--- /dev/null
+from django.conf.urls.defaults import *
+
+urlpatterns = patterns('',
+ (r'^lts/link/(?P<flowcell>.+)/(?P<serial>.+)/$', 'htsworkflow.frontend.inventory.views.link_flowcell_and_device'),
+ )
-# Create your views here.
+from htsworkflow.frontend.inventory.models import Item, LongTermStorage
+from htsworkflow.frontend.experiments.models import FlowCell
+
+from django.core.exceptions import ObjectDoesNotExist
+from django.http import HttpResponse
+
+
+def link_flowcell_and_device(request, flowcell, serial):
+ """
+ Updates database records of a flowcell being archived on a device with a particular serial #
+ """
+ assert flowcell is not None
+ assert serial is not None
+
+ ###########################################
+ # Retrieve Storage Device
+ try:
+ sd = Item.objects.get(barcode_id=serial)
+ except ObjectDoesNotExist, e:
+ msg = "Item with barcode_id of %s not found." % (serial)
+ raise ObjectDoesNotExist(msg)
+
+ ###########################################
+ # Retrieve FlowCell
+ try:
+ fc = FlowCell.objects.get(flowcell_id=flowcell)
+ except ObjectDoesNotExist, e:
+ msg = "FlowCell with flowcell_id of %s not found." % (flowcell)
+ raise ObjectDoesNotExist(msg)
+
+ ###########################################
+ # Retrieve or create LongTermStorage Object
+ count = fc.longtermstorage_set.count()
+ lts = None
+ if count > 1:
+ msg = "There really should only be one longtermstorage object per flowcell"
+ raise ValueError, msg
+ elif count == 1:
+ # lts already attached to flowcell
+ lts = fc.longtermstorage_set.all()[0]
+ else:
+ lts = LongTermStorage()
+ # Attach flowcell
+ lts.flowcell = fc
+ # Need a primary keey before linking to storage devices
+ lts.save()
+
+
+ ############################################
+ # Link Storage to Flowcell
+
+ # Add a link to this storage device if it is not already linked.
+ if sd not in lts.storage_devices.values():
+ lts.storage_devices.add(sd)
+
+ ###########################################
+ # Add Library Links to LTS
+
+ if fc.lane_1_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_1_library)
+
+ if fc.lane_2_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_2_library)
+
+ if fc.lane_3_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_3_library)
+
+ if fc.lane_4_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_4_library)
+
+
+ if fc.lane_5_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_5_library)
+
+ if fc.lane_6_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_6_library)
+
+ if fc.lane_7_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_7_library)
+
+ if fc.lane_8_library not in lts.storage_devices.values():
+ lts.libraries.add(fc.lane_8_library)
+
+ # Save Changes
+ lts.save()
+
+ return HttpResponse("Success")
\ No newline at end of file
# AnalysTrack:
#(r'^analysis/', include('htsworkflow.frontend.analysis.urls')),
# Report Views:
+ (r'^inventory/', include('htsworkflow.frontend.inventory.urls')),
(r'^reports/', include('htsworkflow.frontend.reports.urls')),
# Library browser
(r'^library/$', 'htsworkflow.frontend.samples.views.library'),
--- /dev/null
+#!/usr/bin/env python
+
+#import os
+#os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.frontend.settings'
+
+from htsworkflow.util.hdquery import get_hd_serial_num
+
+#from django.conf import settings
+from optparse import OptionParser
+
+import sys
+import urllib
+
+#FIXME: Remove hard coded URL
+HTSW_URL = "http://localhost:8000/inventory/lts/link/"
+
+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",
+ help="device flowcell is being archived to")
+ parser.add_option("-s", "--serial", action="store", type="string", dest="serial",
+ help="serial num. of archive device")
+
+ return parser
+
+
+def update_db(flowcell, serial):
+ """
+ Creates link between flowcell and storage device over http
+ """
+ www = urllib.urlopen(HTSW_URL+'%s/%s/' % (flowcell, serial))
+ httpcode = www.getcode()
+ if httpcode != 200:
+ print 'ERROR - HTTP OUTPUT:'
+ print www.read()
+ sys.exit(httpcode)
+
+ print "DB Update of %s & %s succeeded" % (flowcell, serial)
+
+
+def process_args(parser):
+ """
+ returns flowcell and serial#
+ """
+ options, args = parser.parse_args()
+
+ msg = []
+
+ # 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 options.flowcell
+ print options.device
+ print options.serial
+
+ if options.flowcell is None:
+ msg.append(" --flowcell required")
+
+ # 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)
+
+ # Update db records
+ if options.device is not None:
+ serial = get_hd_serial_num(options.device)
+ update_db(flowcell=options.flowcell, serial=serial)
+ elif options.serial is not None:
+ update_db(flowcell=options.flowcell, serial=options.serial)
+ else:
+ msg ="FATAL should not happen error occured; i.e. the best kind!"
+ raise ValueError, msg
+
+
+
+def main():
+ """
+ """
+ parser = construct_parser()
+ process_args(parser)
+
+ #print "Database Updated."
+ sys.exit(0)
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
projects / htsworkflow.git / commitdiff