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jameshadfieldjameshadfield
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[test] Unit test createStateFromQueryOrJSONs
This was primarily motivated by the bug identified in <nextstrain/auspice.us#122> and fixed via a one-line patch in <nextstrain#1986>. I confirmed that the tests added here would have flagged this bug (via reverting ece625f). There's a lot of future directions we can take tests such as these, this is only the starting point.
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‎test/data/generic.json‎

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{
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"version": "v2",
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"meta": {
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"title": "Generic (small) feature-rich dataset for testing purposes",
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"updated": "2023-03-28",
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"build_url": "https://github.com/nextstrain/auspice",
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"build_avatar": "https://avatars.githubusercontent.com/u/22159334?s=48&v=4",
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"description": "# Markdown description",
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"warning": "Achtung!",
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"maintainers": [{"name": "The nextstrain team", "url": "https://nextstrain.org"}],
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"genome_annotations": {"nuc": { "end": 100, "start": 1 }},
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"filters": ["subtree"],
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"panels": ["tree", "map", "entropy"],
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"extensions": "any data structure!",
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"geo_resolutions": [{"key": "subtree2", "title": "Subtree2 (demes)", "demes": {"red": {"latitude": 0, "longitude": -125}, "purple": {"latitude": -5, "longitude": -130}}}],
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"colorings": [
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{ "key": "num_date", "title": "Sampling date", "type": "temporal"},
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{ "key": "subtree", "title": "subtree (Colour)", "type": "categorical", "scale": [["blue", "#2c7fb8"], ["green", "#78c679"]]},
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{ "key": "subtree2", "title": "subtree 2 (Colour)", "type": "categorical", "scale": [["red", "#f03b20"], ["purple", "#8856a7"]]},
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{ "key": "ord", "title": "ordinal (string)", "type": "ordinal"},
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{ "key": "bool", "title": "Boolean / Binary", "type": "boolean"}
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],
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"display_defaults": {
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"map_triplicate": false,
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"geo_resolution": "subtree2",
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"color_by": "subtree2",
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"distance_measure": "div",
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"layout": "rect",
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"branch_label": "node_name",
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"label": "node_name:alpha",
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"tip_label": "subtree",
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"stream_label": "river",
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"transmission_lines": true,
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"language": "en",
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"sidebar": "open",
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"panels": ["tree", "map", "entropy"]
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},
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"stream_labels": ["river"],
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"data_provenance": [{"name": "test-data", "url": "https://github.com/nextstrain/auspice"}]
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},
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"tree": {
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"name": "romeo",
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"node_attrs": {"div": 0, "subtree": {"value": "green"}, "subtree2": {"value": "red"}, "ord": {"value": "A"}, "bool": {"value": "True"}, "num_date": {"value": 2000.00}},
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"branch_attrs": {"labels": {"node_name": "romeo"}, "mutations": {"nuc": ["T50A"]}},
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"children": [
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{
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"name": "alpha",
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"node_attrs": {"div": 1, "subtree": {"value": "green"}, "subtree2": {"value": "red"}, "ord": {"value": "A"}, "bool": {"value": "True"},
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"num_date": {"value": 2003.00}},
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"branch_attrs": {"labels": {"node_name": "alpha", "river": "Nile"}, "mutations": {"nuc": []}},
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"children": [
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{
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"name": "bravo",
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"node_attrs": {"div": 2, "subtree": {"value": "green"}, "subtree2": {"value": "red"}, "ord": {"value": "C"}, "bool": {"value": "True"}, "num_date": {"value": 2005.00}},
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"branch_attrs": {"labels": {"node_name": "bravo"}, "mutations": {"nuc": []}}
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},
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{
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"name": "charlie",
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"node_attrs": {"div": 2, "subtree": {"value": "green"}, "subtree2": {"value": "red"}, "num_date": {"value": 2012.00}},
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"branch_attrs": {"labels": {"node_name": "charlie"}, "mutations": {"nuc": []}},
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"children": [
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{
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"name": "delta",
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"node_attrs": {"div": 3, "subtree": {"value": "green"}, "subtree2": {"value": "purple"}, "ord": {"value": "B"}, "bool": {"value": "1"}, "num_date": {"value": 2015.00}},
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"branch_attrs": {"labels": {"node_name": "delta"}, "mutations": {"nuc": []}}
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},
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{
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"name": "echo",
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"node_attrs": {"div": 3, "subtree": {"value": "blue"}, "subtree2": {"value": "purple"}, "ord": {"value": "B"}, "bool": {"value": "True"}, "num_date": {"value": 2018.00}},
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"branch_attrs": {"labels": {"node_name": "echo", "river": "Lena"}, "mutations": {"nuc": ["A50T"]}},
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"children": [
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{
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"name": "foxtrot",
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"node_attrs": {"div": 4, "subtree": {"value": "blue"}, "subtree2": {"value": "purple"}, "ord": {"value": "B"}, "bool": {"value": 0}, "num_date": {"value": 2019.00}},
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"branch_attrs": {"labels": {"node_name": "foxtrot"}, "mutations": {"nuc": []}}
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},
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{
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"name": "golf",
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"node_attrs": {"div": 4, "subtree": {"value": "blue"}, "subtree2": {"value": "purple"}, "ord": {"value": "A"}, "bool": {"value": "False"}, "num_date": {"value": 2020.00}},
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"branch_attrs": {"labels": {"node_name": "golf"}, "mutations": {"nuc": []}}
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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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"root_sequence": "ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC"
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}

‎test/recomputeReduxState.test.js‎

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/**
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* @jest-environment jsdom
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*/
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/* NOTE: We use the jsdom environment since `createStateFromQueryOrJSONs` relies on `window` */
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import { createStateFromQueryOrJSONs } from "../src/actions/recomputeReduxState";
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import genericMainJson from './data/generic.json';
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/**
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* The `createStateFromQueryOrJSONs` function is a large and complex function used at dataset load time
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* as well as to effect narrative slide changes. The aim here is to test it on a number of datasets and
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* different ways the function can be called. Simply testing that the function returns an object (i.e.
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* doesn't throw) is enough to start with, as there's only a single return point in the function.
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*
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* Future directions:
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* - assert dispatch is called in certain circumstances
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* - check console logs (console.error's are expected in many circumstances)
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* - create a similar test for sidecar files
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* - consider using these datasets to smoke test via playright
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* - create state then call `createStateFromQueryOrJSONs` again
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*/
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/**
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* Define a list of dataset permutations, each element being an array with
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* a short description (string) and a function which takes in the mainDataset (object)
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* and returns a modified version.
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*/
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const datasetPermutationSpecifications = [
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["generic dataset JSON", (dataset) => dataset],
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..._modifyJsonToRemoveOptionalMetaKeys(),
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..._modifyJsonToRemoveOptionalDisplayDefaultKeys(),
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]
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function* datasetPermutations() {
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for (const [summary, modify] of datasetPermutationSpecifications) {
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yield [summary, modify(clone(genericMainJson))]
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}
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}
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/**
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* Run through each permutation of the dataset and turn it into react state
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* via the simplest possible call to `createStateFromQueryOrJSONs`
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*/
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for (const [summary, mainDataset] of datasetPermutations()) {
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it(`Basic redux state creation for: ${summary}`, () => {
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const state = createStateFromQueryOrJSONs({
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json: mainDataset,
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query: {},
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dispatch,
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})
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expect(state).toBeInstanceOf(Object)
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})
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}
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/**
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* Test two-trees
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*/
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for (const [summary, modifiedDataset] of datasetPermutations()) {
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it(`Basic redux state creation for two trees: generic + ${summary}`, () => {
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const state = createStateFromQueryOrJSONs({
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json: modifiedDataset,
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query: {},
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dispatch,
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})
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expect(state).toBeInstanceOf(Object)
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})
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}
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function _modifyJsonToRemoveOptionalMetaKeys() {
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return Object.keys(genericMainJson['meta']) // all are optional in the schema
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.filter(() => true) // NOTE: the schema requires "updated", "panels", but auspice can handle cases where these are missing
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.map((key) => [
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`missing .meta key "${key}"`,
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(dataset) => {
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delete dataset['meta'][key];
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return dataset
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}
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])
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}
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function _modifyJsonToRemoveOptionalDisplayDefaultKeys() {
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// Since the dataset works without the `display_defaults` object at all, this seems a little unnecessary,
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// but I guess there's no harm?
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return Object.keys(genericMainJson['meta']['display_defaults']) // all are optional in the schema
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.filter(() => true) // all are optional in the schema
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.map((key) => [
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`missing .meta.display_default key "${key}"`,
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(dataset) => {
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delete dataset['meta']['display_defaults'][key];
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return dataset
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}
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])
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}
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function dispatch() {
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/* no-op */
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}
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/**
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* Clone a (JSON) dataset. We can't use the native `window.structuredClone`
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* because we're in a jsdom test environment, and we can't polyfill it without
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* updating our version of core-js (structuredClone added in v3.20.0). Since the
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* dataset is originally JSON it's fine to use the classic stringify-parse approach.
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*/
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function clone(dataset) {
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return JSON.parse(JSON.stringify(dataset))
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}

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