def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
raise PermissionDenied
if not family.has_data('variation'):
return render(request, 'analysis_unavailable.html', {
'reason': 'This family does not have any variant data.'
})
elif project.project_status == Project.NEEDS_MORE_PHENOTYPES and not request.user.is_staff:
return render(request, 'analysis_unavailable.html', {
'reason': 'Awaiting phenotype data.'
})
has_gene_search = get_project_datastore(project_id).project_collection_is_loaded(project_id)
gene_lists = [project_gene_list.gene_list.toJSON(details=True) for project_gene_list in ProjectGeneList.objects.filter(project=project)]
sys.stderr.write("returning mendelian_variant_search page for %(project_id)s %(family_id)s. has_gene_search = %(has_gene_search)s\n " % locals() )
return render(request, 'mendelian_variant_search.html', {
'gene_lists': json.dumps(gene_lists),
'project': project,
'family': family,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
'has_gene_search': has_gene_search or get_elasticsearch_dataset(project_id) is not None
})
def cohort_variant_search(request, project_id, cohort_id):
project = get_object_or_404(Project, project_id=project_id)
cohort = get_object_or_404(Cohort, project=project, cohort_id=cohort_id)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
return render(request, 'cohort/cohort_variant_search.html', {
'project': project,
'cohort': cohort,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(cohort.xfamily())),
})
def cohort_variant_search(request, project_id, cohort_id):
project = get_object_or_404(Project, project_id=project_id)
cohort = get_object_or_404(Cohort, project=project, cohort_id=cohort_id)
if not project.can_view(request.user):
raise PermissionDenied
return render(request, 'cohort/cohort_variant_search.html', {
'project': project,
'cohort': cohort,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(cohort.xfamily())),
})
def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
if not family.has_data('variation'):
return render(request, 'analysis_unavailable.html', {
'reason': 'This family does not have any variant data.'
})
return render(request, 'mendelian_variant_search.html', {
'project': project,
'family': family,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
})
def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
if not family.has_data('variation'):
return render(request, 'analysis_unavailable.html', {
'reason': 'This family does not have any variant data.'
})
has_gene_search = get_project_datastore(project_id).project_collection_is_loaded(project_id)
sys.stderr.write("Running mendelian_variant_search on %(project_id)s %(family_id)s. has_gene_search = %(has_gene_search)s\n " % locals() )
return render(request, 'mendelian_variant_search.html', {
'project': project,
'family': family,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
'has_gene_search': has_gene_search
})
def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
if not family.has_data('variation'):
return render(
request, 'analysis_unavailable.html',
{'reason': 'This family does not have any variant data.'})
return render(
request, 'mendelian_variant_search.html', {
'project':
project,
'family':
family,
'family_genotype_filters_json':
json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
})
def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
raise PermissionDenied
if not family.has_data('variation'):
return render(
request, 'analysis_unavailable.html',
{'reason': 'This family does not have any variant data.'})
has_gene_search = get_project_datastore(
project).project_collection_is_loaded(project)
gene_lists = [
project_gene_list.gene_list.toJSON(details=True)
for project_gene_list in ProjectGeneList.objects.filter(
project=project)
]
sys.stderr.write(
"returning mendelian_variant_search page for %(project_id)s %(family_id)s. has_gene_search = %(has_gene_search)s\n "
% locals())
return render(
request, 'mendelian_variant_search.html', {
'gene_lists':
json.dumps(gene_lists),
'project':
project,
'family':
family,
'family_genotype_filters_json':
json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
'has_gene_search':
has_gene_search,
'new_page_url':
'/variant_search/family/{0}'.format(family.seqr_family.guid)
if family.seqr_family and family.seqr_family.project.has_new_search
else None,
})
def mendelian_variant_search(request, project_id, family_id):
project = get_object_or_404(Project, project_id=project_id)
family = get_object_or_404(Family, project=project, family_id=family_id)
if not project.can_view(request.user):
raise PermissionDenied
if not family.has_data('variation'):
return render(request, 'analysis_unavailable.html', {
'reason': 'This family does not have any variant data.'
})
has_gene_search = get_project_datastore(project_id).project_collection_is_loaded(project_id)
gene_lists = [project_gene_list.gene_list.toJSON(details=True) for project_gene_list in ProjectGeneList.objects.filter(project=project)]
sys.stderr.write("Running mendelian_variant_search on %(project_id)s %(family_id)s. has_gene_search = %(has_gene_search)s\n " % locals() )
return render(request, 'mendelian_variant_search.html', {
'gene_lists': json.dumps(gene_lists),
'project': project,
'family': family,
'family_genotype_filters_json': json.dumps(x_inheritance.get_genotype_filters(family.xfamily())),
'has_gene_search': has_gene_search
})
