Merge branch 'development' into feature-2642-PlaceOfResidenceFilterStatistics

# Conflicts:
#	sormas-api/src/main/java/de/symeda/sormas/api/statistics/StatisticsCaseAttribute.java
#	sormas-api/src/main/java/de/symeda/sormas/api/statistics/StatisticsCaseCriteria.java
#	sormas-api/src/main/java/de/symeda/sormas/api/statistics/StatisticsCaseSubAttribute.java
#	sormas-backend/src/main/java/de/symeda/sormas/backend/caze/CaseStatisticsFacadeEjb.java
#	sormas-ui/src/main/java/de/symeda/sormas/ui/statistics/StatisticsFilterResidenceElement.java
#	sormas-ui/src/main/java/de/symeda/sormas/ui/statistics/StatisticsFilterValuesElement.java
#	sormas-ui/src/main/java/de/symeda/sormas/ui/statistics/StatisticsView.java

Author: barnabartha

GUIDE_CREATE_CERTIFICATE.md

@@ -0,0 +1,41 @@
+# How to create a new certificate?
+
+This guide explains how to create a new self-signed certificate, used for SORMAS to SORMAS communication.
+   
+### Using the certificate generation script
+
+1. Run ``bash ./generate-cert.sh``
+2. For the generation of the certificate, the following data is needed: a password, a *Common Name* (CN) 
+    and an *Organization* (O). These may be set in environment variables (recommended), or provided 
+    manually as the script executes.
+    * The password environment variable should be named ``SORMAS_S2S_CERT_PASS``.
+    * the *Common Name* environment variable should be named ``SORMAS_S2S_CERT_CN``.<br/>
+    **Important**: for Germany, this value should be the SurvNet Code Site. <br/>
+    E.g. *2.03.1.01.*
+    * the *Organization* (O) environment variable should be named ``SORMAS_S2S_CERT_ORG``.<br/>
+    **Important**: for Germany, this value should be the name of the Health Department (Gesundheitsamt) 
+    to which the SORMAS instance will be assigned. <br/>
+    E.g. *GA Braunschweig*
+3. After providing the requested data, the certificate files will be generated. <br/>
+   The generated certificate has a validity of 3 years. 
+   The certificate files will be available in the root SORMAS directory, in the folder ``/sormas2sormas``.
+4. The generated ``.p12`` file should not be shared with third parties. <br/>
+   The generated ``.crt`` file will be verified and shared with other SORMAS instances, from which this instance
+   will be able to request data. Conversely, in order to enable other SORMAS instances to request data from this 
+   instance, their certificate files should be obtained and added to the local truststore. More details can be found
+   in the next section.
+5. If the ``SORMAS_PROPERTIES`` environment variable is available, the relevant properties will be 
+    automatically set by the script.
+    * Else, the properties which need to be added will be displayed in the console after the script finishes executing.
+    * Please note these properties and add them to the ``sormas.properties`` file. This should be located in the 
+    ``/domains/sormas`` folder.
+    * Example output:
+    ```
+    sormas.properties file was not found. 
+    Please add the following properties to the sormas.properties file:
+    sormas2sormas.keyAlias=mycertificate
+    sormas2sormas.keyPassword=changeit
+    ```
+
+### Adding a new certificate to the Truststore
+

SERVER_CUSTOMIZATION.md

@@ -27,7 +27,7 @@ The following properties are currently configurable:
 * **Name similarity threshold** *(namesimilaritythreshold)*: This is used when comparing cases or contacts to find duplicates in the system, either in retrospection or during creation or import. The higher the value, the more restrictive the algorithm, i.e. less potential duplicates will be found. It is suggested to play around with this setting to see which value works for your country and language.
 * **Dev mode** *(devmode)*: Enabling developer mode will give you access to a tab in the Configuration menu that allows admins to create dummy cases and contacts to quickly fill the database. This is only meant to be used on development or demo systems and should be left disabled for production servers.
 * **Infrastructure sync threshold** *(infrastructuresyncthreshold)*: Synchronizing infrastructure data to mobile apps (e.g. regions or health facilities) is done in chunks to avoid connection timeouts. If you expect your users to have very bad internet connection, lowering this threshold could make it easier for them to synchronize this data.
-* **Archiving thresholds** *(daysAfterCaseGetsArchived and daysAfterEventGetsArchived)*: The number of days without any changes after which cases/events are automatically archived (i.e. they will no longer be displayed in the normal directories, but still count towards statistics or counts on the dashboard and can still be viewed by users with the respective user right).
+* **Archiving thresholds** *(daysAfterCaseGetsArchived and daysAfterEventGetsArchived)*: The number of days without any changes after which cases/events are automatically archived (i.e. they will no longer be displayed in the normal directories, but still count towards statistics or counts on the dashboard and can still be viewed by users with the respective user right). If set to 0, automatic archiving is disabled.
 * **Rscript executable** *(rscript.executable)*: The location of the Rscript executable. If you've installed Rscript on your server and specify the path here (the default should work for Linux systems as long as you've used the default install path), network diagrams for transmission chains will be shown in the web app.
 * **Symptom journal interface**: Properties used to connect to an external symptom journal service. *interface.symptomjournal.url* is the URL to the website that SORMAS should connect to; *interface.symptomjournal.authurl* is the URL used to authenticate SORMAS at the external service; *interface.symptomjournal.clientid* and *interface.symptomjournal.secret* are the credentials used for the authentication process.
 * **Custom branding**: Properties used to apply a custom branding to SORMAS that overrides its name and default logo. Using these properties also alters the sidebar and adds another customizable area to it. If you want to use this feature, set *custombranding* to true. *custombranding.name* is the name that you want to use, *custombranding.logo.path* is the path to the logo that should be used.

SERVER_SETUP.md

@@ -236,6 +236,12 @@ This can be conveniently accomplished by executing the R setup script from the S
 
 * Follow the instructions of the script.
 
+## SORMAS to SORMAS Certificate Setup
+
+To be able to communicate with other SORMAS instances, there are some additional steps which need to be taken, in order to set
+up the certificate and the truststore. Please see the [related guide](GUIDE_CREATE_CERTIFICATE.md) for detailed instructions regarding
+SORMAS to SORMAS setup.
+<br/>
 
 ## Troubleshooting
 

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

@@ -17,12 +17,16 @@
  *******************************************************************************/
 package de.symeda.sormas.api;
 
+import javax.naming.InitialContext;
+import javax.naming.NamingException;
+
 import de.symeda.sormas.api.action.ActionFacade;
 import de.symeda.sormas.api.campaign.CampaignFacade;
 import de.symeda.sormas.api.campaign.data.CampaignFormDataFacade;
 import de.symeda.sormas.api.campaign.form.CampaignFormMetaFacade;
 import de.symeda.sormas.api.caze.CaseFacade;
 import de.symeda.sormas.api.caze.CaseStatisticsFacade;
+import de.symeda.sormas.api.caze.caseimport.CaseImportFacade;
 import de.symeda.sormas.api.caze.classification.CaseClassificationFacade;
 import de.symeda.sormas.api.caze.maternalhistory.MaternalHistoryFacade;
 import de.symeda.sormas.api.clinicalcourse.ClinicalCourseFacade;
@@ -64,9 +68,6 @@
 import de.symeda.sormas.api.visit.VisitFacade;
 import de.symeda.sormas.api.visualization.VisualizationFacade;
 
-import javax.naming.InitialContext;
-import javax.naming.NamingException;
-
 public class FacadeProvider {
 
 	private static final String JNDI_PREFIX = "java:global/sormas-ear/sormas-backend/";
@@ -99,6 +100,10 @@ public static CaseStatisticsFacade getCaseStatisticsFacade() {
 		return get().lookupEjbRemote(CaseStatisticsFacade.class);
 	}
 
+	public static CaseImportFacade getCaseImportFacade() {
+		return get().lookupEjbRemote(CaseImportFacade.class);
+	}
+
 	public static ContactFacade getContactFacade() {
 		return get().lookupEjbRemote(ContactFacade.class);
 	}

sormas-api/src/main/java/de/symeda/sormas/api/caze/caseimport/CaseImportEntities.java

@@ -0,0 +1,75 @@
+/*
+ * 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.caseimport;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import de.symeda.sormas.api.caze.CaseDataDto;
+import de.symeda.sormas.api.person.PersonDto;
+import de.symeda.sormas.api.sample.PathogenTestDto;
+import de.symeda.sormas.api.sample.SampleDto;
+import de.symeda.sormas.api.user.UserReferenceDto;
+
+public class CaseImportEntities implements Serializable {
+
+	private static final long serialVersionUID = -4565794925738392508L;
+
+	private final PersonDto person;
+	private final CaseDataDto caze;
+	private final List<SampleDto> samples;
+	private final List<PathogenTestDto> pathogenTests;
+
+	public CaseImportEntities(UserReferenceDto reportingUser) {
+		person = PersonDto.build();
+		caze = createCase(person, reportingUser);
+
+		samples = new ArrayList<>();
+		pathogenTests = new ArrayList<>();
+	}
+
+	public static CaseDataDto createCase(PersonDto person, UserReferenceDto reportingUser) {
+		CaseDataDto caze = CaseDataDto.build(person.toReference(), null);
+		caze.setReportingUser(reportingUser);
+
+		return caze;
+	}
+
+	public CaseImportEntities(PersonDto person, CaseDataDto caze) {
+		this.person = person;
+		this.caze = caze;
+
+		samples = new ArrayList<>();
+		pathogenTests = new ArrayList<>();
+	}
+
+	public PersonDto getPerson() {
+		return person;
+	}
+
+	public CaseDataDto getCaze() {
+		return caze;
+	}
+
+	public List<SampleDto> getSamples() {
+		return samples;
+	}
+
+	public List<PathogenTestDto> getPathogenTests() {
+		return pathogenTests;
+	}
+}

sormas-api/src/main/java/de/symeda/sormas/api/caze/caseimport/CaseImportFacade.java

@@ -0,0 +1,42 @@
+/*
+ * 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.caseimport;
+
+import javax.ejb.Remote;
+
+import de.symeda.sormas.api.importexport.InvalidColumnException;
+
+@Remote
+public interface CaseImportFacade {
+
+	ImportLineResultDto<CaseImportEntities> importCaseData(
+		String[] values,
+		String[] entityClasses,
+		String[] entityProperties,
+		String[][] entityPropertyPaths,
+		boolean ignoreEmptyEntries)
+		throws InvalidColumnException;
+
+	ImportLineResultDto<CaseImportEntities> updateCaseWithImportData(
+		String personUuid,
+		String caseUuid,
+		String[] values,
+		String[] entityClasses,
+		String[][] entityPropertyPaths)
+		throws InvalidColumnException;
+
+	ImportLineResultDto<CaseImportEntities> saveImportedEntities(CaseImportEntities entities);
+}

sormas-api/src/main/java/de/symeda/sormas/api/caze/caseimport/ImportLineResult.java

@@ -0,0 +1,22 @@
+/*
+ * 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.caseimport;
+
+public enum ImportLineResult {
+
+	SUCCESS,
+	ERROR,
+	DUPLICATE;
+}

sormas-api/src/main/java/de/symeda/sormas/api/caze/caseimport/ImportLineResultDto.java

@@ -0,0 +1,69 @@
+/*
+ * 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.caseimport;
+
+import java.io.Serializable;
+
+public class ImportLineResultDto<E> implements Serializable {
+
+	private static final long serialVersionUID = -9004769653154669800L;
+
+	private final ImportLineResult result;
+	private final String message;
+	private final E importEntities;
+
+	private ImportLineResultDto(ImportLineResult result, String message, E importEntities) {
+		this.result = result;
+		this.message = message;
+		this.importEntities = importEntities;
+	}
+
+	public ImportLineResult getResult() {
+		return result;
+	}
+
+	public String getMessage() {
+		return message;
+	}
+
+	public E getImportEntities() {
+		return importEntities;
+	}
+
+	public boolean isError() {
+		return result == ImportLineResult.ERROR;
+	}
+
+	public boolean isDuplicate() {
+		return result == ImportLineResult.DUPLICATE;
+	}
+
+	public boolean isSuccess() {
+		return result == ImportLineResult.SUCCESS;
+	}
+
+	public static <E> ImportLineResultDto<E> successResult() {
+		return new ImportLineResultDto<>(ImportLineResult.SUCCESS, null, null);
+	}
+
+	public static <E> ImportLineResultDto<E> errorResult(String message) {
+		return new ImportLineResultDto<>(ImportLineResult.ERROR, message, null);
+	}
+
+	public static <E> ImportLineResultDto<E> duplicateResult(E entities) {
+		return new ImportLineResultDto<>(ImportLineResult.DUPLICATE, null, entities);
+	}
+}

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

@@ -42,6 +42,8 @@ public interface ContactFacade {
 
 	ContactDto saveContact(ContactDto dto);
 
+	ContactDto saveContact(ContactDto dto, boolean handleChanges);
+
 	ContactReferenceDto getReferenceByUuid(String uuid);
 
 	List<String> getAllActiveUuids();

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

@@ -460,6 +460,7 @@ public interface Strings {
 	String messageAdditionalTestSaved = "messageAdditionalTestSaved";
 	String messageAggregateReportFound = "messageAggregateReportFound";
 	String messageAllCampaignFormsValid = "messageAllCampaignFormsValid";
+	String messageAlreadyEventParticipant = "messageAlreadyEventParticipant";
 	String messageAnimalContactsHint = "messageAnimalContactsHint";
 	String messageAreaArchived = "messageAreaArchived";
 	String messageAreaArchivingNotPossible = "messageAreaArchivingNotPossible";