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Update to Apache Jena 4.2 #748

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Merged
merged 7 commits into from
Jun 4, 2022
Merged

Update to Apache Jena 4.2 #748

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5e324e0
Updated to Apache Jena 4.2
egonw Sep 21, 2021
9d95752
Fixed the error message: correct writer description
egonw Sep 21, 2021
27af912
Reupdated, resolving merge conflict
egonw Apr 5, 2022
00a7507
Merge branch 'master' into update/jena4.2
johnmay May 16, 2022
ae5e460
Move to Jena 4.4.0 and only include cdk-iordf if you are using Java 11
johnmay May 16, 2022
3ff62d6
Remove stack trace dumping
johnmay May 16, 2022
267a14f
Update to latest dependency versions.
johnmay Jun 4, 2022
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50 changes: 30 additions & 20 deletions bundle/pom.xml
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Expand Up @@ -3,17 +3,17 @@
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>

<parent>
<artifactId>cdk</artifactId>
<groupId>org.openscience.cdk</groupId>
<version>2.8-SNAPSHOT</version>
</parent>

<artifactId>cdk-bundle</artifactId>

<name>cdk-bundle</name>

<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
Expand Down Expand Up @@ -240,11 +240,6 @@
<artifactId>cdk-qm</artifactId>
<version>${project.parent.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>cdk-iordf</artifactId>
<version>${project.parent.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>cdk-libiomd</artifactId>
Expand Down Expand Up @@ -315,17 +310,17 @@
<artifactId>maven-shade-plugin</artifactId>
<version>2.2</version>
<configuration>
<finalName>cdk-${project.parent.version}</finalName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<finalName>cdk-${project.parent.version}</finalName>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
Expand All @@ -335,7 +330,22 @@
</goals>
</execution>
</executions>
</plugin>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<id>jdk11-plus</id>
<activation>
<jdk>[11,)</jdk>
</activation>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>cdk-iordf</artifactId>
<version>${project.parent.version}</version>
</dependency>
</dependencies>
</profile>
</profiles>
</project>
19 changes: 17 additions & 2 deletions storage/iordf/pom.xml
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Expand Up @@ -17,7 +17,22 @@
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>2.7.4</version>
<version>4.5.0</version>
<exclusions>
<exclusion>
<artifactId>slf4j-log4j12</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
<exclusion>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>4.5.0</version>
<exclusions>
<exclusion>
<artifactId>slf4j-log4j12</artifactId>
Expand All @@ -32,7 +47,7 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.7.10</version>
<version>1.7.36</version>
<exclusions>
<exclusion>
<groupId>log4j</groupId>
Expand Down
5 changes: 2 additions & 3 deletions storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLReader.java
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Expand Up @@ -27,6 +27,8 @@
import java.io.InputStreamReader;
import java.io.Reader;

import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObject;
Expand All @@ -35,9 +37,6 @@
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.libio.jena.Convertor;

import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;

/**
* Reads content from a CDK OWL serialization.
*
Expand Down
9 changes: 5 additions & 4 deletions storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLWriter.java
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Expand Up @@ -23,6 +23,9 @@
import java.io.OutputStreamWriter;
import java.io.Writer;

import org.apache.jena.rdf.model.Model;
import org.apache.jena.riot.Lang;
import org.apache.jena.riot.RDFDataMgr;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObject;
Expand All @@ -31,8 +34,6 @@
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.libio.jena.Convertor;

import com.hp.hpl.jena.rdf.model.Model;

/**
* Serializes the data model into CDK OWL.
*
Expand Down Expand Up @@ -107,7 +108,7 @@ public void write(IChemObject object) throws CDKException {
try {
writeMolecule((IAtomContainer) object);
} catch (Exception ex) {
throw new CDKException("Error while writing HIN file: " + ex.getMessage(), ex);
throw new CDKException("Error while writing CDK OWL file: " + ex.getMessage(), ex);
}
} else {
throw new CDKException("CDKOWLWriter only supports output of IAtomContainer classes.");
Expand All @@ -116,7 +117,7 @@ public void write(IChemObject object) throws CDKException {

private void writeMolecule(IAtomContainer mol) {
Model model = Convertor.molecule2Model(mol);
model.write(output, "N3");
RDFDataMgr.write(output, model, Lang.RDFXML);
}

}
8 changes: 4 additions & 4 deletions storage/iordf/src/main/java/org/openscience/cdk/libio/jena/CDK.java
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Expand Up @@ -22,10 +22,10 @@
*/
package org.openscience.cdk.libio.jena;

import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.vocabulary.RDF;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.ResourceFactory;
import org.apache.jena.vocabulary.RDF;

/**
* Helper class to provide a Java API to the CDK OWL ontology, following the design of similar namespace
Expand Down
15 changes: 7 additions & 8 deletions storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java
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Expand Up @@ -26,6 +26,13 @@
import java.util.HashMap;
import java.util.Map;

import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.ResIterator;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import org.apache.jena.vocabulary.RDF;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
Expand All @@ -40,14 +47,6 @@
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IPseudoAtom;

import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.vocabulary.RDF;

/**
* Helper class that converts a CDK {@link IChemObject} into RDF using a
* Jena model and the CDK data model ontology.
Expand Down
3 changes: 1 addition & 2 deletions storage/iordf/src/test/java/org/openscience/cdk/libio/jena/ConvertorTest.java
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Expand Up @@ -22,6 +22,7 @@
*/
package org.openscience.cdk.libio.jena;

import org.apache.jena.rdf.model.Model;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.test.CDKTestCase;
Expand All @@ -38,8 +39,6 @@
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.tools.diff.AtomContainerDiff;

import com.hp.hpl.jena.rdf.model.Model;

/**
* @cdk.module test-iordf
*/
Expand Down
15 changes: 12 additions & 3 deletions storage/pom.xml
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Expand Up @@ -3,7 +3,7 @@
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>

<parent>
<artifactId>cdk</artifactId>
<groupId>org.openscience.cdk</groupId>
Expand All @@ -14,7 +14,6 @@
<module>ctab</module>
<module>io</module>
<module>ioformats</module>
<module>iordf</module>
<module>libiocml</module>
<module>libiomd</module>
<module>pdb</module>
Expand All @@ -25,5 +24,15 @@
</modules>
<packaging>pom</packaging>
<artifactId>cdk-storage</artifactId>

<profiles>
<profile>
<id>jdk11-plus</id>
<activation>
<jdk>[11,)</jdk>
</activation>
<modules>
<module>iordf</module>
</modules>
</profile>
</profiles>
</project>