Commit 081a806e authored by rwm's avatar rwm

Documentation, scripts

parent 71aaf9bb
......@@ -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`
......@@ -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>
......
<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>
......
......@@ -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>
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