Merge branch 'development' into feature-3424-ContactFollowUpCancel

# Conflicts:
#	sormas-backend/src/test/java/de/symeda/sormas/backend/contact/ContactFacadeEjbTest.java

Author: barnabartha

CONTRIBUTING.md

@@ -110,6 +110,18 @@ The GitHub project has been configured to **automatically** move issues that are
 The Development Team is responsible to keep the tickets up to date on this board and to assign the appropriate milestone in which the work is going to be released.
 
 
+### Managing dependencies
+
+For managing Java libraries as dependencies, they are managed by Maven and listed in *sormas-base/pom.xml*.  The purpose of a centralized management is to have an overview of the used libraries and adjust for new versions.
+
+1. **Payara modules**: Provided by Payara in *{payara-home}/glassfish/modules* and used in that version by other libs.
+2. **Domain libs**: Provided in Payara domain under *{payara-domain}/lib* to be usable by deployed artifacts (ear, war). They have to be listed in *sormas-base/dependencies/serverlibs.pom*. Usually for helper libraries that several artifacts need.
+3. **Compile dependencies**: Bundled in respective artifacts who need the dependency explicitly. Usually for dependencies singularly needed in one artifact.
+4. **Test libraries**: Libraries used in automated tests in one or more modules.
+
+Due to the separate build management tool Gradle for *sormas-app*, there exists a redundant listing of compile dependencies in *sormas-app/app/build.gradle*.
+
+
 ### Eclipse Troubleshooting
 
 Unfortunatley, when using eclipse together with the Payara Tools, there are a number of deployment problems that you might run into. Examples of these include:

DEVELOPMENT_ENVIRONMENT.md

@@ -51,7 +51,7 @@
 - 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)
-- Install the Vaadin Designer plugin
+- Install the Vaadin plugin (not the Vaadin Designer plugin!)
 - Make a copy of "build.properties.example" contained in "sormas-base", rename it to "build.properties" and set "glassfish.domain.root" to the location of the sormas domain located in the "glassfish/domains" folder inside your payara installation
 - Run "Maven install" on the sormas-base project
 - Add a Payara server to IntelliJ:

README.md

@@ -27,6 +27,8 @@ SORMAS officially supports and is tested on **Chromium-based browsers** (like Go
 
 #### Is there a ReST API documentation?
 Yes! Please download the [latest release](https://github.com/hzi-braunschweig/SORMAS-Project/releases/latest) and copy the content of /deploy/openapi/sormas-rest.yaml to an editor that generates a visual API documentation (e.g. https://editor.swagger.io/).
+<br/>
+Runtime Swagger documentation of the External Visits Resource (used by external symptom journals such as CLIMEDO or PIA) is also available at ``<<host>>/sormas-rest/visits-external/openapi.json`` or ``<<host>>/sormas-rest/visits-external/openapi.yaml``
 
 <p align="center"><img src="https://user-images.githubusercontent.com/23701005/74659600-ebb8fc00-5194-11ea-836b-a7ca9d682301.png"/></p>
 

SERVER_CUSTOMIZATION.md

@@ -88,3 +88,14 @@ The following features are currently configurable:
 * **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.
+
+## Proxy Settings
+Some SORMAS integrations support proxy settings:
+* **Patient diary interface**
+* **Geocoding**
+* **SORMAS 2 SORMAS**
+
+The proxy can be configured through the following system properties which can be passed as JVM arguments to the server:
+* `org.jboss.resteasy.jaxrs.client.proxy.host`
+* `org.jboss.resteasy.jaxrs.client.proxy.port`
+* `org.jboss.resteasy.jaxrs.client.proxy.scheme`

sormas-api/pom.xml

@@ -67,6 +67,11 @@
 			<artifactId>simmetrics-core</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.jsoup</groupId>
+			<artifactId>jsoup</artifactId>
+		</dependency>
+
 	</dependencies>
 
 </project>

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

@@ -127,6 +127,8 @@ public class CaseDataDto extends PseudonymizableDto {
 	public static final String ADDITIONAL_DETAILS = "additionalDetails";
 	public static final String EXTERNAL_ID = "externalID";
 	public static final String SHARED_TO_COUNTRY = "sharedToCountry";
+	public static final String NOSOCOMIAL_OUTBREAK = "nosocomialOutbreak";
+	public static final String INFECTION_SETTING = "infectionSetting";
 	public static final String QUARANTINE = "quarantine";
 	public static final String QUARANTINE_TYPE_DETAILS = "quarantineTypeDetails";
 	public static final String QUARANTINE_FROM = "quarantineFrom";
@@ -165,6 +167,10 @@ 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 PROHIBITION_TO_WORK = "prohibitionToWork";
+	public static final String PROHIBITION_TO_WORK_FROM = "prohibitionToWorkFrom";
+	public static final String PROHIBITION_TO_WORK_UNTIL = "prohibitionToWorkUntil";
+
 	// Fields are declared in the order they should appear in the import template
 
 	@Outbreaks
@@ -367,6 +373,10 @@ public class CaseDataDto extends PseudonymizableDto {
 		COUNTRY_CODE_SWITZERLAND })
 	private String externalID;
 	private boolean sharedToCountry;
+	@HideForCountriesExcept
+	private boolean nosocomialOutbreak;
+	@HideForCountriesExcept
+	private InfectionSetting infectionSetting;
 	private QuarantineType quarantine;
 	@SensitiveData
 	private String quarantineTypeDetails;
@@ -444,6 +454,13 @@ public class CaseDataDto extends PseudonymizableDto {
 	@SensitiveData
 	private String endOfIsolationReasonDetails;
 
+	@HideForCountriesExcept
+	private YesNoUnknown prohibitionToWork;
+	@HideForCountriesExcept
+	private Date prohibitionToWorkFrom;
+	@HideForCountriesExcept
+	private Date prohibitionToWorkUntil;
+
 	public static CaseDataDto build(PersonReferenceDto person, Disease disease) {
 		return build(person, disease, null);
 	}
@@ -1008,6 +1025,22 @@ public void setSharedToCountry(boolean sharedToCountry) {
 		this.sharedToCountry = sharedToCountry;
 	}
 
+	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 QuarantineType getQuarantine() {
 		return quarantine;
 	}
@@ -1296,6 +1329,30 @@ public void setSormasToSormasOriginInfo(SormasToSormasOriginInfoDto sormasToSorm
 		this.sormasToSormasOriginInfo = sormasToSormasOriginInfo;
 	}
 
+	public YesNoUnknown getProhibitionToWork() {
+		return prohibitionToWork;
+	}
+
+	public void setProhibitionToWork(YesNoUnknown prohibitionToWork) {
+		this.prohibitionToWork = prohibitionToWork;
+	}
+
+	public Date getProhibitionToWorkFrom() {
+		return prohibitionToWorkFrom;
+	}
+
+	public void setProhibitionToWorkFrom(Date prohibitionToWorkFrom) {
+		this.prohibitionToWorkFrom = prohibitionToWorkFrom;
+	}
+
+	public Date getProhibitionToWorkUntil() {
+		return prohibitionToWorkUntil;
+	}
+
+	public void setProhibitionToWorkUntil(Date prohibitionToWorkUntil) {
+		this.prohibitionToWorkUntil = prohibitionToWorkUntil;
+	}
+
 	public boolean isOwnershipHandedOver() {
 		return ownershipHandedOver;
 	}