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Phenopacket reading #30

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Phenopacket reading #30

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6b03daa
Method for reading basic associations out of a PhenoPacket.
balhoff Jun 13, 2016
27d6230
Merge branch 'master' into phenopacket-reading
balhoff Jun 15, 2016
c05cef9
Updated to phenopackets 0.0.4.
balhoff Jun 17, 2016
d4b9575
Added Junit to fix build problems.
balhoff Jun 21, 2016
b19e8e3
Changed junit to be in the main compile.
balhoff Jun 21, 2016
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371 changes: 190 additions & 181 deletions owlsim-core/pom.xml
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Original file line number Diff line number Diff line change
@@ -1,192 +1,201 @@
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>owlsim</artifactId>
<groupId>org.monarchinitiative.owlsim</groupId>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>owlsim-core</artifactId>
<packaging>jar</packaging>
<name>owlsim-core</name>
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<artifactId>owlsim</artifactId>
<groupId>org.monarchinitiative.owlsim</groupId>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>owlsim-core</artifactId>
<packaging>jar</packaging>
<name>owlsim-core</name>

<properties>
<jena.version>2.11.2</jena.version>
</properties>
<properties>
<jena.version>2.11.2</jena.version>
</properties>

<build>
<plugins>
<build>
<plugins>
<!-- Build a bin/owlsim.jar file with all dependencies -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<finalName>owlsim</finalName>
<appendAssemblyId>false</appendAssemblyId>
<attach>false</attach>
<outputDirectory>${project.parent.basedir}/bin</outputDirectory>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<mainClass>org.monarchinitiative.owlsim.compute.runner.RunEngine</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<finalName>owlsim</finalName>
<appendAssemblyId>false</appendAssemblyId>
<attach>false</attach>
<outputDirectory>${project.parent.basedir}/bin</outputDirectory>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<mainClass>org.monarchinitiative.owlsim.compute.runner.RunEngine</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.18.1</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>2.18.1</version>
<executions>
<execution>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>

<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>${jena.version}</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>${jena.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-contract</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-impl</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-parsers</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-tools</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
<exclusions>
<exclusion>
<artifactId>mail</artifactId>
<groupId>javax.mail</groupId>
</exclusion>
<exclusion>
<artifactId>jms</artifactId>
<groupId>javax.jms</groupId>
</exclusion>
<exclusion>
<artifactId>jmxtools</artifactId>
<groupId>com.sun.jdmk</groupId>
</exclusion>
<exclusion>
<artifactId>jmxri</artifactId>
<groupId>com.sun.jmx</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>1.8.2</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>org.semanticweb.elk</groupId>
<artifactId>elk-owlapi</artifactId>
<version>0.4.1</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.2.4</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>jfact</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>jline</groupId>
<artifactId>jline</artifactId>
<version>0.9.93</version>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-javamail_1.4_spec</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>com.googlecode.javaewah</groupId>
<artifactId>JavaEWAH</artifactId>
<version>0.7.7</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.3</version>
</dependency>
<dependency>
<groupId>commons-validator</groupId>
<artifactId>commons-validator</artifactId>
<version>1.4.0</version>
</dependency>
</dependencies>
</plugins>
</build>

<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>${jena.version}</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>${jena.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-contract</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-impl</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-parsers</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-tools</artifactId>
<version>${owlapi.version}</version>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>1.2.17</version>
<exclusions>
<exclusion>
<artifactId>mail</artifactId>
<groupId>javax.mail</groupId>
</exclusion>
<exclusion>
<artifactId>jms</artifactId>
<groupId>javax.jms</groupId>
</exclusion>
<exclusion>
<artifactId>jmxtools</artifactId>
<groupId>com.sun.jdmk</groupId>
</exclusion>
<exclusion>
<artifactId>jmxri</artifactId>
<groupId>com.sun.jmx</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>1.8.2</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>org.semanticweb.elk</groupId>
<artifactId>elk-owlapi</artifactId>
<version>0.4.1</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.2.4</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>jfact</artifactId>
<version>1.0.0</version>
</dependency>
<dependency>
<groupId>jline</groupId>
<artifactId>jline</artifactId>
<version>0.9.93</version>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.geronimo.specs</groupId>
<artifactId>geronimo-javamail_1.4_spec</artifactId>
<version>1.6</version>
</dependency>
<dependency>
<groupId>com.googlecode.javaewah</groupId>
<artifactId>JavaEWAH</artifactId>
<version>0.7.7</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.3</version>
</dependency>
<dependency>
<groupId>commons-validator</groupId>
<artifactId>commons-validator</artifactId>
<version>1.4.0</version>
</dependency>
<dependency>
<groupId>org.phenopackets</groupId>
<artifactId>phenopackets-api</artifactId>
<version>0.0.4</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
</dependencies>

</project>
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