Ticket #1303: ScanImporter.java

/**
  $Id: ScanImporter.java 4551 2008-09-29 07:47:24Z nicklas $

  Copyright (C) 2008 Nicklas Nordborg

  This file is part of BASE - BioArray Software Environment.
  Available at http://base.thep.lu.se/

  BASE is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 3
  of the License, or (at your option) any later version.

  BASE is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with BASE. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sf.basedb.plugins.batchimport;

import java.util.Collections;
import java.util.List;
import java.util.Set;

import net.sf.basedb.core.DbControl;
import net.sf.basedb.core.File;
import net.sf.basedb.core.Hardware;
import net.sf.basedb.core.Hybridization;
import net.sf.basedb.core.Image;
import net.sf.basedb.core.Item;
import net.sf.basedb.core.ItemQuery;
import net.sf.basedb.core.Path;
import net.sf.basedb.core.PathParameterType;
import net.sf.basedb.core.PluginParameter;
import net.sf.basedb.core.Protocol;
import net.sf.basedb.core.ProtocolType;
import net.sf.basedb.core.Scan;
import net.sf.basedb.core.SystemItems;
import net.sf.basedb.core.Version;
import net.sf.basedb.core.plugin.About;
import net.sf.basedb.core.plugin.AboutImpl;
import net.sf.basedb.core.plugin.GuiContext;
import net.sf.basedb.util.parser.FlatFileParser;
import net.sf.basedb.util.parser.Mapper;

/**
  Plug-in for importing scan items in a batch. The plug-in can create new 
  items and updated existing items.

  @author nicklas
  @version 2.8
  @base.modified $Date: 2008-09-29 09:47:24 +0200 (Mon, 29 Sep 2008) $
*/
public class ScanImporterNMC
  extends AbstractItemImporter<Scan>
{

  private static final Set<GuiContext> guiContexts =  
    Collections.singleton(new GuiContext(Item.SCAN, GuiContext.Type.LIST));

  private static final About about =
    new AboutImpl
  (
      "Scan importer with images",
      "Imports and updates scans in a batch (linking with images).",
      Version.getMajor() + "." + Version.getMinor() + "." + Version.getMaintenance(),
      "2008, Base 2 development team",
      null,
      null,
      "http://base.thep.lu.se"
  );

  
  protected static final PluginParameter<String> hardwareColumnMapping = new PluginParameter<String>(
      "hardwareColumnMapping",
      "Scanner",
      "Mapping that picks the name or ID of the array slide scanner from the data columns. " +
      "The plug-in will first try to find a scanner with the given name. If none is found and " +
      "the value is numeric it will try to load by internal ID. " +
      "Example: \\Scanner\\",
      optionalColumnMapping
      );

  protected static final PluginParameter<String> hybridizationColumnMapping = new PluginParameter<String>(
      "hybridizationColumnMapping",
      "Hybridization",
      "Mapping that picks the name or ID of the hybridization from the data columns. " +
      "The plug-in will first try to find a hybridization with the given name. If none is found and " +
      "the value is numeric it will try to load by internal ID. " +
      "Example: \\Hybridization\\",
      optionalColumnMapping
      );
  
  // extra parameter needed for linking with image files
  protected static final PluginParameter<String> fileColumnMapping = new PluginParameter<String>(
      "fileColumnMapping",
      "File",
      "Mapping that picks the path of a image file from the columns. " +
      "The path can be an absolute path (starting with /) or relative " +
      "to the 'Data directory' parameter." +
      "Example: \\File\\",
      optionalColumnMapping
      );
  
  public ScanImporterNMC()
  {}

  /*
    From the Plugin interface
    ------------------------------------
  */
  @Override
  public About getAbout()
  {
    return about;
  }
  // ------------------------------------

  /*
    From the InteractivePlugin interface
    ------------------------------------
  */
  @Override
  public Set<GuiContext> getGuiContexts()
  {
    return guiContexts;
  }
  // ------------------------------------

  /*
    From the AbstractItemImporter class
    ------------------------------------
  */
  
  private Mapper nameMapper;
  private Mapper descriptionMapper;
  private Mapper protocolMapper;
  private Mapper hardwareMapper;
  private Mapper hybridizationMapper;
  //extra mappers for linking with image file
  private Mapper fileMapper;
  private String imagesDirectory;
  
  /**
    Useable methods are:
    <ul>
    <li>{@link PropertyIdMethod#NAME}
    <li>{@link InternalIdMethod#INTERNAL_ID}
    <li>{@link FallbackIdMethod#NAME_OR_ID}
    </ul>
  */
  @Override
  protected IdMethod[] getIdMethods()
  {
    return new IdMethod[] { PropertyIdMethod.NAME,  
        InternalIdMethod.INTERNAL_ID, FallbackIdMethod.NAME_OR_ID};
  }
  
  
  /**
  Add parameter for "Image directory" directory where image files may be located. 
   */
  @Override
  protected void addMoreJobParameters(List<PluginParameter<?>> parameters)
  {
    parameters.add(new PluginParameter<String>(
        "imagesDirectory",
        "Images directory",
        "A base directory were image files are located. Relative file paths are " +
        "resolved against this directory. If no directory is given, only absolute " +
        "paths (=paths starting with /) can be used.",
        new PathParameterType(Path.Type.DIRECTORY))
    );
  }

  
  /**
    Adds column mappings for name, externalId, description,
    protocol, creation date, original quantity, pooled, parent
    and used quantity from parent.
  */
  @Override
  protected void addMoreColumnMappingParameters(List<PluginParameter<?>> parameters)
  {
    parameters.add(internalIdColumnMapping);
    parameters.add(nameColumnMapping);
    parameters.add(descriptionColumnMapping);
    parameters.add(hybridizationColumnMapping);
    parameters.add(protocolColumnMapping);
    parameters.add(hardwareColumnMapping);
    parameters.add(fileColumnMapping);
  }
  
  /**
    Calls {@link Scan#getQuery()}.
  */
  @Override
  protected ItemQuery<Scan> createItemQuery()
  {
    return Scan.getQuery();
  }
  
  @Override
  protected void createColumnMappers(FlatFileParser ffp, boolean cropStrings)
  {
    nameMapper = getMapper(ffp, (String)job.getValue("nameColumnMapping"), 
        cropStrings ? Scan.MAX_NAME_LENGTH : null, null);
    descriptionMapper = getMapper(ffp, (String)job.getValue("descriptionColumnMapping"), 
        cropStrings ? Scan.MAX_DESCRIPTION_LENGTH : null, null);
    protocolMapper = getMapper(ffp, (String)job.getValue("protocolColumnMapping"), null, null);
    hardwareMapper = getMapper(ffp, (String)job.getValue("hardwareColumnMapping"), null, null);
    hybridizationMapper = getMapper(ffp, (String)job.getValue("hybridizationColumnMapping"), null, null); 
    fileMapper = getMapper(ffp, (String)job.getValue("fileColumnMapping"), null, null);
    imagesDirectory = (String)job.getValue("imagesDirectory");
    if (imagesDirectory != null && !imagesDirectory.endsWith("/"))
    {
      imagesDirectory += "/";
    }
  }
  
  @Override
  protected Scan createItem(DbControl dc, FlatFileParser.Data data)
  {
    Hybridization hyb = null;
    if (hybridizationMapper != null) 
    {
      hyb = findHybridization(dc, FallbackIdMethod.NAME_OR_ID, hybridizationMapper.getValue(data));
    }

    Scan scan = Scan.getNew(dc, hyb);
    updateItem(dc, scan, data);
    return scan;
  }
  
  @Override
  protected void updateItem(DbControl dc, Scan scan, FlatFileParser.Data data)
  {
    if (nameMapper != null) scan.setName(nameMapper.getValue(data));
    if (descriptionMapper != null) scan.setDescription(descriptionMapper.getValue(data));
    if (hybridizationMapper != null && scan.isInDatabase()) 
    {
      String nameOrId = hybridizationMapper.getValue(data);
      if (nameOrId != null)
      {
        Hybridization hyb = findHybridization(dc, FallbackIdMethod.NAME_OR_ID, hybridizationMapper.getValue(data));
        scan.setHybridization(hyb);
      }
    }
    if (protocolMapper != null) 
    {
      String nameOrId = protocolMapper.getValue(data);
      ProtocolType type = ProtocolType.getById(dc, SystemItems.getId(ProtocolType.SCANNING));
      Protocol protocol = findProtocol(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, type);
      if (nameOrId == null || protocol != null) scan.setProtocol(protocol);
    }
    if (hardwareMapper != null)
    {
      String nameOrId = hardwareMapper.getValue(data);
      Hardware scanner = findScanner(dc, FallbackIdMethod.NAME_OR_ID, nameOrId);
      if (nameOrId == null || scanner != null) scan.setScanner(scanner);
    }
    
    updateMultiLineItem(dc, scan, data, 0);
  }
  
  protected void updateMultiLineItem(DbControl dc, Scan scan, FlatFileParser.Data data, int multiLineNum)
  {
    
    if (fileMapper != null) {
      String filePath = fileMapper.getValue(data);
      File file = null;
      if (filePath != null)
      {
        if (!filePath.startsWith("/") && imagesDirectory != null) 
        {
          filePath = imagesDirectory + filePath;
        }
        file = File.getByPath(dc, new Path(filePath, Path.Type.FILE), false);
      }
      if (file != null)
      {
        Image image = scan.newImage();
        image.setFile(file);
        image.setName(scan.getName()+"_"+file.getName());
        dc.saveItemIf(scan, image, false);
      }
      
    }
    
  }
  
}