# 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.core.exceptions import ObjectDoesNotExist
from django.core.mail import send_mail, mail_admins
+from django.http import HttpResponse, Http404
+
+from htsworkflow.frontend.auth import require_api_key
+from htsworkflow.frontend import settings
+from htsworkflow.frontend.experiments.models import FlowCell, DataRun, Lane
+from htsworkflow.frontend.samples.models import Library, HTSUser
+
+def flowcell_information(flowcell_id):
+ """
+ Return a dictionary describing a flowcell
+ """
+ try:
+ fc = FlowCell.objects.get(flowcell_id=flowcell_id)
+ except FlowCell.DoesNotExist, e:
+ return None
+
+ lane_set = {}
+ for lane in fc.lane_set.all():
+ lane_set[lane.lane_number] = {
+ '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),
+ '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
+ }
+
+ 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
+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
+
+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'
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) +":" + \
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'):
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 = datetime.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