DatabaseDocument.java

/* DatabaseDocument.java
 *
 * created: 2005
 *
 * This file is part of Artemis
 * 
 * Copyright (C) 2005  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.util;

import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.PartialSequence;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.ReadFormatException;

import uk.ac.sanger.artemis.chado.ArtemisUtils;
import uk.ac.sanger.artemis.chado.ChadoCvTermView;
import uk.ac.sanger.artemis.chado.FeatureForUpdatingResidues;
import uk.ac.sanger.artemis.chado.IBatisDAO;
import uk.ac.sanger.artemis.chado.JdbcDAO;
import uk.ac.sanger.artemis.chado.GmodDAO;
import uk.ac.sanger.artemis.chado.ChadoTransaction;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.components.Splash;

import org.gmod.schema.sequence.Feature;
import org.gmod.schema.sequence.FeatureProp;
import org.gmod.schema.sequence.FeatureLoc;
import org.gmod.schema.sequence.FeaturePub;
import org.gmod.schema.sequence.FeatureRelationship;
import org.gmod.schema.sequence.FeatureSynonym;
import org.gmod.schema.sequence.FeatureCvTerm;
import org.gmod.schema.sequence.FeatureCvTermProp;
import org.gmod.schema.sequence.FeatureCvTermDbXRef;
import org.gmod.schema.sequence.FeatureCvTermPub;
import org.gmod.schema.cv.Cv;
import org.gmod.schema.cv.CvTerm;
import org.gmod.schema.general.Db;
import org.gmod.schema.general.DbXRef;
import org.gmod.schema.organism.Organism;
import org.gmod.schema.pub.PubDbXRef;
import org.gmod.schema.pub.Pub;
import org.postgresql.largeobject.LargeObjectManager;

import com.ibatis.common.jdbc.SimpleDataSource;

import java.sql.*;
import java.text.SimpleDateFormat;
import java.io.*;
import java.net.ConnectException;
import java.net.InetAddress;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Set;
import java.util.Vector;
import java.util.Enumeration;
import java.util.List;
import java.util.Iterator;
import java.util.Collection;

import javax.swing.JOptionPane;
import javax.swing.JPasswordField;

/**
 * Objects of this class are Documents created from a relational database.
 */
public class DatabaseDocument extends Document
{
  private String name = null;

  /** source feature_id */
  private String srcFeatureId = "1";

  /** database schema */
  private String schema = "public";

  private static Hashtable cvterms;
  
  private InputStreamProgressListener progress_listener;

  /** JDBC DAO */
  private JdbcDAO jdbcDAO = null;

  /** iBatis DAO */
  private static IBatisDAO connIB = null;

  private ByteBuffer[] gff_buffer;

  private ByteBuffer gff_buff;

  /** entries to split into - each is given a name and the features within the entry */
  private static String[][][] TYPES = 
  { 
      { {"repeats"}   , {"repeat_region", "direct_repeat"} }, 
      { {"EST"}       , {"EST_match", "match_part"} },
      { {"contig+gap"}, {"contig", "gap"}}
  };

  /** true if splitting the GFF into entries */
  private boolean splitGFFEntry;

  private boolean iBatis = false;

  private JPasswordField pfield;
  
  private boolean singleSchema = true;

  private List schema_list;
  
  private static List organismNames;
  
  private boolean gene_builder;
  
  // include children in reading from the database
  private boolean readChildren = true;
  
  // range to retrieve features for
  private Range range;
  
  private Feature geneFeature;
  
  private Hashtable idFeatureStore;
  
  private boolean lazyFeatureLoad = true;
  
  public static String EXONMODEL  = "exon-model";
  public static String TRANSCRIPT = "mRNA";
  public static boolean CHADO_INFER_CDS = false;
  
  /** list of controlled_curation CV names */
  private static Vector cvControledCuratioNames;
  
  private static CvTermThread cvThread;
  
  // controlled vocabulary
  /** controlled_curation controlled vocabulary */
  public static String CONTROLLED_CURATION_TAG_CVNAME = 
                                 "CC_";
  /**  controlled vocabulary */
  public static String PRODUCTS_TAG_CVNAME = "genedb_products";
  public static String RILEY_TAG_CVNAME = "RILEY";
  
  private static org.apache.log4j.Logger logger4j = 
    org.apache.log4j.Logger.getLogger(DatabaseDocument.class);

  
  /**
   * 
   * Create a new Document from a database.
   * 
   * @param location
   *          This should be a URL string giving:
   *          jdbc:postgresql://host:port/datbase_name?user=username
   * 
   */
  public DatabaseDocument(String location, JPasswordField pfield)
  {
    super(location);
    this.pfield = pfield;

    if(location.indexOf('=') > -1)
      this.schema = location.substring( location.indexOf('=')+ 1);
    
    if(System.getProperty("ibatis") != null ||
       System.getProperty("jdbc") == null)
    {
      iBatis = true;
      System.setProperty("chado", location);
    }
    initMDC(this);
  }

  
  /**
   * 
   * Create a new Document from a database.
   * 
   * @param location