Merge branch '2.8' into missingtranslations

I-TECH-UW · Nov 23, 2023 · fa64291 · fa64291
2 parents 36714ba + c0656ac
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diff --git a/.github/workflows/publish-frontend-dev.yml b/.github/workflows/publish-frontend-dev.yml
@@ -12,8 +12,10 @@ on:
 
 
 env:
-  REGISTRY: ghcr.io
+  REGISTRY: docker.io
   IMAGE_NAME: ${{ github.repository }}-frontend-dev
+  DOCKER_NAME: ${{ vars.DOCKERHUB_USERNAME }}/${{ github.event.repository.name }}-frontend-dev
+
 
 jobs:
   build-and-push-image:
@@ -26,23 +28,33 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        # 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: Login to DockerHub
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          images: ${{ env.DOCKER_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v5
         with:
           context: ./frontend
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{github.repository}}:latest
+          cache-to: type=inline
diff --git a/.github/workflows/publish-frontend.yml b/.github/workflows/publish-frontend.yml
@@ -14,8 +14,9 @@ on:
 
 
 env:
-  REGISTRY: ghcr.io
+  REGISTRY: docker.io
   IMAGE_NAME: ${{ github.repository }}-frontend
+  DOCKER_NAME: ${{ vars.DOCKERHUB_USERNAME }}/${{ github.event.repository.name }}-frontend
 
 jobs:
   build-and-push-image:
@@ -28,24 +29,34 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
+      # 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@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          images: ${{ env.DOCKER_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v5
         with:
           context: ./frontend
           file: ./frontend/Dockerfile.prod
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{github.repository}}:latest
+          cache-to: type=inline
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -14,8 +14,9 @@ on:
 
 
 env:
-  REGISTRY: ghcr.io
+  REGISTRY: docker.io
   IMAGE_NAME: ${{ github.repository }}
+  DOCKER_NAME: ${{ vars.DOCKERHUB_USERNAME }}/${{ github.event.repository.name }}
 
 jobs:
   build-and-push-image:
@@ -28,23 +29,34 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        # 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: Login to DockerHub
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
-          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          images: ${{ env.DOCKER_NAME }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{github.repository}}:latest
+          cache-to: type=inline
diff --git a/README.md b/README.md
@@ -14,10 +14,10 @@ You can find more information on how to set up OpenELIS at our [docs page](http:
 #### Building the docker images directly from source code
     docker-compose -f build.docker-compose.yml up -d --build
 
-#### Running docker containers With locally compiled Artifacts (ie the War file and local frontend Source files)
+#### Running docker containers With locally compiled Artifacts (ie the War file)
 1. Clone the Repository
 
-         git clone https://github.com/I-TECH-UW/OpenELIS-Global-2.git -b 2.8 
+         git clone https://github.com/I-TECH-UW/OpenELIS-Global-2.git 
 
 2. innitialize and build sub modules
 

diff --git a/build.docker-compose.yml b/build.docker-compose.yml
@@ -2,7 +2,7 @@ version: '3.3'
 services:
   certs:
     container_name: oe-certs
-    image: ghcr.io/i-tech-uw/certgen:main
+    image: itechuw/certgen:main
     restart: always
     environment:
       - KEYSTORE_PW="kspass"
@@ -13,26 +13,27 @@ services:
       - key_trust-store-volume:/etc/openelis-global
       - keys-vol:/etc/ssl/private/
       - certs-vol:/etc/ssl/certs/
+
   database:
-    container_name: openelisglobal-database
-    image: postgres:9.5
-    ports:
-      - "15432:5432"
-    restart: always
-    env_file:
-      - ./volume/database/database.env
-    volumes:
-      # preserves the database between containers
-      - db-data:/var/lib/postgresql/data
-      # files here will run on install
-      - ./volume/database/dbInit:/docker-entrypoint-initdb.d
-    networks:
-      - default
-    healthcheck:
-      test: [ "CMD", "pg_isready", "-q", "-d", "clinlims", "-U", "clinlims" ]
-      timeout: 45s
-      interval: 10s
-      retries: 10
+      container_name: openelisglobal-database 
+      image: postgres:9.5
+      ports:
+          - "15432:5432"
+      restart: always
+      env_file:
+          - ./volume/database/database.env
+      volumes:
+              # preserves the database between containers
+          - db-data:/var/lib/postgresql/data                
+              # files here will run on install
+          - ./volume/database/dbInit:/docker-entrypoint-initdb.d
+      networks:
+          - default
+      healthcheck:
+            test: [ "CMD", "pg_isready", "-q", "-d", "clinlims", "-U", "clinlims" ]
+            timeout: 45s
+            interval: 10s
+            retries: 10      
 
   oe.openelis.org:
     build:
@@ -72,8 +73,11 @@ services:
       - default
     restart: always
     environment:
+      spring.datasource.url : jdbc:postgresql://database:5432/clinlims?currentSchema=clinlims
+      spring.datasource.username : clinlims
+      spring.datasource.password : clinlims
+      spring.datasource.driverClassName: org.postgresql.Driver
       TZ: Africa/Nairobi
-
       JAVA_OPTS: "-Djavax.net.ssl.trustStore=/etc/openelis-global/truststore 
                       -Djavax.net.ssl.trustStorePassword=tspass
                       -Djavax.net.ssl.trustStoreType=pkcs12 

diff --git a/dev.docker-compose.yml b/dev.docker-compose.yml
@@ -2,7 +2,7 @@ version: '3.3'
 services:
     certs:
         container_name: oe-certs 
-        image: ghcr.io/i-tech-uw/certgen:main
+        image: itechuw/certgen:main
         restart: always
         environment:
             - KEYSTORE_PW="kspass"
@@ -37,7 +37,7 @@ services:
 
     oe.openelis.org:
         container_name: openelisglobal-webapp 
-        image: ghcr.io/i-tech-uw/openelis-global-2:2.8    
+        image: itechuw/openelis-global-2:2.8    
         depends_on:
             - database
         ports:
@@ -72,6 +72,10 @@ services:
             - default
         restart: always
         environment:
+          spring.datasource.url : jdbc:postgresql://database:5432/clinlims?currentSchema=clinlims
+          spring.datasource.username : clinlims
+          spring.datasource.password : clinlims
+          spring.datasource.driverClassName: org.postgresql.Driver
           TZ: Africa/Nairobi
 
           JAVA_OPTS: "-Djavax.net.ssl.trustStore=/etc/openelis-global/truststore 
@@ -87,7 +91,7 @@ services:
 
 
     frontend.openelis.org:
-        image: ghcr.io/i-tech-uw/openelis-global-2-frontend-dev:2.8
+        image: itechuw/openelis-global-2-frontend-dev:2.8
         container_name: openelisglobal-front-end
         networks:
             - default

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -2,7 +2,7 @@ version: '3.3'
 services:
     certs:
         container_name: oe-certs 
-        image: ghcr.io/i-tech-uw/certgen:main
+        image: itechuw/certgen:main
         restart: always
         environment:
             - KEYSTORE_PW="kspass"
@@ -37,7 +37,7 @@ services:
 
     oe.openelis.org:
         container_name: openelisglobal-webapp 
-        image: ghcr.io/i-tech-uw/openelis-global-2:2.8    
+        image: itechuw/openelis-global-2:2.8    
         depends_on:
             - database
         ports:
@@ -57,6 +57,8 @@ services:
             -  key_trust-store-volume:/etc/openelis-global
             - ./volume/plugins/:/var/lib/openelis-global/plugins
             - ./volume/tomcat/oe_server.xml:/usr/local/tomcat/conf/server.xml
+            #Runing the OpenELIS with the locally compiled war file
+            #- ./target/OpenELIS-Global.war:/usr/local/tomcat/webapps/OpenELIS-Global.war
         secrets:
             - source: datasource.password
             - source: common.properties
@@ -71,6 +73,10 @@ services:
             - default
         restart: always
         environment:
+          spring.datasource.url : jdbc:postgresql://database:5432/clinlims?currentSchema=clinlims
+          spring.datasource.username : clinlims
+          spring.datasource.password : clinlims
+          spring.datasource.driverClassName: org.postgresql.Driver
           TZ: Africa/Nairobi
 
           JAVA_OPTS: "-Djavax.net.ssl.trustStore=/etc/openelis-global/truststore 
@@ -86,7 +92,7 @@ services:
 
 
     frontend.openelis.org:
-        image: ghcr.io/i-tech-uw/openelis-global-2-frontend:2.8
+        image: itechuw/openelis-global-2-frontend:2.8
         container_name: openelisglobal-front-end
         networks:
         - default

diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml
@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#   - requirements: docs/requirements.txt
diff --git a/docs/about.md b/docs/about.md
@@ -8,7 +8,7 @@ The software serves as both an effective laboratory software solution and busine
 ##A Global LIS
 Laboratory Information System for Global Health
 
-The global health version of [OpenELIS Global](http://openelisglobal.org) builds on the foundation provided by the original US Public Health Lab version of OpenELIS Global. Our challenge is to provide the flexibility demanded by different laboratories while maintaining a common code base. Some examples:
+The global health version of [OpenELIS Global](https://openelis-global.org) builds on the foundation provided by the original US Public Health Lab version of OpenELIS Global. Our challenge is to provide the flexibility demanded by different laboratories while maintaining a common code base. Some examples:
 
 Some laboratories refer to the number attached to the sample as an accession number while others refer to it as a laboratory number.
 
@@ -21,4 +21,4 @@ Some laboratories refer to the number attached to the sample as an accession num
 
 Our goal in meeting these challenges is to ensure that the code does not become fractured by each variation in requirements. We have so far been successful and all of the implementations differ only by configuration files. Designed to support quality laboratory services and test results from high volume clinical and reference laboratories.
 
-The work is done in partnership with International Training and Education Center for Health (I-TECH). They provide a wide perspective on the background, goals and collaborators of the work being done worldwide. For specifics of I-TECH’s work in two countries where OpenELIS Global is being implemented: [I-TECH in Haiti](https://www.go2itech.org/where-we-work/haiti/), [I-TECH in Côte d’Ivoire](https://www.go2itech.org/where-we-work/cote-divoire/).
+The work is done in partnership with International Training and Education Center for Health (I-TECH). They provide a wide perspective on the background, goals and collaborators of the work being done worldwide. For specifics of I-TECH’s work in two countries where OpenELIS Global is being implemented: [I-TECH in Haiti](https://www.go2itech.org/where-we-work/haiti/), [I-TECH in Côte d’Ivoire](https://www.go2itech.org/where-we-work/cote-divoire/).