Merge pull request #13889 from SORMAS-Foundation/feature-13814-dengue-enhance-sample-form

Summary: Malaria and Dengue Sample and Pathogentestform changes.

Author: KarnaiahPesula

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

@@ -58,6 +58,8 @@ public class HealthConditionsDto extends PseudonymizableDto {
 	public static final String EXPOSED_TO_MOSQUITO_BORNE_VIRUSES = "exposedToMosquitoBorneViruses";
 	public static final String EXPOSED_TO_MOSQUITO_BORNE_VIRUSES_TEXT = "exposedToMosquitoBorneVirusesText";
 	public static final String VACCINATED_AGAINST_MOSQUITO_BORNE_VIRUSES = "vaccinatedAgainstMosquitoBorneViruses";
+	public static final String MALARIA = "malaria";
+	public static final String MALARIA_INFECTED_YEAR = "malariaInfectedYear";
 
 	@HideForCountries(countries = {
 		CountryHelper.COUNTRY_CODE_GERMANY,
@@ -170,6 +172,14 @@ public class HealthConditionsDto extends PseudonymizableDto {
 		Disease.DENGUE })
 	private YesNoUnknown vaccinatedAgainstMosquitoBorneViruses;
 
+	@Diseases(value = {
+		Disease.MALARIA })
+	private YesNoUnknown malaria;
+
+	@Diseases(value = {
+		Disease.MALARIA })
+	private Integer malariaInfectedYear;
+
 	public static HealthConditionsDto build() {
 		HealthConditionsDto healthConditions = new HealthConditionsDto();
 		healthConditions.setUuid(DataHelper.createUuid());
@@ -447,4 +457,20 @@ public YesNoUnknown getVaccinatedAgainstMosquitoBorneViruses() {
 	public void setVaccinatedAgainstMosquitoBorneViruses(YesNoUnknown vaccinatedAgainstMosquitoBorneViruses) {
 		this.vaccinatedAgainstMosquitoBorneViruses = vaccinatedAgainstMosquitoBorneViruses;
 	}
+
+	public YesNoUnknown getMalaria() {
+		return malaria;
+	}
+
+	public void setMalaria(YesNoUnknown malaria) {
+		this.malaria = malaria;
+	}
+
+	public Integer getMalariaInfectedYear() {
+		return malariaInfectedYear;
+	}
+
+	public void setMalariaInfectedYear(Integer malariaInfectedYear) {
+		this.malariaInfectedYear = malariaInfectedYear;
+	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/disease/DiseaseConfigurationFacade.java

@@ -54,6 +54,8 @@ public interface DiseaseConfigurationFacade {
 
 	int getMinIncubationPeriod(Disease disease);
 
+	DiseaseConfigurationDto getDiseaseConfiguration(Disease disease);
+
 	String getCaseDefinitionText(Disease disease);
 
 	Integer getAutomaticSampleAssignmentThreshold(Disease disease);

sormas-api/src/main/java/de/symeda/sormas/api/epidata/DiseaseTransmission.java

@@ -0,0 +1,36 @@
+/*
+ * 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.epidata;
+
+import de.symeda.sormas.api.i18n.I18nProperties;
+
+public enum DiseaseTransmission {
+
+	TRANSMITTED_WITH_MOSQUITOES_FROM_ENDEMIC_COUNTRY,
+	TRANSMITTED_WITH_MOSQUITOES_BY_AIR,
+	TRANSMITTED_THROUGH_MEDICAL_CARE,
+	TRANSMITTED_WITH_STRONG_EPI_EVIDENCE,
+	TRANSMITTED_WITHOUT_EVIDENCE,
+	TRANSMITTED_FROM_MOTHER_TO_CHILD,
+	TRANSMITTED_BY_LAB,
+	TRANSFUSION_TRANSPLANT_RECIPIENT,
+	OTHER,
+	UNKNOWN;
+
+	@Override
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	}
+}

sormas-api/src/main/java/de/symeda/sormas/api/epidata/EpiDataDto.java

@@ -18,6 +18,7 @@
 package de.symeda.sormas.api.epidata;
 
 import java.util.ArrayList;
+import java.util.Date;
 import java.util.List;
 
 import javax.validation.Valid;

sormas-api/src/main/java/de/symeda/sormas/api/epipulse/EpipulseDiseaseExportEntryDto.java

@@ -87,7 +87,7 @@ public class EpipulseDiseaseExportEntryDto {
 	private Date dateOfLaboratoryResult;
 	private List<String> typeOfSpecimenCollected; // SampleMaterial mapped to EpiPulse codes (repeatable)
 	private String resultOfVirusDetection; // PathogenTestResultType mapped to POS/NEG/EQUI/NOTEST
-	private String genotype; // PathogenTest typingId/genoTypeResult
+	private String genotype; // PathogenTest typingId/genoType
 	private List<String> typeOfSpecimenSerology; // SampleMaterial for serology tests (repeatable)
 	private String resultIgG; // IgG test result
 	private String resultIgM; // IgM test result

sormas-api/src/main/java/de/symeda/sormas/api/epipulse/EpipulseLaboratoryMapper.java

@@ -116,7 +116,7 @@ public static String mapTestResultToEpipulseCode(PathogenTestResultType testResu
 	 * MEASV_C1, MEASV_C2, MEASV_D1-D11, MEASV_E, MEASV_F, MEASV_G1-G3, MEASV_H1-H2, etc.
 	 *
 	 * @param genotypeText
-	 *            SORMAS genotype string (from typingId or genoTypeResult)
+	 *            SORMAS genotype string (from typingId or genoType)
 	 * @return Normalized EpiPulse genotype code, or null if not a valid measles genotype
 	 */
 	public static String normalizeGenotypeForEpipulse(String genotypeText) {

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

@@ -11,7 +11,7 @@
 import de.symeda.sormas.api.feature.FeatureType;
 import de.symeda.sormas.api.i18n.Validations;
 import de.symeda.sormas.api.infrastructure.country.CountryReferenceDto;
-import de.symeda.sormas.api.sample.GenoTypeResult;
+import de.symeda.sormas.api.sample.GenoType;
 import de.symeda.sormas.api.sample.PCRTestSpecification;
 import de.symeda.sormas.api.sample.PathogenSpecie;
 import de.symeda.sormas.api.sample.PathogenStrainCallStatus;
@@ -168,7 +168,7 @@ public class TestReportDto extends EntityDto {
 	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
 	private CountryReferenceDto prescriberCountry;
 	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
-	private GenoTypeResult genoTypeResult;
+	private GenoType genoType;
 	@HideForCountriesExcept(countries = CountryHelper.COUNTRY_CODE_LUXEMBOURG)
 	private RsvSubtype rsvSubtype;
 
@@ -572,12 +572,12 @@ public void setPrescriberCountry(CountryReferenceDto prescriberCountry) {
 		this.prescriberCountry = prescriberCountry;
 	}
 
-	public GenoTypeResult getGenoTypeResult() {
-		return genoTypeResult;
+	public GenoType getGenoType() {
+		return genoType;
 	}
 
-	public void setGenoTypeResult(GenoTypeResult genoTypeResult) {
-		this.genoTypeResult = genoTypeResult;
+	public void setGenoType(GenoType genoType) {
+		this.genoType = genoType;
 	}
 
 	public RsvSubtype getRsvSubtype() {

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

@@ -55,6 +55,7 @@
 import de.symeda.sormas.api.sample.PathogenTestDto;
 import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.SampleDto;
+import de.symeda.sormas.api.sample.Serotype;
 import de.symeda.sormas.api.therapy.DrugSusceptibilityDto;
 import de.symeda.sormas.api.utils.DataHelper;
 import de.symeda.sormas.api.utils.DateHelper;
@@ -705,11 +706,7 @@ public List<String[]> mapToPathogenTest(TestReportDto sourceTestReport, Pathogen
 							pathogenTest.getPrescriberCountry(),
 							sourceTestReport.getPrescriberCountry(),
 							PathogenTestDto.PRESCRIBER_COUNTRY),
-						Mapping.of(
-							pathogenTest::setGenoTypeResult,
-							pathogenTest.getGenoTypeResult(),
-							sourceTestReport.getGenoTypeResult(),
-							PathogenTestDto.GENOTYPE_RESULT),
+						Mapping.of(pathogenTest::setGenoType, pathogenTest.getGenoType(), sourceTestReport.getGenoType(), PathogenTestDto.GENOTYPE),
 						Mapping.of(
 							pathogenTest::setSeroGroupSpecification,
 							pathogenTest.getSeroGroupSpecification(),
@@ -720,7 +717,11 @@ public List<String[]> mapToPathogenTest(TestReportDto sourceTestReport, Pathogen
 							pathogenTest.getSeroGroupSpecificationText(),
 							sourceTestReport.getSeroGroupSpecificationText(),
 							PathogenTestDto.SERO_GROUP_SPECIFICATION),
-						Mapping.of(pathogenTest::setSerotype, pathogenTest.getSerotype(), sourceTestReport.getSerotype(), PathogenTestDto.SEROTYPE),
+						Mapping.of(
+							pathogenTest::setSerotype,
+							pathogenTest.getSerotype(),
+							Serotype.fromString(sourceTestReport.getSerotype()),
+							PathogenTestDto.SEROTYPE),
 						Mapping.of(
 							pathogenTest::setSeroTypingMethod,
 							pathogenTest.getSeroTypingMethod(),

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

@@ -2032,6 +2032,8 @@ public interface Captions {
 	String HealthConditions_immunodeficiencyOtherThanHiv = "HealthConditions.immunodeficiencyOtherThanHiv";
 	String HealthConditions_immunodeficiencyOtherThanHivText = "HealthConditions.immunodeficiencyOtherThanHivText";
 	String HealthConditions_immunodepression = "HealthConditions.immunodepression";
+	String HealthConditions_malaria = "HealthConditions.malaria";
+	String HealthConditions_malariaInfectedYear = "HealthConditions.malariaInfectedYear";
 	String HealthConditions_malignancyChemotherapy = "HealthConditions.malignancyChemotherapy";
 	String HealthConditions_obesity = "HealthConditions.obesity";
 	String HealthConditions_otherConditions = "HealthConditions.otherConditions";
@@ -2271,6 +2273,7 @@ public interface Captions {
 	String outbreakOutbreak = "outbreakOutbreak";
 	String passportNumber = "passportNumber";
 	String PathogenTest = "PathogenTest";
+	String PathogenTest_antibodyTitre = "PathogenTest.antibodyTitre";
 	String PathogenTest_cqValue = "PathogenTest.cqValue";
 	String PathogenTest_ctValueE = "PathogenTest.ctValueE";
 	String PathogenTest_ctValueN = "PathogenTest.ctValueN";
@@ -2283,14 +2286,16 @@ public interface Captions {
 	String PathogenTest_externalId = "PathogenTest.externalId";
 	String PathogenTest_externalOrderId = "PathogenTest.externalOrderId";
 	String PathogenTest_fourFoldIncreaseAntibodyTiter = "PathogenTest.fourFoldIncreaseAntibodyTiter";
-	String PathogenTest_genoTypeResult = "PathogenTest.genoTypeResult";
-	String PathogenTest_genoTypeResultText = "PathogenTest.genoTypeResultText";
+	String PathogenTest_fourFoldIncreaseAntibodyTiter_DENGUE = "PathogenTest.fourFoldIncreaseAntibodyTiter.DENGUE";
+	String PathogenTest_genoType = "PathogenTest.genoType";
+	String PathogenTest_genoTypeText = "PathogenTest.genoTypeText";
 	String PathogenTest_isoniazidResistant = "PathogenTest.isoniazidResistant";
 	String PathogenTest_lab = "PathogenTest.lab";
 	String PathogenTest_labDetails = "PathogenTest.labDetails";
 	String PathogenTest_otherDeletionReason = "PathogenTest.otherDeletionReason";
 	String PathogenTest_patternProfile = "PathogenTest.patternProfile";
 	String PathogenTest_pcrTestSpecification = "PathogenTest.pcrTestSpecification";
+	String PathogenTest_performedByReferenceLaboratory = "PathogenTest.performedByReferenceLaboratory";
 	String PathogenTest_preliminary = "PathogenTest.preliminary";
 	String PathogenTest_prescriber = "PathogenTest.prescriber";
 	String PathogenTest_prescriberAddress = "PathogenTest.prescriberAddress";
@@ -2302,15 +2307,19 @@ public interface Captions {
 	String PathogenTest_prescriberPhysicianCode = "PathogenTest.prescriberPhysicianCode";
 	String PathogenTest_prescriberPostalCode = "PathogenTest.prescriberPostalCode";
 	String PathogenTest_reportDate = "PathogenTest.reportDate";
+	String PathogenTest_resultDetails = "PathogenTest.resultDetails";
+	String PathogenTest_retestRequested = "PathogenTest.retestRequested";
 	String PathogenTest_rifampicinResistant = "PathogenTest.rifampicinResistant";
 	String PathogenTest_rsv_testedDiseaseVariant = "PathogenTest.rsv.testedDiseaseVariant";
 	String PathogenTest_rsv_testedDiseaseVariantDetails = "PathogenTest.rsv.testedDiseaseVariantDetails";
 	String PathogenTest_seroGroupSpecification = "PathogenTest.seroGroupSpecification";
 	String PathogenTest_seroGroupSpecificationText = "PathogenTest.seroGroupSpecificationText";
 	String PathogenTest_serotype = "PathogenTest.serotype";
+	String PathogenTest_serotypeText = "PathogenTest.serotypeText";
 	String PathogenTest_seroTypingMethod = "PathogenTest.seroTypingMethod";
 	String PathogenTest_seroTypingMethodText = "PathogenTest.seroTypingMethodText";
 	String PathogenTest_specie = "PathogenTest.specie";
+	String PathogenTest_specieText = "PathogenTest.specieText";
 	String PathogenTest_strainCallStatus = "PathogenTest.strainCallStatus";
 	String PathogenTest_testDateTime = "PathogenTest.testDateTime";
 	String PathogenTest_testedDisease = "PathogenTest.testedDisease";

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

@@ -402,6 +402,8 @@ public interface Strings {
 	String errorViewNotFound = "errorViewNotFound";
 	String errorWasReported = "errorWasReported";
 	String errorWritingTemplate = "errorWritingTemplate";
+	String exposureEndDate = "exposureEndDate";
+	String exposureStartDate = "exposureStartDate";
 	String externalMessageMultipleSampleReports = "externalMessageMultipleSampleReports";
 	String ExternalSurveillanceToolGateway_confirmDeleteCase = "ExternalSurveillanceToolGateway.confirmDeleteCase";
 	String ExternalSurveillanceToolGateway_confirmDeleteEvent = "ExternalSurveillanceToolGateway.confirmDeleteEvent";