def islandpick_genomes(request, aid):
context = {}
try:
analysis = Analysis.objects.get(pk=aid)
context['accnum'] = analysis.ext_id
context['default_analysis'] = (True if analysis.default_analysis == 1 else False)
except Analysis.DoesNotExist:
if settings.DEBUG:
print "Can't fetch analysis"
return HttpResponse(status = 403)
kwargs = {}
selected = {}
try:
iptask = GIAnalysisTask.objects.get(aid=aid, prediction_method='Islandpick')
parameters = json.loads(iptask.parameters)
context['parameters'] = parameters
if 'min_cutoff' in parameters:
kwargs.update({'min_cutoff': float(parameters['min_cutoff'])})
if 'max_distance' in parameters:
kwargs.update({'max_cutoff': float(parameters['max_cutoff'])})
except Exception as e:
if settings.DEBUG:
print e
return HttpResponse(status = 403)
try:
if request.GET.get('min_cutoff'):
kwargs.update({'min_cutoff': float(request.GET.get('min_cutoff'))})
if request.GET.get('max_cutoff'):
kwargs.update({'max_cutoff': float(request.GET.get('max_cutoff'))})
if request.GET.get('max_dist_single_cutoff'):
kwargs.update({'max_dist_single_cutoff': float(request.GET.get('max_dist_single_cutoff'))})
if request.GET.get('min_compare_cutoff'):
kwargs.update({'min_compare_cutoff': float(request.GET.get('min_compare_cutoff'))})
if request.GET.get('max_compare_cutoff'):
kwargs.update({'max_compare_cutoff': float(request.GET.get('max_compare_cutoff'))})
except ValueError as e:
if settings.DEBUG:
print e
return HttpResponse(status = 403)
if 'comparison_genomes' in parameters:
selected = {x: True for x in parameters['comparison_genomes'].split()}
kwargs.update({'extra_genomes': selected})
else:
context['nogenomesselected'] = True
genomes = Distance.find_genomes(analysis.ext_id, **kwargs)
if request.method == 'GET':
try:
# Now get all the names
ext_ids = [g for g,d in genomes]
cache_names = NameCache.objects.filter(cid__in=ext_ids).values('cid', 'name')
cache_names = {x['cid']:x['name'] for x in cache_names}
cids = [int(x) for x in ext_ids if x.isdigit()]
custom_names = CustomGenome.objects.filter(cid__in=cids).values('cid', 'name')
custom_names = {x['cid']:x['name'] for x in custom_names}
# cluster_list = ext_ids
# cluster_list.insert(0, analysis.ext_id)
# print len(cluster_list)
# context['tree'] = Distance.distance_matrix(cluster_list)
except Exception as e:
print str(e)
pass
genome_list = OrderedDict()
# We need the genomes to display in order
for g,dist in sorted(genomes, key=lambda genome: genome[1]):
# We don't want custom genomes, so skip anything without
# a namecache entry for now
if g not in cache_names:
continue
genome_list.update({g: {'dist': "%0.3f" % dist,
'used': (True if g in selected else False),
'picked' : (True if g in selected and 'reselect' not in request.GET else False),
'name': (cache_names[g] if g in cache_names else custom_names[g] if g in custom_names else "Unknown" )
}
})
if request.GET.get('reselect'):
try:
# If we're re-selecting the candidates, make the call to the backend
picker = send_picker(analysis.ext_id, **kwargs)
if 'code' in picker and picker['code'] == 200:
for acc in picker['data']:
if "picked" in picker['data'][acc] and acc in genome_list:
genome_list[acc]["picked"] = 'true'
context['picker'] = picker
except Exception as e:
if settings.DEBUG:
print "Exception: " + str(e)
context['picker'] = {'code': 500}
context['genomes'] = genome_list
context['status'] = "OK"
data = json.dumps(context, indent=4, sort_keys=False)
return HttpResponse(data, content_type="application/json")
else:
try:
#print request.GET.get('min_gi_size')
accnums = []
min_gi_size = filter(lambda x: x.isdigit(), request.GET.get('min_gi_size') )
for name in request.POST:
#print name, request.POST[name]
if name not in (x[0] for x in genomes):
if settings.DEBUG:
print "Error, " + name + " not in genomes set"
raise Exception("Error, requested genome isn't in the allowed set")
accnums.append(name)
clone_kwargs = { 'args': { 'modules': { 'Islandpick': { 'args': { 'comparison_genomes': ' '.join(accnums), 'MIN_GI_SIZE': min_gi_size } } } } }
# Check if we've run these settings before, if so, just redirect to that
match_aid = Analysis.find_islandpick(analysis.ext_id, accnums, min_gi_size)
if match_aid:
context['status'] = 'success'
context['aid'], token = match_aid
if token:
context['token'] = token
else:
clone_ret = send_clone(aid, **clone_kwargs)
if 'code' in clone_ret and clone_ret['code'] == 200:
if settings.DEBUG:
print "Job submitted, new aid: " + clone_ret['data']
context['status'] = 'success'
aid = clone_ret['data']
context['aid'] = aid
try:
new_analysis = Analysis.objects.get(pk=aid)
if new_analysis.token:
context['token'] = new_analysis.token
except:
pass
except Exception as e:
if settings.DEBUG:
print "Error in post"
print str(e)
return HttpResponse(status = 403)
data = json.dumps(context, indent=4, sort_keys=False)
return HttpResponse(data, content_type="application/json")
def results(request, aid):
# Create the context we're going to add
# our variables for rending to
context = {}
context['container']=request.GET.get('container','circularchart')
try:
analysis = Analysis.objects.get(pk=aid)
context['noanalysis'] = False
except Analysis.DoesNotExist:
context['noanalysis'] = True;
if context['noanalysis'] != True:
context['aid'] = aid
context['default_analysis'] = (True if analysis.default_analysis == 1 else False)
# Check for a security token
if analysis.token and analysis.owner_id != 0:
# We have a security token
if request.GET.get('token'):
token = request.GET.get('token')
if token != analysis.token:
# Uh-oh, the token didn't match!
return HttpResponse(status=403)
else:
# There's a token in the analysis but the user didn't supply one...
return HttpResponse(status=403)
# Fetch the genome name and such
if(analysis.atype == Analysis.CUSTOM):
genome = CustomGenome.objects.get(pk=analysis.ext_id)
context['genomename'] = genome.name
if genome.contigs > 1:
ref_accnum = analysis.find_reference_genome()
ref_genome = Analysis.lookup_genome(ref_accnum)
context['ref_genome'] = ref_genome.name
elif(analysis.atype == Analysis.MICROBEDB):
# gpv_id = Replicon.objects.using('microbedb').filter(rep_accnum=analysis.ext_id)[0].gpv_id
# context['genomename'] = Genomeproject.objects.using('microbedb').get(pk=gpv_id).org_name
context['genomename'] = NameCache.objects.get(cid=analysis.ext_id).name
# context['genomename'] = 'Something from Microbedb'
# Fetch the virulence factors
# island_genes = Genes.objects.filter(ext_id=analysis.ext_id).order_by('start').all()
# vir_list = Virulence.objects.using('microbedb').filter(protein_accnum__in=
# list(island_genes.values_list('name', flat=True))).values_list('source', flat=True).distinct()
# context['vir_types'] = {}
# context['has_vir'] = False
# for vir in VIRULENCE_FACTORS.keys():
# if vir in vir_list:
# context['vir_types'][vir] = True
# context['has_vir'] = True
# else:
# context['vir_types'][vir] = False
# Remember the methods we have available
# context['methods'] = dict.fromkeys(GenomicIsland.objects.filter(aid_id=aid).values_list("prediction_method", flat=True).distinct(), 1)
CHOICES = dict(STATUS_CHOICES)
context['status'] = CHOICES[analysis.status]
if analysis.status == STATUS['PENDING'] or analysis.status == STATUS['RUNNING']:
try:
context['emails'] = ','.join(Notification.objects.filter(analysis=analysis).values_list('email', flat=True))
except Exception as e:
if settings.DEBUG:
print e
pass
if request.GET.get('load'):
context['reload'] = request.GET.get('load')
context['showtour'] = True
return render(request, 'results.html', context)