ReadAndWriteEntry.java

/* ReadAndWriteEntry.java

 * This file is part of Artemis
 *
 * Copyright(C) 2008  Genome Research Limited
 *
 * This program 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 2
 * of the License, or(at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

package uk.ac.sanger.artemis.io;

import java.io.File;
import java.io.IOException;

import javax.swing.JFrame;

import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;

public class ReadAndWriteEntry
{

  private static org.apache.log4j.Logger logger4j = 
    org.apache.log4j.Logger.getLogger(ReadAndWriteEntry.class);

  private static DatabaseEntrySource ENTRY_SOURCE;
  
  /**
   * Read from the database, given a srcFeature uniquename
   * @param uniqueName
   * @return
   * @throws OutOfRangeException
   * @throws NoSequenceException
   * @throws IOException
   */
  public static Entry readEntryFromDatabase(final String uniqueName,
                                            DatabaseEntrySource entry_source) 
         throws OutOfRangeException, NoSequenceException, IOException
  {
    if(entry_source == null)
    {
      ReadAndWriteEntry.ENTRY_SOURCE = new DatabaseEntrySource();
      entry_source = ENTRY_SOURCE;
      boolean promptUser = true;
      //if(System.getProperty("read_only") != null)
      if (UI.mode == UI.UIMode.SCRIPT)
        promptUser = false;

      if(!entry_source.setLocation(promptUser))
        return null;
    }
    
    String url = (String)entry_source.getLocation();
    int index  = url.indexOf("?");
    
    String userName = url.substring(index+1).trim();
    if(userName.startsWith("user="))
      userName = userName.substring(5);
    
    final String srcFeatureId = getFeatureId(entry_source, uniqueName);
    
    final InputStreamProgressListener stream_progress_listener =
        new InputStreamProgressListener() 
    {
      public void progressMade(final InputStreamProgressEvent event) 
      {
        final int char_count = event.getCharCount();
        if(char_count != -1) 
          logger4j.debug("chars read so far: " + char_count);
      }
      public void progressMade(String progress)
      {
        logger4j.debug(progress);
      }
    };
    return entry_source.getEntry(srcFeatureId, userName, 
                                 stream_progress_listener);
  }
  
  /**
   * Read from the database, given a srcFeature uniquename
   * @param uniqueName
   * @return
   * @throws OutOfRangeException
   * @throws NoSequenceException
   * @throws IOException
   */
  public static Entry readEntryFromDatabase(final String uniqueName) 
         throws OutOfRangeException, NoSequenceException, IOException
  {
    return readEntryFromDatabase(uniqueName, null);
  }
  
  /**
   * Write entry to a file
   * @param entry
   * @param file
   * @param flatten Flatten the gene model and combine the qualifiers if true.
   *    If false it will write all features and qualifiers out.
   * @param ignore obsolete features if true
   * @param force invalid qualifiers and any features with invalid keys will 
   *    be quietly thrown away when saving.
   * @param include_diana_extensions false if writing EMBL submission format.
   * @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT,
   *    GFF_FORMAT or ANY_FORMAT.  If ANY_FORMAT then the Entry will
   *    be saved in the same format it was created, otherwise it will be saved
   *    in the given format.
   * @param parent
   * @throws IOException
   * @throws EntryInformationException
   */
  public static void writeDatabaseEntryToFile(final Entry entry, final File file,
                                              final boolean flatten,
                                              final boolean ignoreObsolete,
                                              final boolean force,
                                              final boolean include_diana_extensions,
                                              final boolean removeProductForPseudo,
                                              final int destination_type,
                                              final JFrame parent) 
         throws IOException, EntryInformationException
  {
    GeneUtils.lazyLoadAll(entry, parent);

    EntryInformation artemis_entry_information = Options.getArtemisEntryInformation();
    if(!flatten)
    {
      final FeatureVector features = entry.getAllFeatures();
      for(int i=0; i<features.size(); i++)
        addAllKeysQualifiers(artemis_entry_information, features.elementAt(i).getEmblFeature());
      
      if(entry.getEMBLEntry() instanceof GFFDocumentEntry)
        addQualifierToEntryInfo(artemis_entry_information, 
          (String)PublicDBDocumentEntry.getDatabaseQualifiersToRemove()[0]);
    }
    PublicDBDocumentEntry.IGNORE_OBSOLETE_FEATURES = ignoreObsolete;
    
    if(destination_type == DocumentEntryFactory.EMBL_FORMAT &&
       (entry.getHeaderText() == null || 
        entry.getHeaderText().equals("") ||
        entry.getHeaderText().startsWith("#")))
    {
      String name = file.getName();
      int ind = name.lastIndexOf(".embl.gz");
      if(ind > -1)
        name = name.substring(0, ind);
      else
      {
        ind = name.lastIndexOf(".embl");
        if(ind > -1)
          name = name.substring(0, ind);
        
      }
      
      int length = entry.getBases().getLength();
      String header = "ID   "+name+"; SV ; ; ; ; ; "+length+" BP.";
      if(entry.getFeatureCount() > 0)
        header = header.concat("\nFH   Key             "+
                               "Location/Qualifiers\nFH\n");
      entry.setHeaderText(header);
    }

    if(include_diana_extensions)
      entry.save(file, destination_type, force, artemis_entry_information);
    else
    {
      if(removeProductForPseudo)
      {
        uk.ac.sanger.artemis.io.FeatureVector features = entry.getEMBLEntry().getAllFeatures();
        for(Feature f: features)
        {
          if(f.getKey().equals("polypeptide"))
          {
            Qualifier q = f.getQualifierByName("product");
            if(q != null)
            {
              Feature gene = ((GFFStreamFeature) f).getChadoGene().getGene();
              if(gene.getKey().equals("pseudogene"))
                f.getQualifiers().remove(q);
            }
          }
        }
      }
      
      entry.saveStandardOnly(file, destination_type, force);
    }
  }
  
  
  /**
   * Add all keys and qualifiers for a given feature to the EntryInformation 
   * @param entry_information
   * @param feature
   */
  protected static void addAllKeysQualifiers(final EntryInformation entry_information,
                                           final Feature feature)
  {
    Key new_key = feature.getKey();
    
    new_key = PublicDBDocumentEntry.mapKeys(new_key);
    
    boolean keyAdded = false;
    if(!entry_information.isValidKey(new_key))
    {
      entry_information.addKey(new_key);
      keyAdded = true;
    }
    
    final QualifierVector feature_qualifiers = feature.getQualifiers();
    
    // check the qualifiers
    for(int i = 0 ; i < feature_qualifiers.size() ; ++i)
    {
      final Qualifier this_qualifier = (Qualifier)feature_qualifiers.elementAt(i);
      final String this_qualifier_name = this_qualifier.getName();

      if(!entry_information.isValidQualifier(this_qualifier_name) ||
         !entry_information.isValidQualifier(new_key, this_qualifier_name) ||
         keyAdded) 
      {
        QualifierInfo qualifierInfo = entry_information.getQualifierInfo(this_qualifier_name);
        
        if(qualifierInfo == null)
        {
          KeyVector keys = new KeyVector();
          qualifierInfo = new QualifierInfo(this_qualifier_name, QualifierInfo.QUOTED_TEXT,
                                            keys, null, false);
          try
          {
            entry_information.addQualifierInfo(qualifierInfo);
          }
          catch(QualifierInfoException e)
          {
            e.printStackTrace();
          }
        }
        
        if(qualifierInfo.getValidKeys() != null)
          qualifierInfo.getValidKeys().add(new_key);
      }
    }

  }
  
  protected static void addQualifierToEntryInfo(final EntryInformation entry_information,
                                             final String qualifier_name)
  {
    KeyVector keys = new KeyVector();
    QualifierInfo qualifierInfo = new QualifierInfo(qualifier_name, QualifierInfo.QUOTED_TEXT,
                                      keys, null, false);
    try
    {
      entry_information.addQualifierInfo(qualifierInfo);
    }
    catch(QualifierInfoException e)
    {
      e.printStackTrace();
    }
  }
  
  /**
   * Get feature id
   * @param entry_source
   * @param srcUniqueName
   * @return
   */
  public static String getFeatureId(
      final DatabaseEntrySource entry_source, final String srcUniqueName)
  {
    final DatabaseDocument doc = entry_source.getDatabaseDocument();
    org.gmod.schema.sequence.Feature feature = doc.getFeatureByUniquename(srcUniqueName);
    return Integer.toString(feature.getFeatureId());
  }
  
  /**
   * return the ENTRY_SOURCE
   */
  public static DatabaseEntrySource getEntrySource()
  {
    return ENTRY_SOURCE;
  }

  public static void main(final String args[])
  {
    try
    {
      String names[];
      boolean flatten = true;
      boolean ignoreObsolete = true;
      
      if( (args != null && args.length == 1 && args[0].startsWith("-h")) ||
          (args == null || args.length < 1))
      {
        System.out.println("-h\tshow help");

        System.out.println("-f\t[y|n] flatten the gene model, default is y");
        System.out.println("-i\t[y|n] ignore obsolete features, default is y");
        System.out.println("-s\tspace separated list of sequences to read and write out");
        System.out.println("-o\t[EMBL|GFF] output format, default is EMBL");
        
        // note that read_only and noprompt -D parameters redundant now
        System.out.println("Advanced parameters:");
        System.out.println("-l\tlocation of EMBL mapping files (qualifier_mapping and key_mapping)");
        System.out.println("-z\t[y|n] gzip output, default is y");
        System.out.println("-a\t[y|n] for EMBL submission format change to n, default is y");
        System.out.println("-pp\t[y|n] read polypeptide domain features, default is n");
        System.out.println("-r\t[y|n] remove product qualifiers from pseudogene, default is n");
        System.out.println("-c\tthe URL for your Chado database e.g. db.genedb.org:5432/snapshot?genedb_ro (if not using default)");
        System.out.println("-u\t[swing|console|script] the UI mode : run in swing (with popup dialog boxes) mode, run in console mode (choices entered in the console window), or in script mode (all choices default to continue, all parameters passed on command line) ");
        System.out.println("-p\tthe password for connecting to the Chado database");
        System.out.println("-fp\t the file path (the folder you want to save the files in)");
        System.out.println("-np\t[y|n] do not write out private qualifiers, default is y");
        
        System.exit(0);
      }
      
      
      names = args;
      int format = DocumentEntryFactory.EMBL_FORMAT;
      boolean include_diana_extensions = true;
      String suffix = ".embl";
      boolean gzip = true;
      boolean noprivates = true;
      boolean removeProductForPseudo = false;
      
      String filePath = "";
      
      for(int i = 0; i < args.length; i++)
      {
    	String key = args[i].toLowerCase();
        if (key.equals("-f"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
            flatten = false;
        }
        else if (key.equals("-i"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
            ignoreObsolete = false;
        }
        else if (key.equals("-a"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
            include_diana_extensions = false;
        }
        else if (key.equals("-z"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
            gzip = false;
        }
        else if (key.equals("-np"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
            noprivates = false;
        }
        else if (key.equals("-o"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("gff"))
          {
            format = DocumentEntryFactory.GFF_FORMAT;
            suffix = ".gff";
          }
        }
        else if (key.equals("-pp"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("y"))
            LocalAndRemoteFileManager.domainLoad.setSelected(true);
        }
        
        // GSV :: added these command-line parameters
        // note that read_only and noprompt -D parameters redundant now
        else if (key.equals("-u"))
        {
        	System.setProperty("uimode", args[i + 1]);
        }
        else if (key.equals("-c"))
        {
        	System.setProperty("chado", args[i + 1]);
        }
        else if (key.equals("-r"))
        {
          if(i + 1 < args.length && args[i + 1].toLowerCase().equals("y"))
            removeProductForPseudo = true;
        }
        else if (key.equals("-p"))
        {
        	System.setProperty("chadoPassword", args[i + 1]);
        }
        else if (key.equals("-fp"))
        {
        	filePath = args[i + 1];
        }
      }
      
      // run this after all the system properties have been set
      UI.initalise();
      
      java.util.Vector<String> files = null;
      for(int i = 0; i < args.length; i++)
      {
        if(args[i].toLowerCase().equals("-s"))
        {
          if(files == null)
            files = new java.util.Vector<String>();
          for(int j = i + 1; j < args.length; j++)
          {
            if(args[j].startsWith("-"))
              break;
            files.add(args[j]);
          }
        }
        else if(args[i].startsWith("-"))
        {
          i++;
        }
        else
        {
          if(files == null)
            files = new java.util.Vector<String>();
          if(!files.contains(args[i]))
            files.add(args[i]);
        }
      }
      if(files != null && files.size() > 0)
      {
        names = new String[files.size()];
        files.toArray(names);
      }
     
      if(filePath.length() != 0)
      {
		filePath += "/";
      }

      if(gzip)
        suffix = suffix + ".gz";

      if(noprivates)
        System.setProperty("noprivate", "true");
      
      for(int i=0;i < names.length; i++)
      {
        
        System.out.println("read :: "+names[i]+" write :: "+names[i]+suffix);
        logger4j.info("read :: "+names[i]+" write :: "+names[i]+suffix);
        
        Entry entry = ReadAndWriteEntry.readEntryFromDatabase(names[i], ENTRY_SOURCE);
        
        try
        {
          ReadAndWriteEntry.writeDatabaseEntryToFile(
            entry, new File(filePath + names[i]+suffix), flatten, ignoreObsolete, 
            false, include_diana_extensions, removeProductForPseudo,
            format, null);
          System.out.println("done");
          logger4j.info("done");
        }
        catch(EntryInformationException eie)
        {
        	String label = "Destination format can't handle all keys/qualifiers - continue?";
        	boolean canContinue = UI.booleanUserInput(label, eie.getMessage());
        	
        	if (canContinue)
        	{
        		ReadAndWriteEntry.writeDatabaseEntryToFile(entry, new File(filePath + names[i] + suffix), 
        				flatten, ignoreObsolete, true,
        			include_diana_extensions, removeProductForPseudo, format, null);
        		System.out.println("done");
        		logger4j.info("done");
        	}
        }
        entry.dispose();
      }
    }
    catch(Exception e)
    {
      e.printStackTrace();
    }
    System.exit(0);
  }
  
}