def diagnostic_search(request):
project, family = utils.get_project_and_family_for_user(request.user, request.GET)
if not project.can_view(request.user):
raise PermissionDenied
form = api_forms.DiagnosticSearchForm(family, request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = family.family_id
gene_list = form.cleaned_data['gene_list']
diagnostic_info_list = []
for gene_id in gene_list.gene_id_list():
diagnostic_info = get_gene_diangostic_info(family, gene_id, search_spec.variant_filter)
add_extra_info_to_variants_family(get_reference(), family, diagnostic_info._variants)
diagnostic_info_list.append(diagnostic_info)
return JSONResponse({
'is_error': False,
'gene_diagnostic_info_list': [d.toJSON() for d in diagnostic_info_list],
'gene_list_info': gene_list.toJSON(details=True),
'data_summary': family.get_data_summary(),
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def diagnostic_search(request):
project, family = utils.get_project_and_family_for_user(request.user, request.GET)
if not project.can_view(request.user):
raise PermissionDenied
form = api_forms.DiagnosticSearchForm(family, request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = family.family_id
gene_list = form.cleaned_data['gene_list']
diagnostic_info_list = []
for gene_id in gene_list.gene_id_list():
diagnostic_info = get_gene_diangostic_info(family, gene_id, search_spec.variant_filter)
add_extra_info_to_variants_family(get_reference(), family, diagnostic_info._variants)
diagnostic_info_list.append(diagnostic_info)
return JSONResponse({
'is_error': False,
'gene_diagnostic_info_list': [d.toJSON() for d in diagnostic_info_list],
'gene_list_info': gene_list.toJSON(details=True),
'data_summary': family.get_data_summary(),
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def family_gene_lookup(request):
project, family = utils.get_project_and_family_for_user(request.user, request.GET)
if not project.can_view(request.user):
raise PermissionDenied
gene_id = request.GET.get('gene_id')
if not get_reference().is_valid_gene_id(gene_id):
return JSONResponse({
'is_error': True,
'error': 'Invalid gene',
})
family_gene_data = get_gene_diangostic_info(family, gene_id)
add_extra_info_to_variants_family(get_reference(), family, family_gene_data._variants)
return JSONResponse({
'is_error': False,
'family_gene_data': family_gene_data.toJSON(),
'data_summary': family.get_data_summary(),
'gene': get_reference().get_gene(gene_id),
})
def family_gene_lookup(request):
project, family = utils.get_project_and_family_for_user(request.user, request.GET)
if not project.can_view(request.user):
raise PermissionDenied
gene_id = request.GET.get('gene_id')
if not get_reference().is_valid_gene_id(gene_id):
return JSONResponse({
'is_error': True,
'error': 'Invalid gene',
})
family_gene_data = get_gene_diangostic_info(family, gene_id)
add_extra_info_to_variants_family(get_reference(), family, family_gene_data._variants)
return JSONResponse({
'is_error': False,
'family_gene_data': family_gene_data.toJSON(),
'data_summary': family.get_data_summary(),
'gene': get_reference().get_gene(gene_id),
})
