Merge branch 'development' into 2644-populationDataInCampaignDiagrams

Author: barnabartha

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/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

@@ -181,6 +181,8 @@ 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;
@@ -258,7 +260,7 @@ 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,
+						 String phone, String phoneOwner, String emailAddress, EducationType educationType, String educationDetails,
 						 OccupationType occupationType, String occupationDetails, YesNoUnknown traveled,
 						 YesNoUnknown burialAttended, YesNoUnknown directContactConfirmedCase, YesNoUnknown directContactProbableCase, YesNoUnknown contactWithRodent,
 						 //Date onsetDate,
@@ -324,6 +326,7 @@ 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;
@@ -973,6 +976,16 @@ 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 +999,7 @@ public void setEducationType(String educationType) {
 		this.educationType = educationType;
 	}
 
-	@Order(76)
+	@Order(77)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE,
 		CaseExportType.CASE_MANAGEMENT })
@@ -996,7 +1009,7 @@ public String getOccupationType() {
 		return occupationType;
 	}
 
-	@Order(77)
+	@Order(78)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(TRAVELED)
@@ -1009,7 +1022,7 @@ public void setTraveled(YesNoUnknown traveled) {
 		this.traveled = traveled;
 	}
 
-	@Order(78)
+	@Order(79)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(TRAVEL_HISTORY)
@@ -1018,7 +1031,7 @@ public String getTravelHistory() {
 		return travelHistory;
 	}
 
-	@Order(79)
+	@Order(80)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(EpiDataDto.BURIAL_ATTENDED)
@@ -1031,7 +1044,7 @@ public void setBurialAttended(YesNoUnknown burialAttended) {
 		this.burialAttended = burialAttended;
 	}
 
-	@Order(80)
+	@Order(81)
 	@ExportTarget(caseExportTypes = {
 		CaseExportType.CASE_SURVEILLANCE })
 	@ExportProperty(EpiDataDto.DIRECT_CONTACT_CONFIRMED_CASE)
@@ -1497,6 +1510,10 @@ public void setPhone(String phone) {
 		this.phone = phone;
 	}
 
+	public void setEmailAddress(String emailAddress) {
+		this.emailAddress = emailAddress;
+	}
+
 	public void setOccupationType(String occupationType) {
 		this.occupationType = occupationType;
 	}

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

@@ -25,6 +25,8 @@
 import de.symeda.sormas.api.EntityRelevanceStatus;
 import de.symeda.sormas.api.caze.CaseClassification;
 import de.symeda.sormas.api.caze.CaseReferenceDto;
+import de.symeda.sormas.api.event.EventParticipantReferenceDto;
+import de.symeda.sormas.api.event.EventReferenceDto;
 import de.symeda.sormas.api.person.PersonReferenceDto;
 import de.symeda.sormas.api.person.SymptomJournalStatus;
 import de.symeda.sormas.api.region.CommunityReferenceDto;
@@ -112,6 +114,8 @@ public class ContactCriteria extends BaseCriteria implements Serializable {
 	private String eventUuid;
 	private Boolean includeContactsFromOtherJurisdictions = Boolean.FALSE;
 	private Boolean onlyContactsSharingEventWithSourceCase;
+	private EventParticipantReferenceDto eventParticipant;
+	private EventReferenceDto onlyContactsWithSourceCaseInGivenEvent;
 
 	public UserRole getReportingUserRole() {
 		return reportingUserRole;
@@ -531,4 +535,32 @@ public Boolean getIncludeContactsFromOtherJurisdictions() {
 	public void setIncludeContactsFromOtherJurisdictions(Boolean includeContactsFromOtherJurisdictions) {
 		this.includeContactsFromOtherJurisdictions = includeContactsFromOtherJurisdictions;
 	}
+
+	public void setEventParticipant(EventParticipantReferenceDto eventParticipant) {
+		this.eventParticipant = eventParticipant;
+	}
+
+	@IgnoreForUrl
+	public EventParticipantReferenceDto getEventParticipant() {
+		return eventParticipant;
+	}
+
+	public ContactCriteria eventParticipant(EventParticipantReferenceDto eventParticipant) {
+		this.eventParticipant = eventParticipant;
+		return this;
+	}
+
+	public void setOnlyContactsWithSourceCaseInGivenEvent(EventReferenceDto onlyContactsWithSourceCaseInGivenEvent) {
+		this.onlyContactsWithSourceCaseInGivenEvent = onlyContactsWithSourceCaseInGivenEvent;
+	}
+
+	@IgnoreForUrl
+	public EventReferenceDto getOnlyContactsWithSourceCaseInGivenEvent() {
+		return onlyContactsWithSourceCaseInGivenEvent;
+	}
+
+	public ContactCriteria onlyContactsWithSourceCaseInGivenEvent(EventReferenceDto onlyContactsWithSourceCaseInGivenEvent) {
+		this.onlyContactsWithSourceCaseInGivenEvent = onlyContactsWithSourceCaseInGivenEvent;
+		return this;
+	}
 }

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

@@ -27,6 +27,7 @@
 import de.symeda.sormas.api.caze.CaseReferenceDto;
 import de.symeda.sormas.api.clinicalcourse.HealthConditionsDto;
 import de.symeda.sormas.api.epidata.EpiDataDto;
+import de.symeda.sormas.api.event.EventParticipantDto;
 import de.symeda.sormas.api.person.PersonReferenceDto;
 import de.symeda.sormas.api.region.CommunityReferenceDto;
 import de.symeda.sormas.api.region.DistrictReferenceDto;
@@ -247,27 +248,32 @@ public class ContactDto extends PseudonymizableDto {
 	private String endOfQuarantineReasonDetails;
 
 	public static ContactDto build() {
-		return build(null, null, null);
+		final ContactDto contact = new ContactDto();
+		contact.setUuid(DataHelper.createUuid());
+		contact.setPerson(new PersonReferenceDto(DataHelper.createUuid()));
+		contact.setReportDateTime(new Date());
+		contact.setContactClassification(ContactClassification.UNCONFIRMED);
+		contact.setContactStatus(ContactStatus.ACTIVE);
+		contact.setEpiData(EpiDataDto.build());
+		contact.setHealthConditions(HealthConditionsDto.build());
+
+		return contact;
+	}
+
+	public static ContactDto build(EventParticipantDto eventParticipant) {
+		final ContactDto contact = build();
+		contact.setPerson(eventParticipant.getPerson().toReference());
+
+		return contact;
 	}
 
 	public static ContactDto build(CaseDataDto caze) {
 		return build(caze.toReference(), caze.getDisease(), caze.getDiseaseDetails());
 	}
 
 	public static ContactDto build(CaseReferenceDto caze, Disease disease, String diseaseDetails) {
-		ContactDto contact = new ContactDto();
-		contact.setUuid(DataHelper.createUuid());
-
+		final ContactDto contact = build();
 		contact.assignCase(caze, disease, diseaseDetails);
-		contact.setPerson(new PersonReferenceDto(DataHelper.createUuid()));
-
-		contact.setReportDateTime(new Date());
-		contact.setContactClassification(ContactClassification.UNCONFIRMED);
-		contact.setContactStatus(ContactStatus.ACTIVE);
-
-		contact.setEpiData(EpiDataDto.build());
-
-		contact.setHealthConditions(HealthConditionsDto.build());
 
 		return contact;
 	}

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

@@ -101,6 +101,8 @@ public class ContactExportDto implements Serializable {
 	private String facility;
 	@SensitiveData
 	private String phone;
+	@SensitiveData
+	private String emailAddress;
 	private String occupationType;
 	private int numberOfVisits;
 	private YesNoUnknown lastCooperativeVisitSymptomatic;
@@ -154,7 +156,7 @@ 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, OccupationType occupationType, String occupationDetails,
+							String phone, String phoneOwner, String emailAddress, OccupationType occupationType, String occupationDetails,
 							String region, String district, String community,
 							long epiDataId, YesNoUnknown traveled, YesNoUnknown burialAttended, YesNoUnknown directContactConfirmedCase, YesNoUnknown directContactProbableCase,
 							YesNoUnknown contactWithRodent, YesNoUnknown returningTraveler, long eventCount, String externalID,
@@ -211,6 +213,7 @@ public ContactExportDto(long id, long personId, String uuid, String sourceCaseUu
 		this.postalCode = postalCode;
 		this.facility = FacilityHelper.buildFacilityString(facilityUuid, facility, facilityDetails);
 		this.phone = PersonHelper.buildPhoneString(phone, phoneOwner);
+		this.emailAddress = emailAddress;
 		this.occupationType = PersonHelper.buildOccupationString(occupationType, occupationDetails);
 		this.region = region;
 		this.district = district;
@@ -520,6 +523,11 @@ public String getPhone() {
 		return phone;
 	}
 
+	@Order(53)
+	public String getEmailAddress() {
+		return emailAddress;
+	}
+
 	@Order(60)
 	public String getOccupationType() {
 		return occupationType;
@@ -731,6 +739,10 @@ public void setPhone(String phone) {
 		this.phone = phone;
 	}
 
+	public void setEmailAddress(String emailAddress) {
+		this.emailAddress = emailAddress;
+	}
+
 	public void setOccupationType(String occupationType) {
 		this.occupationType = occupationType;
 	}