Merge pull request #1501 from FZJ-INM1-BDA/staging

2.14.24

Author: AhmetNSimsek

.prepare_release.mjs

@@ -96,7 +96,7 @@ async function updateCodemeta(version){
   // getMonth returns index 0 month...
   // see https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Date/getMonth
   const MM = (date.getMonth() + 1).toString().padStart(2, "0")
-  const DD = date.getDate().toString()
+  const DD = date.getDate().toString().padStart(2, "0")
 
   codemetaContent["dateModified"] = `${YYYY}-${MM}-${DD}`
   await writeFile(pathToCodemeta, JSON.stringify(codemetaContent, null, 4), "utf-8")

.sop/DEPLOYMENT.md

@@ -0,0 +1,26 @@
+# Deployment
+
+This document outline the standard operating procedure of how to rollout a new release on ebrains infrastructure.
+
+## Requirement
+
+node v20+
+
+Go to https://docker-registry.ebrains.eu/harbor/projects/28/summary , and ensure sufficient disk space (> 1GB). If insufficient:
+
+- `siibra/siibra-explorer` namespace: `2.*.*` that is not the latest can be deleted
+- `siibra/siibra-api` namespace: `0.3.*[-worker|-worker-v4|server]` that is not the latest can be deleted
+- above, any untagged image can be deleted
+- if unsure, ask Xiao 
+
+(optional) Ensure siibra-api `-rc` prerelease action completes without error. Ensure in `src/atlasComponents/sapi/sapi.service.ts`, `export const EXPECTED_SIIBRA_API_VERSION = ''` is set to the expected siibra-api version.
+
+## Steps
+
+0. Commit any changes. (Run `npm prepare-release` if necessary) push to staging/branch and PR and merge to staging.
+
+1. Raise PR from staging to master, ensure all check passes
+
+2. Go through the checklist generated by github-bot. This is a manual process, and is meant to take awhile. Ensure all passes.
+
+3. (if siibra-api is also updated) release siibra-api first. When all actions passes, merge staging -> master. 

codemeta.json

@@ -91,7 +91,7 @@
     ],
     "codeRepository": "git+https://github.com/fzj-inm1-bda/siibra-explorer.git",
     "dateCreated": "2024-08-28",
-    "dateModified": "2025-08-20",
+    "dateModified": "2025-09-09",
     "datePublished": "2019-04-26",
     "description": "`siibra-explorer` is a browser based 3D viewer for exploring brain atlases that cover different spatial resolutions and modalities. It is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometers. ",
     "license": "https://spdx.org/licenses/Apache-2.0",
@@ -100,9 +100,9 @@
         "python 3",
         "typescript"
     ],
-    "schema:releaseNotes": "# v2.14.23\n\n## Feature\n\n- show messages when some error occurs (e.g. propagate region selection, spatial transformation)\n- enable von economo atlas\n- enable api select template/parcellation\n- add warning to users outside EU about perf implications\n- (experimental) enable light/dark theme toggling\n\n## Bugfixes\n\n- drag drop JSON pointcloud now checks selected template, and use the appropriate transform\n\n## Behind the scene\n\n- disentangle maps, propagate selected region when change parcellations\n",
+    "schema:releaseNotes": "# v2.14.24\n\n## Feature\n\n- Selecting region will now navigate to the region's centroid\n- Add warning text when warping, region deselection and/or when cortical layers is selected\n\n## Behind the scene\n\n- Fix prepare_release script\n- Added SOP for ebrains deployment\n\n",
     "runtimePlatform": "docker",
-    "version": "2.14.23",
+    "version": "2.14.24",
     "contIntegration": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions",
     "codemeta:continuousIntegration": {
         "id": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions"

docs/releases/v2.14.24.md

@@ -0,0 +1,12 @@
+# v2.14.24
+
+## Feature
+
+- Selecting region will now navigate to the region's centroid
+- Add warning text when warping, region deselection and/or when cortical layers is selected
+
+## Behind the scene
+
+- Fix prepare_release script
+- Added SOP for ebrains deployment
+

mkdocs.yml

@@ -46,6 +46,7 @@ nav:
     - Plugin API: "advanced/api/README.md"
 
   - Release notes:
+    - v2.14.24: 'releases/v2.14.24.md'
     - v2.14.23: 'releases/v2.14.23.md'
     - v2.14.22: 'releases/v2.14.22.md'
     - v2.14.21: 'releases/v2.14.21.md'

package.json

@@ -1,6 +1,6 @@
 {
   "name": "siibra-explorer",
-  "version": "2.14.23",
+  "version": "2.14.24",
   "description": "siibra-explorer - explore brain atlases. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
   "scripts": {
     "lint": "eslint src --ext .ts",

src/atlasComponents/sapi/sapi.service.ts

@@ -19,7 +19,7 @@ export const useViewer = {
 } as const
 
 export const SIIBRA_API_VERSION_HEADER_KEY='x-siibra-api-version'
-export const EXPECTED_SIIBRA_API_VERSION = '0.3.28'
+export const EXPECTED_SIIBRA_API_VERSION = '0.3.29'
 
 type PaginatedResponse<T> = {
   items: T[]

src/state/atlasSelection/effects.ts

@@ -1,13 +1,13 @@
 import { Component, Inject, Injectable, InjectionToken, Injector } from "@angular/core";
 import { Actions, createEffect, ofType } from "@ngrx/effects";
-import { combineLatest, concat, EMPTY, forkJoin, from, NEVER, Observable, of, throwError, TimeoutError } from "rxjs";
+import { combineLatest, concat, forkJoin, from, NEVER, Observable, of, throwError, TimeoutError } from "rxjs";
 import { catchError, debounceTime, distinctUntilChanged, filter, map, mapTo, switchMap, take, timeout, withLatestFrom } from "rxjs/operators";
 import { IDS, SAPI } from "src/atlasComponents/sapi";
 import * as mainActions from "../actions"
 import { select, Store } from "@ngrx/store";
 import { selectors, actions, fromRootStore } from '.'
 import { AtlasSelectionState } from "./const"
-import { atlasAppearance, atlasSelection, generalActions, userPreference } from "..";
+import { atlasAppearance, atlasSelection, generalActions } from "..";
 
 import { InterSpaceCoordXformSvc } from "src/atlasComponents/sapi/core/space/interSpaceCoordXform.service";
 import { SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate } from "src/atlasComponents/sapi/sxplrTypes";
@@ -75,6 +75,20 @@ function sortParc(parcs: SxplrParcellation[]) {
   ]
 }
 
+const SPATIAL_TRANSFORM_SRC = "SPATIAL_TRANSFORM_SRC"
+const SPATIAL_TRANSFORM_RESULT = "SPATIAL_TRANSFORM_RESULT"
+const CORTICAL_LAYERS_WARNING = "CORTICAL_LAYERS_WARNING"
+const REGION_DESELECTED_WARNING = "REGION_DESELECTED_WARNING"
+
+type TPSelectPostHookOptions = {
+  [SPATIAL_TRANSFORM_SRC]?: number[]
+  [SPATIAL_TRANSFORM_RESULT]?: "failed" | "succeeded"
+  [CORTICAL_LAYERS_WARNING]?: string
+  [REGION_DESELECTED_WARNING]?: string
+}
+
+type TPSelectPostHook = Partial<AtlasSelectionState> & { options?: TPSelectPostHookOptions }
+
 @Injectable()
 export class Effect {
 
@@ -96,7 +110,7 @@ export class Effect {
     )
   }
 
-  onTemplateParcSelectionPostHook: ((arg: OnTmplParcHookArg) => Observable<Partial<AtlasSelectionState>>)[] = [
+  onTemplateParcSelectionPostHook: ((arg: OnTmplParcHookArg) => Observable<TPSelectPostHook>)[] = [
     /**
      * This hook gets the region associated with the selected parcellation and template,
      * and then set selectedParcellationAllRegions to it
@@ -130,27 +144,34 @@ export class Effect {
         switchMap(navigation => 
           /**
            * if either space name is undefined, return default state for navigation
+           * else if space name is the same, skip trying to transform
            */
-          !prevSpcName || !currSpcName
+          !prevSpcName || !currSpcName || prevSpcName === currSpcName
           ? of({ navigation })
           : this.interSpaceCoordXformSvc.transform(prevSpcName, currSpcName, navigation.position as [number, number, number]).pipe(
             map(value => {
+              const common: TPSelectPostHookOptions = {
+                [SPATIAL_TRANSFORM_SRC]: navigation.position
+              }
               if (value.status === "error") {
-                this.sxplrSnackBarSvc.open({
-                  message: `spatial transformation failed: ${value.statusText}. Using default navigation`,
-                  
-                  // TODO switch to maticon when material icon css is added
-                  // maticon: "warning"
-                  icon: "fas fa-exclamation-triangle",
-                })
-                return { navigation: null }
+                return {
+                  navigation: null,
+                  options: {
+                    [SPATIAL_TRANSFORM_RESULT]: 'failed',
+                    ...common,
+                  }
+                } as TPSelectPostHook
               }
               return {
                 navigation: {
                   ...navigation,
                   position: value.result,
+                },
+                options: {
+                  SPATIAL_TRANSFORM_RESULT: 'succeeded',
+                  ...common,
                 }
-              } as Partial<AtlasSelectionState>
+              } as TPSelectPostHook
             })
           )
         )
@@ -159,15 +180,11 @@ export class Effect {
     ({ current, previous }) => {
       const prevParcId = previous?.parcellation?.id
       const currentParcId = current?.parcellation?.id
+      const options: Record<string, string> = {}
       if (currentParcId !== prevParcId && currentParcId === IDS.PARCELLATION.CORTICAL_LAYERS) {
-        this.sxplrSnackBarSvc.open({
-          message: `Regional inaccuracies in the automated computation of cortical layers may occur due to limitations in the available training data and algorithm. Regions that deviate from the expected canonical isocortical structure should be examined with caution.`,
-          // TODO switch to maticon when material icon css is added
-          // maticon: "warning"
-          icon: "fas fa-exclamation-triangle",
-        })
+        options[CORTICAL_LAYERS_WARNING] = "Regional inaccuracies in the automated computation of cortical layers may occur due to limitations in the available training data and algorithm. Regions that deviate from the expected canonical isocortical structure should be examined with caution."
       }
-      return of({})
+      return of({ options })
     }
   ]
 
@@ -349,16 +366,6 @@ export class Effect {
             }
           }
           return from(prAskUser()).pipe(
-            switchMap(val => {
-              /** user cancelled */
-              if (!val) {
-                return of(null)
-              }
-              const { atlas, parcellation, template } = val
-              return of({
-                atlas, parcellation, template
-              })
-            }),
             switchMap(current => {
               if (!current) {
                 return of(
@@ -376,29 +383,51 @@ export class Effect {
                     selectedParcellation: current.parcellation,
                     selectedTemplate: current.template
                   }
+                  let talliedOptions: TPSelectPostHookOptions = {}
                   for (const partial of partialState){
+                    const { options, ...rest } = partial
                     state = {
                       ...state,
-                      ...partial,
+                      ...rest,
+                    }
+                    talliedOptions = {
+                      ...talliedOptions,
+                      ...options,
                     }
                   }
 
                   state.selectedRegions = []
                   if (!!regionId) {
                     const selectedRegions = (state.selectedParcellationAllRegions || []).filter(r => r.name === regionId)
                     if (selectedRegions.length === 0) {
-                      
-                      this.sxplrSnackBarSvc.open({
-                        message: `Previously selected region \`${regionId}\` not found in the currently selected parcellation \`${state.selectedParcellation?.name}\`. Region selections were cleared.`,
-                        useMarkdown: true,
-                        // TODO switch to maticon when material icon css is added
-                        // maticon: "warning"
-                        icon: "fas fa-exclamation-triangle",
-                      })
+                      talliedOptions[REGION_DESELECTED_WARNING] = regionId
                     }
                     state.selectedRegions = selectedRegions
                   }
-                  
+
+                  const warningMarkdowns = []
+                  if (talliedOptions[SPATIAL_TRANSFORM_SRC] && talliedOptions[SPATIAL_TRANSFORM_RESULT]) {
+                    let text = `Due to the change of reference space, previous navigation location \`${talliedOptions[SPATIAL_TRANSFORM_SRC].map(v => (v/1e6).toFixed(2) + "mm").join(", ")}\` in \`${template.name}\` `
+                    if (talliedOptions[SPATIAL_TRANSFORM_RESULT] === "succeeded") {
+                      text += `was warped to \`${(state?.navigation?.position || [0, 0, 0]).map(v => (v/1e6).toFixed(2) + "mm").join(", ")}\` in \`${state?.selectedTemplate?.name}\``
+                    } else {
+                      text += `was attempted to be warped to \`${state?.selectedTemplate?.name}\`, but was unsuccessful. The navigation was reset to \`0, 0, 0\``
+                    }
+                    warningMarkdowns.push(text)
+                  }
+                  if (talliedOptions[CORTICAL_LAYERS_WARNING]) {
+                    warningMarkdowns.push(talliedOptions[CORTICAL_LAYERS_WARNING])
+                  }
+                  if (talliedOptions[REGION_DESELECTED_WARNING]) {
+                    warningMarkdowns.push(`Due to the change of reference parcellation, previously selected region \`${talliedOptions[REGION_DESELECTED_WARNING]}\` is not available. Therefore, region selection has been reset.`)
+                  }
+                  if (warningMarkdowns.length > 0) {
+                    this.sxplrSnackBarSvc.open({
+                      message: warningMarkdowns.join(`\n\n---\n\n`),
+                      useMarkdown: true,
+                      icon: "fas fa-info"
+                    })
+                  }
                   return actions.setAtlasSelectionState(state)
                 })
               )
@@ -540,39 +569,31 @@ export class Effect {
     })
   ))
 
-  onRegionSelection = createEffect(() => this.store.pipe(
-    select(userPreference.selectors.showExperimental),
-    switchMap(flag => {
-      if (!flag) {
-        return EMPTY
-      }
-      return this.action.pipe(
-        ofType(actions.selectRegion),
-        map(({ region }) => {
-          
-          if (region) {
-            this.onNavigateToRegion.pipe(
-              take(1)
-            ).subscribe(() => {
-              this.sxplrOverlaySvc.close()
-            })
+  onRegionSelectionNavigateToCentroid = createEffect(() => this.action.pipe(
+    ofType(actions.selectRegion),
+    map(({ region }) => {
+      
+      if (region) {
+        this.onNavigateToRegion.pipe(
+          take(1)
+        ).subscribe(() => {
+          this.sxplrOverlaySvc.close()
+        })
 
-            const injector = Injector.create({
-              providers: [
-                {
-                  provide: REGION_LOADING_TOKEN,
-                  useValue: { region } as RegionLoadingCfg
-                }
-              ]
-            })
-            const portal = new ComponentPortal(LoadingRegionCmp, null, injector)
-            this.sxplrOverlaySvc.openPortal(portal)
-            this.store.dispatch(
-              actions.navigateToRegion({ region, timeout: REGION_LOADING_TIMEOUT })
-            )
-          }
+        const injector = Injector.create({
+          providers: [
+            {
+              provide: REGION_LOADING_TOKEN,
+              useValue: { region } as RegionLoadingCfg
+            }
+          ]
         })
-      )
+        const portal = new ComponentPortal(LoadingRegionCmp, null, injector)
+        this.sxplrOverlaySvc.openPortal(portal)
+        this.store.dispatch(
+          actions.navigateToRegion({ region, timeout: REGION_LOADING_TIMEOUT })
+        )
+      }
     })
   ), { dispatch: false })