DatabaseEntrySource.java

/* DatabaseEntrySource.java
 *
 * created: Mar 2005
 *
 * This file is part of Artemis
 *
 * Copyright (C) 2001  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.components;

import javax.swing.*;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.TreeSelectionModel;
import javax.swing.tree.TreePath;
import java.awt.Container;
import java.awt.GridLayout;
import java.net.*;
import java.io.*;
import java.util.*;

import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.SimpleEntryInformation;
import uk.ac.sanger.artemis.io.InvalidKeyException;
import uk.ac.sanger.artemis.io.EntryInformationException;

/**
 *
 *  This is an EntrySource that reads Entry objects from a relational
 *  database.
 *
 **/

public class DatabaseEntrySource implements EntrySource
{
  private String location;
  private JPasswordField pfield;
  private Hashtable entries;
  private boolean splitGFFEntry;

  /**
   *  Create a new DatabaseEntrySource.
   **/
  public DatabaseEntrySource() 
  {
  }

  /**
   *  @param bases The Bases object to pass to the Entry constructor.
   *  @param show_progress If true a InputStreamProgressDialog will be shown
   *    while loading.  (Not implemented)
   *  @exception OutOfRangeException Thrown if one of the features in
   *    the Entry is out of range of the Bases object.
   *  @return null if and only if the read is cancelled by the user or if the
   *    read fails.
   **/
  public Entry getEntry(final Bases bases, final boolean show_progress)
      throws OutOfRangeException, IOException
  {
    return null;
  }

  public Entry getEntry(final boolean show_progress)
      throws OutOfRangeException, IOException
  {
    return null;
  }

  /**
   *  Get an Entry object from this source.
   *  @param id Feature ID to read in.
   *  @exception OutOfRangeException Thrown if one of the features in
   *    the Entry is out of range of the Bases object.
   *  @exception NoSequenceException Thrown if the entry that we read has no
   *    sequence.
   *  @return null if and only if the user cancels the read or if the read
   *    fails.
   **/
  public Entry getEntry(String id, InputStreamProgressListener progress_listener)
      throws OutOfRangeException, NoSequenceException, IOException
  {
    return makeFromID(null,id,false,progress_listener);
  }

  /**
   *  Returns true if and only if this EntrySource always returns "full"
   *  entries.  ie. entries that contain features and sequence.
   **/
  public boolean isFullEntrySource()
  {
    return true;
  }

  /**
   *  Return the name of this source (for display to the user in menus).
   **/
  public String getSourceName()
  {
    return "Database";
  }


  /**
  *
  * Set the database location as:
  * jdbc:postgresql://localhost:13001/chadoCVS?user=es2
  *
  */
  protected boolean setLocation(final boolean prompt_user)
  {
    Container bacross = new Container();
    bacross.setLayout(new GridLayout(6,2,5,5));

    JLabel lServer = new JLabel("Server : ");
    bacross.add(lServer);
    JTextField inServer = new JTextField("localhost");
    bacross.add(inServer);

    JLabel lPort = new JLabel("Port : ");
    bacross.add(lPort);
    JTextField inPort = new JTextField("5432");
    bacross.add(inPort);

    JLabel lDB = new JLabel("Database : ");
    bacross.add(lDB);
    JTextField inDB = new JTextField("chado");
    bacross.add(inDB);

    JLabel lUser = new JLabel("User : ");
    bacross.add(lUser);
    JTextField inUser = new JTextField("afumigatus");
    bacross.add(inUser);

    JLabel lpasswd = new JLabel("Password : ");
    bacross.add(lpasswd);
    pfield = new JPasswordField(16);
    bacross.add(pfield);

    // given -Dchado=localhost:port/dbname?username
    if(System.getProperty("chado") != null)
    {
      String db_url = System.getProperty("chado").trim();
      int index;
      if((index = db_url.indexOf(":")) > -1)
      {
        inServer.setText(db_url.substring(0,index));
        int index2;
        if((index2 = db_url.indexOf("/")) > -1)
        {
          inPort.setText(db_url.substring(index+1,index2));
          int index3;
          if((index3 = db_url.indexOf("?")) > -1)
          {
            inDB.setText(db_url.substring(index2+1,index3));
            inUser.setText(db_url.substring(index3+1));
            
/*
            if(!prompt_user)
            {
              location = "jdbc:postgresql://"
                 +inServer.getText().trim()+ ":"
                 +inPort.getText().trim()+ "/"
                 +inDB.getText().trim()+ "?user="
                 +inUser.getText().trim();
              return true;
            }
*/
          }
        }
      }
    }

    int n = JOptionPane.showConfirmDialog(null, bacross,
                      "Enter Database Address",
                      JOptionPane.OK_CANCEL_OPTION,
                      JOptionPane.QUESTION_MESSAGE);
    if(n == JOptionPane.CANCEL_OPTION)
      return false;

    location = "jdbc:postgresql://"
      +inServer.getText().trim()+ ":"
      +inPort.getText().trim()+ "/"
      +inDB.getText().trim()+ "?user="
      +inUser.getText().trim();

     
     return true;
  }


  /**
  *
  *  Given the entry name get the seq feature_id
  *
  */
  protected String getEntryID(String name)
  {
    return (String)entries.get(name);
  }

  /**
  *
  * Create database organism JTree.
  *
  */
  protected JTree getDatabaseTree()
  {
    DatabaseDocument doc = new DatabaseDocument(location, pfield);

    entries = doc.getDatabaseEntries();
    Vector organism = doc.getOrganism();

    DefaultMutableTreeNode top =
        new DefaultMutableTreeNode("PSU Organism List");
    createNodes(top,organism,entries);
    final JTree tree = new JTree(top);
    tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);

    return tree;
  }

  /**
  *
  * Get DefaultMutableTreeNode of selected node
  * @return     node that is currently selected
  *
  */
  protected String getSelectedNode(JTree tree)
  {
    TreePath path = tree.getLeadSelectionPath();
    if(path == null)
      return null;

    DefaultMutableTreeNode seq_node  = (DefaultMutableTreeNode)path.getLastPathComponent();
    DefaultMutableTreeNode type_node = (DefaultMutableTreeNode)seq_node.getParent();
    DefaultMutableTreeNode org_node  = (DefaultMutableTreeNode)type_node.getParent();

    return (String)org_node.getUserObject() + " - " +
           (String)type_node.getUserObject() + " - " +
           (String)seq_node.getUserObject();
  }

  /**
  *
  * Create the nodes of the organism JTree
  * @param top		root node
  * @param org  	organism collection
  * @param organism 	sequences collection 
  *
  */
  private void createNodes(DefaultMutableTreeNode top, Vector org,
                           Hashtable organism)
  {
    Enumeration enum_org = org.elements();
    DefaultMutableTreeNode org_node;
    DefaultMutableTreeNode seq_node;
    DefaultMutableTreeNode typ_node;

    final Object v_organism[] = organism.keySet().toArray();
    final int v_organism_size = v_organism.length;
    Arrays.sort(v_organism);

    while(enum_org.hasMoreElements())
    { 
      String name = (String)enum_org.nextElement();
      org_node = new DefaultMutableTreeNode(name);
      top.add(org_node);

      Hashtable seq_type_node = new Hashtable();

      for(int i=0; i<v_organism_size; i++)
      {
        String seq_name = (String)v_organism[i];
        if(seq_name.startsWith(name))
        {
          int ind1 = seq_name.indexOf( "- ");
          int ind2 = seq_name.lastIndexOf("- ");

          String type =  seq_name.substring(ind1+2,ind2-1);
          seq_name = seq_name.substring(ind2+2);

          if(!seq_type_node.containsKey(type))
          {   
            typ_node = new DefaultMutableTreeNode(type);
            seq_type_node.put(type,typ_node);
            org_node.add(typ_node);          
          }
          else
            typ_node= (DefaultMutableTreeNode)seq_type_node.get(type);
         
          seq_node = new DefaultMutableTreeNode(seq_name);
          typ_node.add(seq_node);
        }
      }
    }
  }

  protected void setSplitGFF(final boolean splitGFFEntry)
  {
    this.splitGFFEntry = splitGFFEntry;
  }

  /**
   *
   *  Given an accession number and the handle of an EMBL corba server, this
   *  method will ask the user (using a TextRequester) for the id of a entry
   *  in the server and will then attempt to get it.
   *  @param bases If this is null a new Bases object will be created for the
   *    Entry once it has been read from the server.  If not null then it will
   *    be passed to the Entry constructor.
   *  @param corba_id The id of the entry in the database
   *  @param read_only true if and only if a read-only Entry should be created
   *    (some are always read only).
   *  @exception OutOfRangeException Thrown if one of the features in
   *    the Entry is out of range of the Bases object.
   **/
  protected Entry makeFromID(final Bases bases,
                             final String id,
                             final boolean read_only,
                             InputStreamProgressListener progress_listener)
      throws OutOfRangeException, IOException 
  {
    try 
    {
      DatabaseDocumentEntry db_entry = null;

      if(read_only) 
      {
      } 
      else 
      {
        DatabaseDocument doc = new DatabaseDocument(location, pfield, id, 
                               splitGFFEntry, progress_listener);
        db_entry = new DatabaseDocumentEntry(doc);
      }

      final Bases real_bases;

      if(bases == null)
      {
        if(db_entry.getSequence() == null)
        {
          JOptionPane.showMessageDialog(null,
                       "The selected entry contains no sequence: " + id,
                       "No Sequence",
                       JOptionPane.ERROR_MESSAGE);

          return null; 
        }

        real_bases = new Bases(db_entry.getSequence());
      } 
      else
        real_bases = bases;

      return new Entry(real_bases, db_entry);
    } 
    catch(InvalidKeyException e) 
    {
      JOptionPane.showMessageDialog(null,
                       "Unexpected error while accessing " + id + ": " + e,
                       "Invalid Key",
                       JOptionPane.ERROR_MESSAGE);
    }
    catch(EntryInformationException e) 
    {
      JOptionPane.showMessageDialog(null,
                       "Failed to get entry: " + e,
                       "Entry Information Exception",
                       JOptionPane.ERROR_MESSAGE);
    }

    return null;
  }

  protected DatabaseDocumentEntry[] 
                         makeFromGff(final DatabaseDocument doc, String id)
               throws OutOfRangeException, IOException
  {
    DatabaseDocumentEntry[] db_entry = null;
 
    try
    {
      DatabaseDocument[] new_docs = doc.getGffDocuments(location, id);
      db_entry = new DatabaseDocumentEntry[new_docs.length];

      for(int i=0; i<new_docs.length; i++)
        db_entry[i] = new DatabaseDocumentEntry(new_docs[i]);
    }
    catch(EntryInformationException e)
    {
      JOptionPane.showMessageDialog(null,
                       "Failed to get entry: " + e,
                       "Entry Information Exception",
                       JOptionPane.ERROR_MESSAGE);
    }

    return db_entry;
  }

}