mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-15 20:57:56 +08:00
bkmartinjr/world tests (#306)
First cut at test for stateManager/world. Test data for REST responses factored out into separate file for shared use by Universe and World tests. Also cleaned up some debugging code.
This commit is contained in:
Bruce Martin
116
client/__tests__/util/stateManager/sampleResponses.js
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116
client/__tests__/util/stateManager/sampleResponses.js
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@@ -0,0 +1,116 @@
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/* eslint no-bitwise: "off" */
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import _ from "lodash";
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/*
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test data mocking REST 0.2 API responses. Used in several tests.
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*/
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const nObs = 10;
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const nVar = 32;
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const field4Categories = [83, true, "foo", 2.222222];
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const fieldDCategories = [99, false, "mumble", 3.1415];
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const aConfigResponse = {
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config: {
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features: [
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{ method: "POST", path: "/cluster/", available: false },
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{ method: "POST", path: "/layout/", available: false },
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{ method: "POST", path: "/diffexp/", available: false },
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{ method: "POST", path: "/saveLocal/", available: false }
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],
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displayNames: {
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engine: "the little engine that could",
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dataset: "all your zeros are mine"
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}
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}
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};
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const aSchemaResponse = {
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schema: {
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dataframe: {
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nObs,
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nVar,
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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: "field1", type: "int32" },
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{ name: "field2", type: "float32" },
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{ name: "field3", type: "boolean" },
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{
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name: "field4",
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type: "categorical",
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categories: field4Categories
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}
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],
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var: [
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{ name: "name", type: "string" },
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{ name: "fieldA", type: "int32" },
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{ name: "fieldB", type: "float32" },
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{ name: "fieldC", type: "boolean" },
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{
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name: "fieldD",
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type: "categorical",
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categories: fieldDCategories
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}
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]
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}
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}
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};
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const anAnnotationsObsResponse = {
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names: ["name", "field1", "field2", "field3", "field4"],
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data: _()
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.range(nObs)
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.map(idx => [
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idx,
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`obs${idx}`,
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2 * idx,
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idx + 0.0133,
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!!(idx & 1),
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field4Categories[idx % field4Categories.length]
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])
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.value()
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};
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const anAnnotationsVarResponse = {
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names: ["fieldA", "fieldB", "fieldC", "fieldD", "name"],
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data: _()
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.range(nVar)
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.map(idx => [
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idx,
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10 * idx,
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idx + 2.90143,
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!!(idx & 1),
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fieldDCategories[idx % fieldDCategories.length],
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`var${idx}`
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])
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.value()
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};
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const aLayoutResponse = {
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layout: {
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ndims: 2,
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coordinates: _()
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.range(nObs)
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.map(idx => [idx, Math.random(), Math.random()])
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.value()
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}
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};
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const aDataObsResponse = {
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var: [2, 4, 29],
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obs: _()
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.range(nObs)
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.map(idx => [idx, Math.random(), Math.random(), Math.random()])
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.value()
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};
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export {
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aLayoutResponse as layoutObs,
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aDataObsResponse as dataObs,
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anAnnotationsVarResponse as annotationsVar,
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anAnnotationsObsResponse as annotationsObs,
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aSchemaResponse as schema,
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aConfigResponse as config
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};
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@@ -1,112 +1,6 @@
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/* eslint no-bitwise: "off" */
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import _ from "lodash";
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import * as Universe from "../../../src/util/stateManager/universe";
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/*
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test data mocking REST 0.2 API responses
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*/
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const nObs = 10;
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const nVar = 32;
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const field4Categories = [83, true, "foo", 2.222222];
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const fieldDCategories = [99, false, "mumble", 3.1415];
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const aConfigResponse = {
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config: {
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features: [
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{ method: "POST", path: "/cluster/", available: false },
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{ method: "POST", path: "/layout/", available: false },
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{ method: "POST", path: "/diffexp/", available: false },
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{ method: "POST", path: "/saveLocal/", available: false }
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],
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displayNames: {
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engine: "the little engine that could",
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dataset: "all your zeros are mine"
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}
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}
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};
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const aSchemaResponse = {
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schema: {
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dataframe: {
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nObs,
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nVar,
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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: "field1", type: "int32" },
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{ name: "field2", type: "float32" },
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{ name: "field3", type: "boolean" },
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{
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name: "field4",
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type: "categorical",
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categories: field4Categories
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}
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],
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var: [
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{ name: "name", type: "string" },
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{ name: "fieldA", type: "int32" },
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{ name: "fieldB", type: "float32" },
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{ name: "fieldC", type: "boolean" },
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{
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name: "fieldD",
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type: "categorical",
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categories: fieldDCategories
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}
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]
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}
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}
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};
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const anAnnotationsObsResponse = {
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names: ["name", "field1", "field2", "field3", "field4"],
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data: _()
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.range(nObs)
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.map(idx => [
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idx,
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`obs${idx}`,
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2 * idx,
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idx + 0.0133,
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idx & 1,
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field4Categories[idx % field4Categories.length]
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])
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.value()
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};
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const anAnnotationsVarResponse = {
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names: ["fieldA", "fieldB", "fieldC", "fieldD", "name"],
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data: _()
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.range(nVar)
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.map(idx => [
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idx,
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10 * idx,
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idx + 2.90143,
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idx & 1,
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fieldDCategories[idx % fieldDCategories.length],
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`var${idx}`
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])
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.value()
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};
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const aLayoutResponse = {
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layout: {
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ndims: 2,
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coordinates: _()
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.range(nObs)
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.map(idx => [idx, Math.random(), Math.random()])
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.value()
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}
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};
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const aDataObsResponse = {
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var: [2, 4, 29],
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obs: _()
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.range(nObs)
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.map(idx => [idx, Math.random(), Math.random(), Math.random()])
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.value()
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};
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import * as REST from "./sampleResponses";
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describe("createUniverseFromRestV02Response", () => {
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/*
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@@ -135,13 +29,14 @@ describe("createUniverseFromRestV02Response", () => {
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/*
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create a universe from sample data nad validate its shape & contents
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*/
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const { nObs, nVar } = REST.schema.schema.dataframe;
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const universe = Universe.createUniverseFromRestV02Response(
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aConfigResponse,
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aSchemaResponse,
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anAnnotationsObsResponse,
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anAnnotationsVarResponse,
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aLayoutResponse
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REST.config,
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REST.schema,
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REST.annotationsObs,
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REST.annotationsVar,
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REST.layoutObs
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);
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expect(universe).toBeDefined();
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@@ -150,7 +45,7 @@ describe("createUniverseFromRestV02Response", () => {
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api: "0.2",
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nObs,
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nVar,
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schema: aSchemaResponse.schema,
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schema: REST.schema.schema,
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obsAnnotations: expect.any(Array),
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varAnnotations: expect.any(Array),
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obsNameToIndexMap: expect.any(Object),
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@@ -163,12 +58,12 @@ describe("createUniverseFromRestV02Response", () => {
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})
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);
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expect(_.size(universe.obsAnnotations)).toBe(nObs);
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expect(_.size(universe.obsNameToIndexMap)).toBe(nObs);
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expect(_.size(universe.obsLayout.X)).toBe(nObs);
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expect(_.size(universe.obsLayout.Y)).toBe(nObs);
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expect(_.size(universe.varAnnotations)).toBe(nVar);
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expect(_.size(universe.varNameToIndexMap)).toBe(nVar);
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expect(universe.obsAnnotations).toHaveLength(nObs);
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expect(_.keys(universe.obsNameToIndexMap)).toHaveLength(nObs);
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expect(universe.obsLayout.X).toHaveLength(nObs);
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expect(universe.obsLayout.Y).toHaveLength(nObs);
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expect(universe.varAnnotations).toHaveLength(nVar);
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expect(_.keys(universe.varNameToIndexMap)).toHaveLength(nVar);
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});
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});
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@@ -191,36 +86,32 @@ describe("convertExpressionRESTv02ToObject", () => {
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*/
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test("create from response data", () => {
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const universe = Universe.createUniverseFromRestV02Response(
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aConfigResponse,
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aSchemaResponse,
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anAnnotationsObsResponse,
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anAnnotationsVarResponse,
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aLayoutResponse
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REST.config,
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REST.schema,
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REST.annotationsObs,
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REST.annotationsVar,
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REST.layoutObs
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);
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const expression = Universe.convertExpressionRESTv02ToObject(
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universe,
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aDataObsResponse
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REST.dataObs
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);
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/* Check that the expected keys are present */
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const expectedGeneNames = _.map(
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aDataObsResponse.var,
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v => anAnnotationsVarResponse.data[v][5]
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REST.dataObs.var,
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v => REST.annotationsVar.data[v][5]
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);
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expect(Object.keys(expression)).toEqual(
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expect.arrayContaining(expectedGeneNames)
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);
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const expectedExpressionValues = _.map(
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_.unzip(aDataObsResponse.obs),
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_.unzip(REST.dataObs.obs),
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a => new Float32Array(a)
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);
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// console.log(aDataObsResponse);
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// console.log(expression);
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// console.log(_.unzip(aDataObsResponse.obs));
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_.forEach(aDataObsResponse.var, (varIdx, idx) => {
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_.forEach(REST.dataObs.var, (varIdx, idx) => {
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const varName = universe.varAnnotations[varIdx].name;
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expect(varName).toBeDefined();
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expect(varIdx).toBe(universe.varNameToIndexMap[varName]);
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129
client/__tests__/util/stateManager/world.test.js
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129
client/__tests__/util/stateManager/world.test.js
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@@ -0,0 +1,129 @@
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import _ from "lodash";
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import * as Universe from "../../../src/util/stateManager/universe";
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import * as World from "../../../src/util/stateManager/world";
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import Crossfilter from "../../../src/util/typedCrossfilter";
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import * as REST from "./sampleResponses";
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/*
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TODO: endpoints to test:
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createObsDimensionMap(crossfilter, world)
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subsetVarData(world, universe, varData)
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*/
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describe("createWorldFromEntireUniverse", () => {
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test("create from REST sample", () => {
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const universe = Universe.createUniverseFromRestV02Response(
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REST.config,
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REST.schema,
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REST.annotationsObs,
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REST.annotationsVar,
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REST.layoutObs
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);
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expect(universe).toBeDefined();
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const world = World.createWorldFromEntireUniverse(universe);
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expect(world).toBeDefined();
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expect(world).toMatchObject(
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expect.objectContaining({
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api: "0.2",
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nObs: universe.nObs,
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nVar: universe.nVar,
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schema: universe.schema,
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obsAnnotations: universe.obsAnnotations,
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varAnnotations: universe.varAnnotations,
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obsLayout: universe.obsLayout,
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summary: expect.objectContaining({
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obs: _(REST.schema.schema.annotations.obs)
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.keyBy("name")
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.mapValues(() => expect.any(Object))
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.value(),
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var: {} // TODO: currently unimplemneted
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}),
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varDataCache: expect.any(Object),
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worldObsIndex: null // indicating full universe
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})
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);
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});
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});
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describe("createWorldFromCurrentSelection", () => {
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test("create from REST sample", () => {
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/* create universe */
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const universe = Universe.createUniverseFromRestV02Response(
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REST.config,
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REST.schema,
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REST.annotationsObs,
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REST.annotationsVar,
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REST.layoutObs
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);
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/* create world */
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const originalWorld = World.createWorldFromEntireUniverse(universe);
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/* create crossfilter */
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const crossfilter = Crossfilter(originalWorld.obsAnnotations);
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/* fake a selection */
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const dimensionMap = World.createObsDimensionMap(
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crossfilter,
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originalWorld
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);
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dimensionMap.field1.filterRange([0, 5]);
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dimensionMap.field3.filterExact(false);
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/* create the world from the selection */
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const world = World.createWorldFromCurrentSelection(
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universe,
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originalWorld,
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crossfilter
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);
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expect(world).toBeDefined();
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expect(world.nObs).toEqual(crossfilter.countFiltered());
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/*
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calculate expected values and match against result
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*/
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/* matchFilter must match the dimension filters above */
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const matchFilter = val => val.field1 >= 0 && val.field1 < 5 && !val.field3;
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const universeIndices = _()
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.range(universe.nObs)
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.filter(idx => matchFilter(universe.obsAnnotations[idx]))
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.value();
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const expected = {
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nObs: universeIndices.length,
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obsAnnotations: _.map(universeIndices, i => universe.obsAnnotations[i]),
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obsLayout: {
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X: _.map(universeIndices, i => universe.obsLayout.X[i]),
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Y: _.map(universeIndices, i => universe.obsLayout.Y[i])
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},
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worldObsIndex: _.transform(
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universeIndices,
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(result, univIdx, worldIdx) => {
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result[univIdx] = worldIdx;
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},
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new Array(universe.nObs).fill(-1)
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)
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};
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expect(world).toMatchObject(
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expect.objectContaining({
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api: "0.2",
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nObs: expected.nObs,
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nVar: universe.nVar,
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schema: universe.schema,
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obsAnnotations: expected.obsAnnotations,
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varAnnotations: universe.varAnnotations,
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obsLayout: expected.obsLayout,
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summary: expect.any(Object) /* we could do better! */,
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varDataCache: expect.any(Object),
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worldObsIndex: expected.worldObsIndex
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})
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);
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});
|
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});
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Block a user