import json
except ImportError, 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
+from django.conf import settings
+from django.utils import timezone
-from htsworkflow.frontend import settings
-from htsworkflow.frontend.experiments.models import FlowCell, DataRun
-from htsworkflow.frontend.samples.models import Library
+from htsworkflow.frontend.auth import require_api_key
+from htsworkflow.frontend.experiments.models import \
+ FlowCell, \
+ DataRun, \
+ Lane, \
+ LANE_STATUS_MAP
+from htsworkflow.frontend.samples.models import Library, MultiplexIndex, HTSUser
def flowcell_information(flowcell_id):
"""
Return a dictionary describing a flowcell
"""
try:
- fc = FlowCell.objects.get(flowcell_id=flowcell_id)
+ fc = FlowCell.objects.get(flowcell_id__startswith=flowcell_id)
except FlowCell.DoesNotExist, 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,
- 'pM': float(lane.pM),
+ 'library_id': lane.library.id,
+ 'library_species': lane.library.library_species.scientific_name,
+ 'pM': unicode(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,
'cluster_station': fc.cluster_station.name,
- 'control_lane': int(fc.control_lane),
+ 'control_lane': control_lane,
# 'datarun_set': how should this be represented?,
'flowcell_id': fc.flowcell_id,
'id': fc.id,
'sequencer_id': fc.sequencer_id,
'sequencer': fc.sequencer.name,
}
-
+
return info
-@login_required
+@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')
-
+
+def lanes_for(username=None):
+ """
+ Given a user id try to return recent lanes as a list of dictionaries
+ """
+ query = {}
+ if username is not None:
+ 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_list = [(a.id, a.name) for a in affiliations]
+ result.append({ 'flowcell': l.flowcell.flowcell_id,
+ 'run_date': l.flowcell.run_date.isoformat(),
+ 'lane_number': l.lane_number,
+ 'library': l.library.id,
+ 'library_name': l.library.library_name,
+ 'comment': l.comment,
+ 'affiliations': affiliations_list})
+ return result
+
+@csrf_exempt
+def lanes_for_json(request, username):
+ """
+ Format lanes for a user
+ """
+ require_api_key(request)
+
+ try:
+ result = lanes_for(username)
+ except ObjectDoesNotExist, 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 settings.ALLOWED_IPS.has_key(ClIP)):
return HttpResponse("%s access denied from %s." % (user, ClIP))
# ~~~~~~Parameters for the job ~~~~
fcid = request.REQUEST['fcid']
else:
return HttpResponse('missing fcid')
-
+
if request.REQUEST.has_key('runf'):
runfolder = request.REQUEST['runf']
else:
return HttpResponse('missing runf')
-
+
if request.REQUEST.has_key('updst'):
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 = timezone.now().__str__()
mytimestamp = re.sub(pattern=":[^:]*$",repl="",string=mytimestamp)
if request.REQUEST.has_key('msg'):
rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
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():
- print dir(lane.library.library_species)
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
cnfgfile = 'Nothing found'
runfolder = 'unknown'
request = req.REQUEST
- print request, dir(request)
- print request['fcid'], request.has_key('fcid')
- print request['runf']
if request.has_key('fcid'):
fcid = request['fcid']
if request.has_key('runf'):
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
outputfile = ''
if request.has_key('fcid'):
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__()
mydate = year+month+day
outputfile = '<?xml version="1.0" ?>'
outputfile += '\n<SolexaResult Date="'+mydate+'" Flowcell="'+fcid+'" Client="'+settings.ALLOWED_IPS[ClIP]+'">'
- outputfile += '\n<Lane Index="1" Name="'+rec.lane_1_library.library_name+'" Library="'+rec.lane_1_library.library_id+'" Genome="'+rec.lane_1_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="2" Name="'+rec.lane_2_library.library_name+'" Library="'+rec.lane_2_library.library_id+'" Genome="'+rec.lane_2_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="3" Name="'+rec.lane_3_library.library_name+'" Library="'+rec.lane_3_library.library_id+'" Genome="'+rec.lane_3_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="4" Name="'+rec.lane_4_library.library_name+'" Library="'+rec.lane_4_library.library_id+'" Genome="'+rec.lane_4_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="5" Name="'+rec.lane_5_library.library_name+'" Library="'+rec.lane_5_library.library_id+'" Genome="'+rec.lane_5_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="6" Name="'+rec.lane_6_library.library_name+'" Library="'+rec.lane_6_library.library_id+'" Genome="'+rec.lane_6_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="7" Name="'+rec.lane_7_library.library_name+'" Library="'+rec.lane_7_library.library_id+'" Genome="'+rec.lane_7_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
- outputfile += '\n<Lane Index="8" Name="'+rec.lane_8_library.library_name+'" Library="'+rec.lane_8_library.library_id+'" Genome="'+rec.lane_8_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="1" Name="'+rec.lane_1_library.library_name+'" Library="'+rec.lane_1_library.id+'" Genome="'+rec.lane_1_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="2" Name="'+rec.lane_2_library.library_name+'" Library="'+rec.lane_2_library.id+'" Genome="'+rec.lane_2_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="3" Name="'+rec.lane_3_library.library_name+'" Library="'+rec.lane_3_library.id+'" Genome="'+rec.lane_3_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="4" Name="'+rec.lane_4_library.library_name+'" Library="'+rec.lane_4_library.id+'" Genome="'+rec.lane_4_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="5" Name="'+rec.lane_5_library.library_name+'" Library="'+rec.lane_5_library.id+'" Genome="'+rec.lane_5_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="6" Name="'+rec.lane_6_library.library_name+'" Library="'+rec.lane_6_library.id+'" Genome="'+rec.lane_6_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="7" Name="'+rec.lane_7_library.library_name+'" Library="'+rec.lane_7_library.id+'" Genome="'+rec.lane_7_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
+ outputfile += '\n<Lane Index="8" Name="'+rec.lane_8_library.library_name+'" Library="'+rec.lane_8_library.id+'" Genome="'+rec.lane_8_library.library_species.use_genome_build+'" PrimerName="" PrimerSeq=""/>'
outputfile += '\n</SolexaResult>'
except ObjectDoesNotExist:
outputfile = 'Flowcell entry not found for: '+fcid
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
sequencing_time = timedelta(0, cycles * sequencing_seconds_per_cycle)
analysis_time = timedelta(0, cycles * pipeline_seconds_per_cycle)
estimate_mid = sequencing_time + analysis_time
+
+ return estimate_mid
+
+def estimateFlowcellTimeRemaining(flowcell):
+ estimate_mid = estimateFlowcellDuration(flowcell)
+
+ # offset for how long we've been running
+ running_time = timezone.now() - flowcell.run_date
+ estimate_mid -= running_time
+
+ return estimate_mid
+
+def roundToDays(estimate):
+ """
+ Given a time estimate round up and down in days
+ """
# floor estimate_mid
- estimate_low = timedelta(estimate_mid.days, 0)
+ estimate_low = timedelta(estimate.days, 0)
# floor estimate_mid and add a day
- estimate_high = timedelta(estimate_mid.days+1, 0)
-
+ 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