mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 12:47:56 +08:00
b90447c387
* first flatbuffer schema * do not lint auto-generated files * add flatbuffers package * add flatbuffer module * wire up /data/X/T route * use flatbuffers for matrix data fetc * clarity and comments * add flatbuffer layout route * clean up obsolete code * fix tests * move flake8 config to setup.cfg * add comments * lint * rework layout routes for fbs * add more type support to fbs * lint * add flatbuffer support for annotations * function name improvements * fix botched merge with master * remove unused import * route cleanup for flatbuffers * rename function for clarity * add missing globals to Jest tests * fix client JS tests * fix routes for Python tests * comments for clarity * non-finite floating point hardening * more non-finite number handling * lint * fix tests for summarizeAnnotations * harden diffexp calculation against FP errors * cleanup unused code * lint * add encoding tests for flatbuffers * application type specified as strings * fix spelling error * improve variable names * add note about documentation gap * rename FBS DataFrame to Matrix
895 lines
34 KiB
Python
895 lines
34 KiB
Python
from http import HTTPStatus
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import pkg_resources
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import warnings
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from flask import Blueprint, current_app, jsonify, make_response, request
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from flask_restful_swagger_2 import Api, swagger, Resource
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from werkzeug.datastructures import ImmutableMultiDict
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from server.app.util.constants import (
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Axis,
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DiffExpMode,
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JSON_NaN_to_num_warning_msg,
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)
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from server.app.util.filter import parse_filter, QueryStringError
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from server.app.util.models import FilterModel
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from server.app.util.utils import get_mime_type
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from server.app.util.errors import (
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FilterError,
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InteractiveError,
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JSONEncodingValueError,
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MimeTypeError,
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PrepareError,
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)
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"""
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Sort order for routes
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1. Initialize
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2. Data & Metadata
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3. Computation
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"""
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class SchemaAPI(Resource):
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@swagger.doc(
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{
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"summary": "get schema for dataframe and annotations",
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"tags": ["initialize"],
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"parameters": [],
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"responses": {
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"200": {
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"description": "schema",
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"examples": {
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"application/json": {
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"schema": {
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"dataframe": {
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"nObs": 383,
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"nVar": 19944,
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"type": "float32",
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},
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"annotations": {
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"obs": [
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{"name": "name", "type": "string"},
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{"name": "tissue_type", "type": "string"},
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{"name": "num_reads", "type": "int32"},
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{"name": "sample_name", "type": "string"},
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{
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"name": "clusters",
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"type": "categorical",
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"categories": [99, 1, "unknown cluster"],
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},
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{"name": "QScore", "type": "float32"},
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],
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"var": [
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{"name": "name", "type": "string"},
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{"name": "gene", "type": "string"},
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],
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},
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}
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}
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},
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}
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},
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}
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)
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def get(self):
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return make_response(
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jsonify({"schema": current_app.data.schema}), HTTPStatus.OK
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)
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class ConfigAPI(Resource):
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@swagger.doc(
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{
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"summary": "Configuration information to assist in front-end adaptation"
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" to underlying engine, available functionality, interactive time limits, etc",
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"tags": ["initialize"],
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"parameters": [],
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"responses": {
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"200": {
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"description": "schema",
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"examples": {
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"application/json": {
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"config": {
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"features": [
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{
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"method": "POST",
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"path": "/cluster/",
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"available": False,
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},
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{
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"method": "POST",
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"path": "/layout/obs",
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"available": True,
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"interactiveLimit": 10000,
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},
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{
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"method": "POST",
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"path": "/layout/var",
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"available": False,
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},
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],
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"displayNames": {
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"engine": "ScanPy version 1.33",
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"dataset": "/home/joe/mouse/blorth.csv",
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},
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}
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}
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},
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}
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},
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}
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)
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def get(self):
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config = {
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"config": {
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"features": [
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{
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"method": "POST",
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"path": "/cluster/",
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**current_app.data.features["cluster"],
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},
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{
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"method": "POST",
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"path": "/layout/obs",
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**current_app.data.features["layout"]["obs"],
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},
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{
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"method": "POST",
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"path": "/layout/var",
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**current_app.data.features["layout"]["var"],
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},
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{
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"method": "POST",
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"path": "/diffexp/",
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**current_app.data.features["diffexp"],
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},
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],
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"displayNames": {
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"engine": f"cellxgene Scanpy engine version {pkg_resources.get_distribution('cellxgene').version}",
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"dataset": current_app.config["DATASET_TITLE"],
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},
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"parameters": {
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"max_category_items": current_app.data.max_category_items
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},
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}
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}
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return make_response(jsonify(config), HTTPStatus.OK)
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class AnnotationsObsAPI(Resource):
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@swagger.doc(
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{
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"summary": "Fetch annotations (metadata) for all observations.",
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"tags": ["annotations"],
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"parameters": [
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{
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"in": "query",
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"name": "annotation-name",
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"type": "string",
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"description": "list of 1 or more annotation names",
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}
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],
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"responses": {
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"200": {
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"description": "annotations",
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"examples": {
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"application/json": {
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"names": ["tissue_type", "sex", "num_reads", "clusters"],
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"data": [
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[0, "lung", "F", 39844, 99],
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[1, "heart", "M", 83, 1],
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[49, "spleen", None, 2, "unknown cluster"],
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],
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}
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},
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},
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"400": {
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"description": "one or more of the annotation-name identifiers were not associated with an "
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"annotation name"
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},
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},
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}
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)
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def get(self):
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fields = request.args.getlist("annotation-name", None)
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preferred_mimetype = request.accept_mimetypes.best_match(
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["application/json", "application/octet-stream"],
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"application/json"
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)
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try:
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if preferred_mimetype == "application/json":
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return make_response(
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current_app.data.annotation({}, "obs", fields), HTTPStatus.OK, {"Content-Type": "application/json"}
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)
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elif preferred_mimetype == "application/octet-stream":
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return make_response(current_app.data.annotation_to_fbs_matrix("obs", fields),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"})
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else:
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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except KeyError:
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return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
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except JSONEncodingValueError as e:
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# JSON encoding failure, usually due to bad data
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warnings.warn(JSON_NaN_to_num_warning_msg)
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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except ValueError as e:
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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@swagger.doc(
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{
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"summary": "Fetch annotations (metadata) for filtered subset of observations.",
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"tags": ["annotations"],
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"parameters": [
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{
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"in": "query",
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"name": "annotation-name",
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"type": "string",
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"description": "list of 1 or more annotation names",
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},
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{
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"name": "filter",
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"description": "Complex Filter",
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"in": "body",
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"schema": FilterModel,
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},
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],
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"responses": {
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"200": {
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"description": "annotations",
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"examples": {
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"application/json": {
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"names": ["tissue_type", "sex", "num_reads", "clusters"],
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"data": [
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[0, "lung", "F", 39844, 99],
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[1, "heart", "M", 83, 1],
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[49, "spleen", None, 2, "unknown cluster"],
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],
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}
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},
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},
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"400": {
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"description": "malformed filter or one or more of the annotation-name identifiers were"
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"not associated with an annotation name"
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},
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},
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}
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)
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def put(self):
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fields = request.args.getlist("annotation-name", None)
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try:
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annotation_response = current_app.data.annotation(
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request.get_json()["filter"], "obs", fields
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)
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return make_response(
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annotation_response, HTTPStatus.OK, {"Content-Type": "application/json"}
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)
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except KeyError:
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return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
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except FilterError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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except JSONEncodingValueError as e:
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# JSON encoding failure, usually due to bad data
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warnings.warn(JSON_NaN_to_num_warning_msg)
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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except ValueError as e:
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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class AnnotationsVarAPI(Resource):
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@swagger.doc(
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{
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"summary": "Fetch annotations (metadata) for all variables.",
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"tags": ["annotations"],
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"parameters": [
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{
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"in": "query",
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"name": "annotation-name",
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"type": "string",
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"description": "list of 1 or more annotation names",
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}
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],
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"responses": {
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"200": {
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"description": "annotations",
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"examples": {
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"application/json": {
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"names": ["name", "category"],
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"data": [
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[0, "ATAD3C", 1],
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[1, "RER1", None],
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[49, "S100B", 6],
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],
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}
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},
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},
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"400": {
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"description": "one or more of the annotation-name identifiers were not associated with an"
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" annotation name"
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},
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},
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}
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)
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def get(self):
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fields = request.args.getlist("annotation-name", None)
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preferred_mimetype = request.accept_mimetypes.best_match(
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["application/json", "application/octet-stream"],
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"application/json"
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)
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try:
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if preferred_mimetype == "application/json":
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return make_response(current_app.data.annotation({}, "var", fields),
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HTTPStatus.OK,
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{"Content-Type": "application/json"})
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elif preferred_mimetype == "application/octet-stream":
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return make_response(current_app.data.annotation_to_fbs_matrix("var", fields),
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HTTPStatus.OK,
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{"Content-Type": "application/octet-stream"})
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else:
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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except KeyError:
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return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
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except JSONEncodingValueError as e:
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# JSON encoding failure, usually due to bad data
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warnings.warn(JSON_NaN_to_num_warning_msg)
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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except ValueError as e:
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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|
@swagger.doc(
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{
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"summary": "Fetch annotations (metadata) for filtered subset of variables.",
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"tags": ["annotations"],
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"parameters": [
|
|
{
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|
"in": "query",
|
|
"name": "annotation-name",
|
|
"type": "string",
|
|
"description": "list of 1 or more annotation names",
|
|
},
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|
{
|
|
"name": "filter",
|
|
"description": "Complex Filter",
|
|
"in": "body",
|
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"schema": FilterModel,
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|
},
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|
],
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|
"responses": {
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"200": {
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|
"description": "annotations",
|
|
"examples": {
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|
"application/json": {
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"names": ["name", "category"],
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"data": [
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[0, "ATAD3C", 1],
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[1, "RER1", None],
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[49, "S100B", 6],
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],
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}
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},
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},
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"400": {
|
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"description": "malformed filter or one or more of the annotation-name identifiers were"
|
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"not associated with an annotation name"
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},
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},
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}
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)
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def put(self):
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fields = request.args.getlist("annotation-name", None)
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try:
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annotation_response = current_app.data.annotation(
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request.get_json()["filter"], "var", fields
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)
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return make_response(
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annotation_response, HTTPStatus.OK, {"Content-Type": "application/json"}
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)
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except KeyError:
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return make_response(f"Error bad key in {fields}", HTTPStatus.BAD_REQUEST)
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except FilterError:
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return make_response("Malformed filter", HTTPStatus.BAD_REQUEST)
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except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
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warnings.warn(JSON_NaN_to_num_warning_msg)
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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except ValueError as e:
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return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
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|
|
|
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class DataObsAPI(Resource):
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|
@swagger.doc(
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{
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"summary": "Get data (expression values) from the dataframe.",
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"tags": ["data"],
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|
"parameters": [
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|
{
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"in": "query",
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"name": "filter",
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"type": "string",
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"description": "axis:key:value",
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},
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{
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"in": "query",
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"name": "accept-type",
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"type": "string",
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"description": "MIME type",
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},
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],
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"responses": {
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"200": {
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"description": "expression",
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|
"examples": {
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|
"application/json": {
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"var": [0, 20000],
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"obs": [[1, 39483, 3902, 203, 0, 0, 28]],
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}
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},
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|
},
|
|
"400": {"description": "Malformed filter"},
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|
"406": {"description": "Unacceptable MIME type"},
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|
},
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}
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)
|
|
def get(self):
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accept_type = request.args.get("accept-type", None)
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# request.args is immutable
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args = request.args.copy()
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args.pop("accept-type", None)
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try:
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|
filter_ = parse_filter(
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ImmutableMultiDict(args), current_app.data.schema["annotations"]
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)
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except QueryStringError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
# TODO support CSV
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|
try:
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|
# TODO store mime_type when more than one is supported
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get_mime_type(
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acceptable_types=["application/json"],
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query_param=accept_type,
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header=request.accept_mimetypes,
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)
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except MimeTypeError as e:
|
|
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
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|
try:
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|
return make_response(
|
|
current_app.data.data_frame(filter_, axis=Axis.OBS),
|
|
HTTPStatus.OK,
|
|
{"Content-Type": "application/json"},
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|
)
|
|
except FilterError as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
|
|
warnings.warn(JSON_NaN_to_num_warning_msg)
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except ValueError as e:
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
|
|
@swagger.doc(
|
|
{
|
|
"summary": "Get data (expression values) from the dataframe.",
|
|
"tags": ["data"],
|
|
"parameters": [
|
|
{
|
|
"name": "filter",
|
|
"description": "Complex Filter",
|
|
"in": "body",
|
|
"schema": FilterModel,
|
|
}
|
|
],
|
|
"responses": {
|
|
"200": {
|
|
"description": "expression",
|
|
"examples": {
|
|
"application/json": {
|
|
"var": [0, 20000],
|
|
"obs": [[1, 39483, 3902, 203, 0, 0, 28]],
|
|
}
|
|
},
|
|
},
|
|
"400": {"description": "Malformed filter"},
|
|
"406": {"description": "Unacceptable MIME type"},
|
|
},
|
|
}
|
|
)
|
|
def put(self):
|
|
if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
|
|
return make_response(
|
|
f"Unsupported MIME type '{request.accept_mimetypes}'",
|
|
HTTPStatus.NOT_ACCEPTABLE,
|
|
)
|
|
try:
|
|
get_mime_type(
|
|
acceptable_types=["application/json"], header=request.accept_mimetypes
|
|
)
|
|
except MimeTypeError as e:
|
|
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
|
|
try:
|
|
return make_response(
|
|
(
|
|
current_app.data.data_frame(
|
|
request.get_json()["filter"], axis=Axis.OBS
|
|
)
|
|
),
|
|
HTTPStatus.OK,
|
|
{"Content-Type": "application/json"},
|
|
)
|
|
except FilterError as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
|
|
warnings.warn(JSON_NaN_to_num_warning_msg)
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except ValueError as e:
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
|
|
|
|
class DataVarAPI(Resource):
|
|
@swagger.doc(
|
|
{
|
|
"summary": "Get data (expression values) from the dataframe.",
|
|
"tags": ["data"],
|
|
"parameters": [
|
|
{
|
|
"in": "query",
|
|
"name": "filter",
|
|
"type": "string",
|
|
"description": "axis:key:value",
|
|
},
|
|
{
|
|
"in": "query",
|
|
"name": "accept-type",
|
|
"type": "string",
|
|
"description": "MIME type",
|
|
},
|
|
],
|
|
"responses": {
|
|
"200": {
|
|
"description": "expression",
|
|
"examples": {
|
|
"application/json": {
|
|
"obs": [0, 20000],
|
|
"var": [[1, 39483, 3902, 203, 0, 0, 28]],
|
|
}
|
|
},
|
|
},
|
|
"400": {"description": "Malformed filter"},
|
|
"406": {"description": "Unacceptable MIME type"},
|
|
},
|
|
}
|
|
)
|
|
def get(self):
|
|
accept_type = request.args.get("accept-type", None)
|
|
# request.args is immutable
|
|
args = request.args.copy()
|
|
args.pop("accept-type", None)
|
|
try:
|
|
filter_ = parse_filter(
|
|
ImmutableMultiDict(args), current_app.data.schema["annotations"]
|
|
)
|
|
except QueryStringError as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
try:
|
|
get_mime_type(
|
|
acceptable_types=["application/json"],
|
|
query_param=accept_type,
|
|
header=request.accept_mimetypes,
|
|
)
|
|
except MimeTypeError as e:
|
|
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
|
|
try:
|
|
return make_response(
|
|
current_app.data.data_frame(filter_, axis=Axis.VAR),
|
|
HTTPStatus.OK,
|
|
{"Content-Type": "application/json"},
|
|
)
|
|
except FilterError as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
|
|
warnings.warn(JSON_NaN_to_num_warning_msg)
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except ValueError as e:
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
|
|
@swagger.doc(
|
|
{
|
|
"summary": "Get data (expression values) from the dataframe.",
|
|
"tags": ["data"],
|
|
"parameters": [
|
|
{
|
|
"name": "filter",
|
|
"description": "Complex Filter",
|
|
"in": "body",
|
|
"schema": FilterModel,
|
|
}
|
|
],
|
|
"responses": {
|
|
"200": {
|
|
"description": "expression",
|
|
"examples": {
|
|
"application/json": {
|
|
"obs": [0, 20000],
|
|
"var": [[1, 39483, 3902, 203, 0, 0, 28]],
|
|
}
|
|
},
|
|
},
|
|
"400": {"description": "Malformed filter"},
|
|
"406": {"description": "Unacceptable MIME type"},
|
|
},
|
|
}
|
|
)
|
|
def put(self):
|
|
preferred_mimetype = request.accept_mimetypes.best_match(
|
|
["application/json", "application/octet-stream"],
|
|
"application/json"
|
|
)
|
|
try:
|
|
if preferred_mimetype == "application/json":
|
|
return make_response(
|
|
(
|
|
current_app.data.data_frame(
|
|
request.get_json()["filter"], axis=Axis.VAR
|
|
)
|
|
),
|
|
HTTPStatus.OK,
|
|
{"Content-Type": "application/json"},
|
|
)
|
|
elif preferred_mimetype == "application/octet-stream":
|
|
return make_response(
|
|
current_app.data.data_frame_to_fbs_matrix(
|
|
request.get_json()["filter"], axis=Axis.VAR
|
|
),
|
|
HTTPStatus.OK,
|
|
{"Content-Type": "application/octet-stream"})
|
|
else:
|
|
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
|
|
except FilterError as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
|
|
warnings.warn(JSON_NaN_to_num_warning_msg)
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except ValueError as e:
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
|
|
|
|
class DiffExpObsAPI(Resource):
|
|
@swagger.doc(
|
|
{
|
|
"summary": "Generate differential expression (DE) statistics for two specified subsets of data, "
|
|
"as indicated by the two provided observation complex filters",
|
|
"tags": ["diffexp"],
|
|
# TODO sort out params
|
|
# "parameters": [
|
|
# # {
|
|
# # "in": "body",
|
|
# # "name": "mode",
|
|
# # "type": "string",
|
|
# # "required": True,
|
|
# # "description": "topN or varFilter"
|
|
# # },
|
|
# {
|
|
# "in": "query",
|
|
# "name": "count",
|
|
# "type": "int32",
|
|
# "description": "TopN mode: how many vars to return"
|
|
# },
|
|
# {
|
|
# "in": "body",
|
|
# "name": "varFilter",
|
|
# "schema": FilterModel,
|
|
# "description": "varFilter: Complex filter, only var for which vars to return"
|
|
# },
|
|
# {
|
|
# "in": "body",
|
|
# "name": "set1",
|
|
# "schema": FilterModel,
|
|
# "required": True,
|
|
# "description": "Complex filter, only obs - observations in set1"
|
|
# },
|
|
# {
|
|
# "in": "body",
|
|
# "name": "set2",
|
|
# "schema": FilterModel,
|
|
# "description": "Complex filter, only obs - observations in set2.
|
|
# If not included, inverse of set1."
|
|
# },
|
|
# ],
|
|
"responses": {
|
|
"200": {
|
|
"description": "Statistics are encoded as an array of arrays, with fields ordered as: "
|
|
"varIndex, logfoldchange, pVal, pValAdj",
|
|
"examples": {
|
|
"application/json": [
|
|
[328, -2.569_489, 2.655_706e-63, 3.642_036e-57],
|
|
[1250, -2.569_489, 2.655_706e-63, 3.642_036e-57],
|
|
]
|
|
},
|
|
},
|
|
"400": {"description": "malformed filter"},
|
|
"403": {"description": "non-interactive request"},
|
|
"501": {"description": "diffexp is not implemented"},
|
|
},
|
|
}
|
|
)
|
|
def post(self):
|
|
args = request.get_json()
|
|
# confirm mode is present and legal
|
|
try:
|
|
mode = DiffExpMode(args["mode"])
|
|
except KeyError:
|
|
return make_response("Error: mode is required", HTTPStatus.BAD_REQUEST)
|
|
except ValueError:
|
|
return make_response(
|
|
f"Error: invalid mode option {args['mode']}", HTTPStatus.BAD_REQUEST
|
|
)
|
|
# Validate filters
|
|
if mode == DiffExpMode.VAR_FILTER or "varFilter" in args:
|
|
# not NOT_IMPLEMENTED
|
|
return make_response(
|
|
"mode=varfilter not implemented", HTTPStatus.NOT_IMPLEMENTED
|
|
)
|
|
if mode == DiffExpMode.TOP_N and "count" not in args:
|
|
return make_response(
|
|
"mode=topN requires a count parameter", HTTPStatus.BAD_REQUEST
|
|
)
|
|
|
|
if "set1" not in args:
|
|
return make_response("set1 is required.", HTTPStatus.BAD_REQUEST)
|
|
if Axis.VAR in args["set1"]["filter"]:
|
|
return make_response(
|
|
"Var filter not allowed for set1", HTTPStatus.BAD_REQUEST
|
|
)
|
|
# set2
|
|
if "set2" not in args:
|
|
return make_response(
|
|
"Set2 as inverse of set1 is not implemented", HTTPStatus.NOT_IMPLEMENTED
|
|
)
|
|
if Axis.VAR in args["set2"]["filter"]:
|
|
return make_response(
|
|
"Var filter not allowed for set2", HTTPStatus.BAD_REQUEST
|
|
)
|
|
|
|
set1_filter = args["set1"]["filter"]
|
|
set2_filter = args.get("set2", {"filter": {}})["filter"]
|
|
|
|
# TODO: implement varfilter mode
|
|
|
|
# mode=topN
|
|
count = args.get("count", None)
|
|
try:
|
|
diffexp = current_app.data.diffexp_topN(
|
|
set1_filter,
|
|
set2_filter,
|
|
count,
|
|
current_app.data.features["diffexp"]["interactiveLimit"],
|
|
)
|
|
return make_response(
|
|
diffexp, HTTPStatus.OK, {"Content-Type": "application/json"}
|
|
)
|
|
except (ValueError, FilterError) as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
except InteractiveError:
|
|
return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
|
|
except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
|
|
warnings.warn(JSON_NaN_to_num_warning_msg)
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except ValueError as e:
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
|
|
|
|
class LayoutObsAPI(Resource):
|
|
@swagger.doc(
|
|
{
|
|
"summary": "Get the default layout for all observations.",
|
|
"tags": ["layout"],
|
|
"parameters": [],
|
|
"responses": {
|
|
"200": {
|
|
"description": "layout",
|
|
"examples": {
|
|
"application/json": {
|
|
"layout": {
|
|
"ndims": 2,
|
|
"coordinates": [
|
|
[0, 0.284_483, 0.983_744],
|
|
[1, 0.038_844, 0.739_444],
|
|
],
|
|
}
|
|
}
|
|
},
|
|
},
|
|
"400": {"description": "Data preparation error"},
|
|
},
|
|
}
|
|
)
|
|
def get(self):
|
|
preferred_mimetype = request.accept_mimetypes.best_match(
|
|
["application/json", "application/octet-stream"],
|
|
"application/json"
|
|
)
|
|
try:
|
|
if preferred_mimetype == "application/json":
|
|
return make_response(current_app.data.layout({}), HTTPStatus.OK, {"Content-Type": "application/json"})
|
|
|
|
elif preferred_mimetype == "application/octet-stream":
|
|
return make_response(current_app.data.layout_to_fbs_matrix(),
|
|
HTTPStatus.OK,
|
|
{"Content-Type": "application/octet-stream"})
|
|
else:
|
|
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
|
|
except PrepareError as e:
|
|
return make_response(e.message, HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except JSONEncodingValueError as e:
|
|
# JSON encoding failure, usually due to bad data
|
|
warnings.warn(JSON_NaN_to_num_warning_msg)
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
except ValueError as e:
|
|
return make_response(str(e), HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
|
|
# @swagger.doc({
|
|
# "summary": "Observation layout for filtered subset.",
|
|
# "tags": ["layout"],
|
|
# "parameters": [
|
|
# {
|
|
# "name": "filter",
|
|
# "description": "Complex Filter",
|
|
# "in": "body",
|
|
# "schema": FilterModel
|
|
# }
|
|
# ],
|
|
# "responses": {
|
|
# "200": {
|
|
# "description": "layout",
|
|
# "examples": {
|
|
# "application/json": {
|
|
# "layout": {
|
|
# "ndims": 2,
|
|
# "coordinates": [
|
|
# [0, 0.284483, 0.983744],
|
|
# [1, 0.038844, 0.739444]
|
|
# ]
|
|
# }
|
|
# }
|
|
# }
|
|
# },
|
|
# "400": {
|
|
# "description": "Malformed filter"
|
|
# },
|
|
# "403": {
|
|
# "description": "Non-interactive request"
|
|
# },
|
|
# }
|
|
# })
|
|
# def put(self):
|
|
# try:
|
|
# filter = request.get_json()["filter"]
|
|
# interactive_limit = current_app.data.features["layout"]["obs"]["interactiveLimit"]
|
|
# layout = current_app.data.layout(filter, interactive_limit=interactive_limit)
|
|
# return make_response(layout, HTTPStatus.OK, {"Content-Type": content_type})
|
|
# except FilterError as e:
|
|
# return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
# except InteractiveError:
|
|
# return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
|
|
|
|
|
|
def get_api_resources():
|
|
bp = Blueprint("api", __name__, url_prefix="/api/v0.2")
|
|
api = Api(bp, add_api_spec_resource=False)
|
|
# Initialization routes
|
|
api.add_resource(SchemaAPI, "/schema")
|
|
api.add_resource(ConfigAPI, "/config")
|
|
# Data routes
|
|
api.add_resource(AnnotationsObsAPI, "/annotations/obs")
|
|
api.add_resource(AnnotationsVarAPI, "/annotations/var")
|
|
api.add_resource(DataObsAPI, "/data/obs")
|
|
api.add_resource(DataVarAPI, "/data/var")
|
|
# Computation routes
|
|
api.add_resource(DiffExpObsAPI, "/diffexp/obs")
|
|
api.add_resource(LayoutObsAPI, "/layout/obs")
|
|
return api
|