[GITFLOW]merging 'release-0.7.0' into 'master'

README.md

@@ -48,8 +48,9 @@ For information on what libs are used see pom.xml in sormas-base project: https:
     * ``sudo -u postgres pg_dump -Fc -b sormas_db >  "sormas_db_"`date +"%Y-%m-%d_%H-%M-%S"`".dump"``
     * ``cd /root/deploy/sormas/$(date +%F)``	
 * Update the database schema
-    * make the schema update script executable: ``chmod +x sql/database-update.sh``
-    * execute the update script: ``sql/database-update.sh``
+    * ``cd /root/deploy/sormas/$(date +%F)/sql``
+    * make the schema update script executable: ``chmod +x ./database-update.sh``
+    * execute the update script: ``./database-update.sh``
     * confirm schema update by pressing enter when asked
 * Alternative: Manual database update
     * Find out current schema version of database:

sormas-api/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>0.6.0</version>
+		<version>0.7.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>

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

@@ -1,15 +1,16 @@
 package de.symeda.sormas.api;
 
 public enum Disease {
-	EVD,
-	LASSA,
 	AVIAN_INFLUENCA,
-	CSM,
 	CHOLERA,
-	MEASLES,
-	YELLOW_FEVER,
+	CSM,
 	DENGUE,
+	EVD,
+	LASSA,
+	MEASLES,
 	MONKEYPOX,
+	PLAGUE,
+	YELLOW_FEVER,
 	OTHER
 	;
 
@@ -25,7 +26,4 @@ public String getName() {
 		return this.name();
 	}
 
-	public boolean hasContactFollowUp() {
-		return this == EVD || this == LASSA || this == AVIAN_INFLUENCA || this == MONKEYPOX || this == OTHER;
-	}
 }

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

@@ -0,0 +1,40 @@
+package de.symeda.sormas.api;
+
+import de.symeda.sormas.api.caze.CaseDataDto;
+import de.symeda.sormas.api.symptoms.SymptomState;
+import de.symeda.sormas.api.symptoms.SymptomsDto;
+
+public class DiseaseHelper {
+
+	public static boolean hasContactFollowUp(CaseDataDto caze) {
+		Disease disease = caze.getDisease();
+
+		return disease == Disease.EVD || disease == Disease.LASSA || disease == Disease.AVIAN_INFLUENCA 
+				|| disease == Disease.MONKEYPOX || (disease == Disease.PLAGUE && caze.getPlagueType() == PlagueType.PNEUMONIC) 
+				|| disease == Disease.OTHER;
+	}
+
+	/**
+	 * Checks whether the given symptoms match the clinical criteria of one of the three Plague types.
+	 * 
+	 * @param symptoms The symptoms of a case with the Plague disease
+	 * @return One of the three Plague types if the clinical criteria are met, null otherwise
+	 */
+	public static PlagueType getPlagueTypeForSymptoms(SymptomsDto symptoms) {
+		if (symptoms.getFever() == SymptomState.YES) {
+			if (symptoms.getPainfulLymphadenitis() == SymptomState.YES) {
+				return PlagueType.BUBONIC;
+			} else if (symptoms.getCough() == SymptomState.YES || symptoms.getChestPain() == SymptomState.YES ||
+					symptoms.getCoughingBlood() == SymptomState.YES) {
+				return PlagueType.PNEUMONIC;
+			} else if (symptoms.getChillsSweats() == SymptomState.YES) {
+				return PlagueType.SEPTICAEMIC;
+			} else {
+				return null;
+			}
+		} else {
+			return null;
+		}
+	}
+
+}

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

@@ -0,0 +1,13 @@
+package de.symeda.sormas.api;
+
+public enum PlagueType {
+
+	BUBONIC,
+	PNEUMONIC,
+	SEPTICAEMIC;
+
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	};
+
+}

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

@@ -3,6 +3,7 @@
 import java.util.Date;
 
 import de.symeda.sormas.api.Disease;
+import de.symeda.sormas.api.PlagueType;
 import de.symeda.sormas.api.epidata.EpiDataDto;
 import de.symeda.sormas.api.facility.FacilityReferenceDto;
 import de.symeda.sormas.api.hospitalization.HospitalizationDto;
@@ -21,13 +22,12 @@ public class CaseDataDto extends CaseReferenceDto {
 
 	public static final String I18N_PREFIX = "CaseData";
 
-	public static final String COUNTRY_EPID_CODE = "NIE";
-
 	public static final String CASE_CLASSIFICATION = "caseClassification";
 	public static final String INVESTIGATION_STATUS = "investigationStatus";
 	public static final String PERSON = "person";
 	public static final String DISEASE = "disease";
 	public static final String DISEASE_DETAILS = "diseaseDetails";
+	public static final String PLAGUE_TYPE = "plagueType";
 	public static final String REGION = "region";
 	public static final String DISTRICT = "district";
 	public static final String COMMUNITY = "community";
@@ -49,6 +49,8 @@ public class CaseDataDto extends CaseReferenceDto {
 	public static final String YELLOW_FEVER_VACCINATION = "yellowFeverVaccination";
 	public static final String YELLOW_FEVER_VACCINATION_INFO_SOURCE = "yellowFeverVaccinationInfoSource";
 	public static final String SMALLPOX_VACCINATION_SCAR = "smallpoxVaccinationScar";
+	public static final String SMALLPOX_VACCINATION_RECEIVED = "smallpoxVaccinationReceived";
+	public static final String SMALLPOX_VACCINATION_DATE = "smallpoxVaccinationDate";
 	public static final String EPID_NUMBER = "epidNumber";
 	public static final String REPORT_LAT = "reportLat";
 	public static final String REPORT_LON = "reportLon";
@@ -58,6 +60,7 @@ public class CaseDataDto extends CaseReferenceDto {
 	private InvestigationStatus investigationStatus;
 	private Disease disease;
 	private String diseaseDetails;
+	private PlagueType plagueType;
 	private UserReferenceDto reportingUser;
 	private Date reportDate;
 	private Date investigatedDate;
@@ -86,6 +89,10 @@ public class CaseDataDto extends CaseReferenceDto {
 	private VaccinationInfoSource yellowFeverVaccinationInfoSource;
 	@Diseases({Disease.MONKEYPOX})
 	private YesNoUnknown smallpoxVaccinationScar;
+	@Diseases({Disease.MONKEYPOX})
+	private YesNoUnknown smallpoxVaccinationReceived;
+	@Diseases({Disease.MONKEYPOX})
+	private Date smallpoxVaccinationDate;
 
 	private String epidNumber;
 
@@ -129,6 +136,14 @@ public void setDiseaseDetails(String diseaseDetails) {
 		this.diseaseDetails = diseaseDetails;
 	}
 
+	public PlagueType getPlagueType() {
+		return plagueType;
+	}
+
+	public void setPlagueType(PlagueType plagueType) {
+		this.plagueType = plagueType;
+	}
+
 	public UserReferenceDto getReportingUser() {
 		return reportingUser;
 	}
@@ -297,6 +312,22 @@ public void setSmallpoxVaccinationScar(YesNoUnknown smallpoxVaccinationScar) {
 		this.smallpoxVaccinationScar = smallpoxVaccinationScar;
 	}
 
+	public YesNoUnknown getSmallpoxVaccinationReceived() {
+		return smallpoxVaccinationReceived;
+	}
+
+	public void setSmallpoxVaccinationReceived(YesNoUnknown smallpoxVaccinationReceived) {
+		this.smallpoxVaccinationReceived = smallpoxVaccinationReceived;
+	}
+
+	public Date getSmallpoxVaccinationDate() {
+		return smallpoxVaccinationDate;
+	}
+
+	public void setSmallpoxVaccinationDate(Date smallpoxVaccinationDate) {
+		this.smallpoxVaccinationDate = smallpoxVaccinationDate;
+	}
+
 	public String getEpidNumber() {
 		return epidNumber;
 	}

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

@@ -12,7 +12,6 @@
 import de.symeda.sormas.api.region.DistrictReferenceDto;
 import de.symeda.sormas.api.region.RegionReferenceDto;
 import de.symeda.sormas.api.user.UserReferenceDto;
-import de.symeda.sormas.api.utils.EpiWeek;
 
 @Remote
 public interface CaseFacade {
@@ -47,4 +46,5 @@ public interface CaseFacade {
 	 * @param disease optional
 	 */
 	Map<RegionReferenceDto, Long> getCaseCountPerRegion(Date onsetFromDate, Date onsetToDate, Disease disease);
+
 }

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

@@ -37,13 +37,13 @@ public class ContactDto extends ContactReferenceDto {
 	private Date lastContactDate;
 	private ContactProximity contactProximity;
 	private ContactClassification contactClassification;
-	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.OTHER})
+	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.PLAGUE,Disease.OTHER})
 	private FollowUpStatus followUpStatus;
-	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.OTHER})
+	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.PLAGUE,Disease.OTHER})
 	private String followUpComment;
-	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.OTHER})
+	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.PLAGUE,Disease.OTHER})
 	private Date followUpUntil;
-	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.OTHER})
+	@Diseases({Disease.EVD,Disease.LASSA,Disease.CHOLERA,Disease.MONKEYPOX,Disease.PLAGUE,Disease.OTHER})
 	private UserReferenceDto contactOfficer;
 	private String description;
 	private ContactRelation relationToCase;

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

@@ -42,6 +42,7 @@ public class EpiDataDto extends DataTransferObject {
 	public static final String WATER_BODY = "waterBody";
 	public static final String WATER_BODY_DETAILS = "waterBodyDetails";
 	public static final String TICKBITE = "tickBite";
+	public static final String FLEABITE = "fleaBite";
 	public static final String DATE_OF_LAST_EXPOSURE = "dateOfLastExposure";
 	public static final String PLACE_OF_LAST_EXPOSURE = "placeOfLastExposure";
 	public static final String ANIMAL_CONDITION = "animalCondition";
@@ -53,9 +54,9 @@ public class EpiDataDto extends DataTransferObject {
 	private YesNoUnknown burialAttended;
 	@Diseases({Disease.EVD,Disease.LASSA,Disease.AVIAN_INFLUENCA,Disease.CSM,Disease.CHOLERA,Disease.MEASLES,Disease.YELLOW_FEVER,Disease.DENGUE,Disease.OTHER})
 	private YesNoUnknown gatheringAttended;
-	@Diseases({Disease.EVD,Disease.LASSA,Disease.AVIAN_INFLUENCA,Disease.CSM,Disease.CHOLERA,Disease.MEASLES,Disease.YELLOW_FEVER,Disease.DENGUE,Disease.MONKEYPOX,Disease.OTHER})
+	@Diseases({Disease.EVD,Disease.LASSA,Disease.AVIAN_INFLUENCA,Disease.CSM,Disease.CHOLERA,Disease.MEASLES,Disease.YELLOW_FEVER,Disease.DENGUE,Disease.MONKEYPOX,Disease.PLAGUE,Disease.OTHER})
 	private YesNoUnknown traveled;
-	@Diseases({Disease.EVD,Disease.LASSA,Disease.MONKEYPOX,Disease.OTHER})
+	@Diseases({Disease.EVD,Disease.LASSA,Disease.MONKEYPOX,Disease.PLAGUE,Disease.OTHER})
 	private YesNoUnknown rodents;
 	@Diseases({Disease.EVD,Disease.LASSA,Disease.OTHER})
 	private YesNoUnknown bats;
@@ -103,6 +104,8 @@ public class EpiDataDto extends DataTransferObject {
 	private String waterBodyDetails;
 	@Diseases({Disease.EVD,Disease.LASSA,Disease.OTHER})
 	private YesNoUnknown tickBite;
+	@Diseases({Disease.PLAGUE,Disease.OTHER})
+	private YesNoUnknown fleaBite;
 	@Diseases({Disease.MONKEYPOX,Disease.OTHER})
 	private Date dateOfLastExposure;
 	@Diseases({Disease.MONKEYPOX,Disease.OTHER})	
@@ -324,6 +327,13 @@ public void setAnimalCondition(AnimalCondition animalCondition) {
 		this.animalCondition = animalCondition;
 	}
 
+	public YesNoUnknown getFleaBite() {
+		return fleaBite;
+	}
+	public void setFleaBite(YesNoUnknown fleaBite) {
+		this.fleaBite = fleaBite;
+	}
+
 	public List<EpiDataBurialDto> getBurials() {
 		return burials;
 	}

sormas-api/src/main/java/de/symeda/sormas/api/facility/FacilityDto.java

@@ -104,9 +104,7 @@ public String toString() {
 
 		StringBuilder caption = new StringBuilder();
 		caption.append(name);
-		if (community != null) {
-			caption.append(" (").append(community.getCaption()).append(")");
-		}
+
 		return caption.toString();
 	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/region/GeoShapeProvider.java

@@ -12,5 +12,7 @@ public interface GeoShapeProvider {
 
 	RegionReferenceDto getRegionByCoord(GeoLatLon latLon);
 
+	GeoLatLon getCenterOfAllRegions();
+
 	GeoLatLon getCenterOfRegion(RegionReferenceDto region);
 }

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

@@ -20,6 +20,7 @@ public class SampleTestDto extends SampleTestReferenceDto {
 	public static final String TEST_RESULT = "testResult";
 	public static final String TEST_RESULT_TEXT = "testResultText";
 	public static final String TEST_RESULT_VERIFIED = "testResultVerified";
+	public static final String FOUR_FOLD_INCREASE_ANTIBODY_TITER = "fourFoldIncreaseAntibodyTiter";
 
 	private SampleReferenceDto sample;
 	private SampleTestType testType;
@@ -30,6 +31,7 @@ public class SampleTestDto extends SampleTestReferenceDto {
 	private SampleTestResultType testResult;
 	private String testResultText;
 	private boolean testResultVerified;
+	private boolean fourFoldIncreaseAntibodyTiter;
 
 	public SampleReferenceDto getSample() {
 		return sample;
@@ -85,5 +87,11 @@ public boolean isTestResultVerified() {
 	public void setTestResultVerified(boolean testResultVerified) {
 		this.testResultVerified = testResultVerified;
 	}
+	public boolean isFourFoldIncreaseAntibodyTiter() {
+		return fourFoldIncreaseAntibodyTiter;
+	}
+	public void setFourFoldIncreaseAntibodyTiter(boolean fourFoldIncreaseAntibodyTiter) {
+		this.fourFoldIncreaseAntibodyTiter = fourFoldIncreaseAntibodyTiter;
+	}
 
 }

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

@@ -12,6 +12,7 @@ public enum SampleTestType {
 	VIRUS_ISOLATION,
 	RAPID_TEST,
 	ANTIGEN_DETECTION,
+	SERUM_ANTIBODY_TITER,
 	OTHER,
 	;