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Black -- formatter for python (#508)
* Add black * use black to format code * Black version
This commit is contained in:
Charlotte Weaver
+327
-426
@@ -2,9 +2,7 @@ from http import HTTPStatus
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import pkg_resources
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import warnings
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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 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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@@ -23,83 +21,78 @@ Sort order for routes
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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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@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": {"nObs": 383, "nVar": 19944, "type": "float32"},
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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": [{"name": "name", "type": "string"}, {"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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})
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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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@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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{"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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{"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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},
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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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@@ -111,50 +104,48 @@ class ConfigAPI(Resource):
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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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"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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"parameters": {"max_category_items": current_app.data.max_category_items},
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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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@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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"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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try:
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@@ -168,47 +159,40 @@ class AnnotationsObsAPI(Resource):
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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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@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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@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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{"name": "filter", "description": "Complex Filter", "in": "body", "schema": FilterModel},
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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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"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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)
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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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@@ -226,38 +210,35 @@ class AnnotationsObsAPI(Resource):
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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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@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": [[0, "ATAD3C", 1], [1, "RER1", None], [49, "S100B", 6]],
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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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"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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try:
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@@ -271,45 +252,36 @@ class AnnotationsVarAPI(Resource):
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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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|
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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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@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",
|
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"name": "annotation-name",
|
||||
"type": "string",
|
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"description": "list of 1 or more annotation names",
|
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},
|
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{"name": "filter", "description": "Complex Filter", "in": "body", "schema": FilterModel},
|
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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": [[0, "ATAD3C", 1], [1, "RER1", None], [49, "S100B", 6]],
|
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}
|
||||
},
|
||||
},
|
||||
"400": {
|
||||
"description": "malformed filter or one or more of the annotation-name identifiers were"
|
||||
"not associated with an annotation name"
|
||||
},
|
||||
},
|
||||
{
|
||||
"name": "filter",
|
||||
"description": "Complex Filter",
|
||||
"in": "body",
|
||||
"schema": FilterModel
|
||||
}
|
||||
],
|
||||
"responses": {
|
||||
"200": {
|
||||
"description": "annotations",
|
||||
"examples": {
|
||||
"application/json": {
|
||||
"names": [
|
||||
"name", "category"
|
||||
],
|
||||
"data": [
|
||||
[0, "ATAD3C", 1],
|
||||
[1, "RER1", None],
|
||||
[49, "S100B", 6]
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
"400": {
|
||||
"description": "malformed filter or one or more of the annotation-name identifiers were"
|
||||
"not associated with an annotation name"
|
||||
}
|
||||
}
|
||||
})
|
||||
)
|
||||
def put(self):
|
||||
fields = request.args.getlist("annotation-name", None)
|
||||
try:
|
||||
@@ -327,57 +299,39 @@ class AnnotationsVarAPI(Resource):
|
||||
|
||||
|
||||
class DataObsAPI(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": {
|
||||
"var": [0, 20000],
|
||||
"obs": [
|
||||
[1, 39483, 3902, 203, 0, 0, 28]
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
"400": {
|
||||
"description": "Malformed filter"
|
||||
},
|
||||
"406": {
|
||||
"description": "Unacceptable MIME type"
|
||||
@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": {"var": [0, 20000], "obs": [[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'])
|
||||
filter_ = parse_filter(ImmutableMultiDict(args), current_app.data.schema["annotations"])
|
||||
except QueryStringError as e:
|
||||
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
||||
# TODO support CSV
|
||||
try:
|
||||
# TODO store mime_type when more than one is supported
|
||||
get_mime_type(acceptable_types=["application/json"], query_param=accept_type,
|
||||
header=request.accept_mimetypes)
|
||||
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:
|
||||
@@ -389,37 +343,21 @@ class DataObsAPI(Resource):
|
||||
warnings.warn(JSON_NaN_to_num_warning_msg)
|
||||
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"
|
||||
@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)
|
||||
@@ -428,8 +366,9 @@ class DataObsAPI(Resource):
|
||||
except MimeTypeError as e:
|
||||
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
|
||||
try:
|
||||
return make_response((jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.OBS))),
|
||||
HTTPStatus.OK)
|
||||
return make_response(
|
||||
(jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.OBS))), HTTPStatus.OK
|
||||
)
|
||||
except FilterError as e:
|
||||
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
||||
except ValueError as e:
|
||||
@@ -439,55 +378,37 @@ class DataObsAPI(Resource):
|
||||
|
||||
|
||||
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"
|
||||
@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'])
|
||||
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)
|
||||
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:
|
||||
@@ -499,37 +420,21 @@ class DataVarAPI(Resource):
|
||||
warnings.warn(JSON_NaN_to_num_warning_msg)
|
||||
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"
|
||||
@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):
|
||||
if not request.accept_mimetypes.best_match(["application/json", "text/csv"]):
|
||||
return make_response(f"Unsupported MIME type '{request.accept_mimetypes}'", HTTPStatus.NOT_ACCEPTABLE)
|
||||
@@ -539,8 +444,9 @@ class DataVarAPI(Resource):
|
||||
except MimeTypeError as e:
|
||||
return make_response(e.message, HTTPStatus.NOT_ACCEPTABLE)
|
||||
try:
|
||||
return make_response((jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.VAR))),
|
||||
HTTPStatus.OK)
|
||||
return make_response(
|
||||
(jsonify(current_app.data.data_frame(request.get_json()["filter"], axis=Axis.VAR))), HTTPStatus.OK
|
||||
)
|
||||
except FilterError as e:
|
||||
return make_response(e.message, HTTPStatus.BAD_REQUEST)
|
||||
except ValueError as e:
|
||||
@@ -550,67 +456,64 @@ class DataVarAPI(Resource):
|
||||
|
||||
|
||||
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, -2.569489, 2.655706e-63, 3.642036e-57],
|
||||
[1250, -2.569489, 2.655706e-63, 3.642036e-57],
|
||||
]
|
||||
}
|
||||
@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"},
|
||||
},
|
||||
"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
|
||||
@@ -645,8 +548,9 @@ class DiffExpObsAPI(Resource):
|
||||
# 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"])
|
||||
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:
|
||||
@@ -660,30 +564,27 @@ class DiffExpObsAPI(Resource):
|
||||
|
||||
|
||||
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]
|
||||
]
|
||||
@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"},
|
||||
},
|
||||
"400": {
|
||||
"description": "Data preparation error"
|
||||
}
|
||||
}
|
||||
})
|
||||
)
|
||||
def get(self):
|
||||
try:
|
||||
layout = current_app.data.layout({})
|
||||
|
||||
Reference in New Issue
Block a user