From 91f97ecc4317dc8b4ccb47cac898d608a11cfd00 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Tue, 10 Nov 2020 08:57:19 +0100
Subject: [PATCH] bugfix: remove additional layers
---
deploy/atlas/sanity.spec.js | 106 ++++++++++++++++++
.../browsingForDatasets.prod.e2e-spec.js | 2 +-
e2e/src/selecting/atlas.prod.e2e-spec.js | 56 ++++++++-
e2e/src/selecting/region.prod.e2e-spec.js | 4 +-
e2e/util/selenium/iav.js | 2 +-
e2e/util/selenium/layout.js | 40 ++++---
src/res/ext/waxholmRatV2_0.json | 2 +
.../state/viewerState.store.helper.ts | 29 +++--
.../atlasLayerSelector.template.html | 14 +--
9 files changed, 217 insertions(+), 38 deletions(-)
create mode 100644 deploy/atlas/sanity.spec.js
diff --git a/deploy/atlas/sanity.spec.js b/deploy/atlas/sanity.spec.js
new file mode 100644
index 000000000..21d4be22a
--- /dev/null
+++ b/deploy/atlas/sanity.spec.js
@@ -0,0 +1,106 @@
+const fs = require('fs')
+const path = require('path')
+const { promisify } = require('util')
+const asyncReadfile = promisify(fs.readFile)
+const { expect } = require('chai')
+const { pid } = require('process')
+const { assert } = require('console')
+
+const templateFiles = [
+ 'bigbrain.json',
+ 'colin.json',
+ 'MNI152.json',
+ 'waxholmRatV2_0.json',
+ 'allenMouse.json'
+]
+
+const atlasFiles = [
+ 'atlas_multiLevelHuman.json',
+ 'atlas_waxholmRat.json',
+ 'atlas_allenMouse.json'
+]
+
+const templateIdToParcsMap = new Map()
+const templateIdToTemplateMap = new Map()
+const parcIdToTemplateId = new Map()
+const parcIdToParcMap = new Map()
+
+const rootDir = path.join(__dirname, '../../src/res/ext')
+
+describe('> atlas sanity check', () => {
+ before(async () => {
+ for (const templateFile of templateFiles){
+ const txt = await asyncReadfile(
+ path.join(rootDir, templateFile),
+ 'utf-8'
+ )
+ const template = JSON.parse(txt)
+ const { ['@id']: templateId, name: templateName, parcellations } = template
+ if (!templateId) throw new Error(`${templateFile} / ${templateName} / @id not defined`)
+ templateIdToTemplateMap.set(templateId, template)
+
+ for (const parc of parcellations) {
+ const { ['@id']: parcId, name: parcName } = parc
+ if (!parcId) throw new Error(`${templateFile} / ${parcName} /@id not defined`)
+ parcIdToParcMap.set(parcId, parc)
+
+ const arr = templateIdToParcsMap.get(templateId) || []
+ templateIdToParcsMap.set(templateId, arr.concat(parcId) )
+
+ const arr2 = parcIdToTemplateId.get(parcId) || []
+ parcIdToTemplateId.set(parcId, arr2.concat(templateId))
+ }
+ }
+ })
+
+ for (const atlas of atlasFiles) {
+ describe(`> checking ${atlas}`, () => {
+
+ beforeEach(async () => {
+ const txt = await asyncReadfile(
+ path.join(rootDir, 'atlas', atlas)
+ )
+ const { ['@id']: atlasId, name: atlasName, templateSpaces, parcellations } = JSON.parse(txt)
+
+ describe(`> checking ${atlasName}`, () => {
+ describe('> checking template spaces', () => {
+ for (const { name: tName, ['@id']: tId, availableIn } of templateSpaces) {
+ describe(`> checking ${tName} with id ${tId}`, () => {
+ for (const { ['@id']: pId, name: pName } of availableIn) {
+ describe(`> checking ${pName}, with id ${pId}`, () => {
+ it('> template maps to parc', () => {
+ const arr = templateIdToParcsMap.get(tId)
+ const idx = arr.findIndex(id => id === pId)
+ assert(
+ idx >= 0,
+ 'entry can be found'
+ )
+ arr.splice(idx, 1)
+ })
+
+ it('> parc maps to tmpl', () => {
+
+ const arr = parcIdToTemplateId.get(pId)
+ if (!arr) throw new Error(`${pName} cannot be found`)
+ const idx = arr.findIndex(id => id === tId)
+ assert(
+ idx >= 0,
+ 'entry can be found'
+ )
+ arr.splice(idx, 1)
+ })
+ })
+ }
+ })
+ }
+ })
+ })
+
+ })
+
+ it('> dummy test', () => {
+ expect(true).to.equal(true)
+ })
+ })
+ }
+})
diff --git a/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js b/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js
index fba414f29..28900df32 100644
--- a/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js
+++ b/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js
@@ -75,7 +75,7 @@ describe('> dataset browser', () => {
describe(`> in template: ${template}`, () => {
beforeAll(async () => {
await iavPage.goto()
- await iavPage.selectAtlasTemplateParcellation(atlasName, template)
+ await iavPage.setAtlasSpecifications(atlasName, [ template ])
// account for linear template translation backend
await iavPage.wait(5000)
diff --git a/e2e/src/selecting/atlas.prod.e2e-spec.js b/e2e/src/selecting/atlas.prod.e2e-spec.js
index 75dac89ac..e5b703809 100644
--- a/e2e/src/selecting/atlas.prod.e2e-spec.js
+++ b/e2e/src/selecting/atlas.prod.e2e-spec.js
@@ -19,7 +19,7 @@ describe('> atlases are generally available', () => {
})
})
-describe('> generic atlaes behaviours', () => {
+describe('> generic atlas behaviours', () => {
let atlasPage = new AtlasPage()
beforeEach(async () => {
atlasPage = new AtlasPage()
@@ -30,7 +30,8 @@ describe('> generic atlaes behaviours', () => {
it('> on launch, shows atlas name as a pill', async () => {
await atlasPage.goto()
await atlasPage.clearAlerts()
- await atlasPage.selectAtlasTemplateParcellation(atlas)
+ await atlasPage.setAtlasSpecifications(atlas)
+ await atlasPage.wait(500)
await atlasPage.waitUntilAllChunksLoaded()
const txtArr = await atlasPage.getAllChipsText()
expect(
@@ -40,4 +41,53 @@ describe('> generic atlaes behaviours', () => {
})
})
}
-})
\ No newline at end of file
+})
+
+describe('> in human multi level', () => {
+ let atlasPage = new AtlasPage()
+ beforeAll(async () => {
+ atlasPage = new AtlasPage()
+ await atlasPage.init()
+ await atlasPage.goto()
+ await atlasPage.clearAlerts()
+ })
+ describe('> removal of additional layers should restore base layer', () => {
+ it('> in mni152', async () => {
+ await atlasPage.setAtlasSpecifications(atlases[1], [`Fibre tracts`, `Short Bundle`])
+ await atlasPage.wait(500)
+ await atlasPage.waitForAsync()
+
+ const txtArr = await atlasPage.getAllChipsText()
+ expect(
+ txtArr.find(txt => /short bundle/i.test(txt))
+ ).toBeTruthy()
+
+ await atlasPage.clickChip(/short bundle/i, '.fa-times')
+
+ const txtArr2 = await atlasPage.getAllChipsText()
+ expect(
+ txtArr2.find(txt => /short bundle/i.test(txt))
+ ).toBeFalsy()
+
+ })
+
+ it('> in bigbrain', async () => {
+ await atlasPage.setAtlasSpecifications(atlases[1], [/isocortex/i])
+ await atlasPage.wait(500)
+ await atlasPage.waitForAsync()
+
+ const txtArr = await atlasPage.getAllChipsText()
+ expect(
+ txtArr.find(txt => /isocortex/i.test(txt))
+ ).toBeTruthy()
+
+ await atlasPage.clickChip(/isocortex/i, '.fa-times')
+
+ const txtArr2 = await atlasPage.getAllChipsText()
+ expect(
+ txtArr2.find(txt => /isocortex/i.test(txt))
+ ).toBeFalsy()
+
+ })
+ })
+})
diff --git a/e2e/src/selecting/region.prod.e2e-spec.js b/e2e/src/selecting/region.prod.e2e-spec.js
index d2f63699d..01b30f83e 100644
--- a/e2e/src/selecting/region.prod.e2e-spec.js
+++ b/e2e/src/selecting/region.prod.e2e-spec.js
@@ -14,7 +14,7 @@ describe('> selecting regions', () => {
const newPage = new AtlasPage()
await newPage.init()
await newPage.goto()
- await newPage.selectAtlasTemplateParcellation(duplicatedRegion.atlas, duplicatedRegion.template)
+ await newPage.setAtlasSpecifications(duplicatedRegion.atlas, [ duplicatedRegion.template ])
await newPage.wait(500)
await newPage.waitForAsync()
await newPage.execScript(`interactiveViewer.viewerHandle.setNavigationLoc(${JSON.stringify(duplicatedRegion.position.map(v => v*1e6))}, true)`)
@@ -64,7 +64,7 @@ describe('> selecting regions', () => {
})
it('> on change atlas, multi region panel are dismissed', async () => {
- await newPage.selectAtlasTemplateParcellation(humanAtlasName)
+ await newPage.setAtlasSpecifications(humanAtlasName)
await newPage.wait(500)
await newPage.waitForAsync()
diff --git a/e2e/util/selenium/iav.js b/e2e/util/selenium/iav.js
index 75f011dee..f93946027 100644
--- a/e2e/util/selenium/iav.js
+++ b/e2e/util/selenium/iav.js
@@ -39,7 +39,7 @@ class WdIavPage extends WdLayoutPage{
}
async selectDropdownTemplate(title) {
- throw new Error(`selectDropdownTemplate has been deprecated. use changeTemplate instead`)
+ throw new Error(`selectDropdownTemplate has been deprecated. use setAtlasSpecifications instead`)
}
async _getSearchRegionInput(){
diff --git a/e2e/util/selenium/layout.js b/e2e/util/selenium/layout.js
index 99b7e97c6..e4a01a627 100644
--- a/e2e/util/selenium/layout.js
+++ b/e2e/util/selenium/layout.js
@@ -258,6 +258,20 @@ class WdLayoutPage extends WdBase{
return visibility
}
+ async clickChip(search, cssSelector) {
+ const allChips = await this._getChips()
+ const idx = await _getIndexFromArrayOfWebElements(search, allChips)
+ if (idx < 0) throw new Error(`clickChip ${search.toString()} not found`)
+ if (!cssSelector) {
+ return await allChips[idx].click()
+ }
+ const el = await allChips[idx].findElement(
+ By.css(cssSelector)
+ )
+ if (!el) throw new Error(`clickChip css selector ${cssSelector} not found`)
+ return await el.click()
+ }
+
/**
* Cards
*/
@@ -297,7 +311,7 @@ class WdLayoutPage extends WdBase{
}
async selectTitleTemplateParcellation(templateName, parcellationName){
- throw new Error(`selectTitleTemplateParcellation has been deprecated. use selectAtlasTemplateParcellation`)
+ throw new Error(`selectTitleTemplateParcellation has been deprecated. use setAtlasSpecifications`)
}
/**
@@ -320,17 +334,15 @@ class WdLayoutPage extends WdBase{
}
}
- async changeTemplate(templateName){
- if (!templateName) throw new Error(`templateName needs to be provided`)
+ async selectTile(tileName){
+ if (!tileName) throw new Error(`tileName needs to be provided`)
await this._setAtlasSelectorExpanded(true)
await this.wait(1000)
- const allTiles = await this._browser
- .findElement( By.css('atlas-layer-selector') )
- .findElements( By.css(`mat-grid-tile`) )
+ const allTiles = await this._browser.findElements( By.css(`mat-grid-tile`) )
- const idx = await _getIndexFromArrayOfWebElements(templateName, allTiles)
+ const idx = await _getIndexFromArrayOfWebElements(tileName, allTiles)
if (idx >= 0) await allTiles[idx].click()
- else throw new Error(`#changeTemplate: templateName ${templateName} cannot be found.`)
+ else throw new Error(`#selectTile: tileName ${tileName} cannot be found.`)
}
async changeParc(parcName) {
@@ -341,7 +353,7 @@ class WdLayoutPage extends WdBase{
throw new Error(`changeParcVersion NYI`)
}
- async selectAtlasTemplateParcellation(atlasName, templateName, parcellationName, parcVersion) {
+ async setAtlasSpecifications(atlasName, atlasSpecifications = [], parcVersion = null) {
if (!atlasName) throw new Error(`atlasName needs to be provided`)
try {
/**
@@ -357,16 +369,10 @@ class WdLayoutPage extends WdBase{
await this.selectDropdownOption(`[aria-label="${ARIA_LABELS.SELECT_ATLAS}"]`, atlasName)
}
- if (templateName) {
- await this.wait(1000)
- await this.waitUntilAllChunksLoaded()
- await this.changeTemplate(templateName)
- }
-
- if (parcellationName) {
+ for (const spec of atlasSpecifications) {
await this.wait(1000)
await this.waitUntilAllChunksLoaded()
- await this.changeParc(parcellationName)
+ await this.selectTile(spec)
}
if (parcVersion) {
diff --git a/src/res/ext/waxholmRatV2_0.json b/src/res/ext/waxholmRatV2_0.json
index a6cd785fe..8c07984a4 100644
--- a/src/res/ext/waxholmRatV2_0.json
+++ b/src/res/ext/waxholmRatV2_0.json
@@ -13,6 +13,8 @@
"parcellations": [
{
"ngId": "WHS_SD_rat_atlas_v4_beta",
+ "@id": "juelich/iav/atlas/v1.0.0/9",
+ "fullId": "juelich/iav/atlas/v1.0.0/9",
"type": "parcellation",
"name": "Waxholm Space rat brain atlas v4 beta",
"regions": [
diff --git a/src/services/state/viewerState.store.helper.ts b/src/services/state/viewerState.store.helper.ts
index 16ee0b763..307ea047f 100644
--- a/src/services/state/viewerState.store.helper.ts
+++ b/src/services/state/viewerState.store.helper.ts
@@ -1,6 +1,6 @@
// TODO merge with viewerstate.store.ts when refactor is done
-import { createReducer, on, ActionReducer, createSelector, Store, select } from "@ngrx/store";
-import { generalApplyState } from "../stateStore.helper";
+import { createReducer, on, ActionReducer, Store, select } from "@ngrx/store";
+import { generalActionError, generalApplyState } from "../stateStore.helper";
import { Effect, Actions, ofType } from "@ngrx/effects";
import { Observable } from "rxjs";
import { withLatestFrom, map } from "rxjs/operators";
@@ -112,11 +112,26 @@ export class ViewerStateHelperEffect{
@Effect()
selectParcellationWithId$: Observable<any> = this.actions$.pipe(
ofType(viewerStateRemoveAdditionalLayer.type),
- withLatestFrom(this.store$.pipe(
- select(viewerStateGetSelectedAtlas)
- )),
- map(([ { payload }, selectedAtlas ]) => {
- const baseLayer = selectedAtlas['parcellations'].find(p => p['baseLayer'])
+ withLatestFrom(
+ this.store$.pipe(
+ select(viewerStateGetSelectedAtlas)
+ ),
+ this.store$.pipe(
+ select(viewerStateSelectedTemplateSelector)
+ )
+ ),
+ map(([ { payload }, selectedAtlas, selectedTemplate ]) => {
+ const tmpl = selectedAtlas['templateSpaces'].find(t => t['@id'] === selectedTemplate['@id'])
+ if (!tmpl) {
+ return generalActionError({
+ message: `templateSpace with id ${selectedTemplate['@id']} cannot be found in atlas with id ${selectedAtlas['@id']}`
+ })
+ }
+
+ const eligibleParcIdSet = new Set(
+ tmpl.availableIn.map(p => p['@id'])
+ )
+ const baseLayer = selectedAtlas['parcellations'].find(fullP => fullP['baseLayer'] && eligibleParcIdSet.has(fullP['@id']))
return viewerStateHelperSelectParcellationWithId({ payload: baseLayer })
})
)
diff --git a/src/ui/atlasLayerSelector/atlasLayerSelector.template.html b/src/ui/atlasLayerSelector/atlasLayerSelector.template.html
index c3e55596b..8e1293981 100644
--- a/src/ui/atlasLayerSelector/atlasLayerSelector.template.html
+++ b/src/ui/atlasLayerSelector/atlasLayerSelector.template.html
@@ -171,12 +171,11 @@
hasBackdrop="false">
<ng-template matMenuContent let-layerGroupItems="layerGroupItems">
-
- <div iav-stop="click"
- class="d-flex flex-column align-items-center"
+ <mat-grid-list cols="1"
+ rowHeight="1:1"
+ iav-stop="click"
(iav-outsideClick)="collapseExpandedGroup()">
-
- <div class="single-column-tile" *ngFor="let layer of layerGroupItems">
+ <mat-grid-tile *ngFor="let layer of layerGroupItems">
<ng-container *ngTemplateOutlet="tileTmpl; context: {
tileSrc: layer,
@@ -186,7 +185,8 @@
} ">
</ng-container>
- </div>
- </div>
+ </mat-grid-tile>
+ </mat-grid-list>
+
</ng-template>
</mat-menu>
--
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