diff --git a/angular.json b/angular.json
index dcbadb4911f1203a6204541cc20e00b2ec00947b..46d2ba12824d187f38aab94428da75566e9fccee 100644
--- a/angular.json
+++ b/angular.json
@@ -34,7 +34,13 @@
"styles": [
"src/theme.scss",
"src/overwrite.scss",
- "src/extra_styles.css"
+ "src/extra_styles.css",
+
+ {
+ "input": "export-nehuba/dist/min/main.css",
+ "inject": false,
+ "bundleName": "vanillaMain"
+ }
],
"scripts": [{
"input": "worker/worker.js",
diff --git a/common/constants.js b/common/constants.js
index d3fe2b2b308520de3e5e9142d58b681c9dbc2a5a..d3f6f24546090062459459f82f8652db30691244 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -148,6 +148,9 @@ If you do not accept the Terms & Conditions you are not permitted to access or u
REMOVE_FRONTAL_OCTANT_HELPER_TEXT: `Hide the octant facing the user, and overlaying the slice views.`,
AUXMESH_DESC: `Some templates contain auxiliary meshes, which compliment the appearance of the template in the perspective view.`,
+
+ OVERWRITE_SAPI_ENDPOINT_ATTR: `x-sapi-base-url`,
+ DATA_ERROR_ATTR: `data-error`
}
exports.QUICKTOUR_DESC ={
diff --git a/deploy/app.js b/deploy/app.js
index f4b3dcd07ead1a7cad8f3c987db8619c1d16e219..bc3444df3848e83ef16d9e9a8e9e2d3391cbbb58 100644
--- a/deploy/app.js
+++ b/deploy/app.js
@@ -1,4 +1,3 @@
-const fs = require('fs')
const path = require('path')
const express = require('express')
const app = express.Router()
@@ -6,8 +5,7 @@ const session = require('express-session')
const crypto = require('crypto')
const cookieParser = require('cookie-parser')
const bkwdMdl = require('./bkwdCompat')()
-
-const LOCAL_CDN_FLAG = !!process.env.LOCAL_CDN
+const { CONST } = require("../common/constants")
if (process.env.NODE_ENV !== 'production') {
app.use(require('cors')())
@@ -123,36 +121,6 @@ const PUBLIC_PATH = process.env.NODE_ENV === 'production'
*/
app.use('/.well-known', express.static(path.join(__dirname, 'well-known')))
-if (LOCAL_CDN_FLAG) {
- /*
- * TODO setup local cdn for supported libraries map
- */
- const LOCAL_CDN = process.env.LOCAL_CDN
- const CDN_ARRAY = [
- 'https://stackpath.bootstrapcdn.com',
- 'https://use.fontawesome.com',
- 'https://unpkg.com'
- ]
-
- let indexFile
- fs.readFile(path.join(PUBLIC_PATH, 'index.html'), 'utf-8', (err, data) => {
- if (err) throw err
- if (!LOCAL_CDN) {
- indexFile = data
- return
- }
- const regexString = CDN_ARRAY.join('|').replace(/\/|\./g, s => `\\${s}`)
- const regex = new RegExp(regexString, 'gm')
- indexFile = data.replace(regex, LOCAL_CDN)
- })
-
- app.get('/', bkwdMdl, (_req, res) => {
- if (!indexFile) return res.status(404).end()
- res.setHeader('Content-Type', 'text/html; charset=utf-8')
- return res.status(200).send(indexFile)
- })
-}
-
app.use((_req, res, next) => {
res.setHeader('Referrer-Policy', 'origin-when-cross-origin')
next()
@@ -182,23 +150,42 @@ app.get('/', (req, res, next) => {
middelware(req, res, next)
}
-}, bkwdMdl, cookieParser(), (req, res) => {
+}, bkwdMdl, cookieParser(), async (req, res) => {
+ res.setHeader('Content-Type', 'text/html')
+
+ let returnIndex = indexTemplate
+
+ if (!!process.env.LOCAL_CDN) {
+ const CDN_ARRAY = [
+ 'https://stackpath.bootstrapcdn.com',
+ 'https://use.fontawesome.com',
+ 'https://unpkg.com'
+ ]
+
+ const regexString = CDN_ARRAY.join('|').replace(/\/|\./g, s => `\\${s}`)
+ const regex = new RegExp(regexString, 'gm')
+ returnIndex = returnIndex.replace(regex, process.env.LOCAL_CDN)
+ }
const iavError = req.cookies && req.cookies['iav-error']
- res.setHeader('Content-Type', 'text/html')
+ const attributeToAppend = {}
if (iavError) {
res.clearCookie('iav-error', { httpOnly: true, sameSite: 'strict' })
+ attributeToAppend[CONST.DATA_ERROR_ATTR] = iavError
+ }
- const returnTemplate = indexTemplate
- .replace(/\$\$NONCE\$\$/g, res.locals.nonce)
- .replace('<atlas-viewer>', `<atlas-viewer data-error="${iavError.replace(/"/g, '"')}">`)
- res.status(200).send(returnTemplate)
- } else {
- const returnTemplate = indexTemplate
- .replace(/\$\$NONCE\$\$/g, res.locals.nonce)
- res.status(200).send(returnTemplate)
+ if (!!process.env.OVERWRITE_API_ENDPOING) {
+ attributeToAppend[CONST.OVERWRITE_SAPI_ENDPOINT_ATTR] = process.env.OVERWRITE_API_ENDPOING
}
+
+ const attr = Object.entries(attributeToAppend).map(([key, value]) => `${key}="${value.replace(/"/g, '"')}"`).join(" ")
+
+ const returnTemplate = returnIndex
+ .replace(/\$\$NONCE\$\$/g, res.locals.nonce)
+ .replace('<atlas-viewer>', `<atlas-viewer ${attr}>`)
+
+ res.status(200).send(returnTemplate)
})
app.get('/ready', async (req, res) => {
diff --git a/docs/releases/v2.12.0.md b/docs/releases/v2.12.0.md
index ba23e2fa1c0a5e1dc3cdb00fdfef918654e02bf0..99ad15e06c399f56481ee50d135ecb889ae3e1ec 100644
--- a/docs/releases/v2.12.0.md
+++ b/docs/releases/v2.12.0.md
@@ -13,4 +13,5 @@
## Behind the scene
- update spotlight mechanics from in-house to angular CDK
-- Updated neuroglancer/nehuba dependency. This allows volumes with non-rigid affine to be displayed properly.
+- updated neuroglancer/nehuba dependency. This allows volumes with non-rigid affine to be displayed properly.
+- allow siibra-api endpoint to be configured at runtime
diff --git a/src/atlasComponents/sapi/sapi.service.ts b/src/atlasComponents/sapi/sapi.service.ts
index b5aaf5bc4a03501f57dda3e3312240f67b800343..0750c09315d429dee2d64b41680eecdd6288b35a 100644
--- a/src/atlasComponents/sapi/sapi.service.ts
+++ b/src/atlasComponents/sapi/sapi.service.ts
@@ -13,6 +13,7 @@ import {
import { FeatureType, PathReturn, RouteParam, SapiRoute } from "./typeV3";
import { BoundingBox, SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate, VoiFeature, Feature } from "./sxplrTypes";
import { parcBanList, speciesOrder } from "src/util/constants";
+import { CONST } from "common/constants"
export const useViewer = {
THREESURFER: "THREESURFER",
@@ -94,7 +95,12 @@ export class SAPI{
*/
static get BsEndpoint$(): Observable<string> {
if (!!BS_ENDPOINT_CACHED_VALUE) return BS_ENDPOINT_CACHED_VALUE
- const endpoints = environment.SIIBRA_API_ENDPOINTS.split(',')
+ const rootEl = document.querySelector('atlas-viewer')
+ const overwriteSapiUrl = rootEl?.getAttribute(CONST.OVERWRITE_SAPI_ENDPOINT_ATTR)
+
+ const endpoints = overwriteSapiUrl
+ ? [ overwriteSapiUrl ]
+ : environment.SIIBRA_API_ENDPOINTS.split(',')
if (endpoints.length === 0) {
SAPI.ErrorMessage = `No siibra-api endpoint defined!`
return NEVER
diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts
index c28d15f9a80133259294b4de407a543014adcf78..b80a7c4de7fa4836e9916ccff47e5aa228385fdf 100644
--- a/src/atlasViewer/atlasViewer.component.ts
+++ b/src/atlasViewer/atlasViewer.component.ts
@@ -76,11 +76,11 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
@Inject(DARKTHEME) private darktheme$: Observable<boolean>
) {
- const error = this.el.nativeElement.getAttribute('data-error')
+ const error = this.el.nativeElement.getAttribute(CONST.DATA_ERROR_ATTR)
if (error) {
this.snackbar.open(error, 'Dismiss', { duration: 5000 })
- this.el.nativeElement.removeAttribute('data-error')
+ this.el.nativeElement.removeAttribute(CONST.DATA_ERROR_ATTR)
}
}
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
index 7db5392a46b74554df8c9e2db2ab8d5e221ab44b..f5bea95d183a58649bb52caedbd27430cfc2b47c 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.spec.ts
@@ -107,6 +107,10 @@ describe('> mesh.service.ts', () => {
[labelIndex2]: fits2
}
})
+ const mockStore = TestBed.inject(MockStore)
+
+ mockStore.overrideSelector(atlasSelection.selectors.selectedTemplate, {} as any)
+ mockStore.overrideSelector(atlasSelection.selectors.selectedParcellation, {} as any)
})
describe("> auxMesh defined", () => {
diff --git a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.spec.ts b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.spec.ts
index ed281a389241e4a8fbaec5c004557601f2af1aa2..89b3a42f99d93c8222d314784bfa9b6057de5aa1 100644
--- a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.spec.ts
+++ b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.spec.ts
@@ -307,8 +307,10 @@ describe('> nehubaViewer.component.ts', () => {
describe('> # setColorMap', () => {
let nehubaViewerSpy: any
let ngViewerStatechildrenGetSpy = jasmine.createSpy('get')
- let toJsonSpy = jasmine.createSpy('toJsonSpy')
- let restoreStateSpy = jasmine.createSpy('restoreStateSpy')
+ let layersMngerToJsonSpy = jasmine.createSpy('layersMngerToJsonSpy')
+ let posToJsonSpy = jasmine.createSpy('posToJsonSpy')
+ let layerMgerRestoreStateSpy = jasmine.createSpy('layerMgerRestoreStateSpy')
+ let posRestoreStateSpy = jasmine.createSpy("posRestoreStateSpy")
const ngId1 = 'foo-bar'
const ngId2 = 'hello-world'
@@ -326,11 +328,23 @@ describe('> nehubaViewer.component.ts', () => {
}
}
- ngViewerStatechildrenGetSpy.and.returnValue({
- toJSON: toJsonSpy,
- restoreState: restoreStateSpy,
+ ngViewerStatechildrenGetSpy.and.callFake(prop => {
+ if (prop === "position") {
+ return {
+ toJSON: posToJsonSpy,
+ restoreState: posRestoreStateSpy
+ }
+ }
+ if (prop === "layers") {
+ return {
+ toJSON: layersMngerToJsonSpy,
+ restoreState: layerMgerRestoreStateSpy,
+ }
+ }
+ throw new Error(`prop ${prop} is not anticipated`)
})
- toJsonSpy.and.returnValue([{
+ posToJsonSpy.and.returnValue([1.1, 2.2, 3.3])
+ layersMngerToJsonSpy.and.returnValue([{
name: ngId1
}, {
name: ngId2
@@ -338,8 +352,8 @@ describe('> nehubaViewer.component.ts', () => {
})
afterEach(() => {
ngViewerStatechildrenGetSpy.calls.reset()
- toJsonSpy.calls.reset()
- restoreStateSpy.calls.reset()
+ layersMngerToJsonSpy.calls.reset()
+ layerMgerRestoreStateSpy.calls.reset()
})
it('> calls nehubaViewer.restoreState', () => {
const fixture = TestBed.createComponent(NehubaViewerUnit)
@@ -359,7 +373,7 @@ describe('> nehubaViewer.component.ts', () => {
fixture.componentInstance['setColorMap'](mainMap)
- expect(restoreStateSpy).toHaveBeenCalledOnceWith([{
+ expect(layerMgerRestoreStateSpy).toHaveBeenCalledOnceWith([{
name: ngId1,
segmentColors: {
1: rgbToHex([100, 100, 100]),
@@ -372,6 +386,10 @@ describe('> nehubaViewer.component.ts', () => {
2: rgbToHex([20, 20, 20]),
}
}])
+
+ expect(posRestoreStateSpy).toHaveBeenCalledOnceWith(
+ [ 1.1, 2.2, 3.3 ]
+ )
})
})
diff --git a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
index 017187edb71c29fc59bc0dd589790a6dc3bb4e02..0bee1941f311aee0df808e66678299649bcc6128 100644
--- a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
@@ -505,7 +505,6 @@ export class NehubaViewerUnit implements OnDestroy {
...rest,
...(transform ? { transform } : {})
}
- console.log(combined)
viewer.layerManager.addManagedLayer(
viewer.layerSpecification.getLayer(key, combined))
@@ -820,7 +819,14 @@ export class NehubaViewerUnit implements OnDestroy {
*/
}
+ /**
+ * n.b. 2
+ * updating layer colormap seems to also mess up the position ()
+ */
+
const layersManager = this.nehubaViewer.ngviewer.state.children.get("layers")
+ const position = this.nehubaViewer.ngviewer.state.children.get("position")
+ const prevPos = position.toJSON()
const layerJson = layersManager.toJSON()
for (const layer of layerJson) {
if (layer.name in mainDict) {
@@ -828,6 +834,7 @@ export class NehubaViewerUnit implements OnDestroy {
}
}
layersManager.restoreState(layerJson)
+ position.restoreState(prevPos)
this.#triggerMeshLoad$.next(null)
}
}
diff --git a/third_party/vanilla.html b/third_party/vanilla.html
index be223e1e38ab861e649e4c4666e894d0a48c6f8c..5513962d41c1a6cb07e54a164e06a6bae15784f5 100644
--- a/third_party/vanilla.html
+++ b/third_party/vanilla.html
@@ -9,6 +9,7 @@
<script src="main.bundle.js"></script>
<link rel="stylesheet" href="vanilla_styles.css">
<link rel="stylesheet" href="main.css">
+ <link rel="stylesheet" href="vanillaMain.css">
</head>
<body>
<div id="neuroglancer-container"></div>