Merge branch 'development' into feature-3253-SendSMSToCases

# Conflicts:
#	sormas-backend/src/main/resources/META-INF/persistence.xml
#	sormas-backend/src/main/resources/sql/sormas_schema.sql
#	sormas-backend/src/test/resources/META-INF/persistence.xml
#	sormas-ui/src/test/resources/META-INF/persistence.xml

Author: barnabartha

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

@@ -24,13 +24,23 @@ public enum CaseClassification
 	implements
 	StatisticsGroupingKey {
 
-	NOT_CLASSIFIED,
-	SUSPECT,
-	PROBABLE,
-	CONFIRMED,
-	CONFIRMED_NO_SYMPTOMS,
-	CONFIRMED_UNKNOWN_SYMPTOMS,
-	NO_CASE;
+	NOT_CLASSIFIED(1),
+	SUSPECT(2),
+	PROBABLE(3),
+	CONFIRMED(6),
+	CONFIRMED_NO_SYMPTOMS(4),
+	CONFIRMED_UNKNOWN_SYMPTOMS(5),
+	NO_CASE(0);
+
+	/**
+	 * Severity of the case classification; confirmed has the highest severity in terms of the classification process
+	 * while no_case has the lowest.
+	 */
+	private final int severity;
+
+	CaseClassification(int severity) {
+		this.severity = severity;
+	}
 
 	public String getName() {
 		return this.name();
@@ -57,4 +67,8 @@ public int keyCompareTo(StatisticsGroupingKey o) {
 
 		return this.toString().compareTo(o.toString());
 	}
+
+	public int getSeverity() {
+		return severity;
+	}
 }

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

@@ -85,6 +85,7 @@ public class CaseExportDto implements Serializable {
 	public static final String ADDRESS_REGION = "addressRegion";
 	public static final String ADDRESS_COMMUNITY = "addressCommunity";
 	public static final String ADDRESS_GPS_COORDINATES = "addressGpsCoordinates";
+	public static final String BURIAL_ATTENDED = "burialAttended";
 	public static final String TRAVELED = "traveled";
 	public static final String TRAVEL_HISTORY = "travelHistory";
 	public static final String NUMBER_OF_PRESCRIPTIONS = "numberOfPrescriptions";
@@ -186,11 +187,9 @@ public class CaseExportDto implements Serializable {
 	private String occupationType;
 	private String educationType;
 	private String travelHistory;
-	private YesNoUnknown traveled;
-	private YesNoUnknown burialAttended;
-	private YesNoUnknown directContactConfirmedCase;
-	private YesNoUnknown directContactProbableCase;
-	private YesNoUnknown contactWithRodent;
+	private boolean traveled;
+	private boolean burialAttended;
+	private YesNoUnknown contactWithSourceCaseKnown;
 	private SymptomsDto symptoms;
 	//	private Date onsetDate;
 //	private String symptoms;
@@ -261,8 +260,7 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
 						 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, EducationType educationType, String educationDetails,
-						 OccupationType occupationType, String occupationDetails, YesNoUnknown traveled,
-						 YesNoUnknown burialAttended, YesNoUnknown directContactConfirmedCase, YesNoUnknown directContactProbableCase, YesNoUnknown contactWithRodent,
+						 OccupationType occupationType, String occupationDetails, YesNoUnknown contactWithSourceCaseKnown,
 						 //Date onsetDate,
 						 Vaccination vaccination, String vaccinationDoses, Date vaccinationDate,
 						 VaccinationInfoSource vaccinationInfoSource, YesNoUnknown postpartum, Trimester trimester,
@@ -329,11 +327,7 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
 		this.emailAddress = emailAddress;
 		this.educationType = PersonHelper.buildEducationString(educationType, educationDetails);
 		this.occupationType = PersonHelper.buildOccupationString(occupationType, occupationDetails);
-		this.traveled = traveled;
-		this.burialAttended = burialAttended;
-		this.directContactConfirmedCase = directContactConfirmedCase;
-		this.directContactProbableCase = directContactProbableCase;
-		this.contactWithRodent = contactWithRodent;
+		this.contactWithSourceCaseKnown = contactWithSourceCaseKnown;
 //		this.onsetDate = onsetDate;
 		this.vaccination = vaccination;
 		this.vaccinationDoses = vaccinationDoses;
@@ -1014,11 +1008,11 @@ public String getOccupationType() {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(TRAVELED)
 	@ExportGroup(ExportGroupType.EPIDEMIOLOGICAL)
-	public YesNoUnknown getTraveled() {
+	public boolean isTraveled() {
 		return traveled;
 	}
 
-	public void setTraveled(YesNoUnknown traveled) {
+	public void setTraveled(boolean traveled) {
 		this.traveled = traveled;
 	}
 
@@ -1034,49 +1028,27 @@ public String getTravelHistory() {
 	@Order(80)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
-	@ExportProperty(EpiDataDto.BURIAL_ATTENDED)
+	@ExportProperty(BURIAL_ATTENDED)
 	@ExportGroup(ExportGroupType.EPIDEMIOLOGICAL)
-	public YesNoUnknown getBurialAttended() {
+	public boolean isBurialAttended() {
 		return burialAttended;
 	}
 
-	public void setBurialAttended(YesNoUnknown burialAttended) {
+	public void setBurialAttended(boolean burialAttended) {
 		this.burialAttended = burialAttended;
 	}
 
 	@Order(81)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
-	@ExportProperty(EpiDataDto.DIRECT_CONTACT_CONFIRMED_CASE)
-	@ExportGroup(ExportGroupType.EPIDEMIOLOGICAL)
-	public YesNoUnknown getDirectContactConfirmedCase() {
-		return directContactConfirmedCase;
-	}
-
-	public void setDirectContactConfirmedCase(YesNoUnknown directContactConfirmedCase) {
-		this.directContactConfirmedCase = directContactConfirmedCase;
-	}
-
-	@Order(90)
-	@ExportTarget(caseExportTypes = {
-		CaseExportType.CASE_SURVEILLANCE })
-	@ExportProperty(EpiDataDto.DIRECT_CONTACT_PROBABLE_CASE)
+	@ExportProperty(EpiDataDto.CONTACT_WITH_SOURCE_CASE_KNOWN)
 	@ExportGroup(ExportGroupType.EPIDEMIOLOGICAL)
-	public YesNoUnknown getDirectContactProbableCase() {
-		return directContactProbableCase;
+	public YesNoUnknown getContactWithSourceCaseKnown() {
+		return contactWithSourceCaseKnown;
 	}
 
-	public void setDirectContactProbableCase(YesNoUnknown directContactProbableCase) {
-		this.directContactProbableCase = directContactProbableCase;
-	}
-
-	@Order(91)
-	@ExportTarget(caseExportTypes = {
-		CaseExportType.CASE_SURVEILLANCE })
-	@ExportProperty(EpiDataDto.RODENTS)
-	@ExportGroup(ExportGroupType.EPIDEMIOLOGICAL)
-	public YesNoUnknown getContactWithRodent() {
-		return contactWithRodent;
+	public void setContactWithSourceCaseKnown(YesNoUnknown contactWithSourceCaseKnown) {
+		this.contactWithSourceCaseKnown = contactWithSourceCaseKnown;
 	}
 
 	@Order(92)
@@ -1522,10 +1494,6 @@ public void setTravelHistory(String travelHistory) {
 		this.travelHistory = travelHistory;
 	}
 
-	public void setContactWithRodent(YesNoUnknown contactWithRodent) {
-		this.contactWithRodent = contactWithRodent;
-	}
-
 	public void setInitialDetectionPlace(String initialDetectionPlace) {
 		this.initialDetectionPlace = initialDetectionPlace;
 	}
@@ -1546,10 +1514,6 @@ public void setVaccinationInfoSource(VaccinationInfoSource vaccinationInfoSource
 		this.vaccinationInfoSource = vaccinationInfoSource;
 	}
 
-//	public void setOnsetDate(Date onsetDate) {
-//		this.onsetDate = onsetDate;
-//	}
-
 	public void setSymptoms(SymptomsDto symptoms) {
 		this.symptoms = symptoms;
 	}

sormas-api/src/main/java/de/symeda/sormas/api/caze/classification/CaseClassificationFacade.java

@@ -30,7 +30,7 @@
 @Remote
 public interface CaseClassificationFacade {
 
-	CaseClassification getClassification(CaseDataDto caze, List<PathogenTestDto> sampleTests);
+	CaseClassification getClassification(CaseDataDto caze, List<PathogenTestDto> pathogenTests);
 
 	DiseaseClassificationCriteriaDto getByDisease(Disease disease);
 

sormas-api/src/main/java/de/symeda/sormas/api/caze/classification/ClassificationCaseCriteriaDto.java

@@ -35,6 +35,7 @@
 	@JsonSubTypes.Type(value = ClassificationEpiDataCriteriaDto.class, name = "ClassificationEpiDataCriteriaDto"),
 	@JsonSubTypes.Type(value = ClassificationNotInStartDateRangeCriteriaDto.class, name = "ClassificationNotInStartDateRangeCriteriaDto"),
 	@JsonSubTypes.Type(value = ClassificationPathogenTestCriteriaDto.class, name = "ClassificationPathogenTestCriteriaDto"),
+	@JsonSubTypes.Type(value = ClassificationExposureCriteriaDto.class, name = "ClassificationExposureCriteriaDto"),
 	@JsonSubTypes.Type(value = ClassificationSymptomsCriteriaDto.class, name = "ClassificationSymptomsCriteriaDto"), })
 public class ClassificationCaseCriteriaDto extends ClassificationCriteriaDto {
 
@@ -61,7 +62,7 @@ protected Object getInvokeObject(CaseDataDto caze) {
 	}
 
 	@Override
-	public boolean eval(CaseDataDto caze, PersonDto person, List<PathogenTestDto> sampleTests) {
+	public boolean eval(CaseDataDto caze, PersonDto person, List<PathogenTestDto> pathogenTests) {
 
 		try {
 			Method method = getInvokeClass().getMethod("get" + propertyId.substring(0, 1).toUpperCase() + propertyId.substring(1));

sormas-api/src/main/java/de/symeda/sormas/api/caze/classification/ClassificationCriteriaDto.java

@@ -55,7 +55,7 @@ public abstract class ClassificationCriteriaDto implements Serializable {
 
 	private static final long serialVersionUID = -3686569295881034008L;
 
-	public abstract boolean eval(CaseDataDto caze, PersonDto person, List<PathogenTestDto> sampleTests);
+	public abstract boolean eval(CaseDataDto caze, PersonDto person, List<PathogenTestDto> pathogenTests);
 
 	public abstract String buildDescription();
 

sormas-api/src/main/java/de/symeda/sormas/api/caze/classification/ClassificationExposureCriteriaDto.java

@@ -0,0 +1,99 @@
+/*
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2020 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
+ * 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.caze.classification;
+
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.List;
+
+import org.apache.commons.collections.CollectionUtils;
+
+import de.symeda.sormas.api.EntityDto;
+import de.symeda.sormas.api.caze.CaseDataDto;
+import de.symeda.sormas.api.exposure.ExposureDto;
+import de.symeda.sormas.api.exposure.ExposureType;
+import de.symeda.sormas.api.i18n.I18nProperties;
+import de.symeda.sormas.api.i18n.Strings;
+import de.symeda.sormas.api.person.PersonDto;
+import de.symeda.sormas.api.sample.PathogenTestDto;
+import de.symeda.sormas.api.utils.YesNoUnknown;
+
+public class ClassificationExposureCriteriaDto extends ClassificationCaseCriteriaDto {
+
+	private ExposureType exposureType;
+
+	public ClassificationExposureCriteriaDto() {
+		super();
+	}
+
+	public ClassificationExposureCriteriaDto(String propertyId, ExposureType exposureType, Object... propertyValues) {
+
+		super(propertyId, propertyValues);
+		this.exposureType = exposureType;
+	}
+
+	@Override
+	protected Class<? extends EntityDto> getInvokeClass() {
+		return ExposureDto.class;
+	}
+
+	@Override
+	public boolean eval(CaseDataDto caze, PersonDto person, List<PathogenTestDto> pathogenTests) {
+
+		for (ExposureDto exposure : caze.getEpiData().getExposures()) {
+			if (exposureType != null && exposure.getExposureType() != exposureType) {
+				continue;
+			}
+
+			Method method;
+			try {
+				method = getInvokeClass().getMethod("get" + propertyId.substring(0, 1).toUpperCase() + propertyId.substring(1));
+			} catch (NoSuchMethodException e) {
+				try {
+					method = getInvokeClass().getMethod("is" + propertyId.substring(0, 1).toUpperCase() + propertyId.substring(1));
+				} catch (NoSuchMethodException newE) {
+					throw new RuntimeException(newE);
+				}
+			} catch (SecurityException e) {
+				throw new RuntimeException(e);
+			}
+
+			try {
+				Object value = method.invoke(exposure);
+				if (propertyValues.contains(value) || CollectionUtils.isEmpty(propertyValues) && YesNoUnknown.YES.equals(value)) {
+					return true;
+				}
+			} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException | SecurityException e) {
+				throw new RuntimeException(e);
+			}
+		}
+
+		return false;
+	}
+
+	@Override
+	public String buildDescription() {
+
+		StringBuilder sb = new StringBuilder();
+		sb.append(I18nProperties.getPrefixCaption(ExposureDto.I18N_PREFIX, propertyId));
+		if (exposureType != null) {
+			sb.append(" ").append(I18nProperties.getString(Strings.classificationCriteriaForExposureType)).append(exposureType.toString());
+		}
+
+		return sb.toString();
+	}
+
+}

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

@@ -69,6 +69,7 @@ public class ContactCriteria extends BaseCriteria implements Serializable {
 	private UserRole reportingUserRole;
 	private Disease disease;
 	private CaseReferenceDto caze;
+	private CaseReferenceDto resultingCase;
 	private RegionReferenceDto region;
 	private DistrictReferenceDto district;
 	private CommunityReferenceDto community;
@@ -148,6 +149,15 @@ public ContactCriteria caze(CaseReferenceDto caze) {
 		return this;
 	}
 
+	public CaseReferenceDto getResultingCase() {
+		return resultingCase;
+	}
+
+	public ContactCriteria resultingCase(CaseReferenceDto resultingCase) {
+		this.resultingCase = resultingCase;
+		return this;
+	}
+
 	public RegionReferenceDto getRegion() {
 		return region;
 	}