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| | ==Dazzle Example adaptor for 1.6 spec source compliant with the registry == | | ==Dazzle Example adaptor for 1.6 spec source compliant with the registry == |
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| − | <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
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| − | *
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| − | * This code may be freely distributed and modified under the
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| − | * terms of the GNU Lesser General Public Licence. This should
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| − | * be distributed with the code. If you do not have a copy,
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| − | * see:
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| − | *
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| − | * http://www.gnu.org/copyleft/lesser.html
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| − | *
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| − | * Copyright for this code is held jointly by the individual
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| − | * authors. These should be listed in @author doc comments.
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| − | *
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| − | * For more information on the BioJava project and its aims,
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| − | * or to join the biojava-l mailing list, visit the home page
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| − | * at:
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| − | *
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| − | * http://www.biojava.org/
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| − | *
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| − | * Created on 10.09.2009
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| − | * @author Jonathan Warren
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| − | *
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| − | */
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| − | | |
| − | package uk.ac.sanger.dazzle.datasource;
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| − | import java.sql.Connection;
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| − | import java.sql.PreparedStatement;
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| − | import java.sql.ResultSet;
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| − | import java.sql.SQLException;
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| − | import java.util.ArrayList;
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| − | import java.util.Collections;
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| − | import java.util.HashSet;
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| − | import java.util.List;
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| − | import java.util.Set;
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| − | | |
| − | import javax.naming.Context;
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| − | import javax.naming.InitialContext;
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| − | import javax.servlet.ServletContext;
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| − | import javax.sql.DataSource;
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| − | | |
| − | import org.biojava.servlets.dazzle.Segment;
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| − | import org.biojava.servlets.dazzle.datasource.Abstract16FeatureSource;
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| − | import org.biojava.servlets.dazzle.datasource.AbstractGFFFeatureSource;
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| − | import org.biojava.servlets.dazzle.datasource.DASGFFGroup;
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| − | import org.biojava.servlets.dazzle.datasource.DataSourceException;
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| − | import org.biojava.servlets.dazzle.datasource.GFF16Feature;
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| − | import org.biojava.servlets.dazzle.datasource.GFFFeature;
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| − | import org.biojava.servlets.dazzle.datasource.Type16MetadataSource;
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| − | import org.biojava.servlets.dazzle.datasource.TypeMetadataSource;
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| − | | |
| − | public class DazzleTest16Source extends Abstract16FeatureSource implements Type16MetadataSource {
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| − | DataSource dataSource;
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| − | String dataSourceName;
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| − |
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| − | public String getDataSourceName() {
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| − | return dataSourceName;
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| − | }
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| − | | |
| − | | |
| − | | |
| − | public void setDataSourceName(String dataSourceName) {
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| − | this.dataSourceName = dataSourceName;
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| − | }
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| − | | |
| − | | |
| − | | |
| − | public void init (ServletContext ctx) throws DataSourceException{
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| − | System.out.println("init DazzleTest15Source " + dataSourceName);
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| − |
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| − | super.init(ctx);
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| − |
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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");
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| − | System.out.println("trying to get datasource from context");
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| − | dataSource = (DataSource) env.lookup(dataSourceName) ;
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| − | } catch (Exception ex) {
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| − | throw new DataSourceException (ex);
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| − | }
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| − | }
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| − | | |
| − | | |
| − | | |
| − | public GFF16Feature[] getFeatures(Segment seg, String[] types)
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| − | throws DataSourceException {
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| − | //all types are the same for this source so filtering on tyes is unecessary
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| − | Connection conn =null;
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| − |
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| − | List <GFF16Feature>gffFeatures = new ArrayList<GFF16Feature>();
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| − | try {
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| − | conn = dataSource.getConnection();
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| − | | |
| − | // create Structure object from MSD database query.
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| − | } catch (SQLException e) {
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| − | e.printStackTrace();
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| − |
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| − | }
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| − | //get data from segment object
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| − | String ref=seg.getReference();
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| − | String start=Integer.toString(seg.getStart());
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| − | String stop=Integer.toString(seg.getStop());
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| − | //this source is attached to the generic grouped_db database schema
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| − | //proserver sourceAdapter grouped_db.pm
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| − | //for the proserver_vertres_mouse_snps_WSB_EiJ database they could just have had one table
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| − | //the feature table and not fgroup as they only have same id and everything else is null!!!
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| − | //as a generic source we will leave the query as it is though!!
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| − | //maybe i need another example with groups in !! especially for 1.6 testing!!!
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| − | String sql="SELECT * FROM feature, fgroup "+
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| − | " WHERE segment = ? "+
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| − | " AND start <= ? "+" AND end >=? "+
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| − | " AND feature.group_id = fgroup.group_id "+
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| − | " ORDER BY start;";
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| − | //System.out.println(sql);
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| − | try {
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| − | PreparedStatement ps=conn.prepareStatement(sql);
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| − | ps.setString(1,ref);
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| − | ps.setString(2,stop);
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| − | ps.setString(3, start);
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| − | ResultSet results=ps.executeQuery();
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| − |
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| − | while(results.next()){
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| − | GFF16Feature feature=new GFF16Feature();
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| − | feature.setName(results.getString("id"));
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| − | //System.out.println("adding id="+results.getString("id"));
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| − | feature.setStart(results.getString("start"));
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| − | feature.setEnd(results.getString("end"));
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| − |
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| − | DASGFFGroup group=new DASGFFGroup(results.getString("group_id"),"Coding SNP");
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| − | feature.setLabel(results.getString("id"));
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| − | feature.setMethod("samtools");//can get it from database but they are all same in this source
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| − | feature.setOrientation(results.getString("orient"));
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| − | //feature.setType(results.getString("type_id"));
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| − | //actually type should be ontology from SO for snp it's SO:0000694
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| − | feature.setType(results.getString("type_id"));
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| − | //feature.setTypeCategory(results.getString("type_catagory"));
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| − | //ECO:0000053 inferred from reviewed computational analysis
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| − | feature.setTypeCategory(results.getString("type_cat"));//"ECO:0000053");//normally would come from the database
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| − | feature.setTypeId(results.getString("type_id"));//"SO:0000694");//normally would come from the database
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| − |
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| − | feature.setGroup(group);
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| − |
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| − | //filter by types if on the end of the url has ;type=exon
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| − | if (types!=null) {
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| − | for (String type : types) {
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| − | //System.out.println("types=" + type);
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| − | if(type.equals(results.getString("type_id"))){
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| − | gffFeatures.add(feature);
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| − | }
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| − | }
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| − | }else{
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| − | gffFeatures.add(feature);
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| − | }
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| − | }
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| − |
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| − |
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| − | | |
| − |
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| − |
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| − | ps.close();
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| − | conn.close();
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| − |
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| − | } catch (SQLException e) {
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| − | // TODO Auto-generated catch block
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| − | e.printStackTrace();
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| − | }
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| − |
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| − |
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| − | GFF16Feature[] gffs = gffFeatures.toArray(new GFF16Feature[gffFeatures.size()]) ;
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| − |
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| − |
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| − | return gffs;
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| − | }
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| − |
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| − |
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| − | public String getFeatureID(GFFFeature f) {
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| − | //override this method as our feature ids are unique and same as name anyway
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| − | StringBuffer sb = new StringBuffer();
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| − |
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| − | sb.append(f.getName());
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| − |
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| − | return sb.toString();
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| − |
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| − | }
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| − |
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| − | public Set<String> getAllTypes(){
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| − | Set<String> list=new HashSet<String>();
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| − | Connection conn =null;
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| − |
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| − | try {
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| − | conn = dataSource.getConnection();
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| − | | |
| − | // create Structure object from MSD database query.
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| − | } catch (SQLException e) {
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| − | e.printStackTrace();
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| − |
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| − | }
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| − | //the type_id and category in the database are the wrong way around
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| − | //ie the type_id will be better as the category "variation" while the type_id is non_synonymous or synonymous
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| − | //this is because the id needs to be unique and have one category
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| − | String sql="SELECT distinct type_id FROM feature";
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| − | //System.out.println(sql);
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| − | try {
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| − | PreparedStatement ps=conn.prepareStatement(sql);
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| − |
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| − | ResultSet results=ps.executeQuery();
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| − |
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| − | while(results.next()){
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| − | String type_id=results.getString("type_id");
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| − | list.add(type_id);
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| − | //String type_category=results.getString("type_category");
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| − |
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| − | }
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| − |
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| − | | |
| − |
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| − |
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| − | ps.close();
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| − |
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| − |
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| − | } catch (SQLException e) {
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| − | // TODO Auto-generated catch block
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| − | e.printStackTrace();
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| − | }
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| − |
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| − |
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| − |
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| − | //list.add("Coding SNP");
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| − | return Collections.unmodifiableSet(list);
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| − | }
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| − | | |
| − | | |
| − | | |
| − | public String getCategory(String arg0) {
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| − | Connection conn =null;
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| − | String type_category=null;
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| − | try {
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| − | conn = dataSource.getConnection();
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| − | | |
| − | // create Structure object from MSD database query.
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| − | } catch (SQLException e) {
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| − | e.printStackTrace();
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| − |
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| − | }
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| − |
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| − | String sql="SELECT type_cat FROM feature where type_id=?";
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| − | System.out.println(sql);
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| − | try {
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| − | PreparedStatement ps=conn.prepareStatement(sql);
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| − | ps.setString(1, arg0);
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| − | ResultSet results=ps.executeQuery();
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| − | | |
| − | while(results.next()){
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| − | type_category=results.getString("type_cat");
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| − |
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| − | //String type_category=results.getString("type_category");
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| − |
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| − | }
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| − |
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| − | | |
| − |
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| − |
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| − | ps.close();
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| − |
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| − |
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| − | } catch (SQLException e) {
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| − |
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| − | e.printStackTrace();
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| − | }
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| − |
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| − | return type_category;
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| − | }
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| − | | |
| − | | |
| − | public String getTypeCvId(String type) {
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| − |
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| − | return "cvId here";
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| − | }
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| − | | |
| − | | |
| − | | |
| − | public int getTypeCount(String t) {
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| − | //some database call should go here
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| − | int typeCount=0;
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| − | Connection conn =null;
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| − | String type_category=null;
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| − | try {
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| − | conn = dataSource.getConnection();
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| − | | |
| − | // create Structure object from MSD database query.
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| − | } catch (SQLException e) {
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| − | e.printStackTrace();
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| − |
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| − | }
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| − |
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| − | String sql="select type_id, COUNT(*) from feature where type_id=?";
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| − | //System.out.println(sql);
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| − | try {
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| − | PreparedStatement ps=conn.prepareStatement(sql);
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| − | ps.setString(1, t);
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| − | ResultSet results=ps.executeQuery();
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| − |
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| − | while(results.next()){
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| − | typeCount=results.getInt(2);
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| − |
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| − | //String type_category=results.getString("type_category");
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| − |
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| − | }
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| − |
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| − | | |
| − |
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| − |
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| − | ps.close();
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| − | conn.close();
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| − |
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| − |
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| − | } catch (SQLException e) {
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| − |
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| − | e.printStackTrace();
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| − | }
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| − | return typeCount;
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| − | }
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| − | | |
| − | | |
| − | | |
| − |
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| − | | |
| − |
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| − | }
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| − | </pre>
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This is a working document and a proposal for a reworked DAS specification which hopes to:
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.
