def on_modified(self, event):
'''
Listens for modifications of the given log file and executes QC workflow on the newly copied file.
@param event: is triggered on any file modification within the directory monitored
'''
# Only watch for changes on file 'robocopy'
event_file = event.__dict__['_src_path']
if not 'robocopy' in event_file:
return
self.service.log("{0} New robocopy event".format(self.get_time()))
# Actually process the robocopy log file and any new RAW files, which will take some time
qc_pipeline(self.indir, self.outdir, event_file)
# Call function again in case new file(s) were copied during the run.
# It will return without running if now new files are ready for processing
qc_pipeline(self.indir, self.outdir, event_file)
self.service.log("{0} Monitoring for new RAW files..".format(self.get_time()))
if __name__ == "__main__":
# Program can be called with 'install' as only argument which triggers a service installation
if sys.argv[1] == 'install':
instart(QCMonitorService, 'ctmm-qc', 'ctmm_qc-monitor')
else:
# Create and parse command line arguments
parser = ArgumentParser(description='QC-workflow monitor for MS data using NIST metrics')
parser.add_argument('indir', type=str,
help='Input folder containing (Thermo) RAW files outputted by a mass-spectrometer')
parser.add_argument('outdir', type=str, help='Folder in which output (report) PDF files will be written')
# If no copylog folder is supplied, the QC pipeline will be ran a single time on the indir
# directory and will process all non-processed RAW files within this folder. After processing
# the process will stop
parser.add_argument('copylogdir', type=str, help=('(Optional) Directory containing logfile (local) that'
' Robocopy uses to write status messages (should be named:'
' "robocopy.*". If missing, the QC tool will process all'
' RAW files in the given indir and uses the QC'
' log file for tracking already processed files'),
nargs='?')
#Extract arguments
args = parser.parse_args()
# If no copylogdir is given, process all files in indir
if args.copylogdir == None:
qc_pipeline(args.indir, args.outdir, None)
else:
# Create new monitor checking for changes in the given robocopy logfile
monitor = QCMonitor(args.indir, args.outdir, args.copylogdir)
monitor.start()
'''
Sets paths to input / output directories etc.
@param indir: directory to monitor for file changes
@param outdir: directory to store output (passed to QC tool)
'''
self.indir = indir
self.outdir = outdir
print "Monitoring: \nInput Dir: {0}\nOutput Dir: {1}".format(self.indir, self.outdir)
if __name__ == "__main__":
# Program can be called with 'install' as only argument which triggers a service installation
# Create and parse command line arguments
parser = ArgumentParser(description='QC-workflow monitor for MS data using NIST metrics')
parser.add_argument('indir', type=str,
help='Input folder containing (Thermo) RAW files outputted by a mass-spectrometer')
parser.add_argument('outdir', type=str, help='Folder in which temporary folders and files will be created')
# If no copylog folder is supplied, the QC pipeline will be ran a single time on the indir
# directory and will process all non-processed RAW files within this folder. After processing
# the process will stop
#Extract arguments
args = parser.parse_args()
try:
while True:
status = qc_pipeline(args.indir, args.outdir)
if status == False:
print"Finished QC processing of existing files from {0}.\n reinvoking QC pipeline after 1 minute.".format(args.indir)
sleep(60)
except KeyboardInterrupt:
print "Shutdown requested...exiting"
sys.exit(0)
