#13204 - RSV disease variants - add support for similar Customizable … (

#13219) * #13204 - RSV disease variants - add support for similar Customizable disease values * #13204 RSV disease variants - fix values without disease * #13204 - RSV disease variants - add support for similar Customizable disease values * #13204 RSV disease variants - basic disease variant converter tests --------- Co-authored-by: SergiuPacurariu <[email protected]> Co-authored-by: Levente Gal <[email protected]>
SORMAS-Foundation · Dec 19, 2024 · 7865ae3 · 7865ae3
1 parent bb67f2a
commit 7865ae3
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Showing 65 changed files with 490 additions and 208 deletions.
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/bagexport/BAGExportCaseDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/bagexport/BAGExportCaseDto.java
@@ -24,6 +24,7 @@
 import de.symeda.sormas.api.contact.QuarantineType;
 import de.symeda.sormas.api.infrastructure.facility.FacilityType;
 import de.symeda.sormas.api.person.OccupationType;
+import de.symeda.sormas.api.person.OccupationTypeConverter;
 import de.symeda.sormas.api.person.Sex;
 import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.PathogenTestType;
@@ -32,6 +33,7 @@
 import de.symeda.sormas.api.utils.YesNoUnknown;
 
 public class BAGExportCaseDto implements Serializable {
+
 	private Integer caseIdIsm;
 	private Long caseId;
 	private Long personId;
@@ -124,7 +126,7 @@ public BAGExportCaseDto(Integer caseIdIsm, Long caseId, Long personId,
 							String homeAddressStreet, String homeAddressHouseNumber, String homeAddressCity, String homeAddressPostalCode, String homeAddressCountry,
 							String phoneNumber, String mobileNumber, String emailAddress,
 							Sex sex, Integer birthdateDD, Integer birthdateMM, Integer birthdateYYYY,
-							OccupationType occupationType,
+							String occupationType,
 							boolean symptomatic, Date symptomOnsetDate,
 							String activityMappingYn,
 							Date contactTracingContactDate,
@@ -148,7 +150,7 @@ public BAGExportCaseDto(Integer caseIdIsm, Long caseId, Long personId,
 		this.emailAddress = emailAddress;
 		this.sex = sex;
 		this.birthDate = new BirthDateDto(birthdateDD, birthdateMM, birthdateYYYY);
-		this.occupationType = occupationType;
+		this.occupationType = new OccupationTypeConverter().convertToEntityAttribute(null, occupationType);
 		this.symptomatic = symptomatic ? YesNoUnknown.YES : YesNoUnknown.NO;
 		this.symptomOnsetDate = symptomOnsetDate;
 		this.activityMappingYn = activityMappingYn;

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/bagexport/BAGExportContactDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/bagexport/BAGExportContactDto.java
@@ -23,6 +23,7 @@
 import de.symeda.sormas.api.contact.QuarantineType;
 import de.symeda.sormas.api.infrastructure.facility.FacilityType;
 import de.symeda.sormas.api.person.OccupationType;
+import de.symeda.sormas.api.person.OccupationTypeConverter;
 import de.symeda.sormas.api.person.Sex;
 import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.PathogenTestType;
@@ -91,7 +92,7 @@ public BAGExportContactDto(Long contactId, Long personId, String lastName, Strin
 							   String homeAddressStreet, String homeAddressHouseNumber, String homeAddressCity, String homeAddressPostalCode,
 							   String phoneNumber, String mobileNumber, Sex sex,
 							   Integer birthdateDD, Integer birthdateMM, Integer birthdateYYYY,
-							   OccupationType occupationType,
+							   String occupationType,
 							   QuarantineType quarantineType, String quarantineDetails,
 							   Integer caseLinkCaseIdIsm, Long caseLinkCaseId, Date caseLinkContactDate,
 							   Date startOfQuarantineDate, Date endOfQuarantineDate, EndOfQuarantineReason endOfQuarantineReason, String endOfQuarantineReasonDetails
@@ -112,7 +113,7 @@ public BAGExportContactDto(Long contactId, Long personId, String lastName, Strin
 		this.mobileNumber = mobileNumber;
 		this.sex = sex;
 		this.birthDate = new BirthDateDto(birthdateDD, birthdateMM, birthdateYYYY);
-		this.occupationType = occupationType;
+		this.occupationType = new OccupationTypeConverter().convertToEntityAttribute(null, occupationType);
 
 		this.quarantineType = quarantineType;
 		this.quarantineDetails = quarantineDetails;

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseExportDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseExportDto.java
@@ -28,6 +28,7 @@
 import de.symeda.sormas.api.contact.FollowUpStatus;
 import de.symeda.sormas.api.contact.QuarantineType;
 import de.symeda.sormas.api.disease.DiseaseVariant;
+import de.symeda.sormas.api.disease.DiseaseVariantConverter;
 import de.symeda.sormas.api.epidata.EpiDataDto;
 import de.symeda.sormas.api.event.EventStatus;
 import de.symeda.sormas.api.feature.FeatureType;
@@ -49,6 +50,7 @@
 import de.symeda.sormas.api.person.BurialConductor;
 import de.symeda.sormas.api.person.EducationType;
 import de.symeda.sormas.api.person.OccupationType;
+import de.symeda.sormas.api.person.OccupationTypeConverter;
 import de.symeda.sormas.api.person.PersonDto;
 import de.symeda.sormas.api.person.PresentCondition;
 import de.symeda.sormas.api.person.Salutation;
@@ -362,7 +364,7 @@ public class CaseExportDto extends AbstractUuidDto implements IsCase {
 	@SuppressWarnings("unchecked")
 	public CaseExportDto(long id, long personId, Double personAddressLatitude, Double personAddressLongitude, Float personAddressLatLonAcc, long epiDataId, long symptomsId,
 						 long hospitalizationId, long healthConditionsId, String uuid, String epidNumber,
-						 Disease disease, DiseaseVariant diseaseVariant, String diseaseDetails, String diseaseVariantDetails,
+						 Disease disease, String diseaseVariant, String diseaseDetails, String diseaseVariantDetails,
 						 String personUuid, String firstName, String lastName, Salutation salutation, String otherSalutation, Sex sex, YesNoUnknown pregnant,
 						 Integer approximateAge, ApproximateAgeType approximateAgeType, Integer birthdateDD, Integer birthdateMM,
 						 Integer birthdateYYYY, Date reportDate, String region, String district, String community,
@@ -389,7 +391,7 @@ public CaseExportDto(long id, long personId, Double personAddressLatitude, Doubl
 						 String addressRegion, String addressDistrict, String addressCommunity, String city, String street, String houseNumber, String additionalInformation, String postalCode,
 						 String facility, String facilityUuid, String facilityDetails,
 						 String phone, String phoneOwner, String emailAddress, String otherContactDetails, EducationType educationType, String educationDetails,
-						 OccupationType occupationType, String occupationDetails, ArmedForcesRelationType ArmedForcesRelationType, YesNoUnknown contactWithSourceCaseKnown,
+						 String occupationType, String occupationDetails, ArmedForcesRelationType ArmedForcesRelationType, YesNoUnknown contactWithSourceCaseKnown,
 						 //Date onsetDate,
 						 VaccinationStatus vaccinationStatus, YesNoUnknown postpartum, Trimester trimester,
 						 long eventCount, Long prescriptionCount, Long treatmentCount, Long clinicalVisitCount,
@@ -419,7 +421,7 @@ public CaseExportDto(long id, long personId, Double personAddressLatitude, Doubl
 		this.armedForcesRelationType = ArmedForcesRelationType;
 		this.disease = disease;
 		this.diseaseDetails = diseaseDetails;
-		this.diseaseVariant = diseaseVariant;
+		this.diseaseVariant = new DiseaseVariantConverter().convertToEntityAttribute(disease, diseaseVariant);
 		this.diseaseVariantDetails = diseaseVariantDetails;
 		this.personUuid = personUuid;
 		this.firstName = firstName;
@@ -501,7 +503,7 @@ public CaseExportDto(long id, long personId, Double personAddressLatitude, Doubl
 		this.otherContactDetails = otherContactDetails;
 		this.educationType = educationType;
 		this.educationDetails = educationDetails;
-		this.occupationType = occupationType;
+		this.occupationType = new OccupationTypeConverter().convertToEntityAttribute(null, occupationType);
 		this.occupationDetails = occupationDetails;
 		this.contactWithSourceCaseKnown = contactWithSourceCaseKnown;
 //		this.onsetDate = onsetDate;

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseIndexDetailedDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseIndexDetailedDto.java
@@ -75,7 +75,7 @@ public class CaseIndexDetailedDto extends CaseIndexDto {
 
 	//@formatter:off
 	public CaseIndexDetailedDto(long id, String uuid, String epidNumber, String externalID, String externalToken, String internalToken,String caseReferenceNumber, String personUuid, String personFirstName, String personLastName,
-								Disease disease, DiseaseVariant diseaseVariant, String diseaseDetails, CaseClassification caseClassification, InvestigationStatus investigationStatus,
+								Disease disease, String diseaseVariant, String diseaseDetails, CaseClassification caseClassification, InvestigationStatus investigationStatus,
 								PresentCondition presentCondition, Date reportDate, Date creationDate,
 								String regionUuid, String districtUuid,
 								String healthFacilityUuid, String healthFacilityName, String healthFacilityDetails,

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseIndexDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseIndexDto.java
@@ -25,6 +25,7 @@
 import de.symeda.sormas.api.common.DeletionReason;
 import de.symeda.sormas.api.contact.FollowUpStatus;
 import de.symeda.sormas.api.disease.DiseaseVariant;
+import de.symeda.sormas.api.disease.DiseaseVariantConverter;
 import de.symeda.sormas.api.infrastructure.InfrastructureHelper;
 import de.symeda.sormas.api.infrastructure.facility.FacilityHelper;
 import de.symeda.sormas.api.person.ApproximateAgeType;
@@ -141,7 +142,7 @@ public class CaseIndexDto extends PseudonymizableIndexDto implements MergeableIn
 
 	//@formatter:off
 	public CaseIndexDto(long id, String uuid, String epidNumber, String externalID, String externalToken, String internalToken, String caseReferenceNumber, String personUuid, String personFirstName, String personLastName, Disease disease,
-						DiseaseVariant diseaseVariant, String diseaseDetails, CaseClassification caseClassification, InvestigationStatus investigationStatus,
+						String diseaseVariant, String diseaseDetails, CaseClassification caseClassification, InvestigationStatus investigationStatus,
 						PresentCondition presentCondition, Date reportDate, Date creationDate, String regionUuid,
 						String districtUuid, String healthFacilityUuid, String healthFacilityName, String healthFacilityDetails,
 						String pointOfEntryUuid, String pointOfEntryName, String pointOfEntryDetails, String surveillanceOfficerUuid, CaseOutcome outcome,
@@ -166,7 +167,7 @@ public CaseIndexDto(long id, String uuid, String epidNumber, String externalID,
 		this.personFirstName = personFirstName;
 		this.personLastName = personLastName;
 		this.disease = disease;
-		this.diseaseVariant = diseaseVariant;
+		this.diseaseVariant = new DiseaseVariantConverter().convertToEntityAttribute(disease, diseaseVariant);
 		this.diseaseDetails = diseaseDetails;
 		this.caseClassification = caseClassification;
 		this.investigationStatus = investigationStatus;

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseMergeIndexDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseMergeIndexDto.java
@@ -21,7 +21,7 @@ public class CaseMergeIndexDto extends CaseIndexDto {
 	//@formatter:off
 	public CaseMergeIndexDto(
 			long id, String uuid, String epidNumber, String externalID, String externalToken, String internalToken, String caseReferenceNumber, String personUuid, String personFirstName, String personLastName, Disease disease,
-			DiseaseVariant diseaseVariant, String diseaseDetails, CaseClassification caseClassification, InvestigationStatus investigationStatus,
+			String diseaseVariant, String diseaseDetails, CaseClassification caseClassification, InvestigationStatus investigationStatus,
 			PresentCondition presentCondition, Date reportDate, Date creationDate, String regionUuid,
 			String districtUuid, String healthFacilityUuid, String healthFacilityName, String healthFacilityDetails,
 			String pointOfEntryUuid, String pointOfEntryName, String pointOfEntryDetails, String surveillanceOfficerUuid, CaseOutcome outcome,

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/caze/PreviousCaseDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/caze/PreviousCaseDto.java
@@ -17,7 +17,9 @@
 
 import java.util.Date;
 
+import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.disease.DiseaseVariant;
+import de.symeda.sormas.api.disease.DiseaseVariantConverter;
 import de.symeda.sormas.api.uuid.AbstractUuidDto;
 
 public class PreviousCaseDto extends AbstractUuidDto {
@@ -29,11 +31,11 @@ public class PreviousCaseDto extends AbstractUuidDto {
 	private final DiseaseVariant diseaseVariant;
 	private final Date onsetDate;
 
-	public PreviousCaseDto(String uuid, Date reportDate, String externalToken, DiseaseVariant diseaseVariant, Date onsetDate) {
+	public PreviousCaseDto(String uuid, Date reportDate, String externalToken, Disease disease, String diseaseVariant, Date onsetDate) {
 		super(uuid);
 		this.reportDate = reportDate;
 		this.externalToken = externalToken;
-		this.diseaseVariant = diseaseVariant;
+		this.diseaseVariant = new DiseaseVariantConverter().convertToEntityAttribute(disease, diseaseVariant);
 		this.onsetDate = onsetDate;
 	}
 

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/contact/ContactExportDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/contact/ContactExportDto.java
@@ -46,6 +46,7 @@
 import de.symeda.sormas.api.person.ApproximateAgeType.ApproximateAgeHelper;
 import de.symeda.sormas.api.person.ArmedForcesRelationType;
 import de.symeda.sormas.api.person.OccupationType;
+import de.symeda.sormas.api.person.OccupationTypeConverter;
 import de.symeda.sormas.api.person.PersonDto;
 import de.symeda.sormas.api.person.PresentCondition;
 import de.symeda.sormas.api.person.Salutation;
@@ -259,7 +260,7 @@ public ContactExportDto(long id, long personId, String uuid, String sourceCaseUu
 							PresentCondition presentCondition, Date deathDate,
 							String addressRegion, String addressDistrict, String addressCommunity, String city, String street, String houseNumber, String additionalInformation, String postalCode,
 							String facility, String facilityUuid, String facilityDetails,
-							String phone, String phoneOwner, String emailAddress, String otherContactDetails, OccupationType occupationType, String occupationDetails, ArmedForcesRelationType armedForcesRelationType,
+							String phone, String phoneOwner, String emailAddress, String otherContactDetails, String occupationType, String occupationDetails, ArmedForcesRelationType armedForcesRelationType,
 							String region, String district, String community,
 							long epiDataId, YesNoUnknown contactWithSourceCaseKnown, YesNoUnknown returningTraveler,
 							VaccinationStatus vaccinationStatus, String externalID, String externalToken, String internalToken, String caseReferenceNumber,
@@ -337,7 +338,7 @@ public ContactExportDto(long id, long personId, String uuid, String sourceCaseUu
 //			this.otherContactDetails += this.otherContactDetails.equals("") ? otherContactDetail : ", " + otherContactDetail;
 //		}
 		this.otherContactDetails = otherContactDetails;
-		this.occupationType = occupationType;
+		this.occupationType = new OccupationTypeConverter().convertToEntityAttribute(null, occupationType);
 		this.occupationDetails = occupationDetails;
 		this.armedForcesRelationType = armedForcesRelationType;
 		this.region = region;

diff --git a/...izableenum/CustomizableEnumConverter.java → ...izableenum/CustomizableEnumConverter.java b/...izableenum/CustomizableEnumConverter.java → ...izableenum/CustomizableEnumConverter.java
@@ -13,17 +13,14 @@
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
  */
 
-package de.symeda.sormas.backend.customizableenum;
+package de.symeda.sormas.api.customizableenum;
 
 import javax.naming.InitialContext;
 import javax.naming.NamingException;
-import javax.persistence.AttributeConverter;
 
 import org.apache.commons.lang3.StringUtils;
 
-import de.symeda.sormas.api.customizableenum.CustomizableEnum;
-import de.symeda.sormas.api.customizableenum.CustomizableEnumFacade;
-import de.symeda.sormas.api.customizableenum.CustomizableEnumType;
+import de.symeda.sormas.api.Disease;
 
 /**
  * JPA Converter that converts a JSON String stored in the database to an instance of {@link CustomizableEnum} and vice versa.
@@ -36,7 +33,7 @@
  * @param <T>
  *            The specific extension of {@link CustomizableEnum} for type safety
  */
-public abstract class CustomizableEnumConverter<T extends CustomizableEnum> implements AttributeConverter<T, String> {
+public abstract class CustomizableEnumConverter<T extends CustomizableEnum> {
 
 	private final Class<T> enumClass;
 	private CustomizableEnumFacade customizableEnumFacade;
@@ -45,13 +42,11 @@ public CustomizableEnumConverter(Class<T> enumClass) {
 		this.enumClass = enumClass;
 	}
 
-	@Override
 	public String convertToDatabaseColumn(T enumValue) {
 		return enumValue != null ? enumValue.getValue() : null;
 	}
 
-	@Override
-	public T convertToEntityAttribute(String enumString) {
+	public T convertToEntityAttribute(Disease disease, String enumString) {
 		if (StringUtils.isBlank(enumString)) {
 			return null;
 		}
@@ -66,7 +61,11 @@ public T convertToEntityAttribute(String enumString) {
 				throw new RuntimeException("No CustomizableEnumType for given enumClass " + enumClass + "found");
 			}
 
-			return customizableEnumFacade.getEnumValue(CustomizableEnumType.getByEnumClass(enumClass), enumString);
+			T enumValue = customizableEnumFacade.getEnumValue(enumType, disease, enumString);
+			if (enumValue == null && disease != null) {
+				enumValue = customizableEnumFacade.getEnumValue(enumType, null, enumString);
+			}
+			return enumValue;
 		} catch (NamingException e) {
 			throw new RuntimeException(e);
 		}

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/customizableenum/CustomizableEnumFacade.java b/sormas-api/src/main/java/de/symeda/sormas/api/customizableenum/CustomizableEnumFacade.java
@@ -46,11 +46,11 @@ public interface CustomizableEnumFacade
 	 *            The specific extension of {@link CustomizableEnum} for type safety
 	 * @return The enum instance containing its value, internationalized caption, and optional properties
 	 */
-	<T extends CustomizableEnum> T getEnumValue(CustomizableEnumType type, String value);
+	<T extends CustomizableEnum> T getEnumValue(CustomizableEnumType type, Disease disease, String value);
 
 	/**
 	 * Works similar to the {@link CustomizableEnumFacade#getEnumValues(CustomizableEnumType, Disease)}, but looks up a specific value.
-	 * Unlike the {@link CustomizableEnumFacade#getEnumValue(CustomizableEnumType, String)}, this method does not throw a RuntimeException
+	 * Unlike the {@link CustomizableEnumFacade#getEnumValue(CustomizableEnumType, Disease, String)}, this method does not throw a RuntimeException
 	 * when an enum can not be found.
 	 * 
 	 * @param type
@@ -106,7 +106,7 @@ public interface CustomizableEnumFacade
 
 	/**
 	 * Clears the caches and reloads the customizable enum values from the database. Does not load enum values by language
-	 * or disease as those are retrieved on demand by using {@link #getEnumValue(CustomizableEnumType, String)} and
+	 * or disease as those are retrieved on demand by using {@link #getEnumValue(CustomizableEnumType, Disease, String)} and
 	 * {@link #getEnumValues(CustomizableEnumType, Disease)}. Exposed to this facade to allow reloading the caches without
 	 * having to restart the server.
 	 */

diff --git a/...kend/disease/DiseaseVariantConverter.java → .../api/disease/DiseaseVariantConverter.java b/...kend/disease/DiseaseVariantConverter.java → .../api/disease/DiseaseVariantConverter.java
@@ -13,10 +13,9 @@
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
  */
 
-package de.symeda.sormas.backend.disease;
+package de.symeda.sormas.api.disease;
 
-import de.symeda.sormas.api.disease.DiseaseVariant;
-import de.symeda.sormas.backend.customizableenum.CustomizableEnumConverter;
+import de.symeda.sormas.api.customizableenum.CustomizableEnumConverter;
 
 public class DiseaseVariantConverter extends CustomizableEnumConverter<DiseaseVariant> {
 

diff --git a/...as/backend/disease/PathogenConverter.java → ...sormas/api/disease/PathogenConverter.java b/...as/backend/disease/PathogenConverter.java → ...sormas/api/disease/PathogenConverter.java
@@ -13,10 +13,10 @@
  * along with this program. If not, see <https://www.gnu.org/licenses/>.
  */
 
-package de.symeda.sormas.backend.disease;
+package de.symeda.sormas.api.disease;
 
 import de.symeda.sormas.api.environment.environmentsample.Pathogen;
-import de.symeda.sormas.backend.customizableenum.CustomizableEnumConverter;
+import de.symeda.sormas.api.customizableenum.CustomizableEnumConverter;
 
 public class PathogenConverter extends CustomizableEnumConverter<Pathogen> {
 

diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/event/EventActionExportDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/event/EventActionExportDto.java
@@ -25,6 +25,7 @@
 import de.symeda.sormas.api.action.ActionPriority;
 import de.symeda.sormas.api.action.ActionStatus;
 import de.symeda.sormas.api.disease.DiseaseVariant;
+import de.symeda.sormas.api.disease.DiseaseVariantConverter;
 import de.symeda.sormas.api.importexport.format.ExportFormat;
 import de.symeda.sormas.api.importexport.format.ImportExportFormat;
 import de.symeda.sormas.api.user.UserReferenceDto;
@@ -64,7 +65,7 @@ public EventActionExportDto(
 		String eventUuid,
 		String eventTitle,
 		Disease eventDisease,
-		DiseaseVariant eventDiseaseVariant,
+		String eventDiseaseVariant,
 		String eventDiseaseDetails,
 		String eventDesc,
 		EventIdentificationSource eventIdentificationSource,
@@ -98,7 +99,7 @@ public EventActionExportDto(
 		this.eventUuid = eventUuid;
 		this.eventTitle = eventTitle;
 		this.eventDisease = eventDisease;
-		this.eventDiseaseVariant = eventDiseaseVariant;
+		this.eventDiseaseVariant = new DiseaseVariantConverter().convertToEntityAttribute(eventDisease, eventDiseaseVariant);
 		this.eventDiseaseDetails = eventDiseaseDetails;
 		this.eventDesc = eventDesc;
 		this.eventIdentificationSource = eventIdentificationSource;