Merge pull request #1312 from FZJ-INM1-BDA/dev

v2.11.0 push to staging

.github/workflows/docker_img.yml

@@ -7,7 +7,7 @@ on:
       # changes to .openshift directory... mostly devops config
       - '.openshift/*'
       # docs (docs are built on readthedocs any way)
-      - 'docs/*'
+      - 'docs/**/*'
 
 jobs:
   build-docker-img:
@@ -18,14 +18,22 @@ jobs:
       PRODUCTION: 'true'
       DOCKER_REGISTRY: 'docker-registry.ebrains.eu/siibra/'
 
-      SIIBRA_API_STABLE: 'https://siibra-api-stable.apps.hbp.eu/v3_0,https://siibra-api-stable-ns.apps.hbp.eu/v3_0,https://siibra-api-stable.apps.jsc.hbp.eu/v3_0'
+      SIIBRA_API_STABLE: 'https://siibra-api-stable.apps.hbp.eu/v3_0,https://siibra-api-stable.apps.jsc.hbp.eu/v3_0'
       SIIBRA_API_RC: 'https://siibra-api-rc.apps.hbp.eu/v3_0'
       SIIBRA_API_LATEST: 'https://siibra-api-latest.apps-dev.hbp.eu/v3_0'
 
+      SIIBRA_API_LOCAL: 'http://localhost:10081/v3_0'
+      LOCAL_TAG: 'local-10081'
+
+    strategy:
+      matrix:
+        build: [ 'local', 'prod' ]
 
     steps:
     - uses: actions/checkout@v2
     - name: 'Set matomo env var'
+      # if matrix.build is local, only run if master or dev
+      if: ${{ !(matrix.build == 'local' && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/dev') }} 
       run: |
         echo "Using github.ref: $GITHUB_REF"
 
@@ -52,8 +60,17 @@ jobs:
             echo "SIIBRA_API_ENDPOINTS=${{ env.SIIBRA_API_LATEST }}" >> $GITHUB_ENV
           fi
         fi
+        
+        if [[ "${{ matrix.build }}" == "local" ]]
+        then
+          echo "SIIBRA_API_ENDPOINTS=${{ env.SIIBRA_API_LOCAL }}" >> $GITHUB_ENV
+          echo "MATOMO_URL=" >> $GITHUB_ENV
+          echo "MATOMO_ID=" >> $GITHUB_ENV
+        fi
 
     - name: 'Set version variable & expmt feature flag'
+      # if matrix.build is local, only run if master or dev
+      if: ${{ !(matrix.build == 'local' && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/dev') }} 
       run: |
         if [[ "$GITHUB_REF" == 'refs/heads/master' ]] || [[ "$GITHUB_REF" == 'refs/heads/staging' ]]
         then
@@ -63,8 +80,14 @@ jobs:
           echo "EXPERIMENTAL_FEATURE_FLAG=true" >> $GITHUB_ENV
         fi
     - name: 'Build docker image'
+      # if matrix.build is local, only run if master or dev
+      if: ${{ !(matrix.build == 'local' && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/dev') }} 
       run: |
         DOCKER_BUILT_TAG=${{ env.DOCKER_REGISTRY }}siibra-explorer:$BRANCH_NAME
+        if [[ "${{ matrix.build }}" == "local" ]]
+        then
+          DOCKER_BUILT_TAG="$DOCKER_BUILT_TAG"-${{ env.LOCAL_TAG }}
+        fi
         echo "Building $DOCKER_BUILT_TAG"
         docker build \
           --build-arg MATOMO_URL=$MATOMO_URL \
@@ -77,6 +100,8 @@ jobs:
         echo "DOCKER_BUILT_TAG=$DOCKER_BUILT_TAG" >> $GITHUB_ENV
 
     - name: 'Push to docker registry'
+      # if matrix.build is local, only run if master or dev
+      if: ${{ !(matrix.build == 'local' && github.ref != 'refs/heads/master' && github.ref != 'refs/heads/dev') }} 
       run: |
         echo "Login to docker registry"
         docker login \

.github/workflows/release.yml

@@ -32,6 +32,7 @@ jobs:
       with:
         tag_name: ${{ needs.check-version.outputs.package-version }}
         release_name: Release ${{ needs.check-version.outputs.package-version }}
+        body_path: docs/releases/v${{ needs.check-version.outputs.package-version }}.md
         draft: false
         prerelease: false
         

Dockerfile

@@ -4,7 +4,7 @@ ARG BACKEND_URL
 ENV BACKEND_URL=${BACKEND_URL}
 
 ARG SIIBRA_API_ENDPOINTS
-ENV SIIBRA_API_ENDPOINTS=${SIIBRA_API_ENDPOINTS:-https://siibra-api-stable.apps.hbp.eu/v2_0,https://siibra-api-stable-ns.apps.hbp.eu/v2_0,https://siibra-api-stable.apps.jsc.hbp.eu/v2_0}
+ENV SIIBRA_API_ENDPOINTS=${SIIBRA_API_ENDPOINTS:-https://siibra-api-stable.apps.hbp.eu/v3_0,https://siibra-api-stable.apps.jsc.hbp.eu/v3_0}
 
 ARG STRICT_LOCAL
 ENV STRICT_LOCAL=${STRICT_LOCAL:-false}
@@ -74,7 +74,7 @@ COPY --from=builder /iv/common /common
 # Copy the express server
 COPY --from=builder /iv/deploy .
 
-# Copy built interactive viewer
+# Copy built siibra explorer
 COPY --from=compressor /iv ./public
 
 RUN chown -R node:node /iv-app

README.md

@@ -4,7 +4,7 @@
 [![Documentation Status](https://readthedocs.org/projects/siibra-explorer/badge/?version=latest)](https://siibra-explorer.readthedocs.io/)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
-# siibra-explorer - Interactive viewer for multilevel brain atlases
+# siibra-explorer - Interactive atlas viewer for multilevel brain atlases
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH*
 
@@ -14,11 +14,11 @@ Copyright 2020-2021, Forschungszentrum Jülich GmbH
 
 ## Getting Started
 
-A live version of the Interactive Atlas Viewer is available at [https://atlases.ebrains.eu/viewer/](https://atlases.ebrains.eu/viewer/). This section is useful for developers who would like to develop this project.
+A live version of the siibra explorer is available at [https://atlases.ebrains.eu/viewer/](https://atlases.ebrains.eu/viewer/). This section is useful for developers who would like to develop this project.
 
 ### General information
 
-Interactive atlas viewer is built with [Angular (v13.0)](https://angular.io/), [Bootstrap (v4)](http://getbootstrap.com/), and [fontawesome icons](https://fontawesome.com/). Some other notable packages used are [ngrx/store](https://github.com/ngrx/platform) for state management. 
+Siibra explorer is built with [Angular (v14.0)](https://angular.io/), [Bootstrap (v4)](http://getbootstrap.com/), and [fontawesome icons](https://fontawesome.com/). Some other notable packages used are [ngrx/store](https://github.com/ngrx/platform) for state management. 
 
 Releases newer than [v0.2.9](https://github.com/HumanBrainProject/interactive-viewer/tree/v0.2.9) also uses a nodejs backend, which uses [passportjs](http://www.passportjs.org/) for user authentication, [express](https://expressjs.com/) as a http framework.
 

build_env.md

 # Build-time environment variables
 
-As interactive atlas viewer uses [webpack define plugin](https://webpack.js.org/plugins/define-plugin/), where necessary, the environmental variables are `JSON.stringify`'ed and directly replaced in the code.
+As siibra-explorer uses [webpack define plugin](https://webpack.js.org/plugins/define-plugin/), where necessary, the environmental variables are `JSON.stringify`'ed and directly replaced in the code.
 
 | name | description | default | example |
 | --- | --- | --- | --- |

common/constants.js

@@ -90,7 +90,7 @@
   }
 
   exports.CONST = {
-    KG_TOS: `The interactive viewer queries HBP Knowledge Graph Data Platform ("KG") for published datasets.
+    KG_TOS: `Siibra explorer queries EBRAINS Knowledge Graph Data Platform ("KG") for published datasets.
 
 
 Access to the data and metadata provided through KG requires that you cite and acknowledge said data and metadata according to the Terms and Conditions of the Platform.

common/helpOnePager.md

-# Quickstart
-
-
 | Action | Desktop | Touch devices |
-| --- | --- |
+| --- | --- | --- |
 | Translate / Pan | `[drag]` any of the slice views | `[drag]` any of the slice views |
 | Oblique rotation | `<shift>` + `[drag]` any of the slice views | `[rotate]` any of the slice views |
 | Zoom | `[mousewheel]` | `[pinch zoom]` |
@@ -11,6 +8,8 @@
 | Next 10 slice | `<ctrl>` + `<shift>` + `[mousewheel]` | - |
 | Toggle delineation | `[q]` | - |
 | Toggle cross hair | `[a]` | - |
+| Multiple region select | `<ctrl>` + `[click]` on region | - |
+| Context menu | `[right click]` | - |
 
 ---
 

deploy/README.md

 # Deployment
 
-Latest stable version of interactive atlas viewer is continously deployed to the following URL:
+Latest stable version of siibra explorer is continously deployed to the following URL:
 
 - <https://interactive-viewer.apps.hbp.eu/>
 - <https://atlases.ebrains.eu/viewer/>
 
 ## Dependency monitoring
 
-Interactive atlas viewer interacts with a number of other ebrains services. Monitoring these services contributes to the stability of the webapplication.
+Siibra explorer interacts with a number of other ebrains services. Monitoring these services contributes to the stability of the webapplication.
 
 ### Probability & continuous maps availability
 

deploy/quickstart/index.js

@@ -26,7 +26,7 @@ const getQuickStartMdPr = (async () => {
   <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
   <script src="https://unpkg.com/dompurify@latest/dist/purify.min.js"></script>
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  <title>Interactive Atlas Viewer Quickstart</title>
+  <title>Siibra Explorer Quickstart</title>
   <style>
     .padded { padding: 1.5rem; }
   </style>

docs/develop/deploy_plugin.md

+# Deploy plugin
+
+This section details how plugins can be deployed on ebrains infrastructure (openshift). It should also apply more generally to other infrastructure providers with openshift and/or k8s flavors.
+
+## Prerequisite
+
+- Docker
+- Access to self hosted docker registry (e.g. docker-registry.ebrains.eu) [1]
+- Access to openshift cluster (e.g. okd.hbp.eu)
+- openshift cli `oc` installed [https://github.com/openshift/origin/releases/tag/v3.11.0](https://github.com/openshift/origin/releases/tag/v3.11.0) (for CLI approach)
+
+
+## How
+
+!!! warning
+    This guide assumes the plugin developers are using the template repo provided at [https://github.com/FZJ-INM1-BDA/siibra-toolbox-template](https://github.com/FZJ-INM1-BDA/siibra-toolbox-template), such as [https://github.com/fzj-inm1-bda/siibra-jugex/tree/feat_workerFrontend](https://github.com/fzj-inm1-bda/siibra-jugex/tree/feat_workerFrontend)
+
+!!! info
+    This guide assumes plugin developers successfully tested their plugin locally.
+
+!!! info
+    This guide is suitable for deploying the application for the initial deployment of the application. Documentation on updating of deployed services can be found at [update_plugin_deployment.md](update_plugin_deployment.md)
+
+You can deploy the plugin either via GUI or CLI.
+
+## How (via CLI)
+
+0. (can be skipped if project already created) Goto https://docker-registry.ebrains.eu/ , create a project (hereafter referred to as `<project_name>`). Decide a namespace for your current project, hereafter referred to as `<app_name>`
+
+1. In root working directory, build server image with
+
+    ```sh
+    docker build \
+        -f http.server.dockerfile \
+        -t docker-registry.ebrains.eu/<project_name>/<app_name>:latest-server \
+        .
+    ```
+2. In root working directory, build worker image with
+
+    ```sh
+    docker build \
+        -f http.worker.dockerfile \
+        -t docker-registry.ebrains.eu/<project_name>/<app_name>:latest-worker \
+        .
+    ```
+3. Login to docker registry via CLI
+
+    ```sh
+    docker login -u <USERNAME> -p <PASSWORD> docker-registry.ebrains.eu
+    ```
+
+    !!! info
+        Most docker registry do **not** require you to use your actual password. In docker-registry.ebrains.eu (Harbor), you can obtain a token with auto expiry by clicking your profile > CLI Secret.
+
+4. Push both worker and server images to docker registry
+
+    ```sh
+    docker push docker-registry.ebrains.eu/<project_name>/<app_name>:latest-worker 
+    docker push docker-registry.ebrains.eu/<project_name>/<app_name>:latest-server 
+    ```
+
+5. Login to openshift admin dashboard. (Create a project if you haven't already, hereafter referred to as `<okd_project_name>`). Enter your project by clicking it.
+
+6. Copy `openshift-service-tmpl.yml` to our working directory, or `cd` into this directory
+
+7. Copy the login command via `(top right) [Your Username]` > `Copy Login Command`. Launch a terminal, paste the login command and hit enter.
+
+8. Select the project with `oc project <okd_project_name>`
+
+9. Start the service with 
+    ```sh
+    oc new-app \
+    -f openshift-service-tmpl.yml \
+    -p TOOLBOX_NAME=my_app \
+    -p TOOLBOX_ROUTE=https://my_app_route.apps.hbp.eu \
+    -p TOOLBOX_WORKER_IMAGE=docker-registry.ebrains.eu/<project_name>/<app_name>:latest-worker \
+    -p TOOLBOX_SERVER_IMAGE=docker-registry.ebrains.eu/<project_name>/<app_name>:latest-server
+
+    ```
+
+## How (via GUI)
+
+for 0. - 5. (follow How (via CLI))
+
+6. Deploy a redis instance via GUI:
+    - `(top right) Add to project` > `Deploy Image` > `(radio button) Image Name`
+    - enter `docker-registry.ebrains.eu/monitoring/redis:alpine3.17` in the text field
+    - click `(button) [magnifying glass]`
+    - change or remember the `name` attribute. Hereafter this attribute will be referred to as `<redis_instance_name>`
+    - click `(primary button) Deploy`
+
+7. Deploy the server via GUI:
+
+    - `(top right) Add to project` > `Deploy Image` > `(radio button) Image Name`
+    - enter `docker-registry.ebrains.eu/<project_name>/<app_name>:latest-server` in the text field
+    - click `(button) [magnifying glass]`
+    - under `Environment Variables`, add the following environment variables[2]:
+        - `SIIBRA_TOOLBOX_CELERY_BROKER`=`redis://<redis_instance_name>:6379`
+        - `SIIBRA_TOOLBOX_CELERY_RESULT`=`redis://<redis_instance_name>:6379`
+    - under `Labels`, add the following labels:
+        - `app_role`=`server`
+    - click `(primary button) Deploy`
+
+8. Deploy worker via GUI: repeat 7. but
+    - use `docker-registry.ebrains.eu/<project_name>/<app_name>:latest-worker` as the image
+    - under `Labels` use the following labels:
+        - `app_role`=`worker`
+
+9. Create route (TBD)
+
+
+[1] dockerhub rate/count limits pulls from IP addresses. It is likely that the openshift cluster would easily exceed the quota. 
+[2] you may have to adjust the variable names if you have changed them in your project
+

docs/develop/docker-compose.yml

+version: '3'
+services:
+
+  redis:
+    image: redis
+    restart: always
+
+  siibra-api:
+    depends_on:
+    - redis
+    image: docker-registry.ebrains.eu/siibra/siibra-api:0.3
+    ports:
+    - '10081:5000'
+    environment:
+      REDIS_HOST: redis
+      REDIS_PORT: '6379'
+
+    # comment out below to run siibra with default configuration
+      SIIBRA_USE_CONFIGURATION: /data/siibra-configuration
+    volumes:
+      - </path/to/your/volume/>:/data/siibra-configuration
+    # comment out above to run siibra with default configuration
+
+  siibra-explorer:
+    ports:
+    - '10082:3000'
+    depends_on:
+    - siibra-api
+    image: docker-registry.ebrains.eu/siibra/siibra-explorer:dev-local-10081
+    environment:
+      PORT: '3000'

docs/develop/localsiibraconfig.md

+# Local configuration
+
+This documentation outlines how advanced users can run siibra-explorer targeted at a siibra-configuration directory on their own machine
+
+!!! info
+    siibra-configuration only contain atlas metadata. As a result, the procedure described in this document still requires an active internet connection to function.
+
+## Why
+
+Advanced users may wish to run local instances of siibra-explorer against local siibra-configuration for any number of reasons:
+
+- Data cannot yet be made public
+- Testing the integration of atlas/template/parcellation/features
+- etc
+
+## Prerequisite
+
+- This document assumes the user validated that the configuration is visible in siibra-python (TODO add link).
+- Docker & docker-compose
+
+## Steps
+
+- copy the [docker-compose.yml](docker-compose.yml) file to your working directory
+- replace `</path/to/your/volume/>` with path to siibra-configuration on your machine
+- run `docker-compose up -d`
+- siibra-explorer should be running on http://localhost:10082
+- to teardown, run `docker-compose down`
+
+!!! info
+    First visit of each endpoints of cold started siibra-api often takes very long. The result is cached by by redis middleware, and subsequent visits will result in millisecond response time. If at first the page does not load, try refreshing once every 5 second.
+
+!!! info
+    If you make any changes to the configuration, you will have to teardown and restart.

docs/develop/openshift-service-tmpl.yml

+apiVersion: template.openshift.io/v1
+kind: Template
+labels:
+  template: siibra-toolbox-deploy-template
+metadata:
+  annotations:
+    description: Deploy siibra toolbox
+    tags: python,async
+  name: siibra-toolbox-deploy-template
+objects:
+- apiVersion: v1
+  kind: DeploymentConfig
+  metadata:
+    labels:
+      app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+    name: siibra-toolbox-deploy-${TOOLBOX_NAME}-redis
+      spec:
+    replicas: 3
+    revisionHistoryLimit: 10
+    selector:
+      deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-redis
+    template:
+      metadata:
+        labels:
+          app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+          deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-redis
+      spec:
+        containers:
+        - image: docker-registry.ebrains.eu/monitoring/redis:alpine3.17
+          imagePullPolicy: Always
+          name: redis
+          resources: {}
+          terminationMessagePath: /dev/termination-log
+          terminationMessagePolicy: File
+
+        dnsPolicy: ClusterFirst
+        restartPolicy: Always
+        schedulerName: default-scheduler
+        securityContext: {}
+        terminationGracePeriodSeconds: 30
+
+- apiVersion: v1
+  kind: DeploymentConfig
+  metadata:
+    labels:
+      app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+      app_role: worker
+    name: siibra-toolbox-deploy-${TOOLBOX_NAME}-worker
+  spec:
+    replicas: 3
+    revisionHistoryLimit: 10
+    selector:
+      deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-worker
+    template:
+      metadata:
+        labels:
+          app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+          app_role: worker
+          deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-worker
+      spec:
+        containers:
+        - env:
+          - name: SIIBRA_TOOLBOX_NAME
+            value: ${SIIBRA_TOOLBOX_NAME}
+          - name: SIIBRA_TOOLBOX_CELERY_BROKER
+            value: redis://redis:6379
+          - name: SIIBRA_JURGEX_CELERY_RESULT
+            value: redis://redis:6379
+
+          # see [2]
+          
+          # - name: SIIBRA_TOOLBOX_DATA_DIR
+          #   value: ${SHARED_VOLUME_MOUNT}
+
+          # see [1]
+
+          # - name: SIIBRA_TOOLBOX_LOG_DIR
+          #   value: ${LOG_VOLUME_MOUNT}
+
+          image: ${TOOLBOX_WORKER_IMAGE}
+          imagePullPolicy: Always
+          name: siibra-toolbox-deploy-${TOOLBOX_NAME}-worker
+          resources: {}
+          terminationMessagePath: /dev/termination-log
+          terminationMessagePolicy: File
+          volumeMounts:
+
+          # see [2]
+
+          # - mountPath: ${SHARED_VOLUME_MOUNT}
+          #   name: volume-${SHARED_VOLUME_WORKER_VOLUME_NAME}
+
+          # see [1]
+          
+          # - mountPath: ${LOG_VOLUME_MOUNT}
+          #   name: volume-${LOG_VOLUME_WORKER_VOLUME_NAME}
+
+        dnsPolicy: ClusterFirst
+        restartPolicy: Always
+        schedulerName: default-scheduler
+        securityContext: {}
+        terminationGracePeriodSeconds: 30
+        volumes:
+
+        # see [2]
+        
+        # - name: volume-${SHARED_VOLUME_WORKER_VOLUME_NAME}
+        #   persistentVolumeClaim:
+        #     claimName: toolbox-storage
+
+        
+        # see [1]
+
+        # - name: volume-${LOG_VOLUME_WORKER_VOLUME_NAME}
+        #   persistentVolumeClaim:
+        #     claimName: log-volume
+
+- apiVersion: v1
+  kind: DeploymentConfig
+  metadata:
+    labels:
+      app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+      app_role: server
+    name: siibra-toolbox-deploy-${TOOLBOX_NAME}-server
+  spec:
+    replicas: 1
+    revisionHistoryLimit: 10
+    selector:
+      deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-server
+    template:
+      metadata:
+        labels:
+          app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+          app_role: server
+          deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-server
+      spec:
+        containers:
+        - env:
+          - name: SIIBRA_TOOLBOX_NAME
+            value: ${SIIBRA_TOOLBOX_NAME}
+          - name: SIIBRA_TOOLBOX_CELERY_BROKER
+            value: redis://redis:6379
+          - name: SIIBRA_JURGEX_CELERY_RESULT
+            value: redis://redis:6379
+            
+          # see [2]
+
+          # - name: SIIBRA_TOOLBOX_DATA_DIR
+          #   value: ${SHARED_VOLUME_MOUNT}
+
+          # see [1]
+
+          # - name: SIIBRA_TOOLBOX_LOG_DIR
+          #   value: ${LOG_VOLUME_MOUNT}
+          image: ${TOOLBOX_SERVER_IMAGE}
+          imagePullPolicy: Always
+
+          # You can choose to have a liveness probe.
+          # Here, it is at /ready
+          # uncomment if you have
+
+          # livenessProbe:
+          #   failureThreshold: 3
+          #   httpGet:
+          #     path: /ready
+          #     port: 6001
+          #     scheme: HTTP
+          #   initialDelaySeconds: 10
+          #   periodSeconds: 10
+          #   successThreshold: 1
+          #   timeoutSeconds: 1
+
+          name: siibra-toolbox-deploy-${TOOLBOX_NAME}-server
+          ports:
+          - containerPort: 6001
+            protocol: TCP
+
+            
+
+          # You can choose to have a readiness probe.
+          # Here, it is at /ready
+          # uncomment if you have
+
+          # readinessProbe:
+          #   failureThreshold: 3
+          #   httpGet:
+          #     path: /ready
+          #     port: 6001
+          #     scheme: HTTP
+          #   initialDelaySeconds: 3
+          #   periodSeconds: 10
+          #   successThreshold: 1
+          #   timeoutSeconds: 6
+
+          resources: {}
+          terminationMessagePath: /dev/termination-log
+          terminationMessagePolicy: File
+          volumeMounts:
+          
+          # see [2]
+          
+          # - mountPath: ${SHARED_VOLUME_MOUNT}
+          #   name: volume-${SHARED_VOLUME_SERVER_VOLUME_NAME}
+          
+          # see [1]
+
+          # - mountPath: ${LOG_VOLUME_MOUNT}
+          #   name: volume-${LOG_VOLUME_SERVER_VOLUME_NAME}
+
+        dnsPolicy: ClusterFirst
+        restartPolicy: Always
+        schedulerName: default-scheduler
+        securityContext: {}
+        terminationGracePeriodSeconds: 30
+        volumes:
+
+        # see [2]
+
+        # - name: volume-${SHARED_VOLUME_SERVER_VOLUME_NAME}
+        #   persistentVolumeClaim:
+        #     claimName: toolbox-storage
+
+        # see [1]
+
+        # - name: volume-${LOG_VOLUME_SERVER_VOLUME_NAME}
+        #   persistentVolumeClaim:
+        #     claimName: log-volume
+
+- apiVersion: v1
+  kind: Service
+  metadata:
+    labels:
+      app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+    name: siibra-toolbox-deploy-${TOOLBOX_NAME}-service
+  spec:
+    ports:
+    - name: 6001-tcp
+      port: 6001
+      protocol: TCP
+      targetPort: 6001
+    selector:
+      deploymentconfig: siibra-toolbox-deploy-${TOOLBOX_NAME}-server
+    type: ClusterIP
+
+- apiVersion: v1
+  kind: Route
+  metadata:
+    labels:
+      app: siibra-toolbox-deploy-${TOOLBOX_NAME}
+    name: siibra-toolbox-deploy-${TOOLBOX_NAME}-route
+  spec:
+    host: ${TOOLBOX_ROUTE}
+    port:
+      targetPort: 6001-tcp
+    tls:
+      insecureEdgeTerminationPolicy: Redirect
+      termination: edge
+    to:
+      kind: Service
+      name: siibra-toolbox-deploy-${TOOLBOX_NAME}-service
+      weight: 100
+    wildcardPolicy: None
+
+parameters:
+- description: Toolbox name
+  name: TOOLBOX_NAME
+  required: true
+- description: Toolbox Route, without scheme (i.e. no https?://). should be [a-z0-9][a-z0-9-][a-z0-9].apps(-dev)?.hbp.eu
+  name: TOOLBOX_ROUTE
+  required: true
+- description: Docker image for the worker
+  name: TOOLBOX_WORKER_IMAGE
+  required: true
+- description: Docker image for the server
+  name: TOOLBOX_SERVER_IMAGE
+  required: true
+
+- description: Randomly generated volume name. Do not overwrite
+  from: '[a-z0-9]{8}'
+  generate: expression
+  name: SHARED_VOLUME_SERVER_VOLUME_NAME
+- description: Randomly generated volume name. Do not overwrite
+  from: '[a-z0-9]{8}'
+  generate: expression
+  name: SHARED_VOLUME_WORKER_VOLUME_NAME
+- description: Randomly generated volume name. Do not overwrite
+  from: '[a-z0-9]{8}'
+  generate: expression
+  name: LOG_VOLUME_SERVER_VOLUME_NAME
+- description: Path where shared volume will be mounted. Applies to both server and
+    worker pods.
+  name: SHARED_VOLUME_MOUNT
+  value: /siibra_toolbox_volume
+- description: Randomly generated volume name. Do not overwrite
+  from: '[a-z0-9]{8}'
+  generate: expression
+  name: LOG_VOLUME_WORKER_VOLUME_NAME
+- description: Randomly generated volume name. Do not overwrite
+  from: '[a-z0-9]{8}'
+  generate: expression
+  name: LOG_VOLUME_SERVER_VOLUME_NAME
+- description: Path where shared volume will be mounted. Applies to both server and
+    worker pods.
+  name: LOG_VOLUME_MOUNT
+  value: /siibra_toolbox_logs
+
+
+
+# [1] enabling logging volume
+# 
+# If you would like shared log storage between worker and server
+# create a persistent log storage named `log-volume`
+# Then uncomment this block
+
+
+# [2] enabling shared data volume
+# 
+# If you would like shared data storage between worker and server
+# create a persistent data storage named `toolbox-storage`
+# Then uncomment this block

docs/develop/update_plugin_deployment.md

+TBD
\ No newline at end of file

docs/index.md

-# Interactive Atlas Viewer
+# Siibra Explorer
 
-The interactive atlas viewer is a browser based viewer of brain atlases. Tight integration with the Human Brain Project Knowledge Graph allows seamless querying of semantically and spatially anchored datasets. 
+The siibra explorer is a browser based viewer of brain atlases. Tight integration with the ebrains Knowledge Graph allows seamless querying of semantically and spatially anchored datasets. 
 
 ![](images/desktop_bigbrain_cortical.png)
 
 ## Links
 
-- production: <https://interactive-viewer.apps.hbp.eu>
 - production: <https://atlases.ebrains.eu/viewer/>
 - support: [support@ebrains.eu](mailto:support@ebrains.eu?subject=[interactive%20atlas%20viewer]%20queries)

docs/releases/v2.11.0.md

+# v2.11.0
+
+## Feature
+
+- Automatically selects human multilevel atlas on startup, if no atlases are selected
+- Allow multiple region selection for visualization purposes (`<ctrl>` + `[click]` on region)
+- Allow point to be selected (`[right click]`) and enabling map assignment
+- Allow atlas download
+
+## Behind the scenes
+
+- fixed unit tests
+- updated checklist.md, removed outdated checklist item
+- Reorganised help, quick tour and about page
+- Simplify volume of interest wireframe show/hide

docs/requirements.md

 # System requirements
 
-Interactive atlas viewer relies on [WebGL2.0](https://en.wikipedia.org/wiki/WebGL). Whilst a large proportion of modern browsers support this technology, some browser vendors do not. Most notably, __none__ of the Apple browsers (Safari on MacOS, [**any** browser on iOS](https://developer.apple.com/app-store/review/guidelines/#software-requirements)) support WebGL2.0.
+Siibra exporer relies on [WebGL2.0](https://en.wikipedia.org/wiki/WebGL). 
 
 !!! info
     To check if your device and browser combination support webgl 2.0, visit <https://get.webgl.org/webgl2/>.
@@ -8,11 +8,9 @@ Interactive atlas viewer relies on [WebGL2.0](https://en.wikipedia.org/wiki/WebG
 ## Desktop
 
 - PC (Windows/Linux/MacOS)
-- Latest Chrome/Firefox
+- Latest Chrome/Firefox/Safari
 - Dedicated graphics card (optional, but will drastically improve the performance)
 
 ## Mobile
 
-- Android Smartphone
-- Latest Chrome/Firefox
-
+- Latest Chrome/Firefox/Safari

docs/usage/connectivity.md

 # Exploring a connectivity matrix for the selected brain parcellation
 
-Via the <https://github.com/FZJ-INM1-BDA/HBP-connectivity-component>, the interactive atlas viewer allows interactive exploration of a connectivity matrix, that is defined for the currently selected brain parcellation and available from the HBP Knowledge Graph. As of now, this function is only available for the `JuBrain Cytoarchitectonic Atlas.
+Via the <https://github.com/FZJ-INM1-BDA/HBP-connectivity-component>, the siibra explorer allows interactive exploration of a connectivity matrix, that is defined for the currently selected brain parcellation and available from the HBP Knowledge Graph. As of now, this function is only available for the `JuBrain Cytoarchitectonic Atlas.
 
 ## Launching the connectivity browser
 

docs/usage/navigating.md

@@ -2,7 +2,7 @@
 
 ## Navigating the viewer
 
-The interactive atlas viewer can be accessed from either a desktop or an Android mobile device. The navigation scheme vary slightly between the two platforms.
+The siibra explorer can be accessed from either a desktop or an Android mobile device. The navigation scheme vary slightly between the two platforms.
 
 | | Desktop | Mobile |
 | --- | --- | --- |
@@ -41,6 +41,6 @@ From here, `click` on `Navigate`.
 
 ## Navigation status panel
 
-You can find the navigation status in the lower left corner of the interactive atlas viewer. You can reset the `position`, `rotation` and/or `zoom`, as well as toggling the units between `physical` (mm) and `voxel`.
+You can find the navigation status in the lower left corner of the siibra explorer. You can reset the `position`, `rotation` and/or `zoom`, as well as toggling the units between `physical` (mm) and `voxel`.
 
 [![](images/navigation_status.png)](images/navigation_status.png)

docs/usage/search.md

 # Searching
 
-The interactive viewer fetches datasets semantically linked to [selected regions](selecting.md#selecting-deselecting-regions). If no regions are selected, all datasets associated with a parcellation will be returned.
+Siibra explorer fetches datasets semantically linked to [selected regions](selecting.md#selecting-deselecting-regions). If no regions are selected, all datasets associated with a parcellation will be returned.
 
 [![](images/bigbrain_search_interface.png)](images/bigbrain_search_interface.png)