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Phenopacket reading #30
| @@ -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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