Merge branch 'releases/version-0.0.1'

# Conflicts:
#	README.md

.gitignore

@@ -0,0 +1,15 @@
+*.project
+*.classpath
+*.settings
+*target
+*.metadata
+*.recommenders
+*.idea
+/sormas-backend/bin
+/sormas-rest/bin
+/sormas-surveillance-ui/bin
+/sormas-widgetset/bin
+/deploy/bundles
+deploy
+/sormas-base/build.properties
+/sormas-ui/bin

README.md

@@ -1,55 +1,96 @@
-sormas
-===============
-Project Structure
-
-The project consists of the following modules:
-
-    sormas-api: general business logic and definitions for data exchange between app and server
-    sormas-app: the android app
-    sormas-backend: server entity services, facades, etc.
-    sormas-base: base project that also contains build scripts
-    sormas-ear: the ear needed to build the application
-    sormas-rest: the rest interface
-    sormas-ui: the web application
-
-Getting Started
-SORMAS Server & Domain
-
-    Download payara 4.1.1.161 (http://bit.ly/2aY0aEX - possible issues with more recent versions) and extract it to a folder on your hard drive (e.g. /srv/payara-sormas)
-    Create a PostgreSQL database named "sormas_db" (password: "sormas_db") with user "sormas_user" (password: "sormas_db") as its owner, and run the SQL scripts contained in "/sormas-base/sql/sormas_schema.sql"
-    Get the latest SORMAS build from github: https://github.com/hzi-braunschweig/SORMAS-Open/releases/ (deploy.zip and app-debug.apk)
-    Open "deploy/glassfish-config.bat" (or glassfish-config.sh on linux) in a text editor and change GLASSFISH_HOME to the location of the Glassfish folder inside your payara installation
-    Set up a payara domain called "sormas" by executing glassfish-config.bat from the command line
-
-Updating the SORMAS domain
-
-(ignore this when you are setting up a whole development enviroment, as described below)
-
-    Get the latest SORMAS build from github: https://github.com/hzi-braunschweig/SORMAS-Open/releases/ (deploy.zip and app-debug.apk)
-    locate the server domain directory (domain-dir). Mostly /srv/payara-sormas/glassfish/domains/sormas
-    make sure the server is not running
-    delete the content from the following subfolders: domain-dir/autodeploy/bundles/... domain-dir/osgi-cache/felix
-    copy the files from deploy/bundles to domain-dir/autodeploy/bundles
-    update database: open sormas_schema.sql and execute ONLY the new part (compare based on table schema_version)
-    start server: /srv/payara-sormas/glassfish/bin/startserv.bat
-    copy sormas-ear.ear, sormas-rest.war, sormas-ui.war to domain-dir\autodeploy after some seconds the server should be updated (wait until nothing happens in the log)
-    try to login at https://localhost:6081/sormas-ui if it doesn't work: restart the server
-    update the mobile app with the new apk file
-
-Development Environment
-
-    Install the latest Eclipse version, Git for Windows and (optional) a Git client such as TortoiseGit if you don't want to handle version control from the command line/separately for the Eclipse and Android Studio projects
-    Open the Git Bash and execute the command git config --global branch.development.rebase true (which ensures that rebase is used when pulling rather than merge)
-    Clone the SORMAS-Open repository and import the projects to Eclipse
-        If you're using Eclipse to clone, choose "File -> Import -> Git -> Projects from Git" and continue until you're asked to create a new project from the cloned repository; click cancel instead and use "File -> Import -> Maven -> Existing Maven Projects" to import the separate projects into your workspace
-        If you've cloned the repository from the command line or a Git client, you obviously only need to perform the last step
-    Highlight all Eclipse projects and choose "Maven -> Update Project" from the right click menu; perform the update for all projects
-    Install Glassfish Tools and (recommended) the Vaadin Plugin for Eclipise (make sure to untick the option to also install the commercial UI designer)
-    Set up a Glassfish 4 server in Eclipse and enter the credentials you specified when setting up the server
-    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
-    Install the latest Android Studio version (to avoid any errors, make sure to start the installation with admin rights and choose a path for the Android SDK that contains no whitespaces)
-    Open Android Studio and import the "sormas-app" project from Eclipse
-    Drag the "build.xml" file contained in "sormas-base" into the Ant view in Eclipse and execute the "install [default]", "deploy-serverlibs" and "deploy-bundles" scripts
-    Build the Android Studio project by executing the gradle build (this may be done automatically)
-    Start the Glassfish server and deploy "sormas-ear", "sormas-rest" and "sormas-ui" by dragging the respective projects onto it
-    Open your browser and type in "https://localhost:6081/sormas-ui" to test whether everything has been set up correctly (and to use the application)
+Project Structure
+========
+The project consists of the following modules:
+
+- sormas-api: general business logic and definitions for data exchange between app and server
+- sormas-app: the android app
+- sormas-backend: server entity services, facades, etc.
+- sormas-base: base project that also contains build scripts
+- sormas-ear: the ear needed to build the application
+- sormas-rest: the rest interface
+- sormas-ui: the web application
+
+
+Getting Started
+========
+SORMAS Server & Domain
+--------
+1. Install PostgreSQL (currently we are using 9.6) on your system
+2. Install the "temporal tables" addon for Postgres (https://github.com/arkhipov/temporal_tables)
+  * Windows: Download latest version for your postgres version: https://github.com/arkhipov/temporal_tables/releases/latest Then you must copy the DLL from the project into the PostgreSQL's lib directory and the .sql and .control files into the directory share\extension.
+  * Linux: <code>pgxn install temporal_tables</code> (see https://github.com/arkhipov/temporal_tables#installation)
+3. Download payara 4.1.2.172 (https://www.payara.fish/all_downloads) and extract it to a folder on your hard drive (e.g. /srv/payara-sormas)
+4. Create a PostgreSQL database named "sormas_db" (password: "sormas_db") with user "sormas_user" (password: "sormas_db") as its owner, and run the SQL scripts contained in "/sormas-base/sql/sormas_schema.sql"
+5. Get the latest SORMAS build from github: https://github.com/hzi-braunschweig/SORMAS-Open/releases/latest (deploy.zip and app-debug.apk)
+6. Open "deploy/glassfish-config.bat" (or glassfish-config.sh on linux) in a text editor and change GLASSFISH_HOME to the location of the Glassfish folder inside your payara installation
+7. Set up a payara domain called "sormas" by executing "deploy/glassfish-config.bat" (or glassfish-config.sh on linux) from the command line
+
+Updating Payara Version
+--------
+If you are using an older version of payara as mentioned below, please do the following:
+1. Make sure the server is not running
+2. Rename the server directory (e.g. /srv/payara-sormas-162)
+3. Download payara 4.1.2.172 (https://www.payara.fish/all_downloads) and extract it to the path previously used by your server (e.g. /srv/payara-sormas)
+4. Copy the domain from the old to the new server (e.g. ''cp -R /srv/payara-sormas-162/glassfish/domains/sormas /srv/payara-sormas/glassfish/domains/sormas'')
+5. Update the domain (as explained below).
+
+Updating the SORMAS domain
+--------
+(ignore this when you are setting up a whole development enviroment, as described below)
+
+1. Get the latest SORMAS build from github: https://github.com/hzi-braunschweig/SORMAS-Open/releases/ (deploy.zip and app-debug.apk)
+2. locate the server domain directory (domain-dir). Mostly /srv/payara-sormas/glassfish/domains/sormas
+3. make sure the server is not running
+4. delete the content from the following subfolders: 
+   domain-dir/autodeploy/bundles/... 
+   domain-dir/osgi-cache/felix
+5. copy the files from deploy/bundles to domain-dir/autodeploy/bundles
+6. update database: open sormas_schema.sql and execute ONLY the new part (compare based on table schema_version)
+7. start server: /srv/payara-sormas/glassfish/bin/startserv.bat
+8. copy sormas-ear.ear, sormas-rest.war, sormas-ui.war to domain-dir\autodeploy
+   after some seconds the server should be updated (wait until nothing happens in the log)
+9. try to login at https://localhost:6081/sormas-ui
+   if it doesn't work: restart the server
+10. update the mobile app with the new apk file 
+
+Development Environment
+--------
+- Install the latest Eclipse version, Git for Windows and (optional) a Git client such as TortoiseGit if you don't want to handle version control from the command line/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)
+- Clone the SORMAS-Open repository and import the projects to Eclipse
+	- If you're using Eclipse to clone, choose "File -> Import -> Git -> Projects from Git" and continue until you're asked to create a new project from the cloned repository; click cancel instead and use "File -> Import -> Maven -> Existing Maven Projects" to import the separate projects into your workspace
+	- If you've cloned the repository from the command line or a Git client, you obviously only need to perform the last step
+- Highlight all Eclipse projects and choose "Maven -> Update Project" from the right click menu; perform the update for all projects
+- Install Glassfish Tools and (recommended) the Vaadin Plugin for Eclipise (make sure to untick the option to also install the commercial UI designer)
+- Set up a Glassfish 4 server in Eclipse and enter the credentials you specified when setting up the server
+- 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
+- Install the latest Android Studio version (to avoid any errors, make sure to start the installation with admin rights and choose a path for the Android SDK that contains no whitespaces)
+- Open Android Studio and import the "sormas-app" project from Eclipse
+- Drag the "build.xml" file contained in "sormas-base" into the Ant view in Eclipse and execute the "install [default]", "deploy-serverlibs" and "deploy-bundles" scripts
+- Build the Android Studio project by executing the gradle build (this may be done automatically)
+- Start the Glassfish server and deploy "sormas-ear", "sormas-rest" and "sormas-ui" by dragging the respective projects onto it
+- Open your browser and type in "https://localhost:6081/sormas-ui" to test whether everything has been set up correctly (and to use the application)
+
+Apache Server
+--------
+When you are using SORMAS in a production environment you should use a http server like Apache 2 instead of putting the payara server in the first line.
+Here are some things that you should do to configure the apache server as proxy:
+
+* Force SSL secured connections (redirect from http to https)
+* Add a proxy pass to the local port:
+
+		ProxyRequests Off
+		ProxyPass /sormas-ui http://localhost:5080/sormas-ui
+		ProxyPassReverse /sormas-ui http://localhost:5080/sormas-ui
+		ProxyPass /sormas-rest http://localhost:5080/sormas-rest
+		ProxyPassReverse /sormas-rest http://localhost:5080/sormas-rest
+* Activate output compression (very important!): 
+
+        <IfModule mod_deflate.c>
+                AddOutputFilterByType DEFLATE text/plain text/html text/xml
+                AddOutputFilterByType DEFLATE text/css text/javascript
+                AddOutputFilterByType DEFLATE application/json
+                AddOutputFilterByType DEFLATE application/xml application/xhtml+xml
+                AddOutputFilterByType DEFLATE application/javascript application/x-javascript
+                DeflateCompressionLevel 1
+        </IfModule></code>

sormas-api/.gitignore

@@ -0,0 +1 @@
+/bin/

sormas-api/pom.xml

@@ -0,0 +1,50 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<parent>
+		<groupId>de.symeda.sormas</groupId>
+		<artifactId>sormas-base</artifactId>
+		<version>0.0.1</version>
+		<relativePath>../sormas-base</relativePath>
+	</parent>
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>sormas-api</artifactId>
+
+
+	<build>
+		<finalName>${project.artifactId}</finalName>
+		<resources>
+		    <resource>
+		      <directory>src/main/resources</directory>
+		      <filtering>true</filtering>
+		      <includes>
+		        <include>**/version.txt</include>
+		      </includes>
+		    </resource>
+		    <resource>
+		      <directory>src/main/resources</directory>
+		      <filtering>false</filtering>
+		      <excludes>
+		        <exclude>**/version.txt</exclude>
+		      </excludes>
+		    </resource>
+		</resources>		
+	</build>
+
+	<properties>
+		<maven.compiler.source>1.7</maven.compiler.source>
+		<maven.compiler.target>1.7</maven.compiler.target>
+	</properties>
+
+	<name>${project.artifactId}</name>
+	<dependencies>
+		<dependency>
+			<groupId>javax</groupId>
+			<artifactId>javaee-web-api</artifactId>
+		</dependency>
+		<dependency>
+		  <groupId>joda-time</groupId>
+		  <artifactId>joda-time</artifactId>
+		  <version>2.9.4</version>
+		</dependency>		
+	</dependencies>
+</project>

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

@@ -0,0 +1,78 @@
+package de.symeda.sormas.api;
+
+import java.io.Serializable;
+import java.util.Date;
+
+public abstract class DataTransferObject implements Serializable, Cloneable {
+
+	private static final long serialVersionUID = -1L;
+
+	public static final String CREATION_DATE = "creationDate";
+	public static final String CHANGE_DATE = "changeDate";
+	public static final String UUID = "uuid";
+
+	private Date creationDate;
+	private Date changeDate;
+	private String uuid;
+
+	public Date getCreationDate() {
+		return creationDate;
+	}
+
+	public void setCreationDate(Date creationDate) {
+		this.creationDate = creationDate;
+	}
+
+	public Date getChangeDate() {
+		return changeDate;
+	}
+
+	public void setChangeDate(Date changeDate) {
+		this.changeDate = changeDate;
+	}
+
+	public String getUuid() {
+		return uuid;
+	}
+
+	public void setUuid(String uuid) {
+		this.uuid = uuid;
+	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) {
+			return true;
+		}
+		if (o == null) {
+			return false;
+		}
+
+		if (getUuid() != null && o instanceof DataTransferObject
+				&& ((DataTransferObject) o).getUuid() != null) {
+			// this works, because we are using UUIDs
+			DataTransferObject ado = (DataTransferObject) o;
+			return getUuid().equals(ado.getUuid());
+		} else {
+			return false;
+		}
+	}
+
+	@Override
+	public int hashCode() {
+		if (getUuid() != null) {
+			return getUuid().hashCode();
+		}
+		return 0;
+	}
+
+	@Override
+	public DataTransferObject clone() throws CloneNotSupportedException {
+		if (getUuid() == null) {
+			throw new CloneNotSupportedException("DataTransferObject must have uuid in order to be cloneable");
+		}
+		return (DataTransferObject) super.clone();
+	}
+}
+
+

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

@@ -0,0 +1,23 @@
+package de.symeda.sormas.api;
+
+public enum Disease {
+	EVD,
+	LASSA,
+	AVIAN_INFLUENCA,
+	CSM,
+	CHOLERA,
+	MEASLES
+	;
+
+	public String toString() {
+		return I18nProperties.getEnumCaption(this);
+	};
+
+	public String toShortString() {
+		return I18nProperties.getEnumCaption(this, "Short");
+	}
+
+	public String getName() {
+		return this.name();
+	}
+}