def test_stderr(self):
""" Stderr should be printed to stderr and logged"""
tmp_file = os.path.join(tmp_dir_path, 'tmp_log')
saved_stderr = sys.stderr
tmp_stderr = os.path.join(tmp_dir_path, 'tmp_stderr')
with open(tmp_stderr, 'w') as sys.stderr:
with EppLogger(tmp_file, prepend=False) as epp_logger:
print('stderr nosetest', file=sys.stderr)
sys.stderr = saved_stderr
with open(tmp_stderr, 'r') as stderr:
stream_lines = stderr.readlines()
assert 'stderr nosetest' in stream_lines[-1]
with open(tmp_file, 'r') as log_file:
log_lines = log_file.readlines()
assert 'stderr nosetest' in log_lines[-1]
def test_stdout(self):
""" Stdout should be logged but not printed"""
tmp_file = os.path.join(tmp_dir_path, 'tmp_log')
saved_stdout = sys.stdout
tmp_stdout = os.path.join(tmp_dir_path, 'tmp_stdout')
with open(tmp_stdout, 'w') as sys.stdout:
with EppLogger(tmp_file, prepend=False) as epp_logger:
print('stdout nosetest', file=sys.stdout)
sys.stdout = saved_stdout
with open(tmp_stdout, 'r') as stdout:
stream_lines = stdout.readlines()
assert not stream_lines
with open(tmp_file, 'r') as log_file:
log_lines = log_file.readlines()
assert 'stdout nosetest' in log_lines[-1]
x for x in io if x[1]['output-generation-type'] == 'PerInput'
]
# Fetch the first input-output artifact pair
(input, output) = io_filtered[0]
# Instantiate the output artifact
output_artifact = Artifact(output['limsid'])
# Attach the file
attach_file(args.file, output_artifact)
if __name__ == "__main__":
parser = ArgumentParser()
# Arguments that are useful in all EPP scripts
parser.add_argument("--log", default=sys.stdout, help="Log file")
# Arguments specific for this scripts task
parser.add_argument("--pid", help="Process id")
parser.add_argument("--file", help="File to upload")
args = parser.parse_args()
# Log everything to log argument
with EppLogger(args.log):
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
main(lims, args.pid, args.file)
"measurement!".format(R2))
else:
QiT.missing_udfs.append('Linearity of standards')
if QiT.missing_samps:
QiT.abstract.append("The following samples are missing in Quant-iT "
"result File 1 or 2: {0}.".format(', '.join(
QiT.missing_samps)))
if QiT.missing_udfs:
QiT.abstract.append("Are all of the following udfs set? : {0}".format(
', '.join(QiT.missing_udfs)))
print >> sys.stderr, ' '.join(QiT.abstract)
if __name__ == "__main__":
parser = ArgumentParser(description=DESC)
parser.add_argument('--pid',
default=None,
dest='pid',
help='Lims id for current Process')
parser.add_argument('--log',
dest='log',
help=('File name for standard log file, '
'for runtime information and problems.'))
args = parser.parse_args()
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
with EppLogger(log_file=args.log, lims=lims, prepend=True) as epp_logger:
main(lims, args.pid, epp_logger)
elif lines: # Avoid printing empty files
lp_args = ["lp"]
if args.hostname:
#remove that when all the calls to this script have been updated
if args.hostname == 'homer.scilifelab.se:631':
args.hostname='homer2.scilifelab.se:631'
lp_args += ["-h",args.hostname]
if args.destination:
lp_args += ["-d",args.destination]
lp_args.append("-") # lp accepts stdin if '-' is given as filename
logging.info('Ready to call lp for printing.')
sp = subprocess.Popen(lp_args,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sp.stdin.write(str('\n'.join(lines)))
logging.info('lp command is called for printing.')
stdout,stderr = sp.communicate() # Will wait for sp to finish
logging.info('lp stdout: {0}'.format(stdout))
logging.info('lp stderr: {0}'.format(stderr))
logging.info('lp command finished')
sp.stdin.close()
if __name__ == '__main__':
arguments = getArgs()
lims = Lims(BASEURI,USERNAME,PASSWORD)
lims.check_version()
prepend = not arguments.no_prepend
with EppLogger(arguments.log,lims=lims,prepend=prepend) as epp_logger:
main(arguments,lims,epp_logger)