def run_server(self):
'this method blocks, so run it in a separate thread'
cmdArgs = (sys.executable, self.server_script) + tuple(sys.argv) \
+ ('--port-file=' + self.port_file,
'--pygrdatapath=' + self.pygrDataPath,
'--downloadDB=' + self.downloadDB,
'--resources=' + ':'.join(self.pygrDataNames))
if self.port: # only add port argument if set
cmdArgs += ('--port=' + str(self.port), )
p = classutil.FilePopen(cmdArgs,
stdout=classutil.PIPE,
stderr=classutil.PIPE)
try:
logger.debug('Starting XML-RPC server: ')
logger.debug(repr(cmdArgs))
if p.wait():
logger.warn('XML-RPC server command failed!')
output = p.stdout.read()
errout = p.stderr.read()
logger.debug('XML-RPC server output: %s' % output)
logger.debug('XML-RPC server error out: %s' % errout)
finally:
p.close()
logger.debug('server stopped')
def check_results(results, correct, formatter, delta=0.01, reformatCorrect=False, reformatResults=True):
if reformatResults:
results = reformat_results(results, formatter)
if reformatCorrect: # reformat these data too
correct = reformat_results(correct, formatter)
else:
correct.sort()
# this is to help troubleshooting the mismatches if there are any
mismatch = [(a, b) for a, b in zip(correct, results) if testutil.approximate_cmp([a], [b], delta)]
if mismatch:
logger.warn("blast mismatches found")
for m in mismatch:
logger.warn("%s != %s" % m)
# this is the actual test
assert testutil.approximate_cmp(correct, results, delta) == 0
def check_results(results, correct, formatter, delta=0.01):
found = []
for result in results:
for t in result.edges():
found.append(formatter(t))
# order it identically
correct.sort()
found.sort()
# this is to help troubleshooting the mismatches if there are any
mismatch = [ (a, b) for a, b in zip(correct, found) if
testutil.approximate_cmp([a], [b], delta)]
if mismatch:
logger.warn('blast mismatches found')
for m in mismatch:
logger.warn('%s != %s' % m)
# this is the actual test
assert testutil.approximate_cmp(correct, found, delta) == 0
def run_server(self):
'this method blocks, so run it in a separate thread'
cmdArgs = (sys.executable, self.server_script) + tuple(sys.argv) \
+ ('--port=' + str(self.port),
'--port-file=' + self.port_file,
'--pygrdatapath=' + self.pygrDataPath,
'--downloadDB=' + self.downloadDB,
'--resources=' + ':'.join(self.pygrDataNames))
p = classutil.FilePopen(cmdArgs, stdout=classutil.PIPE,
stderr=classutil.PIPE)
try:
logger.debug('Starting XML-RPC server: ')
logger.debug(repr(cmdArgs))
if p.wait():
logger.warn('XML-RPC server command failed!')
output = p.stdout.read()
errout = p.stderr.read()
logger.debug('XML-RPC server output: %s' % output)
logger.debug('XML-RPC server error out: %s' % errout)
finally:
p.close()
logger.debug('server stopped')