edu.scripps.fl.pubchem.xml.extract.CategorizedCommentExtractor.java Source code

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Here is the source code for edu.scripps.fl.pubchem.xml.extract.CategorizedCommentExtractor.java

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/*
 * Copyright 2010 The Scripps Research Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.scripps.fl.pubchem.xml.extract;

import java.util.ArrayList;
import java.util.List;
import java.util.Map;

import org.apache.commons.beanutils.BeanUtils;
import org.dom4j.Document;
import org.dom4j.Node;

import com.googlecode.exceltablemodel.ExcelTableModel;

import edu.scripps.fl.pubchem.xml.PubChemXMLUtils;
import edu.scripps.fl.pubchem.xml.model.CategorizedComment;

public class CategorizedCommentExtractor {

    public void fillCategorizedCommentExcelTemplate(ExcelTableModel model, List<CategorizedComment> cComments)
            throws Exception {
        model.setSheet("Categorized Comments");
        Map<Integer, String> map = new XMLExtractor().getColumnsMap(model);
        String[] categorizedCommentsProps = { "commentTag", "commentValue" };
        for (int ii = 0; ii <= cComments.size() - 1; ii++) {
            CategorizedComment cComment = cComments.get(ii);
            for (String property : categorizedCommentsProps) {
                for (int jj = 0; jj <= map.size() - 1; jj++) {
                    if (property.equalsIgnoreCase(map.get(jj)))
                        model.setValueAt(BeanUtils.getProperty(cComment, property), ii, jj);
                }
            }
        }
    }

    public List<CategorizedComment> getCategorizedCommentsFromXML(Document doc) throws Exception {
        List<CategorizedComment> comments = new ArrayList<CategorizedComment>();
        List<Node> nodes = doc.selectNodes("//PC-AssayDescription_categorized-comment/PC-CategorizedComment");
        PubChemXMLUtils utils = new PubChemXMLUtils();
        for (Node nn : nodes) {
            CategorizedComment comment = new CategorizedComment();
            comment.setCommentTag(nn.selectSingleNode("PC-CategorizedComment_title").getText());
            List<Node> valueNodes = nn.selectNodes("PC-CategorizedComment_comment/PC-CategorizedComment_comment_E");
            String text = "";
            for (Node valeuNode : valueNodes) {
                if (null != valeuNode.getText())
                    text = text + valeuNode.getText() + "\n";
            }
            comment.setCommentValue(text);
            comments.add(comment);
        }
        return comments;
    }

}