Feature 14233 mumps samples and pathogen test form changes

sormas-api/src/main/java/de/symeda/sormas/api/Disease.java

@@ -98,6 +98,8 @@ public enum Disease
 	SALMONELLOSIS(true, true, true, false, true, 14, false, false, false, true, 1, 3, false, 0, 0),
 	SYPHILIS(true, true, true, false, false, 0, true, false, false, true, 10, 90, false, 0, 0),
 	YERSINIOSIS(true, true, true, false, true, 14, false, false, false, true, 1, 14, false, 0, 0),
+	// As per the requested requirement, setting the follow-up duration 21 and min and max incubation period as 12 and 25.
+	MUMPS(true, true, true, false, true, 21, false, false, false, true, 12, 25, true, 3, 9),
 	OTHER(true, true, true, false, true, 21, false, false, false, false, 0, 0, false, 0, 0),
 	UNDEFINED(true, true, true, false, true, 0, false, false, false, false, 0, 0, false, 0, 0);
 

sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseDataDto.java

@@ -249,6 +249,8 @@ public class CaseDataDto extends SormasToSormasShareableDto implements IsCase {
 	public static final String TREATMENT_STARTED = "treatmentStarted";
 	public static final String TREATMENT_NOT_APPLICABLE = "treatmentNotApplicable";
 	public static final String TREATMENT_START_DATE = "treatmentStartDate";
+	// Mumps changes
+	public static final String REPORTING_EXCLUDED = "reportingExcluded";
 
 	// Fields are declared in the order they should appear in the import template
 
@@ -722,6 +724,10 @@ public class CaseDataDto extends SormasToSormasShareableDto implements IsCase {
 	private RadiographyCompatibility radiographyCompatibility;
 	private String otherDiagnosticCriteria;
 
+	@Diseases(value = {
+		Disease.MUMPS })
+	private YesNoUnknown reportingExcluded;
+
 	public static CaseDataDto build(PersonReferenceDto person, Disease disease) {
 		return build(person, disease, HealthConditionsDto.build());
 	}
@@ -2006,6 +2012,14 @@ public void setTreatmentStartDate(Date treatmentStartDate) {
 		this.treatmentStartDate = treatmentStartDate;
 	}
 
+	public YesNoUnknown getReportingExcluded() {
+		return reportingExcluded;
+	}
+
+	public void setReportingExcluded(YesNoUnknown reportingExcluded) {
+		this.reportingExcluded = reportingExcluded;
+	}
+
 	@JsonIgnore
 	public String i18nPrefix() {
 		return I18N_PREFIX;

sormas-api/src/main/java/de/symeda/sormas/api/contact/ContactDto.java

@@ -33,6 +33,7 @@
 import de.symeda.sormas.api.MappingException;
 import de.symeda.sormas.api.caze.CaseDataDto;
 import de.symeda.sormas.api.caze.CaseReferenceDto;
+import de.symeda.sormas.api.caze.Trimester;
 import de.symeda.sormas.api.caze.VaccinationStatus;
 import de.symeda.sormas.api.clinicalcourse.HealthConditionsDto;
 import de.symeda.sormas.api.common.DeletionReason;
@@ -166,6 +167,9 @@ public class ContactDto extends SormasToSormasShareableDto implements IsContact
 
 	public static final String VACCINATION_DOSE_ONE_DATE = "vaccinationDoseOneDate";
 	public static final String VACCINATION_DOSE_TWO_DATE = "vaccinationDoseTwoDate";
+	public static final String PREGNANT = "pregnant";
+	public static final String POSTPARTUM = "postpartum";
+	public static final String TRIMESTER = "trimester";
 
 	@EmbeddedPersonalData
 	private CaseReferenceDto caze;
@@ -437,6 +441,12 @@ public class ContactDto extends SormasToSormasShareableDto implements IsContact
 	@HideForCountriesExcept(countries = {
 		COUNTRY_CODE_LUXEMBOURG })
 	private boolean immuneGlobulinProposed;
+	@SensitiveData
+	private YesNoUnknown pregnant;
+	@SensitiveData
+	private YesNoUnknown postpartum;
+	@SensitiveData
+	private Trimester trimester;
 
 	public static ContactDto build() {
 		final ContactDto contact = new ContactDto();
@@ -1227,4 +1237,28 @@ public boolean isImmuneGlobulinProposed() {
 	public void setImmuneGlobulinProposed(boolean immuneGlobulinProposed) {
 		this.immuneGlobulinProposed = immuneGlobulinProposed;
 	}
+
+	public YesNoUnknown getPregnant() {
+		return pregnant;
+	}
+
+	public void setPregnant(YesNoUnknown pregnant) {
+		this.pregnant = pregnant;
+	}
+
+	public YesNoUnknown getPostpartum() {
+		return postpartum;
+	}
+
+	public void setPostpartum(YesNoUnknown postpartum) {
+		this.postpartum = postpartum;
+	}
+
+	public Trimester getTrimester() {
+		return trimester;
+	}
+
+	public void setTrimester(Trimester trimester) {
+		this.trimester = trimester;
+	}
 }

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

@@ -17,18 +17,21 @@
 import de.symeda.sormas.api.i18n.I18nProperties;
 
 public enum ClusterType {
-    KINDERGARTEN_OR_CHILDCARE,
-    FAMILY,
-    MILITARY,
-    NOSOCOMIAL,
-    SCHOOL,
-    SPORTS_TEAM,
-    UNIVERSITY,
-    OTHER;
 
-    @Override
-    public String toString() {
-        return I18nProperties.getEnumCaption(this);
-    }
+	KINDERGARTEN_OR_CHILDCARE,
+	FAMILY,
+	MILITARY,
+	NOSOCOMIAL,
+	SCHOOL,
+	SPORTS_TEAM,
+	UNIVERSITY,
+	NOT_APPLICABLE,
+	UNKNOWN,
+	OTHER;
+
+	@Override
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	}
 
 }

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

@@ -74,6 +74,7 @@ public class EpiDataDto extends PseudonymizableDto {
 	public static final String HEALTHCARE_PROFESSIONAL = "healthcareProfessional";
 	public static final String PLACE_OF_INFECTION = "placeOfInfection";
 	public static final String RESIDENCE_AT_ONSET = "residenceAtOnset";
+	public static final String CLUSTER_IDENTIFIER = "clusterIdentifier";
 	public static final String PROBABLE_ROUTE_OF_TRANSMISSION = "probableRouteOfTransmission";
 	public static final String MOTHER_COUNTRY_OF_BIRTH = "motherCountryOfBirth";
 	public static final String MOTHER_CITIZENSHIP = "motherCitizenship";
@@ -93,19 +94,22 @@ public class EpiDataDto extends PseudonymizableDto {
 	@Diseases({
 		Disease.GIARDIASIS,
 		Disease.SALMONELLOSIS,
-		Disease.SHIGELLOSIS })
+		Disease.SHIGELLOSIS,
+		Disease.MUMPS })
 	private YesNoUnknown importedCase;
 
 	@HideForCountriesExcept(countries = {
 		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	@Diseases({
-		Disease.MEASLES })
+		Disease.MEASLES,
+		Disease.MUMPS })
 	private ClusterType clusterType;
 
 	@HideForCountriesExcept(countries = {
 		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	@Diseases({
-		Disease.MEASLES })
+		Disease.MEASLES,
+		Disease.MUMPS })
 	private boolean clusterRelated;
 
 	@HideForCountriesExcept(countries = {
@@ -114,6 +118,11 @@ public class EpiDataDto extends PseudonymizableDto {
 		Disease.MEASLES })
 	private String clusterTypeText;
 
+	@Diseases({
+		Disease.MUMPS })
+	@Size(max = FieldConstraints.CHARACTER_LIMIT_DEFAULT, message = Validations.textTooLong)
+	private String clusterIdentifier;
+
 	@Diseases({
 		Disease.AFP,
 		Disease.GUINEA_WORM,
@@ -153,7 +162,8 @@ public class EpiDataDto extends PseudonymizableDto {
 	@Diseases({
 		Disease.GIARDIASIS,
 		Disease.SALMONELLOSIS,
-		Disease.SHIGELLOSIS })
+		Disease.SHIGELLOSIS,
+		Disease.MUMPS })
 	private CountryReferenceDto country;
 
 	@Valid
@@ -453,6 +463,14 @@ public void setContactWithSexWorker(YesNoUnknown contactWithSexWorker) {
 		this.contactWithSexWorker = contactWithSexWorker;
 	}
 
+	public String getClusterIdentifier() {
+		return clusterIdentifier;
+	}
+
+	public void setClusterIdentifier(String clusterIdentifier) {
+		this.clusterIdentifier = clusterIdentifier;
+	}
+
 	private static void validateDateRange(Date from, Date to, String fromName, String toName) {
 		if (from != null && to != null && from.after(to)) {
 			throw new IllegalArgumentException(fromName + " must be before or equal to " + toName);

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

@@ -31,6 +31,7 @@ public enum ExposureCategory {
 	WATER_BORNE,
 	MEDICAL_CARE,
 	LAB,
+	RESPIRATORY_DROPLET,
 	OTHER;
 
 	public boolean hasNoSetting() {

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

@@ -40,8 +40,8 @@ public enum ExposureSetting {
 
 	PREGNANCY_OR_DELIVERY(ExposureCategory.VERTICAL_TRANSMISSION),
 
-	OTHER(ExposureCategory.AIR_BORNE),
-	UNKNOWN(ExposureCategory.AIR_BORNE);
+	OTHER(ExposureCategory.AIR_BORNE, ExposureCategory.RESPIRATORY_DROPLET),
+	UNKNOWN(ExposureCategory.AIR_BORNE, ExposureCategory.RESPIRATORY_DROPLET);
 
 	private final Set<ExposureCategory> categories;
 

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

@@ -792,6 +792,7 @@ public interface Captions {
 	String CaseData_reinfectionStatus = "CaseData.reinfectionStatus";
 	String CaseData_reportDate = "CaseData.reportDate";
 	String CaseData_reportingDistrict = "CaseData.reportingDistrict";
+	String CaseData_reportingExcluded = "CaseData.reportingExcluded";
 	String CaseData_reportingUser = "CaseData.reportingUser";
 	String CaseData_reportLat = "CaseData.reportLat";
 	String CaseData_reportLatLonAccuracy = "CaseData.reportLatLonAccuracy";
@@ -1082,6 +1083,8 @@ public interface Captions {
 	String Contact_overwriteFollowUpUntil = "Contact.overwriteFollowUpUntil";
 	String Contact_person = "Contact.person";
 	String Contact_personUuid = "Contact.personUuid";
+	String Contact_postpartum = "Contact.postpartum";
+	String Contact_pregnant = "Contact.pregnant";
 	String Contact_prescribedDrug = "Contact.prescribedDrug";
 	String Contact_prescribedDrugText = "Contact.prescribedDrugText";
 	String Contact_previousQuarantineTo = "Contact.previousQuarantineTo";
@@ -1123,6 +1126,7 @@ public interface Captions {
 	String Contact_symptomJournalStatus = "Contact.symptomJournalStatus";
 	String Contact_tracingApp = "Contact.tracingApp";
 	String Contact_tracingAppDetails = "Contact.tracingAppDetails";
+	String Contact_trimester = "Contact.trimester";
 	String Contact_uuid = "Contact.uuid";
 	String Contact_vaccinationDoseOneDate = "Contact.vaccinationDoseOneDate";
 	String Contact_vaccinationDoseTwoDate = "Contact.vaccinationDoseTwoDate";
@@ -1640,6 +1644,7 @@ public interface Captions {
 	String EpiData_airportWorker = "EpiData.airportWorker";
 	String EpiData_areaInfectedAnimals = "EpiData.areaInfectedAnimals";
 	String EpiData_caseImportedStatus = "EpiData.caseImportedStatus";
+	String EpiData_clusterIdentifier = "EpiData.clusterIdentifier";
 	String EpiData_clusterRelated = "EpiData.clusterRelated";
 	String EpiData_clusterType = "EpiData.clusterType";
 	String EpiData_clusterTypeText = "EpiData.clusterTypeText";
@@ -2450,6 +2455,8 @@ public interface Captions {
 	String PathogenTest_rsv_testedDiseaseVariant = "PathogenTest.rsv.testedDiseaseVariant";
 	String PathogenTest_rsv_testedDiseaseVariantDetails = "PathogenTest.rsv.testedDiseaseVariantDetails";
 	String PathogenTest_rsvSubtype = "PathogenTest.rsvSubtype";
+	String PathogenTest_sequenceId = "PathogenTest.sequenceId";
+	String PathogenTest_seroConversion = "PathogenTest.seroConversion";
 	String PathogenTest_seroGroupSpecification = "PathogenTest.seroGroupSpecification";
 	String PathogenTest_seroGroupSpecificationText = "PathogenTest.seroGroupSpecificationText";
 	String PathogenTest_serotype = "PathogenTest.serotype";
@@ -3241,6 +3248,7 @@ public interface Captions {
 	String Symptoms_neckStiffness = "Symptoms.neckStiffness";
 	String Symptoms_nephroticSyndrome = "Symptoms.nephroticSyndrome";
 	String Symptoms_neurologicalManifestations = "Symptoms.neurologicalManifestations";
+	String Symptoms_noComplications = "Symptoms.noComplications";
 	String Symptoms_nocturnalCough = "Symptoms.nocturnalCough";
 	String Symptoms_noseBleeding = "Symptoms.noseBleeding";
 	String Symptoms_ocularManifestations = "Symptoms.ocularManifestations";
@@ -3251,12 +3259,15 @@ public interface Captions {
 	String Symptoms_onsetSymptom = "Symptoms.onsetSymptom";
 	String Symptoms_opisthotonus = "Symptoms.opisthotonus";
 	String Symptoms_oralUlcers = "Symptoms.oralUlcers";
+	String Symptoms_orchitis = "Symptoms.orchitis";
 	String Symptoms_otherClinicalPresentation = "Symptoms.otherClinicalPresentation";
 	String Symptoms_otherClinicalPresentationText = "Symptoms.otherClinicalPresentationText";
 	String Symptoms_otherComplications = "Symptoms.otherComplications";
 	String Symptoms_otherComplications_CryptoGiardia = "Symptoms.otherComplications.CryptoGiardia";
 	String Symptoms_otherComplicationsText = "Symptoms.otherComplicationsText";
 	String Symptoms_otherComplicationsText_CryptoGiardia = "Symptoms.otherComplicationsText.CryptoGiardia";
+	String Symptoms_otherGeneralSymptoms = "Symptoms.otherGeneralSymptoms";
+	String Symptoms_otherGeneralSymptomsText = "Symptoms.otherGeneralSymptomsText";
 	String Symptoms_otherHemorrhagicSymptoms = "Symptoms.otherHemorrhagicSymptoms";
 	String Symptoms_otherHemorrhagicSymptomsText = "Symptoms.otherHemorrhagicSymptomsText";
 	String Symptoms_otherMajorSiteDetails = "Symptoms.otherMajorSiteDetails";
@@ -3272,6 +3283,7 @@ public interface Captions {
 	String Symptoms_palpableLiver = "Symptoms.palpableLiver";
 	String Symptoms_palpableSpleen = "Symptoms.palpableSpleen";
 	String Symptoms_palpitations = "Symptoms.palpitations";
+	String Symptoms_pancreatitis = "Symptoms.pancreatitis";
 	String Symptoms_paradoxicalBreathing = "Symptoms.paradoxicalBreathing";
 	String Symptoms_paralysis = "Symptoms.paralysis";
 	String Symptoms_parentTimeOffWork = "Symptoms.parentTimeOffWork";
@@ -3299,6 +3311,7 @@ public interface Captions {
 	String Symptoms_respiratoryRate = "Symptoms.respiratoryRate";
 	String Symptoms_restlessness = "Symptoms.restlessness";
 	String Symptoms_runnyNose = "Symptoms.runnyNose";
+	String Symptoms_salivarySwelling = "Symptoms.salivarySwelling";
 	String Symptoms_scantHemorrhage = "Symptoms.scantHemorrhage";
 	String Symptoms_seizures = "Symptoms.seizures";
 	String Symptoms_sepsis = "Symptoms.sepsis";
@@ -3340,6 +3353,7 @@ public interface Captions {
 	String Symptoms_tremor = "Symptoms.tremor";
 	String Symptoms_unexplainedBleeding = "Symptoms.unexplainedBleeding";
 	String Symptoms_unilateralCataracts = "Symptoms.unilateralCataracts";
+	String Symptoms_unknownComplications = "Symptoms.unknownComplications";
 	String Symptoms_unknownSymptom = "Symptoms.unknownSymptom";
 	String Symptoms_uproariousness = "Symptoms.uproariousness";
 	String Symptoms_urinaryRetention = "Symptoms.urinaryRetention";

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

@@ -104,6 +104,44 @@ public enum GenoType {
 	@Diseases({
 		Disease.CRYPTOSPORIDIOSIS })
 	CRYPTOSPORIDIUM_SPECIES,
+	// mumps genotypes
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_A,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_B,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_C,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_D,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_F,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_G,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_H,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_I,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_J,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_K,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_L,
+	@Diseases({
+		Disease.MUMPS })
+	MUMPV_N,
+
 	OTHER,
 	UNKNOWN;