Merge branch '2.8' into 2.8feature

.github/workflows/ci.yml

@@ -21,37 +21,21 @@ jobs:
         key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
         restore-keys: |
             ${{ runner.os }}-maven- 
-    - name: Log in to the Container registry
-      uses: docker/login-action@v1
-      with:
-        registry: ghcr.io
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}         
-    - name: Checkout dataexport module
-      uses: actions/checkout@v2
-      with:
-        repository: I-TECH-UW/dataexport
-        ref: develop    
-    - name: install dataexport module
-      run: mvn clean install  
     
     - name: Checkout OpenELIS-Global2
       uses: actions/checkout@v2
       with:
         repository: ${{github.repository}} 
+        submodules: recursive
+    - name: Initialize and build submodules
+      run: |
+            cd dataexport
+            mvn clean install  
+            cd ..
+    
     - name: Build OpenELIS-Global2
       run: mvn clean install  
 
     - name: Run OpenELS image 
       run : docker-compose -f build.docker-compose.yml up -d
 
-    - name: Sleep for 3 minutes for OpenELIS to start
-      run: sleep 3m
-      shell: bash
-
-    - name: check containers
-      run : docker ps 
-
-    - name: Show OpenELIS Logs
-      run : docker-compose logs oe.openelis.org
-

.github/workflows/publish-frontend-dev.yml

@@ -0,0 +1,48 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish 3.X Dev FrontEnd Docker image
+
+on:
+  push:
+    branches: [ '2.8']
+  workflow_dispatch:
+
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}-frontend-dev
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: ./frontend
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

README.md

@@ -8,12 +8,32 @@ You can find more information on how to set up OpenELIS at our [docs page](http:
 [![Publish Docker Image Status](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/publish.yml/badge.svg)](https://github.com/I-TECH-UW/OpenELIS-Global-2/actions/workflows/publish.yml)
 
 ### Running OpenELIS in Docker
-#### Running with published docker images
+#### Running with docker compose
     docker-compose up -d
 
-#### Building the docker images from source code
+#### 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)
+1. Clone the Repository
+
+         git clone https://github.com/I-TECH-UW/OpenELIS-Global-2.git -b 2.8 
+
+2. innitialize and build sub modules
+
+        git submodule update --init --recursive
+        cd OpenELIS-Global-2/dataexport
+        mvn clean install -DskipTests
+
+3.   Build the War file
+
+            cd OpenELIS-Global-2
+            mvn clean install -DskipTests
+
+4. Start the containers to mount the locally compiled artifacts
+
+        docker-compose -f dev.docker-compose.yml up -d    
+
 #### The Instaces can be accesed at 
 
 | Instance  |     URL       | credentials (user : password)|

build.docker-compose.yml

@@ -114,6 +114,8 @@ services:
       - certs-vol:/etc/nginx/certs/
       - keys-vol:/etc/nginx/keys/
       - ./volume/nginx/nginx.conf:/etc/nginx/nginx.conf:ro
+    networks:
+      - default  
     restart: unless-stopped
     depends_on:
       - certs

dev.docker-compose.yml

@@ -0,0 +1,134 @@
+version: '3.3'
+services:
+    certs:
+        container_name: oe-certs 
+        image: ghcr.io/i-tech-uw/certgen:main
+        restart: always
+        environment:
+            - KEYSTORE_PW="kspass"
+            - TRUSTSTORE_PW="tspass"
+        networks:
+            - default
+        volumes:
+            -  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 
+
+    oe.openelis.org:
+        container_name: openelisglobal-webapp 
+        image: ghcr.io/i-tech-uw/openelis-global-2:2.8    
+        depends_on:
+            - database
+        ports:
+            - "8080:8080"
+            - "8443:8443"
+        restart: always
+        networks:
+          default:
+              ipv4_address: 172.20.1.121
+
+        environment:
+            - DEFAULT_PW=adminADMIN! 
+            - TZ=Africa/Nairobi
+              # context.xml doesn't seem to be able to pick up environment variables directly, so we are passing them in as CATALINA_OPTS
+            - CATALINA_OPTS= -Ddatasource.url=jdbc:postgresql://database:5432/clinlims -Ddatasource.username=clinlims
+        volumes:
+            -  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
+            - ./target/OpenELIS-Global.war:/usr/local/tomcat/webapps/OpenELIS-Global.war
+        secrets:
+            - source: datasource.password
+            - source: common.properties
+
+    fhir.openelis.org:
+        container_name: external-fhir-api
+        image: hapiproject/hapi:v5.5.1
+        ports:
+            - "8081:8080"
+            - "8444:8443"
+        networks:
+            - default
+        restart: always
+        environment:
+          TZ: Africa/Nairobi
+
+          JAVA_OPTS: "-Djavax.net.ssl.trustStore=/etc/openelis-global/truststore 
+                      -Djavax.net.ssl.trustStorePassword=tspass
+                      -Djavax.net.ssl.trustStoreType=pkcs12 
+                      -Djavax.net.ssl.keyStore=/etc/openelis-global/keystore 
+                      -Djavax.net.ssl.keyStorePassword=kspass 
+                      -Djavax.net.ssl.keyStoreType=pkcs12"            
+
+        volumes:
+            -  key_trust-store-volume:/etc/openelis-global
+            - ./volume/tomcat/hapi_server.xml:/usr/local/tomcat/conf/server.xml
+
+
+    frontend.openelis.org:
+        image: ghcr.io/i-tech-uw/openelis-global-2-frontend-dev:2.8
+        container_name: openelisglobal-front-end
+        networks:
+            - default
+        volumes:
+            - './frontend/src:/app/src'
+            - './frontend/public:/app/public'
+        environment:
+            - CHOKIDAR_USEPOLLING=true
+        tty: true
+
+    proxy:
+        image: nginx:1.15-alpine
+        container_name: openelisglobal-proxy
+        ports:
+            - 80:80
+            - 443:443
+        volumes:
+            - certs-vol:/etc/nginx/certs/
+            - keys-vol:/etc/nginx/keys/
+            - ./volume/nginx/nginx.conf:/etc/nginx/nginx.conf:ro
+        networks:
+            - default
+        restart: unless-stopped
+        depends_on:
+        - certs        
+
+secrets:
+  datasource.password:
+    file: ./volume/properties/datasource.password  
+  common.properties:
+    file:  ./volume/properties/common.properties  
+
+networks:
+  default:
+    driver: bridge
+    ipam:
+      config:
+        - subnet: 172.20.1.0/24  
+
+volumes:
+  db-data:
+  key_trust-store-volume:
+  certs-vol:
+  keys-vol:

docker-compose.yml

@@ -88,13 +88,8 @@ services:
     frontend.openelis.org:
         image: ghcr.io/i-tech-uw/openelis-global-2-frontend:2.8
         container_name: openelisglobal-front-end
-        # ports:
-        #   - 80:80
         networks:
         - default
-        volumes:
-        - './react-ui/src:/app/src'
-        - './react-ui/public:/app/public'
         environment:
         - CHOKIDAR_USEPOLLING=true
         tty: true
@@ -103,12 +98,14 @@ services:
         image: nginx:1.15-alpine
         container_name: openelisglobal-proxy
         ports:
-        - 80:80
-        - 443:443
+            - 80:80
+            - 443:443
         volumes:
-        - certs-vol:/etc/nginx/certs/
-        - keys-vol:/etc/nginx/keys/
-        - ./volume/nginx/nginx-prod.conf:/etc/nginx/nginx.conf:ro
+            - certs-vol:/etc/nginx/certs/
+            - keys-vol:/etc/nginx/keys/
+            - ./volume/nginx/nginx-prod.conf:/etc/nginx/nginx.conf:ro
+        networks:
+            - default
         restart: unless-stopped
         depends_on:
         - certs        

frontend/src/components/addOrder/AddOrder.js

@@ -31,10 +31,9 @@ const AddOrder = (props) => {
   const [siteNames, setSiteNames] = useState([]);
   const [innitialized, setInnitialized] = useState(false);
   const [phoneFormat, setPhoneFormat] = useState("");
-  const configurationProperties = useContext(ConfigurationContext);
+  const { configurationProperties } = useContext(ConfigurationContext);
   const [departments, setDepartments] = useState([]);
 
-
   const handleDatePickerChange = (datePicker, date) => {
     let obj = null;
     switch (datePicker) {
@@ -246,9 +245,9 @@ const AddOrder = (props) => {
       loadDepartments,
     );
   }
-  const loadDepartments =(data) => {
+  const loadDepartments = (data) => {
     setDepartments(data);
-  }
+  };
 
   function handleLabNo(e) {
     setOrderFormValues({
@@ -308,7 +307,6 @@ const AddOrder = (props) => {
     });
   }
 
-
   useEffect(() => {
     if (!innitialized) {
       setPhoneFormat(configurationProperties.phoneFormat);
@@ -332,7 +330,6 @@ const AddOrder = (props) => {
     if (orderFormValues.sampleOrderItems.requestDate != "") {
       setInnitialized(true);
     }
-
   }, [orderFormValues]);
 
   function handlePriority(e) {
@@ -445,7 +442,7 @@ const AddOrder = (props) => {
               id={"order_receivedDate"}
               labelText={<FormattedMessage id="sample.receivedDate" />}
               className="inputDate"
-               autofillDate={true}
+              autofillDate={true}
               value={orderFormValues.sampleOrderItems.receivedDateForDisplay}
               onChange={(date) => handleDatePickerChange("receivedDate", date)}
             />
@@ -667,7 +664,10 @@ const AddOrder = (props) => {
             if (sample.tests.length > 0) {
               return (
                 <div key={index}>
-                  <h4> <FormattedMessage id="label.button.sample" /> {index + 1}</h4>
+                  <h4>
+                    {" "}
+                    <FormattedMessage id="label.button.sample" /> {index + 1}
+                  </h4>
                   <OrderResultReporting
                     selectedTests={sample.tests}
                     reportingNotifications={reportingNotifications}

frontend/src/components/addOrder/Index.js

@@ -54,6 +54,7 @@ const Index = () => {
         <FormattedMessage id="save.order.success.msg" />,
         NotificationKinds.success,
       );
+      setPage(page + 1);
     } else {
       showAlertMessage(
         <FormattedMessage id="server.error.msg" />,
@@ -63,7 +64,6 @@ const Index = () => {
   };
   const handleSubmitOrderForm = (e) => {
     e.preventDefault();
-    setPage(page + 1);
     console.log(JSON.stringify(orderFormValues))
     postToOpenElisServer(
       "/rest/SamplePatientEntry",