From: Rajarshi G. <raj...@us...> - 2006-01-16 00:20:46
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3929/src/org/openscience/cdk/qsar Modified Files: DescriptorEngine.java Log Message: Updated the deserialization of the OWL descriptor dictionary to recognize the correct XOM element, Descriptor, and not IDescriptor. Also updated the DescriptorEngine. Added an extra test to the DictDB test and fixed the DescriptorEngine test Index: DescriptorEngine.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/DescriptorEngine.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- DescriptorEngine.java 15 Jan 2006 19:34:12 -0000 1.25 +++ DescriptorEngine.java 16 Jan 2006 00:20:34 -0000 1.26 @@ -167,10 +167,14 @@ Entry[] dictEntries = dict.getEntries(); String specRef = getSpecRef(identifier); + logger.debug("Got identifier: "+identifier); + logger.debug("Final spec ref: "+specRef); + for (int j = 0; j < dictEntries.length; j++) { - if (!dictEntries[j].getClassName().equals("IDescriptor")) continue; + if (!dictEntries[j].getClassName().equals("Descriptor")) continue; if (dictEntries[j].getID().equals(specRef.toLowerCase())) { Element rawElement = (Element) dictEntries[j].getRawContent(); + assert(rawElement != null); Elements classifications = rawElement.getChildElements("isClassifiedAs", dict.getNS()); for (int i = 0; i < classifications.size(); i++) { @@ -236,7 +240,7 @@ List dictClasses = new ArrayList(); for (int j = 0; j < dictEntries.length; j++) { - if (!dictEntries[j].getClassName().equals("IDescriptor")) continue; + if (!dictEntries[j].getClassName().equals("Descriptor")) continue; if (dictEntries[j].getID().equals(specRef.toLowerCase())) { Element rawElement = (Element) dictEntries[j].getRawContent(); Elements classifications = rawElement.getChildElements("isClassifiedAs", dict.getNS()); @@ -299,7 +303,7 @@ String definition = null; for (int j = 0; j < dictEntries.length; j++) { - if (!dictEntries[j].getClassName().equals("IDescriptor")) continue; + if (!dictEntries[j].getClassName().equals("Descriptor")) continue; if (dictEntries[j].getID().equals(specRef.toLowerCase())) { definition = dictEntries[j].getDefinition(); break; @@ -378,7 +382,7 @@ * @param packageName The name of the package containing the required descriptor * @return A list containing the classes in the specified package */ - private List getDescriptorClassNameByPackage(String packageName) { + private List getDescriptorClassNameByPackage(String packageName) { if (packageName == null || packageName.equals("")) { packageName = "org.openscience.cdk.qsar.descriptors"; @@ -389,6 +393,7 @@ ArrayList classlist = new ArrayList(); for (int i = 0; i < jars.length; i++) { + logger.debug("Looking in "+jars[i]); JarFile j; try { j = new JarFile(jars[i]); @@ -421,10 +426,10 @@ descriptors.add(descriptor); logger.info("Loaded descriptor: ", descriptorName); } catch (ClassNotFoundException exception) { - logger.error("Could not find this IDescriptor: ", descriptorName); + logger.error("Could not find this Descriptor: ", descriptorName); logger.debug(exception); } catch (Exception exception) { - logger.error("Could not load this IDescriptor: ", descriptorName); + logger.error("Could not load this Descriptor: ", descriptorName); logger.debug(exception); } } |