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11 several ontologies of tib fail in ingestion #18

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merged 4 commits into from
Jul 24, 2024
Merged

11 several ontologies of tib fail in ingestion #18

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9124d45
added logic to convert ontologies to RDF/XML format before parsing
deepananbu Jun 12, 2024
061f546
added logic to convert ontologies to rdf format. Added "convertToRDF" as
deepananbu Jun 18, 2024
20bcaf9
owl & ttl files required for the conversion
deepananbu Jun 18, 2024
882cb46
Merge remote-tracking branch 'origin/dev' into
deepananbu Jun 24, 2024
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212 changes: 112 additions & 100 deletions dataload/rdf2json/pom.xml
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Original file line number Diff line number Diff line change
@@ -1,117 +1,129 @@
<?xml version="1.0" encoding="UTF-8"?>
<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>uk.ac.ebi.spot</groupId>
<artifactId>rdf2json</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>
<groupId>uk.ac.ebi.spot</groupId>
<artifactId>rdf2json</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>

<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>3.17.0</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.7</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>31.1-jre</version>
</dependency>
</dependencies>
<dependencies>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<version>3.17.0</version>
<type>pom</type>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
<version>2.7</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>31.1-jre</version>
</dependency>
<dependency>
<groupId>org.obolibrary.robot</groupId>
<artifactId>robot-core</artifactId>
<version>1.9.6</version>
</dependency>
</dependencies>

<properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
</properties>
<properties>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
</properties>

<build>
<plugins>
<build>
<plugins>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<shadedArtifactAttached>false</shadedArtifactAttached>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<shadedArtifactAttached>false</shadedArtifactAttached>

<!--
<!--
https://issues.apache.org/jira/browse/LOG4J2-954
Multiple Log4j2Plugins.dat
jena-fuseki-server only pick up one Log4j2Plugins.dat (from log4j-core-2.13.2)
No need to run the transformer to merge them.
If it becomes necessary, see: https://github.com/edwgiz/maven-shaded-log4j-transformer
If it becomes necessary, see:
https://github.com/edwgiz/maven-shaded-log4j-transformer
-->

<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>uk.ac.ebi.rdf2json.RDF2JSON</mainClass>
<!-- https://issues.apache.org/jira/browse/LOG4J2-2537 -->
<manifestEntries>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer" />
<transformer implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
<addHeader>false</addHeader>
</transformer>
</transformers>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>uk.ac.ebi.rdf2json.RDF2JSON</mainClass>
<!--
https://issues.apache.org/jira/browse/LOG4J2-2537 -->
<manifestEntries>
<Multi-Release>true</Multi-Release>
</manifestEntries>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
<transformer
implementation="org.apache.maven.plugins.shade.resource.ApacheLicenseResourceTransformer" />
<transformer
implementation="org.apache.maven.plugins.shade.resource.ApacheNoticeResourceTransformer">
<addHeader>false</addHeader>
</transformer>
</transformers>

<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<!-- Some jars are signed but shading breaks that. Don't
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<!-- Some jars are signed but shading breaks
that. Don't
include signing files. -->
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<!--<phase /><!- - Switch off -->
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- <plugin>-->
<!-- <groupId>org.apache.maven.plugins</groupId>-->
<!-- <artifactId>maven-assembly-plugin</artifactId>-->
<!-- <executions>-->
<!-- <execution>-->
<!-- <phase>package</phase>-->
<!-- <goals>-->
<!-- <goal>single</goal>-->
<!-- </goals>-->
<!-- <configuration>-->
<!-- <archive>-->
<!-- <manifest>-->
<!-- <mainClass>-->
<!-- RDF2JSON-->
<!-- </mainClass>-->
<!-- </manifest>-->
<!-- </archive>-->
<!-- <descriptorRefs>-->
<!-- <descriptorRef>jar-with-dependencies</descriptorRef>-->
<!-- </descriptorRefs>-->
<!-- </configuration>-->
<!-- </execution>-->
<!-- </executions>-->
<!-- </plugin>-->
</plugins>
</build>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<!--<phase /><!- - Switch off -->
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- <plugin>-->
<!-- <groupId>org.apache.maven.plugins</groupId>-->
<!-- <artifactId>maven-assembly-plugin</artifactId>-->
<!-- <executions>-->
<!-- <execution>-->
<!-- <phase>package</phase>-->
<!-- <goals>-->
<!-- <goal>single</goal>-->
<!-- </goals>-->
<!-- <configuration>-->
<!-- <archive>-->
<!-- <manifest>-->
<!-- <mainClass>-->
<!-- RDF2JSON-->
<!-- </mainClass>-->
<!-- </manifest>-->
<!-- </archive>-->
<!-- <descriptorRefs>-->
<!-- <descriptorRef>jar-with-dependencies</descriptorRef>-->
<!-- </descriptorRefs>-->
<!-- </configuration>-->
<!-- </execution>-->
<!-- </executions>-->
<!-- </plugin>-->
</plugins>
</build>
</project>
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