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| − | '''Note: this is NOT the official version of the [http://biodas.org/documents/spec.html DAS specification].'''
| + | DAS 1.6 is, as of 19th October 2010, the latest official version of DAS. The specification document is found here: |
| | + | [http://www.biodas.org/documents/spec-1.6.html DAS 1.6 specification] |
| | | | |
| − | =Distributed Annotation System (DAS) 1.6=
| + | 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. |
| | | | |
| − | This is a working document and a proposal for a reworked DAS specification which hopes to:
| + | ==Purpose== |
| − | * clarify the existing DAS spec | + | |
| | + | It is the first official version published in several years, and aims to: |
| | + | * clarify ambiguities in the previous DAS specification |
| | * better reflect how DAS is being used in the community today | | * 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) | | * better reflect the use of DAS beyond the genome-centric arena (protein sequences and structures) |
| − | * ratify commands from the [http://www.dasregistry.org/spec_1.53E.jsp 1.53E spec] | + | * ratify commands from the [http://www.dasregistry.org/spec_1.53E.jsp 1.53E extended spec] |
| | * introduce some ideas inspired by DAS/2 | | * introduce some ideas inspired by DAS/2 |
| | * formally introduce the DAS registry | | * formally introduce the DAS registry |
| | * migrate from the use of DTDs for describing the XML formats to RelaxNG | | * 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 list of changes is listed here: [[DAS 1.6 Changes]]. |
| − | | |
| − | The specification has been written as a number of drafts:
| |
| − | * [http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html Draft 1]
| |
| − | * [http://www.ebi.ac.uk/~aj/1.6_draft2/documents/spec.html Draft 2]
| |
| − | * [http://www.ebi.ac.uk/~aj/1.6_draft3/documents/spec.html Draft 3]
| |
| − | * [http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html Draft 5]
| |
| − | Last modified: 29th Jan 2010
| |
| | | | |
| | + | ==Compatibility== |
| | | | |
| − | =(DAS) 1.6 Development and Tutorials=
| + | Software developers wanting to know more about supporting or migrating between different versions of the specification may wish to consult the [[DAS 1.6 Migration]] page. |
| − | ==Dazzle Example adaptor for 1.6 spec source compliant with the registry ==
| |
| | | | |
| − | <pre>
| + | ==Extensions== |
| − | /*
| |
| − | * 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;
| + | Several extensions to the 1.6 are proposed by community members. See the [[DAS1.6E]] page for more details. |
| − | 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;
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| − |
| |
| − | 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);
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| − |
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| − |
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| − |
| |
| − | try {
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| − | 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;
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| − |
| |
| − | List <GFF16Feature>gffFeatures = new ArrayList<GFF16Feature>();
| |
| − | try {
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| − | conn = dataSource.getConnection();
| |
| − | | |
| − | // create Structure object from MSD database query.
| |
| − | } catch (SQLException e) {
| |
| − | e.printStackTrace();
| |
| − |
| |
| − | }
| |
| − | //get data from segment object
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| − | 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"));
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| − |
| |
| − | 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);
| |
| − | }
| |
| − | }
| |
| − |
| |
| − |
| |
| − | | |
| − |
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| − |
| |
| − | ps.close();
| |
| − | conn.close();
| |
| − |
| |
| − | } catch (SQLException e) {
| |
| − | // TODO Auto-generated catch block
| |
| − | e.printStackTrace();
| |
| − | }
| |
| − |
| |
| − |
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| − | 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);
| |
| − |
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| − | 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");
| |
| − |
| |
| − | }
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| − |
| |
| − | | |
| − |
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| − |
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| − | 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");
| |
| − |
| |
| − | }
| |
| − |
| |
| − | | |
| − |
| |
| − |
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| − | ps.close();
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| − | conn.close();
| |
| − |
| |
| − |
| |
| − | } catch (SQLException e) {
| |
| − |
| |
| − | e.printStackTrace();
| |
| − | }
| |
| − | return typeCount;
| |
| − | }
| |
| | | | |
| | + | ==Development== |
| | | | |
| | + | The specification was developed as a community collaboration via progression through a number of drafts: |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft1/documents/spec.html Draft 1] |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft2/documents/spec.html Draft 2] |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft3/documents/spec.html Draft 3] |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft4/documents/spec.html Draft 4] |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft5/documents/spec.html Draft 5] |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft6/documents/spec.html Draft 6] |
| | + | * [http://www.ebi.ac.uk/~aj/1.6_draft7/documents/spec.html Draft 7] |
| | | | |
| − |
| + | ==Links== |
| | | | |
| − |
| + | [[DAS 1.6 in Dazzle]] |
| − | }
| |
| − | </pre>
| |
DAS 1.6 is, as of 19th October 2010, the latest official version of DAS. The specification document is found here:
DAS 1.6 specification
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.
Software developers wanting to know more about supporting or migrating between different versions of the specification may wish to consult the DAS 1.6 Migration page.
The specification was developed as a community collaboration via progression through a number of drafts:
