eu.eubrazilcc.lvl.core.xml.ESearchXmlBinder.java Source code

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Here is the source code for eu.eubrazilcc.lvl.core.xml.ESearchXmlBinder.java

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/*
 * Copyright 2014 EUBrazilCC (EU?Brazil Cloud Connect)
 * 
 * Licensed under the EUPL, Version 1.1 or - as soon they will be approved by 
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at:
 * 
 *   http://ec.europa.eu/idabc/eupl
 * 
 * Unless required by applicable law or agreed to in writing, software 
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing permissions and 
 * limitations under the Licence.
 * 
 * This product combines work with different licenses. See the "NOTICE" text
 * file for details on the various modules and licenses.
 * The "NOTICE" text file is part of the distribution. Any derivative works
 * that you distribute must include a readable copy of the "NOTICE" text file.
 */

package eu.eubrazilcc.lvl.core.xml;

import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkState;
import static com.google.common.base.Predicates.notNull;
import static com.google.common.collect.FluentIterable.from;
import static com.google.common.collect.Lists.newArrayList;
import static org.apache.commons.lang.StringUtils.trimToNull;

import java.util.List;

import javax.xml.bind.JAXBElement;

import com.google.common.base.Function;

import eu.eubrazilcc.lvl.core.xml.ncbi.esearch.Count;
import eu.eubrazilcc.lvl.core.xml.ncbi.esearch.ESearchResult;
import eu.eubrazilcc.lvl.core.xml.ncbi.esearch.Id;
import eu.eubrazilcc.lvl.core.xml.ncbi.esearch.IdList;
import eu.eubrazilcc.lvl.core.xml.ncbi.esearch.ObjectFactory;

/**
 * NCBI Entrez ESearch XML binding helper.
 * @author Erik Torres <ertorser@upv.es>
 */
public class ESearchXmlBinder extends XmlBinder {

    private static final Class<?>[] SUPPORTED_CLASSES = { ESearchResult.class };

    public static final ObjectFactory ESEARCH_XML_FACTORY = new ObjectFactory();

    public static final ESearchXmlBinder ESEARCH_XMLB = new ESearchXmlBinder();

    private ESearchXmlBinder() {
        super(SUPPORTED_CLASSES);
    }

    @Override
    @SuppressWarnings("unchecked")
    protected <T> JAXBElement<T> createType(final T obj) {
        Object element = null;
        Class<? extends Object> clazz = obj.getClass();
        if (clazz.equals(ESearchResult.class)) {
            element = ESEARCH_XML_FACTORY.createESearchResult();
        } else {
            throw new IllegalArgumentException("Unsupported type: " + clazz.getCanonicalName());
        }
        return (JAXBElement<T>) element;
    }

    public static int getCount(final ESearchResult result) {
        checkArgument(result != null, "Uninitialized result");
        int count = -1;
        final List<Object> elements = result
                .getCountOrRetMaxOrRetStartOrQueryKeyOrWebEnvOrIdListOrTranslationSetOrTranslationStackOrQueryTranslationOrERROR();
        if (elements != null) {
            for (int i = 0; i < elements.size() && count < 0; i++) {
                if (elements.get(i) instanceof Count) {
                    count = Integer.parseInt(((Count) elements.get(i)).getvalue());
                }
            }
        }
        checkState(count >= 0, "Count node not found");
        return count;
    }

    public static List<String> getIds(final ESearchResult result) {
        checkArgument(result != null, "Uninitialized result");
        List<String> ids = null;
        final List<Object> elements = result
                .getCountOrRetMaxOrRetStartOrQueryKeyOrWebEnvOrIdListOrTranslationSetOrTranslationStackOrQueryTranslationOrERROR();
        if (elements != null) {
            for (int i = 0; i < elements.size() && ids == null; i++) {
                if (elements.get(i) instanceof IdList) {
                    ids = from(((IdList) elements.get(i)).getId()).transform(new Function<Id, String>() {
                        @Override
                        public String apply(final Id id) {
                            return id != null ? trimToNull(id.getvalue()) : null;
                        }
                    }).filter(notNull()).toList();
                }
            }
        }
        if (ids == null) {
            ids = newArrayList();
        }
        return ids;
    }

}