Merge pull request #126 from FZJ-INM1-BDA/fsdavid-patch-1

Upload to docker pipeline for staging
FZJ-INM1-BDA · Jul 7, 2022 · 529037d · 529037d
2 parents 7f3d720 + 16b454b
commit 529037d
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diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -0,0 +1,62 @@
+name: '[docker image] - Staging'
+
+on:
+  push:
+    branches:
+      - staging
+
+    # do not rebuild if...
+    paths-ignore:
+      # use_docs (use_docs are built on readthedocs any way)
+      - 'use_docs/*'
+
+jobs:
+  build-docker-img:
+    runs-on: ubuntu-latest
+    env:
+      DOCKERIMG: voluba:latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: 'Setup tags'
+      run: |
+        DOCKER_IMGSTREAM=${{ secrets.EBRAINS_DOCKER_REG_VOLUBA_NSP }}/${{ env.DOCKERIMG }}
+        echo "Setting docker image stream to $DOCKER_IMGSTREAM"
+        echo "DOCKER_IMGSTREAM=$DOCKER_IMGSTREAM" >> $GITHUB_ENV
+    - name: 'Set matomo env var'
+      run: |
+        echo "Using github.ref: $GITHUB_REF"
+        echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
+        
+        echo "MATOMO_URL=${{ secrets.MATOMO_URL_PROD }}" >> $GITHUB_ENV
+        echo "MATOMO_ID=${{ secrets.MATOMO_ID_PROD }}" >> $GITHUB_ENV
+    - name: 'Set version variable & expmt feature flag'
+      run: |
+        GIT_HASH=$(git rev-parse --short HEAD)
+        echo "Setting GIT_HASH: $GIT_HASH"
+        echo "GIT_HASH=$GIT_HASH" >> $GITHUB_ENV
+        # VERSION=$(jq -r '.version' package.json)
+        # echo "Setting VERSION: $VERSION"
+        # echo "VERSION=$VERSION" >> $GITHUB_ENV
+        # VUE_APP_ENABLE_EXPERIMENTAL_FEATURES="{}"
+    - name: 'Build docker image'
+      run: |
+        
+        echo "Building $DOCKER_IMGSTREAM"
+        docker build \
+          --build-arg MATOMO_URL=$MATOMO_URL \
+          --build-arg MATOMO_ID=$MATOMO_ID \
+          --build-arg VUE_APP_BACKEND_URL=${{ secrets.VUE_APP_BACKEND_URL }} \
+          --build-arg VUE_APP_UPLOAD_URL=${{ secrets.VUE_APP_UPLOAD_URL }} \
+          -t $DOCKER_IMGSTREAM \
+          .
+        echo "Successfully built $DOCKER_IMGSTREAM"
+    - name: 'Push to docker registry'
+      run: |
+        echo "Login to docker registry"
+        docker login \
+          -u '${{ secrets.EBRAINS_DOCKER_REG_USER }}' \
+          -p '${{ secrets.EBRAINS_DOCKER_REG_TOKEN }}' \
+          docker-registry.ebrains.eu
+        echo "Pushing $DOCKER_IMGSTREAM"
+        docker push $DOCKER_IMGSTREAM
diff --git a/.github/workflows/dockerimg.yml b/.github/workflows/dockerimg.yml
@@ -0,0 +1,69 @@
+name: '[docker image]'
+
+on:
+  push:
+    branches:
+      - master
+
+    # do not rebuild if...
+    paths-ignore:
+      # use_docs (use_docs are built on readthedocs any way)
+      - 'use_docs/*'
+
+jobs:
+  build-docker-img:
+    runs-on: ubuntu-latest
+    env:
+      DOCKERIMG: voluba:latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: 'Setup tags'
+      run: |
+
+        DOCKER_IMGSTREAM=${{ secrets.EBRAINS_DOCKER_REG_VOLUBA_NSP }}/${{ env.DOCKERIMG }}
+        echo "Setting docker image stream to $DOCKER_IMGSTREAM"
+        echo "DOCKER_IMGSTREAM=$DOCKER_IMGSTREAM" >> $GITHUB_ENV
+    - name: 'Set matomo env var'
+      run: |
+        echo "Using github.ref: $GITHUB_REF"
+
+        echo "BRANCH_NAME=${GITHUB_REF#refs/heads/}" >> $GITHUB_ENV
+        
+        echo "MATOMO_URL=${{ secrets.MATOMO_URL_PROD }}" >> $GITHUB_ENV
+        echo "MATOMO_ID=${{ secrets.MATOMO_ID_PROD }}" >> $GITHUB_ENV
+
+    - name: 'Set version variable & expmt feature flag'
+      run: |
+        GIT_HASH=$(git rev-parse --short HEAD)
+        echo "Setting GIT_HASH: $GIT_HASH"
+        echo "GIT_HASH=$GIT_HASH" >> $GITHUB_ENV
+
+        # VERSION=$(jq -r '.version' package.json)
+        # echo "Setting VERSION: $VERSION"
+        # echo "VERSION=$VERSION" >> $GITHUB_ENV
+
+        # VUE_APP_ENABLE_EXPERIMENTAL_FEATURES="{}"
+
+    - name: 'Build docker image'
+      run: |
+        
+        echo "Building $DOCKER_IMGSTREAM"
+        docker build \
+          --build-arg MATOMO_URL=$MATOMO_URL \
+          --build-arg MATOMO_ID=$MATOMO_ID \
+          --build-arg VUE_APP_BACKEND_URL=${{ secrets.VUE_APP_BACKEND_URL }} \
+          --build-arg VUE_APP_UPLOAD_URL=${{ secrets.VUE_APP_UPLOAD_URL }} \
+          -t $DOCKER_IMGSTREAM \
+          .
+        echo "Successfully built $DOCKER_IMGSTREAM"
+
+    - name: 'Push to docker registry'
+      run: |
+        echo "Login to docker registry"
+        docker login \
+          -u '${{ secrets.EBRAINS_DOCKER_REG_USER }}' \
+          -p '${{ secrets.EBRAINS_DOCKER_REG_TOKEN }}' \
+          docker-registry.ebrains.eu
+        echo "Pushing $DOCKER_IMGSTREAM"
+        docker push $DOCKER_IMGSTREAM
diff --git a/Dockerfile b/Dockerfile
@@ -1,58 +1,39 @@
 FROM node:12 as builder
 
-ARG HOSTNAME
-ARG VUE_APP_ALLOW_UPLOAD
-ARG IV_HOST
+ARG VUE_APP_ALLOW_UPLOAD=true
 ARG VUE_APP_BACKEND_URL
 ARG VUE_APP_NONLINEAR_BACKEND
 ARG VUE_APP_UPLOAD_URL
-ARG PORT
-ARG VUE_APP_DEBUG
+ARG VUE_APP_DEBUG=false
 ARG MATOMO_URL
 ARG MATOMO_ID
 ARG VUE_APP_ENABLE_EXPERIMENTAL_FEATURES
-ARG VUE_APP_INC_VOL_IDS
 
 ENV MATOMO_URL=$MATOMO_URL
 ENV MATOMO_ID=$MATOMO_ID
-ENV HOSTNAME=$HOSTNAME
 ENV VUE_APP_ALLOW_UPLOAD=$VUE_APP_ALLOW_UPLOAD
-ENV IV_HOST=$IV_HOST
+
 ENV VUE_APP_BACKEND_URL=$VUE_APP_BACKEND_URL
 ENV VUE_APP_NONLINEAR_BACKEND=$VUE_APP_NONLINEAR_BACKEND
 ENV VUE_APP_ENABLE_EXPERIMENTAL_FEATURES=$VUE_APP_ENABLE_EXPERIMENTAL_FEATURES
 ENV VUE_APP_UPLOAD_URL=$VUE_APP_UPLOAD_URL
-ENV PORT=$PORT
 ENV VUE_APP_DEBUG=$VUE_APP_DEBUG
-ENV VUE_APP_INC_VOL_IDS=$VUE_APP_INC_VOL_IDS
 
 COPY . /frontend
 WORKDIR /frontend/app
 RUN npm i
 
 RUN npm run build
 
-# build doc
-FROM python:3.7 as doc-builder
-
-COPY . /voluba
-WORKDIR /voluba
-
-RUN pip install mkdocs mkdocs-material mdx_truly_sane_lists
-RUN mkdocs build
-
 # 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 -p /frontend/app
 
 # copy frontend
 COPY --from=builder /frontend/app/dist /frontend/app/dist
 
-# copy docs to container
-COPY --from=doc-builder /voluba/site /frontend/app/dist/doc
-
 WORKDIR /frontend/app/dist
 
 RUN for f in $(find . -type f); do gzip < $f > $f.gz && brotli < $f > $f.br; done
@@ -77,4 +58,7 @@ COPY --from=builder /frontend/deploy .
 
 RUN npm i
 
+# DEPLOY ENV
+# IV_HOST, HOSTNAME
+
 ENTRYPOINT ["node", "server/server.js"]
diff --git a/app/src/App.vue b/app/src/App.vue
@@ -139,6 +139,52 @@ export default {
     if (DEBUG) {
       window.setProduction = (arg) => this.setProduction(arg)
     }
+
+    /**
+     * get voluba temp volume, if running on http
+     */
+    if (window.location.protocol === "http") {
+
+      const { appendToIncomingVolumes } = this
+
+      fetch(`http://ime178.ime.kfa-juelich.de/voluba/voluba.json`)
+        .then(res => res.json())
+        .then(({ voluba_sources }) => {
+          return Promise.all(
+            voluba_sources.map(({ name, url }) => {
+              const pingUrl = url.replace(/^precomputed:\/\//, '') + '/info'
+              return fetch(pingUrl)
+                .then(res => res.json())
+                .then(info => {
+                  const { size, resolution } = info.scales[0]
+                  const dim = [0, 1, 2].map(idx => size[idx] * resolution[idx]) // dimension in nm
+                  return {
+                    name,
+                    url,
+                    dim
+                  }
+                })
+            })
+          )
+        })
+        .then(voluba_sources => {
+          appendToIncomingVolumes({ 
+            volumes: voluba_sources.map(({ name, url, dim }, idx) => {
+              return {
+                name,
+                imageSource: url,
+                dim,
+                id: `voluba-custom-source-fzj-${name}-${idx}`
+              }
+            })
+          })
+        })
+        .catch(e => {
+          console.error(`fetching http://ime178.ime.kfa-juelich.de/voluba/voluba.json error`)
+        })
+
+    }
+    
     this.initAppendNehuba();
     this.$store.subscribeAction(({ type = '', payload = {} } = {}) => {
       switch (type) {
@@ -226,6 +272,9 @@ export default {
     ...mapActions('nehubaStore', [
       'redrawNehuba'
     ]),
+    ...mapActions('dataSelectionStore', [
+      'appendToIncomingVolumes'
+    ]),
     startRegistration: function () {
       this.showSelectVolumesModal = false
     },

diff --git a/app/src/components/LandmarkControlBodyV2.vue b/app/src/components/LandmarkControlBodyV2.vue
@@ -548,6 +548,9 @@ export default {
 .lm-wrapper
 {
   display:flex;
+  max-height:50vh;
+  overflow-y: scroll;
+  overflow-x: hidden;
 }
 
 .lm-wrapper > .ref-lm-wrapper

diff --git a/app/src/components/Nehuba.vue b/app/src/components/Nehuba.vue
@@ -61,6 +61,19 @@
       class="statusCardWrapper">
       <NehubaStatusCard>
         <template>
+          <div>
+            <span>rotation:</span>
+            <b-button-group>
+              <b-button size="sm"
+                @click="resetViewerOrientation()">
+                reset
+              </b-button>
+              <b-button size="sm"
+                @click="resetViewerOrientation('incomingVolume')">
+                set to inc
+              </b-button>
+            </b-button-group>
+          </div>
           <div>
             {{ navStatusText }}
           </div>
@@ -93,7 +106,7 @@
 <script>
 import { mapState, mapGetters, mapActions, mapMutations } from 'vuex'
 
-import { REFERENCE_COLOR, transposeMat4, UNPAIRED_COLOR, INCOMING_COLOR, annotationColorBlur, annotationColorFocus, testBigbrain, determineElement, getRotationVec3, incomingTemplateActiveOpacity, identityMat, identityMatFlattened } from '@//constants'
+import { REFERENCE_COLOR, transposeMat4, UNPAIRED_COLOR, INCOMING_COLOR, annotationColorFocus, testBigbrain, determineElement, getRotationVec3, identityMat, invertQuat } from '@//constants'
 
 import { incompatibleBrowserText } from '@/text'
 
@@ -364,13 +377,20 @@ export default {
     ]),
     ...mapActions('nehubaStore', [
       'setTranslInc',
-      'rotIncBy'
+      'rotIncBy',
     ]),
     ...mapMutations('nehubaStore', [
       'setReferenceTemplateTransform',
       'setIncomingVolumeHighlighted',
       'setPrimaryNehubaNavigationPosition'
     ]),
+    resetViewerOrientation: function(target){
+      const orientation =  target === 'incomingVolume'
+        ? invertQuat(Array.from(this.incRotQuat))
+        : [0, 0, 0, 1]
+      
+      this.nehubaBase__setOrientation(orientation)
+    },
     rerenderOpacity: function () {
       if (this.$options.nonReactiveData.ngUserLayer) {
         const layer = this.$options.nonReactiveData.ngUserLayer

diff --git a/app/src/constants.js b/app/src/constants.js
@@ -628,6 +628,10 @@ export const openFileDialog = (type, acceptedMimeType, fileHandler = null, conte
   file_selector.click()
 }
 
+export function invertQuat(q){
+  const { quat } = window.export_nehuba
+  return quat.invert(q, q)
+}
 
 export const testLandmarks = {
   referenceLandmarks: [{
@@ -784,7 +788,7 @@ export const oldJson = [
 export const annotationColorBlur = `grey`
 export const annotationColorFocus = `yellow`
 
-export const UPLOAD_URL = process.env.VUE_APP_UPLOAD_URL || `http://ime178.ime.kfa-juelich.de:7300`
+export const UPLOAD_URL = process.env.VUE_APP_UPLOAD_URL || `https://zam10143.zam.kfa-juelich.de/chumni`
 export const NONLINEAR_BACKEND = process.env.VUE_APP_NONLINEAR_BACKEND || `http://localhost:5000`
 
 export const processImageMetaData = ({id:defaultId, visibility = 'public', name = 'Untitled', links = {}, extra = {}, uploadUrl } = {}) => {

diff --git a/app/src/mixins/NehubaBase.js b/app/src/mixins/NehubaBase.js
@@ -200,6 +200,9 @@ export default {
       ) {
         this.nehubaBase__navigationChanged()
       }
+    },
+    nehubaBase__setOrientation: function(orientation){    
+      this.$options.nehubaBase.nehubaBase__nehubaViewer.ngviewer.navigationState.pose.orientation.restoreState( orientation )
     }
   }
 }