Merge branch 'I-TECH-UW:develop' into Add-intergattion-test-for-Sampl…

…eHumanService

.github/workflows/ci.yml

@@ -31,11 +31,11 @@ jobs:
       - name: check formatting
         run: mvn spotless:check
 
-      - name: Initialize and build submodules
-        run: |
-          cd dataexport
-          mvn clean install  
-          cd ..
+      # - name: Initialize and build submodules
+      #   run: |
+      #     cd dataexport
+      #     mvn clean install  
+      #     cd ..
 
       - name: Build OpenELIS-Global2
         run: mvn clean install -Dspotless.check.skip=true

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "plugins"]
 	path = plugins
-	url = https://github.com/openelisglobal/openelisglobal-plugins.git
+	url = https://github.com/I-TECH-UW/openelisglobal-plugins.git
 [submodule "tools/Liquibase-Outdated"]
 	path = tools/Liquibase-Outdated
 	url = https://github.com/I-TECH-UW/Liquibase-Outdated.git

Dockerfile

@@ -20,18 +20,21 @@ RUN ./install/createDefaultPassword.sh -c -p ${DEFAULT_PW}
 ##
 # Build DataExport
 #
-COPY ./dataexport /build/dataexport
-WORKDIR /build/dataexport/dataexport-core
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn dependency:go-offline 
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn clean install -DskipTests
-WORKDIR /build/dataexport/
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn dependency:go-offline 
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn clean install -DskipTests
+# COPY ./dataexport /build/dataexport
+# WORKDIR /build/dataexport/dataexport-core
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn dependency:go-offline 
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn clean install -DskipTests
+# WORKDIR /build/dataexport/
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn dependency:go-offline 
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn clean install -DskipTests
 
+##
+# Build the Project
+#  
 WORKDIR /build
 
 COPY ./pom.xml /build/pom.xml

Dockerfile.dev

@@ -16,7 +16,7 @@ RUN --mount=target=/var/lib/apt/lists,type=cache,sharing=locked \
 ADD ./pom.xml /build/pom.xml
 ADD ./tools /build/tools
 ADD ./src /build/src
-ADD ./dataexport /build/dataexport
+# ADD ./dataexport /build/dataexport
 
 WORKDIR /build
 
@@ -28,17 +28,20 @@ RUN ./install/createDefaultPassword.sh -c -p ${DEFAULT_PW}
 ##
 # Build DataExport
 #
-WORKDIR /build/dataexport/dataexport-core
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn dependency:go-offline 
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn clean install -DskipTests
-WORKDIR /build/dataexport/
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn dependency:go-offline 
-RUN --mount=type=cache,target=/root/.m2,sharing=locked \
-    mvn clean install -DskipTests
+# WORKDIR /build/dataexport/dataexport-core
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn dependency:go-offline 
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn clean install -DskipTests
+# WORKDIR /build/dataexport/
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn dependency:go-offline 
+# RUN --mount=type=cache,target=/root/.m2,sharing=locked \
+#     mvn clean install -DskipTests
 
+##
+# Build the Project
+#    
 WORKDIR /build
 
 RUN --mount=type=cache,target=/root/.m2,sharing=locked \

frontend/src/components/admin/Admin.js

@@ -30,6 +30,7 @@ import {
   User,
   BatchJob,
   Popup,
+  Search,
 } from "@carbon/icons-react";
 import PathRoute from "../utils/PathRoute";
 import CalculatedValue from "./calculatedValue/CalculatedValueForm";
@@ -57,6 +58,7 @@ import ManageMethod from "./testManagement/ManageMethod.js";
 import BatchTestReassignmentAndCancelation from "./BatchTestReassignmentAndCancellation/BatchTestReassignmentAndCancelation.js";
 import TestNotificationConfigMenu from "./testNotificationConfigMenu/TestNotificationConfigMenu.js";
 import TestNotificationConfigEdit from "./testNotificationConfigMenu/TestNotificationConfigEdit.js";
+import SearchIndexManagement from "./searchIndexManagement/SearchIndexManagement";
 
 function Admin() {
   const intl = useIntl();
@@ -200,6 +202,9 @@ function Admin() {
           <SideNavLink href="#NotifyUser" renderIcon={Bullhorn}>
             <FormattedMessage id="Notify User" />
           </SideNavLink>
+          <SideNavLink href="#SearchIndexManagement" renderIcon={Search}>
+            <FormattedMessage id="searchindexmanagement.label" />
+          </SideNavLink>
           <SideNavLink
             renderIcon={Catalog}
             target="_blank"
@@ -343,6 +348,9 @@ function Admin() {
       <PathRoute path="#PluginFile">
         <PluginList />
       </PathRoute>
+      <PathRoute path="#SearchIndexManagement">
+        <SearchIndexManagement />
+      </PathRoute>
     </>
   );
 }

frontend/src/components/admin/searchIndexManagement/SearchIndexManagement.js

@@ -0,0 +1,96 @@
+import React, { useState, useContext } from "react";
+import { Button, Loading, Grid, Column, Section, Heading } from "@carbon/react";
+import { FormattedMessage, useIntl, injectIntl } from "react-intl";
+import { getFromOpenElisServer } from "../../utils/Utils";
+import PageBreadCrumb from "../../common/PageBreadCrumb";
+import { NotificationContext } from "../../layout/Layout";
+import {
+  AlertDialog,
+  NotificationKinds,
+} from "../../common/CustomNotification";
+
+function SearchIndexManagement() {
+  const [loading, setLoading] = useState(false);
+  const { notificationVisible, setNotificationVisible, addNotification } =
+    useContext(NotificationContext);
+  const intl = useIntl();
+  const rebuildIndex = async (res) => {
+    setNotificationVisible(true);
+    if (res) {
+      addNotification({
+        kind: NotificationKinds.success,
+        title: intl.formatMessage({ id: "notification.title" }),
+        message: intl.formatMessage({
+          id: "searchindexmanagement.reindex.success",
+        }),
+      });
+    } else {
+      addNotification({
+        kind: NotificationKinds.error,
+        title: intl.formatMessage({ id: "notification.title" }),
+        message: intl.formatMessage({
+          id: "searchindexmanagement.reindex.error",
+        }),
+      });
+    }
+    setLoading(false);
+  };
+  const handleReindexClick = async () => {
+    setLoading(true);
+    getFromOpenElisServer("/rest/reindex", rebuildIndex);
+  };
+
+  const breadcrumbs = [
+    { label: "home.label", link: "/" },
+    {
+      label: "breadcrums.admin.managment",
+      link: "/MasterListsPage",
+    },
+    {
+      label: "searchindexmanagement.label",
+      link: "/MasterListsPage#SearchIndexManagement",
+    },
+  ];
+
+  return (
+    <>
+      {notificationVisible === true ? <AlertDialog /> : ""}
+      {loading && <Loading />}
+      <div className="adminPageContent">
+        <PageBreadCrumb breadcrumbs={breadcrumbs} />
+        <Grid fullWidth={true}>
+          <Column lg={16} md={8} sm={4}>
+            <Section>
+              <Heading>
+                <FormattedMessage id="searchindexmanagement.label" />
+              </Heading>
+            </Section>
+          </Column>
+        </Grid>
+        <div className="orderLegendBody">
+          <Grid>
+            <Column lg={16} md={8} sm={4}>
+              <Section>
+                <Section>
+                  <Heading>
+                    <FormattedMessage id="searchindexmanagement.reindex" />
+                  </Heading>
+                </Section>
+              </Section>
+              <br />
+              <Section>
+                <FormattedMessage id="searchindexmanagement.description" />
+              </Section>
+              <br />
+              <Button onClick={handleReindexClick} disabled={loading}>
+                <FormattedMessage id="searchindexmanagement.reindex" />
+              </Button>
+            </Column>
+          </Grid>
+        </div>
+      </div>
+    </>
+  );
+}
+
+export default injectIntl(SearchIndexManagement);

frontend/src/components/admin/testNotificationConfigMenu/TestNotificationConfigMenu.js

@@ -58,7 +58,7 @@ function TestNotificationConfigMenu() {
 
   const componentMounted = useRef(false);
   const [page, setPage] = useState(1);
-  const [pageSize, setPageSize] = useState(20);
+  const [pageSize, setPageSize] = useState(25);
   const [loading, setLoading] = useState(true);
   const [saveButton, setSaveButton] = useState(true);
   const [testNamesList, setTestNamesList] = useState([]);
@@ -170,7 +170,7 @@ function TestNotificationConfigMenu() {
 
     setTestNotificationConfigMenuDataPost((prevData) => {
       const updatedMenuList = prevData.menuList.map((item) => {
-        if (item.id === rowId) {
+        if (item.testId === rowId) {
           switch (header) {
             case "patientEmail":
               return {
@@ -225,9 +225,13 @@ function TestNotificationConfigMenu() {
       return (
         <TableCell key={cell.id}>
           <Checkbox
-            id={cell.id}
+            id={`checkbox-${row.id}-${cell.info.header}`}
             labelText=""
-            checked={cell.value === "true"}
+            checked={
+              testNotificationConfigMenuDataPost?.menuList.find(
+                (item) => item.testId === row.id,
+              )?.[cell.info.header]?.active || false
+            }
             onChange={(e) => {
               setSaveButton(false);
               handleCheckboxChange(e, row.id, cell.info.header);
@@ -304,7 +308,7 @@ function TestNotificationConfigMenu() {
                   testNotificationConfigMenuDataPost?.menuList
                     ?.slice((page - 1) * pageSize, page * pageSize)
                     ?.map((item) => ({
-                      id: item.id,
+                      id: item.testId,
                       testId: item.testId,
                       patientEmail: item.patientEmail.active ? "true" : "false",
                       patientSMS: item.patientSMS.active ? "true" : "false",

frontend/src/languages/en.json

@@ -1271,5 +1271,10 @@
   "testnotification.testdefault.template": "Default Message for Test",
   "testnotification.testdefault.editIcon": "Edit Test Notification",
   "testnotification.bcc": "BCC",
-  "column.name.testId": "Test Id"
+  "column.name.testId": "Test Id",
+  "searchindexmanagement.label": "Search Index Management",
+  "searchindexmanagement.reindex.success": "Reindexing completed successfully",
+  "searchindexmanagement.reindex.error": "Reindexing failed",
+  "searchindexmanagement.description": "The search index updates automatically when data is added or modified. If you need to manually update the search index, click the Start Reindexing button. This may take some time.",
+  "searchindexmanagement.reindex": "Start Reindexing"
 }

pom.xml

@@ -522,6 +522,11 @@
       <version>4.13.1</version>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>pl.pragmatists</groupId>
+      <artifactId>JUnitParams</artifactId>
+      <version>1.1.0</version>
+    </dependency>
     <dependency>
       <groupId>org.postgresql</groupId>
       <artifactId>postgresql</artifactId>

src/main/java/org/openelisglobal/hibernate/search/massindexer/MassIndexerRestController.java

@@ -15,13 +15,12 @@ public class MassIndexerRestController {
     MassIndexerService massIndexerService;
 
     @GetMapping("/reindex")
-    public ResponseEntity<String> reindex() {
+    public ResponseEntity<Boolean> reindex() {
         try {
             massIndexerService.reindex();
-            return ResponseEntity.ok("Reindexing completed successfully.");
+            return ResponseEntity.ok(true);
         } catch (Exception e) {
-            return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR)
-                    .body("Error occurred during reindexing: " + e.getMessage());
+            return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body(false);
         }
     }
 }

src/main/java/org/openelisglobal/testcalculated/action/util/TestCalculatedUtil.java

@@ -202,9 +202,12 @@ public List<Analysis> addNewTestsToDBForCalculatedTests(List<ResultSet> resultSe
                         ScriptEngine scriptEngine = scriptEngineManager.getEngineByName("JavaScript");
                         String value = null;
                         try {
+                            Log.debug("Caliculation Rule: " + calculation.getName() + " Function : "
+                                    + function.toString());
                             value = scriptEngine.eval(function.toString()).toString();
+                            Log.debug("Caliculation Rule: " + calculation.getName() + " Value  : " + value);
                         } catch (ScriptException e) {
-                            Log.error("Invalid Calication Rule: " + calculation.getName(), e);
+                            Log.error("Invalid Caliculation Rule: " + calculation.getName(), e);
                         }
                         Analysis analysis = createCalculatedResult(resultCalculation, resultSet, calculation, value,
                                 sysUserId);
@@ -257,6 +260,9 @@ private Analysis createCalculatedResult(ResultCalculation resultCalculation, Res
                 result.setMaxNormal(resultLimit.getHighNormal());
                 result.setMinNormal(resultLimit.getLowNormal());
             }
+            if (testResult.getSignificantDigits() != null) {
+                result.setSignificantDigits(Integer.valueOf(testResult.getSignificantDigits()));
+            }
             result.setResultType(testService.getResultType(test));
             result.setSysUserId(systemUserId);
             Boolean resultCalculated = false;
@@ -276,6 +282,10 @@ private Analysis createCalculatedResult(ResultCalculation resultCalculation, Res
                         result.setValue("");
                     }
                 } else if ("N".equals(resultType)) {
+                    if (testResult.getSignificantDigits() != null) {
+                        double factor = Math.pow(10, Double.valueOf(testResult.getSignificantDigits()));
+                        value = String.valueOf(Math.round(Double.valueOf(value) * factor) / factor);
+                    }
                     result.setValue(value);
                     resultCalculated = true;
                 }
@@ -360,7 +370,8 @@ private TestResult getTestResultForCalculation(Calculation calculation) {
             // we are assuming there is only one testResult for a numeric
             // type result
             if (!testResultList.isEmpty()) {
-                return testResultList.get(0);
+                // get the latest modified test result
+                return testResultList.get(testResultList.size() - 1);
             }
         }