"""Genotype browser routes for browsing and listing variants in studies."""
import itertools
import logging
from typing import Union
from datasets_api.permissions import (
handle_partial_permissions,
user_has_permission,
)
from django.http.response import FileResponse, StreamingHttpResponse
from query_base.query_base import QueryDatasetView
from rest_framework import status
from rest_framework.request import Request
from rest_framework.response import Response
from studies.study_wrapper import StudyWrapperBase
from utils.expand_gene_set import expand_gene_set, expand_gene_syms
from utils.logger import request_logging
from utils.query_params import parse_query_params
from utils.streaming_response_util import iterator_to_json
from dae.utils.dae_utils import join_line
logger = logging.getLogger(__name__)
[docs]class GenotypeBrowserQueryView(QueryDatasetView):
"""Genotype browser queries view."""
MAX_SHOWN_VARIANTS = 1000
[docs] @request_logging(logger)
def post(self, request: Request) -> Response:
"""
Query for variants from a dataset.
Request:
POST /genotype_browser/preview/variants HTTP/1.1
Host: example.com
Content-Type: application/json
Accept: text/event-stream
{
"datasetId": "iossifov_2014",
"maxVariantsCount": 1000
}
Response:
HTTP/1.1 200 OK
Vary: Accept
Content-Type: text/event-stream
[
[col1,col2,col3,col4.....]
,
[col1,col2,col3,col4.....]
,
......
,
[col1,col2,col3,col4.....]
]
Status codes:
200: Successfully fetched variants
403: User has no permissions for dataset
400: Invalid request body
404: Dataset does not exist
Request JSON parameters:
datasetId (string): ID of the dataset to query.
download (boolean): Change response type for easier download.
genomicScores (json): Genomic score range filter.
maxVariantsCount (integer): Maximum amount of variants to query.
sources (list): List of name-source objects: columns to fetch.
summaryVariantIds (list): List of summary variant IDs for filter.
querySummary (boolean): True if should query only summary variants.
uniqueFamilyVariants (boolean): Query for unique variants only.
regions (list): List of regions as strings to filter with.
presentInChild (json): Roles object to filter with.
presentInParent (json): Roles object to filter with.
inheritanceTypeFilter (list): Inheritance filtering.
geneScores (list): Gene score range filter.
gender (list): Gender filter.
variantTypes (list): Filter by variant type.
effectTypes (list): Filter by effect type.
studyFilters (list): Filter by study ID (dataset only).
personFilters (list): Filter with person filters.
familyFilters (list): Filter with family filters.
personIds (list): Filter by person IDs.
familyTypes (list): Filter by family type.
familyIds (list): Filter by family IDs.
affectedStatus (list): Filter by affected status.
tagIntersection (boolean): Change Family tags interesection mode
selectedFamilyTags (list): Family tags to include
deselectedFamilyTags (list): Family tags to exlude
"""
# pylint: disable=too-many-branches
logger.info("query v3 variants request: %s", str(request.data))
data = request.data
user = request.user
if "queryData" in data:
data = parse_query_params(data)
dataset_id = data.get("datasetId", None)
if dataset_id is None:
return Response(status=status.HTTP_400_BAD_REQUEST)
if not user_has_permission(self.instance_id, request.user, dataset_id):
return Response(status=status.HTTP_403_FORBIDDEN)
if "genomicScores" in data:
scores = data["genomicScores"]
for score in scores:
if score["rangeStart"] is None and score["rangeEnd"] is None:
return Response(status=status.HTTP_400_BAD_REQUEST)
is_download = data.pop("download", False)
if "maxVariantsCount" in data:
max_variants = data["maxVariantsCount"]
else:
if is_download:
max_variants = 10000
if not user.is_anonymous and \
(user.is_staff or user.has_unlimited_download):
max_variants = None
else:
max_variants = self.MAX_SHOWN_VARIANTS + 1
if max_variants == -1:
# unlimited variants preview
max_variants = None
dataset = self.gpf_instance.get_wdae_wrapper(dataset_id)
if dataset is None:
return Response(status=status.HTTP_404_NOT_FOUND)
if not dataset.is_remote:
data = expand_gene_set(data, user)
elif "geneSet" in data:
gene_set = expand_gene_syms(data, user)
data["geneSymbols"] = list(gene_set["syms"])
del data["geneSet"]
if "sources" in data:
sources = data.pop("sources")
else:
# TODO Handle summary variant preview and download sources
if is_download:
cols = dataset.config.genotype_browser.download_columns
else:
cols = dataset.config.genotype_browser.preview_columns
sources = StudyWrapperBase.get_columns_as_sources(
dataset.config, cols,
)
handle_partial_permissions(self.instance_id, user, dataset_id, data)
response: Union[FileResponse, StreamingHttpResponse, None] = None
if is_download:
result = dataset.query_variants_wdae(
data, sources,
max_variants_count=max_variants,
max_variants_message=is_download,
)
columns = [s.get("name", s["source"]) for s in sources]
result = map(
join_line, itertools.chain([columns], result)) # type: ignore
response = FileResponse(
result, filename="variants.tsv",
as_attachment=True, content_type="text/tsv",
)
response["Content-Disposition"] = \
"attachment; filename=variants.tsv"
response["Expires"] = "0"
else:
stream = dataset.query_variants_wdae_streaming(
data, sources,
max_variants_count=max_variants,
max_variants_message=is_download,
)
response = StreamingHttpResponse(
iterator_to_json(stream),
status=status.HTTP_200_OK,
content_type="text/event-stream",
)
response["Cache-Control"] = "no-cache"
return response