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

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Here is the source code for edu.scripps.fl.pubchem.xml.extract.PanelExtractor.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.HashMap;
import java.util.List;
import java.util.Map;

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

import com.googlecode.exceltablemodel.ExcelTableModel;

import edu.scripps.fl.pubchem.xml.model.Panel;
import edu.scripps.fl.pubchem.xml.model.PanelTarget;

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

    public void fillPanelExcelTemplate(ExcelTableModel model, List<Panel> panelValues) throws Exception {
        model.setSheet("Panel");
        Map<Integer, String> map = new XMLExtractor().getColumnsMap(model);
        String[] panelProperties = { "panelName", "panelGene", "panelTaxonomy" };
        String[] panelTargetProperties = { "panelTargetGi", "panelTargetName", "panelTargetType" };
        for (int ii = 0; ii <= panelValues.size() - 1; ii++) {
            Panel panelValue = panelValues.get(ii);
            List<PanelTarget> panelTargets = panelValue.getPanelTarget();
            if (panelTargets != null && panelTargets.size() > 0) {
                List<Integer> gis = new ArrayList<Integer>();
                List<String> names = new ArrayList<String>();
                List<String> types = new ArrayList<String>();
                for (PanelTarget target : panelTargets) {
                    gis.add(target.getPanelTargetGi());
                    names.add(target.getPanelTargetName());
                    types.add(target.getPanelTargetType());
                }
                Map<String, List<?>> valueMap = new HashMap<String, List<?>>();
                valueMap.put(panelTargetProperties[0], gis);
                valueMap.put(panelTargetProperties[1], names);
                valueMap.put(panelTargetProperties[2], types);
                for (String targetProperty : panelTargetProperties) {
                    for (int kk = 0; kk <= map.size() - 1; kk++) {
                        if (targetProperty.equalsIgnoreCase(map.get(kk))) {
                            model.setValueAt(StringUtils.join(valueMap.get(targetProperty), "|"), ii, kk);
                        }
                    }
                }
            }
            for (String property : panelProperties) {
                for (int jj = 0; jj <= map.size() - 1; jj++) {
                    if (property.equalsIgnoreCase(map.get(jj))) {
                        if (property.equalsIgnoreCase("panelGene"))
                            model.setValueAt(StringUtils.join(panelValue.getPanelGene(), "|"), ii, jj);
                        else if (property == "panelTaxonomy")
                            model.setValueAt(StringUtils.join(panelValue.getPanelTaxonomy(), "|"), ii, jj);
                        else
                            model.setValueAt(BeanUtils.getProperty(panelValue, property), ii, jj);
                    }
                }
            }
        }
        new XMLExtractor().autoSizeSheet(model);
    }

    public List<Panel> getPanelValuesFromXML(Document doc) throws Exception {
        List<Panel> panelValues = new ArrayList<Panel>();
        List<Node> nodes = doc.selectNodes(
                "//PC-AssayDescription_panel-info/PC-AssayPanel/PC-AssayPanel_member/PC-AssayPanelMember");
        for (Node nn : nodes) {
            Panel panelValue = new Panel();
            panelValue.setPanelName(nn.selectSingleNode("PC-AssayPanelMember_name").getText());
            List<Node> targetNodes = nn.selectNodes("PC-AssayPanelMember_target/PC-AssayTargetInfo");
            if (targetNodes != null && targetNodes.size() > 0) {
                List<PanelTarget> targets = new ArrayList<PanelTarget>();
                for (Node targetNode : targetNodes) {
                    PanelTarget target = new PanelTarget();
                    target.setPanelTargetName(targetNode.selectSingleNode("PC-AssayTargetInfo_name").getText());
                    BeanUtils.setProperty(target, "panelTargetGi",
                            targetNode.selectSingleNode("PC-AssayTargetInfo_mol-id").getText());
                    target.setPanelTargetType(
                            targetNode.selectSingleNode("PC-AssayTargetInfo_molecule-type").valueOf("@value"));
                    targets.add(target);
                }
                panelValue.setPanelTarget(targets);
            }

            Node p = nn.selectSingleNode("PC-AssayPanelMember_xref");
            if (p != null) {
                List<Integer> taxonomies = getXrefValues(
                        "PC-AnnotatedXRef/PC-AnnotatedXRef_xref/PC-XRefData/PC-XRefData_taxonomy", p);
                panelValue.setPanelTaxonomy(taxonomies);
                List<Integer> genes = getXrefValues(
                        "PC-AnnotatedXRef/PC-AnnotatedXRef_xref/PC-XRefData/PC-XRefData_gene", p);
                panelValue.setPanelGene(genes);
            }
            panelValues.add(panelValue);
        }
        return panelValues;
    }

    private List<Integer> getXrefValues(String nodeName, Node parent) {
        List<Node> nodes = parent.selectNodes(nodeName);
        List<Integer> list = new ArrayList<Integer>();
        if (nodes != null) {
            for (Node node : nodes)
                list.add(Integer.parseInt(node.getText()));
        }
        return list;
    }
}