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Raphael
histream
Commits
081a806e
Commit
081a806e
authored
May 22, 2015
by
rwm
Browse files
Documentation, scripts
parent
71aaf9bb
Changes
4
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README.md
View file @
081a806e
...
...
@@ -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
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081a806e
...
...
@@ -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
View file @
081a806e
<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
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081a806e
...
...
@@ -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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