# some core functions of the exp tracker module
-from django.http import HttpResponse
-from datetime import datetime
-from string import *
+from datetime import datetime, timedelta
+try:
+ import json
+except ImportError, e:
+ import simplejson as json
+
+import os
import re
-from htsworkflow.frontend import settings
-from htsworkflow.frontend.experiments.models import FlowCell, DataRun
-from htsworkflow.frontend.samples.models import Library
+
+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.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__startswith=flowcell_id)
+ except FlowCell.DoesNotExist, e:
+ return None
+
+ lane_set = {}
+ for lane in fc.lane_set.all():
+ 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': 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),
+ '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': control_lane,
+ # 'datarun_set': how should this be represented?,
+ 'flowcell_id': fc.flowcell_id,
+ 'id': fc.id,
+ 'lane_set': lane_set,
+ 'notes': fc.notes,
+ 'paired_end': fc.paired_end,
+ 'read_length': fc.read_length,
+ 'run_date': fc.run_date.isoformat(),
+ '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')
+
+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=''
fcid = 'none'
runfolder = 'unknown'
ClIP = request.META['REMOTE_ADDR']
- granted = False
- if request.has_key('user'):
- user = request['user']
-
- #Check access permission
- if (user == 'rami' and settings.ALLOWED_IPS.has_key(ClIP)): granted = True
- if not granted: return HttpResponse("access denied.")
+ if hasattr(request, 'user'):
+ user = request.user
+ #Check access permission
+ 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 ~~~~
- if request.has_key('fcid'):
- fcid = request['fcid']
+ if request.REQUEST.has_key('fcid'):
+ fcid = request.REQUEST['fcid']
else:
return HttpResponse('missing fcid')
-
- if request.has_key('runf'):
- runfolder = request['runf']
+
+ if request.REQUEST.has_key('runf'):
+ runfolder = request.REQUEST['runf']
else:
return HttpResponse('missing runf')
-
- if request.has_key('updst'):
- UpdatedStatus = request['updst']
+
+ 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.has_key('msg'):
- rec.run_note += ", "+request['msg']+" ("+mytimestamp+")"
+ if request.REQUEST.has_key('msg'):
+ rec.run_note += ", "+request.REQUEST['msg']+" ("+mytimestamp+")"
else :
if UpdatedStatus == '1':
rec.run_note = "Started ("+mytimestamp+")"
#if not granted: return HttpResponse("access denied.")
- cnfgfile = 'READ_LENGTH 25\n'
- cnfgfile += 'ANALYSIS eland\n'
- cnfgfile += 'GENOME_FILE all_chr.fa\n'
- cnfgfile += 'ELAND_MULTIPLE_INSTANCES 8\n'
+ config = ['READ_LENGTH 25']
+ config += ['ANALYSIS eland']
+ config += ['GENOME_FILE all_chr.fa']
+ config += ['ELAND_MULTIPLE_INSTANCES 8']
genome_dir = 'GENOME_DIR /Volumes/Genomes/'
eland_genome = 'ELAND_GENOME /Volumes/Genomes/'
-
- try:
- rec = FlowCell.objects.get(flowcell_id=fcid)
-
- cnfgfile += '1:'+genome_dir+rec.lane_1_library.library_species.use_genome_build+'\n'
- cnfgfile += '1:'+eland_genome+rec.lane_1_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '2:'+genome_dir+rec.lane_2_library.library_species.use_genome_build+'\n'
- cnfgfile += '2:'+eland_genome+rec.lane_2_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '3:'+genome_dir+rec.lane_3_library.library_species.use_genome_build+'\n'
- cnfgfile += '3:'+eland_genome+rec.lane_3_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '4:'+genome_dir+rec.lane_4_library.library_species.use_genome_build+'\n'
- cnfgfile += '4:'+eland_genome+rec.lane_4_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '5:'+genome_dir+rec.lane_5_library.library_species.use_genome_build+'\n'
- cnfgfile += '5:'+eland_genome+rec.lane_5_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '6:'+genome_dir+rec.lane_6_library.library_species.use_genome_build+'\n'
- cnfgfile += '6:'+eland_genome+rec.lane_6_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '7:'+genome_dir+rec.lane_7_library.library_species.use_genome_build+'\n'
- cnfgfile += '7:'+eland_genome+rec.lane_7_library.library_species.use_genome_build+'\n'
-
- cnfgfile += '8:'+genome_dir+rec.lane_8_library.library_species.use_genome_build+'\n'
- cnfgfile += '8:'+eland_genome+rec.lane_8_library.library_species.use_genome_build
+
+ 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:
- cnfgfile = 'Entry not found for fcid = '+fcid
+ config = 'Entry not found for fcid = '+fcid
- return cnfgfile
+ return os.linesep.join(config)
def getConfile(req):
granted = False
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
else: outputfile = 'Missing input: flowcell id'
return HttpResponse(outputfile, mimetype='text/plain')
+
+def estimateFlowcellDuration(flowcell):
+ """
+ Attempt to estimate how long it will take to run a flowcell
+
+ """
+ # (3600 seconds * 1.5 hours per cycle )
+ 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.days, 0)
+ # floor estimate_mid and add a day
+ estimate_high = timedelta(estimate.days+1, 0)
+
+ return (estimate_low, estimate_high)
+
+
+def makeUserLaneMap(flowcell):
+ """
+ Given a flowcell return a mapping of users interested in
+ the libraries on those lanes.
+ """
+ users = {}
+
+ for lane in flowcell.lane_set.all():
+ for affiliation in lane.library.affiliations.all():
+ for user in affiliation.users.all():
+ users.setdefault(user,[]).append(lane)
+
+ return users
+
+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):
+ affs = {}
+
+ for lane in flowcell.lane_set.all():
+ for affiliation in lane.library.affiliations.all():
+ affs.setdefault(affiliation,[]).append(lane)
+
+ return affs
+
+def makeEmailLaneMap(flowcell):
+ """
+ Create a list of email addresses and the lanes associated with those users.
+
+ The email addresses can come from both the "users" table and the "affiliations" table.
+ """
+ emails = {}
+ for lane in flowcell.lane_set.all():
+ for affiliation in lane.library.affiliations.all():
+ if affiliation.email is not None and len(affiliation.email) > 0:
+ emails.setdefault(affiliation.email,set()).add(lane)
+ for user in affiliation.users.all():
+ if user.email is not None and len(user.email) > 0:
+ emails.setdefault(user.email,set()).add(lane)
+
+ return emails
projects / htsworkflow.git / blobdiff