Documentation, scripts

README.md

@@ -5,12 +5,27 @@ HIStream
 Building from source
 ---------------------
 Build requirements: JDK 8, Maven
-Run `mvn clean install`
 
+Run `mvn clean install` to download dependencies and build all sub-modules.
+The binary distribution zip files can then be found in distribution/target.
 
-Running HIStream from JAR
--------------------------
-`
-java -Djava.util.logging.config.file=target\classes\logging.properties -cp target\histream-0.0.1-SNAPSHOT.jar;target\dependency\postgresql-9.4-1201-jdbc41.jar de.sekmi.histream.impl.RunConfiguration
-`
 
+Running HIStream
+================
+
+Import Data into the i2b2 Data Warehouse
+----------------------------------------
+
+Easy way: 
+1. copy/unzip the binary distribution ..-i2b2.zip (or ..-full.zip) from distribution/target.
+2. adjust the database settings in histream.xml
+3. To import data into i2b2 run `startup examples/dwh-eav.xml` or `startup examples/dwh-eav.xml`
+
+Import SKOS ontology into i2b2
+------------------------------
+Incomplete.
+1. copy/unzip the binary distribution ..-full.zip from distribution/target. 
+The plugins histream-skos and histream-i2b2 are needed.
+2. adjust examples/ontology-import.properties
+3. adjust paths to RDF files in example/skos-ontology.properties
+4. Run `java -cp "lib\*" de.sekmi.histream.i2b2.OntologyImport de.sekmi.histream.ontology.skos.Store example/skos-ontology.properties examples/ontology-import.properties`

distribution/pom.xml

@@ -35,7 +35,7 @@
 						</goals>
 						<configuration>
 							<descriptors>
-								<descriptor>src/assembly/assembly.xml</descriptor>
+								<descriptor>src/assembly/i2b2.xml</descriptor>
 								<descriptor>src/assembly/full.xml</descriptor>
 							</descriptors>
 						</configuration>

distribution/src/assembly/assembly.xml → distribution/src/assembly/i2b2.xml

 <assembly>
-    <id>bin</id>
+    <id>i2b2</id>
     <!-- Specifies that our binary distribution is a zip package -->
     <formats>
         <format>zip</format>
@@ -21,6 +21,15 @@
         <outputDirectory>lib</outputDirectory>
         <unpack>false</unpack>
       </binaries>
+      <sources>
+	<includeModuleDirectory>false</includeModuleDirectory>
+	<fileSets>
+		<fileSet>
+			<outputDirectory>examples</outputDirectory>
+			<directory>src/main/examples</directory>
+		</fileSet>
+	</fileSets>
+      </sources>
     </moduleSet>
   </moduleSets>
 

distribution/src/main/scripts/startup/histream.xml

@@ -46,31 +46,15 @@
 			<property name="project">demo</property>					
 			<property name="nullProvider">LCS-I2B2:PROVIDERS</property>					
 		</plugin>
+		<!-- needed to parse XML files -->
 		<plugin class="de.sekmi.histream.io.XMLProviderFactory"/>
+		<!-- needed to parse flat text files -->
 		<plugin class="de.sekmi.histream.io.FlatProviderFactory"/>
 		
-		<!-- 
-		<plugin class="de.sekmi.histream.i2b2.services.HiveServer">
-			<property name="user">i2b2demodata</property>
-		</plugin>
-		<plugin class="de.sekmi.histream.hl7.MLLPListener">
-			<property name="port">123</property>
-		</plugin> -->
 	</plugins>
-	<!-- Wie kann die Konfiguration benutzt werden, wenn z.B. Dateien von der Kommandozeile
-	gelesen werden sollen und dann das Programm beendet werden soll?
-	 -->
+	<!-- source not needed, files are specified at command line -->
 	<!-- 
 	<source plugin="de.sekmi.histream.hl7.MLLPListener" />
-	<source plugin="de.sekmi.histream.impl.SAXObservationProvider" />
 	-->
-	<!-- TODO source umbenennen in listener (fuer netzwerkschnittstellen) -->
-	
 	<destination plugin="de.sekmi.histream.i2b2.I2b2Inserter" />
-	
-	<!-- kann dateien von Kommandozeile lesen -->
-	<filehandler  type="text/xml" plugin-ref="de.sekmi.histream.hl7.MLLPListener">
-		<url src="file://....xml" />
-	</filehandler>
-		
 </histream>