#!/usr/bin/env python
-#import os
-#os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.frontend.settings'
-
from htsworkflow.util.hdquery import get_hd_serial_num
from htsworkflow.frontend import settings
-#from django.conf import settings
from optparse import OptionParser
-
+import os
+import re
import sys
-import urllib
+import urllib2
+import urlparse
+runfolder_pattern = re.compile(r'[0-9]{6}_[-A-Za-z\d]+_\d+_(?P<flowcell>[A-Z\d]+)\.tgz')
+def extract_flowcell(runfolder_name):
+ path, basename = os.path.split(runfolder_name)
+ match = runfolder_pattern.match(basename)
+ if match is not None:
+ return match.group('flowcell')
+ else:
+ return None
+
def construct_parser():
"""
"""
- parser = OptionParser("usage: %prog -f <flowcell> -d </dev/sdX> OR\n\t %prog -f <flowcell> -s <dev_serial_num>")
- parser.add_option("-f", "--flowcell", action="store", type="string", dest="flowcell",
- help="flowcell being archived")
- parser.add_option("-d", "--device", action="store", type="string", dest="device",
+ msg = "usage: %prog [-d </dev/sdX> | -s <serial_number] [-f <flowcell>] [archived dirs]"
+ parser = OptionParser()
+ parser.add_option('-u', '--url', default=None,
+ help="Alternate url for marking archived flowcells")
+ parser.add_option("-f", "--flowcell", type="string", help="flowcell being archived")
+ parser.add_option("-d", "--device", type="string",
help="device flowcell is being archived to")
- parser.add_option("-s", "--serial", action="store", type="string", dest="serial",
- help="serial num. of archive device")
- parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=False)
+ parser.add_option("-s", "--serial", type="string", help="serial num. of archive device")
+ parser.add_option("-v", "--verbose", action="store_true", default=False)
return parser
-def update_db(flowcell, serial, debug=False):
+def update_db(root_url, flowcells, serial, debug=False):
"""
Creates link between flowcell and storage device over http
"""
- www = urllib.urlopen(settings.LINK_FLOWCELL_STORAGE_DEVICE_URL+'%s/%s/' % (flowcell, serial))
- httpcode = www.getcode()
- if httpcode != 200:
- print 'ERROR - HTTP OUTPUT (Return Code: %s); use -v/--verbose for more details.' % (httpcode)
- if debug:
- print www.read()
- sys.exit(httpcode)
+ for fc in flowcells:
+ url = urlparse.urljoin(root_url, '%s/%s/' % (fc, serial))
+
+ req = urllib2.Request(url)
+ try:
+ response = urllib2.urlopen(req)
+ except urllib2.URLError, e:
+ print 'ERROR - HTTP OUTPUT (Return Code: %s); use -v/--verbose for more details.' % (e.code)
+ if debug:
+ print e.read()
+ sys.exit(e.code)
+
+ print "DB Update of %s & %s succeeded" % (fc, serial)
+ print response.read()
- print "DB Update of %s & %s succeeded" % (flowcell, serial)
- print www.read()
-
def process_args(parser):
"""
# Only provide device or serial
if options.device is not None and options.serial is not None:
- print "ERROR: Please only provide --device or --serial.\n" \
- " The serial number is extracted automatically if the device is provided."
- sys.exit(2)
-
- print 'Flowcell:', options.flowcell
- print ' Device:', options.device
- print ' Serial:', options.serial
-
- if options.flowcell is None:
- msg.append(" --flowcell required")
-
+ parser.error("Please provide only --device or --serial.\n"\
+ "The serial number is extracted automatically if the"\
+ "device is provided.")
+
+ # allow user to override the default destination URL
+ if options.url is not None:
+ root_url = options.url
+ else:
+ root_url = settings.LINK_FLOWCELL_STORAGE_DEVICE_URL
+
# if device and serial missing:
if options.device is None and options.serial is None:
- msg.append(" --device OR --serial required")
-
- if len(msg) > 0:
- print '\n'.join(msg)
- sys.exit(3)
+ parser.error('One of --device or --serial is required')
+
+ flowcells = []
+ # sanitize args
+ for runfolder in args:
+ flowcell_id = extract_flowcell(runfolder)
+ if flowcell_id is None:
+ parser.error('archive names must look like YYMMDD_MACHINE_RUN_FLOWCELLID.tgz\n'\
+ '(got %s)' % (runfolder,))
+ else:
+ flowcells.append(flowcell_id)
+
+ if options.flowcell is not None:
+ flowcells.append(options.flowcell)
+
+ if len(flowcells) == 0:
+ parser.error('please specify a --flowcell or list of runfolder archives\n'\
+ 'for archival. I need something to do.')
+
# Update db records
if options.device is not None:
serial = get_hd_serial_num(options.device)
- update_db(flowcell=options.flowcell, serial=serial, debug=options.verbose)
+ update_db(root_url, flowcells, serial=serial, debug=options.verbose)
elif options.serial is not None:
- update_db(flowcell=options.flowcell, serial=options.serial, debug=options.verbose)
+ update_db(root_url, flowcells, serial=options.serial, debug=options.verbose)
else:
msg ="FATAL should not happen error occured; i.e. the best kind!"
raise ValueError, msg
sys.exit(0)
if __name__ == '__main__':
- main()
\ No newline at end of file
+ main()
projects / htsworkflow.git / blobdiff