Revision as of 16:15, 29 January 2010

Note: this is NOT the official version of the DAS specification.

Distributed Annotation System (DAS) 1.6

This is a working document and a proposal for a reworked DAS specification which hopes to:

• clarify the existing DAS spec
• better reflect how DAS is being used in the community today
• better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures)
• ratify commands from the 1.53E spec
• introduce some ideas inspired by DAS/2
• formally introduce the DAS registry
• migrate from the use of DTDs for describing the XML formats to RelaxNG

Note: the DAS specification is a technical document but with some effort should hopefully be readable and understandable by people without a deep understanding of broader technical issues and other system architectures. That is, it makes only basic assumptions.

The specification has been written as a number of drafts:

• Draft 1
• Draft 2
• Draft 3
• Draft 5

Last modified: 29th Jan 2010

(DAS) 1.6 Development and Tutorials

Dazzle Example adaptor for 1.6 spec source compliant with the registry

/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on 10.09.2009
 * @author Jonathan Warren
 *
 */

package uk.ac.sanger.dazzle.datasource;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import javax.naming.Context;
import javax.naming.InitialContext;
import javax.servlet.ServletContext;
import javax.sql.DataSource;

import org.biojava.servlets.dazzle.Segment;
import org.biojava.servlets.dazzle.datasource.Abstract16FeatureSource;
import org.biojava.servlets.dazzle.datasource.AbstractGFFFeatureSource;
import org.biojava.servlets.dazzle.datasource.DASGFFGroup;
import org.biojava.servlets.dazzle.datasource.DataSourceException;
import org.biojava.servlets.dazzle.datasource.GFF16Feature;
import org.biojava.servlets.dazzle.datasource.GFFFeature;
import org.biojava.servlets.dazzle.datasource.Type16MetadataSource;
import org.biojava.servlets.dazzle.datasource.TypeMetadataSource;

public class DazzleTest16Source extends Abstract16FeatureSource implements Type16MetadataSource {
	DataSource dataSource;
	String dataSourceName;
	
	public String getDataSourceName() {
		return dataSourceName;
	}



	public void setDataSourceName(String dataSourceName) {
		this.dataSourceName = dataSourceName;
	}



	public void init (ServletContext ctx) throws DataSourceException{
	System.out.println("init DazzleTest15Source " + dataSourceName);
	
	super.init(ctx);
	
	
	
	try {
		Context env = (Context) new InitialContext().lookup("java:comp/env");
		System.out.println("trying to get datasource from context");
		dataSource = (DataSource) env.lookup(dataSourceName) ;
	} catch (Exception ex) {
		throw new DataSourceException (ex);
	}
	}



	public GFF16Feature[] getFeatures(Segment seg, String[] types)
			throws DataSourceException {
		//all types are the same for this source so filtering on tyes is unecessary
		Connection conn =null;
		
		List <GFF16Feature>gffFeatures = new ArrayList<GFF16Feature>();
		try {
			conn = dataSource.getConnection();

			// create Structure object from MSD database query.
		} catch (SQLException e) {
			e.printStackTrace();
			
		}
		//get data from segment object
		String ref=seg.getReference();
		String start=Integer.toString(seg.getStart());
		String stop=Integer.toString(seg.getStop());
		//this source is attached to the generic grouped_db database schema
		//proserver sourceAdapter grouped_db.pm
		//for the proserver_vertres_mouse_snps_WSB_EiJ database they could just have had one table
		//the feature table and not fgroup as they only have same id and everything else is null!!!
		//as a generic source we will leave the query as it is though!!
		//maybe i need another example with groups in !! especially for 1.6 testing!!!
		String sql="SELECT * FROM feature, fgroup "+
        " WHERE  segment = ? "+
        " AND start <= ? "+" AND end >=? "+ 
        " AND    feature.group_id = fgroup.group_id "+
        " ORDER BY start;";
		//System.out.println(sql);
		try {
			PreparedStatement ps=conn.prepareStatement(sql);
			ps.setString(1,ref);
			ps.setString(2,stop);
			ps.setString(3, start);
		ResultSet results=ps.executeQuery();
		
			while(results.next()){
				GFF16Feature feature=new GFF16Feature();
				feature.setName(results.getString("id"));
				//System.out.println("adding id="+results.getString("id"));
				feature.setStart(results.getString("start"));
				feature.setEnd(results.getString("end"));
				
				DASGFFGroup group=new DASGFFGroup(results.getString("group_id"),"Coding SNP");
				feature.setLabel(results.getString("id"));
				feature.setMethod("samtools");//can get it from database but they are all same in this source
				feature.setOrientation(results.getString("orient"));
				//feature.setType(results.getString("type_id"));
				//actually type should be ontology from SO for snp it's SO:0000694
				feature.setType(results.getString("type_id"));
				//feature.setTypeCategory(results.getString("type_catagory"));
				//ECO:0000053 inferred from reviewed computational analysis
				feature.setTypeCategory(results.getString("type_cat"));//"ECO:0000053");//normally would come from the database
				feature.setTypeId(results.getString("type_id"));//"SO:0000694");//normally would come from the database
				
				feature.setGroup(group);
				
				//filter by types if on the end of the url has ;type=exon
				if (types!=null) {
					for (String type : types) {
						//System.out.println("types=" + type);
						if(type.equals(results.getString("type_id"))){
							gffFeatures.add(feature);
						}
					}
				}else{
				gffFeatures.add(feature);
				}
			}
			
			

			
				
				ps.close();
				conn.close();
			
		} catch (SQLException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
		
		
		GFF16Feature[] gffs = gffFeatures.toArray(new GFF16Feature[gffFeatures.size()]) ;
		
		
		return gffs;
	}
	
	
	public String getFeatureID(GFFFeature f) {
		//override this method as our feature ids are unique and same as name anyway
        StringBuffer sb = new StringBuffer();
        
        sb.append(f.getName());
       
        return sb.toString();
		 
	}
	
	public Set<String> getAllTypes(){
		Set<String> list=new HashSet<String>();
Connection conn =null;
		
		try {
			conn = dataSource.getConnection();

			// create Structure object from MSD database query.
		} catch (SQLException e) {
			e.printStackTrace();
			
		}
		//the type_id and category in the database are the wrong way around
		//ie the type_id will be better as the category "variation" while the type_id is non_synonymous or synonymous
		//this is because the id needs to be unique and have one category
		String sql="SELECT distinct type_id FROM feature";
		//System.out.println(sql);
		try {
			PreparedStatement ps=conn.prepareStatement(sql);
			
		ResultSet results=ps.executeQuery();
	
			while(results.next()){
				String type_id=results.getString("type_id");
				list.add(type_id);
				//String type_category=results.getString("type_category");
				
			}
			

			
				
				ps.close();
			
			
		} catch (SQLException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
		}
		
		
		
		//list.add("Coding SNP");
		return Collections.unmodifiableSet(list);
	}



	public String getCategory(String arg0) {
Connection conn =null;
String type_category=null;
		try {
			conn = dataSource.getConnection();

			// create Structure object from MSD database query.
		} catch (SQLException e) {
			e.printStackTrace();
			
		}
		
		String sql="SELECT type_cat FROM feature where type_id=?";
		System.out.println(sql);
		try {
			PreparedStatement ps=conn.prepareStatement(sql);
			ps.setString(1, arg0);
		ResultSet results=ps.executeQuery();

			while(results.next()){
				type_category=results.getString("type_cat");
				
				//String type_category=results.getString("type_category");
				
			}
			

			
				
				ps.close();
			
			
		} catch (SQLException e) {
			
			e.printStackTrace();
		}
		
		return type_category;
	}


	public String getTypeCvId(String type) {
		
		return "cvId here";
	}



	public int getTypeCount(String t) {
		//some database call should go here
		int typeCount=0;
		Connection conn =null;
		String type_category=null;
				try {
					conn = dataSource.getConnection();

					// create Structure object from MSD database query.
				} catch (SQLException e) {
					e.printStackTrace();
					
				}
				
				String sql="select type_id, COUNT(*) from feature where type_id=?";
				//System.out.println(sql);
				try {
					PreparedStatement ps=conn.prepareStatement(sql);
				ps.setString(1, t);	
				ResultSet results=ps.executeQuery();
				
					while(results.next()){
						typeCount=results.getInt(2);
						
						//String type_category=results.getString("type_category");
						
					}
					

					
						
						ps.close();
						conn.close();
					
					
				} catch (SQLException e) {
					
					e.printStackTrace();
				}
		return typeCount;
	}



	

	
}