maint: clarify release ci, also checks code meta

maint: add service meta endpoint
feat: always listen on root
fix: angular material column name
doc: added regression notice
fix: added message when user activates cheat code

.github/workflows/release-ci.yml

@@ -11,9 +11,9 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - run: |
-        MASTER_VERSION=$(git show origin/master:package.json | jq '.version')
-        THIS_VERSION=$(jq '.version' < package.json)
-        test "$MASTER_VERSION" == "$THIS_VERSION" && exit 1 || exit 0
+        MASTER_VERSION=$(git show origin/master:package.json | jq -r '.version')
+        THIS_VERSION=$(jq -r '.version' < package.json)
+        test "$MASTER_VERSION" == "$THIS_VERSION" && exit 1
 
   check_release:
     if: always()
@@ -21,10 +21,8 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - run: |
-        VERSION_NUM=$(jq '.version' < package.json)
-        VERSION_NUM=${VERSION_NUM#\"}
-        VERSION_NUM=${VERSION_NUM%\"}
-        test -f docs/releases/v$VERSION_NUM.md && exit 0 || exit 1
+        VERSION_NUM=$(jq -r '.version' < package.json)
+        test -f docs/releases/v$VERSION_NUM.md || exit 1
   
   release_linked_mkdocs:
     if: always()
@@ -32,11 +30,24 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - run: |
-        VERSION_NUM=$(jq '.version' < package.json)
-        VERSION_NUM=${VERSION_NUM#\"} 
-        VERSION_NUM=${VERSION_NUM%\"} 
+        VERSION_NUM=$(jq -r '.version' < package.json)
         echo "VERSION_NUM: $VERSION_NUM"
         cat mkdocs.yml
         GREP_VERSION_NUM=$(cat mkdocs.yml | grep $VERSION_NUM)
         echo GREP_VERSION_NUM: $GREP_VERSION_NUM
-        test -z "$GREP_VERSION_NUM" && exit 1 || exit 0
\ No newline at end of file
+        test -z "$GREP_VERSION_NUM" && exit 1
+  
+  check_code_meta:
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - run: |
+        VERSION_NUM=$(jq -r '.version' < package.json)
+        CODEMETA_VERSION=$(jq -r '.version' < codemeta.json)
+        test "$VERSION_NUM" == "$CODEMETA_VERSION" && echo "Version matches" || exit 1
+
+        RELEASE_NOTES=$(< docs/releases/v${VERSION_NUM}.md)
+        CODEMETA_RELEASE_NOTES=$(jq -r '.["schema:releaseNotes"]' codemeta.json)
+
+        test "$RELEASE_NOTES" == "$CODEMETA_RELEASE_NOTES" || exit 1

Dockerfile

@@ -59,6 +59,7 @@ WORKDIR /iv-app
 COPY --from=builder /iv/backend .
 RUN pip install -r requirements.txt
 COPY --from=builder /iv/dist/aot /iv/backend/public
+COPY --from=builder /iv/codemeta.json /iv/backend/public/codemeta.json
 
 ENV PATH_TO_PUBLIC=/iv/backend/public
 

backend/app/app.py

 from pathlib import Path
+import json
+
 from fastapi import FastAPI, Request
 from fastapi.responses import RedirectResponse, Response
 from fastapi.staticfiles import StaticFiles
@@ -16,6 +18,7 @@ from app.config import HOST_PATHNAME
 from app.logger import logger
 from app.bkwdcompat import BkwdCompatMW
 from app.version_header import VersionHeaderMW
+from app.const import DOCUMENTATION_URL, INPUT_FORMAT, OUTPUT_FORMAT
 
 app = FastAPI()
 
@@ -25,6 +28,39 @@ ready_flag = False
 def ready():
     return Response(None, 204 if ready_flag else 500)
 
+
+_cached_code_meta = None
+@app.get("/about")
+def about():
+    global _cached_code_meta
+    if _cached_code_meta is None:
+        try:
+            with open(Path(__file__).parent.parent.parent / "codemeta.json", "r") as fp:
+                _cached_code_meta = json.load(fp=fp)
+        except:
+            ...
+    if _cached_code_meta is None:
+        try:
+            with open(Path(PATH_TO_PUBLIC) / "codemeta.json", "r") as fp:
+                _cached_code_meta = json.load(fp=fp)
+        except:
+            ...
+    if _cached_code_meta is None:
+        raise Exception(f"codemeta.json not found, cannot populate service meta")
+    
+    return {
+        "@context": "https://gitlab.ebrains.eu/lauramble/servicemeta/-/raw/main/data/contexts/servicemeta.jsonld",
+        "type": "WebApplication",
+        "author": _cached_code_meta["author"],
+        "dateModified": _cached_code_meta["dateModified"],
+        "documentation": DOCUMENTATION_URL,
+        "name": _cached_code_meta["name"],
+        "version": _cached_code_meta["version"],
+        "inputFormat": INPUT_FORMAT,
+        "outputFormat": OUTPUT_FORMAT
+    }
+
+
 app.add_middleware(SessionMiddleware, secret_key=SESSION_SECRET)
 app.add_middleware(BkwdCompatMW)
 app.add_middleware(VersionHeaderMW)
@@ -56,11 +92,14 @@ app.mount("/", StaticFiles(directory=Path(PATH_TO_PUBLIC)), name="static")
 if HOST_PATHNAME:
     assert HOST_PATHNAME[0] == "/", f"HOST_PATHNAME, if defined, must start with /: {HOST_PATHNAME!r}"
     assert HOST_PATHNAME[-1] != "/", f"HOST_PATHNAME, if defined, must not end with /: {HOST_PATHNAME!r}"
-    logger.info(f"listening on path {HOST_PATHNAME}")
+    logger.info(f"listening on path {HOST_PATHNAME}, also falls back to root")
     _app = app
     app = FastAPI()
     app.mount(HOST_PATHNAME, _app)
 
+    # fallback, also listen on root
+    app.mount("", _app)
+
 ready_flag = True
 
 DO_NOT_LOGS = (

backend/app/const.py

@@ -22,3 +22,8 @@ OVERWRITE_SAPI_ENDPOINT_ATTR = "x-sapi-base-url"
 
 OVERWRITE_SPATIAL_BACKEND_ATTR = "x-spatial-backend-url"
 
+DOCUMENTATION_URL = "https://siibra-explorer.readthedocs.io/en/stable/"
+
+INPUT_FORMAT = ["nifti", "json", "swc"]
+
+OUTPUT_FORMAT = ["json"]

codemeta.json

+{
+    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+    "type": "SoftwareSourceCode",
+    "author": [
+        {
+            "id": "_:author_1",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Forschungszentrum Juelich"
+            },
+            "email": "x.gui@fz-juelich.de",
+            "familyName": "Gui",
+            "givenName": "Xiaoyun"
+        },
+        {
+            "id": "_:author_2",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Forshungszentrum Juelich"
+            },
+            "familyName": "Gogshelidze",
+            "givenName": "Daviti"
+        },
+        {
+            "id": "https://orcid.org/0000-0002-9051-3701",
+            "type": "Person",
+            "affiliation": {
+                "type": "Organization",
+                "name": "Forschungszentrum Juelich"
+            },
+            "email": "t.dickscheid@fz-juelich.de",
+            "familyName": "Dickscheid",
+            "givenName": "Timo"
+        }
+    ],
+    "codeRepository": "git+https://github.com/fzj-inm1-bda/siibra-explorer.git",
+    "dateCreated": "2024-08-28",
+    "dateModified": "2024-08-28",
+    "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",
+    "name": "siibra-explorer",
+    "programmingLanguage": [
+        "python 3",
+        "typescript"
+    ],
+    "schema:releaseNotes": "# v2.14.10\n\n## Bugfix\n\n- Fix deployment scripts\n- Fix region update to updated siibra-api endpoint\n\n## Behind the scenes\n\n- Re-enable siibra-api warning mismatch warning\n- Adapt to siibra-api v0.3.18 point assignment rhetoric\n- Enable cheat code, removing obsolete experimental flags\n",
+    "runtimePlatform": "docker",
+    "version": "2.14.10",
+    "contIntegration": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions",
+    "codemeta:continuousIntegration": {
+        "id": "https://github.com/FZJ-INM1-BDA/siibra-explorer/actions"
+    },
+    "issueTracker": "https://github.com/fzj-inm1-bda/siibra-explorer/issues"
+}

docs/releases/v2.14.10.md

@@ -10,3 +10,9 @@
 - Re-enable siibra-api warning mismatch warning
 - Adapt to siibra-api v0.3.18 point assignment rhetoric
 - Enable cheat code, removing obsolete experimental flags
+- If `HOST_PATHNAME` env is provided, also listens on root path
+- Added servicemeta endpoint
+
+## Known regressions
+
+- Labelled assignment now takes a little longer. Additionally, the assigned value does not match that of the index label. This will be addressed in a future update. (The temporary regression allows for significant performant statistical assignment, as well more accurate label assignment.)

src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.html

@@ -41,6 +41,9 @@
     </ng-template>
 </mat-action-list>
 
+<div class="sxplr-m-2" *ngIf="warningMessage$ | async; let warningMessage">
+    <markdown-dom [markdown]="warningMessage"></markdown-dom>
+</div>
 
 <div class="sxplr-m-2" *ngIf="busy$ | async as busyMessage">
     <spinner-cmp class="sxplr-d-inline-block"></spinner-cmp>
@@ -62,7 +65,7 @@
         matSort
         class="sxplr-w-100"
         #simpleTblSort="matSort"
-        matSortActive="map value"
+        matSortActive="map_value"
         matSortDirection="desc">
         <ng-container matColumnDef="region">
             <th mat-header-cell *matHeaderCellDef mat-sort-header>
@@ -78,7 +81,7 @@
                 </button>
             </td>
         </ng-container>
-        <ng-container matColumnDef="map value">
+        <ng-container matColumnDef="map_value">
             <th mat-header-cell *matHeaderCellDef mat-sort-header>
                 map value
             </th>
@@ -98,7 +101,7 @@
         <table mat-table [dataSource]="df$ | async | dfToDs : comphTableSort"
             matSort
             #comphTableSort="matSort"
-            matSortActive="map value"
+            matSortActive="map_value"
             matSortDirection="desc">
             
             <ng-container matColumnDef="region">

src/atlasComponents/sapiViews/volumes/point-assignment/point-assignment.component.ts

 import { Component, Input, OnDestroy, Output, TemplateRef, EventEmitter } from '@angular/core';
 import { Clipboard, MatDialog, MatDialogRef, MatSnackBar } from 'src/sharedModules/angularMaterial.exports';
 import { BehaviorSubject, EMPTY, Observable, Subscription, combineLatest, concat, of } from 'rxjs';
-import { catchError, map, shareReplay, switchMap, tap } from 'rxjs/operators';
+import { catchError, filter, map, shareReplay, switchMap, take, tap } from 'rxjs/operators';
 import { SAPI, EXPECTED_SIIBRA_API_VERSION } from 'src/atlasComponents/sapi/sapi.service';
 import { SxplrParcellation, SxplrTemplate } from 'src/atlasComponents/sapi/sxplrTypes';
 import { translateRegionName } from 'src/atlasComponents/sapi/translateV3';
@@ -15,6 +15,10 @@ import { atlasSelection } from 'src/state';
 const DOING_PROB_ASGMT = "Performing probabilistic assignment ..."
 const DOING_LABEL_ASGMT = "Probabilistic assignment failed. Performing labelled assignment ..."
 
+const LABELLED_MAP_ASSIGNMENT_REGRESSION = `Labelled point assignment is currently experiencing some regression. For more detail, please visit
+
+[https://siibra-explorer.readthedocs.io/en/stable/releases/v2.14.10/](https://siibra-explorer.readthedocs.io/en/stable/releases/v2.14.10/)`
+
 @Component({
   selector: 'sxplr-point-assignment',
   templateUrl: './point-assignment.component.html',
@@ -24,7 +28,7 @@ export class PointAssignmentComponent implements OnDestroy {
 
   SIMPLE_COLUMNS = [
     "region",
-    "map value",
+    "map_value",
   ]
   
   #busy$ = new BehaviorSubject<string>(null)
@@ -58,6 +62,11 @@ export class PointAssignmentComponent implements OnDestroy {
   @Output()
   clickOnRegionName = new EventEmitter<{ target: string, event: MouseEvent }>()
 
+  warningMessage$ = this.busy$.pipe(
+    filter(busyWith => !!busyWith),
+    map(busyWith => busyWith === DOING_LABEL_ASGMT && LABELLED_MAP_ASSIGNMENT_REGRESSION)
+  )
+
   df$: Observable<PathReturn<"/map/assign">> = combineLatest([
     this.point$,
     this.#parcellation,
@@ -227,5 +236,5 @@ function generateCsv(df: PathReturn<"/map/assign">) {
   return [
     df.columns.map(escapeDoubleQuotes).map(v => `"${v}"`).join(","),
     ...df.data.map(processRow)
-  ].join("\n")
+  ].join("\r\n")
 }

src/atlasComponents/sapiViews/volumes/volumes.module.ts

@@ -7,6 +7,7 @@ import { ZipFilesOutputModule } from 'src/zipFilesOutput/module';
 import { SandsToNumPipe } from "./sandsToNum.pipe"
 import { SapiViewsUtilModule } from '../util';
 import { AngularMaterialModule } from 'src/sharedModules';
+import { MarkdownModule } from 'src/components/markdown';
 
 
 
@@ -22,6 +23,7 @@ import { AngularMaterialModule } from 'src/sharedModules';
     ZipFilesOutputModule,
     SapiViewsUtilModule,
     AngularMaterialModule,
+    MarkdownModule,
   ],
   exports: [
     PointAssignmentComponent

src/experimental/experimental.module.ts

@@ -2,6 +2,7 @@ import { DOCUMENT } from "@angular/common";
 import { APP_INITIALIZER, InjectionToken, NgModule } from "@angular/core";
 import { BehaviorSubject, fromEvent, Observable } from "rxjs";
 import { filter, scan, take } from "rxjs/operators";
+import { MatSnackBar } from "src/sharedModules";
 
 const CODE_DICT = {
   ArrowUp: "ArrowUp",
@@ -41,7 +42,7 @@ const showXmptToggle = new BehaviorSubject<boolean>(false)
   providers: [
     {
       provide: APP_INITIALIZER,
-      useFactory: (document: Document) => {
+      useFactory: (document: Document, snackbar: MatSnackBar) => {
         fromEvent(document, "keydown", { capture: true }).pipe(
           scan((acc, curr: KeyboardEvent) => {
             const key = curr.key
@@ -57,11 +58,12 @@ const showXmptToggle = new BehaviorSubject<boolean>(false)
           take(1)
         ).subscribe(() => {
           showXmptToggle.next(true)
+          snackbar.open(`Cheat mode activated`, "Dismiss", { duration: 5000 })
         })
         return () => Promise.resolve()
       },
       multi: true,
-      deps: [DOCUMENT]
+      deps: [DOCUMENT, MatSnackBar]
     },
     {
       provide: SHOW_EXPERIMENTAL_TOKEN,

src/ui/cookieAgreement/data/info.md

@@ -2,6 +2,8 @@ Siibra explorer uses 'cookies' (text files placed on your computer) to verify lo
 
 Siibra explorer uses at least the following cookies:
 
-- **connect.sid**  verify login details
+- **MATOMO_SESSID**: used by ebrains hosted matomo instance to store whether user opt out of tracking
+- **_pk_id**: used by ebrains hosted matommo instance to identify user 
+- **_pk_sess**: used by ebrains hosted matommo instance to identify user session
 
-To find out more about cookies, including how to determine the cookies that have been set on your computer and how to manage or delete them, visit <www.aboutcookies.org>
\ No newline at end of file
+To find out more about cookies, including how to determine the cookies that have been set on your computer and how to manage or delete them, visit <www.aboutcookies.org>