SORMAS-Foundation#3416 add nosocomial outbreak and infection setting to cases

Author: lgal

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

@@ -165,6 +165,9 @@ public class CaseDataDto extends PseudonymizableDto {
 	public static final String END_OF_ISOLATION_REASON = "endOfIsolationReason";
 	public static final String END_OF_ISOLATION_REASON_DETAILS = "endOfIsolationReasonDetails";
 
+	public static final String NOSOCOMIAL_OUTBREAK = "nosocomialOutbreak";
+	public static final String INFECTION_SETTING = "infectionSetting";
+
 	// Fields are declared in the order they should appear in the import template
 
 	@Outbreaks
@@ -443,6 +446,10 @@ public class CaseDataDto extends PseudonymizableDto {
 	@HideForCountriesExcept(countries = COUNTRY_CODE_SWITZERLAND)
 	@SensitiveData
 	private String endOfIsolationReasonDetails;
+	@HideForCountriesExcept
+	private boolean nosocomialOutbreak;
+	@HideForCountriesExcept
+	private InfectionSetting infectionSetting;
 
 	public static CaseDataDto build(PersonReferenceDto person, Disease disease) {
 		return build(person, disease, null);
@@ -1288,6 +1295,22 @@ public void setEndOfIsolationReasonDetails(String endOfIsolationReasonDetails) {
 		this.endOfIsolationReasonDetails = endOfIsolationReasonDetails;
 	}
 
+	public boolean isNosocomialOutbreak() {
+		return nosocomialOutbreak;
+	}
+
+	public void setNosocomialOutbreak(boolean nosocomialOutbreak) {
+		this.nosocomialOutbreak = nosocomialOutbreak;
+	}
+
+	public InfectionSetting getInfectionSetting() {
+		return infectionSetting;
+	}
+
+	public void setInfectionSetting(InfectionSetting infectionSetting) {
+		this.infectionSetting = infectionSetting;
+	}
+
 	public SormasToSormasOriginInfoDto getSormasToSormasOriginInfo() {
 		return sormasToSormasOriginInfo;
 	}

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

@@ -0,0 +1,60 @@
+/*
+ * 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;
+
+import de.symeda.sormas.api.i18n.I18nProperties;
+
+public enum InfectionSetting {
+
+	UNKNOWN(null),
+	AMBULANT(null),
+	MEDICAL_PRACTICE(AMBULANT),
+	OPERATIVE_1200(AMBULANT),
+	HOSPITAL_1300(AMBULANT),
+	OTHER_OUTPATIENT_FACILITY(AMBULANT),
+	STATIONARY(null),
+	HOSPITAL_2100(STATIONARY),
+	NORMAL_WARD(HOSPITAL_2100),
+	OPERATIVE_2111(NORMAL_WARD),
+	NOT_OPERATIVE(NORMAL_WARD),
+	HEMATOLOGICAL_ONCOLOGY(NORMAL_WARD),
+	CHILDREN_WARD(HOSPITAL_2100),
+	NEONATOLOGY(HOSPITAL_2100),
+	INTENSIVE_CARE_UNIT(HOSPITAL_2100),
+	OTHER_STATION(HOSPITAL_2100),
+	NURSING_HOME(STATIONARY),
+	REHAB_FACILITY(STATIONARY),
+	OTHER_STATIONARY_FACILITY(STATIONARY);
+
+	private final InfectionSetting parent;
+
+	InfectionSetting(InfectionSetting parent) {
+		this.parent = parent;
+	}
+
+	public InfectionSetting getParent() {
+		return this.parent;
+	}
+
+	public String toString() {
+		String caption = I18nProperties.getEnumCaption(this);
+		if (this.parent != null) {
+			caption = this.parent.toString() + " / " + caption;
+		}
+
+		return caption;
+	}
+}

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

@@ -222,6 +222,7 @@ public interface Captions {
 	String CaseData_healthFacilityDetails = "CaseData.healthFacilityDetails";
 	String CaseData_healthFacilityName = "CaseData.healthFacilityName";
 	String CaseData_hospitalization = "CaseData.hospitalization";
+	String CaseData_infectionSetting = "CaseData.infectionSetting";
 	String CaseData_investigatedDate = "CaseData.investigatedDate";
 	String CaseData_investigationStatus = "CaseData.investigationStatus";
 	String CaseData_laboratoryDiagnosticConfirmation = "CaseData.laboratoryDiagnosticConfirmation";
@@ -231,6 +232,7 @@ public interface Captions {
 	String CaseData_maternalHistory = "CaseData.maternalHistory";
 	String CaseData_nationalLevelDate = "CaseData.nationalLevelDate";
 	String CaseData_noneHealthFacilityDetails = "CaseData.noneHealthFacilityDetails";
+	String CaseData_nosocomialOutbreak = "CaseData.nosocomialOutbreak";
 	String CaseData_notifyingClinic = "CaseData.notifyingClinic";
 	String CaseData_notifyingClinicDetails = "CaseData.notifyingClinicDetails";
 	String CaseData_numberOfVisits = "CaseData.numberOfVisits";

sormas-api/src/main/resources/captions.properties

@@ -393,6 +393,8 @@ CaseData.quarantineReasonBeforeIsolationDetails=Other reason
 CaseData.endOfIsolationReason=Reason for end of isolation
 CaseData.endOfIsolationReasonDetails=Other reason
 CaseData.sormasToSormasOriginInfo=Shared by
+CaseData.nosocomialOutbreak=Nosocomial outbreak
+CaseData.infectionSetting=Infection setting
 
 # CaseExport
 CaseExport.address=Address

sormas-api/src/main/resources/captions_de-DE.properties

@@ -390,6 +390,8 @@ CaseData.quarantineReasonBeforeIsolationDetails=Anderer Grund
 CaseData.endOfIsolationReason=Grund für das Ende der Isolation
 CaseData.endOfIsolationReasonDetails=Anderer Grund
 CaseData.sormasToSormasOriginInfo=Geteilt von
+CaseData.nosocomialOutbreak=Nosocomialer Ausbruch
+CaseData.infectionSetting=Infektionsumfeld
 
 # CaseExport
 CaseExport.address=Adresse

sormas-api/src/main/resources/enum.properties

@@ -1214,3 +1214,23 @@ EndOfQuarantineReason.ASYMPTOMATIC=Asymptomatic after 10 days
 EndOfQuarantineReason.ISOLATED_AS_CASE=Isolated as Case
 EndOfQuarantineReason.LOST_TO_FOLLOWUP=Lost to follow-up
 EndOfQuarantineReason.OTHER=Other
+
+InfectionSetting.UNKNOWN=Unknown
+InfectionSetting.AMBULANT=Ambulant
+InfectionSetting.MEDICAL_PRACTICE=Medical practice
+InfectionSetting.OPERATIVE_1200=Operative
+InfectionSetting.HOSPITAL_1300=Hospital
+InfectionSetting.OTHER_OUTPATIENT_FACILITY=Other outpatient facility
+InfectionSetting.STATIONARY=In-patient
+InfectionSetting.HOSPITAL_2100=Hospital
+InfectionSetting.NORMAL_WARD=Normal ward
+InfectionSetting.OPERATIVE_2111=Operative
+InfectionSetting.NOT_OPERATIVE=Non-operative
+InfectionSetting.HEMATOLOGICAL_ONCOLOGY=Hematological oncology
+InfectionSetting.CHILDREN_WARD=Children's ward
+InfectionSetting.NEONATOLOGY=Neonatology
+InfectionSetting.INTENSIVE_CARE_UNIT=Intensive Care Unit
+InfectionSetting.OTHER_STATION=Other station
+InfectionSetting.NURSING_HOME=Nursing home
+InfectionSetting.REHAB_FACILITY=Rehab facility
+InfectionSetting.OTHER_STATIONARY_FACILITY=Other in-patient facililty

sormas-api/src/main/resources/enum_de-DE.properties

@@ -1209,3 +1209,23 @@ EndOfQuarantineReason.ASYMPTOMATIC=Asymptomatisch nach 10 Tagen
 EndOfQuarantineReason.ISOLATED_AS_CASE=Als Fall isoliert
 EndOfQuarantineReason.LOST_TO_FOLLOWUP=Keine Nachverfolgung möglich
 EndOfQuarantineReason.OTHER=Sonstiges
+
+InfectionSetting.UNKNOWN=Nicht erhoben
+InfectionSetting.AMBULANT=Ambulant
+InfectionSetting.MEDICAL_PRACTICE=Arztpraxis
+InfectionSetting.OPERATIVE_1200=Operativ
+InfectionSetting.HOSPITAL_1300=Krankenhaus
+InfectionSetting.OTHER_OUTPATIENT_FACILITY=Sonstige Ambulante Einrichtung
+InfectionSetting.STATIONARY=Stationär
+InfectionSetting.HOSPITAL_2100=Krankenhaus
+InfectionSetting.NORMAL_WARD=Normalstation
+InfectionSetting.OPERATIVE_2111=Operativ
+InfectionSetting.NOT_OPERATIVE=Nicht Operativ
+InfectionSetting.HEMATOLOGICAL_ONCOLOGY=Hamatoonkologie
+InfectionSetting.CHILDREN_WARD=Kinderstation
+InfectionSetting.NEONATOLOGY=Neonatologie
+InfectionSetting.INTENSIVE_CARE_UNIT=Intensivstation
+InfectionSetting.OTHER_STATION=Sonstige Station
+InfectionSetting.NURSING_HOME=Pflege Einrichtung
+InfectionSetting.REHAB_FACILITY=Reha-Einrichtung
+InfectionSetting.OTHER_STATIONARY_FACILITY=Sonstige Stationare Einrichtung

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/caze/Case.java

@@ -38,6 +38,7 @@
 import de.symeda.sormas.api.caze.DengueFeverType;
 import de.symeda.sormas.api.caze.EndOfIsolationReason;
 import de.symeda.sormas.api.caze.HospitalWardType;
+import de.symeda.sormas.api.caze.InfectionSetting;
 import de.symeda.sormas.api.caze.InvestigationStatus;
 import de.symeda.sormas.api.caze.PlagueType;
 import de.symeda.sormas.api.caze.QuarantineReason;
@@ -333,6 +334,10 @@ public class Case extends PseudonymizableAdo {
 	private EndOfIsolationReason endOfIsolationReason;
 	@Column(length = COLUMN_LENGTH_DEFAULT)
 	private String endOfIsolationReasonDetails;
+	@DatabaseField
+	private boolean nosocomialOutbreak;
+	@Enumerated(EnumType.STRING)
+	private InfectionSetting infectionSetting;
 
 	@DatabaseField(foreign = true, foreignAutoRefresh = true)
 	private SormasToSormasOriginInfo sormasToSormasOriginInfo;
@@ -1103,6 +1108,22 @@ public void setEndOfIsolationReasonDetails(String endOfIsolationReasonDetails) {
 		this.endOfIsolationReasonDetails = endOfIsolationReasonDetails;
 	}
 
+	public boolean isNosocomialOutbreak() {
+		return nosocomialOutbreak;
+	}
+
+	public void setNosocomialOutbreak(boolean nosocomialOutbreak) {
+		this.nosocomialOutbreak = nosocomialOutbreak;
+	}
+
+	public InfectionSetting getInfectionSetting() {
+		return infectionSetting;
+	}
+
+	public void setInfectionSetting(InfectionSetting infectionSetting) {
+		this.infectionSetting = infectionSetting;
+	}
+
 	public SormasToSormasOriginInfo getSormasToSormasOriginInfo() {
 		return sormasToSormasOriginInfo;
 	}

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/caze/CaseDtoHelper.java

@@ -196,6 +196,8 @@ public void fillInnerFromDto(Case target, CaseDataDto source) {
 		target.setQuarantineReasonBeforeIsolationDetails(source.getQuarantineReasonBeforeIsolationDetails());
 		target.setEndOfIsolationReason(source.getEndOfIsolationReason());
 		target.setEndOfIsolationReasonDetails(source.getEndOfIsolationReasonDetails());
+		target.setNosocomialOutbreak(source.isNosocomialOutbreak());
+		target.setInfectionSetting(source.getInfectionSetting());
 
 		target.setSormasToSormasOriginInfo(
 			sormasToSormasOriginInfoDtoHelper.fillOrCreateFromDto(target.getSormasToSormasOriginInfo(), source.getSormasToSormasOriginInfo()));
@@ -399,6 +401,8 @@ public void fillInnerFromAdo(CaseDataDto target, Case source) {
 		target.setQuarantineReasonBeforeIsolationDetails(source.getQuarantineReasonBeforeIsolationDetails());
 		target.setEndOfIsolationReason(source.getEndOfIsolationReason());
 		target.setEndOfIsolationReasonDetails(source.getEndOfIsolationReasonDetails());
+		target.setNosocomialOutbreak(source.isNosocomialOutbreak());
+		target.setInfectionSetting(source.getInfectionSetting());
 
 		if (source.getSormasToSormasOriginInfo() != null) {
 			target.setSormasToSormasOriginInfo(sormasToSormasOriginInfoDtoHelper.adoToDto(source.getSormasToSormasOriginInfo()));

sormas-app/app/src/main/java/de/symeda/sormas/app/backend/common/DatabaseHelper.java

@@ -152,7 +152,7 @@ public class DatabaseHelper extends OrmLiteSqliteOpenHelper {
 	public static final String DATABASE_NAME = "sormas.db";
 	// any time you make changes to your database objects, you may have to increase the database version
 
-	public static final int DATABASE_VERSION = 247;
+	public static final int DATABASE_VERSION = 249;
 
 	private static DatabaseHelper instance = null;
 
@@ -1779,6 +1779,12 @@ public void onUpgrade(SQLiteDatabase db, ConnectionSource connectionSource, int
 				getDao(Contact.class).executeRaw("ALTER TABLE contacts ADD column multidaycontact boolean default false;");
 				getDao(Contact.class).executeRaw("ALTER TABLE contacts ADD column firstcontactdate timestamp;");
 
+				case 248:
+				currentVersion = 248;
+
+				getDao(Case.class).executeRaw("ALTER TABLE cases ADD COLUMN nosocomialOutbreak boolean DEFAULT false");
+				getDao(Case.class).executeRaw("ALTER TABLE cases ADD COLUMN infectionSetting varchar(255)");
+
 				// ATTENTION: break should only be done after last version
 				break;
 			default: