diff --git a/e2e/src/iv.e2e-spec.js b/e2e/src/iv.e2e-spec.js
new file mode 100644
index 0000000000000000000000000000000000000000..34fdb7c386b2c97e8f1858bd2c7356810bf0d820
--- /dev/null
+++ b/e2e/src/iv.e2e-spec.js
@@ -0,0 +1,98 @@
+const url = 'http://localhost:8081/'
+
+const noErrorLog = require('./noErrorLog')
+const { getSelectedTemplate, getSelectedParcellation } = require('./ivApi')
+const { getSearchParam, wait } = require('./util')
+
+describe('protractor works', () => {
+ it('protractor works', () => {
+ expect(true).toEqual(true)
+ })
+})
+
+describe('Home screen', () => {
+ beforeEach(() => {
+ browser.waitForAngularEnabled(false)
+ browser.get(url)
+ })
+
+ it('get title works', () => {
+ browser.getTitle()
+ .then(title => {
+ expect(title).toEqual('Interactive Atlas Viewer')
+ })
+ .catch(error => {
+ console.error('error', error)
+ })
+
+ browser.executeScript('window.interactiveViewer')
+ .then(result => expect(result).toBeDefined())
+ browser.executeScript('window.viewer')
+ .then(result => expect(result).toBeNull())
+
+ noErrorLog(browser)
+ })
+})
+
+describe('Query param: ', () => {
+
+ it('correctly defined templateSelected and selectedParcellation works', async () => {
+
+ const searchParam = '?templateSelected=MNI+Colin+27&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas'
+ browser.get(url + searchParam)
+ browser.executeScript('window.interactiveViewer').then(result => expect(result).toBeDefined())
+ browser.executeScript('window.viewer').then(result => expect(result).toBeDefined())
+
+ await wait(browser)
+
+ getSelectedTemplate(browser)
+ .then(template => {
+ expect(template.name).toBe('MNI Colin 27')
+ })
+
+ getSelectedParcellation(browser)
+ .then(parcellation => {
+ expect(parcellation.name).toBe('JuBrain Cytoarchitectonic Atlas')
+ })
+
+ noErrorLog(browser)
+ })
+
+ it('correctly defined templateSelected but incorrectly defined selectedParcellation work', async () => {
+ const searchParam = '?templateSelected=MNI+Colin+27&parcellationSelected=NoName'
+ browser.get(url + searchParam)
+
+ await wait(browser)
+
+ getSelectedTemplate(browser)
+ .then(template => {
+ expect(template.name).toBe('MNI Colin 27')
+ })
+ .catch(fail)
+
+ Promise.all([
+ getSelectedTemplate(browser),
+ getSelectedParcellation(browser)
+ ])
+ .then(([template, parcellation]) => {
+ expect(parcellation.name).toBe(template.parcellations[0].name)
+ })
+ .catch(fail)
+
+ noErrorLog(browser)
+ })
+
+ it('incorrectly defined templateSelected should clear searchparam', async () => {
+ const searchParam = '?templateSelected=NoName2&parcellationSelected=NoName'
+ browser.get(url + searchParam)
+
+ await wait(browser)
+
+ getSearchParam(browser)
+ .then(searchParam => {
+ const templateSelected = searchParam.get('templateSelected')
+ expect(templateSelected).toBeNull()
+ })
+ .catch(fail)
+ })
+})
\ No newline at end of file
diff --git a/e2e/src/ivApi.js b/e2e/src/ivApi.js
new file mode 100644
index 0000000000000000000000000000000000000000..825bee506911fff68b5dfd80924b73ed3f83df2f
--- /dev/null
+++ b/e2e/src/ivApi.js
@@ -0,0 +1,11 @@
+exports.getSelectedTemplate = (browser) => new Promise((resolve, reject) => {
+ browser.executeAsyncScript('let sub = window.interactiveViewer.metadata.selectedTemplateBSubject.subscribe(obj => arguments[arguments.length - 1](obj));sub.unsubscribe()')
+ .then(resolve)
+ .catch(reject)
+})
+
+exports.getSelectedParcellation = (browser) => new Promise((resolve, reject) => {
+ browser.executeAsyncScript('let sub = window.interactiveViewer.metadata.selectedParcellationBSubject.subscribe(obj => arguments[arguments.length - 1](obj));sub.unsubscribe()')
+ .then(resolve)
+ .catch(reject)
+})
\ No newline at end of file
diff --git a/e2e/src/niftilayer.e2e-spec.js b/e2e/src/niftilayer.e2e-spec.js
deleted file mode 100644
index 0fab4ed54b424adc59a5b1830f564500a186ca84..0000000000000000000000000000000000000000
--- a/e2e/src/niftilayer.e2e-spec.js
+++ /dev/null
@@ -1,25 +0,0 @@
-const url = 'http://localhost:8080/'
-
-describe('protractor works', () => {
- it('getting title works', () => {
- browser.get(url)
- browser.getTitle().then(function(title){
- expect(title).toBe('Interactive Atlas Viewer')
- browser.executeScript('window.interactiveViewer').then(result => expect(result).toBeDefined())
- browser.executeScript('window.viewer').then(result => expect(result).toBeNull())
- })
- })
-})
-
-describe('URL works', () => {
-
- it('templateSelected existing template works', () => {
-
- const searchParam = '?templateSelected=MNI+Colin+27'
- browser.get(url + searchParam)
- browser.executeScript('window.interactiveViewer').then(result => expect(result).toBeDefined())
- browser.executeScript('window.viewer').then(result => expect(result).toBeDefined())
- browser.executeAsyncScript('window.interactiveViewer.metadata.selectedTemplateBSubject.subscribe(obj => arguments[arguments.length - 1](obj))')
- .then(obj => expect(obj.name).toBe('MNI Colin 27'))
- })
-})
\ No newline at end of file
diff --git a/e2e/src/noErrorLog.js b/e2e/src/noErrorLog.js
new file mode 100644
index 0000000000000000000000000000000000000000..d7bc1ef7dc223d3f66aece5994623fbaea239823
--- /dev/null
+++ b/e2e/src/noErrorLog.js
@@ -0,0 +1,14 @@
+module.exports = (browser) => {
+ if (!browser) {
+ fail('browser not defined')
+ throw new Error('browser not defined')
+ }
+ browser.manage().logs().get('browser')
+ .then(browserLogs => {
+ const errorLogs = browserLogs
+ .filter(log => !(/favicon/.test(log.message)))
+ .filter(log => log.level.value > 900)
+ expect(errorLogs.length).toEqual(0)
+ })
+ .catch(fail)
+}
\ No newline at end of file
diff --git a/e2e/src/util.js b/e2e/src/util.js
new file mode 100644
index 0000000000000000000000000000000000000000..030f2ccad62151ce4392c95704b211d57fb7af43
--- /dev/null
+++ b/e2e/src/util.js
@@ -0,0 +1,20 @@
+const {URLSearchParams} = require('url')
+
+exports.getSearchParam = (browser) => {
+ const script = `
+ const search = window.location.search;
+ return search
+ `
+ return browser.executeScript(script)
+ .then(search => new URLSearchParams(search))
+}
+
+exports.wait = (browser) => new Promise(resolve => {
+
+ /**
+ * TODO figure out how to wait until the select parcellation is populated
+ */
+
+ browser.sleep(1000)
+ .then(resolve)
+})
\ No newline at end of file
diff --git a/package.json b/package.json
index 1ed24602b17406726b4cf9a24183da38b1d1b097..de42925f1316dc751433170342d6ad34e95096c6 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,8 @@
"dev-server-aot": "PRODUCTION=true GIT_HASH=`git log --pretty=format:'%h' --invert-grep --grep=^.ignore -1` webpack-dev-server --config webpack.aot.js",
"dev-server-all-interfaces": "webpack-dev-server --config webpack.dev.js --mode development --hot --host 0.0.0.0",
"serve-plugins": "node src/plugin_examples/server.js",
- "test": "karma start spec/karma.conf.js"
+ "test": "karma start spec/karma.conf.js",
+ "e2e": "protractor e2e/protractor.conf"
},
"keywords": [],
"author": "",
diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts
index 594b28c22891efa9ebff8edd14730d4b3efb1bd8..cc1e6b0bf5c315b7b927c2caf49ec45cbbc3a2a0 100644
--- a/src/atlasViewer/atlasViewer.constantService.service.ts
+++ b/src/atlasViewer/atlasViewer.constantService.service.ts
@@ -55,7 +55,8 @@ export class AtlasViewerConstantsServices{
'res/json/colin.json',
'res/json/MNI152.json',
'res/json/waxholmRatV2_0.json',
- 'res/json/allenMouse.json'
+ 'res/json/allenMouse.json',
+ 'res/json/test.json'
]
/* to be provided by KG in future */
@@ -189,6 +190,14 @@ Interactive atlas viewer requires **webgl2.0**, and the \`EXT_color_buffer_float
raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}">${this.repoUrl}</a>`
}
+ incorrectParcellationNameSearchParam(title) {
+ return `The selected parcellation - ${title} - is not available. The the first parcellation of the template is selected instead.`
+ }
+
+ incorrectTemplateNameSearchParam(title) {
+ return `The selected template - ${title} - is not available.`
+ }
+
private supportEmailAddress = `x.gui@fz-juelich.de`
private repoUrl = `https://github.com/HumanBrainProject/interactive-viewer`
diff --git a/src/atlasViewer/atlasViewer.urlService.service.ts b/src/atlasViewer/atlasViewer.urlService.service.ts
index 9087930a30aea98f5baf1fc04237c202d8241a73..5aa63426f2d52de25b01b7bcf3d5a2a226d8eec6 100644
--- a/src/atlasViewer/atlasViewer.urlService.service.ts
+++ b/src/atlasViewer/atlasViewer.urlService.service.ts
@@ -6,6 +6,7 @@ import { filter, map, scan, distinctUntilChanged, skipWhile, take } from "rxjs/o
import { getActiveColorMapFragmentMain } from "../ui/nehubaContainer/nehubaContainer.component";
import { PluginServices } from "./atlasViewer.pluginService.service";
import { AtlasViewerConstantsServices } from "./atlasViewer.constantService.service";
+import { ToastService } from "src/services/toastService.service";
declare var window
@@ -21,7 +22,8 @@ export class AtlasViewerURLService{
constructor(
private store : Store<ViewerStateInterface>,
private pluginService : PluginServices,
- private constantService:AtlasViewerConstantsServices
+ private constantService:AtlasViewerConstantsServices,
+ private toastService: ToastService
){
this.pluginState$ = this.store.pipe(
@@ -85,28 +87,65 @@ export class AtlasViewerURLService{
/* first, check if any template and parcellations are to be loaded */
const searchedTemplatename = searchparams.get('templateSelected')
const searchedParcellationName = searchparams.get('parcellationSelected')
+
+ if (!searchedTemplatename) {
+ const urlString = window.location.href
+ /**
+ * TODO think of better way of doing this
+ */
+ history.replaceState(null, '', urlString.split('?')[0])
+ return
+ }
const templateToLoad = fetchedTemplates.find(template=>template.name === searchedTemplatename)
- if(!templateToLoad)
+ if (!templateToLoad) {
+ this.toastService.showToast(
+ this.constantService.incorrectTemplateNameSearchParam(searchedTemplatename),
+ {
+ timeout: 5000
+ }
+ )
+ const urlString = window.location.href
+ /**
+ * TODO think of better way of doing this
+ */
+ history.replaceState(null, '', urlString.split('?')[0])
return
- const parcellationToLoad = templateToLoad ?
- templateToLoad.parcellations.find(parcellation=>parcellation.name === searchedParcellationName) :
- templateToLoad.parcellations[0]
+ }
+
+ /**
+ * TODO if search param of either template or parcellation is incorrect, wrong things are searched
+ */
+ const parcellationToLoad = templateToLoad.parcellations.find(parcellation=>parcellation.name === searchedParcellationName)
+
+ if (!parcellationToLoad) {
+ this.toastService.showToast(
+ this.constantService.incorrectParcellationNameSearchParam(searchedParcellationName),
+ {
+ timeout: 5000
+ }
+ )
+ }
this.store.dispatch({
type : NEWVIEWER,
selectTemplate : templateToLoad,
- selectParcellation : parcellationToLoad
+ selectParcellation : parcellationToLoad || templateToLoad.parcellations[0]
})
/* selected regions */
- const labelIndexMap = getLabelIndexMap(parcellationToLoad.regions)
- const selectedRegions = searchparams.get('regionsSelected')
- if(selectedRegions){
- this.store.dispatch({
- type : SELECT_REGIONS,
- selectRegions : selectedRegions.split('_').map(labelIndex=>labelIndexMap.get(Number(labelIndex)))
- })
+ if (parcellationToLoad && parcellationToLoad.regions) {
+ /**
+ * either or both parcellationToLoad and .regions maybe empty
+ */
+ const labelIndexMap = getLabelIndexMap(parcellationToLoad.regions)
+ const selectedRegions = searchparams.get('regionsSelected')
+ if(selectedRegions){
+ this.store.dispatch({
+ type : SELECT_REGIONS,
+ selectRegions : selectedRegions.split('_').map(labelIndex=>labelIndexMap.get(Number(labelIndex)))
+ })
+ }
}
/* now that the parcellation is loaded, load the navigation state */
diff --git a/src/res/cvtLyon.js b/src/res/cvtLyon.js
new file mode 100644
index 0000000000000000000000000000000000000000..073d04bca2c38e6bb48d2f436f1ef00d0da386c4
--- /dev/null
+++ b/src/res/cvtLyon.js
@@ -0,0 +1,23 @@
+const fs = require('fs')
+fs.readFile(
+ './ext/***REMOVED***.json',
+ // './ext/***REMOVED***.json',
+ 'utf-8', (err, data) => {
+ const json = JSON.parse(data)
+ const newFile = json.map(item => {
+ return {
+ name: item.name.replace('DESj', 'item2'),
+ // name: item.name.replace('BATg', 'item1'),
+ templateSpace: item.templateSpace,
+ geometry: item.geometry
+ }
+ })
+
+ fs.writeFile(
+ './raw/exportForOliver/item2.json',
+ // './raw/exportForOliver/item1.json',
+ JSON.stringify(newFile), 'utf-8', err => {
+ if (err) throw err
+ console.log('done')
+ })
+})
\ No newline at end of file
diff --git a/src/res/ext/test.json b/src/res/ext/test.json
new file mode 100644
index 0000000000000000000000000000000000000000..9d9e02858246fb04e3872496b5f22426692d2cba
--- /dev/null
+++ b/src/res/ext/test.json
@@ -0,0 +1,14 @@
+{
+ "name": "test",
+ "type": "template",
+ "species": "Human",
+ "useTheme": "dark",
+ "ngId": "greyscale",
+ "nehubaConfigURL": "res/json/testNehubaConfig.json",
+ "parcellations": [
+ ],
+ "properties": {
+ "name": "test",
+ "description": "test description"
+ }
+}
\ No newline at end of file
diff --git a/src/res/ext/testNehubaConfig.json b/src/res/ext/testNehubaConfig.json
new file mode 100644
index 0000000000000000000000000000000000000000..2a42671d7a955b6300ccd372f1b496d702063cbd
--- /dev/null
+++ b/src/res/ext/testNehubaConfig.json
@@ -0,0 +1,66 @@
+{
+ "globals": {
+ "hideNullImageValues": true,
+ "useNehubaLayout": true,
+ "useNehubaMeshLayer": true,
+ "useCustomSegmentColors": true
+ },
+ "zoomWithoutCtrl": true,
+ "hideNeuroglancerUI": true,
+ "rightClickWithCtrl": true,
+ "rotateAtViewCentre": true,
+ "zoomAtViewCentre": true,
+ "enableMeshLoadingControl": true,
+ "layout": {
+ "useNehubaPerspective": {
+ "fixedZoomPerspectiveSlices": {
+ "sliceViewportWidth": 300,
+ "sliceViewportHeight": 300,
+ "sliceZoom": 724698.1843689409,
+ "sliceViewportSizeMultiplier": 2
+ },
+ "centerToOrigin": true,
+ "mesh": {
+ "removeBasedOnNavigation": true,
+ "flipRemovedOctant": true,
+ "surfaceParcellation": true
+ },
+ "removePerspectiveSlicesBackground": {
+ "mode": "=="
+ },
+ "waitForMesh": true,
+ "drawSubstrates": {
+ "color": [
+ 0.5,
+ 0.5,
+ 1,
+ 0.2
+ ]
+ },
+ "drawZoomLevels": {
+ "cutOff": 150000
+ },
+ "restrictZoomLevel": {
+ "minZoom": 2500000,
+ "maxZoom": 3500000
+ }
+ }
+ },
+ "dataset": {
+ "imageBackground": [
+ 0,
+ 0,
+ 0,
+ 1
+ ],
+ "initialNgState": {
+ "showDefaultAnnotations": false,
+ "layers": {
+ "greyscale": {
+
+ "source": "dvid://http://dvid-dev.humanbrainproject.org:/5b666a3cc19344f29025c65e829f98f2/grayscale"
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/ui/banner/banner.component.ts b/src/ui/banner/banner.component.ts
index 29088073bf540a99ae51db17acc6011576f65127..fc75046e2c26bedc769d8f8624e20543b3bf48f5 100644
--- a/src/ui/banner/banner.component.ts
+++ b/src/ui/banner/banner.component.ts
@@ -132,6 +132,9 @@ export class AtlasBanner implements OnDestroy, OnInit {
}
handleParcellationChange(parcellation) {
+ if (!(parcellation && parcellation.regions)) {
+ return
+ }
this.selectedParcellation = parcellation
this.regionsLabelIndexMap = getLabelIndexMap(parcellation.regions)
}
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts
index 560b8c825f999d20cd209fcd00753b94b5df2bd6..f97f445181d8f8f357c72bbcaabf86b5d5310072 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.ts
@@ -353,6 +353,9 @@ export class NehubaContainer implements OnInit, OnDestroy{
map(state => {
const deepCopiedState = JSON.parse(JSON.stringify(state))
const navigation = deepCopiedState.templateSelected.nehubaConfig.dataset.initialNgState.navigation
+ if (!navigation) {
+ return deepCopiedState
+ }
navigation.zoomFactor = calculateSliceZoomFactor(navigation.zoomFactor)
deepCopiedState.templateSelected.nehubaConfig.dataset.initialNgState.navigation = navigation
return deepCopiedState
@@ -646,6 +649,12 @@ export class NehubaContainer implements OnInit, OnDestroy{
}
private handleParcellation(parcellation:any){
+ /**
+ * parcellaiton may be undefined
+ */
+ if ( !(parcellation && parcellation.regions)) {
+ return
+ }
this.regionsLabelIndexMap = getLabelIndexMap(parcellation.regions)
this.nehubaViewer.regionsLabelIndexMap = this.regionsLabelIndexMap
diff --git a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
index 3d46a0226dab5d2ea445651da46bb03c4d5ceaec..b20c2edb87a12a326546cb1258408859e0dca424 100644
--- a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
+++ b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
@@ -80,9 +80,12 @@ export class NehubaViewerUnit implements OnDestroy{
this.constantService.loadExportNehubaPromise
.then(() => {
- const { sliceZoom, sliceViewportWidth, sliceViewportHeight } = this.config.layout.useNehubaPerspective.fixedZoomPerspectiveSlices
- const dim = Math.min(sliceZoom * sliceViewportWidth, sliceZoom * sliceViewportHeight)
- this._dim = [dim, dim, dim]
+ const fixedZoomPerspectiveSlices = this.config && this.config.layout && this.config.layout.useNehubaPerspective && this.config.layout.useNehubaPerspective.fixedZoomPerspectiveSlices
+ if (fixedZoomPerspectiveSlices) {
+ const { sliceZoom, sliceViewportWidth, sliceViewportHeight } = fixedZoomPerspectiveSlices
+ const dim = Math.min(sliceZoom * sliceViewportWidth, sliceZoom * sliceViewportHeight)
+ this._dim = [dim, dim, dim]
+ }
this.patchNG()
this.loadNehuba()
})
@@ -300,6 +303,7 @@ export class NehubaViewerUnit implements OnDestroy{
loadNehuba(){
this.nehubaViewer = window['export_nehuba'].createNehubaViewer(this.config, (err)=>{
/* print in debug mode */
+ console.log(err)
})
if(this.regionsLabelIndexMap){