DatabaseDocument.java

        // PMID
        Pub pub = feature_cvterm.getPub();
        
        // internal check
        checkPubDbXRef(pubDbXRefs, pub.getPubId(), pub, feature_cvterm);
        
        attr_buff.append("db_xref="+ pub.getUniqueName());
        nfound_dbxref++;
      }
      
      if(featureCvTermDbXRefs != null &&
              featureCvTermDbXRefs.size() > 0)
      {
        for(int i=0; i<featureCvTermDbXRefs.size(); i++)
        {
          FeatureCvTermDbXRef featureCvTermDbXRef =
            (FeatureCvTermDbXRef)featureCvTermDbXRefs.get(i);
    
          if(feature_cvterm.getFeatureCvTermId() != 
            featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
            continue;
      
          if(nfound_dbxref == 0)
            attr_buff.append("db_xref=");
          else if(nfound_dbxref > 0)
            attr_buff.append("|");
          
          DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
          attr_buff.append(fc_dbXRef.getDb().getName()+":");
          attr_buff.append(fc_dbXRef.getAccession());
          nfound_dbxref++;
        }
      }
      
      if(nfound_dbxref > 0)
        attr_buff.append("%3B");
      
      List feature_cvtermprops = (List) feature_cvterm.getFeatureCvTermProps();
      for(int i = 0; i < feature_cvtermprops.size(); i++)
      {
        FeatureCvTermProp feature_cvtermprop = 
          (FeatureCvTermProp)feature_cvtermprops.get(i);
        attr_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
            .getCvTermId(), dao));
        attr_buff.append("=");
        attr_buff.append(feature_cvtermprop.getValue());
        if(i < feature_cvtermprops.size()-1)
          attr_buff.append("%3B");
      }
      
      attr_buff.append(";");
    }
    else if(cvterm.getCv().getName().equals(DatabaseDocument.PRODUCTS_TAG_CVNAME))
    {
      attr_buff.append("product=");
      attr_buff.append(feature_cvterm.getCvTerm().getName()+";");
    }
    else
    {
      attr_buff.append("GO=");

      if(cvterm.getCv().getName().equals("molecular_function"))
        attr_buff.append("aspect=F%3B");
      else if(cvterm.getCv().getName().equals("cellular_component"))
        attr_buff.append("aspect=C%3B");
      else if(cvterm.getCv().getName().equals("biological_process"))
        attr_buff.append("aspect=P%3B");

      if(feature_cvterm.isNot())
        attr_buff.append("qualifier=NOT%3B");

      attr_buff.append("GOid="+dbXRef.getDb().getName() + ":"
          + dbXRef.getAccession() + "%3B");
      
      attr_buff.append("term="+feature_cvterm.getCvTerm().getName()+"%3B");
      
      // PMID
      int nfound_pub = 0;
      if(feature_cvterm.getPub() != null &&
         feature_cvterm.getPub().getUniqueName() != null &&
         !feature_cvterm.getPub().getUniqueName().equals("NULL"))
      {
        Pub pub = feature_cvterm.getPub();
        attr_buff.append("db_xref="+
            pub.getUniqueName());
        nfound_pub++;
      }
      
      if(featureCvTermPubs != null &&
          featureCvTermPubs.size() > 0)
      {
        for(int i=0; i<featureCvTermPubs.size(); i++)
        {
          FeatureCvTermPub featureCvTermPub =
            (FeatureCvTermPub)featureCvTermPubs.get(i);
          
          if(feature_cvterm.getFeatureCvTermId() != 
            featureCvTermPub.getFeatureCvTerm().getFeatureCvTermId())
            continue;
          
          if(nfound_pub == 0)
            attr_buff.append("db_xref=");
          else if(nfound_pub > 0)
            attr_buff.append("|");

          attr_buff.append(featureCvTermPub.getPub().getUniqueName());
          nfound_pub++;
        }
      }
      
      if(nfound_pub > 0)
        attr_buff.append("%3B");
      
      if(featureCvTermDbXRefs != null &&
          featureCvTermDbXRefs.size() > 0 )
      {  
        int nfound = 0;
        for(int i=0; i<featureCvTermDbXRefs.size(); i++)
        {
          FeatureCvTermDbXRef featureCvTermDbXRef =
            (FeatureCvTermDbXRef)featureCvTermDbXRefs.get(i);
          
          
          if(feature_cvterm.getFeatureCvTermId() != 
            featureCvTermDbXRef.getFeatureCvTerm().getFeatureCvTermId())
          {
            continue;
          }
          
          if(nfound == 0)
            attr_buff.append("with=");
          else if(nfound > 1)
            attr_buff.append("|");
          
          DbXRef fc_dbXRef = featureCvTermDbXRef.getDbXRef();
          attr_buff.append(fc_dbXRef.getDb().getName()+":");
          attr_buff.append(fc_dbXRef.getAccession());
          nfound++;
        }
        
        if(nfound > 0)
          attr_buff.append("%3B");
      }
      
      List feature_cvtermprops = (List)feature_cvterm
          .getFeatureCvTermProps();
      for(int i = 0; i < feature_cvtermprops.size(); i++)
      {
        FeatureCvTermProp feature_cvtermprop = 
          (FeatureCvTermProp)feature_cvtermprops.get(i);
        
        if(feature_cvtermprop.getValue() == null)
          continue;
        
        attr_buff.append(getCvtermName(feature_cvtermprop.getCvTerm()
            .getCvTermId(), dao));
        attr_buff.append("=");
        attr_buff.append(feature_cvtermprop.getValue());
        if(i < feature_cvtermprops.size()-1)
          attr_buff.append("%3B");
      }
      
      attr_buff.append(";");
    }
  }
  
  /**
   * Check the PubDbXref contains the Pub in FeatureCvTerm
   * @param pubDbXRefs
   * @param pubId
   * @param pub
   * @param feature_cvterm
   */
  private static void checkPubDbXRef(final List pubDbXRefs, final int pubId,
                                     final Pub pub, final FeatureCvTerm feature_cvterm)
  {
    PubDbXRef pubDbXRef = null;
    for(int i = 0; i < pubDbXRefs.size(); i++)
    {
      pubDbXRef = (PubDbXRef) pubDbXRefs.get(i);
      if(pubDbXRef.getPub().getPubId() == pubId)
      {
        DbXRef dbxref = pubDbXRef.getDbXRef();
        Splash.logger4j.debug("Checking PubDbXRef and found Pub "+dbxref.getDb().getName()+
                              ":"+dbxref.getAccession());
        break;
      }
    }
    
    if(pubDbXRef == null || 
        !pub.getUniqueName().endsWith(pubDbXRef.getDbXRef().getAccession()))
     {
       Splash.logger4j.debug("Checking PubDbXRef and not found Pub "+
                           feature_cvterm.getPub().getUniqueName());
      
       JOptionPane.showMessageDialog(null, "Cannot find pub_dbxref for:\n"+
           feature_cvterm.getPub().getUniqueName(), 
           "Database Error",
           JOptionPane.ERROR_MESSAGE);
     }
  }
  
  /**
   * Look up the cvterm_id for a controlled vocabulary name.
   * @param name  
   * @return
   */
  public static Integer getCvtermID(String name)
  {
    Enumeration enum_cvterm = cvterms.keys();
    while(enum_cvterm.hasMoreElements())
    {
      Integer key = (Integer)enum_cvterm.nextElement();
      if(name.equals( ((CvTerm)cvterms.get(key)).getName() ))
        return key;
    }
    return null;
  }

  /**
   * Look up a cvterm name from the collection of cvterms.
   * @param id  a cvterm_id  
   * @return    the cvterm name
   */
  private static String getCvtermName(int id, GmodDAO dao)
  {
    return getCvTerm(id, dao).getName();
  }
  
  private static CvTerm getCvTerm(int id, GmodDAO dao)
  {
    if(cvterms == null)
      getCvterms(dao);

    return (CvTerm)cvterms.get(new Integer(id));
  }
  
  public static CvTerm getCvTermByCvTermName(String cvterm_name)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvterm_name.equals( cvterm.getName() ))
        return cvterm;
    }
    
    return null;
  }
  
  public static CvTerm getCvTermByCvAndCvTerm(final String cvterm_name,
                                              final String cvName)
  {
    Enumeration enum_cvterm = cvterms.elements();
    while(enum_cvterm.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)enum_cvterm.nextElement();
      if(cvName.equals( cvterm.getCv().getName() ) &&
         cvterm_name.equals( cvterm.getName() ))
        return cvterm;
    }
    return null;
  }

  /**
   * Look up cvterms names and id and return in a hashtable.
   * @param dao the data access object
   * @return    the cvterm <code>Hashtable</code>
   */
  private static Hashtable getCvterms(GmodDAO dao)
  {
    cvterms = new Hashtable();

    try
    {
      List cvterm_list = dao.getCvTerms();
      Iterator it = cvterm_list.iterator();

      while(it.hasNext())
      {
        CvTerm cvterm = (CvTerm)it.next();
        cvterms.put(new Integer(cvterm.getCvTermId()), cvterm);
      }
    }
    catch(RuntimeException sqle)
    {
      System.err.println("SQLException retrieving CvTerms");
      System.err.println(sqle);
    }

    return cvterms;
  }
  
  public static Vector getCvterms(final String search_str, final String cv_name)
  {
    final Vector cvterm_match = new Vector();
    
    Enumeration enum_cvterm = cvterms.keys();
    while(enum_cvterm.hasMoreElements())
    {
      Integer key = (Integer)enum_cvterm.nextElement();
      CvTerm cvterm = (CvTerm)cvterms.get(key);
      
      if(cvterm.getCv().getName().startsWith(cv_name))
      {
        if(cvterm.getName().indexOf(search_str) > -1)
          cvterm_match.add(cvterm);
      }
    }
    
    return cvterm_match;
  }

  /**
   * Look up synonym type names e.g. synonym, systematic_id.
   * @return    the synonym tag names
   */
  public static String[] getSynonymTypeNames(String cv_name)
  {
    Vector synonym_names = new Vector();
    Enumeration cvterm_enum = cvterms.elements();
    while(cvterm_enum.hasMoreElements())
    {
      CvTerm cvterm = (CvTerm)cvterm_enum.nextElement();
      if(cvterm.getCv().getName().equals(cv_name))
        synonym_names.add(cvterm.getName());
    }
    
    return (String[])synonym_names.toArray(
                       new String[synonym_names.size()]);
  }
  
  
  /**
   * Get the sequence for a feature.
   * @param dao   the data access object
   * @param buff  the buffer to add the sequence to
   * @return      the resulting buffer
   * @throws java.sql.SQLException
   */
  private ByteBuffer getChadoSequence(GmodDAO dao, ByteBuffer buff)
  {
    Feature feature = dao.getFeatureById(Integer.parseInt(srcFeatureId));
 
    buff.append("##FASTA\n>");
    buff.append(feature.getUniqueName());
    buff.append("\n");
    buff.append(feature.getResidues());
    return buff;
  }

  /**
   * Get the <code>List</code> of available schemas.
   * @return  the <code>List</code> of available schemas
   */
  public List getSchema()
  {
    return schema_list;
  }
  
  
  /**
   * Create a hashtable of the available entries with residues.
   * @return a <code>Hashtable</code> of the <code>String</code>
   *          representation (schema-type-feature_name) and the
   *          corresponding feature_id
   * @throws ConnectException
   * @throws java.sql.SQLException
   */
  public HashMap getDatabaseEntries()
                   throws ConnectException, java.sql.SQLException
  {
    String schema = null;

    try
    { 
      GmodDAO dao = null;
      dao = getDAO();
      schema_list = dao.getOrganisms();
      
      
/*      Organism o = new Organism();
      o.setCommonName("web");
      schema_list.add(o);*/
      
      
      Iterator it = schema_list.iterator();
      db = new HashMap();
      
      while(it.hasNext())
      {
        Organism organism = (Organism)it.next();
        schema = organism.getCommonName();
        
        reset((String)getLocation(),  schema);

        try
        {
          dao = getDAO();
          List list_residue_features = dao.getResidueFeatures();
          
          Iterator it_residue_features = list_residue_features.iterator();
          while(it_residue_features.hasNext())
          {
            Feature feature = (Feature)it_residue_features.next();
            String typeName = getCvtermName(feature.getCvTerm().getCvTermId(), getDAO()); 
          
            db.put(schema + " - " + typeName + " - " + feature.getUniqueName(),
                   Integer.toString(feature.getFeatureId()));
          }
        }
        catch(RuntimeException e)
        { 
        }
        catch(java.sql.SQLException sqlExp)
        {
        }
      }
      
    }
    catch(RuntimeException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems...\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      sqlExp.printStackTrace();
    }
    catch(ConnectException exp)
    {
      JOptionPane.showMessageDialog(null, "Connection Problems...\n"+
            exp.getMessage(), 
            "Connection Error",
            JOptionPane.ERROR_MESSAGE);
      throw exp;
    }
    catch(java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "SQL Problems....\n"+
                                    sqlExp.getMessage(), 
                                    "SQL Error",
                                    JOptionPane.ERROR_MESSAGE);
      throw sqlExp;
    }
    
    return db;
  }
  
  
  /**
   * Get the data access object (DAO).
   * @return data access object
   */
  private GmodDAO getDAO()
     throws java.net.ConnectException, SQLException
  { 
    if(!iBatis)
    {
      if(jdbcDAO == null)
       jdbcDAO = new JdbcDAO((String)getLocation(), pfield); 
      return jdbcDAO;
    }
    else
    {   
      if(connIB == null)
      {
        System.setProperty("chado", (String)getLocation());
        connIB = new IBatisDAO(pfield);
      }
      return connIB;
    }
  }


  /**
   * Create a new OutputStream object from this Document. The contents of the
   * Document can be written from the stream.
   * 
   * @exception IOException
   *              Thrown if the Document can't be written.
   */
  public OutputStream getOutputStream() throws IOException
  {
    final File write_file = new File(System.getProperty("user.dir")+
                                     System.getProperty("file.separator")+
                                     getName());

    final FileOutputStream file_output_stream =
      new FileOutputStream(write_file);

    if(write_file.getName().endsWith(".gz")) 
    {
      // assume this file should be gzipped
      return new java.util.zip.GZIPOutputStream (file_output_stream);
    } 
    else 
      return file_output_stream;
  }

  /**
   * Commit the <code>ChadoTransaction</code> SQL back to the
   * database.
   * @param sql the collection of <code>ChadoTransaction</code> objects
   * @return
   */
  public int commit(Vector sql)
  {
    int i = 0;

    try
    {
      
      GmodDAO dao = getDAO();
      if(dao instanceof IBatisDAO)
        ((IBatisDAO) dao).startTransaction();
      boolean unchanged;
      
      //
      // check feature timestamps have not changed
      Vector names_checked = new Vector();
      for(i = 0; i < sql.size(); i++)
      {
        ChadoTransaction tsn = (ChadoTransaction)sql.get(i);
        if( (tsn.getType() == ChadoTransaction.INSERT ||
             tsn.getType() == ChadoTransaction.DELETE) && 
             tsn.getFeatureObject() instanceof Feature )
          continue;
            
        final String uniquename = tsn.getUniquename();
        
        if(uniquename == null)
          continue;
        
        if(names_checked.contains(uniquename))
          continue;

        names_checked.add(uniquename);
        
        String keyName = tsn.getFeatureKey();
        unchanged = checkFeatureTimestamp(schema, 
                         uniquename, 
                         tsn.getLastModified(), dao, 
                         keyName, tsn.getFeatureObject());
        if(!unchanged)
          return 0;
      }  
      
      try
      {
        //
        // commit to database
        for(i = 0; i < sql.size(); i++)
        {
          ChadoTransaction tsn = (ChadoTransaction) sql.get(i);

          if(tsn.getType() == ChadoTransaction.UPDATE)
          {
            if(tsn.getFeatureObject() instanceof Feature)
            {
              Feature feature = (Feature)tsn.getFeatureObject();
              
              if(feature.getUniqueName() != null)
              {
                final String uniquename;
                if(tsn.getOldUniquename() != null)
                  uniquename = (String)tsn.getOldUniquename();
                else
                  uniquename = feature.getUniqueName();
                
                Feature old_feature
                    = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey());
                
                if(old_feature != null)
                  feature.setFeatureId( old_feature.getFeatureId() );
                
                tsn.setOldUniquename(feature.getUniqueName());
              }
            }
            dao.merge(tsn.getFeatureObject());
            //dao.updateAttributes(tsn);
          }
          else if(tsn.getType() == ChadoTransaction.INSERT)
          {
            if(tsn.getFeatureObject() instanceof FeatureCvTerm)
              ArtemisUtils.inserFeatureCvTerm(dao, (FeatureCvTerm)tsn.getFeatureObject());
            else
            {
              // set srcfeature_id
              if(tsn.getFeatureObject() instanceof Feature)
              {
                FeatureLoc featureloc = ((Feature) tsn.getFeatureObject()).getFeatureLoc();
                Feature featureBySrcFeatureId = new Feature();
                featureBySrcFeatureId.setFeatureId(Integer.parseInt(srcFeatureId));
                featureloc.setFeatureBySrcFeatureId(featureBySrcFeatureId);
              }
              dao.persist(tsn.getFeatureObject());
            }
            
          }
          else if(tsn.getType() == ChadoTransaction.DELETE)
          {
            if(tsn.getFeatureObject() instanceof FeatureCvTerm)
              ArtemisUtils.deleteFeatureCvTerm(dao, (FeatureCvTerm)tsn.getFeatureObject());
            else
              dao.delete(tsn.getFeatureObject());
          }
        }

        //
        // update timelastmodified timestamp
        Timestamp ts = new Timestamp(new java.util.Date().getTime());
        names_checked = new Vector();
        for(int j = 0; j < sql.size(); j++)
        {
          ChadoTransaction tsn = (ChadoTransaction)sql.get(j);
          
          if( (tsn.getType() == ChadoTransaction.INSERT ||
              tsn.getType() == ChadoTransaction.DELETE) && 
              tsn.getFeatureObject() instanceof Feature )
           continue;
          
          final String uniquename = tsn.getUniquename();
          if(uniquename == null)
            continue;
            
          if(names_checked.contains(uniquename))
            continue;

          names_checked.add(uniquename);

          Feature feature = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey());
          if(feature != null)
          {
            feature.setTimeLastModified(ts);
            dao.merge(feature);
          }

          GFFStreamFeature gff_feature = (GFFStreamFeature) tsn
              .getGff_feature();
          gff_feature.setLastModified(ts);
        }
        
        if(dao instanceof IBatisDAO && 
           System.getProperty("nocommit") == null)
           ((IBatisDAO) dao).commitTransaction();
      }
      finally
      {
        if(dao instanceof IBatisDAO)
          ((IBatisDAO) dao).endTransaction();
      }
    }
    catch (java.sql.SQLException sqlExp)
    {
      JOptionPane.showMessageDialog(null, "Problems Writing...\n" +
                                    sqlExp.getMessage(),
                                    "Problems Writing to Database ",
                                    JOptionPane.ERROR_MESSAGE);
      sqlExp.printStackTrace();
    }
    catch (java.net.ConnectException conn_ex)
    {
      JOptionPane.showMessageDialog(null, "Problems connecting..."+
                                    conn_ex.getMessage(),
                                    "Database Connection Error - Check Server",
                                    JOptionPane.ERROR_MESSAGE);
      conn_ex.printStackTrace();
    }

      
    return i;
  }
  
  /**
   * Check the <code>Timestamp</code> on a feature (for versioning).
   * @param schema      the schema
   * @param uniquename  the feature uniquename
   * @param timestamp   the last read feature timestamp
   */
  public boolean checkFeatureTimestamp(final String schema,
                                       final String uniquename,
                                       final Timestamp timestamp,
                                       final GmodDAO dao,
                                       final String keyName,
                                       final Object featureObject)
  {
    Feature feature = dao.getFeatureByUniqueName(uniquename, keyName);
    if(feature == null)
      return true;
    
    if(featureObject instanceof FeatureProp)
      ((FeatureProp)featureObject).setFeature(feature);
    else if(featureObject instanceof FeatureLoc)
      ((FeatureLoc)featureObject).setFeatureByFeatureId(feature);
      
    Timestamp now = feature.getTimeLastModified();
    
    if(now != null && timestamp != null)
    {
      now.setNanos(0);
      timestamp.setNanos(0);
      
      if(now.compareTo(timestamp) != 0)
      {
        SimpleDateFormat date_format = 
                   new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
        
        //System.out.println(date_format.format(now)+"   "+
        //                   date_format.format(timestamp));
        int select = JOptionPane.showConfirmDialog(null, uniquename +
                                      " has been altered at :\n"+
                                      date_format.format(now)+"\nOverwite?", 
                                      "Feature Changed", 
                                      JOptionPane.OK_CANCEL_OPTION);
        if(select == JOptionPane.OK_OPTION)
          return true;
        else
          return false;
      }
    }
    return true;
  }

  
  public static void main(String args[])
  {
    try
    {
      GmodDAO dao;
      DatabaseEntrySource src = new DatabaseEntrySource();
      src.setLocation(true);
      
      if(System.getProperty("ibatis") == null)
        dao = new JdbcDAO(src.getLocation(), src.getPfield()); 
      else
        dao = new IBatisDAO(src.getPfield());
      
      Feature feature = new Feature();
      feature.setUniqueName(args[0]);
      List schemas = new Vector();
      schemas.add(args[1]);
      List featureList = new Vector();
      featureList.add(dao.getFeatureByUniqueName(args[0], "polypeptide")); 
      System.out.println("FINISHED getFeature()");
      for(int i = 0; i < featureList.size(); i++)
      {
        feature = (Feature)featureList.get(i);
        
        String abb  = feature.getOrganism().getAbbreviation();
        String type = feature.getCvTerm().getName();
        int fmin    = feature.getFeatureLoc().getFmin().intValue() + 1;
        int fmax    = feature.getFeatureLoc().getFmax().intValue();
        String featprop = 
          ((FeatureProp)(new Vector(feature.getFeatureProps()).get(0))).getCvTerm().getName();
        
        System.out.print(fmin+".."+fmax);
        System.out.print(" "+type);
        System.out.print(" "+featprop);
        System.out.print(" "+feature.getFeatureLoc().getStrand());
        System.out.print(" "+feature.getUniqueName());
        System.out.print(" "+abb);
        System.out.println(" "+Integer.toString(feature.getFeatureId()));
        
/*      Hashtable synonyms = getAllFeatureSynonyms(dao, null);
        Vector syns = (Vector)synonyms.get(new Integer(feature.getId()));
        for(int j=0; j<syns.size(); j++)
        {
          FeatureSynonym alias = (FeatureSynonym)syns.get(j);
          System.out.print(" "+alias.getSynonym().getCvterm().getName()+
                           "="+alias.getSynonym().getName());
        }*/
        
        System.out.println(" "); 
      }
    }
    catch(SQLException sqle)
    {
      sqle.printStackTrace();
    }
    catch(RuntimeException re)
    {
      re.printStackTrace();
    }
    catch(ConnectException e)
    {
      e.printStackTrace();
    }
  }

  public Document getParent()
  {
    return null;
  }
  
  public static FeatureLoc getFeatureLoc(List locs, int srcfeature_id)
  {
    for(int i=0; i<locs.size(); i++)
    {
      FeatureLoc loc = (FeatureLoc)locs.get(i);
      if(loc.getFeatureBySrcFeatureId().getFeatureId() == srcfeature_id)
        return loc;
    }
    return null;
  }


  public String getSrcFeatureId()
  {
    return srcFeatureId;
  }
}