Merge branch 'develop' of github.com:I-TECH-UW/OpenELIS-Global-2 into…

… develop
I-TECH-UW · Nov 4, 2024 · 36bf8ec · 36bf8ec
2 parents 29e56da + 633eb2e
commit 36bf8ec
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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
@@ -389,6 +389,7 @@ jobs:
           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
@@ -431,6 +432,7 @@ jobs:
           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

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:

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/src/components/addOrder/OrderEntryAdditionalQuestions.js b/frontend/src/components/addOrder/OrderEntryAdditionalQuestions.js
@@ -381,18 +381,20 @@ const OrderEntryAdditionalQuestions = ({
 
   function setAdditionalQuestions(res, event) {
     console.debug(res);
-    setQuestionnaire(res);
-    var convertedQuestionnaireResponse = convertQuestionnaireToResponse(res);
-    setQuestionnaireResponse(convertedQuestionnaireResponse);
-    setOrderFormValues({
-      ...orderFormValues,
-      sampleOrderItems: {
-        ...orderFormValues.sampleOrderItems,
-        questionnaire: res,
-        programId: event ? event.target.value : "",
-        additionalQuestions: convertedQuestionnaireResponse,
-      },
-    });
+    if ("item" in res) {
+      setQuestionnaire(res);
+      var convertedQuestionnaireResponse = convertQuestionnaireToResponse(res);
+      setQuestionnaireResponse(convertedQuestionnaireResponse);
+      setOrderFormValues({
+        ...orderFormValues,
+        sampleOrderItems: {
+          ...orderFormValues.sampleOrderItems,
+          questionnaire: res,
+          programId: event ? event.target.value : "",
+          additionalQuestions: convertedQuestionnaireResponse,
+        },
+      });
+    }
   }
   const getAnswer = (linkId) => {
     var responseItem = questionnaireResponse?.item?.find(

diff --git a/frontend/src/components/admin/reflexTests/ReflexStyles.css b/frontend/src/components/admin/reflexTests/ReflexStyles.css
@@ -26,12 +26,17 @@ body {
   margin-left: 0px;
   overflow-y: auto;
   padding-left: 0px;
-  width: 30%;
+  width: 100%;
   z-index: 10;
   position: absolute;
   background-color: #ffffff;
 }
 
+.suggestions-container {
+  position: relative;
+  width: 100%;
+}
+
 .suggestions li {
   padding: 0.5rem;
   z-index: 99 !important;

diff --git a/frontend/src/components/common/AutoComplete.js b/frontend/src/components/common/AutoComplete.js
@@ -88,24 +88,26 @@ function AutoComplete(props) {
   if (showSuggestions && userInput) {
     if (filteredSuggestions.length) {
       suggestionsListComponent = (
-        <ul className="suggestions">
-          {filteredSuggestions.map((suggestion, index) => {
-            let className;
-            // Flag the active suggestion with a class
-            if (index === activeSuggestion) {
-              className = "suggestion-active";
-            }
-            return (
-              <li
-                className={className}
-                key={index}
-                onClick={(e) => onClick(e, suggestion.id, suggestion)}
-              >
-                {suggestion.value}
-              </li>
-            );
-          })}
-        </ul>
+        <div className="suggestions-container">
+          <ul className="suggestions">
+            {filteredSuggestions.map((suggestion, index) => {
+              let className;
+              // Flag the active suggestion with a class
+              if (index === activeSuggestion) {
+                className = "suggestion-active";
+              }
+              return (
+                <li
+                  className={className}
+                  key={index}
+                  onClick={(e) => onClick(e, suggestion.id, suggestion)}
+                >
+                  {suggestion.value}
+                </li>
+              );
+            })}
+          </ul>
+        </div>
       );
     } else {
       suggestionsListComponent = (

diff --git a/frontend/src/components/common/PatientHeader.js b/frontend/src/components/common/PatientHeader.js
@@ -32,7 +32,7 @@ const PatientHeader = (props) => {
             {id ? (
               <div className={className}>
                 <Grid>
-                  <Column lg={4} md={2} sm={2}>
+                  <Column lg={4} md={2} sm={1}>
                     <div
                       className={
                         referringFacility ? "patientAvatar2" : "patientAvatar"
@@ -55,7 +55,7 @@ const PatientHeader = (props) => {
                       />
                     </div>
                   </Column>
-                  <Column lg={10} md={5} sm={2}>
+                  <Column lg={10} md={5} sm={3}>
                     <div className="patient-name">
                       {patientName ? patientName : lastName + " " + firstName}
                     </div>
@@ -137,7 +137,7 @@ const PatientHeader = (props) => {
             ) : (
               <div className={className}>
                 <Grid>
-                  <Column lg={4} md={2} sm={2}>
+                  <Column lg={4} md={2} sm={1}>
                     <Avatar
                       alt={"Patient avatar"}
                       color="rgba(0,0,0,0)"

diff --git a/frontend/src/components/layout/search/searchBar.css b/frontend/src/components/layout/search/searchBar.css
@@ -7,7 +7,7 @@
 .search-bar-container {
   position: absolute;
   display: flex;
-  width: 430px;
+  width: 100%;
   top: 10px;
   right: -30px;
   box-shadow: 0em 0.1em 0.05em #ccc;
@@ -24,11 +24,12 @@
 
 .patients {
   overflow-y: auto;
-  width: 700px;
+  width: 100%;
   max-height: 250px;
-  position: relative;
+  position: absolute;
   background-color: #f0e7e7;
   top: 45px;
+  right: -30px;
   box-shadow: 0em 0.1em 0.5em #ccc;
 }
 

diff --git a/frontend/src/components/patient/resultsViewer/results-viewer.styles.scss b/frontend/src/components/patient/resultsViewer/results-viewer.styles.scss
@@ -203,3 +203,19 @@
   height: 5rem;
   border-radius: 1px;
 }
+@media screen and (max-width: 673px) {
+  .patient-name {
+    font-size: 16px;
+    margin-left: 5%;
+  }
+
+  .patient-dob {
+    font-size: 14px;
+    margin-left: 5%;
+  }
+
+  .patient-id {
+    font-size: 12px;
+    margin-left: 5%;
+  }
+}
diff --git a/frontend/src/components/patient/resultsViewer/results-viewer.tsx b/frontend/src/components/patient/resultsViewer/results-viewer.tsx
@@ -88,7 +88,7 @@ const RoutedResultsViewer: React.FC<ResultsViewerProps> = () => {
       <>
         <Loading></Loading>
         <Grid fullWidth={true}>
-          <Column lg={16}>
+          <Column lg={16} md={8} sm={4}>
             <EmptyState
               headerTitle={intl.formatMessage({ id: "label.test.results" })}
               displayText={intl.formatMessage({
@@ -104,7 +104,7 @@ const RoutedResultsViewer: React.FC<ResultsViewerProps> = () => {
   return (
     <>
       <Grid fullWidth={true}>
-        <Column lg={16}>
+        <Column lg={16} md={8} sm={4}>
           <Breadcrumb>
             <BreadcrumbItem href="/">
               {intl.formatMessage({ id: "home.label" })}
@@ -116,7 +116,7 @@ const RoutedResultsViewer: React.FC<ResultsViewerProps> = () => {
         </Column>
       </Grid>
       <Grid fullWidth={true}>
-        <Column lg={16}>
+        <Column lg={16} md={8} sm={4}>
           <Section>
             <Section>
               <Heading>
@@ -127,7 +127,7 @@ const RoutedResultsViewer: React.FC<ResultsViewerProps> = () => {
         </Column>
       </Grid>
       <Grid fullWidth={true}>
-        <Column lg={16}>
+        <Column lg={16} md={8} sm={4}>
           <PatientHeader
             id={patient.patientPK}
             lastName={patient.lastName}
@@ -145,7 +145,7 @@ const RoutedResultsViewer: React.FC<ResultsViewerProps> = () => {
 
       {roots?.length ? (
         <Grid fullWidth={true} className="orderLegendBody">
-          <Column lg={16}>
+          <Column lg={16} md={8} sm={4}>
             <FilterProvider roots={loading ? roots : []}>
               <ResultsViewer
                 patientId={patientId}