def detail_study(request, pk=None):
"""
Detailed view of a single study
"""
study = Study.objects.published().get(id=pk)
# Check if RNASeq or Phenotypes:
if len(Phenotype.objects.published().filter(study__id=pk)) > 0:
phenotype_table = ReducedPhenotypeTable(
Phenotype.objects.published().filter(study__id=pk),
order_by="-name")
else:
phenotype_table = RNASeqTable(RNASeq.objects.filter(study__id=pk),
order_by="-name")
RequestConfig(request, paginate={
"per_page": 20
}).configure(phenotype_table)
variable_dict = {}
variable_dict["phenotype_table"] = phenotype_table
variable_dict["study"] = study
variable_dict['to_data'] = study.phenotype_set.values(
'to_term__name').annotate(count=Count('to_term__name'))
variable_dict['eo_data'] = study.phenotype_set.values(
'eo_term__name').annotate(count=Count('eo_term__name'))
variable_dict['uo_data'] = study.phenotype_set.values(
'uo_term__name').annotate(count=Count('uo_term__name'))
return render(request, 'phenotypedb/study_detail.html', variable_dict)
def list_rnaseqs(request):
"""
Displays table of all published RNASeq
"""
table = RNASeqTable(RNASeq.objects.all(), order_by="-name")
RequestConfig(request, paginate={"per_page": 50}).configure(table)
return render(request, 'phenotypedb/rnaseq_data_list.html',
{"rnaseq_table": table})
def list_rnaseqs(request):
"""
Displays table of all published RNASeq
"""
table = RNASeqTable(RNASeq.objects.all(), order_by="name")
RequestConfig(request, paginate={"per_page":50}).configure(table)
context = { 'rnaseq_table': table, 'is_rnaseq': True }
context.update(base_context(request))
return render(request, 'phenotypedb/rnaseq_data_list.html', context)
def SearchResultsRNASeq(request, query=None):
studies = Study.objects.published().annotate(
pheno_count=Count('phenotype')).annotate(rna_count=Count('rnaseq'))
studies = studies.filter(pheno_count=0).filter(rna_count__gt=0)
if query == None:
rnaseqs = RNASeq.objects.all()
studies = studies.all()
accessions = Accession.objects.all()
download_url = "/rest/rnaseq_search"
else:
rnaseqs = RNASeq.objects.filter(
Q(name__icontains=query) | Q(growth_conditions__icontains=query))
studies = studies.filter(name__icontains=query)
accessions = Accession.objects.filter(name__icontains=query)
download_url = "/rest/rnaseq_search/" + str(query)
rnaseq_table = RNASeqTable(rnaseqs, order_by="-name")
RequestConfig(request, paginate={"per_page": 10}).configure(rnaseq_table)
study_table = RNASeqStudyTable(studies, order_by="-name")
RequestConfig(request, paginate={"per_page": 10}).configure(study_table)
accession_table = AccessionTable(accessions, order_by="-name")
RequestConfig(request, paginate={
"per_page": 10
}).configure(accession_table)
variable_dict = {}
variable_dict['query'] = query
variable_dict['nrnaseqs'] = rnaseqs.count()
variable_dict['rnaseq_table'] = rnaseq_table
variable_dict['accession_table'] = accession_table
variable_dict['study_table'] = study_table
variable_dict['nstudies'] = studies.count()
variable_dict['naccessions'] = accessions.count()
variable_dict['download_url'] = download_url
print(variable_dict)
return render(request, 'home/rnaseq_search_results.html', variable_dict)