def test_json_for_saved_variant(self):
variant = SavedVariant.objects.first()
json = get_json_for_saved_variant(variant)
fields = {'variantGuid', 'variantId', 'familyGuids', 'xpos', 'ref', 'alt'}
self.assertSetEqual(set(json.keys()), fields)
fields.update({'tags', 'functionalData', 'notes', 'liftedOverGenomeVersion', 'clinvar', 'originalAltAlleles',
'liftedOverPos', 'genomeVersion', 'mainTranscript', 'hgmd', 'liftedOverChrom', 'genotypeFilters',
'genotypes', 'transcripts', 'populations', 'predictions', 'chrom', 'pos', 'rsid'})
json = get_json_for_saved_variant(variant, add_tags=True, add_details=True)
self.assertSetEqual(set(json.keys()), fields)
def test_json_for_saved_variant(self):
variant = SavedVariant.objects.first()
json = get_json_for_saved_variant(variant)
fields = {'variantGuid', 'variantId', 'familyGuids', 'xpos', 'ref', 'alt'}
self.assertSetEqual(set(json.keys()), fields)
fields.update({'tags', 'functionalData', 'notes', 'liftedOverGenomeVersion', 'clinvar', 'originalAltAlleles',
'liftedOverPos', 'genomeVersion', 'mainTranscript', 'hgmd', 'liftedOverChrom', 'genotypeFilters',
'genotypes', 'transcripts', 'populations', 'predictions', 'chrom', 'pos', 'rsid'})
json = get_json_for_saved_variant(variant, add_tags=True, add_details=True)
self.assertSetEqual(set(json.keys()), fields)
def test_json_for_saved_variant(self):
variant = SavedVariant.objects.first()
json = get_json_for_saved_variant(variant)
fields = {
'variantId', 'familyGuid', 'xpos', 'ref', 'alt', 'chrom', 'pos'
}
self.assertSetEqual(set(json.keys()), fields)
fields.update({'tags', 'functionalData', 'notes'})
json = get_json_for_saved_variant(variant, add_tags=True)
self.assertSetEqual(set(json.keys()), fields)
def saved_variant_data(request, project_guid, variant_guid=None):
project = get_project_and_check_permissions(project_guid, request.user)
variants = {}
variant_query = SavedVariant.objects.filter(project=project)\
.select_related('family')\
.only('xpos_start', 'ref', 'alt', 'saved_variant_json', 'family__guid', 'guid')\
.prefetch_related('varianttag_set', 'varianttag_set__created_by', 'varianttag_set__variant_tag_type',
'variantfunctionaldata_set', 'variantfunctionaldata_set__created_by', 'variantnote_set',
'variantnote_set__created_by')
if request.GET.get('families'):
variant_query = variant_query.filter(
family__guid__in=request.GET.get('families').split(','))
if variant_guid:
variant_query = variant_query.filter(guid=variant_guid)
if variant_query.count() < 1:
return create_json_response(
{},
status=404,
reason='Variant {} not found'.format(variant_guid))
for saved_variant in variant_query:
variant = get_json_for_saved_variant(saved_variant, add_tags=True)
if variant['tags'] or variant['notes']:
variant_json = json.loads(saved_variant.saved_variant_json or '{}')
variant.update(variant_details(variant_json, project,
request.user))
variants[variant['variantId']] = variant
genes = _saved_variant_genes(variants)
_add_locus_lists(project, variants, genes)
return create_json_response({
'savedVariants': variants,
'genesById': genes,
})
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json.pop('familyGuid')
non_variant_json = {
k: variant_json.pop(k, None) for k in ['searchHash', 'tags', 'functionalData', 'notes', 'note', 'submitToClinvar']
}
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
xpos = variant_json['xpos']
ref = variant_json['ref']
alt = variant_json['alt']
# TODO remove project field from saved variants
saved_variant = SavedVariant.objects.create(
xpos=xpos,
xpos_start=xpos,
xpos_end=xpos + len(ref) - 1,
ref=ref,
alt=alt,
family=family,
project=family.project,
saved_variant_json=json.dumps(variant_json)
)
if non_variant_json.get('note'):
_create_variant_note(saved_variant, non_variant_json, request.user)
elif non_variant_json.get('tags'):
_create_new_tags(saved_variant, non_variant_json, request.user)
variant_json.update(get_json_for_saved_variant(saved_variant, add_tags=True, project_guid=family.project.guid))
return create_json_response({
'savedVariantsByGuid': {saved_variant.guid: variant_json},
})
def test_json_for_saved_variant(self):
variant = SavedVariant.objects.get(guid='SV0000001_2103343353_r0390_100')
json = get_json_for_saved_variant(variant)
self.assertSetEqual(set(json.keys()), SAVED_VARIANT_FIELDS)
self.assertListEqual(json['familyGuids'], ["F000001_1"])
self.assertEqual(json['variantId'], '21-3343353-GAGA-G')
fields = set()
fields.update(SAVED_VARIANT_FIELDS)
fields.update(list(variant.saved_variant_json.keys()))
json = get_json_for_saved_variant(variant, add_details=True)
self.assertSetEqual(set(json.keys()), fields)
self.assertListEqual(json['familyGuids'], ["F000001_1"])
self.assertEqual(json['variantId'], '21-3343353-GAGA-G')
self.assertEqual(json['mainTranscriptId'], 'ENST00000258436')
def test_json_for_saved_variant(self):
variant = SavedVariant.objects.get(
guid='SV0000001_2103343353_r0390_100')
json = get_json_for_saved_variant(variant)
fields = {
'variantGuid', 'variantId', 'familyGuids', 'xpos', 'ref', 'alt',
'selectedMainTranscriptId'
}
self.assertSetEqual(set(json.keys()), fields)
self.assertListEqual(json['familyGuids'], ["F000001_1"])
self.assertEqual(json['variantId'], '21-3343353-GAGA-G')
fields.update(variant.saved_variant_json.keys())
fields.update({'tags', 'functionalData', 'notes'})
json = get_json_for_saved_variant(variant,
add_tags=True,
add_details=True)
self.assertSetEqual(set(json.keys()), fields)
self.assertListEqual(json['familyGuids'], ["F000001_1"])
self.assertEqual(json['variantId'], 'abc123')
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json.pop('familyGuid')
non_variant_json = {
k: variant_json.pop(k, None)
for k in [
'searchHash', 'tags', 'functionalData', 'notes', 'note',
'submitToClinvar'
]
}
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
if 'xpos' not in variant_json:
variant_json['xpos'] = get_xpos(variant_json['chrom'],
variant_json['pos'])
xpos = variant_json['xpos']
ref = variant_json['ref']
alt = variant_json['alt']
var_length = variant_json['pos_end'] - variant_json[
'pos'] if 'pos_end' in variant_json else len(ref) - 1
saved_variant = SavedVariant.objects.create(
xpos=xpos,
xpos_start=xpos,
xpos_end=xpos + var_length,
ref=ref,
alt=alt,
family=family,
saved_variant_json=variant_json)
if non_variant_json.get('note'):
_create_variant_note(saved_variant, non_variant_json, request.user)
elif non_variant_json.get('tags'):
_create_new_tags(saved_variant, non_variant_json, request.user)
variant_json.update(
get_json_for_saved_variant(saved_variant, add_tags=True))
return create_json_response({
'savedVariantsByGuid': {
saved_variant.guid: variant_json
},
})
def create_saved_variant_handler(request):
variant_json = json.loads(request.body)
family_guid = variant_json.pop('familyGuid')
non_variant_json = {
k: variant_json.pop(k, None)
for k in [
'searchHash', 'tags', 'functionalData', 'notes', 'note',
'submitToClinvar'
]
}
family = Family.objects.get(guid=family_guid)
check_permissions(family.project, request.user, CAN_VIEW)
xpos = variant_json['xpos']
ref = variant_json['ref']
alt = variant_json['alt']
# TODO remove project field from saved variants
saved_variant = SavedVariant.objects.create(
xpos=xpos,
xpos_start=xpos,
xpos_end=xpos + len(ref) - 1,
ref=ref,
alt=alt,
family=family,
project=family.project,
saved_variant_json=json.dumps(variant_json))
if non_variant_json.get('note'):
_create_variant_note(saved_variant, non_variant_json, request.user)
elif non_variant_json.get('tags'):
_create_new_tags(saved_variant, non_variant_json, request.user)
variant_json.update(
get_json_for_saved_variant(saved_variant,
add_tags=True,
project_guid=family.project.guid))
return create_json_response({
'savedVariantsByGuid': {
saved_variant.guid: variant_json
},
})
def _get_json_for_variant_tag_types(project):
project_variant_tags = []
discovery_tags = []
tag_counts_by_type_and_family = VariantTag.objects.filter(
saved_variant__project=project).values(
'saved_variant__family__guid',
'variant_tag_type__name').annotate(count=Count('*'))
for variant_tag_type in VariantTagType.objects.filter(
Q(project=project) | Q(project__isnull=True)):
current_tag_type_counts = [
counts for counts in tag_counts_by_type_and_family
if counts['variant_tag_type__name'] == variant_tag_type.name
]
num_tags = sum(count['count'] for count in current_tag_type_counts)
if variant_tag_type.category == 'CMG Discovery Tags' and num_tags > 0:
for tag in VariantTag.objects.filter(
saved_variant__project=project,
variant_tag_type=variant_tag_type).select_related(
'saved_variant'):
tag_data = get_json_for_saved_variant(tag.saved_variant)
tag_data.update(
json.loads(tag.saved_variant.saved_variant_json or '{}'))
discovery_tags.append(tag_data)
project_variant_tags.append({
'variantTagTypeGuid': variant_tag_type.guid,
'name': variant_tag_type.name,
'category': variant_tag_type.category,
'description': variant_tag_type.description,
'color': variant_tag_type.color,
'order': variant_tag_type.order,
'is_built_in': variant_tag_type.is_built_in,
'numTags': num_tags,
'numTagsPerFamily': {
count['saved_variant__family__guid']: count['count']
for count in current_tag_type_counts
},
})
project_functional_tags = []
for category, tags in VariantFunctionalData.FUNCTIONAL_DATA_CHOICES:
project_functional_tags += [{
'category':
category,
'name':
name,
'metadataTitle':
json.loads(tag_json).get('metadata_title'),
'color':
json.loads(tag_json)['color'],
'description':
json.loads(tag_json).get('description'),
} for name, tag_json in tags]
return {
'variantTagTypes':
sorted(project_variant_tags,
key=lambda variant_tag_type: variant_tag_type['order']),
'variantFunctionalTagTypes':
project_functional_tags,
'discoveryTags':
discovery_tags,
}
