Merge branch 'development' into 2644-populationDataInCampaignDiagrams

# Conflicts:
#	sormas-api/src/main/resources/strings.properties

Author: danRosca

SERVER_CUSTOMIZATION.md

@@ -19,7 +19,7 @@ The following properties are currently configurable:
 * **EPID prefix** `country.epidprefix`: SORMAS automatically generates EPID numbers for new cases. This is the prefix your country is using for all of these numbers. Most of the time it will be some sort of country code and should be three characters long.
 * **Country center/zoom** `country.center.latitude`, `country.center.longitude` and `map.zoom`: These are the geo coordinates of the geographical center of the country or region you're using SORMAS in. Used to set the initial location of the maps used in dashboards and statistics.
 * **App URL** `app.url`: The directory on your server where the mobile .apk file is stored that is used to automatically update the Android app after a new release. You should be able to copy the example given in the properties file and only have to replace the SERVER-NAME placeholder.
-* **File paths** `temp.path`, `generated.path` and `custom.path`: The folders that SORMAS stores files in, either temporarily during case export or permanently like import templates. Files in temp.path are automatically deleted at midnight. Files in custom.path can be used to customize the login page, e.g. to provide default logins for demo servers or add additional contributors to the right sidebar.
+* **File paths** `documents.path`, `temp.path`, `generated.path` and `custom.path`: The folders that SORMAS stores files in, either temporarily during case export or permanently like import templates or documents. Files in temp.path are automatically deleted at midnight. Files in custom.path can be used to customize the login page, e.g. to provide default logins for demo servers or add additional contributors to the right sidebar.
 * **Automatic case classification** `feature.automaticcaseclassification`: Determines whether SORMAS automatically classifies cases based on a number of criteria that are defined in the code.
 * **Email settings** `email.sender.address` and `email.sender.name`: The email address and sender name that should be used when SORMAS is sending out emails, e.g. to notify users about specific events.
 * **SMS settings** `sms.sender.name, sms.auth.key and sms.auth.secret`: Besides emails, SORMAS also supports sending automatic SMS to users at the same time (e.g. when a case has been classified as confirmed). The SMS provider SORMAS is using is the Vonage SMS API (https://www.vonage.com/communications-apis/sms/). If you have an account there, you can use your key and secret here to enable sending out SMS. Leaving these properties empty will disable this feature.
@@ -87,3 +87,4 @@ The following features are currently configurable:
 * **Area Infrastructure** `INFRASTRUCTURE_TYPE_AREA`: Enables an additional infrastructure level above region that is called area by default. Currently only used in the campaigns module.
 * **Case Follow-Up** `CASE_FOLLOWUP`: Enables the contact follow-up module for cases as well to allow a more detailed daily documentation of symptoms.
 * **Line Listing** `LINE_LISTING`: Whether or not using line listing for case entry is enabled in the specified jurisdiction for the specified disease. Configurable from the UI, no database interaction needed.
+* **Documents** `DOCUMENTS`: Enables document storage.

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

@@ -1,20 +1,17 @@
-/*******************************************************************************
+/*
  * SORMAS® - Surveillance Outbreak Response Management & Analysis System
- * Copyright © 2016-2018 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
- *
+ * 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;
 
 import javax.ejb.Remote;
@@ -50,6 +47,8 @@ public interface ConfigFacade {
 
 	String getSmsAuthSecret();
 
+	String getDocumentFilesPath();
+
 	String getTempFilesPath();
 
 	String getGeneratedFilesPath();
@@ -113,4 +112,7 @@ public interface ConfigFacade {
 	boolean isExternalJournalActive();
 
 	int getDashboardMapMarkerLimit();
+
+	boolean isSmsServiceSetUp();
+
 }

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

@@ -1,20 +1,17 @@
-/*******************************************************************************
+/*
  * SORMAS® - Surveillance Outbreak Response Management & Analysis System
- * Copyright © 2016-2018 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
- *
+ * 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;
 
 import javax.naming.InitialContext;
@@ -37,6 +34,7 @@
 import de.symeda.sormas.api.disease.DiseaseConfigurationFacade;
 import de.symeda.sormas.api.disease.DiseaseFacade;
 import de.symeda.sormas.api.docgeneneration.QuarantineOrderFacade;
+import de.symeda.sormas.api.document.DocumentFacade;
 import de.symeda.sormas.api.epidata.EpiDataFacade;
 import de.symeda.sormas.api.event.EventFacade;
 import de.symeda.sormas.api.event.EventParticipantFacade;
@@ -54,6 +52,7 @@
 import de.symeda.sormas.api.person.PersonFacade;
 import de.symeda.sormas.api.region.AreaFacade;
 import de.symeda.sormas.api.region.CommunityFacade;
+import de.symeda.sormas.api.region.CountryFacade;
 import de.symeda.sormas.api.region.DistrictFacade;
 import de.symeda.sormas.api.region.GeoShapeProvider;
 import de.symeda.sormas.api.region.RegionFacade;
@@ -158,6 +157,9 @@ public static FacilityFacade getFacilityFacade() {
 		return get().lookupEjbRemote(FacilityFacade.class);
 	}
 
+	public static CountryFacade getCountryFacade() {
+		return get().lookupEjbRemote(CountryFacade.class);
+	}
 	public static RegionFacade getRegionFacade() {
 		return get().lookupEjbRemote(RegionFacade.class);
 	}
@@ -310,11 +312,15 @@ public static QuarantineOrderFacade getQuarantineOrderFacade() {
 		return get().lookupEjbRemote(QuarantineOrderFacade.class);
 	}
 
-  public static ExternalJournalFacade getExternalJournalFacade() {
+	public static ExternalJournalFacade getExternalJournalFacade() {
 		return get().lookupEjbRemote(ExternalJournalFacade.class);
-  }
+	}
+
+	public static DocumentFacade getDocumentFacade() {
+		return get().lookupEjbRemote(DocumentFacade.class);
+	}
 
-  @SuppressWarnings("unchecked")
+	@SuppressWarnings("unchecked")
 	public <P> P lookupEjbRemote(Class<P> clazz) {
 		try {
 			return (P) get().ic.lookup(buildJndiLookupName(clazz));

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/CaseDataDto.java

@@ -505,7 +505,7 @@ public CaseReferenceDto toReference() {
 	 * Returns true if the case is an original point of entry case and has not yet
 	 * been assigned a health facility.
 	 */
-	public boolean isUnreferredPortHealthCase() {
+	public boolean checkIsUnreferredPortHealthCase() {
 		return caseOrigin == CaseOrigin.POINT_OF_ENTRY && healthFacility == null;
 	}
 

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";
@@ -181,14 +182,14 @@ public class CaseExportDto implements Serializable {
 	private String facility;
 	@SensitiveData
 	private String phone;
+	@SensitiveData
+	private String emailAddress;
 	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;
@@ -258,9 +259,8 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
 						 Date deathDate, Date burialDate, BurialConductor burialConductor, String burialPlaceDescription,
 						 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, EducationType educationType, String educationDetails,
-						 OccupationType occupationType, String occupationDetails, YesNoUnknown traveled,
-						 YesNoUnknown burialAttended, YesNoUnknown directContactConfirmedCase, YesNoUnknown directContactProbableCase, YesNoUnknown contactWithRodent,
+						 String phone, String phoneOwner, String emailAddress, EducationType educationType, String educationDetails,
+						 OccupationType occupationType, String occupationDetails, YesNoUnknown contactWithSourceCaseKnown,
 						 //Date onsetDate,
 						 Vaccination vaccination, String vaccinationDoses, Date vaccinationDate,
 						 VaccinationInfoSource vaccinationInfoSource, YesNoUnknown postpartum, Trimester trimester,
@@ -324,13 +324,10 @@ public CaseExportDto(long id, long personId, long personAddressId, long epiDataI
 		this.postalCode = postalCode;
 		this.facility = FacilityHelper.buildFacilityString(facilityUuid, facility, facilityDetails);
 		this.phone = PersonHelper.buildPhoneString(phone, phoneOwner);
+		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;
@@ -973,6 +970,16 @@ public String getPhone() {
 	}
 
 	@Order(75)
+	@ExportTarget(caseExportTypes = {
+			CaseExportType.CASE_SURVEILLANCE,
+			CaseExportType.CASE_MANAGEMENT })
+	@ExportProperty(PersonDto.EMAIL_ADDRESS)
+	@ExportGroup(ExportGroupType.SENSITIVE)
+	public String getEmailAddress() {
+		return emailAddress;
+	}
+
+	@Order(76)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -986,7 +993,7 @@ public void setEducationType(String educationType) {
 		this.educationType = educationType;
 	}
 
-	@Order(76)
+	@Order(77)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -996,20 +1003,20 @@ public String getOccupationType() {
 		return occupationType;
 	}
 
-	@Order(77)
+	@Order(78)
 	@ExportTarget(caseExportTypes = {
 		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;
 	}
 
-	@Order(78)
+	@Order(79)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(TRAVEL_HISTORY)
@@ -1018,52 +1025,30 @@ public String getTravelHistory() {
 		return travelHistory;
 	}
 
-	@Order(79)
+	@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(80)
-	@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)
+	@Order(81)
 	@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 void setDirectContactProbableCase(YesNoUnknown directContactProbableCase) {
-		this.directContactProbableCase = directContactProbableCase;
+	public YesNoUnknown getContactWithSourceCaseKnown() {
+		return contactWithSourceCaseKnown;
 	}
 
-	@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)
@@ -1497,6 +1482,10 @@ public void setPhone(String phone) {
 		this.phone = phone;
 	}
 
+	public void setEmailAddress(String emailAddress) {
+		this.emailAddress = emailAddress;
+	}
+
 	public void setOccupationType(String occupationType) {
 		this.occupationType = occupationType;
 	}
@@ -1505,10 +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;
 	}
@@ -1529,10 +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);