/**
 *
 * C O P Y R I G H T   N O T I C E
 *  Copyright (c) 2001 by:
 *    * The MicroArray Gene Expression Database group (MGED)
 *    * Rosetta Inpharmatics
 * 
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation files
 * (the "Software"), to deal in the Software without restriction,
 * including without limitation the rights to use, copy, modify, merge,
 * publish, distribute, sublicense, and/or sell copies of the Software,
 * and to permit persons to whom the Software is furnished to do so,
 * subject to the following conditions:
 * 
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * 
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
 * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
 * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 *
 *
 * @author $Author: rhubley $
 * @version $Revision: 1.6 $
 *
 */
package org.biomage.tools.generate_dtd;

import java.util.Vector;

import org.biomage.tools.generate_classes.CreateClassFile;
import org.biomage.tools.generate_classes.CreateFile;
import org.biomage.tools.helpers.StringOutputHelpers;
import org.biomage.tools.generate_classes.XMIParseHelpers;

import org.w3c.dom.*;

/**
 * <b>Description:</b>
 *      Class that is resposible for transforming the class list passed in.
 *      Modifies the BioAssayData classes to better capture the data in XML.
 */
public
class
TransformBioAssayData implements WriteDTDFile.CreateClassTransformer
{
    /**
     * <b>Description:</b>
     *      Transform the BioAssayData class for producing modified DTD for its 
     *      associations and attributes.
     *
     *      NOTE: The transformation modifies the list itself
     *
     *      Modified 7/14/02 to change the transform so that the dimensions were
     *      note moved (MAGE issue 11) --mm
     *
     *<p>
     *  @param createFileList: the list of CreateFiles to transform.
     *<p>
     */
    public 
    void
    transform(
        Vector createFileList
    ) throws Exception
    {
        // There are four create class files to find
        CreateClassFile bioAssayData   = null;
        CreateClassFile bioDataCube    = null;
        CreateClassFile bioDataTuples  = null;
        CreateClassFile bioAssayDatum  = null;
        
        for (int i = createFileList.size() - 1; -1 < i; i--)
        {
            CreateFile createFile = (CreateFile) createFileList.get(i);
            if ( "BioAssayData".equals(createFile.getClassFileName()) &&
                 CreateFile.UML_CLASS == createFile.getFileType() )
            {
                StringOutputHelpers.writeOutput("Transform found BioAssayData class.", 3);
                bioAssayData = (CreateClassFile) createFile;
            }
            else if ( "BioDataCube".equals(createFile.getClassFileName()) )
            {
                StringOutputHelpers.writeOutput("Transform found bioDataCube class.", 3);
                bioDataCube = (CreateClassFile) createFile;
            }
            else if ( "BioDataTuples".equals(createFile.getClassFileName()) )
            {
                StringOutputHelpers.writeOutput("Transform found BioDataTuples class.", 3);
                bioDataTuples = (CreateClassFile) createFile;
            }
            else if ( "BioAssayDatum".equals(createFile.getClassFileName()) )
            {
                StringOutputHelpers.writeOutput("Transform found BioAssayDatum class.", 3);
                bioAssayDatum = (CreateClassFile) createFile;
                createFileList.remove(i);
            }
            else if ( "HasBioAssayDatum".equals(createFile.getClassFileName()) )
            {
                StringOutputHelpers.writeOutput("Transform found HasBioAssayDatum class.", 3);
                createFileList.remove(i);
            }
        }
        
        if (null == bioAssayData || null == bioDataCube || null == bioDataTuples || null == bioAssayDatum)
        {
            // throw new Exception("TransformBioAssayData.transform(): Did not find expected CreateFiles to transform.");
            StringOutputHelpers.writeOutput("TransformBioAssayData.transform(): Did not find expected CreateFiles to transform.", 3);
            return;
        }
        
        // Obtain and remove the dimension associations from the BioAssayData
        int BIOASSAY_DIM         = 0;
        int DESIGNELEMENT_DIM    = 1;
        int QUANTITATIONTYPE_DIM = 2;
        Vector assns = bioAssayData.getAssociationInfo();
        
        // Go backwards to avoid having remove() disturb the iteration
        for (int i = assns.size() - 1; -1 < i; i--)
        {
            CreateFile.AssociationAttrInformation assn = (CreateFile.AssociationAttrInformation) assns.get(i);
            if ("BioAssayDimension".equals(assn.getOriginalType()))
            {
                assn.makeOptional();
            }
            else if ("DesignElementDimension".equals(assn.getOriginalType()))
            {
                assn.makeOptional();
            }
            else if ("QuantitationTypeDimension".equals(assn.getOriginalType()))
            {
                assn.makeOptional();
            }
        }
        
        // remove the attribute, which is the data cube that is captured in these new elements
        Vector attrs = bioDataCube.getAttrInfo();
        if ( null == attrs || 2 != attrs.size() ||
             (!"cube".equals(((CreateFile.AttrInformation) attrs.get(0)).getName()) && 
              !"order".equals(((CreateFile.AttrInformation) attrs.get(1)).getName())))
        {
            throw new Exception("TransformBioAssayData.transform(): bioDataCube has unexpected attributes.");
        }
        attrs.remove(0);
        
        // Create the new classes for the Cube
        String comment = "Transformed class to associate whitespaced delimited data to the BioAssayDataCube";
        CreateClassFile dataInternal = new CreateClassFile("DataInternal", "BioAssayData", comment, XMIParseHelpers.COMPOSITE);
        
        comment = "Transformed class to associate external data to the BioAssayDataCube";
        CreateClassFile dataExternal = new CreateClassFile("DataExternal", "BioAssayData", comment, XMIParseHelpers.COMPOSITE);
     
        // add them to the cube
        comment = "Transformed class to associate white spaced delimited data to the BioAssayDataCube";
        bioDataCube.addAssociation("dataInternal", "private", "dataInternal", comment, 1, 1, 1, 1, 
                                    XMIParseHelpers.COMPOSITE, false, new Integer(2), false, false, 
				   true, true);	// these are bogus
        comment = "Transformed class to associate external data to the BioAssayDataCube";
        dataInternal.addRoleName("dataInternal", 1, XMIParseHelpers.COMPOSITE);
        
        bioDataCube.addAssociation("dataExternal", "private", "DataExternal", comment, 1, 1, 1, 1, 
                                    XMIParseHelpers.COMPOSITE, false, new Integer(2), false, false, 
				   true, true);	// these are bogus

        dataExternal.addRoleName("dataExternal", 1, XMIParseHelpers.COMPOSITE);
    
        // Finish off the Internal data
        comment = "The tab delimited data.";
        dataInternal.addAssociation("#PCDATA", "private", "#PCDATA", comment, 1, 1, 1, 1, 
                                    XMIParseHelpers.COMPOSITE, false, new Integer(2), false, false,
				    true, true); // these are bogus
    
        // Finish off the External Data
        comment = "The format of the external file, whitespace delimited, tab delimited, netcdf, etc...";
        dataExternal.addAttribute("dataFormat", "private", "String", comment, "whitespace", true);
        
        comment = "Location for documentation on the data format";
        dataExternal.addAttribute("dataFormatInfoURI", "private", "String", comment, null, false);
        
        comment = "The name and location of the file containing the external data";
        dataExternal.addAttribute("filenameURI", "private", "String", comment, null, true);
        
        // Move the dimension associations out of the BioAssayData and into the Tuples
        assns = bioDataTuples.getAssociationInfo();
        if ( null == assns || 1 != assns.size() ||
             !"BioAssayDatum".equals(((CreateFile.AssociationAttrInformation) assns.get(0)).getOriginalType()) )
        {
            throw new Exception("TransformBioAssayData.transform(): BioDataTuples has unexpected associations.");
        }
        
        assns.remove(0);
        
        // From BioAssayDatum, get the tuple associations to hand off to the new classes
        // Obtain and remove the dimension associations from the BioAssayData
        assns = bioAssayDatum.getAssociationInfo();
        CreateFile.AssociationAttrInformation dims[] = new CreateFile.AssociationAttrInformation[3];
        
        for (int i = assns.size() - 1; -1 < i; i--)
        {
            CreateFile.AssociationAttrInformation assn = (CreateFile.AssociationAttrInformation) assns.get(i);
            if ("BioAssay".equals(assn.getOriginalType()))
            {
                dims[BIOASSAY_DIM] = assn;
            }
            else if ("DesignElement".equals(assn.getOriginalType()))
            {
                dims[DESIGNELEMENT_DIM] = assn;
            }
            else if ("QuantitationType".equals(assn.getOriginalType()))
            {
                dims[QUANTITATIONTYPE_DIM] = assn;
            }
        }
        
        // create the new classes for the BioDataTuples
        comment = "Transformed container to hold a value.  QuantitationType will " +
                  "determine the type of this value.";
        CreateClassFile datum = new CreateClassFile("Datum", "BioAssayData", comment, XMIParseHelpers.COMPOSITE);
        comment = "Value for the BioAssay, DesignElement and QuantitationType specified by the " +
                  "parent tuple elements.";
        datum.addAttribute("value", "private", "any", comment, null, true);
        
        comment = "Transformed container to specify a Quantitation Type and the value for that Type.";
        CreateClassFile qtTuple = new CreateClassFile("QuantitationTypeTuple", "BioAssayData", comment, XMIParseHelpers.COMPOSITE);
        qtTuple.addAssociation(dims[QUANTITATIONTYPE_DIM], new Integer(1), 
			       1, 1, 
			       1, 1, // these are bogus
			       true, true); // these are bogus

        
        comment = "The value to associate with the Quantitation Type.";
        qtTuple.addAssociation("datum", "private", "Datum", comment, 1, 1, 
			       1, 1, // these are bogus 
                               XMIParseHelpers.COMPOSITE, false, 
			       new Integer(2), false, false,
			       true, true); // these are bogus

        datum.addRoleName("datum", 1, XMIParseHelpers.COMPOSITE);

        comment = "Transformed container to specify a DesignElement and QuantitationTypes for that Element.";
        CreateClassFile deTuple = new CreateClassFile("DesignElementTuple", "BioAssayData", comment, XMIParseHelpers.COMPOSITE);
        deTuple.addAssociation(dims[DESIGNELEMENT_DIM], new Integer(1), 1, 1, 
			       1, 1, // these are bogus
			       true, true); // these are bogus
        
        comment = "A QuantitationType and the value associated with it";
        deTuple.addAssociation("quantitationTypeTuples", "private", 
			       "QuantitationTypeTuple", comment, 1, -1, 
			       0, 0, // these are bogus
                               XMIParseHelpers.COMPOSITE, false, 
			       new Integer(2), false, false,
			       true, true); // these are bogus
        qtTuple.addRoleName("quantitationTypeTuples", -1, XMIParseHelpers.COMPOSITE);
        
        comment = "Transformed container to specify a BioAssay and the Design Elements and their data for " +
                  "that BioAssay.";
        CreateClassFile baTuple = new CreateClassFile("BioAssayTuple", "BioAssayData", comment, XMIParseHelpers.COMPOSITE);
        baTuple.addAssociation(dims[BIOASSAY_DIM], new Integer(1), 1, 1, 1, 1,
			       true, true); // these are bogus
        comment = "DesignElement with the QuantitationTypes and their values for this BioAssay";
        baTuple.addAssociation("designElementTuples", "private", 
			       "DesignElementTuple", comment, 1, -1, 
			       0, 0, // these are bogus
                               XMIParseHelpers.COMPOSITE, false, 
			       new Integer(2), false, false,
			       true, true); // these are bogus
        deTuple.addRoleName("designElementTuples", -1, XMIParseHelpers.COMPOSITE);
        
        comment = "Each BioAssayTuple contains the the Data for a BioAssay.";
        bioDataTuples.addAssociation("bioAssayTuples", "private", 
				     "BioAssayTuple", comment, 0, -1, 
				     0, 0, // these are bogus
				     XMIParseHelpers.COMPOSITE, false, 
				     new Integer(4), false, false,
			       true, true); // these are bogus
        baTuple.addRoleName("bioAssayTuples", -1, XMIParseHelpers.COMPOSITE);
        
        createFileList.add(dataInternal);
        createFileList.add(dataExternal);
        createFileList.add(baTuple);
        createFileList.add(deTuple);
        createFileList.add(qtTuple);
        createFileList.add(datum);
    }
}