mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 20:57:56 +08:00
00a68276a2
* new diffexp REST API spec * new diffexp REST API; faster diffexp and dataframe slicing * first draft of fast diffexp * convert variance calculation to two-pass method * lint * update front-end use of API * fix typo in spec * disable content compression * catch index filter format errors * clean up of dead code * resolve PR review comments
713 lines
26 KiB
Python
713 lines
26 KiB
Python
from http import HTTPStatus
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import pkg_resources
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from flask import (
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Blueprint, current_app, jsonify, make_response, request
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)
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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 Axis, DiffExpMode
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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 MimeTypeError, FilterError, InteractiveError, PrepareError
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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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"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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def get(self):
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return make_response(jsonify({"schema": current_app.data.schema}), HTTPStatus.OK)
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class ConfigAPI(Resource):
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@swagger.doc({
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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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{"method": "POST", "path": "/cluster/", "available": False},
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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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{"method": "POST", "path": "/layout/var", "available": False}
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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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def get(self):
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config = {
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"config": {
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"features": [
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{"method": "POST", "path": "/cluster/", **current_app.data.features["cluster"]},
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{"method": "POST", "path": "/layout/obs", **current_app.data.features["layout"]["obs"]},
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{"method": "POST", "path": "/layout/var", **current_app.data.features["layout"]["var"]},
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{"method": "POST", "path": "/diffexp/", **current_app.data.features["diffexp"]},
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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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"summary": "Fetch annotations (metadata) for all observations.",
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"tags": ["annotations"],
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"parameters": [{
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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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"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": [
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"tissue_type", "sex", "num_reads", "clusters"
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],
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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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def get(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({}, "obs", fields)
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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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return make_response(jsonify(annotation_response), HTTPStatus.OK)
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@swagger.doc({
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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": [
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"tissue_type", "sex", "num_reads", "clusters"
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],
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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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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(request.get_json()["filter"], "obs", fields)
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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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return make_response(jsonify(annotation_response), HTTPStatus.OK)
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class AnnotationsVarAPI(Resource):
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@swagger.doc({
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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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"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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"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": [
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"name", "category"
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],
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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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def get(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({}, "var", fields)
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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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return make_response(jsonify(annotation_response), HTTPStatus.OK)
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@swagger.doc({
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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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{
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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": [
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"name", "category"
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],
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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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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(request.get_json()["filter"], "var", fields)
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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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return make_response(jsonify(annotation_response), HTTPStatus.OK)
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class DataObsAPI(Resource):
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@swagger.doc({
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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": [
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[1, 39483, 3902, 203, 0, 0, 28]
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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"
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},
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"406": {
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"description": "Unacceptable MIME type"
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},
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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 = dict(request.args)
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args.pop("accept-type", None)
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try:
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filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])
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except QueryStringError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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# 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(acceptable_types=["application/json"], query_param=accept_type,
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header=request.accept_mimetypes)
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except MimeTypeError as e:
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return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
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try:
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return make_response((jsonify(current_app.data.data_frame(filter_, axis=Axis.OBS))), HTTPStatus.OK)
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except FilterError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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@swagger.doc({
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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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'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": "expression",
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"examples": {
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"application/json": {
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"var": [0, 20000],
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"obs": [
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[1, 39483, 3902, 203, 0, 0, 28]
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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"
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},
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"406": {
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"description": "Unacceptable MIME type"
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},
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}
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})
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def put(self):
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if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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try:
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get_mime_type(acceptable_types=["application/json"], header=request.accept_mimetypes)
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except MimeTypeError as e:
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return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
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try:
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return make_response((jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.OBS))),
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HTTPStatus.OK)
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except FilterError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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class DataVarAPI(Resource):
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@swagger.doc({
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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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"obs": [0, 20000],
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"var": [
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[1, 39483, 3902, 203, 0, 0, 28]
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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"
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},
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"406": {
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"description": "Unacceptable MIME type"
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},
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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 = dict(request.args)
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args.pop("accept-type", None)
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try:
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filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema['annotations'])
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except QueryStringError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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try:
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get_mime_type(acceptable_types=["application/json"], query_param=accept_type,
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header=request.accept_mimetypes)
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except MimeTypeError as e:
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return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
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try:
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return make_response((jsonify(current_app.data.data_frame(filter_, axis=Axis.VAR))), HTTPStatus.OK)
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except FilterError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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@swagger.doc({
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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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'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": "expression",
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"examples": {
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"application/json": {
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"obs": [0, 20000],
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"var": [
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[1, 39483, 3902, 203, 0, 0, 28]
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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"
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},
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"406": {
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"description": "Unacceptable MIME type"
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},
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}
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})
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def put(self):
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if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
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return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
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# TODO support CSV
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try:
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get_mime_type(acceptable_types=["application/json"], header=request.accept_mimetypes)
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except MimeTypeError as e:
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return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
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try:
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return make_response((jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.VAR))),
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HTTPStatus.OK)
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except FilterError as e:
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return make_response(e.message, HTTPStatus.BAD_REQUEST)
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|
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class DiffExpObsAPI(Resource):
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@swagger.doc({
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"summary": "Generate differential expression (DE) statistics for two specified subsets of data, "
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"as indicated by the two provided observation complex filters",
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"tags": ["diffexp"],
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# TODO sort out params
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# "parameters": [
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# # {
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# # "in": "body",
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# # "name": "mode",
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# # "type": "string",
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# # "required": True,
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# # "description": "topN or varFilter"
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# # },
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# {
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# "in": "query",
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# "name": "count",
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# "type": "int32",
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# "description": "TopN mode: how many vars to return"
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# },
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# {
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# "in": "body",
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# "name": "varFilter",
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# "schema": FilterModel,
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# "description": "varFilter: Complex filter, only var for which vars to return"
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# },
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# {
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# "in": "body",
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# "name": "set1",
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# "schema": FilterModel,
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# "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, -2.569489, 2.655706e-63, 3.642036e-57],
|
|
[1250, -2.569489, 2.655706e-63, 3.642036e-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"])
|
|
except (ValueError, FilterError) as e:
|
|
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
|
except InteractiveError:
|
|
return make_response("Non-interactive request", HTTPStatus.FORBIDDEN)
|
|
return make_response(jsonify(diffexp), HTTPStatus.OK)
|
|
|
|
|
|
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, 0.284483, 0.983744],
|
|
[1, 0.038844, 0.739444]
|
|
]
|
|
}
|
|
}
|
|
}
|
|
},
|
|
"400": {
|
|
"description": "Data preparation error"
|
|
}
|
|
}
|
|
})
|
|
def get(self):
|
|
try:
|
|
layout = current_app.data.layout({})
|
|
except PrepareError as e:
|
|
return make_response(e.message, HTTPStatus.INTERNAL_SERVER_ERROR)
|
|
return make_response((jsonify({"layout": layout})), HTTPStatus.OK)
|
|
|
|
# @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(jsonify({"layout": layout}), HTTPStatus.OK)
|
|
# 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
|