some changes in python
This commit is contained in:
anil
@@ -99,8 +99,8 @@ def exportCore(bugName):
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if os.path.exists(join(BUGDIR, bugName,'diffs')):
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shutil.rmtree(join(BUGDIR, bugName,'diffs'))
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# os.makedirs(join(BUGDIR, bugName,'diffs'))
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if os.path.exists(join(BUGDIR, bugName, 'src')):
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shutil.rmtree(join(BUGDIR, bugName,'src'))
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# if os.path.exists(join(BUGDIR, bugName, 'src')):
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# shutil.rmtree(join(BUGDIR, bugName,'src'))
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# os.makedirs(join(BUGDIR, bugName, 'src'))
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#
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cmd = 'docker create -ti --name dummy '+output.strip()+' bash'
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@@ -114,10 +114,10 @@ def exportCore(bugName):
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cmd = 'docker cp dummy:/experiment/src '+join(BUGDIR,bugName)
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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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# cmd = 'docker cp dummy:/experiment/src '+join(BUGDIR,bugName)
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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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cmd = 'docker cp dummy:/experiment/diffs '+join(BUGDIR,bugName)
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logging.info(cmd)
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+13
-3
@@ -33,7 +33,7 @@ if __name__ == '__main__':
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# subject = 'ALL'
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# rootType = 'if'
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# job = 'patterns'
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job = 'indexClusters'
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print(job)
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@@ -107,6 +107,12 @@ if __name__ == '__main__':
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from sprinferIndex import removeDuplicates
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removeDuplicates()
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elif job =='mergeCoccis':
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# from sprinferIndex import mergeCoccis
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# mergeCoccis()
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from sprinferIndex import removeDuplicates2
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removeDuplicates2()
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elif job == 'evalManyBugs':
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# from patchManyBugs import patchCore
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# patchCore()
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@@ -176,8 +182,12 @@ if __name__ == '__main__':
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from stats import defects4jStats
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defects4jStats()
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elif job == 'patterns':
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from stats import exportAbstractPatterns
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exportAbstractPatterns()
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coccis = load_zipped_pickle(join(DATA_PATH, 'allCocciPatterns2.pickle'))
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coccis['family'] = coccis.cid.apply(lambda x: x.split('.cocci')[0])
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# from stats import exportAbstractPatterns
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# exportAbstractPatterns()
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elif job == 'travis':
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if isfile(join(DATA_PATH,'repoList')):
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+57
-27
@@ -4,7 +4,7 @@ import csv
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import os
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from common.commons import *
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DATA_PATH = os.environ["DATA_PATH"]
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ROOT_DIR = os.environ["ROOT_DIR"]
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def readTestSuite(testPath):
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regex = r"([p|n0-9]+)\)"
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with open(testPath,mode='r') as testFile:
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@@ -127,7 +127,15 @@ def myvalidateCore(t):
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def validateCore(t):
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bugName, port = t
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container = None
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with bugzoo.server.ephemeral(port=port, verbose=False, timeout_connection=30000) as client:
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cmd = 'bash {} {}'.format(join(ROOT_DIR, 'data', 'startBugzoo.sh'), port)
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with Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True) as myProcess:
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# o,e = shellGitCheckout(cmd)
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url = "http://127.0.0.1:{}".format(port)
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timeout_connection = 3000
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client = Client(url, timeout_connection=timeout_connection)
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# with bugzoo.server.ephemeral(port=port, verbose=False, timeout_connection=30000) as client:
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try:
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bug = client.bugs[bugName]
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@@ -144,22 +152,22 @@ def validateCore(t):
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preId, postId = bugName.split(':')[-1].split('-')[-2:]
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failing = join(DATA_PATH, 'manybugs', bugName, 'failing.tests.txt')
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passing = join(DATA_PATH, 'manybugs', bugName, 'passing.tests.txt')
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if not (isfile(failing)):
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return
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cmd = 'docker cp ' +failing+ ' '+container.id +':/experiment/failing.tests.txt '
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o,e = shellGitCheckout(cmd)
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cmd = 'sudo chown $(whoami):$(whoami) "{}"'
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cmd = cmd.format('failing.tests.txt')
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o = client.containers.exec(container=container, command=cmd, context='/experiment/')
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cmd = 'docker cp ' +passing+ ' '+container.id +':/experiment/passing.tests.txt '
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o,e = shellGitCheckout(cmd)
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cmd = 'sudo chown $(whoami):$(whoami) "{}"'
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cmd = cmd.format('passing.tests.txt')
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o = client.containers.exec(container=container, command=cmd, context='/experiment/')
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# failing = join(DATA_PATH, 'manybugs', bugName, 'failing.tests.txt')
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# passing = join(DATA_PATH, 'manybugs', bugName, 'passing.tests.txt')
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#
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# if not (isfile(failing)):
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# return
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#
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# cmd = 'docker cp ' +failing+ ' '+container.id +':/experiment/failing.tests.txt '
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# o,e = shellGitCheckout(cmd)
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# cmd = 'sudo chown $(whoami):$(whoami) "{}"'
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# cmd = cmd.format('failing.tests.txt')
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# o = client.containers.exec(container=container, command=cmd, context='/experiment/')
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# cmd = 'docker cp ' +passing+ ' '+container.id +':/experiment/passing.tests.txt '
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# o,e = shellGitCheckout(cmd)
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# cmd = 'sudo chown $(whoami):$(whoami) "{}"'
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# cmd = cmd.format('passing.tests.txt')
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# o = client.containers.exec(container=container, command=cmd, context='/experiment/')
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originalBugs = get_filepaths(join(DATA_PATH, 'manybugs', bugName, 'diffs'), preId)
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for ob in originalBugs:
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@@ -180,7 +188,25 @@ def validateCore(t):
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filepath = ob.split('diffs')[-1]
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cmd = 'cp diffs' + filepath + ' src' + filepath.replace('-' + postId, '')
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client.containers.exec(container=container, command=cmd, context='/experiment/')
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client.containers.build(container)
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times = 0
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name = ob
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patch_result = client.containers.build(container)
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if patch_result.successful:
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failure_cases, failure, total, test_outcomes = test_all(bug, container, client,validTests)
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if failure == 0:
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times += 1
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output += ' fixed by {}'.format(name)
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else:
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output += ' {}'.format(failure_cases)
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else:
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output += ' {}'.format('build error')
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output += ' times:{}'.format(times)
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if times > 0:
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output += ' success'
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else:
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output += ' failure'
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# client.containers.build(container)
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# diff_files = get_diff(bug.name, client, container)
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# patch_result = patch_application(client, container, diff_files)
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# if not patch_result:
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@@ -191,13 +217,13 @@ def validateCore(t):
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#
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# print("Second_test:",end=' ')
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# post_test_outcomes = {}
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post_failure_cases, post_failure, total, post_test_outcomes = test_all(bug, container, client,validTests)
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output += ','.join(post_failure) + ' '
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if len(post_failure) == 0:
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# times += 1
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fix = 'success'
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# print("fix {} by {}".format(bugName, patch_name))
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output += 'fix {} '.format(bugName)
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# post_failure_cases, post_failure, total, post_test_outcomes = test_all(bug, container, client,validTests)
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# output += ','.join(post_failure) + ' '
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# if len(post_failure) == 0:
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# # times += 1
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# fix = 'success'
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# # print("fix {} by {}".format(bugName, patch_name))
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# output += 'fix {} '.format(bugName)
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# patch_names = os.listdir(join(DATA_PATH,'manybugs',bugName,'patched'))
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@@ -245,6 +271,10 @@ def validateCore(t):
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# ''
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cmd = 'docker stop {}'.format(container.id)
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out, e = shellGitCheckout(cmd)
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try:
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client.shutdown()
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except Exception as e:
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logging.error(e)
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# docker stop $(docker ps -q)
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@@ -276,7 +306,7 @@ def patch_validate():
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if isinstance(v,logging.Logger):
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v.setLevel(logging.ERROR)
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buglist = listdir(join(DATA_PATH,'manybugs'))
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buglist = listdir(join(DATA_PATH,'manybugs_sos'))
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# for i in range(0,len(bugList)):
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bugList = []
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@@ -5,6 +5,7 @@ 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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ROOT_DIR = os.environ["ROOT_DIR"]
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def indexCore():
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@@ -157,6 +158,43 @@ def runSpinfer():
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# output,e = shellGitCheckout(cmd)
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# logging.info(output)
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def mergeCoccis():
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DATA = '/Users/anil.koyuncu/projects/fixminer/fixminer-data2'
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folders = os.listdir(DATA)
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coccis = [i for i in folders if 'cocci' in i]
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allCoccis = [get_filepaths(join(DATA, i), '') for i in coccis]
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for cocci in list(itertools.chain.from_iterable(allCoccis)):
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_,srcFolder,cocciName = cocci.split(DATA)[-1].split('/')
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with open(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(DATA, 'merged', cocciName+str(i)+'-'+srcFolder), '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(DATA, 'merged', cocciName + str(i)+'-'+srcFolder), 'w') as iFile:
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iFile.writelines(idx[t[1]:])
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else:
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shutil.copy2(cocci,join(DATA, 'merged', cocciName + '-'+srcFolder))
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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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@@ -200,6 +238,58 @@ def getFreqPatterns():
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re.search(r"// Recall:(.*), Precision:(.*), Matching recall:(.*)")
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def removeDuplicates2():
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commentPattern = r"(/\*([^*]|[\r\n]|(\*+([^*/]|[\r\n])))*\*+/)|(//.*)"
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DATA = '/Users/anil.koyuncu/projects/fixminer/fixminer-data2'
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coccis =os.listdir(join(DATA, 'merged'))
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cocciPatterns = pd.DataFrame(columns=['cid', 'pattern','inferedFrom','recall','precision','matchingRecall'])
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ind = 0
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for cocci in coccis:
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try:
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if cocci == '.DS_Store':
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continue
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with open(join(DATA, 'merged', 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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recall,precision, matchingRecall = re.search(r"// Recall:(.*), Precision:(.*), Matching recall:(.*)",idx).groups()
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pattern = re.sub(commentPattern, '', idx, re.DOTALL)
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cocciPatterns.loc[ind] = [cocci,pattern,inferedFrom,recall.strip(),precision.strip(),matchingRecall.strip()]
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ind = ind +1
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except Exception as e:
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shutil.move(join(DATA,'merged',cocci),join(DATA,'mergedBroken',cocci))
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continue
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# logging.error(e)
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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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save_zipped_pickle(cocciPatterns,join(DATA,'allCocciPatternsMerge.pickle'))
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cocciPatterns['dup'] = cocciPatterns.duplicated(subset=['pattern'], keep=False)
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duplicates = cocciPatterns[cocciPatterns.dup == True]
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duplicateDF = duplicates.groupby(by=['pattern'], as_index=False).agg(lambda x: x.tolist())
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pattern2keep= duplicateDF.cid.apply(lambda x: min(x, key=len)).values.tolist()
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allDuplicates = list(itertools.chain.from_iterable(duplicateDF.cid.values.tolist()))
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toRemove = list(set(allDuplicates).difference(set(pattern2keep)))
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for tr in toRemove:
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shutil.move(join(DATA,'merged',tr),join(DATA,'mergedDuplicate',tr))
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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 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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+10
-4
@@ -473,12 +473,18 @@ def exportAbstractPatterns():
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if 'java' == PROJECT_TYPE:
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isJava = True
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for id, members in df[['cid','members']].values.tolist():
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if (len(members) == 0):
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continue
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try:
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dKey = '/'.join(id[0].split('-')[:-1]) + "/" + members[0]
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lines = redis_db.hget("dump",dKey )
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dKey = '/'.join(id[0].split('-')[:-1]) + "/" + members[0]
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lines = redis_db.hget("dump",dKey )
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cid = id[0].replace("-",'#')
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abstractPattern(cid,lines.decode(),isJava,members)
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cid = id[0].replace("-",'#')
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abstractPattern(cid,lines.decode(),isJava,members)
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except Exception as e:
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logging.error(e)
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def abstractPattern(cid,lines,isJava,cMembers):
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+71
-17
@@ -6,7 +6,34 @@ import signal
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# from common.commons import shellGitCheckout
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DATA_PATH = os.environ["DATA_PATH"]
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ROOT_DIR = os.environ["ROOT_DIR"]
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DATASET = os.environ["dataset"]
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introClassFile = join(DATA_PATH,'introClassData.txt')
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COCCI_PATH = join(os.environ["coccinelle"],'spatch')
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def patchSourceFile(bugPath,spfile,bugName):
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# print(bugPath)
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srcName = bugPath.split('/')[-1].split(':')[1]
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srcPath = join(bugPath,srcName + '.c')
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patchName = srcName+'.c'
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if(isfile(join(DATA_PATH,"introclass",bugName,'patched',patchName+spfile+'.c'))):
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return join(DATA_PATH,"introclass",bugName,'patched',patchName+spfile+'.c')
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if not (isfile(join(DATA_PATH,"introclass",bugName,'patches',patchName+spfile+'.txt'))):
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cmd = COCCI_PATH + ' --sp-file ' + join(DATASET, 'cocci', spfile) + ' ' + srcPath + ' --patch -o' + join(
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DATA_PATH, "introclass", bugName, 'patches', patchName) + ' > ' + join(DATA_PATH, "introclass", bugName,
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'patches',
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patchName + spfile + '.txt')
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output, e = shellGitCheckout(cmd)
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# logging.info(output)
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patchSize = os.path.getsize(join(DATA_PATH,"introclass",bugName,'patches',patchName+spfile+'.txt'))
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if patchSize == 0 :
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# os.remove(join(DATA_PATH,"introclass",bugName,'patches',patchName+spfile+'.txt'))
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return None
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else:
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cmd = 'patch -d '+join(DATA_PATH, "introclass", bugName)+' -i '+join(DATA_PATH,"introclass",bugName,'patches',patchName+spfile+'.txt')+' -o '+join(DATA_PATH,"introclass",bugName,'patched',patchName+spfile+'.c')
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o,e = shellGitCheckout(cmd)
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return join(DATA_PATH, "introclass", bugName, 'patched', patchName + spfile + '.c')
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def testCore(t):
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bugName, port = t
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@@ -14,7 +41,7 @@ def testCore(t):
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# with bugzoo.server.ephemeral(port=port, verbose=False,bugzooPath="/Users/anil.koyuncu/anaconda3/envs/python36/bin/bugzood", timeout_connection=3000) as client:
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cmd = 'bash {} {}'.format(join(ROOT_DIR,'data','startBugzoo.sh'),port)
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with Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True) as process:
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with Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True) as myProcess:
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# o,e = shellGitCheckout(cmd)
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url = "http://127.0.0.1:{}".format(port)
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@@ -56,27 +83,39 @@ def testCore(t):
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return ''
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output += '@fail:' + str(pre_failure) + '@total:' + str(total) + ', '
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# print("patching...")
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path = join(DATA_PATH,'introclass',bugName)
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patch_path = join(path ,'patched')
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# avaliable_patch = os.path.abspath('data') + '/introclass2/' + bugName + '/' + 'patches'
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patch_names = os.listdir(patch_path)
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spfiles = listdir(join(DATASET, 'cocci'))
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# print("patching... " + bugName)
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for idx,spfile in enumerate(spfiles):
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||||
if spfile == '.DS_Store':
|
||||
continue
|
||||
|
||||
times = 0
|
||||
for patch_name in patch_names:
|
||||
path = join(DATA_PATH,'introclass',bugName)
|
||||
patch = patchSourceFile(path,spfile,bugName)
|
||||
|
||||
if patch is None:
|
||||
continue
|
||||
# print(patch)
|
||||
# print(str(idx) + '..'+str(len(spfiles)))
|
||||
# patch_path = join(path ,'patched')
|
||||
# # avaliable_patch = os.path.abspath('data') + '/introclass2/' + bugName + '/' + 'patches'
|
||||
# patch_names = os.listdir(patch_path)
|
||||
#
|
||||
times = 0
|
||||
# for patch_name in patch_names:
|
||||
# if patch_name not in os.listdir(avaliable_patch):
|
||||
# continue
|
||||
patch = join(patch_path,patch_name)
|
||||
# patch = join(patch_path,patch_name)
|
||||
|
||||
patch_result = patched_application(path, bug.name, patch, client, container)
|
||||
if patch_result == -1 or patch_result.code != 0:
|
||||
# print("@{}@".format('False'), end='')
|
||||
# print("{}".format('F'), end=' ')
|
||||
output += '@False@F '
|
||||
# output += '@False@F '
|
||||
output += '@False:' + str(idx) + ':' + patch.split('/')[-1] + '@'
|
||||
continue
|
||||
# print("@{}@".format('True'), end='')
|
||||
output += '@True@'
|
||||
|
||||
# output += '@True@'
|
||||
output += '@True:' + str(idx) + ':' + patch.split('/')[-1] + '@'
|
||||
# print("Second_test:", end=' ')
|
||||
post_test_outcomes = {}
|
||||
post_failure_cases, post_failure, total, post_test_outcomes = test_all(bug, container, client)
|
||||
@@ -86,7 +125,8 @@ def testCore(t):
|
||||
times += 1
|
||||
fix = 'success'
|
||||
# print("fix {} by {}".format(bugName, patch_name))
|
||||
output += 'fix {} by {} '.format(bugName, patch_name)
|
||||
output += 'fix {} by {} '.format(bugName, patch)
|
||||
break
|
||||
# print("@fail:{}@total:{}".format(post_failure, total),end=' ')
|
||||
# print("@post_failure_cases:{}".format(post_failure_cases))
|
||||
|
||||
@@ -103,8 +143,12 @@ def testCore(t):
|
||||
# ''
|
||||
cmd = 'docker stop {}'.format(container.id)
|
||||
out, e = shellGitCheckout(cmd)
|
||||
client.shutdown()
|
||||
os.killpg(process.pid, signal.SIGTERM)
|
||||
try:
|
||||
client.shutdown()
|
||||
except Exception as e:
|
||||
logging.error(e)
|
||||
# print(myProcess.pid)
|
||||
# os.killpg(myProcess.pid, signal.SIGTERM)
|
||||
# docker stop $(docker ps -q)
|
||||
|
||||
|
||||
@@ -124,6 +168,10 @@ def patch_validate():
|
||||
# bug = client.bugs['introclass:checksum:08c7ea:006']
|
||||
bugList = []
|
||||
|
||||
nonFail = ['introclass:syllables:93f87b:005','introclass:smallest:f94e26:004','introclass:smallest:d25c71:001','introclass:median:d25c71:002','introclass:smallest:d25c71:000'
|
||||
,'introclass:median:d6364e:007','introclass:median:489253:007','introclass:syllables:d12048:004','introclass:smallest:d9e7ea:002','introclass:syllables:035fe9:000'
|
||||
,'introclass:syllables:c9d718:002','introclass:syllables:ea67b8:007','introclass:median:48b829:000','introclass:syllables:d9e7ea:001']
|
||||
|
||||
# cmd = 'bash ' + join(DATA_PATH,'startBugzoo.sh')
|
||||
# cmd = "/Users/anil.koyuncu/anaconda3/envs/python36/bin/bugzood --debug -p " + str(port)
|
||||
# output, errors = shellGitCheckout(cmd)
|
||||
@@ -131,6 +179,11 @@ def patch_validate():
|
||||
port = 6000
|
||||
bugs2test= listdir(join(DATA_PATH, "introclass"))
|
||||
for b in bugs2test:
|
||||
if b == '.DS_Store':
|
||||
continue
|
||||
|
||||
if b in nonFail:
|
||||
continue
|
||||
t = b, port
|
||||
bugList.append(t)
|
||||
if port == 6300:
|
||||
@@ -149,8 +202,9 @@ def patch_validate():
|
||||
# t = 'introclass:syllables:93f87b:005',6000
|
||||
# t = 'introclass:syllables:99cbb4:000',6000
|
||||
# testCore(t)
|
||||
results = parallelRunMerge(testCore, bugList,max_workers=10)
|
||||
# print('\n'.join(results))
|
||||
# results = parallelRunMerge(testCore, bugList,max_workers=10)
|
||||
results = parallelRunMerge(testCore, bugList)
|
||||
print('\n'.join(results))
|
||||
with open(join(DATA_PATH, 'introTestResults'), 'w',
|
||||
encoding='utf-8') as writeFile:
|
||||
# if levelPatch == 0:
|
||||
|
||||
@@ -75,7 +75,7 @@ def patch_validate(t):
|
||||
finally:
|
||||
cmd = 'docker stop {}'.format(container.id)
|
||||
out, e = shellGitCheckout(cmd)
|
||||
client.shutdown()
|
||||
# client.shutdown()
|
||||
os.killpg(process.pid, signal.SIGTERM)
|
||||
|
||||
from bugzoo import Patch, Client
|
||||
|
||||
Reference in New Issue
Block a user