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* Add RDKitRuntimeExceptionHandler class to allow RDKit version before 4.1 or after 4.1 to work seemlessly
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...nalis.knime.chem.core/src/com/vernalis/knime/chem/rdkit/RDKitRuntimeExceptionHandler.java
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| /******************************************************************************* | ||
| * Copyright (c) 2020, Vernalis (R&D) Ltd | ||
| * This program is free software; you can redistribute it and/or modify it | ||
| * under the terms of the GNU General Public License, Version 3, as | ||
| * published by the Free Software Foundation. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, but | ||
| * WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | ||
| * See the GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program; if not, see <http://www.gnu.org/licenses> | ||
| ******************************************************************************/ | ||
| package com.vernalis.knime.chem.rdkit; | ||
|
|
||
| import java.lang.reflect.InvocationTargetException; | ||
| import java.lang.reflect.Method; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
||
| import org.RDKit.AtomKekulizeException; | ||
| import org.RDKit.AtomSanitizeException; | ||
| import org.RDKit.AtomValenceException; | ||
| import org.RDKit.ChemicalReactionException; | ||
| import org.RDKit.ChemicalReactionParserException; | ||
| import org.RDKit.ConformerException; | ||
| import org.RDKit.GenericRDKitException; | ||
| import org.RDKit.KekulizeException; | ||
| import org.RDKit.KeyErrorException; | ||
| import org.RDKit.MolPicklerException; | ||
| import org.RDKit.MolSanitizeException; | ||
| import org.RDKit.MolSanitizeException_Vect; | ||
| import org.RDKit.SmilesParseException; | ||
|
|
||
| /** | ||
| * This class wraps RDKit {@link RuntimeException}s and obtains the message via | ||
| * reflection from either the {@code message} or {@code what} methods. If | ||
| * neither method is found, it falls back on the standard {@link #getMessage()} | ||
| * method. The original 'cause' RDKit exception is available via | ||
| * {@link #getCause()} | ||
| * | ||
| * @author S.Roughley knime@vernalis.com | ||
| * @since com.vernalis.knime.chem.core 1.27.4 | ||
| */ | ||
| @SuppressWarnings("serial") | ||
| public class RDKitRuntimeExceptionHandler extends RuntimeException { | ||
|
|
||
| // The following from RDKitExceptions.i | ||
| /** | ||
| * Constructor from {@link ChemicalReactionException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(ChemicalReactionException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link ChemicalReactionParserException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(ChemicalReactionParserException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link ConformerException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(ConformerException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link MolPicklerException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(MolPicklerException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link MolSanitizeException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(MolSanitizeException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link SmilesParseException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(SmilesParseException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link KeyErrorException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(KeyErrorException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link GenericRDKitException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(GenericRDKitException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| // The following subclasses of MolSanitizeException are defined in | ||
| // SanitException.i | ||
| /** | ||
| * Constructor from {@link AtomSanitizeException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(AtomSanitizeException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link AtomValenceException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(AtomValenceException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link AtomKekulizeException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(AtomKekulizeException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| /** | ||
| * Constructor from {@link KekulizeException} | ||
| * | ||
| * @param e | ||
| * The cause | ||
| */ | ||
| public RDKitRuntimeExceptionHandler(KekulizeException e) { | ||
| this((RuntimeException) e); | ||
| } | ||
|
|
||
| private RDKitRuntimeExceptionHandler(RuntimeException cause) { | ||
| super(getRDKitMessage(cause), cause); | ||
|
|
||
| } | ||
|
|
||
| /** | ||
| * @return The class of the initial RDKit Exception | ||
| */ | ||
| public Class<?> getRDKitExceptionClass() { | ||
| return getCause().getClass(); | ||
| } | ||
|
|
||
| private static String getRDKitMessage(RuntimeException cause) { | ||
| Class<?> clazz = cause.getClass(); | ||
| String msg = null; | ||
| Method mtd = null; | ||
| methodloop: for (Method m : clazz.getMethods()) { | ||
| switch (m.getName()) { | ||
| case "what": | ||
| case "message": | ||
| mtd = m; | ||
| break methodloop; | ||
| default: | ||
| // Nothing to do | ||
| } | ||
| } | ||
| if (mtd != null) { | ||
| mtd.setAccessible(true); | ||
| try { | ||
| msg = (String) mtd.invoke(cause); | ||
| } catch (ClassCastException | IllegalAccessException | ||
| | IllegalArgumentException | InvocationTargetException e) { | ||
| // Do nothing | ||
| } | ||
| } | ||
| if (msg == null) { | ||
| msg = cause.getMessage(); | ||
| } | ||
| return msg; | ||
| } | ||
|
|
||
| /** | ||
| * Static factory method to handle {@link MolSanitizeException_Vect} | ||
| * | ||
| * @param msev | ||
| * The cause vector | ||
| * @return A List of handlers for the individual | ||
| * {@link MolSanitizeException}s | ||
| */ | ||
| public static List<RDKitRuntimeExceptionHandler> | ||
| fromMolSanitizeExceptionVect(MolSanitizeException_Vect msev) { | ||
| List<RDKitRuntimeExceptionHandler> retVal = new ArrayList<>(); | ||
| for (int i = 0; i < msev.size(); i++) { | ||
| retVal.add(new RDKitRuntimeExceptionHandler(msev.get(i))); | ||
| } | ||
| return retVal; | ||
| } | ||
| } |
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