Array Index Issue while running Demo

[OGalOz]

I got this error while running the demo through a Docker container:

''' =========== Setting gate parts according to assigned gate names =========== Setting gate parts according to assigned gate names [WARNING] java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.IndexOutOfBoundsException: Index: 1, Size: 1 at java.util.ArrayList.rangeCheck(ArrayList.java:657) at java.util.ArrayList.get(ArrayList.java:433) at org.cellocad.MIT.dnacompiler.PlasmidUtil.setTxnUnits(PlasmidUtil.java:520) at org.cellocad.MIT.dnacompiler.DNACompiler.generatePlasmids(DNACompiler.java:1136) at org.cellocad.MIT.dnacompiler.DNACompiler.run(DNACompiler.java:1068) at org.cellocad.MIT.dnacompiler.CelloMain.main(CelloMain.java:15) ... 6 more [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 17.077 s [INFO] Finished at: 2019-11-15T00:01:12+00:00 [INFO] Final Memory: 39M/271M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.4.0:java (default) on project cellocad: An exception occured while executing the Java class. null: InvocationTargetException: Index: 1, Size: 1 -> [Help 1] org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.4.0:java (default) on project cellocad: An exception occured while executing the Java class. null '''

A possible fix is to replace the code in org.cellocad.MIT.dnacompiler.PlasmidUtil.setTxnUnits to the following:

        else {
        boolean f1 = g.getChildren().size() > 0 && (
        g.system.equals("CRISPRi") || g.getChildren().get(0).system.equals("CRISPRi") ||
        g.system.equals("Ecoligenome") || g.getChildren().get(0).system.equals("Ecoligenome") ||
        g.system.equals("Yeast") || g.getChildren().get(0).system.equals("Yeast")
    );

    boolean f2 = g.getChildren().size() > 1 && (
        g.getChildren().get(1).system.equals("Ecoligenome") ||
        g.getChildren().get(1).system.equals("Yeast")
    );

    /*
       if(g.system.equals("CRISPRi") || g.getChildren().get(0).system.equals("CRISPRi")
       || g.system.equals("Ecoligenome") || g.getChildren().get(0).system.equals("Ecoligenome") || g.getChildren().get(1).system.equals("Ecoligenome")
       || g.system.equals("Yeast") || g.getChildren().get(0).system.equals("Yeast") || g.getChildren().get(1).system.equals("Yeast")) {
       */
    if(f1 || f2) {

                for(String var: g.get_variable_names()) {

                    for(Wire w: g.get_variable_wires().get(var)) {
                        ArrayList<Part> txn_unit = new ArrayList<>();

                        txn_unit.add(w.to.get_regulable_promoter());

                        ArrayList<Part> expression_cassette = g.get_downstream_parts().get(var);

                        txn_unit.addAll(expression_cassette);

                        g.get_txn_units().add(txn_unit);
                    }

                }

The original conditional statement is commented out but left there to show where the change occurs.