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

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Here is the source code for edu.scripps.fl.pubchem.xml.extract.AssayExtractor.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.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.List;

import org.apache.commons.beanutils.BeanUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.CellStyle;
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.Assay;

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

    public void fillAssayExcelTemplate(ExcelTableModel model, Assay assay)
            throws IllegalAccessException, InvocationTargetException, NoSuchMethodException {
        model.setSheet("Assay");
        model.setUseFirstRowAsColumnHeadings(false);
        String[] tags = { "AID", "Name", "External Reg Id", "Grant Number", "Project Category", "Hold Until Date",
                "Activity Outcome Method", "Source" };
        Integer count = tags.length;

        for (int ii = 0; ii < count; ii++) {
            model.setValueAt(tags[ii], ii, 0);
            String property = StringUtils.uncapitalize(tags[ii].replaceAll(" ", ""));
            if (tags[ii].equals("AID"))
                property = property.toLowerCase();
            if (property.equals("holdUntilDate"))
                model.setValueAt(assay.getHoldUntilDate(), ii, 1);
            else {
                Object value = BeanUtils.getProperty(assay, property);
                model.setValueAt(value, ii, 1);
            }
        }
        List<String> descriptionS = assay.getDescription();
        putStringListInModel(model, descriptionS, count, "Description");

        List<String> protocolS = assay.getProtocol();
        count = count + descriptionS.size();
        putStringListInModel(model, protocolS, count, "Protocol");

        List<String> commentS = assay.getComment();
        count = count + protocolS.size();
        putStringListInModel(model, commentS, count, "Comment");

        //      Sheet sheet = model.getSheet();
        //      for(int ii = 0; ii <= model.getColumnCount(); ii++)
        //         sheet.autoSizeColumn(ii);
    }

    private void putStringListInModel(ExcelTableModel model, List<String> strings, Integer count, String name) {
        for (int hh = 0; hh < strings.size(); hh++) {
            String ss = strings.get(hh);
            Integer row = hh + count;
            model.setValueAt(name, row, 0);
            model.setValueAt(ss, row, 1);
            Cell cell = model.getCellAt(row, 1);
            CellStyle style = cell.getCellStyle();
            style.setWrapText(true);
            cell.setCellStyle(style);
        }
    }

    public Assay getAssayValuesFromXML(Document doc)
            throws ParseException, IllegalAccessException, InvocationTargetException {
        Assay assay = new Assay();
        PubChemXMLUtils utils = new PubChemXMLUtils();

        utils.getElementText(assay, "//PC-DBTracking_source-id/Object-id/Object-id_str", doc, "externalRegId");
        utils.getElementText(assay, "//PC-AssayDescription_name", doc, "name");
        utils.getListofElementsText(assay, "//PC-AssayDescription_description_E", doc, "description");
        utils.getListofElementsText(assay, "//PC-AssayDescription_protocol_E", doc, "protocol");
        utils.getListofElementsText(assay, "//PC-AssayDescription_comment_E", doc, "comment");
        utils.getElementText(assay, "//PC-ID_id", doc, "aid");
        utils.getElementText(assay, "//PC-AssayDescription_grant-number_E", doc, "grantNumber");
        utils.getElementText(assay, "//PC-DBTracking_name", doc, "source");

        String attribute = utils.getElementAttribute("//PC-AssayDescription_activity-outcome-method", doc);
        if (!attribute.equals(""))
            assay.setActivityOutcomeMethod(attribute);
        attribute = utils.getElementAttribute("//PC-AssayDescription_project-category", doc);
        if (!attribute.equals(""))
            assay.setProjectCategory(attribute);
        Node node = doc.selectSingleNode("//PC-DBTracking_date/Date/Date_std/Date-std");
        if (node != null)
            assay.setHoldUntilDate(
                    new SimpleDateFormat("MM/dd/yyyy").parse(node.selectSingleNode("Date-std_month").getText() + "/"
                            + node.selectSingleNode("Date-std_day").getText() + "/"
                            + node.selectSingleNode("Date-std_year").getText()));

        return assay;
    }

}