION_OPERATOR] ")
file_for_src2abs_name = vul_id + "_" + class_name.replace(".java","") + "_" + str(mut_id) + ".txt"
file_for_src2abs = open(PATH_ML_DATASET_DIR + "/" + file_for_src2abs_name, "w")
file_for_src2abs.write(original_seq_with_mutation_operator)
file_for_src2abs.close()
command_to_execute = ["java", "-jar", PATH_SRC2ABS, "single", "method", PATH_ML_DATASET_DIR + "/" + file_for_src2abs_name, PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name, PATH_IDIOMS]
execute_command_with_timeout(command_to_execute)
command_to_execute = ["rm", PATH_ML_DATASET_DIR + "/" + file_for_src2abs_name]
execute_command_with_timeout(command_to_execute)
if os.path.exists(PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name + ".map"):
command_to_execute = ["rm", PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name + ".map"]
execute_command_with_timeout(command_to_execute)
if os.path.exists(PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name) is False:
continue
file_from_src2abs = open(PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name, "r")
abstracted_seq_with_mutation_operator = file_from_src2abs.read()
file_from_src2abs.close()
if abstracted_seq_with_mutation_operator is None or abstracted_seq_with_mutation_operator == "":
continue
if "[ MUTATION_OPERATOR ]" not in abstracted_seq_with_mutation_operator:
continue
abstracted_seq_final = abstracted_seq_with_mutation_operator.replace("[ MUTATION_OPERATOR ]", mut_operator)
command_to_execute = ["rm", PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name]
execute_command_with_timeout(command_to_execute)
file_from_src2abs = open(PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name, "w")
file_from_src2abs.write(abstracted_seq_final)
file_from_src2abs.close()
file_from_src2abs = open(PATH_ML_DATASET_DIR + "/" + file_from_src2abs_name, "r")
abstracted_seq_final = file_from_src2abs.read()
file_from_src2abs.close()
if abstracted_seq_final is None or abstracted_seq_final == "":
continue
row_vul_id = df_compilable_mutants['vul_id'][df_compilable_mutants_index]
row_cve_id = df_compilable_mutants['cve_id'][df_compilable_mutants_index]
row_class = df_compilable_mutants['class'][df_compilable_mutants_index]
row_mut_id = df_compilable_mutants['mut_id'][df_compilable_mutants_index]
row_did_mutant_compile = df_compilable_mutants['did_mutant_compile'][df_compilable_mutants_index]
row_did_tests_fail = df_compilable_mutants['did_tests_fail'][df_compilable_mutants_index]
row_imitates_vuln = df_compilable_mutants['imitates_vuln'][df_compilable_mutants_index]
row_ochiai = df_compilable_mutants['ochiai'][df_compilable_mutants_index]
row_failed_tests_intersection = df_compilable_mutants['failed_tests_intersection'][df_compilable_mutants_index]
row_failed_tests = df_compilable_mutants['failed_tests'][df_compilable_mutants_index]
row_failures = df_compilable_mutants['failures'][df_compilable_mutants_index]
df_ml_dataset = df_ml_dataset.append({'vul_id' : row_vul_id,
'cve_id' : row_cve_id,
'class' : row_class,
'mut_id' : row_mut_id,
'did_mutant_compile': row_did_mutant_compile,
'did_tests_fail' : row_did_tests_fail,
'imitates_vuln' : row_imitates_vuln,
'ochiai' : row_ochiai,
'failed_tests_intersection' : row_failed_tests_intersection,
'failed_tests' : row_failed_tests,
'failures' : row_failures,
'abs_seq' : "\"" + abstracted_seq_final + "\""}, ignore_index = True)
df_ml_dataset.to_csv(PATH_ML_DATASET_DIR + "/" + ML_DATASET_CSV_NAME, index = False)
def get_changed_code_files_and_methods_nums (vul_id):
lst_changed_files = []
lst_changed_methods = []
path_patches_dir_for_vulnerability = PATH_PATCHES_DIR + "/" + vul_id
lst_changed_code_files_paths = []
if os.path.exists(path_patches_dir_for_vulnerability + "/" + CHANGED_METHODS_CSV_NAME):
df_changed_methods = pd.read_csv(path_patches_dir_for_vulnerability + "/" + CHANGED_METHODS_CSV_NAME)
for df_changed_methods_ind in df_changed_methods.index:
file_path = df_changed_methods["file_path"][df_changed_methods_ind]
long_name = df_changed_methods["long_name"][df_changed_methods_ind]
if ("/test/" not in file_path) and ("/tests/" not in file_path) and (".java" in file_path) and (file_path not in lst_changed_code_files_paths):
if file_path not in lst_changed_files:
lst_changed_files.append(file_path)
if long_name not in lst_changed_methods:
lst_changed_methods.append(long_name)
return len(lst_changed_files), len(lst_changed_methods)
def analyze_csvs_at_high_level ():
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR + "/" + HIGH_LEVEL_ANALYSIS_CSV_NAME):
df_analysis_csv = pd.read_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + HIGH_LEVEL_ANALYSIS_CSV_NAME)
return df_analysis_csv
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR) is False:
os.mkdir(PATH_MUTANTS_ANALYSIS_DIR)
df_analysis_csv = pd.DataFrame(columns = ['vul_id', 'cve_id', 'changed_files_num', 'changed_methods_num', 'failed_tests_by_vuln', 'total_mutants', 'mutants_failing_tests_num', 'mutants_imitating_vuln_num', 'ochiai_avg'])
for vul_id in os.listdir(PATH_MUTANTS_DIR):
if os.path.isdir(PATH_MUTANTS_DIR + "/" + vul_id) is False:
continue
dict_changed_files_with_path = {}
lst_changed_code_files_paths = get_changed_code_files_paths (vul_id)
changed_files_num, changed_methods_num = get_changed_code_files_and_methods_nums (vul_id)
for changed_code_file_path in lst_changed_code_files_paths:
arr_changed_code_file_path = changed_code_file_path.split("/")
changed_code_file_name = arr_changed_code_file_path[len(arr_changed_code_file_path) - 1]
if changed_code_file_name not in dict_changed_files_with_path:
dict_changed_files_with_path[changed_code_file_name] = changed_code_file_path
total_mutants = 0
mutants_failing_tests_num = 0
mutants_imitating_vuln_num = 0
ochiai_sum = 0
total_strong_substitution = 0
total_strong_substitution_with_add_tests_failed = 0
total_test_substitution = 0
total_test_substitution_with_add_tests_failed = 0
total_partial_substitution = 0
total_partial_substitution_with_add_tests_failed = 0
total_partial_test_substitution = 0
total_partial_test_substitution_with_add_tests_failed = 0
total_no_substitution = 0
total_mutant_not_killed = 0
total_compilation_error = 0
for changed_file in dict_changed_files_with_path:
print("\nanalyzing vul_id:", vul_id, "| class:", changed_file)
dir_class_mutants = changed_file.replace(".java","_mutants")
path_mutants_dir_for_vulnerability = PATH_MUTANTS_DIR + "/" + vul_id + "/" + dir_class_mutants
if os.path.exists(path_mutants_dir_for_vulnerability) is False:
continue
cve_id, dict_failed_tests_by_vuln = get_cve_id_and_failed_test_details(PATH_CODE_DIR, vul_id)
failed_tests_by_vuln = len(dict_failed_tests_by_vuln)
if len(dict_failed_tests_by_vuln) == 0:
continue
for mutant_id in os.listdir(path_mutants_dir_for_vulnerability):
if os.path.isdir(path_mutants_dir_for_vulnerability + "/" + mutant_id) is False:
continue
did_mutant_compile, did_tests_fail, imitates_vuln, ochiai, failed_tests_intersection, failed_tests, failures, failed_tests_vuln, failures_vuln, vuln_coupling_result = \
get_mutant_vulnerability_comparison_scores(vul_id, dir_class_mutants, mutant_id, dict_failed_tests_by_vuln)
if did_mutant_compile == True:
total_mutants = total_mutants + 1
if did_tests_fail == True:
mutants_failing_tests_num = mutants_failing_tests_num + 1
if imitates_vuln == True:
mutants_imitating_vuln_num = mutants_imitating_vuln_num + 1
ochiai_sum = ochiai_sum + ochiai
if vuln_coupling_result == keyword_strong_substitution:
total_strong_substitution = total_strong_substitution + 1
elif vuln_coupling_result == keyword_strong_substitution_with_add_tests_failed:
total_strong_substitution_with_add_tests_failed = total_strong_substitution_with_add_tests_failed + 1
elif vuln_coupling_result == keyword_test_substitution:
total_test_substitution = total_test_substitution + 1
elif vuln_coupling_result == keyword_test_substitution_with_add_tests_failed:
total_test_substitution_with_add_tests_failed = total_test_substitution_with_add_tests_failed + 1
elif vuln_coupling_result == keyword_partial_substitution:
total_partial_substitution = total_partial_substitution + 1
elif vuln_coupling_result == keyword_partial_substitution_with_add_tests_failed:
total_partial_substitution_with_add_tests_failed = total_partial_substitution_with_add_tests_failed + 1
elif vuln_coupling_result == keyword_partial_test_substitution:
total_partial_test_substitution = total_partial_test_substitution + 1
elif vuln_coupling_result == keyword_partial_test_substitution_with_add_tests_failed:
total_partial_test_substitution_with_add_tests_failed = total_partial_test_substitution_with_add_tests_failed + 1
elif vuln_coupling_result == keyword_no_substitution:
total_no_substitution = total_no_substitution + 1
elif vuln_coupling_result == keyword_mutant_not_killed:
total_mutant_not_killed = total_mutant_not_killed + 1
else:
total_compilation_error = total_compilation_error + 1
if total_mutants == 0:
ochiai_avg = 0
else:
ochiai_avg = ochiai_sum / total_mutants
df_analysis_csv = df_analysis_csv.append({'vul_id' : vul_id,
'cve_id' : cve_id,
'changed_files_num' : changed_files_num,
'changed_methods_num' : changed_methods_num,
'failed_tests_by_vuln' : failed_tests_by_vuln,
'total_mutants': total_mutants,
'mutants_failing_tests_num' : mutants_failing_tests_num,
'mutants_imitating_vuln_num' : mutants_imitating_vuln_num,
'ochiai_avg' : ochiai_avg,
'total_strong_substitution' : total_strong_substitution,
'total_strong_substitution_with_add_tests_failed' : total_strong_substitution_with_add_tests_failed,
'total_test_substitution' : total_test_substitution,
'total_test_substitution_with_add_tests_failed' : total_test_substitution_with_add_tests_failed,
'total_partial_substitution' : total_partial_substitution,
'total_partial_substitution_with_add_tests_failed' : total_partial_substitution_with_add_tests_failed,
'total_partial_test_substitution' : total_partial_test_substitution,
'total_partial_test_substitution_with_add_tests_failed' : total_partial_test_substitution_with_add_tests_failed,
'total_no_substitution' : total_no_substitution,
'total_mutant_not_killed' : total_mutant_not_killed,
'total_compilation_error' : total_compilation_error}, ignore_index = True)
print("writing", HIGH_LEVEL_ANALYSIS_CSV_NAME, "in", PATH_MUTANTS_ANALYSIS_DIR)
df_analysis_csv.to_csv(PATH_MUTANTS_ANALYSIS_DIR + "/" + HIGH_LEVEL_ANALYSIS_CSV_NAME, index = False)
return df_analysis_csv
def plot (df_analysis_csv):
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR + "/" + PLOT_FILE_NAME) == False:
df = df_analysis_csv.loc[(df_analysis_csv['did_mutant_compile'] == True) & (df_analysis_csv['did_tests_fail'] == True)]
df = df.sort_values(by='cve_id', ascending=True)
rcParams['figure.figsize'] = 15,7
f = plt.figure(1)
ax = sns.boxplot(x=df["cve_id"], y=df["ochiai"] )
ax.set_xticklabels(ax.get_xticklabels(),rotation=70)
plt.xlabel('CVE', fontsize=16);
plt.ylabel('Ochiai', fontsize=16);
plt.tick_params(axis='both', which='major', labelsize=12)
plt.tight_layout()
plt.savefig(PATH_MUTANTS_ANALYSIS_DIR + "/" + PLOT_FILE_NAME)
def plot_coupling (df_analysis_csv):
if os.path.exists(PATH_MUTANTS_ANALYSIS_DIR + "/" + PLOT_COUPLING_FILE_NAME) == False:
exclude_categories = [keyword_compilation_error, keyword_mutant_not_killed, keyword_no_substitution]
data = df_analysis_csv[~df_analysis_csv['vuln_coupling_result'].isin(exclude_categories)]
category_order = [keyword_strong_substitution, keyword_strong_substitution_with_add_tests_failed, keyword_test_substitution, \
keyword_test_substitution_with_add_tests_failed, keyword_partial_substitution, \
keyword_partial_substitution_with_add_tests_failed, keyword_partial_test_substitution, \
keyword_partial_test_substitution_with_add_tests_failed]
data['vuln_coupling_result'] = pd.Categorical(
data['vuln_coupling_result'], categories=category_order, ordered=True)
grouped_data = data.groupby(['cve_id', 'vuln_coupling_result']).size().unstack(fill_value=0)
grouped_data_percentage = grouped_data.div(grouped_data.sum(axis=1), axis=0) * 100
grouped_data_percentage = grouped_data_percentage.sort_values(by='cve_id', ascending=False)
ax = grouped_data_percentage.plot(kind='barh', stacked=True, figsize=(10, 7))
plt.xlabel('Coupling Mutants(%)')
plt.ylabel('CVE')
category_labels = {keyword_strong_substitution: "Strong Coupling",
keyword_strong_substitution_with_add_tests_failed: "Strong Coupling + Additional",
keyword_test_substitution: "Test Coupling",
keyword_test_substitution_with_add_tests_failed: "Test Coupling + Additional",
keyword_partial_substitution: "Partial Coupling",