def update_variant_tags_handler(request, variant_guids):
request_json = json.loads(request.body)
family_guid = request_json.pop('familyGuid')
family = Family.objects.get(guid=family_guid)
check_project_permissions(family.project, request.user)
all_variant_guids = set(variant_guids.split(','))
saved_variants = SavedVariant.objects.filter(guid__in=all_variant_guids)
if len(saved_variants) != len(all_variant_guids):
error = 'Unable to find the following variant(s): {}'.format(
', '.join([guid for guid in all_variant_guids if guid not in {sv.guid for sv in saved_variants}]))
return create_json_response({'error': error}, status=400, reason=error)
deleted_tag_guids = _delete_removed_tags(saved_variants, all_variant_guids, request_json.get('tags', []), request.user)
created_tags = _create_new_tags(saved_variants, request_json, request.user)
tag_updates = {tag['tagGuid']: tag for tag in get_json_for_variant_tags(created_tags)}
tag_updates.update({guid: None for guid in deleted_tag_guids})
saved_variants_by_guid = {}
for saved_variant in saved_variants:
tags = saved_variant.varianttag_set.all()
saved_variants_by_guid[saved_variant.guid] = {'tagGuids': [t.guid for t in tags]}
if not tags:
if not saved_variant.variantnote_set.count() > 0:
saved_variant.delete_model(request.user, user_can_delete=True)
saved_variants_by_guid[saved_variant.guid] = None
return create_json_response({
'savedVariantsByGuid': saved_variants_by_guid,
'variantTagsByGuid': tag_updates,
})
def test_json_for_variant_tags(self):
tags = VariantTag.objects.all()[:1]
json = get_json_for_variant_tags(tags)[0]
self.assertSetEqual(set(json.keys()), TAG_FIELDS)
def _get_saved_variants(variants, families, include_discovery_tags=False):
if not variants:
return {}, {}
variants = _flatten_variants(variants)
prefetch_related_objects(families, 'project')
hg37_family_guids = {
family.guid
for family in families
if family.project.genome_version == GENOME_VERSION_GRCh37
}
variant_q = Q()
discovery_variant_q = Q()
variants_by_id = {}
for variant in variants:
variants_by_id[_get_variant_key(**variant)] = variant
variant_q |= Q(xpos_start=variant['xpos'],
ref=variant['ref'],
alt=variant['alt'],
family__guid__in=variant['familyGuids'])
discovery_variant_q |= Q(
Q(xpos_start=variant['xpos'],
ref=variant['ref'],
alt=variant['alt'])
& ~Q(family__guid__in=variant['familyGuids']))
if variant[
'liftedOverGenomeVersion'] == GENOME_VERSION_GRCh37 and hg37_family_guids:
variant_hg37_families = [
family_guid for family_guid in variant['familyGuids']
if family_guid in hg37_family_guids
]
if variant_hg37_families:
lifted_xpos = get_xpos(variant['liftedOverChrom'],
variant['liftedOverPos'])
variant_q |= Q(xpos_start=lifted_xpos,
ref=variant['ref'],
alt=variant['alt'],
family__guid__in=variant_hg37_families)
variants_by_id[_get_variant_key(
xpos=lifted_xpos,
ref=variant['ref'],
alt=variant['alt'],
genomeVersion=variant['liftedOverGenomeVersion']
)] = variant
saved_variants = SavedVariant.objects.filter(variant_q)
json = get_json_for_saved_variants_with_tags(saved_variants,
add_details=True)
variants_to_saved_variants = {}
for saved_variant in json['savedVariantsByGuid'].values():
family_guids = saved_variant['familyGuids']
searched_variant = variants_by_id.get(
_get_variant_key(**saved_variant))
if not searched_variant:
# This can occur when an hg38 family has a saved variant that did not successfully lift from hg37
continue
saved_variant.update(searched_variant)
# For saved variants only use family it was saved for, not all families in search
saved_variant['familyGuids'] = family_guids
json['savedVariantsByGuid'][
saved_variant['variantGuid']] = saved_variant
if searched_variant['variantId'] not in variants_to_saved_variants:
variants_to_saved_variants[searched_variant['variantId']] = {}
for family_guid in family_guids:
variants_to_saved_variants[searched_variant['variantId']][
family_guid] = saved_variant['variantGuid']
if include_discovery_tags:
discovery_tags = get_json_for_variant_tags(
VariantTag.objects.filter(
variant_tag_type__category='CMG Discovery Tags',
saved_variants__in=SavedVariant.objects.filter(
discovery_variant_q)),
include_variant_details=True)
if discovery_tags:
family_guids = set()
for tag in discovery_tags:
for variant in tag['variants']:
family_guids.update(variant['familyGuids'])
families_by_guid = {
f.guid: f
for f in Family.objects.filter(
guid__in=family_guids).prefetch_related('project')
}
for tag in discovery_tags:
for variant in tag.pop('variants'):
variant_family = families_by_guid[variant['familyGuids']
[0]]
searched_variant = variants_by_id.get(
_get_variant_key(genomeVersion=variant_family.project.
genome_version,
**variant))
if searched_variant:
if not searched_variant.get('discoveryTags'):
searched_variant['discoveryTags'] = []
tag_json = {
'savedVariant': {
'variantGuid': variant['variantGuid'],
'familyGuid': variant_family.guid,
'projectGuid': variant_family.project.guid,
}
}
tag_json.update(tag)
searched_variant['discoveryTags'].append(tag_json)
json['familiesByGuid'] = {
f['familyGuid']: f
for f in _get_json_for_families(families_by_guid.values())
}
return json, variants_to_saved_variants
