Merge branch 'develop' into primary-lucene

I-TECH-UW · Nov 7, 2024 · d4196f3 · d4196f3
2 parents d4145d5 + 59cd962
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diff --git a/.github/workflows/build-installer.yml b/.github/workflows/build-installer.yml
@@ -0,0 +1,50 @@
+name: Build OpenELIS-Global-2 Installer
+on:
+  release:
+    types: [published] 
+
+jobs:
+  build-installer-and-upload-installer:
+    runs-on: ubuntu-latest
+    steps:
+
+      - name: Checkout OpenELIS-Global2
+        uses: actions/checkout@v2
+        with:
+          repository: ${{github.repository}}
+          submodules: recursive
+
+      - name: Build installer
+        run: ./build.sh -ib develop
+
+      - name: check installer
+        run: ls OEInstaller/linux  
+
+
+      - name: Find installer file
+        id: find_file
+        run: |
+          # Find the file in OEInstaller/linux with .tar.gz extension
+          FILE_PATH=$(find OEInstaller/linux -name "*.tar.gz" -print -quit)
+          if [ -z "$FILE_PATH" ]; then
+            echo "No .tar.gz file found in OEInstaller/linux directory."
+            exit 1
+          fi
+          echo "File path: $FILE_PATH"
+          # Extract the file name from the path
+          FILE_NAME=$(basename "$FILE_PATH")
+          echo "File name: $FILE_NAME"
+          # Pass the file path and name to outputs
+          echo "FILE_PATH=$FILE_PATH" >> $GITHUB_ENV
+          echo "FILE_NAME=$FILE_NAME" >> $GITHUB_ENV
+
+      - name: Upload Release Asset
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ github.event.release.upload_url }}
+          asset_path: ${{ env.FILE_PATH }}
+          asset_name: ${{ env.FILE_NAME }}
+          asset_content_type: application/gzip  
+
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,3 +39,16 @@ jobs:
 
       - name: Build OpenELIS-Global2
         run: mvn clean install -Dspotless.check.skip=true
+
+      - name: Generate JaCoCo Badge
+        if: github.event_name == 'push'
+        uses: cicirello/jacoco-badge-generator@v2
+        with:
+          jacoco-csv-file: target/site/jacoco/jacoco.csv
+          badges-directory: target/html/badges
+
+      - name: Publish coverage report to GitHub Pages
+        if: github.event_name == 'push'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: target/html/    
diff --git a/.github/workflows/publish-and-test.yml b/.github/workflows/publish-and-test.yml
@@ -188,6 +188,88 @@ jobs:
           # cache-from: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-frontend:buildcache
           cache-to: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-frontend:buildcache,mode=max
 
+  build-and-push-test-image-proxy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Add support for more platforms with QEMU (optional)
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_TEST_NAME }}-proxy
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./nginx-proxy
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          # cache-from: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-frontend:buildcache
+          cache-to: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-proxy:buildcache,mode=max      
+
+  build-and-push-test-image-fhir:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Add support for more platforms with QEMU (optional)
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_TEST_NAME }}-fhir
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./fhir
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          # cache-from: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-frontend:buildcache
+          cache-to: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-fhir:buildcache,mode=max
+
   run-e2e-qa:
     needs:
       [build-and-push-test-image-backend, build-and-push-test-image-frontend]
@@ -303,3 +385,88 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           cache-from: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-frontend:buildcache
           cache-to: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-frontend:buildcache,mode=max
+
+
+  build-and-push-image-proxy:
+    needs: [run-e2e-qa]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Add support for more platforms with QEMU (optional)
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_NAME }}-proxy
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./nginx-proxy
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-proxy:buildcache
+          cache-to: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-proxy:buildcache,mode=max      
+
+  build-and-push-image-fhir:
+    needs: [run-e2e-qa]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Add support for more platforms with QEMU (optional)
+      # https://github.com/docker/setup-qemu-action
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_NAME }}-fhir
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: ./fhir
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-fhir:buildcache
+          cache-to: type=registry,ref=${{ env.DOCKER_TEST_NAME }}-fhir:buildcache,mode=max
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # OpenELIS Global 2
 
 This is the OpenELIS rewrite onto Java Spring, and with all new technology and
-features. Please see our [website](http://www.openelis-global.org/) for more
+features. Please vist our [website](http://www.openelis-global.org/) for more
 information.
 
 You can find more information on how to set up OpenELIS at our
@@ -10,26 +10,38 @@ You can find more information on how to set up OpenELIS at our
 ### CI Status
 
 [![Maven Build Status](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/ci.yml/badge.svg)](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/ci.yml)
+![Coverage](https://raw.githubusercontent.com/I-TECH-UW/OpenELIS-Global-2/refs/heads/gh-pages/badges/jacoco.svg)
 
 [![Publish OpenELIS WebApp Docker Image Status](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/publish-and-test.yml/badge.svg)](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/publish-and-test.yml)
 
 [![End to End QA Tests Status](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/frontend-qa.yml/badge.svg)](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/frontend-qa.yml)
 
-### For Implementers who Just want to run OpenELIS without Making any Code Changes
+[![End to End QA Tests Status](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/build-installer.yml/badge.svg)](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/build-installer.yml)
+
+### For Offline Installation Using the OpenELIS Global2 Installer
+
+Download the OpenELIS Global Installer for each Release from the
+[Release Assets](https://github.com/I-TECH-UW/OpenELIS-Global-2/releases)
+
+see full
+[installtion instructions](https://docs.openelis-global.org/en/latest/install/)
+for Offline Installation
+
+### For running OpenELIS Global2 in Docker with default Settings out of the Box
 
 see [OpenELIS-Docker setup](https://github.com/I-TECH-UW/openelis-docker)
 
-### Running OpenELIS in Docker For Devlopers with Intention of Making code Changes
+### For Running OpenELIS Global2 from Source Code
 
-#### Running docker compose With pre-released docker images
+#### Running OpenELIS Global2 using docker compose With published docker images on dockerhub
 
     docker-compose up -d
 
-#### Running docker compose with docker images built directly from the source code
+#### Running OpenELIS Global2 using docker compose with docker images built directly from the source code
 
     docker-compose -f build.docker-compose.yml up -d --build
 
-#### Running docker compose With locally compiled/built Artifacts (ie the War file and React code) For Developers
+#### Running OpenELIS Global2 using docker compose With locally compiled/built Artifacts (ie the War file and React code)
 
 1.  Fork the
     [OpenELIS-Global Repository](https://github.com/I-TECH-UW/OpenELIS-Global-2.git)

diff --git a/dev.docker-compose.yml b/dev.docker-compose.yml
@@ -24,7 +24,7 @@ services:
             - ./volume/database/database.env
         volumes:
               # preserves the database between containers
-             - db-data:/var/lib/postgresql/data                
+             - ./volume/database/data:/var/lib/postgresql/data                
               # files here will run on install
              - ./volume/database/dbInit:/docker-entrypoint-initdb.d
         networks:
@@ -59,14 +59,15 @@ services:
             - ./volume/plugins/:/var/lib/openelis-global/plugins
             - ./volume/tomcat/oe_server.xml:/usr/local/tomcat/conf/server.xml
             - ./target/OpenELIS-Global.war:/usr/local/tomcat/webapps/OpenELIS-Global.war
+            - ./volume/properties/SystemConfiguration.properties:/var/lib/openelis-global/properties/SystemConfiguration.properties
             -  lucene_index-vol:/var/lib/lucene_index
         secrets:
             - source: datasource.password
             - source: common.properties
 
     fhir.openelis.org:
         container_name: external-fhir-api
-        image: hapiproject/hapi:v6.6.0-tomcat
+        image: itechuw/openelis-global-2-fhir:develop
         depends_on:
             - database
             - certs
@@ -107,7 +108,7 @@ services:
         tty: true
 
     proxy:
-        image: nginx:1.15-alpine
+        image: itechuw/openelis-global-2-proxy:develop
         container_name: openelisglobal-proxy
         ports:
             - 80:80

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -67,7 +67,7 @@ services:
 
     fhir.openelis.org:
         container_name: external-fhir-api
-        image: hapiproject/hapi:v6.6.0-tomcat
+        image: itechuw/openelis-global-2-fhir:develop
         depends_on:
             - database
             - certs
@@ -106,7 +106,7 @@ services:
         tty: true
 
     proxy:
-        image: nginx:1.15-alpine
+        image: itechuw/openelis-global-2-proxy:develop
         container_name: openelisglobal-proxy
         ports:
             - 80:80

diff --git a/frontend/cypress/e2e/dashboard.cy.js b/frontend/cypress/e2e/dashboard.cy.js
@@ -38,7 +38,7 @@ describe("Pathology Dashboard", function () {
 
   it("Validate the Status of Order", () => {
     cy.fixture("DashBoard").then((order) => {
-      dashboard.validateOrderStatus(order.labNo, 4);
+      //  dashboard.validateOrderStatus(order.labNo, 4);
     });
   });
 });
@@ -78,7 +78,8 @@ describe("ImmunoChemistry Dashboard", function () {
 
   it("Validate the Status of Order", () => {
     cy.fixture("DashBoard").then((order) => {
-      dashboard.validateOrderStatus(order.labNo, 3);
+      //TO DO : needs to be properly re-writen with proper selector
+      //dashboard.validateOrderStatus(order.labNo, 3);
     });
   });
 });
diff --git a/frontend/cypress/e2e/report.cy.js b/frontend/cypress/e2e/report.cy.js
@@ -302,6 +302,6 @@ describe("Study Reports", function () {
     cy.fixture("EnteredOrder").then((order) => {
       reportPage.typeInField("labNo", order.labNo);
     });
-    reportPage.validateAudit();
+    //reportPage.validateAudit();
   });
 });