Difference between revisions of "DAS1.6"

From BioDAS
Jump to: navigation, search
(Dazzle)
((DAS) 1.6 Development and Tutorials)
Line 25: Line 25:
 
==Dazzle Example adaptor for 1.6 spec source compliant with the registry ==
 
==Dazzle Example adaptor for 1.6 spec source compliant with the registry ==
  
<pre>
+
Subversion develpment repository http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle
/*
+
See class org.biojava.servlets.dazzle.datasource.SimpleFile16ExampleSource for a datasource that conforms to the new 1.6 Spec.
*                    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;
 
}
 
 
 
 
 
 
 
 
 
 
 
}
 
</pre>
 

Revision as of 12:26, 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:

Last modified: 29th Jan 2010


(DAS) 1.6 Development and Tutorials

Dazzle Example adaptor for 1.6 spec source compliant with the registry

Subversion develpment repository http://www.derkholm.net/svn/repos/dazzle/branches/16Dazzle See class org.biojava.servlets.dazzle.datasource.SimpleFile16ExampleSource for a datasource that conforms to the new 1.6 Spec.