Merge pull request #13988 from SORMAS-Foundation/feature-13965-shigellosis-lab-messages

Shigellosis lab message processing + minor defects.

Author: KarnaiahPesula

sormas-api/src/main/java/de/symeda/sormas/api/clinicalcourse/HealthConditionsDto.java

@@ -60,7 +60,7 @@ public class HealthConditionsDto extends PseudonymizableDto {
 	public static final String VACCINATED_AGAINST_MOSQUITO_BORNE_VIRUSES = "vaccinatedAgainstMosquitoBorneViruses";
 	public static final String MALARIA = "malaria";
 	public static final String MALARIA_INFECTED_YEAR = "malariaInfectedYear";
-	public static final String UNDER_MEDICATION = "underMedication";
+	public static final String ON_MEDICATION = "onMedication";
 	public static final String MEDICATION_DETAILS = "medicationDetails";
 	public static final String CHRONIC_DISEASE = "chronicDisease";
 	public static final String CHRONIC_DISEASE_DETAILS = "chronicDiseaseDetails";
@@ -201,7 +201,7 @@ public class HealthConditionsDto extends PseudonymizableDto {
 	private Integer malariaInfectedYear;
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
-	private YesNoUnknown underMedication;
+	private YesNoUnknown onMedication;
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
 	private String medicationDetails;
@@ -506,12 +506,12 @@ public void setMalariaInfectedYear(Integer malariaInfectedYear) {
 		this.malariaInfectedYear = malariaInfectedYear;
 	}
 
-	public YesNoUnknown getUnderMedication() {
-		return underMedication;
+	public YesNoUnknown getOnMedication() {
+		return onMedication;
 	}
 
-	public void setUnderMedication(YesNoUnknown underMedication) {
-		this.underMedication = underMedication;
+	public void setOnMedication(YesNoUnknown onMedication) {
+		this.onMedication = onMedication;
 	}
 
 	public String getMedicationDetails() {

sormas-api/src/main/java/de/symeda/sormas/api/exposure/ExposureDto.java

@@ -142,6 +142,7 @@ public class ExposureDto extends PseudonymizableDto {
 	public static final String TRAVEL_PURPOSE = "travelPurpose";
 	public static final String TRAVEL_PURPOSE_DETAILS = "travelPurposeDetails";
 	public static final String SHOPPING_FOR_FOOD_DETAILS = "shoppingForFoodDetails";
+	public static final String SEXUAL_CONTACT = "sexualContact";
 
 	@SensitiveData
 	private UserReferenceDto reportingUser;
@@ -466,6 +467,11 @@ public class ExposureDto extends PseudonymizableDto {
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_DEFAULT, message = Validations.textTooLong)
 	private String shoppingForFoodDetails;
 
+	@Diseases({
+		Disease.SHIGELLOSIS })
+	@SensitiveData
+	private SexualContact sexualContact;
+
 	public static ExposureDto build(ExposureType exposureType) {
 
 		ExposureDto exposure = new ExposureDto();
@@ -1169,6 +1175,14 @@ public void setShoppingForFoodDetails(String shoppingForFoodDetails) {
 		this.shoppingForFoodDetails = shoppingForFoodDetails;
 	}
 
+	public SexualContact getSexualContact() {
+		return sexualContact;
+	}
+
+	public void setSexualContact(SexualContact sexualContact) {
+		this.sexualContact = sexualContact;
+	}
+
 	@Override
 	public ExposureDto clone() throws CloneNotSupportedException {
 		ExposureDto clone = (ExposureDto) super.clone();

sormas-api/src/main/java/de/symeda/sormas/api/exposure/ExposureSubSetting.java

@@ -51,6 +51,9 @@ public enum ExposureSubSetting {
 
 	EATING_AT_HOME(ExposureCategory.FOOD_BORNE, null),
 	EATING_OUTSIDE(ExposureCategory.FOOD_BORNE, null),
+	@Diseases({
+		Disease.SHIGELLOSIS })
+	HOUSEHOLD_CONTACT(ExposureCategory.DIRECT_CONTACT, ExposureSetting.PERSON_TO_PERSON),
 	@Diseases({
 		Disease.SALMONELLOSIS })
 	SHOPPING_FOR_FOOD(ExposureCategory.FOOD_BORNE, null),

sormas-api/src/main/java/de/symeda/sormas/api/exposure/SexualContact.java

@@ -0,0 +1,35 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2026 SORMAS Foundation gGmbH
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ */
+package de.symeda.sormas.api.exposure;
+
+import de.symeda.sormas.api.i18n.I18nProperties;
+
+/**
+ * Enum for sexual contact types.
+ */
+public enum SexualContact {
+
+	MALE,
+	FEMALE,
+	BOTH,
+	NOT_ANSWERED,
+	UNKNOWN,
+	OTHER;
+
+	@Override
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	}
+}

sormas-api/src/main/java/de/symeda/sormas/api/externalmessage/labmessage/TestReportDto.java

@@ -15,6 +15,7 @@
 import de.symeda.sormas.api.sample.PCRTestSpecification;
 import de.symeda.sormas.api.sample.PathogenSpecie;
 import de.symeda.sormas.api.sample.PathogenStrainCallStatus;
+import de.symeda.sormas.api.sample.PathogenTestCategory;
 import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.PathogenTestType;
 import de.symeda.sormas.api.sample.RsvSubtype;
@@ -217,6 +218,8 @@ public class TestReportDto extends EntityDto {
 	@Size(max = FieldConstraints.CHARACTER_LIMIT_SMALL, message = Validations.textTooLong)
 	private String serotypeText;
 
+	private PathogenTestCategory pathogenTestCategory;
+
 	public SampleReportReferenceDto getSampleReport() {
 		return sampleReport;
 	}
@@ -912,4 +915,11 @@ public void setSerotypeText(String serotypeText) {
 		this.serotypeText = serotypeText;
 	}
 
+	public PathogenTestCategory getPathogenTestCategory() {
+		return pathogenTestCategory;
+	}
+
+	public void setPathogenTestCategory(PathogenTestCategory pathogenTestCategory) {
+		this.pathogenTestCategory = pathogenTestCategory;
+	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java

@@ -1968,6 +1968,7 @@ public interface Captions {
 	String Exposure_rawFoodContactText = "Exposure.rawFoodContactText";
 	String Exposure_riskArea = "Exposure.riskArea";
 	String Exposure_seatNumber = "Exposure.seatNumber";
+	String Exposure_sexualContact = "Exposure.sexualContact";
 	String Exposure_sexualExposureText = "Exposure.sexualExposureText";
 	String Exposure_shoppingForFoodDetails = "Exposure.shoppingForFoodDetails";
 	String Exposure_shortDistance = "Exposure.shortDistance";
@@ -2139,13 +2140,13 @@ public interface Captions {
 	String HealthConditions_malignancyChemotherapy = "HealthConditions.malignancyChemotherapy";
 	String HealthConditions_medicationDetails = "HealthConditions.medicationDetails";
 	String HealthConditions_obesity = "HealthConditions.obesity";
+	String HealthConditions_onMedication = "HealthConditions.onMedication";
 	String HealthConditions_otherConditions = "HealthConditions.otherConditions";
 	String HealthConditions_previousTuberculosisTreatment = "HealthConditions.previousTuberculosisTreatment";
 	String HealthConditions_recurrentBronchiolitis = "HealthConditions.recurrentBronchiolitis";
 	String HealthConditions_sickleCellDisease = "HealthConditions.sickleCellDisease";
 	String HealthConditions_tuberculosis = "HealthConditions.tuberculosis";
 	String HealthConditions_tuberculosisInfectionYear = "HealthConditions.tuberculosisInfectionYear";
-	String HealthConditions_underMedication = "HealthConditions.underMedication";
 	String HealthConditions_vaccinatedAgainstMosquitoBorneViruses = "HealthConditions.vaccinatedAgainstMosquitoBorneViruses";
 	String humanSampleViewType = "humanSampleViewType";
 	String Immunization = "Immunization";

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

@@ -172,27 +172,37 @@ public enum PathogenSpecie {
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
 	@ApplicableToPathogenTests(value = {
-		PathogenTestType.SEROGROUPING })
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING,
+		PathogenTestType.BACTERIAL_CULTURE })
 	BOYDII,
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
 	@ApplicableToPathogenTests(value = {
-		PathogenTestType.SEROGROUPING })
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING,
+		PathogenTestType.BACTERIAL_CULTURE })
 	DYSENTERIAE,
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
 	@ApplicableToPathogenTests(value = {
-		PathogenTestType.SEROGROUPING })
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING,
+		PathogenTestType.BACTERIAL_CULTURE })
 	FLEXNERI,
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
 	@ApplicableToPathogenTests(value = {
-		PathogenTestType.SEROGROUPING })
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING,
+		PathogenTestType.BACTERIAL_CULTURE })
 	SONNEI,
 	@Diseases(value = {
 		Disease.SHIGELLOSIS })
 	@ApplicableToPathogenTests(value = {
-		PathogenTestType.SEROGROUPING })
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING,
+		PathogenTestType.BACTERIAL_CULTURE })
 	SHIGELLA_SPP,
 	@Diseases({
 		Disease.MALARIA,
@@ -206,7 +216,10 @@ public enum PathogenSpecie {
 		PathogenTestType.Q_PCR,
 		PathogenTestType.LAMP,
 		PathogenTestType.OTHER_MOLECULAR_ASSAY,
-		PathogenTestType.OTHER_SEROLOGICAL_TEST })
+		PathogenTestType.OTHER_SEROLOGICAL_TEST,
+		PathogenTestType.BACTERIAL_CULTURE,
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING })
 	OTHER,
 	@Diseases({
 		Disease.TUBERCULOSIS,
@@ -223,7 +236,10 @@ public enum PathogenSpecie {
 		PathogenTestType.Q_PCR,
 		PathogenTestType.LAMP,
 		PathogenTestType.OTHER_MOLECULAR_ASSAY,
-		PathogenTestType.OTHER_SEROLOGICAL_TEST })
+		PathogenTestType.OTHER_SEROLOGICAL_TEST,
+		PathogenTestType.BACTERIAL_CULTURE,
+		PathogenTestType.SEROGROUPING,
+		PathogenTestType.SEROTYPING })
 	UNKNOWN,
 	@Diseases({
 		Disease.TUBERCULOSIS,