def update_locus_list_handler(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
check_user_created_object_permissions(locus_list,
request.user,
permission_level=CAN_EDIT)
request_json = json.loads(request.body)
genes_by_id, intervals, invalid_items = parse_locus_list_items(
request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items},
status=400,
reason=INVALID_ITEMS_ERROR)
update_model_from_json(locus_list, request_json, allow_unknown_keys=True)
if genes_by_id is not None:
_update_locus_list_items(locus_list, genes_by_id, intervals,
request_json)
return create_json_response({
'locusListsByGuid': {
locus_list.guid: get_json_for_locus_list(locus_list, request.user)
},
'genesById': genes_by_id or {},
})
def create_locus_list_handler(request):
request_json = json.loads(request.body)
if not request_json.get('name'):
return create_json_response({},
status=400,
reason='"Name" is required')
genes_by_id, intervals, invalid_items = parse_locus_list_items(
request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items},
status=400,
reason=INVALID_ITEMS_ERROR)
locus_list = LocusList.objects.create(
name=request_json['name'],
description=request_json.get('description') or '',
is_public=request_json.get('isPublic') or False,
created_by=request.user,
)
_update_locus_list_items(locus_list, genes_by_id, intervals, request_json)
return create_json_response({
'locusListsByGuid': {
locus_list.guid: get_json_for_locus_list(locus_list, request.user)
},
'genesById': genes_by_id,
})
def create_locus_list_handler(request):
request_json = json.loads(request.body)
if not request_json.get('name'):
return create_json_response({},
status=400,
reason='"Name" is required')
genes_by_id, intervals, invalid_items = parse_locus_list_items(
request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items},
status=400,
reason=INVALID_ITEMS_ERROR)
try:
locus_list = create_model_from_json(
LocusList, {
'name': request_json['name'],
'description': request_json.get('description') or '',
'is_public': request_json.get('isPublic') or False,
}, request.user)
except IntegrityError:
return create_json_response({'error': 'This list already exists'},
status=400)
_update_locus_list_items(locus_list, genes_by_id, intervals, request_json,
request.user)
return create_json_response({
'locusListsByGuid': {
locus_list.guid: get_json_for_locus_list(locus_list, request.user)
},
'genesById': genes_by_id,
})
def create_locus_list_handler(request):
request_json = json.loads(request.body)
if not request_json.get('name'):
return create_json_response({}, status=400, reason='"Name" is required')
new_genes, existing_gene_ids, new_intervals, existing_interval_guids, invalid_items = _parse_list_items(request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items}, status=400, reason=INVALID_ITEMS_ERROR)
locus_list = create_seqr_model(
LocusList,
name=request_json['name'],
description=request_json.get('description') or '',
is_public=request_json.get('isPublic') or False,
created_by=request.user,
)
_update_locus_list_items(locus_list, new_genes, existing_gene_ids, new_intervals, existing_interval_guids,
request_json, request.user)
add_locus_list_user_permissions(locus_list)
return create_json_response({
'locusListsByGuid': {locus_list.guid: get_json_for_locus_list(locus_list, request.user)},
'genesById': new_genes,
})
def test_json_for_locus_list(self):
locus_list = LocusList.objects.first()
user = User.objects.filter().first()
json = get_json_for_locus_list(locus_list, user)
fields = {
'locusListGuid', 'description', 'lastModifiedDate', 'numEntries', 'isPublic', 'createdBy', 'createdDate',
'canEdit', 'name', 'items', 'intervalGenomeVersion'
}
self.assertSetEqual(set(json.keys()), fields)
def test_json_for_locus_list(self):
locus_list = LocusList.objects.first()
user = User.objects.filter().first()
json = get_json_for_locus_list(locus_list, user)
fields = {
'locusListGuid', 'description', 'lastModifiedDate', 'numEntries', 'isPublic', 'createdBy', 'createdDate',
'canEdit', 'name', 'items', 'intervalGenomeVersion'
}
self.assertSetEqual(set(json.keys()), fields)
def locus_list_info(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
check_public_object_permissions(locus_list, request.user)
locus_list_json = get_json_for_locus_list(locus_list, request.user)
gene_ids = [item['geneId'] for item in locus_list_json['items'] if item.get('geneId')]
return create_json_response({
'locusListsByGuid': {locus_list_guid: locus_list_json},
'genesById': get_genes(gene_ids, add_dbnsfp=True, add_omim=True, add_constraints=True)
})
def locus_list_info(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
check_public_object_permissions(locus_list, request.user)
locus_list_json = get_json_for_locus_list(locus_list, request.user)
gene_ids = [item['geneId'] for item in locus_list_json['items'] if item.get('geneId')]
return create_json_response({
'locusListsByGuid': {locus_list_guid: locus_list_json},
'genesById': get_genes(gene_ids, add_dbnsfp=True, add_omim=True, add_constraints=True)
})
def locus_list_info(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
if not locus_list.is_public:
check_multi_project_permissions(locus_list, request.user)
locus_list_json = get_json_for_locus_list(locus_list, request.user)
gene_ids = [
item['geneId'] for item in locus_list_json['items']
if item.get('geneId')
]
return create_json_response({
'locusListsByGuid': {
locus_list_guid: locus_list_json
},
'genesById': get_genes(gene_ids)
})
def update_locus_list_handler(request, locus_list_guid):
locus_list = LocusList.objects.get(guid=locus_list_guid)
check_object_permissions(locus_list, request.user, permission_level=CAN_EDIT)
request_json = json.loads(request.body)
genes_by_id, intervals, invalid_items = parse_locus_list_items(request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items}, status=400, reason=INVALID_ITEMS_ERROR)
update_model_from_json(locus_list, request_json, allow_unknown_keys=True)
if genes_by_id is not None:
_update_locus_list_items(locus_list, genes_by_id, intervals, request_json, request.user)
return create_json_response({
'locusListsByGuid': {locus_list.guid: get_json_for_locus_list(locus_list, request.user)},
'genesById': genes_by_id or {},
})
def create_locus_list_handler(request):
request_json = json.loads(request.body)
if not request_json.get('name'):
return create_json_response({}, status=400, reason='"Name" is required')
genes_by_id, intervals, invalid_items = parse_locus_list_items(request_json)
if invalid_items and not request_json.get('ignoreInvalidItems'):
return create_json_response({'invalidLocusListItems': invalid_items}, status=400, reason=INVALID_ITEMS_ERROR)
locus_list = create_seqr_model(
LocusList,
name=request_json['name'],
description=request_json.get('description') or '',
is_public=request_json.get('isPublic') or False,
created_by=request.user,
)
_update_locus_list_items(locus_list, genes_by_id, intervals, request_json, request.user)
add_locus_list_user_permissions(locus_list)
return create_json_response({
'locusListsByGuid': {locus_list.guid: get_json_for_locus_list(locus_list, request.user)},
'genesById': genes_by_id,
})
def test_json_for_locus_list(self):
locus_list = LocusList.objects.first()
user = User.objects.filter().first()
json = get_json_for_locus_list(locus_list, user)
self.assertSetEqual(set(json.keys()), LOCUS_LIST_DETAIL_FIELDS)
