org.biopax.validator.impl.ExceptionsAspect.java Source code

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Here is the source code for org.biopax.validator.impl.ExceptionsAspect.java

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package org.biopax.validator.impl;

/*
 * #%L
 * BioPAX Validator
 * %%
 * Copyright (C) 2008 - 2013 University of Toronto (baderlab.org) and Memorial Sloan-Kettering Cancer Center (cbio.mskcc.org)
 * %%
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as 
 * published by the Free Software Foundation, either version 3 of the 
 * License, or (at your option) any later version.
 * 
 * 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 Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU General Lesser Public 
 * License along with this program.  If not, see
 * <http://www.gnu.org/licenses/lgpl-3.0.html>.
 * #L%
 */

import java.lang.reflect.Method;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.aspectj.lang.JoinPoint;
import org.aspectj.lang.ProceedingJoinPoint;
import org.aspectj.lang.annotation.*;
import org.springframework.beans.factory.annotation.Configurable;
import org.biopax.paxtools.controller.PropertyEditor;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler.Triple;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.Model;
import org.biopax.validator.api.AbstractAspect;

/**
 * This is the central aspect to report 
 * all the validation exceptions together with 
 * external exceptions that may happen in the PaxTools
 * and other libraries. 
 *
 * @author rodche
 */
@Configurable
@Aspect
public class ExceptionsAspect extends AbstractAspect {

    private static final Log log = LogFactory.getLog(ExceptionsAspect.class);

    /**
     * This captures the exceptions that occur 
     * during the model build and, more important,
     * associates the just created model
     * with the corresponding validation result
     * (this is the earliest possibility to do so)!
     * 
     * @param jp
     */
    @Around("execution(void org.biopax.paxtools.io.SimpleIOHandler.createAndBind(*)) " + "&& args(model)")
    public void adviseCreateAndBind(ProceedingJoinPoint jp, Model model) {
        SimpleIOHandler reader = (SimpleIOHandler) jp.getTarget();

        // associate the model with the reader (and validation results)
        validator.indirectlyAssociate(reader, model);

        try {
            jp.proceed();
        } catch (Throwable ex) {
            reportException(ex, reader, "syntax.error", "SimpleIOHandler.createAndBind interceptor", null);
        }
    }

    @Around("execution(* org.biopax.paxtools.io.SimpleIOHandler.processIndividual(*)) " + "&& args(model)")
    public String adviseProcessIndividual(ProceedingJoinPoint jp, Model model) {
        String id = null;
        SimpleIOHandler reader = (SimpleIOHandler) jp.getThis();

        try {
            id = (String) jp.proceed();
        } catch (Throwable ex) {
            reportException(ex, reader, "syntax.error", "SimpleIOHandler.processIndividual interceptor", null);
        }
        return id;
    }

    @Around("execution(private void org.biopax.paxtools.io.SimpleIOHandler.bindValue(..))"
            + " && args(triple, model)")
    public void adviseBindValue(ProceedingJoinPoint jp, Triple triple, Model model) {
        if (log.isDebugEnabled())
            log.debug("adviseBindValue, triple: " + triple);

        SimpleIOHandler reader = (SimpleIOHandler) jp.getTarget();
        // try to find the best object to report about...
        Object o = reader;
        BioPAXElement el = model.getByID(triple.domain);
        if (el != null) {
            o = el;
            PropertyEditor<?, ?> editor = reader.getEditorMap().getEditorForProperty(triple.property,
                    el.getModelInterface());
            if (editor == null) {
                // auto-fix (for some)
                if (triple.property.equals("taxonXref")) {
                    report(el, "unknown.property", "SimpleIOHandler.bindValue interceptor", true,
                            triple.property + " - replaced with 'xref'");
                    triple.property = "xref";
                } else {
                    report(el, "unknown.property", "SimpleIOHandler.bindValue interceptor", false,
                            triple.property + " - skipped");
                }
            }
        }

        try {
            jp.proceed();
        } catch (Throwable t) {
            reportException(t, o, "syntax.error", "SimpleIOHandler.bindValue interceptor", triple.toString());
        }
    }

    @Around("execution(protected void org.biopax.paxtools.controller.PropertyEditor*+.checkRestrictions(..)) "
            + "&& args(value, bean)")
    public void adviseCheckRestrictions(ProceedingJoinPoint jp, Object value, BioPAXElement bean) {
        try {
            jp.proceed();
        } catch (Throwable ex) {
            reportException(ex, bean, "syntax.error", "PropertyEditor.checkRestrictions interceptor",
                    String.valueOf(value));
        }
    }

    @Around("execution(protected void org.biopax.paxtools.controller.PropertyEditor*+.invokeMethod(..)) "
            + "&& args(method, bean, value)")
    public void adviseInvokeMethod(ProceedingJoinPoint jp, Method method, BioPAXElement bean, Object value) {
        try {
            jp.proceed();
        } catch (Throwable ex) {
            reportException(ex, bean, "syntax.error", "PropertyEditor.invokeMethod interceptor",
                    "method: " + method + ", value: " + value);
        }
    }

    @Around("execution(* org.biopax.paxtools.io.BioPAXIOHandler*+.convertFromOWL(*))")
    public Object adviseConvertFromOwl(ProceedingJoinPoint jp) {
        Object model = null;
        try {
            model = jp.proceed();
        } catch (Throwable ex) {
            reportException(ex, jp.getTarget(), "syntax.error", "BioPAXIOHandler.convertFromOWL interceptor", null);
        }

        return model;
    }

    @Before("execution(* org.biopax.paxtools.io.SimpleIOHandler.skip(..))")
    public void adviseUnknownClass(JoinPoint jp) {
        SimpleIOHandler reader = (SimpleIOHandler) jp.getTarget();
        String loc = reader.getXmlStreamInfo();
        report(reader, "unknown.class", "SimpleIOHandler.skip interceptor", false, loc);
    }

}