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Updated to suppot later Java versions
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@cjmyers
cjmyers committed Nov 27, 2024
1 parent 040aa01 commit b11268e
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Showing 13 changed files with 198 additions and 161 deletions.
2 changes: 1 addition & 1 deletion analysis/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
</configuration>
<phase>package</phase>
<goals>
<goal>assembly</goal>
<goal>single</goal>
</goals>
</execution>
</executions>
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21 changes: 21 additions & 0 deletions analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/properties/PropertiesUtil.java
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Expand Up @@ -47,6 +47,17 @@ static Algorithm getAlgorithm(AnalysisProperties properties) {
algorithm = new Algorithm(GlobalConstants.KISAO_EULER);
} else if (sim.contains("rk8pd")) {
algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND);
} else if (sim.contains("rk4imp")) {
algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_IMPLICIT);
} else if (sim.contains("gear1")||sim.contains("gear2")) {
algorithm = new Algorithm(GlobalConstants.KISAO_GEAR);
AlgorithmParameter order;
if (sim.contains("gear1")) {
order = new AlgorithmParameter(GlobalConstants.KISAO_ORDER, "1");
} else {
order = new AlgorithmParameter(GlobalConstants.KISAO_ORDER, "2");
}
algorithm.addAlgorithmParameter(order);
} else if (sim.contains("rkf45") || sim.contains("Runge-Kutta-Fehlberg")) {
algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_FEHLBERG);
para.setAttribute("method", sim);
Expand All @@ -57,6 +68,10 @@ static Algorithm getAlgorithm(AnalysisProperties properties) {
} else if (properties.isSsa()) {
if (sim.equals("gillespie")) {
algorithm = new Algorithm(GlobalConstants.KISAO_GILLESPIE_DIRECT);
} else if (sim.equals("bunker")) {
algorithm = new Algorithm(GlobalConstants.KISAO_BUNKER);
} else if (sim.equals("emc")) {
algorithm = new Algorithm(GlobalConstants.KISAO_EMC);
}

else if (sim.contains("Mixed")) {
Expand Down Expand Up @@ -146,6 +161,12 @@ static void setAlgorithm(Algorithm algorithm, AnalysisProperties properties) {
} else if (kisaoId.equals(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND)) {
properties.setOde();
properties.setSim("rk8pd");
} else if (kisaoId.equals(GlobalConstants.KISAO_BUNKER)) {
properties.setOde();
properties.setSim("bunker");
} else if (kisaoId.equals(GlobalConstants.KISAO_EMC)) {
properties.setOde();
properties.setSim("emc");
} else if (kisaoId.equals(GlobalConstants.KISAO_GILLESPIE) || kisaoId.equals(GlobalConstants.KISAO_GILLESPIE_DIRECT)) {
properties.setSsa();
properties.setSim("gillespie");
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2 changes: 1 addition & 1 deletion bin/iBioSim.mac64
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Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,4 @@ export PATH=$BIOSIM/bin:/usr/local/lib:$PATH
export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH
export DDLD_LIBRARY_PATH=/usr/local/lib:$DDLD_LIBRARY_PATH

exec java -Xmx2048M -Xms2048M -Djava.library.path=/usr/local/lib -XX:+UseSerialGC -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/src/main/resources/edu/utah/ece/async/ibiosim/gui/icons/iBioSim.jpg -jar iBioSim.jar
java --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx2048M -Xms2048M -Djava.library.path=/usr/local/lib -XX:+UseSerialGC -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/src/main/resources/edu/utah/ece/async/ibiosim/gui/icons/iBioSim.jpg -jar iBioSim.jar
12 changes: 11 additions & 1 deletion conversion/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
</configuration>
<phase>package</phase>
<goals>
<goal>assembly</goal>
<goal>single</goal>
</goals>
</execution>
</executions>
Expand Down Expand Up @@ -69,6 +69,16 @@
<groupId>org.apache.jena</groupId>
<artifactId>jena-arq</artifactId>
<version>3.0.0</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<repositories>
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111 changes: 95 additions & 16 deletions dataModels/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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 -->
Expand All @@ -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>
Expand All @@ -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>
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7 changes: 4 additions & 3 deletions dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/graphData/GraphData.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,6 @@

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;
Expand Down Expand Up @@ -53,7 +51,8 @@
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;
Expand Down Expand Up @@ -301,6 +300,7 @@ else if (output == 3) {
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);
Expand All @@ -311,6 +311,7 @@ else if (output == 4) {
svgGenerator.stream(out, useCSS);
out.close();
outStream.close();
*/
}
else if ((output == 5) || (output == 6) || (output == 7)) {
exportDataFile(file, output);
Expand Down
31 changes: 15 additions & 16 deletions gui/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,39 +30,24 @@
</configuration>
<phase>package</phase>
<goals>
<goal>assembly</goal>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<repositories>
<repository>
<id>staging</id>
<name>staging</name>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
</repository>
<repository>
<id>ossrh</id>
<name>ossrh</name>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</repository>
<repository>
<id>ebi</id>
<name>ebi</name>
<url>https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
</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>https://bits.netbeans.org/maven2/</url>
</repository>
<repository>
<id>osgeo</id>
<name>osgeo</name>
Expand Down Expand Up @@ -92,6 +77,20 @@
<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>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
<exclusion>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</exclusion>
</exclusions>
</dependency>

<dependency>
Expand Down
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