Merge pull request #767 from VirtualFlyBrain/alpha

Alpha tested release
VirtualFlyBrain · Nov 8, 2020 · 04a55af · 04a55af
2 parents 0bb30c3 + f157ba9
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -0,0 +1,188 @@
+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the action will run. Triggers the workflow on push only. ToDo: handle pull requests for testing only
+on:
+  push:
+    branches: '*'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # Deploy the local and remote versions of geppetto-vfb
+  deploy-test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    # total job timeout:
+    timeout-minutes: 60
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      # Decide based on branch which servers to use
+      - name: Pass branch
+        id: branch
+        run: echo "::set-output name=value::${GITHUB_REF##*/}";
+      - name: Setup local servers
+        id: local-servers
+        shell: bash
+        run: if [ "${GITHUB_REF##*/}" == master ] ; then
+            echo "::debug::Set to master setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
+            echo "::debug::Set to dev setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-dev.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::development";
+          elif [ "${GITHUB_REF##*/}" == alpha ] ; then
+            echo "::debug::Set to alpha setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-alpha.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-alpha.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::staging";
+          else 
+            echo "::debug::Set to default setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          fi
+      - name: Setup remote servers
+        id: remote-servers
+        shell: bash
+        run: if [ "${GITHUB_REF##*/}" == master ] ; then
+            echo "::debug::Set to master setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
+            echo "::debug::Set to dev setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl-dev.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-dev.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          elif [ "${GITHUB_REF##*/}" == alpha ] ; then
+            echo "::debug::Set to alpha setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb-alpha.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl-alpha.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-alpha.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-alpha.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          else 
+            echo "::debug::Set to default setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          fi
+
+      # Output the chosen servers
+      - name: Used remote servers
+        run: |
+          echo PDB:${{ steps.remote-servers.outputs.VFB_PDB_SERVER }}
+          echo OWL:${{ steps.remote-servers.outputs.VFB_OWL_SERVER }}
+          echo SOLR:${{ steps.remote-servers.outputs.SOLR_SERVER }}
+          echo TREE_PDB:${{ steps.remote-servers.outputs.VFB_TREE_PDB_SERVER }}
+          echo R:${{ steps.remote-servers.outputs.VFB_R_SERVER }}
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build and push local wss
+        id: docker_build_local
+        timeout-minutes: 15
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-local.wss"
+          build-args: |
+            VFB_TREE_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_TREE_PDB_SERVER }}
+            SOLR_SERVER_ARG=${{ steps.local-servers.outputs.SOLR_SERVER }}
+            VFB_R_SERVER_ARG=${{ steps.local-servers.outputs.VFB_R_SERVER }}
+            VFB_OWL_SERVER_ARG=${{ steps.local-servers.outputs.VFB_OWL_SERVER }}
+            VFB_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_PDB_SERVER }}
+            build_type=${{ steps.local-servers.outputs.BUILD_TYPE }} 
+            targetBranch=${{ steps.branch.outputs.value }} 
+            originBranch=${{ steps.branch.outputs.value }}
+            defaultBranch=development
+            finalBuild=true
+      
+      - name: Build and push remote
+        id: docker_build_remote
+        timeout-minutes: 15
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"
+          build-args: |
+            VFB_TREE_PDB_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_TREE_PDB_SERVER }}
+            SOLR_SERVER_ARG=${{ steps.remote-servers.outputs.SOLR_SERVER }}
+            VFB_R_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_R_SERVER }}
+            VFB_OWL_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_OWL_SERVER }}
+            VFB_PDB_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_PDB_SERVER }}
+            build_type=${{ steps.remote-servers.outputs.BUILD_TYPE }} 
+            targetBranch=${{ steps.branch.outputs.value }}
+            originBranch=${{ steps.branch.outputs.value }} 
+            defaultBranch=development
+            finalBuild=false
+      
+      - name: Image digest
+        run: |
+          echo "local:${{ steps.docker_build_local.outputs.digest }}"
+          echo "remote:${{ steps.docker_build_remote.outputs.digest }}"
+                
+      - name: Install Puppeteer
+        run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
+      - name: Start VFB server
+        run: docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
+      - name: Wait for VFB server to spin up
+        run: |  
+          export LANDING_PAGE="http://localhost:8080/org.geppetto.frontend/geppetto"  
+          Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
+          Test;
+      - name: Test batch 1   
+        run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
+      - name: Test batch 2   
+        run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'
+      - name: Test batch 3   
+        run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch3/.*js'
+      - name: Test under review  
+        continue-on-error: true
+        run: |
+          if [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] || [[ "${GITHUB_REF##*/}" =~ ^(fix|feature).* ]] ; then
+            npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/review/.*js';
+          fi
+      - name: Stop VFB server   
+        run: docker stop testServer
diff --git a/.travis.yml b/.travis.yml