def saved_variant_data(request, project_guid, variant_guids=None):
project = get_project_and_check_permissions(project_guid, request.user)
family_guids = request.GET['families'].split(',') if request.GET.get('families') else None
variant_guids = variant_guids.split(',') if variant_guids else None
if family_guids:
variant_query = SavedVariant.objects.filter(family__guid__in=family_guids)
else:
variant_query = SavedVariant.objects.filter(family__project=project)
if variant_guids:
variant_query = variant_query.filter(guid__in=variant_guids)
if variant_query.count() < 1:
return create_json_response({}, status=404, reason='Variant {} not found'.format(', '.join(variant_guids)))
discovery_tags_query = None
if user_is_analyst(request.user):
discovery_tags_query = Q()
for variant in variant_query:
discovery_tags_query |= Q(Q(variant_id=variant.variant_id) & ~Q(family_id=variant.family_id))
discovery_tags_query &= Q(family__project__projectcategory__name=ANALYST_PROJECT_CATEGORY)
response = get_json_for_saved_variants_with_tags(variant_query, add_details=True, discovery_tags_query=discovery_tags_query)
variants = list(response['savedVariantsByGuid'].values())
genes = saved_variant_genes(variants)
response['locusListsByGuid'] = _add_locus_lists([project], genes)
discovery_tags = response.pop('discoveryTags', None)
if discovery_tags:
_add_discovery_tags(variants, discovery_tags)
response['genesById'] = genes
return create_json_response(response)
def saved_variant_data(request, project_guid, variant_guids=None):
project = get_project_and_check_permissions(project_guid, request.user)
family_guids = request.GET['families'].split(',') if request.GET.get('families') else None
variant_guids = variant_guids.split(',') if variant_guids else None
if family_guids:
variant_query = SavedVariant.objects.filter(family__guid__in=family_guids)
else:
get_note_only = bool(request.GET.get('includeNoteVariants'))
variant_query = SavedVariant.objects.filter(family__project=project, varianttag__isnull=get_note_only).distinct()
if variant_guids:
variant_query = variant_query.filter(guid__in=variant_guids)
if variant_query.count() < 1:
return create_json_response({}, status=404, reason='Variant {} not found'.format(', '.join(variant_guids)))
response = get_json_for_saved_variants_with_tags(variant_query, add_details=True)
discovery_tags = None
if user_is_analyst(request.user):
discovery_tags, discovery_response = get_json_for_discovery_tags(response['savedVariantsByGuid'].values())
response.update(discovery_response)
variants = list(response['savedVariantsByGuid'].values())
genes = saved_variant_genes(variants)
response['locusListsByGuid'] = _add_locus_lists([project], genes)
if discovery_tags:
_add_discovery_tags(variants, discovery_tags)
response['genesById'] = genes
return create_json_response(response)
def saved_variants_page(request, tag):
gene = request.GET.get('gene')
if tag == 'ALL':
saved_variant_models = SavedVariant.objects.exclude(varianttag=None)
else:
tag_type = VariantTagType.objects.get(name=tag, project__isnull=True)
saved_variant_models = SavedVariant.objects.filter(varianttag__variant_tag_type=tag_type)
saved_variant_models = saved_variant_models.filter(family__project__in=get_projects_user_can_view(request.user))
if gene:
saved_variant_models = saved_variant_models.filter(saved_variant_json__transcripts__has_key=gene)
elif saved_variant_models.count() > MAX_SAVED_VARIANTS:
return create_json_response({'error': 'Select a gene to filter variants'}, status=400)
prefetch_related_objects(saved_variant_models, 'family__project')
response_json = get_json_for_saved_variants_with_tags(saved_variant_models, add_details=True, include_missing_variants=True)
project_models_by_guid = {variant.family.project.guid: variant.family.project for variant in saved_variant_models}
families = {variant.family for variant in saved_variant_models}
individuals = Individual.objects.filter(family__in=families)
saved_variants = list(response_json['savedVariantsByGuid'].values())
genes = saved_variant_genes(saved_variants)
locus_lists_by_guid = _add_locus_lists(list(project_models_by_guid.values()), genes, include_all_lists=True)
projects_json = get_json_for_projects(list(project_models_by_guid.values()), user=request.user, add_project_category_guids_field=False)
functional_tag_types = get_json_for_variant_functional_data_tag_types()
variant_tag_types = VariantTagType.objects.filter(Q(project__in=project_models_by_guid.values()) | Q(project__isnull=True))
prefetch_related_objects(variant_tag_types, 'project')
variant_tags_json = _get_json_for_models(variant_tag_types)
tag_projects = {vt.guid: vt.project.guid for vt in variant_tag_types if vt.project}
for project_json in projects_json:
project_guid = project_json['projectGuid']
project_variant_tags = [
vt for vt in variant_tags_json if tag_projects.get(vt['variantTagTypeGuid'], project_guid) == project_guid]
project_json.update({
'locusListGuids': list(locus_lists_by_guid.keys()),
'variantTagTypes': sorted(project_variant_tags, key=lambda variant_tag_type: variant_tag_type['order'] or 0),
'variantFunctionalTagTypes': functional_tag_types,
})
families_json = _get_json_for_families(list(families), user=request.user, add_individual_guids_field=True)
individuals_json = _get_json_for_individuals(individuals, add_hpo_details=True, user=request.user)
for locus_list in get_json_for_locus_lists(LocusList.objects.filter(guid__in=locus_lists_by_guid.keys()), request.user):
locus_lists_by_guid[locus_list['locusListGuid']].update(locus_list)
response_json.update({
'genesById': genes,
'projectsByGuid': {project['projectGuid']: project for project in projects_json},
'familiesByGuid': {family['familyGuid']: family for family in families_json},
'individualsByGuid': {indiv['individualGuid']: indiv for indiv in individuals_json},
'locusListsByGuid': locus_lists_by_guid,
})
return create_json_response(response_json)
def _process_variants(variants, families, user):
if not variants:
return {'searchedVariants': variants}
prefetch_related_objects(families, 'project')
genes = saved_variant_genes(variants)
projects = {family.project for family in families}
locus_lists_by_guid = _add_locus_lists(projects, genes)
response_json, _ = _get_saved_variants(variants, families, include_discovery_tags=user_is_analyst(user))
response_json.update({
'searchedVariants': variants,
'genesById': genes,
'locusListsByGuid': locus_lists_by_guid,
})
return response_json
