from datetime import datetime, timedelta
try:
import json
-except ImportError, e:
+except ImportError as e:
import simplejson as json
-
+
import os
import re
from django.contrib.auth.decorators import login_required
+from django.views.decorators.csrf import csrf_exempt
from django.core.exceptions import ObjectDoesNotExist
from django.core.mail import send_mail, mail_admins
from django.http import HttpResponse, Http404
DataRun, \
Lane, \
LANE_STATUS_MAP
-from htsworkflow.frontend.samples.models import Library, HTSUser
+from htsworkflow.frontend.samples.models import Library, MultiplexIndex, HTSUser
def flowcell_information(flowcell_id):
"""
"""
try:
fc = FlowCell.objects.get(flowcell_id__startswith=flowcell_id)
- except FlowCell.DoesNotExist, e:
+ except FlowCell.DoesNotExist as e:
return None
lane_set = {}
for lane in fc.lane_set.all():
- lane_set[lane.lane_number] = {
+ lane_item = {
'cluster_estimate': lane.cluster_estimate,
'comment': lane.comment,
'experiment_type': lane.library.experiment_type.name,
'experiment_type_id': lane.library.experiment_type_id,
'flowcell': lane.flowcell.flowcell_id,
- 'lane_number': int(lane.lane_number),
+ 'lane_number': lane.lane_number,
'library_name': lane.library.library_name,
'library_id': lane.library.id,
'library_species': lane.library.library_species.scientific_name,
- 'pM': unicode(lane.pM),
+ 'pM': str(lane.pM),
'read_length': lane.flowcell.read_length,
'status_code': lane.status,
'status': LANE_STATUS_MAP[lane.status]
}
+ sequences = lane.library.index_sequences()
+ if sequences is not None:
+ lane_item['index_sequence'] = sequences
+
+ lane_set.setdefault(lane.lane_number,[]).append(lane_item)
if fc.control_lane is None:
control_lane = None
else:
control_lane = int(fc.control_lane)
-
+
info = {
'advanced_run': fc.advanced_run,
'cluster_station_id': fc.cluster_station_id,
'sequencer_id': fc.sequencer_id,
'sequencer': fc.sequencer.name,
}
-
+
return info
+@csrf_exempt
def flowcell_json(request, fc_id):
"""
Return a JSON blob containing enough information to generate a config file.
"""
require_api_key(request)
-
+
fc_dict = flowcell_information(fc_id)
if fc_dict is None:
raise Http404
-
+
fc_json = json.dumps(fc_dict)
return HttpResponse(fc_json, mimetype = 'application/json')
"""
query = {}
if username is not None:
- user = HTSUser.objects.get(username=username)
+ user = HTSUser.objects.get(username=username)
query.update({'library__affiliations__users__id': user.id})
-
+
lanes = Lane.objects.filter(**query).order_by('-flowcell__run_date')
-
+
result = []
for l in lanes:
affiliations = l.library.affiliations.all()
'affiliations': affiliations_list})
return result
+@csrf_exempt
def lanes_for_json(request, username):
"""
Format lanes for a user
try:
result = lanes_for(username)
- except ObjectDoesNotExist, e:
+ except ObjectDoesNotExist as e:
raise Http404
-
+
#convert query set to python structure
-
+
result_json = json.dumps(result)
return HttpResponse(result_json, mimetype='application/json')
-
+
+
def updStatus(request):
output=''
user = 'none'
user = request.user
#Check access permission
- if not (user.is_superuser and settings.ALLOWED_IPS.has_key(ClIP)):
+ if not (user.is_superuser and ClIP in settings.ALLOWED_IPS):
return HttpResponse("%s access denied from %s." % (user, ClIP))
# ~~~~~~Parameters for the job ~~~~
- if request.REQUEST.has_key('fcid'):
+ if 'fcid' in request.REQUEST:
fcid = request.REQUEST['fcid']
else:
return HttpResponse('missing fcid')
-
- if request.REQUEST.has_key('runf'):
+
+ if 'runf' in request.REQUEST:
runfolder = request.REQUEST['runf']
else:
return HttpResponse('missing runf')
-
- if request.REQUEST.has_key('updst'):
+
+ if 'updst' in request.REQUEST:
UpdatedStatus = request.REQUEST['updst']
else:
return HttpResponse('missing status')
-
- # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Update Data Run status in DB
- # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
+ # Try get rec. If not found return 'entry not found + <fcid><runfolder>', if found try update and return updated
try:
rec = DataRun.objects.get(run_folder=runfolder)
rec.run_status = UpdatedStatus
#if there's a message update that too
mytimestamp = datetime.now().__str__()
mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
- if request.REQUEST.has_key('msg'):
+ if 'msg' in request.REQUEST:
rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
else :
if UpdatedStatus == '1':
config += ['ELAND_MULTIPLE_INSTANCES 8']
genome_dir = 'GENOME_DIR /Volumes/Genomes/'
eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
-
- try:
+
+ try:
fc = FlowCell.objects.get(flowcell_id=fcid)
for lane in fc.lane_set.all():
config += [ str(lane.lane_number) +":" + \
genome_dir + lane.library.library_species.scientific_name ]
config += [ str(lane.lane_number) +":" + \
eland_genome + lane.library.library_species.scientific_name ]
-
+
except ObjectDoesNotExist:
config = 'Entry not found for fcid = '+fcid
def getConfile(req):
granted = False
ClIP = req.META['REMOTE_ADDR']
- if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
+ if (ClIP in settings.ALLOWED_IPS): granted = True
if not granted: return HttpResponse("access denied. IP: "+ClIP)
cnfgfile = 'Nothing found'
runfolder = 'unknown'
request = req.REQUEST
- if request.has_key('fcid'):
+ if 'fcid' in request:
fcid = request['fcid']
- if request.has_key('runf'):
+ if 'runf' in request:
runfolder = request['runf']
try:
rec = DataRun.objects.get(run_folder=runfolder) #,flowcell_id=fcid)
rec.config_params = cnfgfile
rec.save()
else:
- cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
-
+ cnfgfile = 'Failed generating config params for RunFolder = '+runfolder +', Flowcell id = '+ fcid+ ' Config Text:\n'+cnfgfile
+
except ObjectDoesNotExist:
cnfgfile = 'Entry not found for RunFolder = '+runfolder
def getLaneLibs(req):
granted = False
ClIP = req.META['REMOTE_ADDR']
- if (settings.ALLOWED_IPS.has_key(ClIP)): granted = True
+ if (ClIP in settings.ALLOWED_IPS): granted = True
if not granted: return HttpResponse("access denied.")
request = req.REQUEST
fcid = 'none'
outputfile = ''
- if request.has_key('fcid'):
+ if 'fcid' in request:
fcid = request['fcid']
- try:
+ try:
rec = FlowCell.objects.get(flowcell_id=fcid)
#Ex: 071211
year = datetime.today().year.__str__()
year = replace(year,'20','')
month = datetime.today().month
if month < 10: month = "0"+month.__str__()
- else: month = month.__str__()
+ else: month = month.__str__()
day = datetime.today().day
if day < 10: day = "0"+day.__str__()
else: day = day.__str__()
sequencing_seconds_per_cycle= 3600 * 1.5
# 800 is a rough guess
pipeline_seconds_per_cycle = 800
-
+
cycles = flowcell.read_length
if flowcell.paired_end:
cycles *= 2
def estimateFlowcellTimeRemaining(flowcell):
estimate_mid = estimateFlowcellDuration(flowcell)
-
+
# offset for how long we've been running
running_time = datetime.now() - flowcell.run_date
estimate_mid -= running_time
estimate_low = timedelta(estimate.days, 0)
# floor estimate_mid and add a day
estimate_high = timedelta(estimate.days+1, 0)
-
+
return (estimate_low, estimate_high)
-
+
def makeUserLaneMap(flowcell):
"""
def getUsersForFlowcell(flowcell):
users = set()
-
+
for lane in flowcell.lane_set.all():
for affiliation in lane.library.affiliations.all():
for user in affiliation.users.all():
users.add(user)
-
+
return users
-
+
def makeUserLibraryMap(libraries):
"""
Given an interable set of libraries return a mapping or
users interested in those libraries.
"""
users = {}
-
+
for library in libraries:
for affiliation in library.affiliations.all():
for user in affiliation.users.all():
users.setdefault(user,[]).append(library)
-
+
return users
def makeAffiliationLaneMap(flowcell):
projects / htsworkflow.git / blobdiff