[GITFLOW]merging 'release-1.47.0' into 'master'

Author: jenkins

.travis.yml

@@ -2,4 +2,4 @@ language: java
 jdk:
   - openjdk8
 before_install: cd sormas-base
-install: mvn test -B
+install: mvn test -B -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn

DEVELOPMENT_ENVIRONMENT.md

@@ -9,6 +9,16 @@
 - Recommended: Install a Git client such as [TortoiseGit](https://tortoisegit.org/) if you don't want to handle version control from the command line or separately for the Eclipse and Android Studio projects
 - Open the Git Bash and execute the command <code>git config --global branch.development.rebase true</code> (which ensures that rebase is used when pulling rather than merge)
 
+## Java
+- Download and install the Java 8 **JDK** (not JRE) for your operating system. We suggest to use Zulu OpenJDK: https://www.azul.com/downloads/zulu/
+  * **Linux**: https://docs.azul.com/zulu/zuludocs/#ZuluUserGuide/PrepareZuluPlatform/AttachAPTRepositoryUbuntuOrDebianSys.htm
+        
+		sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xB1998361219BD9C9
+		sudo apt-add-repository 'deb http://repos.azulsystems.com/ubuntu stable main'
+		sudo apt-get update
+		sudo apt-get install zulu-8
+  - **Windows**: For testing and development environments we suggest to download and run the installer of the Java 8 **JDK** for 32 or 64 bit client systems (depending on your system).
+
 ## Eclipse
 - Install the latest Eclipse version
 - Set the default JRE of Eclipse to the installed Zulu Java SDK: [Assigning the default JRE for the workbench ](https://help.eclipse.org/kepler/index.jsp?topic=%2Forg.eclipse.jdt.doc.user%2Ftasks%2Ftask-assign_default_jre.htm)
@@ -35,7 +45,7 @@
 
 ## IntelliJ
 - Install the latest Ultimate edition IntelliJ
-- Set the project SDK to use the installed Zulu Java SDK
+- Set the project SDK to use the installed Zulu Java 8 SDK
 - Clone the SORMAS-Project repository and open the project in IntelliJ
 	- make sure the under "File -> Project Structure -> Modules" all the modules (except the android app - this should not be added) are recognized, if not add the modules with +
 - Make sure under "File -> Settings -> Plugins" Glassfish & Ant integrations are enabled (look into the "Installed" tab)
@@ -60,9 +70,9 @@
 	- install Eclipse Code Formatter for IntelliJ (https://plugins.jetbrains.com/plugin/6546-eclipse-code-formatter)
 	- open the plugin settings (Other Settings -> Eclipse Code Formatter) and select "Use the Eclipse Code Formatter"
 	- under "Eclipse Formatter config file", select ``sormas-base/java-formatter-profile.xml``
-	- check optimize imports and, for "Iport order", select ``sormas-base/java-importorder-profile.importorder``
+	- check optimize imports and, for "Import order", select ``sormas-base/java-importorder-profile.importorder``
 	- **Important:** select "Do not format other file types by IntelliJ formatter"
-	- go to Preferences -> Editor -> Code style -> Java : set class and static names counts for import with * to 99
+	- go to Preferences -> Editor -> Code style -> Java -> Imports: set class and static names counts for import with * to 99
 	- for IntelliJ, code formatting is usually done with Ctrl+Alt+L. For automatic formatting, it's recommended to use the plugin Save Actions (https://plugins.jetbrains.com/plugin/7642-save-actions)
 
 ## Android Studio

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/pom.xml

@@ -2,7 +2,7 @@
 	<parent>
 		<groupId>de.symeda.sormas</groupId>
 		<artifactId>sormas-base</artifactId>
-		<version>1.46.0</version>
+		<version>1.47.0</version>
 		<relativePath>../sormas-base</relativePath>
 	</parent>
 	<modelVersion>4.0.0</modelVersion>
@@ -11,7 +11,7 @@
 
 	<build>
 		<finalName>${project.artifactId}</finalName>
-		<resources>
+        <resources>
 			<resource>
 				<directory>src/main/resources</directory>
 				<filtering>true</filtering>

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

@@ -17,10 +17,10 @@
  *******************************************************************************/
 package de.symeda.sormas.api;
 
-import de.symeda.sormas.api.region.GeoLatLon;
-
 import javax.ejb.Remote;
 
+import de.symeda.sormas.api.region.GeoLatLon;
+
 @Remote
 public interface ConfigFacade {
 
@@ -30,6 +30,8 @@ public interface ConfigFacade {
 
 	boolean isGermanServer();
 
+	boolean isSwissServer();
+
 	String getEpidPrefix();
 
 	String getAppUrl();

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

@@ -17,12 +17,17 @@
  *******************************************************************************/
 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.diagram.CampaignDiagramDefinitionFacade;
 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 +69,6 @@
 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 +101,10 @@ 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);
 	}
@@ -267,6 +273,10 @@ public static CampaignFacade getCampaignFacade() {
 		return get().lookupEjbRemote(CampaignFacade.class);
 	}
 
+	public static CampaignDiagramDefinitionFacade getCampaignDiagramDefinitionFacade() {
+		return get().lookupEjbRemote(CampaignDiagramDefinitionFacade.class);
+	}
+
 	public static CampaignFormMetaFacade getCampaignFormMetaFacade() {
 		return get().lookupEjbRemote(CampaignFormMetaFacade.class);
 	}

sormas-api/src/main/java/de/symeda/sormas/api/campaign/data/CampaignFormDataEntry.java

@@ -15,16 +15,18 @@
 
 package de.symeda.sormas.api.campaign.data;
 
+import java.io.Serializable;
+
 import de.symeda.sormas.api.i18n.I18nProperties;
 import de.symeda.sormas.api.i18n.Strings;
 
-import java.io.Serializable;
-import java.util.Objects;
-
 public class CampaignFormDataEntry implements Serializable {
 
 	private static final long serialVersionUID = -3096020120349257398L;
 
+	public static final String ID = "id";
+	public static final String VALUE = "value";
+
 	private String id;
 	private Object value;
 
@@ -53,20 +55,21 @@ public void setValue(Object value) {
 		this.value = value;
 	}
 
-	@Override
-	public boolean equals(Object o) {
-		if (this == o)
-			return true;
-		if (o == null || getClass() != o.getClass())
-			return false;
-		CampaignFormDataEntry that = (CampaignFormDataEntry) o;
-		return Objects.equals(id, that.id);
-	}
-
-	@Override
-	public int hashCode() {
-		return Objects.hash(id);
-	}
+	// does not make sense. Leads to hibernate not persisting any changes in value
+//	@Override
+//	public boolean equals(Object o) {
+//		if (this == o)
+//			return true;
+//		if (o == null || getClass() != o.getClass())
+//			return false;
+//		CampaignFormDataEntry that = (CampaignFormDataEntry) o;
+//		return Objects.equals(id, that.id);
+//	}
+//
+//	@Override
+//	public int hashCode() {
+//		return Objects.hash(id);
+//	}
 
 	@Override
 	public String toString() {
@@ -80,5 +83,4 @@ public String toString() {
 
 		return value.toString();
 	}
-
 }

sormas-api/src/main/java/de/symeda/sormas/api/campaign/data/CampaignFormDataFacade.java

@@ -20,10 +20,14 @@
 
 package de.symeda.sormas.api.campaign.data;
 
-import de.symeda.sormas.api.utils.SortProperty;
+import java.util.List;
 
 import javax.ejb.Remote;
-import java.util.List;
+
+import de.symeda.sormas.api.campaign.diagram.CampaignDiagramCriteria;
+import de.symeda.sormas.api.campaign.diagram.CampaignDiagramDataDto;
+import de.symeda.sormas.api.campaign.diagram.CampaignDiagramSeries;
+import de.symeda.sormas.api.utils.SortProperty;
 
 @Remote
 public interface CampaignFormDataFacade {
@@ -45,4 +49,6 @@ public interface CampaignFormDataFacade {
 	List<CampaignFormDataIndexDto> getIndexList(CampaignFormDataCriteria criteria, Integer first, Integer max, List<SortProperty> sortProperties);
 
 	long count(CampaignFormDataCriteria criteria);
+
+	List<CampaignDiagramDataDto> getDiagramData(List<CampaignDiagramSeries> diagramSeriesList, CampaignDiagramCriteria campaignDiagramCriteria);
 }