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Fix dgarijo#303; Fix dgarijo#373; Fix dgarijo#375; #fix dgarijo#393
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@dgarijo
dgarijo committed May 25, 2020
1 parent 1db804f commit 3f3c970
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Showing 24 changed files with 1,028 additions and 595 deletions.
106 changes: 19 additions & 87 deletions pom.xml
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Expand Up @@ -4,20 +4,14 @@
<groupId>es.oeg</groupId>
<artifactId>widoco</artifactId>
<packaging>jar</packaging>
<version>1.4.13</version>
<version>1.4.14</version>
<name>Widoco</name>

<properties>
<ver.log4j>1.2.16</ver.log4j>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<java.version>1.8</java.version>
<jena.version>2.11.1</jena.version>
<jena-sdb.version>1.3.6</jena-sdb.version>
<jena-tdb.version>0.10.1</jena-tdb.version>
<jena-iri.version>0.9.6</jena-iri.version>
<jena-fuseki.version>0.2.7</jena-fuseki.version>
</properties>

<dependencies>
Expand All @@ -28,84 +22,22 @@
<version>0.3.5</version>
</dependency>

<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>${ver.log4j}</version>
<exclusions>
<!-- Exclude things that don't resolve in some versions of log4j -->
<exclusion>
<groupId>javax.jms</groupId>
<artifactId>jms</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.jdmk</groupId>
<artifactId>jmxtools</artifactId>
</exclusion>
<exclusion>
<groupId>com.sun.jmx</groupId>
<artifactId>jmxri</artifactId>
</exclusion>
<exclusion>
<groupId>javax.mail</groupId>
<artifactId>mail</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.30</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>1.7.30</version>
</dependency>

<!-- We use "provided" scope because we are exporting the contents of these
libraries, and we don't want our bundle consumers to see and be confused
by these additional copies of the classes, as transitive dependencies. "provided"
prevents that from happening. -->

<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>apache-jena-libs</artifactId>
<type>pom</type>
<version>${jena.version}</version>

<scope>provided</scope>
<exclusions>
<exclusion>
<artifactId>lucene-core</artifactId>
<groupId>org.apache.lucene</groupId>
</exclusion>
<exclusion>
<artifactId>stax-api</artifactId>
<groupId>stax</groupId>
</exclusion>
<exclusion>
<artifactId>wstx-asl</artifactId>
<groupId>org.codehaus.woodstox</groupId>
</exclusion>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
</exclusion>
<exclusion>
<artifactId>icu4j</artifactId>
<groupId>com.ibm.icu</groupId>
</exclusion>
<exclusion>
<artifactId>slf4j-log4j12</artifactId>
<groupId>org.slf4j</groupId>
</exclusion>
</exclusions>
</dependency>


<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-core</artifactId>
<version>${jena.version}</version>
<exclusions>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>log4j</groupId>
</exclusion>
</exclusions>
</dependency>

prevents that from happening.
-->
<dependency>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
Expand All @@ -115,7 +47,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
<version>5.1.11</version>
<version>5.1.14</version>
</dependency>

<dependency>
Expand All @@ -136,11 +68,11 @@
<scope>test</scope>
</dependency>

<dependency>
<!--<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.13</version>
</dependency>
</dependency>-->
</dependencies>

<dependencyManagement>
Expand Down Expand Up @@ -205,11 +137,11 @@
<!-- Environment settings -->
<repositories>

<repository>
<!--<repository>
<id>maven-restlet</id>
<name>Restlet Framework repository</name>
<url>https://maven.restlet.org</url>
</repository>
<url>http://maven.restlet.org</url>
</repository>-->

<repository>
<id>jitpack.io</id>
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7 changes: 0 additions & 7 deletions src/main/java/diagram/DiagramGeneration.java
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Expand Up @@ -27,11 +27,4 @@ public static void generateOntologyDiagram(String outFolder, Configuration c) {
logger.error("FAILED TO LOAD " + e.getMessage());
}
}

// public static void main(String[] args){
// File webvowl = new File("mydoc"+File.separator+"webvowl");
// boolean t = webvowl.mkdirs();
// WidocoUtils.unZipIt(Constants.WEBVOWL_RESOURCES, webvowl.getAbsolutePath());
// }

}
18 changes: 9 additions & 9 deletions src/main/java/diff/CompareOntologies.java
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Expand Up @@ -37,17 +37,17 @@ public class CompareOntologies {
private final Logger logger = LoggerFactory.getLogger(this.getClass());

//classes
private ArrayList<OWLAxiomInfo> modifiedClasses = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> newClasses = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> deletedClasses = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> modifiedClasses = new ArrayList<>();
private ArrayList<OWLAxiomInfo> newClasses = new ArrayList<>();
private ArrayList<OWLAxiomInfo> deletedClasses = new ArrayList<>();
//properties
private ArrayList<OWLAxiomInfo> modifiedProperties = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> newProperties = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> deletedProperties = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> modifiedProperties = new ArrayList<>();
private ArrayList<OWLAxiomInfo> newProperties = new ArrayList<>();
private ArrayList<OWLAxiomInfo> deletedProperties = new ArrayList<>();
//data properties
private ArrayList<OWLAxiomInfo> modifiedDataProperties = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> newDataProperties = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> deletedDataProperties = new ArrayList<OWLAxiomInfo>();
private ArrayList<OWLAxiomInfo> modifiedDataProperties = new ArrayList<>();
private ArrayList<OWLAxiomInfo> newDataProperties = new ArrayList<>();
private ArrayList<OWLAxiomInfo> deletedDataProperties = new ArrayList<>();

private String oldVersion, newVersion;

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7 changes: 4 additions & 3 deletions src/main/java/lode/LODEGeneration.java
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Expand Up @@ -36,24 +36,25 @@
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import org.apache.log4j.Logger;
import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat;
import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
import org.semanticweb.owlapi.io.StringDocumentTarget;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLOntologyManager;

import widoco.Configuration;

/**
*
* @author Silvio Peroni, adpated to Widoco (and modified) by Daniel Garijo
*/
public class LODEGeneration {

final static Logger logger = Logger.getLogger(LODEGeneration.class);
private static final Logger logger = LoggerFactory.getLogger(LODEGeneration.class);

public static String getLODEhtml(Configuration c, File lodeResources) throws Exception {
try {
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