ANIL KOYUNCU
457 lines
20 KiB
Python
457 lines
20 KiB
Python
from common.commons import *
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DATA_PATH = os.environ["DATA_PATH"]
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SPINFER_PATH = os.environ["spinfer"]
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SPINFER_INDEX_PATH = os.environ["dataset"]
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COCCI_PATH = join(os.environ["coccinelle"],'spatch')
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DATASET = os.environ["dataset"]
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def indexCore():
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print(SPINFER_INDEX_PATH)
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# dbDir = join(DATA_PATH, 'redis')
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# startDB(dbDir, "6399", "ALLdumps-gumInput.rdb")
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# import redis
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# redis_db = redis.StrictRedis(host="localhost", port=6399, db=0)
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# keys = redis_db.hkeys("dump")#hkeys "dump"
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# # keys = redis_db.scan(0, match='*', count='1000000')
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#
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# matches = pd.DataFrame(keys, columns=['pairs_key'])
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#
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# # matches = load_zipped_pickle(join(DATA_PATH,'singleHunks'))
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# matches['pairs_key'] = matches['pairs_key'].apply(lambda x: x.decode())
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# matches['root'] = matches['pairs_key'].apply(lambda x: x.split('/')[0])
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# matches['size'] = matches['pairs_key'].apply(lambda x: x.split('/')[1])
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# matches['file'] = matches['pairs_key'].apply(lambda x: x.split('/')[2])
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# matches['hunk'] = matches['pairs_key'].apply(lambda x: x.split('/')[2].split('_')[-1])
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# matches['fileName'] = matches['pairs_key'].apply(lambda x: '_'.join(x.split('/')[2].split('_')[:-1]))
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# test = matches[['fileName', 'hunk']]
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# df = test.groupby(by=['fileName'], as_index=False).agg(lambda x: x.tolist())
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# # sDF = df[df.hunk.apply(lambda x: True if x == ['0'] else False)]
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# sDF = df[df.hunk.apply(lambda x: True if len(x)<10005 else False)]
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# singleHunkedFiles = sDF.fileName.unique().tolist()
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# singleHunkedFiles = [i.replace('.txt', '') for i in singleHunkedFiles]
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clusterPath = join(DATA_PATH, 'shapes')
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roots = listdir(clusterPath)
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roots = [i for i in roots if not (i.startswith('.') or i.endswith('.pickle'))]
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for root in roots:
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root
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sizes = listdir(join(clusterPath,root))
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sizes = [f for f in sizes if not f.startswith('.')]
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for size in sizes:
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# actions = listdir(join(clusterPath,root,size))
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# for action in actions:
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clusters = listdir(join(clusterPath,root,size))
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clusters = [f for f in clusters if not f.startswith('.')]
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for cluster in clusters:
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members = listdir(join(clusterPath,root,size,cluster))
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members= [f for f in members if not f.startswith('.')]
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# members = [re.sub('^linux_','',i) for i in members]
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# csMembers = {}
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# for j in [i.split('.txt_') for i in members]:
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# k,v = j
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# k = k +'.txt'
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# if k in csMembers:
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# tmp = csMembers[k]
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# tmp.append(v)
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# csMembers[k] = tmp
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# else:
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# csMembers[k] = [v]
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#
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# splitMembers = []
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# for k,v in csMembers.items():
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# hunks = df[df.fileName == k].iloc[0].hunk
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# if set(hunks) == set(v):
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# splitMembers.append(k)
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members = [re.sub('\.txt\_\d+','',i) for i in members]
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members = list(set(members))
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# members = [i for i in members if i in singleHunkedFiles or i in splitMembers]
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if len(members) > 1:
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lines = []
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for member in members:
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split =member.split('_')
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pj = split[0]
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member ='_'.join(split[1:])
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line = pj+'/prevFiles/prev_' + member + ' ' + pj+'/revFiles/' + member + '\n'
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lines.append(line)
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if len(lines)>0:
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with open(join(SPINFER_INDEX_PATH, root+"_"+size +'_'+cluster+'.index'), 'w', encoding='utf-8') as writeFile:
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# if levelPatch == 0:
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writeFile.write(''.join(lines))
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def test():
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indexes = listdir(SPINFER_INDEX_PATH)
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indexes = [i for i in indexes if i.endswith('.index')]
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coccis = listdir(join(SPINFER_INDEX_PATH,'cocci'))
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if not os.path.exists(join(SPINFER_INDEX_PATH,'indexNC')):
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os.mkdir(join(SPINFER_INDEX_PATH,'indexNC'))
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for i in indexes:
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if re.sub('\.index', '.cocci', i) not in coccis:
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shutil.move(join(SPINFER_INDEX_PATH,i),join(SPINFER_INDEX_PATH,'indexNC',i))
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def runSpinfer():
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indexCore()
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indexes = listdir(SPINFER_INDEX_PATH)
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indexes = [i for i in indexes if i.endswith('.index')]
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# indexes = ['if_9_44.index']
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if not os.path.exists(join(SPINFER_INDEX_PATH,'cocci')):
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os.mkdir(join(SPINFER_INDEX_PATH,'cocci'))
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os.chdir(SPINFER_INDEX_PATH)
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pairs = []
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for i in indexes:
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pairs.append((os.path.getsize(i),i))
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pairs.sort(key=lambda s:s[0])
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coccis = listdir(join(SPINFER_INDEX_PATH,'cocci'))
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cmdList = []
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bigCmdList = []
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for t in pairs:
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sizes, idx = t
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cocciName = re.sub('\.index', '.cocci', idx)
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if cocciName in coccis:
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continue
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# cmd = SPINFER_PATH + " --no-progress -f " + idx + " -o cocci/" + cocciName
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# bigCmdList.append(cmd)
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if sizes < 500:
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# #cmd = SPINFER_PATH + " -j 16 -f " + idx + " -o cocci/" + re.sub('\.index', '.cocci', idx)
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# # cmd = SPINFER_PATH + " --no-progress --genericity 1 -j 16 -f " + idx + " -o cocci/" + cocciName
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cmd = SPINFER_PATH + " --no-progress -f " + idx + " -o cocci/" + cocciName
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cmdList.append(cmd)
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else:
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# # cmd = SPINFER_PATH + " --no-progress --genericity 1 -j 1 -f " + idx + " -o cocci/" + cocciName
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cmd = SPINFER_PATH + " --no-progress -f " + idx + " -o cocci/" + cocciName
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bigCmdList.append(cmd)
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# for cmd in cmdList:
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# logging.info(cmd)
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# output, e = shellGitCheckout(cmd)
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# logging.info(output)
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parallelRun(callSpinfer,cmdList)
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# logging.info('big commands')
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# for cmd in bigCmdList:
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# # logging.info(cmd)
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# # output, e = shellGitCheckout(cmd)
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# # logging.info(output)
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parallelRun(callSpinfer,bigCmdList)
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# if not os.path.exists(join(DATA_PATH,'cocci')):
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# os.mkdir(join(DATA_PATH,'cocci'))
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# logging.info(cmd)
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# output,e = shellGitCheckout(cmd)
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# logging.info(output)
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def divideCoccis():
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import datetime
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shutil.copytree(join(SPINFER_INDEX_PATH,'cocci'),join(DATA_PATH,'cocci'+ datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')))
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coccis =os.listdir(join(SPINFER_INDEX_PATH,'cocci'))
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for cocci in coccis:
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with open(join(SPINFER_INDEX_PATH,'cocci',cocci), 'r') as iFile:
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idx = iFile.readlines()
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idx
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values = np.array(idx)
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points = np.where(values == '@@\n')
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points = list(itertools.chain.from_iterable(points))
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if len(points) == 0:
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os.remove(join(SPINFER_INDEX_PATH, 'cocci', cocci))
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# patches = list(zip(*([iter(points)] * 2)))
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patches = list(pairwise(points[::2]))# every second element in list
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if len(patches) > 0:
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i = 0;
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for t in patches :
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t
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with open(join(SPINFER_INDEX_PATH, 'cocci', cocci+str(i)), 'w') as iFile:
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iFile.writelines(idx[t[0]:t[1]])
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i=i+1
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t
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with open(join(SPINFER_INDEX_PATH, 'cocci', cocci + str(i)), 'w') as iFile:
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iFile.writelines(idx[t[1]:])
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os.remove(join(SPINFER_INDEX_PATH, 'cocci', cocci))
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def removeDuplicates():
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commentPattern = r"(/\*([^*]|[\r\n]|(\*+([^*/]|[\r\n])))*\*+/)|(//.*)"
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coccis =os.listdir(join(SPINFER_INDEX_PATH, 'cocci'))
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cocciPatterns = pd.DataFrame(columns=['cid', 'pattern','inferedFrom'])
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ind = 0
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for cocci in coccis:
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with open(join(SPINFER_INDEX_PATH, 'cocci', cocci), 'r') as iFile:
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idx = iFile.read()
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idx
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inferedFrom = re.search(r"// Infered from:(.*)\n",idx).groups()
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pattern = re.sub(commentPattern, '', idx, re.DOTALL)
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cocciPatterns.loc[ind] = [cocci,pattern,inferedFrom]
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ind = ind +1
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cocciPatterns['iFiles'] = cocciPatterns.inferedFrom.apply(lambda x: getInferred(x[0]))
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cocciPatterns['freq'] = cocciPatterns.iFiles.apply(lambda x: len(x))
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cocciPatterns['project'] = cocciPatterns.iFiles.apply(lambda x: list(set([i.split('/{')[0].replace('(','') for i in x])))
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cocciPatterns.sort_values(by='freq', inplace=True, ascending=False)
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save_zipped_pickle(cocciPatterns,join(DATA_PATH,'allCocciPatterns.pickle'))
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allPatterns = cocciPatterns.cid.values.tolist()
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uniquePatterns = cocciPatterns.drop_duplicates(subset=['pattern']).cid.values.tolist()
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toRemove = list(set(allPatterns).difference(uniquePatterns))
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print(toRemove)
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for p in toRemove:
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os.remove(join(SPINFER_INDEX_PATH, 'cocci', p))
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print(len(uniquePatterns))
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def filterPatterns():
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cocciPatterns = load_zipped_pickle(join(DATA_PATH,'allCocciPatterns.pickle'))
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cocciPatterns['filtered'] = cocciPatterns.iFiles.apply(lambda x: [i for i in x if (
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i.startswith('(libtiff') or i.startswith('(php-src') or i.startswith('(cpython'))])
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return cocciPatterns[cocciPatterns.filtered.str.len() > 0].cid.values.tolist()
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def getInferred(x):
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regex = r"\(.*?\)"
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matches = re.finditer(regex, x)
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results = []
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for matchNum, match in enumerate(matches, start=1):
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results.append(match.group())
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return results
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def getNegLines(x):
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negLines = r"^-(.*)"
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matches = re.finditer(negLines, x, re.MULTILINE)
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res = []
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for matchNum, match in enumerate(matches, start=1):
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for groupNum in range(0, len(match.groups())):
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groupNum = groupNum + 1
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# print("Group {groupNum} found at {start}-{end}: {group}".format(groupNum=groupNum,
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# start=match.start(groupNum),
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# end=match.end(groupNum),
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# group=match.group(groupNum)))
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res.append(match.group(groupNum))
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from common.preprocessing import getTokensForPatterns
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tokens = getTokensForPatterns(res)
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return tokens
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def patternOperations():
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cocciPatterns = load_zipped_pickle(join(DATA_PATH, 'allCocciPatterns.pickle'))
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# cocciPatterns.pattern.apply(lambda x:re.search(r"@@(.*)@@",x,re.DOTALL|re.M).groups())
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cocciPatterns['patternTokens'] = cocciPatterns.pattern.apply(lambda x:getNegLines(x))
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#set(getTokensForPatterns(lines)).intersection(set(tokens))
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save_zipped_pickle(cocciPatterns,join(DATA_PATH, 'allCocciPatterns.pickle'))
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# import html
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# def getTokensForPatterns(res):
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# if isinstance(res, list):
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# merged = str()
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# for r in res:
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# if isinstance(r, list):
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# merged = merged + ' ' + ' '.join(r)
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# else:
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# merged = merged +' ' + r
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# else:
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# merged=res
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#
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# res = html.unescape(merged)
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#
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# tokens = getTokens(res,False)
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#
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# stripped = []
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# for t in tokens:
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# splits = re.split('\.|\(|\)|:|>|<|:|=|/|\\\\|\'|-|,|\]|\[|}|{|;',t)
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# for s in splits:
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# stripped.append(s)
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# non_empty = [i for i in stripped if i != '']
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# return non_empty
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# from nltk.tokenize import RegexpTokenizer
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#
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# def getTokens(re,printDetail=False):
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# tokenizer = RegexpTokenizer(r'\S+')
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# tokens = tokenizer.tokenize(re)
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# if printDetail:
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# print('=====TOKENS=========')
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# print(tokens)
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#
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# return tokens
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def filterCore(t):
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# cocciPatterns = load_zipped_pickle(join(DATA_PATH, 'allCocciPatterns.pickle'))
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src,spfile = t
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srcPath = src
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patchName = src.split('/')[-1]
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manybug = src.split('/')[-2]
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# with open(srcPath, mode='r') as srcFile:
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# lines = srcFile.read()
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# scTokens = getTokensForPatterns(lines)
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# tokens = cocciPatterns[cocciPatterns.cid == spfile].iloc[0].patternTokens
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# patternFilter = set(scTokens).intersection(set(tokens))
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# if len(patternFilter) > 0:
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cmd = COCCI_PATH + ' --sp-file ' + join(DATASET, 'cocci', spfile) + ' ' + srcPath + ' --patch -o' + join(
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DATA_PATH, "introclass", manybug, 'patches', patchName) + ' > ' + join(DATA_PATH, "introclass", manybug,
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'patches',
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patchName + spfile + '.txt')
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# cmd = COCCI_PATH + ' --sp-file ' + join(DATASET,'cocci',spfile) + ' ' + srcPath + ' -o ' + join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt')
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t = cmd, manybug, patchName, spfile, srcPath
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return t
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# return None
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def patchCoreIntro():
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manybugs = listdir(join(DATA_PATH,"introclass"))
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spfiles = listdir(join(DATASET,'cocci'))
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# workList = []
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filterList =[]
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for manybug in manybugs:
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# files = listdir(join(join(DATA_PATH,"manybugs",manybug,'diffs')))
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if os.path.exists(join(DATA_PATH, "introclass", manybug, 'patches')):
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shutil.rmtree(join(DATA_PATH, "introclass", manybug, 'patches'))
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os.mkdir(join(DATA_PATH, "introclass", manybug, 'patches'))
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else:
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os.mkdir(join(DATA_PATH, "introclass", manybug, 'patches'))
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if os.path.exists(join(DATA_PATH, "introclass", manybug, 'patched')):
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shutil.rmtree(join(DATA_PATH, "introclass", manybug, 'patched'))
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os.mkdir(join(DATA_PATH, "introclass", manybug, 'patched'))
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else:
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os.mkdir(join(DATA_PATH, "introclass", manybug, 'patched'))
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files = get_filepaths(join(DATA_PATH, "introclass", manybug), '.c')
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sources = [i for i in files if not (i.endswith('oracle.c.patch') or i.endswith('oracle.c'))]
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filterList.extend(list(itertools.product(sources, spfiles)))
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print(len(filterList))
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workList = parallelRunMerge(filterCore,filterList)
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# for src in sources:
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# # srcPath = src.replace('/diffs/','/src/')
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# srcPath = src
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#
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#
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# with open(srcPath, mode='r') as srcFile:
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# lines = srcFile.read()
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# scTokens = getTokensForPatterns(lines)
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#
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# patchName = src.split('/')[-1]
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# for spfile in spfiles:
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# tokens = cocciPatterns[cocciPatterns.cid == spfile].iloc[0].patternTokens
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# patternFilter = set(scTokens).intersection(set(tokens))
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# if len(patternFilter) > 0:
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# cmd = COCCI_PATH + ' --sp-file ' + join(DATASET,'cocci',spfile) + ' ' + srcPath + ' --patch -o' + join(DATA_PATH,"introclass",manybug,'patches',patchName) + ' > ' + join(DATA_PATH, "introclass", manybug, 'patches', patchName + spfile + '.txt')
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# # cmd = COCCI_PATH + ' --sp-file ' + join(DATASET,'cocci',spfile) + ' ' + srcPath + ' -o ' + join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt')
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# t = cmd,manybug,patchName,spfile,srcPath
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# workList.append(t)
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# else:
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# logging.info("Skip "+ srcPath + " " + spfile)
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workList = list(filter(None, workList))
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print(len(workList))
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# for l in workList:
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# cocciCore2(l)
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parallelRun(cocciCore2,workList)
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def patched():
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manybugs = listdir(join(DATA_PATH,"introclass"))
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# spfiles = listdir(join(DATASET,'cocci'))
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workList = []
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for manybug in manybugs:
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# files = listdir(join(join(DATA_PATH,"manybugs",manybug,'diffs')))
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if os.path.exists(join(DATA_PATH, "introclass_patched", manybug, 'patches')):
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shutil.rmtree(join(DATA_PATH, "introclass_patched", manybug, 'patches'))
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os.makedirs(join(DATA_PATH, "introclass_patched", manybug, 'patches'))
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else:
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os.makedirs(join(DATA_PATH, "introclass_patched", manybug, 'patches'))
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files = get_filepaths(join(DATA_PATH, "introclass", manybug), '.c')
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sources = [i for i in files if not (i.endswith('oracle.c.patch') or i.endswith('oracle.c'))]
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for src in sources:
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# srcPath = src.replace('/diffs/','/src/')
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srcPath = src
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patchName = src.split('/')[-1]
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spfiles = listdir(join(DATA_PATH,"introclass",manybug,'patches'))
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for spfile in spfiles:
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spfile =spfile.replace(patchName,'').replace('.txt','')
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cmd = COCCI_PATH + ' --sp-file ' + join(DATASET,'cocci',spfile) + ' ' + srcPath + ' -o ' + join(DATA_PATH,"introclass_patched",manybug,'patches',patchName+spfile+'.c')
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t = cmd,manybug,patchName,spfile
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workList.append(t)
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parallelRun(cocciCore,workList)
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def cocciCore2(t):
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cmd,manybug,patchName,spfile,srcPath = t
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# cocciPatterns = load_zipped_pickle(join(DATA_PATH, 'allCocciPatterns.pickle'))
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# tokens = cocciPatterns[cocciPatterns.cid == spfile].iloc[0].patternTokens
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# with open(srcPath, mode='r') as srcFile:
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# lines = srcFile.read()
|
|
|
|
# patternFilter = set(getTokensForPatterns(lines)).intersection(set(tokens))
|
|
# if len(patternFilter) > 0:
|
|
|
|
# logging.info(cmd)
|
|
output, e = shellGitCheckout(cmd)
|
|
# logging.info(output)
|
|
patchSize = os.path.getsize(join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt'))
|
|
if patchSize == 0 :
|
|
os.remove(join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt'))
|
|
else:
|
|
cmd = 'patch -d '+join(DATA_PATH, "introclass", manybug)+' -i '+join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt')+' -o '+join(DATA_PATH,"introclass",manybug,'patched',patchName+spfile+'.c')
|
|
o,e = shellGitCheckout(cmd)
|
|
|
|
def cocciCore(t):
|
|
cmd, manybug, patchName, spfile = t
|
|
# logging.info(cmd)
|
|
output, e = shellGitCheckout(cmd)
|
|
# logging.info(output)
|
|
patchSize = os.path.getsize(join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt'))
|
|
if patchSize == 0 :
|
|
os.remove(join(DATA_PATH,"introclass",manybug,'patches',patchName+spfile+'.txt'))
|
|
# def patchCore():
|
|
# manybugs = listdir(join(DATA_PATH,"manybugs"))
|
|
# spfiles = listdir(join(DATASET,'cocci'))
|
|
# for manybug in manybugs:
|
|
# # files = listdir(join(join(DATA_PATH,"manybugs",manybug,'diffs')))
|
|
# if not os.path.exists(join(DATA_PATH, "manybugs", manybug, 'patches')):
|
|
# os.mkdir(join(DATA_PATH, "manybugs", manybug, 'patches'))
|
|
# if not os.path.exists(join(DATA_PATH, "manybugs", manybug, 'patched')):
|
|
# os.mkdir(join(DATA_PATH, "manybugs", manybug, 'patched'))
|
|
#
|
|
# files = get_filepaths(join(DATA_PATH,"manybugs",manybug,'diffs'),'.patch')
|
|
# sources = [i.replace('.c.patch','.c') for i in files if i.endswith('.c.patch')]
|
|
# for src in sources:
|
|
# srcPath = src.replace('/diffs/','/src/')
|
|
# patchName = src.split('/')[-1]
|
|
# for spfile in spfiles:
|
|
# cmd = COCCI_PATH + ' -j 16 --sp-file ' + join(DATASET,'cocci',spfile) + ' ' + srcPath + ' -o ' + join(DATA_PATH,"manybugs",manybug,'patches',patchName+spfile+'.txt')
|
|
# logging.info(cmd)
|
|
# output, e = shellGitCheckout(cmd)
|
|
# logging.info(output)
|
|
# patchSize = os.path.getsize(join(DATA_PATH,"manybugs",manybug,'patches',patchName+spfile+'.txt'))
|
|
# if patchSize == 0 :
|
|
# os.remove(join(DATA_PATH,"manybugs",manybug,'patches',patchName+spfile+'.txt'))
|
|
|