Merge pull request #1151 from FZJ-INM1-BDA/staging

Staging

.github/workflows/ci.yml

@@ -2,10 +2,6 @@ name: '[ci]'
 
 on:
   push:
-    branches-ignore:
-    - 'dev'
-    - 'staging'
-    - 'master'
 
     # ignore changes to docs and mkdocs.yml
     paths-ignore:
@@ -66,4 +62,4 @@ jobs:
         cd deploy
         npm i
         npm run test
-  
\ No newline at end of file
+  

.github/workflows/docker_img.yml

@@ -120,43 +120,65 @@ jobs:
             echo "BUILD_TEXT=$BRANCH_NAME" >> $GITHUB_ENV
           fi
 
+          # DEPLOY_ID == remove _ / and lowercase everything from branch
+          DEPLOY_ID=$(echo ${BRANCH_NAME//[_\/]/} | awk '{ print tolower($0) }')
+          echo "DEPLOY_ID=$DEPLOY_ID" >> $GITHUB_ENV
+
           if [[ "$BRANCH_NAME" == 'master' ]] || [[ "$BRANCH_NAME" == 'staging' ]]
           then
             echo "OKD_URL=https://okd.hbp.eu:443" >> $GITHUB_ENV
             echo "OKD_SECRET=${{ secrets.OKD_PROD_SECRET }}" >> $GITHUB_ENV
             echo "OKD_PROJECT=interactive-viewer" >> $GITHUB_ENV
             echo "ROUTE_HOST=siibra-explorer.apps.hbp.eu" >> $GITHUB_ENV
-            echo "Deploy on prod cluster..."
+
+            if [[ "$BRANCH_NAME" == 'master' ]]
+            then
+              FULL_DEPLOY_ID=siibra-explorer-branch-deploy-2-prodpathviewer
+              FULL_DEPLOY_ID2=siibra-explorer-branch-deploy-2-iav-legacy
+              echo "FULL_DEPLOY_ID=$FULL_DEPLOY_ID" >> $GITHUB_ENV
+              echo "FULL_DEPLOY_ID2=$FULL_DEPLOY_ID2" >> $GITHUB_ENV
+            else
+              FULL_DEPLOY_ID=siibra-explorer-branch-deploy-2-stagingpathed
+              echo "FULL_DEPLOY_ID=$FULL_DEPLOY_ID" >> $GITHUB_ENV
+            fi
+
+            echo "Deploy on **prod** cluster..."
+            echo "Deploy id: **${FULL_DEPLOY_ID}** ..."
+            if [ ! -z "$FULL_DEPLOY_ID2" ]
+            then
+              echo "Secondary deploy id: **$FULL_DEPLOY_ID2** ..."
+            fi
           else
             echo "OKD_URL=https://okd-dev.hbp.eu:443" >> $GITHUB_ENV
             echo "OKD_SECRET=${{ secrets.OKD_DEV_SECRET }}" >> $GITHUB_ENV
             echo "OKD_PROJECT=interactive-atlas-viewer" >> $GITHUB_ENV
             echo "ROUTE_HOST=siibra-explorer.apps-dev.hbp.eu" >> $GITHUB_ENV
             echo "BUILD_TEXT=$BRANCH_NAME" >> $GITHUB_ENV
-            echo "Deploy on dev cluster..."
+            FULL_DEPLOY_ID=${{ env.OC_TEMPLATE_NAME }}-$DEPLOY_ID
+            echo "FULL_DEPLOY_ID=$FULL_DEPLOY_ID" >> $GITHUB_ENV
+            echo "Deploy on **dev** cluster ..."
+            echo "Deploy id: **${FULL_DEPLOY_ID}** ..."
           fi
       - name: 'Login via oc cli & deploy'
         run: |
           oc login $OKD_URL --token=$OKD_SECRET
           oc project $OKD_PROJECT
-
-          # DEPLOY_ID == remove _ / and lowercase everything from branch
-          DEPLOY_ID=$(echo ${BRANCH_NAME//[_\/]/} | awk '{ print tolower($0) }')
-          echo "DEPLOY_ID=$DEPLOY_ID" >> $GITHUB_ENV
           
           ROUTE_PATH=/$DEPLOY_ID
           echo "ROUTE_PATH=$ROUTE_PATH" >> $GITHUB_ENV
 
           echo "Working branch name: $BRANCH_NAME, deploy_id: $DEPLOY_ID"
+          echo "full deploy id: $FULL_DEPLOY_ID, secondary deploy id: $FULL_DEPLOY_ID2"
 
           # check if the deploy already exist
-          if oc get dc ${{ env.OC_TEMPLATE_NAME }}-$DEPLOY_ID; then
+
+          if oc get dc $FULL_DEPLOY_ID; then
             # trigger redeploy if deployconfig exists already
-            echo "dc ${{ env.OC_TEMPLATE_NAME }}-$DEPLOY_ID already exist, redeploy..."
-            oc rollout latest dc/${{ env.OC_TEMPLATE_NAME }}-$DEPLOY_ID
+            echo "dc $FULL_DEPLOY_ID already exist, redeploy..."
+            oc rollout latest dc/$FULL_DEPLOY_ID
           else 
             # create new app if deployconfig does not yet exist
-            echo "dc ${{ env.OC_TEMPLATE_NAME }}-$DEPLOY_ID does not yet exist, create new app..."
+            echo "dc $FULL_DEPLOY_ID does not yet exist, create new app..."
             oc new-app --template ${{ env.OC_TEMPLATE_NAME }} \
               -p BRANCH_NAME=$BRANCH_NAME \
               -p DEPLOY_ID=$DEPLOY_ID \
@@ -164,6 +186,13 @@ jobs:
               -p ROUTE_PATH=$ROUTE_PATH \
               -p BUILD_TEXT=$BUILD_TEXT
           fi
+
+          if [ ! -z "$FULL_DEPLOY_ID2" ]
+          then
+            echo "FULL_DEPLOY_ID2 is defined, trying to redeploy $FULL_DEPLOY_ID2 ..."
+            oc rollout latest dc/$FULL_DEPLOY_ID2
+          fi
+          
       - name: 'Update status badge'
         if: success()
         run: |

.openshift/v2/okd_branch_tmpl_v2.yaml

@@ -48,6 +48,8 @@ objects:
                 name: plugins
             - configMapRef:
                 name: other-deploy-config
+            - configMapRef:
+                name: obj-storage-cred
 
             image: "docker-registry.ebrains.eu/siibra/siibra-explorer:${BRANCH_NAME}"
             imagePullPolicy: Always

Dockerfile

@@ -44,7 +44,7 @@ RUN npm i
 RUN npm run build-aot
 
 # gzipping container
-FROM ubuntu:20.10 as compressor
+FROM ubuntu:22.04 as compressor
 RUN apt upgrade -y && apt update && apt install brotli
 
 RUN mkdir /iv

angular.json

@@ -29,7 +29,6 @@
             "tsConfig": "tsconfig.app.json",
             "inlineStyleLanguage": "css",
             "assets": [
-              "src/favicon.ico",
               "src/assets"
             ],
             "styles": [
@@ -49,6 +48,10 @@
               "input": "worker/worker-nifti.js",
               "inject": false,
               "bundleName": "worker-nifti"
+            },{
+              "input": "worker/worker-typedarray.js",
+              "inject": false,
+              "bundleName": "worker-typedarray"
             },
             
             {
@@ -60,7 +63,11 @@
               "inject": false,
               "bundleName": "syntaxError"
             },
-          
+            {
+              "input": "third_party/extra_js.js",
+              "inject": false,
+              "bundleName": "extra_js"
+            },
             {
               "input": "third_party/vanilla_nehuba.js",
               "inject": false,

deploy/package.json

@@ -29,7 +29,7 @@
     "passport": "^0.4.0",
     "rate-limit-redis": "^2.1.0",
     "redis": "^3.1.2",
-    "request": "^2.88.0",
+    "request": "^2.88.2",
     "showdown": "^1.9.1",
     "soswrap": "^0.0.2",
     "through2": "^3.0.1"
@@ -40,7 +40,7 @@
     "cookie": "^0.4.0",
     "cors": "^2.8.5",
     "dotenv": "^6.2.0",
-    "mocha": "^6.1.4",
+    "mocha": "^9.1.3",
     "nock": "^12.0.3",
     "sinon": "^8.0.2"
   }

deploy/saneUrl/store.js

@@ -48,6 +48,7 @@ class GitlabSnippetStore {
           'PRIVATE-TOKEN': this.token,
           ...headers
         },
+        qs: { per_page: 1000 },
         ...opt
       }, (err, resp, body) => {
         if (err) return rj(err)

docs/releases/v2.6.1.md

+# v2.6.1
+
+## Bugfix
+
+- Fixed perspective view orientation button colors
\ No newline at end of file

docs/releases/v2.6.2.md

+# v2.6.2
+
+## Bugfixes
+
+- Added indication when annotations were overwritten (partial fix to #1128)
+
+## Under the hood stuff
+
+- update deploy depedencies
+- update deployment configurations
+- fixed some CSP issues
+- fixed favicons
+- added build debug messages
+- increment siibra-api version expectation
+- remove unused tests
+- update compressor image to 22.04

docs/releases/v2.6.3.md

+# v2.6.3
+
+## Bugfixes
+
+- Fixed an issue where inter-space selection of parcellation was not possible.
+

docs/releases/v2.6.4.md

+# v2.6.4
+
+## Bugfixes
+
+- Temporarily fixed an issue where saneurl queries were paginated
+

docs/releases/v2.6.5.md

+# v2.6.4
+
+## Feature
+
+- Re-enabled autoradiographs for receptor datasets

e2e/checklist.md

@@ -2,7 +2,7 @@
 
 **use incognito browser**
 
-[home page](https://siibra-explorer.apps.hbp.eu/staging/)
+[home page](https://atlases.ebrains.eu/viewer-staging/)
 
 ## General
 
@@ -44,9 +44,13 @@
     - [ ] Explore in other templates exists, and has MNI152 and big brain
       - [ ] clicking on the respective space will load julich 2.9 in that space
       - [ ] the navigation should be preserved
+  - [ ] switching template/parc
+    - [ ] mni152 julich brain 29 (big brain) -> big brain julich brain 29
+    - [ ] mni152 julich brain 29 (cortical layer) -> big brain cortical layer
+    - [ ] mni152 long bundle (dismiss) -> mni152 julich brain 29
   - [ ] in big brain v2.9 (or latest)
     - [ ] high res hoc1, hoc2, hoc3, lam1-6 are visible
-    - [ ] pli dataset [link](https://siibra-explorer.apps.hbp.eu/staging/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Grey%2FWhite+matter&cNavigation=0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..1uaTK.Bq5o~.lKmo~..NBW&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22minds%2Fcore%2Fdataset%2Fv1.0.0%2Fb08a7dbc-7c75-4ce7-905b-690b2b1e8957%22%2C%22filename%22%3A%22Overlay+of+data+modalities%22%7D%5D)
+    - [ ] pli dataset [link](https://atlases.ebrains.eu/viewer-staging/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Grey%2FWhite+matter&cNavigation=0.0.0.-W000.._eCwg.2-FUe3._-s_W.2_evlu..7LIx..1uaTK.Bq5o~.lKmo~..NBW&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22minds%2Fcore%2Fdataset%2Fv1.0.0%2Fb08a7dbc-7c75-4ce7-905b-690b2b1e8957%22%2C%22filename%22%3A%22Overlay+of+data+modalities%22%7D%5D)
       - [ ] redirects fine
       - [ ] shows fine
   - [ ] fsaverage
@@ -56,9 +60,9 @@
   - [ ] on hover, show correct region name(s)
   - [ ] whole mesh loads
 ## saneURL
-- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/bigbrainGreyWhite) redirects to big brain
-- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/julichbrain) redirects to julich brain (colin 27)
-- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/whs4) redirects to waxholm v4
-- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/allen2017) redirects to allen 2017
-- [ ] [saneUrl](https://siibra-explorer.apps.hbp.eu/staging/saneUrl/mebrains) redirects to monkey
+- [ ] [saneUrl](https://atlases.ebrains.eu/viewer-staging/saneUrl/bigbrainGreyWhite) redirects to big brain
+- [ ] [saneUrl](https://atlases.ebrains.eu/viewer-staging/saneUrl/julichbrain) redirects to julich brain (colin 27)
+- [ ] [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
 

mkdocs.yml

@@ -16,13 +16,6 @@ markdown_extensions:
 
 plugins:
   - search
-  # - errandkun:
-  #     extract_path: docs/autogen_images
-  #     external_resources:
-  #     - type: github
-  #       owner: fzj-inm1-bda
-  #       repo: interactive-viewer
-  #       workflow_name: e2e
 
 pages:
   - Home: 'index.md'
@@ -40,6 +33,11 @@ pages:
     - Fetching datasets: 'advanced/datasets.md'
     - Display non-atlas volumes: 'advanced/otherVolumes.md'
   - Release notes:
+    - v2.6.5: 'releases/v2.6.5.md'
+    - v2.6.4: 'releases/v2.6.4.md'
+    - v2.6.3: 'releases/v2.6.3.md'
+    - v2.6.2: 'releases/v2.6.2.md'
+    - v2.6.1: 'releases/v2.6.1.md'
     - v2.6.0: 'releases/v2.6.0.md'
     - v2.5.8: 'releases/v2.5.8.md'
     - v2.5.7: 'releases/v2.5.7.md'

package.json

 {
   "name": "interactive-viewer",
-  "version": "2.6.0",
+  "version": "2.6.5",
   "description": "HBP interactive atlas viewer. Integrating KG query, dataset previews & more. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
   "scripts": {
     "build-aot": "ng build && node ./third_party/matomo/processMatomo.js",
@@ -20,9 +20,9 @@
   "author": "FZJ-INM1-BDA <inm1-bda@fz-juelich.de>",
   "license": "apache-2.0",
   "devDependencies": {
-    "@angular-devkit/build-angular": "~12.2.1",
-    "@angular/cli": "~12.2.1",
-    "@angular/compiler-cli": "~12.2.0",
+    "@angular-devkit/build-angular": "^12.2.13",
+    "@angular/cli": "^12.2.13",
+    "@angular/compiler-cli": "^12.2.13",
     "@types/jasmine": "~3.8.0",
     "@types/node": "^12.11.1",
     "@typescript-eslint/eslint-plugin": "^4.29.2",