Merge branch 'development' into 13461-chest-pain-missing-from-symptoms-for-plague

Author: KarnaiahPesula

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-        <version>1.102.0-SNAPSHOT</version>
+        <version>1.103.0-SNAPSHOT</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

sormas-api/src/main/java/de/symeda/sormas/api/adverseeventsfollowingimmunization/AefiCriteria.java

@@ -71,6 +71,7 @@ public class AefiCriteria extends BaseCriteria implements Serializable {
 	private Date toDate;
 	private EntityRelevanceStatus relevanceStatus;
 
+	private Boolean gisMapCriteria = false;
 	private Boolean showSeriousAefiForMap = false;
 	private Boolean showNonSeriousAefiForMap = false;
 
@@ -230,6 +231,11 @@ public AefiCriteria aefiType(AefiType aefiType) {
 		return this;
 	}
 
+	public AefiCriteria gisMapCriteria(Boolean gisMapCriteria) {
+		this.gisMapCriteria = gisMapCriteria;
+		return this;
+	}
+
 	public AefiCriteria showSeriousAefiForMap(Boolean showSeriousAefi) {
 		this.showSeriousAefiForMap = showSeriousAefi;
 		return this;
@@ -240,6 +246,10 @@ public AefiCriteria showNonSeriousAefiForMap(Boolean showNonSeriousAefi) {
 		return this;
 	}
 
+	public Boolean isGisMapCriteria() {
+		return gisMapCriteria;
+	}
+
 	public Boolean isShowSeriousAefiForMap() {
 		return showSeriousAefiForMap;
 	}

sormas-api/src/main/java/de/symeda/sormas/api/dashboard/AefiDashboardCriteria.java

@@ -23,6 +23,7 @@ public class AefiDashboardCriteria extends BaseDashboardCriteria<AefiDashboardCr
 	private AefiDashboardFilterDateType aefiDashboardFilterDateType;
 	private AefiType aefiType;
 
+	private boolean gisMapCriteria;
 	private boolean showSeriousAefiForMap;
 	private boolean showNonSeriousAefiForMap;
 
@@ -38,6 +39,10 @@ public AefiType getAefiType() {
 		return aefiType;
 	}
 
+	public boolean isGisMapCriteria() {
+		return gisMapCriteria;
+	}
+
 	public boolean isShowSeriousAefiForMap() {
 		return showSeriousAefiForMap;
 	}
@@ -56,6 +61,11 @@ public AefiDashboardCriteria aefiType(AefiType aefiType) {
 		return self;
 	}
 
+	public AefiDashboardCriteria gisMapCriteria(boolean gisMapCriteria) {
+		this.gisMapCriteria = gisMapCriteria;
+		return self;
+	}
+
 	public AefiDashboardCriteria showSeriousAefiForMap(boolean showSeriousAefi) {
 		this.showSeriousAefiForMap = showSeriousAefi;
 		return self;

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/processing/doctordeclaration/AbstractDoctorDeclarationMessageProcessingFlow.java

@@ -13,7 +13,7 @@
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
  */
 
-package de.symeda.sormas.api.externalmessage.processing.labmessage;
+package de.symeda.sormas.api.externalmessage.processing.doctordeclaration;
 
 import java.util.ArrayList;
 import java.util.Date;

sormas-api/src/main/java/de/symeda/sormas/api/importexport/DatabaseTable.java

@@ -158,7 +158,9 @@ public enum DatabaseTable {
 	SYSTEM_CONFIGURATION_VALUES(DatabaseTableType.CONFIGURATION, "system_configuration_values", null),
 	SYSTEM_CONFIGURATION_CATEGORIES(DatabaseTableType.CONFIGURATION, "system_configuration_categories", null),
 
-	NOTIFIER(DatabaseTableType.SORMAS, "notifier", null);
+	NOTIFIER(DatabaseTableType.SORMAS, "notifier", null),
+
+	DRUG_SUSCEPTIBILITY(DatabaseTableType.SORMAS, "drug_susceptibility", null);
 
 	private static BiFunction<List<FeatureConfigurationDto>, ConfigFacade, Boolean> dependingOnFeature(FeatureType... featureTypes) {
 		return (featureConfigurations, configFacade) -> featureConfigurations.stream()

sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestDto.java

@@ -267,7 +267,8 @@ public static PathogenTestDto build(EnvironmentSampleDto environmentSample, User
 		PathogenTestDto pathogenTest = new PathogenTestDto();
 		pathogenTest.setUuid(DataHelper.createUuid());
 		pathogenTest.setEnvironmentSample(environmentSample.toReference());
-
+		// Initialize with an empty drug susceptibility to avoid multiple unnecessary conditional addFields ana checks of the drug susceptibility field in the form
+		pathogenTest.setDrugSusceptibility(DrugSusceptibilityDto.build());
 		pathogenTest.setLab(currentUser.getLaboratory());
 		if (pathogenTest.getLab() == null) {
 			pathogenTest.setLab(environmentSample.getLaboratory());

sormas-api/src/main/java/de/symeda/sormas/api/utils/AnnotationFieldHelper.java

@@ -41,31 +41,32 @@ public static List<String> getFieldNamesWithMatchingDiseaseAndTestAnnotations(
 		Field[] fields = clazz.getDeclaredFields();
 
 		for (Field field : fields) {
-			boolean matches = false;
+			boolean diseaseMatches = false;
+			boolean pathogenTestMatches = false;
 
 			// Check @Diseases annotation
 			if (diseases != null && !diseases.isEmpty()) {
 				Diseases diseasesAnnotation = field.getAnnotation(Diseases.class);
 				if (diseasesAnnotation != null) {
 					List<Disease> fieldDiseases = Arrays.asList(diseasesAnnotation.value());
 					if (fieldDiseases.stream().anyMatch(diseases::contains)) {
-						matches = true;
+						diseaseMatches = true;
 					}
 				}
 			}
 
 			// Check @ApplicableToPathogenTests annotation
-			if (matches && pathogenTestTypes != null && !pathogenTestTypes.isEmpty()) {
+			if (diseaseMatches && pathogenTestTypes != null && !pathogenTestTypes.isEmpty()) {
 				ApplicableToPathogenTests pathogenTestsAnnotation = field.getAnnotation(ApplicableToPathogenTests.class);
 				if (pathogenTestsAnnotation != null) {
 					List<PathogenTestType> fieldTestTypes = Arrays.asList(pathogenTestsAnnotation.value());
 					if (fieldTestTypes.stream().anyMatch(pathogenTestTypes::contains)) {
-						matches = true;
+						pathogenTestMatches = true;
 					}
 				}
 			}
 
-			if (matches) {
+			if (diseaseMatches && pathogenTestMatches) {
 				matchingFieldNames.add(field.getName());
 			}
 		}

sormas-api/src/main/resources/enum.properties

@@ -2649,7 +2649,7 @@ RadiographyCompatibility.NOT_COMPATIBLE_WITH_TB = Not compatible with TB regardl
 
 # ClinicalPresentationStatus
 ClinicalPresentationStatus.ASYMPTOMATIC=Asymtomatic
-ClinicalPresentationStatus.COMPATIBLE=Signs and symptoms compatible with %s regardless of the anatomical site
+ClinicalPresentationStatus.COMPATIBLE=Signs and symptoms compatible regardless of the anatomical site
 ClinicalPresentationStatus.UNKNOWN=Unknown
 
 # InfectionSite

sormas-app/README.md

@@ -4,7 +4,7 @@ The SORMAS Android app is designed for use by users at the level of hospitals, c
 These have only limited access to the overall data of the system, so it is possible to transfer the relevant data set and make it available offline.
 
 The **offline** functionality was also one of the core requirements in the development of the app, as it is also to be used in areas where no or hardly any mobile data network is available.
-This makes it possible for users to use the app freely and, for example, to synchronise the recorded data with the server in the evening.
+This makes it possible for users to use the app freely and, for example, to synchronize the recorded data with the server in the evening.
 
 The app covers **all essential functionalities of SORMAS** and the complete data collection in the areas of
 cases, contacts, events, samples, messages, aggregate reports and tasks.
@@ -14,9 +14,9 @@ To manage the large number of devices used within a country and to simplify supp
 
 ## Data Synchronization
 
-For synchronisation, the Android app accesses the **SORMAS ReST** interface.
+For synchronization, the Android app accesses the **SORMAS ReST** interface.
 
-First, all data that has changed since the last synchronisation is retrieved from the server.
+First, all data that has changed since the last synchronization is retrieved from the server.
 In the app, a three-way merge takes place for all data that the user has changed himself in the meantime.
 For each individual field (e.g. gender of a person), it is checked whether the value on the server has changed compared to the original status on the device.
 If so, this change is adopted, otherwise any existing change of the user is retained.
@@ -48,7 +48,7 @@ During the update **existing data is automatically migrated** using the commands
 
 ## Device Encryption
 
-Each Android device using SORMAS should ahve device encryption enabled. This is currently not enforced.
+Each Android device using SORMAS should have device encryption enabled. This is currently not enforced.
 
 ## Data Storage
 

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/common/DatabaseHelper.java

@@ -3179,9 +3179,33 @@ public void onUpgrade(SQLiteDatabase db, ConnectionSource connectionSource, int
 				getDao(UserRole.class)
 					.executeRaw("ALTER TABLE userroles ADD COLUMN restrictAccessToAssignedEntities boolean NOT NULL DEFAULT false;");
 
+			case 359:
+				currentVersion = 359;
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN apnoea varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN arthritis varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN asymptomatic varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN clinicalpresentationstatus varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN coughingbouts varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN coughsprovokevomiting varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN dateofonsetknown varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN diagnosis varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN hemorrhagicrash varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN majorsite varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN meningitis varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN minorsite varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN nocturnalcough varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN otherclinicalpresentation varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN otherclinicalpresentationtext varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN othermajorsitedetails varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN otherminorsitedetails varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN septicaemia varchar(255);");
+				getDao(Symptoms.class).executeRaw("ALTER TABLE symptoms ADD COLUMN whoopsound varchar(255);");
+
 				// ATTENTION: break should only be done after last version
 				break;
 
+
+
 			default:
 				throw new IllegalStateException("onUpgrade() with unknown oldVersion " + oldVersion);
 			}