def run(source,
source_extension,
compile_commands,
run_commands,
test_cases=default_testcase_array):
result = []
current_directory = os.getcwd()
temp_dir = uuid.uuid4().hex
os.makedirs(temp_dir)
os.chdir(temp_dir)
try:
source_file_name = create_source_file(source, source_extension)
out_compile = compile_source(compile_commands, source_file_name,
result)
execute_tests(run_commands, test_cases, out_compile, result)
except Exception as e:
out_exception = Output()
result.append(out_exception)
out_exception.status = Status.ENV_CRASH
out_exception.stderr = str(e)
print(os.sys.exc_info())
os.chdir(current_directory)
shutil.rmtree(temp_dir, True)
return result
def execute_tests(run_command, test_cases, out_compile, result):
if out_compile.status == Status.COMPILE_ERROR:
return ("Compilation Error")
else:
#run each test case and add the output to the list
for test_case in test_cases:
out_test = Output()
out_test.test_case_id = test_case.id
if run_command:
start_time = time.time()
completed = subprocess.run(run_command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
input=test_case.input.encode('utf-8'),
timeout=test_case.timeout,
check = True)
out_test.stderr = completed.stderr.decode('utf-8').rstrip()
out_test.stdout = completed.stdout.decode('utf-8').rstrip()
out_test.time = time.time() - start_time
if completed.returncode:
out_test.status = Status.RUNTIME_ERROR
else:
out_test.status = Status.OK
result.append(out_test)
else:
raise ValueError("Test cases must have a run command")
def generate_routes(job, clustering_parameters, objective_coefficients):
output_routes = []
un_routed_orders = job.orders[0:]
while True:
clustered_orders = SectorClustering.get_next_cluster(un_routed_orders, clustering_parameters)
if len(clustered_orders) == 0:
continue
route = initiate_new_route(clustered_orders, job.depot, job.vehicles[0], job.locationMatrix, job.configuration)
if route is None:
break
if len(clustered_orders) > 0:
apply_best_feasible_insertion(route, clustered_orders, job.depot, job.vehicles[0], job.locationMatrix,
job.configuration,
objective_coefficients)
if len(route.orders) > 0:
output_routes.append(route)
un_routed_orders = [order for order in un_routed_orders if order not in route.orders]
else:
break
if len(un_routed_orders) <= 0:
break
return Output(output_routes, un_routed_orders)
def main(inputParams: Input = None) -> None:
getcontext().traps[FloatOperation] = True
if inputParams is None:
inputParams = GetInput()
columnNames = PeptideColumns()
rawPeptideTables = RawPeptideTables(columnNames,
inputDir=inputParams.inputPath)
# TODO: FDR filter
FDRFilter(rawPeptideTables=rawPeptideTables).ApplyDefaultFilter()
if inputParams.blackList is not None:
ApplyBlackList(rawPeptideTables, inputParams.blackList[1])
TestFastaAccessions(inputParams.seqDB, rawPeptideTables)
peptideTables = PeptideTables(rawPeptideTables, seqDB=inputParams.seqDB)
if inputParams.isProteinConfidence is True:
ApplyProteinConfidenceFilter(inputParams.proteinConfidence,
peptideTables)
ApplyPeptideConfidenceFilter(inputParams.confPeptide, peptideTables)
accessionTables = AccessionTables(inputParams.seqDB, peptideTables)
accessionTables.sortedTableNums = peptideTables.GetSortedTableNums()
filesSumms = GetScPsigAndNormFilesSumm(accessionTables)
CalculateAccessionsNormRatios(accessionTables, filesSumms)
ApplyGroupFilter(
accessionTables,
inputParams.maxGroupAbsence,
inputParams.minGroupsWithAccession,
)
Output(
inputParams,
seqDB=inputParams.seqDB,
accessionTables=accessionTables,
proteinGroupsDB=None,
)
def compile_source(compile_commands, source_file_name, result):
out_compile = Output()
if compile_commands:
compile_commands.append(source_file_name)
completed = subprocess.run(compile_commands,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
if completed.returncode:
result.append(out_compile)
out_compile.status = Status.COMPILE_ERROR
out_compile.stdout = completed.stdout.decode('utf-8').rstrip()
out_compile.stderr = completed.stderr.decode('utf-8').rstrip()
else:
out_compile.status = Status.OK
return out_compile
def execute_tests(run_command, test_cases, out_compile, result):
if out_compile.status != Status.COMPILE_ERROR:
for test_case in test_cases:
out_test = Output()
out_test.test_case_id = test_case.id
if run_command:
completed = subprocess.run(
run_command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
input=test_case.input.encode('utf-8'),
timeout=test_case.timeout)
out_test.stdout = completed.stdout.decode('utf-8').rstrip()
out_test.stderr = completed.stderr.decode('utf-8').rstrip()
if completed.returncode:
out_test.status = Status.RUNTIME_ERROR
else:
out_test.status = Status.OK
result.append(out_test)