def cohort_variant_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
if not project.can_view(request.user):
return PermissionDenied
form = api_forms.CohortVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = cohort.cohort_id
sys.stderr.write("cohort_variant_search - starting: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
list_of_variants = [v.toJSON() for v in variants]
sys.stderr.write("cohort_variant_search - done calculate_mendelian_variant_search: %s %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id, len(list_of_variants)))
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), list_of_variants)
sys.stderr.write("cohort_variant_search - done save_results_for_spec: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
sys.stderr.write("cohort_variant_search - done add_extra_info_to_variants_cohort: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_variant_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
if not project.can_view(request.user):
return PermissionDenied
form = api_forms.CohortVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = cohort.cohort_id
sys.stderr.write("cohort_variant_search - starting: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
list_of_variants = [v.toJSON() for v in variants]
sys.stderr.write("cohort_variant_search - done calculate_mendelian_variant_search: %s %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id, len(list_of_variants)))
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), list_of_variants)
sys.stderr.write("cohort_variant_search - done save_results_for_spec: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
sys.stderr.write("cohort_variant_search - done add_extra_info_to_variants_cohort: %s %s\n" % (json.dumps(search_spec.toJSON()), cohort.xfamily().family_id))
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_variant_search(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
if not project.can_view(request.user):
return HttpResponse('unauthorized')
form = api_forms.CohortVariantSearchForm(request.GET)
if form.is_valid():
search_spec = form.cleaned_data['search_spec']
search_spec.family_id = cohort.cohort_id
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
search_hash = cache_utils.save_results_for_spec(project.project_id, search_spec.toJSON(), [v.toJSON() for v in variants])
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_hash': search_hash,
})
else:
return JSONResponse({
'is_error': True,
'error': server_utils.form_error_string(form)
})
def cohort_variant_search_spec(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
# TODO: use form
search_spec_dict, variants = cache_utils.get_cached_results(project.project_id, request.GET.get('search_hash'))
search_spec = MendelianVariantSearchSpec.fromJSON(search_spec_dict)
if variants is None:
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
else:
variants = [Variant.fromJSON(v) for v in variants]
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_spec': search_spec.toJSON(),
})
def cohort_variant_search_spec(request):
project, cohort = get_project_and_cohort_for_user(request.user, request.GET)
# TODO: use form
search_spec_dict, variants = cache_utils.get_cached_results(project.project_id, request.GET.get('search_hash'))
search_spec = MendelianVariantSearchSpec.fromJSON(search_spec_dict)
if variants is None:
variants = api_utils.calculate_mendelian_variant_search(search_spec, cohort.xfamily())
else:
variants = [Variant.fromJSON(v) for v in variants]
api_utils.add_extra_info_to_variants_cohort(get_reference(), cohort, variants)
return JSONResponse({
'is_error': False,
'variants': [v.toJSON() for v in variants],
'search_spec': search_spec.toJSON(),
})
