Dear KNIME Users and Developers,
I am trying to integrate my code into KNIME workflow using JavaSnippet. I have exported the code into a jar and put it into the KNIME jre/lib/endorsed folder. The code references CDK 1.4.19 and I have also placed the corresponding jar file into the same directory. I do not have CDK node extensions installed in KNIME and using them is also not an option in my case.
The code starts with:
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
SmilesParser sp= new SmilesParser(builder);
When I try to execute JavaSnippet I get the following exception message:
Evaluation of java snippet failed for row "Row0". Exception message: Could not initialize class org.openscience.cdk.smiles.SmilesParser
I have read the forum and I know that some other people had the same problem(http://tech.knime.org/forum/knime-general/using-external-jar-in-java-snippet-node-workflow-not-able-to-initialize-class-of) but it was of little help.
When I just try
IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
It works and I get no exception message. I have checked, the builder is not a null. However, when I try to initialize SmilesParser, it fails. This class is public. It has no default constructor and has one public constructor that takes IChemObjectBuilder as a parameter.
I have tried to use class loader:
URL[] classLoaderUrls = new URL[]{new URL("file:///path on my computer/knime_2.9.4/jre/lib/endorsed/cdk-1.4.19.jar")};
URLClassLoader urlClassLoader = new URLClassLoader(classLoaderUrls);
Class<?> parserClass = urlClassLoader.loadClass("org.openscience.cdk.smiles.SmilesParser");
Class[] classParameters = new Class[] {IChemObjectBuilder.class};
Constructor<?> constructor = parserClass.getConstructor(classParameters); //until this line there are no problems
Object parser = constructor.newInstance(builder); //fails here with the same exception message: Could not initialize class org.openscience.cdk.smiles.SmilesParser
I am sure that this is not a CDK error because I can execute the code in Eclipse.
Why can a constructor of one class be called from KNIME without any problems and a constructor of another class can not?
I would be very grateful if you could suggest a solution or a probable reason why this exception occurs.
Thank you!
Maria