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Updated to suppot later Java versions

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This commit is contained in:
Chris Myers 2024-11-26 20:27:58 -07:00
parent 040aa01d2f
commit b11268ec9c
13 changed files with 198 additions and 161 deletions
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111
dataModels/pom.xml
View file

@ -16,21 +16,11 @@
<name>The JSBML Snapshot repository</name>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
<repository>
<id>ebi</id>
<name>ebi</name>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
</repository>
<repository>
<repository>
<id>jboss</id>
<name>jboss</name>
<url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
</repository>
<repository>
<id>netbeans</id>
<name>netbeans</name>
<url>http://bits.netbeans.org/maven2/</url>
</repository>
<repository>
<id>osgeo</id>
<name>osgeo</name>
@ -54,8 +44,26 @@
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>1.1.4</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
<exclusion>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
</exclusion>
<exclusion>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
@ -85,6 +93,20 @@
<groupId>org.sbolstandard</groupId>
<artifactId>libSBOLj</artifactId>
<version>2.4.1-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
<exclusion>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
@ -98,17 +120,56 @@
<groupId>org.jfree</groupId>
<artifactId>jfreechart</artifactId>
<version>1.0.14</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis-ext</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-dom</artifactId>
<version>1.8</version>
<version>1.16</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis-ext</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.xmlgraphics</groupId>
<artifactId>batik-svggen</artifactId>
<version>1.8</version>
<version>1.16</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@ -122,11 +183,29 @@
<artifactId>VectorGraphics2D</artifactId>
<version>0.13</version>
</dependency>
<dependency>
<groupId>org.jlibsedml</groupId>
<artifactId>jlibsedml</artifactId>
<version>2.3.0-SNAPSHOT</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
<exclusion>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
</exclusion>
<exclusion>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>

7
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/graphData/GraphData.java
View file

@ -19,8 +19,6 @@ import java.util.Scanner;
import javax.swing.JComboBox;
import org.apache.batik.dom.GenericDOMImplementation;
import org.apache.batik.svggen.SVGGraphics2D;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
@ -53,7 +51,8 @@ import org.jlibsedml.SEDMLDocument;
import org.jlibsedml.SedML;
import org.jlibsedml.Variable;
import org.jlibsedml.modelsupport.SBMLSupport;
import org.w3c.dom.DOMImplementation;
import org.apache.batik.svggen.SVGGraphics2D;
import org.apache.batik.dom.GenericDOMImplementation;
import com.lowagie.text.Document;
import com.lowagie.text.Rectangle;
@ -301,6 +300,7 @@ public class GraphData extends CoreObservable {
doc.writeTo(new FileOutputStream(file));
}
else if (output == 4) {
/*
DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
org.w3c.dom.Document document = domImpl.createDocument(null, "svg", null);
SVGGraphics2D svgGenerator = new SVGGraphics2D(document);
@ -311,6 +311,7 @@ public class GraphData extends CoreObservable {
svgGenerator.stream(out, useCSS);
out.close();
outStream.close();
*/
}
else if ((output == 5) || (output == 6) || (output == 7)) {
exportDataFile(file, output);