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

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Here is the source code for edu.scripps.fl.pubchem.xml.extract.ResultTidExtractor.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.lang.reflect.InvocationTargetException;
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.model.ResultTid;

/*
 * @author S Canny (scanny at scripps dot edu)
 */
public class ResultTidExtractor {

    public void fillTidExcelTemplate(ExcelTableModel model, List<ResultTid> tidValues)
            throws IllegalAccessException, InvocationTargetException, NoSuchMethodException {
        model.setSheet("Tids");
        Map<Integer, String> map = new XMLExtractor().getColumnsMap(model);
        String[] tidProperties = { "tidName", "tidDescription", "tidType", "tidUnit", "tidConcentration", "tidPlot",
                "tidPanelNum", "tidPanelReadout", "isActiveConcentration" };
        for (int ii = 0; ii <= tidValues.size() - 1; ii++) {
            ResultTid tidValue = tidValues.get(ii);
            for (String property : tidProperties) {
                for (int jj = 0; jj <= map.size() - 1; jj++) {
                    if (property.equalsIgnoreCase(map.get(jj)))
                        model.setValueAt(BeanUtils.getProperty(tidValue, property), ii, jj);
                }
            }
        }
        new XMLExtractor().autoSizeSheet(model);
    }

    public List<ResultTid> getTidValuesFromXML(Document doc)
            throws IllegalAccessException, InvocationTargetException {

        List<ResultTid> tidValues = new ArrayList<ResultTid>();
        List<Node> nodes = doc.selectNodes("//PC-AssayDescription_results/PC-ResultType");
        for (Node nn : nodes) {
            ResultTid tidValue = new ResultTid();
            tidValue.setTidName(nn.selectSingleNode("PC-ResultType_name").getText());
            tidValue.setTidType(nn.selectSingleNode("PC-ResultType_type").valueOf("@value"));
            Node node = nn.selectSingleNode("PC-ResultType_unit");
            if (node != null)
                tidValue.setTidUnit(node.valueOf("@value"));
            node = nn.selectSingleNode("PC-ResultType_description/PC-ResultType_description_E");
            if (node != null)
                tidValue.setTidDescription(node.getText());
            node = nn.selectSingleNode("PC-ResultType_ac");
            if (node != null)
                tidValue.setIsActiveConcentration(true);
            node = nn.selectSingleNode("PC-ResultType_tc");
            if (node != null) {
                Node node2 = node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_dr-id");
                if (node2 != null) {
                    BeanUtils.setProperty(tidValue, "tidPlot", node2.getText());
                }
                BeanUtils.setProperty(tidValue, "tidConcentration",
                        node.selectSingleNode("PC-ConcentrationAttr/PC-ConcentrationAttr_concentration").getText());
            }
            node = nn.selectSingleNode("PC-ResultType_panel-info/PC-AssayPanelTestResult");
            if (node != null) {
                BeanUtils.setProperty(tidValue, "tidPanelNum",
                        node.selectSingleNode("PC-AssayPanelTestResult_mid").getText());
                tidValue.setTidPanelReadout(
                        node.selectSingleNode("PC-AssayPanelTestResult_readout-annot").valueOf("@value"));
            }
            tidValues.add(tidValue);
        }
        return tidValues;
    }

}