def eventsummary(request):
response = HttpResponse()
# get genes out of request
try:
genes = [int(g) for g in request.GET['genes'].split(',')]
except (KeyError, ValueError):
genes = None
# get abstracts
query = request.GET.get('q')
if query:
abstracts = get_abstracts(query)
else:
abstracts = None
# get gene combinations
try:
outergenes = get_gene_combinations(genes=genes, abstracts=abstracts)
except KeyError:
# error if no gene or abstracts
json.dump({'validresult': False, 'errormsg': 'You must supply either genes or a keyword query'}, response)
return response
# get sorter function from request
orderby = request.GET.get('orderby', 'abstracts').lower()
sorter = {'abstracts': lambda g: -g.count, 'symbol': lambda g: g.symbol}[orderby]
# sort data structure before rendering it
outergenes_sorted = []
for og in sorted(outergenes.values(), key=sorter):
og.innergenes.sort(key=sorter)
outergenes_sorted.append(og)
# apply limit
try:
limit = int(request.GET.get('limit'))
outergenes_sorted = outergenes_sorted[:limit]
except (TypeError, ValueError):
pass
# render and return JSON response
if outergenes_sorted:
json.dump({'validresult': True,
'result': render_to_string("eventsummary.html",
{'outergenes': outergenes_sorted, 'genes': genes, 'orderby': orderby})}, response)
else:
json.dump({'validresult': False, 'errormsg': 'No genes found'}, response)
return response
def eventlist(request):
"""Find and return events matching a query"""
maxlimit = 500 # maximum number of events to fetch at once
# get genes out of request. First check for internal gene ids, then entrez
# ids, then gene symbols.
try:
genes = [int(g) for g in request.GET['genes'].split(',')]
except (KeyError, ValueError):
try:
gene_eids = [int(i.strip()) for i in request.GET['gene_entrez_ids'].split(',') if i != '']
genes = [g.id for g in Gene.objects.filter(entrez_id__in=gene_eids)]
# workaround for database mess
if genes == []:
raise Http404
except (KeyError, ValueError):
try:
genes = [g.id for g in gene_lookup(request.GET['gene_symbols'])]
except (KeyError, ValueError):
genes = None
# get abstracts
query = request.GET.get('q')
if query:
abstracts = get_abstracts(query)
else:
abstracts = None
# get limit and offset
try:
limit = int(request.GET['limit'])
if limit > maxlimit:
limit = maxlimit
except (KeyError, ValueError):
limit = maxlimit
try:
offset = int(request.GET['offset'])
except (KeyError, ValueError):
offset = 0
# get events, 404 if we don't supply either genes or abstracts
try:
events = get_events(genes=genes, abstracts=abstracts, limit=limit, offset=offset)
except KeyError:
events = []
# return the appropriate response
if request.GET.get('preview'):
genesyms = [g.symbol for g in Gene.objects.filter(id__in=genes).only('symbol')] if genes else []
# show more information about a specific gene
# TODO: clean this up during the next re-organization of the event search
detail = gene_lookup(request.GET.get('detail'))
if len(detail) > 0:
summaryrow = get_gene_combinations(genes=genes, abstracts=abstracts).get(detail[0].id)
if summaryrow:
summaryrow.innergenes.sort(key=lambda g: -g.count)
else:
summaryrow = None
return render_to_response("eventpreview.html",
{'events': events, 'geneids':genes, 'genesyms': genesyms, 'q': query, 'summaryrow':summaryrow})
# 404 if there were no events
if not events:
raise Http404
dl = request.GET.get('download')
if dl:
if dl.lower() == 'xml':
# return xml file
response = HttpResponse('<?xml version="1.0" ?>\n<!DOCTYPE eventlist SYSTEM "http://gadget.biostat.wisc.edu/static/eventlist.dtd">\n<eventlist>\n')
response.write(xmldescription(query=query, genes=genes, limit=limit, offset=offset))
for ev in events:
try:
# wrap each event in a try block so if something goes wrong,
# we still get all the other events. take this out when debugging.
response.write('\n')
response.write(ev.xml(indent=2))
except:
print "event {0} failed to render XML".format(ev.id)
response.write('</eventlist>')
response['Content-Type'] = 'text/xml'
return response
if dl.lower() == 'csv':
# create, package, and return a CSV file
response = HttpResponse(mimetype='text/csv')
response['Content-Disposition'] = 'attachment; filename=gadget-events.csv'
response.write('event_id,gene_entrez_ids,gene_symbols,event_types,abstract_count\n'
+ '\n'.join([ev.tablerow() for ev in events]))
return response
# render HTML
return render_to_response("eventlist.html", {'events':events, 'q':query})