From b15998aebc3f9339d7eb9b0d13bf5b8146793a3b Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Mon, 18 Sep 2023 10:34:09 +0200
Subject: [PATCH] fix: annotation in saneurl
---
backend/app/sane_url.py | 14 +++++--
docs/releases/v2.13.2.md | 5 +++
e2e/checklist.md | 3 ++
mkdocs.yml | 1 +
package.json | 2 +-
.../annotations/annotation.service.ts | 7 ++++
.../userAnnotations/tools/service.ts | 42 +++++++++++--------
src/util/fn.ts | 15 +++++++
.../layerCtrl.service/layerCtrl.service.ts | 18 ++++++++
.../layerCtrl.service/layerCtrl.util.ts | 7 ++++
.../nehubaViewer/nehubaViewer.component.ts | 10 ++++-
.../nehubaViewerGlue.component.ts | 6 ++-
12 files changed, 105 insertions(+), 25 deletions(-)
create mode 100644 docs/releases/v2.13.2.md
diff --git a/backend/app/sane_url.py b/backend/app/sane_url.py
index 947466933..dc4a4e347 100644
--- a/backend/app/sane_url.py
+++ b/backend/app/sane_url.py
@@ -4,7 +4,7 @@ from fastapi.exceptions import HTTPException
from authlib.integrations.requests_client import OAuth2Session
import requests
import json
-from typing import Union, Dict, Optional
+from typing import Union, Dict, Optional, Any
import time
from io import StringIO
from pydantic import BaseModel
@@ -126,11 +126,19 @@ data_proxy_store = SaneUrlDPStore()
@router.get("/{short_id:str}")
async def get_short(short_id:str, request: Request):
try:
- existing_json = data_proxy_store.get(short_id)
+ existing_json: Dict[str, Any] = data_proxy_store.get(short_id)
accept = request.headers.get("Accept", "")
if "text/html" in accept:
hashed_path = existing_json.get("hashPath")
- return RedirectResponse(f"{HOST_PATHNAME}/#{hashed_path}")
+ extra_routes = []
+ for key in existing_json:
+ if key.startswith("x-"):
+ extra_routes.append(f"{key}:{short_id}")
+ continue
+
+ extra_routes_str = "" if len(extra_routes) == 0 else ("/" + "/".join(extra_routes))
+
+ return RedirectResponse(f"{HOST_PATHNAME}/#{hashed_path}{extra_routes_str}")
return JSONResponse(existing_json)
except DataproxyStore.NotFound as e:
raise HTTPException(404, str(e))
diff --git a/docs/releases/v2.13.2.md b/docs/releases/v2.13.2.md
new file mode 100644
index 000000000..d0fe9ede6
--- /dev/null
+++ b/docs/releases/v2.13.2.md
@@ -0,0 +1,5 @@
+# v2.13.2
+
+## Bugfixes
+
+- fixed displaying annotation in `saneurl`
diff --git a/e2e/checklist.md b/e2e/checklist.md
index 5e740efa8..8378541a0 100644
--- a/e2e/checklist.md
+++ b/e2e/checklist.md
@@ -72,10 +72,13 @@
- [ ] [saneUrl](https://atlases.ebrains.eu/viewer-staging/saneUrl/whs4) redirects to waxholm v4
- [ ] [saneUrl](https://atlases.ebrains.eu/viewer-staging/saneUrl/allen2017) redirects to allen 2017
- [ ] [saneUrl](https://atlases.ebrains.eu/viewer-staging/saneUrl/mebrains) redirects to monkey
+- [ ] [saneUrl](https://atlases.ebrains.eu/viewer-staging/saneUrl/stnr) redirects to URL that contains annotations
+
## VIP URL
- [ ] [vipUrl](https://atlases.ebrains.eu/viewer-staging/human) redirects to human mni152
- [ ] [vipUrl](https://atlases.ebrains.eu/viewer-staging/monkey) redirects mebrains
- [ ] [vipUrl](https://atlases.ebrains.eu/viewer-staging/rat) redirects to waxholm v4
- [ ] [vipUrl](https://atlases.ebrains.eu/viewer-staging/mouse) redirects allen mouse 2017
+
## plugins
- [ ] jugex plugin works
diff --git a/mkdocs.yml b/mkdocs.yml
index da0c7cd79..af8c5c51f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -33,6 +33,7 @@ nav:
- Fetching datasets: 'advanced/datasets.md'
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
+ - v2.13.2: 'releases/v2.13.2.md'
- v2.13.1: 'releases/v2.13.1.md'
- v2.13.0: 'releases/v2.13.0.md'
- v2.12.5: 'releases/v2.12.5.md'
diff --git a/package.json b/package.json
index 4a5fc8a31..8ad925aa3 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "siibra-explorer",
- "version": "2.13.1",
+ "version": "2.13.2",
"description": "siibra-explorer - explore brain atlases. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
"scripts": {
"lint": "eslint src --ext .ts",
diff --git a/src/atlasComponents/annotations/annotation.service.ts b/src/atlasComponents/annotations/annotation.service.ts
index d133671c3..fd19915d2 100644
--- a/src/atlasComponents/annotations/annotation.service.ts
+++ b/src/atlasComponents/annotations/annotation.service.ts
@@ -2,6 +2,7 @@ import { BehaviorSubject, Observable } from "rxjs";
import { distinctUntilChanged } from "rxjs/operators";
import { getUuid, waitFor } from "src/util/fn";
import { PeriodicSvc } from "src/util/periodic.service";
+import { NehubaLayerControlService } from "src/viewerModule/nehuba/layerCtrl.service";
export type TNgAnnotationEv = {
pickedAnnotationId: string
@@ -54,6 +55,10 @@ interface NgAnnotationLayer {
registerDisposer(fn: () => void): void
}
setVisible(flag: boolean): void
+ layerChanged: {
+ add(cb: () => void): void
+ }
+ visible: boolean
}
export class AnnotationLayer {
@@ -109,11 +114,13 @@ export class AnnotationLayer {
this.nglayer.layer.registerDisposer(() => {
this.dispose()
})
+ NehubaLayerControlService.RegisterLayerName(this.name)
}
setVisible(flag: boolean){
this.nglayer && this.nglayer.setVisible(flag)
}
dispose() {
+ NehubaLayerControlService.DeregisterLayerName(this.name)
AnnotationLayer.Map.delete(this.name)
this._onHover.complete()
while(this.onDestroyCb.length > 0) this.onDestroyCb.pop()()
diff --git a/src/atlasComponents/userAnnotations/tools/service.ts b/src/atlasComponents/userAnnotations/tools/service.ts
index 5fa7acf92..f1e2e2689 100644
--- a/src/atlasComponents/userAnnotations/tools/service.ts
+++ b/src/atlasComponents/userAnnotations/tools/service.ts
@@ -2,12 +2,12 @@ import { Injectable, OnDestroy, Type } from "@angular/core";
import { ARIA_LABELS } from 'common/constants'
import { Inject, Optional } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { BehaviorSubject, combineLatest, fromEvent, merge, Observable, of, Subject, Subscription } from "rxjs";
+import { BehaviorSubject, combineLatest, from, fromEvent, merge, Observable, of, Subject, Subscription } from "rxjs";
import {map, switchMap, filter, shareReplay, pairwise, withLatestFrom } from "rxjs/operators";
import { NehubaViewerUnit } from "src/viewerModule/nehuba";
import { NEHUBA_INSTANCE_INJTKN } from "src/viewerModule/nehuba/util";
import { AbsToolClass, ANNOTATION_EVENT_INJ_TOKEN, IAnnotationEvents, IAnnotationGeometry, INgAnnotationTypes, INJ_ANNOT_TARGET, TAnnotationEvent, ClassInterface, TCallbackFunction, TSands, TGeometryJson, TCallback, DESC_TYPE } from "./type";
-import { getExportNehuba, switchMapWaitFor } from "src/util/fn";
+import { getExportNehuba, switchMapWaitFor, retry } from "src/util/fn";
import { Polygon } from "./poly";
import { Line } from "./line";
import { Point } from "./point";
@@ -455,14 +455,13 @@ export class ModularUserAnnotationToolService implements OnDestroy{
store.pipe(
select(atlasSelection.selectors.viewerMode),
withLatestFrom(this.#voxelSize),
- ).subscribe(([viewerMode, voxelSize]) => {
- this.currMode = viewerMode
- if (viewerMode === ModularUserAnnotationToolService.VIEWER_MODE) {
- if (this.annotationLayer) this.annotationLayer.setVisible(true)
- else {
- if (!voxelSize) throw new Error(`voxelSize of ${this.selectedTmpl.id} cannot be found!`)
+ switchMap(([viewerMode, voxelSize]) => from(
+ retry(() => {
if (this.annotationLayer) {
- this.annotationLayer.dispose()
+ return this.annotationLayer
+ }
+ if (!voxelSize) {
+ throw new Error(`voxelSize of ${this.selectedTmpl.id} cannot be found!`)
}
this.annotationLayer = new AnnotationLayer(
ModularUserAnnotationToolService.ANNOTATION_LAYER_NAME,
@@ -479,15 +478,22 @@ export class ModularUserAnnotationToolService implements OnDestroy{
: null
})
})
- /**
- * on template changes, the layer gets lost
- * force redraw annotations if layer needs to be recreated
- */
- this.forcedAnnotationRefresh$.next(null)
- }
- } else {
- if (this.annotationLayer) this.annotationLayer.setVisible(false)
- }
+
+ return this.annotationLayer
+ })
+ ).pipe(
+ map(annotationLayer => ({viewerMode, voxelSize, annotationLayer}))
+ )
+ )
+ ).subscribe(({viewerMode, voxelSize, annotationLayer}) => {
+ this.currMode = viewerMode
+
+ /**
+ * on template changes, the layer gets lost
+ * force redraw annotations if layer needs to be recreated
+ */
+ this.forcedAnnotationRefresh$.next(null)
+ annotationLayer.setVisible(viewerMode === ModularUserAnnotationToolService.VIEWER_MODE)
})
)
diff --git a/src/util/fn.ts b/src/util/fn.ts
index 45a4f4be5..1508dc630 100644
--- a/src/util/fn.ts
+++ b/src/util/fn.ts
@@ -5,6 +5,21 @@ import { filter, mapTo, take } from 'rxjs/operators'
// eslint-disable-next-line @typescript-eslint/no-empty-function
export function noop(){}
+export async function retry<T>(fn: () => T, config={timeout: 1000, retries:3}){
+ let retryNo = 0
+ const { retries, timeout } = config
+ while (retryNo < retries) {
+ retryNo ++
+ try {
+ return await fn()
+ } catch (e) {
+ console.warn(`fn failed, retry after ${timeout} milliseconds`)
+ await (() => new Promise(rs => setTimeout(rs, timeout)))()
+ }
+ }
+ throw new Error(`fn failed ${retries} times, aborting`)
+}
+
export async function getExportNehuba() {
// eslint-disable-next-line no-constant-condition
while (true) {
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index be87e8eee..dffa37da9 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -397,4 +397,22 @@ export class NehubaLayerControlService implements OnDestroy{
]).pipe(
map(([ expectedLayerNames, customLayerNames, pmapName ]) => [...expectedLayerNames, ...customLayerNames, ...pmapName, ...AnnotationLayer.Map.keys()])
)
+
+
+ static ExternalLayerNames = new Set<string>()
+
+ /**
+ * @description Occationally, a layer can be managed by external components. Register the name of such layers so it will be ignored.
+ * @param layername
+ */
+ static RegisterLayerName(layername: string) {
+ NehubaLayerControlService.ExternalLayerNames.add(layername)
+ }
+ /**
+ * @description Once external component is done with the layer, return control back to the service
+ * @param layername
+ */
+ static DeregisterLayerName(layername: string) {
+ NehubaLayerControlService.ExternalLayerNames.delete(layername)
+ }
}
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.util.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.util.ts
index 1e18596e9..d0e9069d3 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.util.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.util.ts
@@ -61,12 +61,19 @@ export type TNgLayerCtrl<T extends keyof INgLayerCtrl> = {
payload: INgLayerCtrl[T]
}
+export interface IExternalLayerCtl {
+ RegisterLayerName(layername: string): void
+ DeregisterLayerName(layername: string): void
+ readonly ExternalLayerNames: Set<string>
+}
+
export const SET_COLORMAP_OBS = new InjectionToken<Observable<IColorMap>>('SET_COLORMAP_OBS')
export const SET_LAYER_VISIBILITY = new InjectionToken<Observable<string[]>>('SET_LAYER_VISIBILITY')
export const SET_SEGMENT_VISIBILITY = new InjectionToken<Observable<string[]>>('SET_SEGMENT_VISIBILITY')
export const NG_LAYER_CONTROL = new InjectionToken<TNgLayerCtrl<keyof INgLayerCtrl>>('NG_LAYER_CONTROL')
export const Z_TRAVERSAL_MULTIPLIER = new InjectionToken<Observable<number>>('Z_TRAVERSAL_MULTIPLIER')
export const CURRENT_TEMPLATE_DIM_INFO = new InjectionToken<Observable<TemplateInfo>>('CURRENT_TEMPLATE_DIM_INFO')
+export const EXTERNAL_LAYER_CONTROL = new InjectionToken<IExternalLayerCtl>("EXTERNAL_LAYER_CONTROL")
export type TemplateInfo = {
transform: number[][]
diff --git a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
index 2a06e3f2d..3bede3ea1 100644
--- a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
@@ -11,7 +11,7 @@ import { IColorMap, SET_COLORMAP_OBS, SET_LAYER_VISIBILITY } from "../layerCtrl.
/**
* import of nehuba js files moved to angular.json
*/
-import { INgLayerCtrl, NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY, TNgLayerCtrl, Z_TRAVERSAL_MULTIPLIER } from "../layerCtrl.service/layerCtrl.util";
+import { EXTERNAL_LAYER_CONTROL, IExternalLayerCtl, INgLayerCtrl, NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY, TNgLayerCtrl, Z_TRAVERSAL_MULTIPLIER } from "../layerCtrl.service/layerCtrl.util";
import { NgCoordinateSpace, Unit } from "../types";
import { PeriodicSvc } from "src/util/periodic.service";
import { ViewerInternalStateSvc, AUTO_ROTATE } from "src/viewerModule/viewerInternalState.service";
@@ -131,6 +131,7 @@ export class NehubaViewerUnit implements OnDestroy {
@Optional() @Inject(SET_SEGMENT_VISIBILITY) private segVis$: Observable<string[]>,
@Optional() @Inject(NG_LAYER_CONTROL) private layerCtrl$: Observable<TNgLayerCtrl<keyof INgLayerCtrl>>,
@Optional() @Inject(Z_TRAVERSAL_MULTIPLIER) multiplier$: Observable<number>,
+ @Optional() @Inject(EXTERNAL_LAYER_CONTROL) private externalLayerCtrl: IExternalLayerCtl,
@Optional() intViewerStateSvc: ViewerInternalStateSvc,
) {
if (multiplier$) {
@@ -261,7 +262,12 @@ export class NehubaViewerUnit implements OnDestroy {
* on switch from freesurfer -> volumetric viewer, race con results in managed layer not necessarily setting layer visible correctly
*/
const managedLayers = this.nehubaViewer.ngviewer.layerManager.managedLayers
- managedLayers.forEach(layer => layer.setVisible(false))
+ managedLayers.forEach(layer => {
+ if (this.externalLayerCtrl && this.externalLayerCtrl.ExternalLayerNames.has(layer.name)) {
+ return
+ }
+ layer.setVisible(false)
+ })
for (const layerName of layerNames) {
const layer = this.nehubaViewer.ngviewer.layerManager.getLayerByName(layerName)
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
index c3bc899bd..1f47b5680 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
@@ -5,7 +5,7 @@ import { distinctUntilChanged } from "rxjs/operators";
import { IViewer, TViewerEvent } from "../../viewer.interface";
import { NehubaMeshService } from "../mesh.service";
import { NehubaLayerControlService, SET_COLORMAP_OBS, SET_LAYER_VISIBILITY } from "../layerCtrl.service";
-import { NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY } from "../layerCtrl.service/layerCtrl.util";
+import { EXTERNAL_LAYER_CONTROL, NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY } from "../layerCtrl.service/layerCtrl.util";
import { SxplrRegion } from "src/atlasComponents/sapi/sxplrTypes";
import { NehubaConfig } from "../config.service";
import { SET_MESHES_TO_LOAD } from "../constants";
@@ -25,6 +25,10 @@ import { atlasSelection, userInteraction } from "src/state";
useFactory: (meshService: NehubaMeshService) => meshService.loadMeshes$,
deps: [ NehubaMeshService ]
},
+ {
+ provide: EXTERNAL_LAYER_CONTROL,
+ useValue: NehubaLayerControlService
+ },
NehubaMeshService,
{
provide: SET_COLORMAP_OBS,
--
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