[Biojava-l] 2 problems found in org.biojava.bio.seq.db.biosql code

[Frederik Decouttere]

Hi,

After doing some tests with the biojava - biosql code I think there are
2 (little) bugs in there:

- when persisting a Sequence which contains a Feature with
BetweenLocation this Location gets converted to a RangeLocation upon
retrieval

- when persisting a Sequence which contains (a) Feature(s) in 2
different biodatabases an exception is thrown in the ontology code part
of biojava

You can find an example for both cases below

Environment: biojava.jar build from cvs, hsqldb database + biosql
schema, jdk1.4

If someone with knowledge of the biosql persistence code finds some time
to have a look...
Dont think it's very hard to fix

Ciao
Frederik

######test
code##################################################################
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.biosql.*;
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.symbol.*;

public class BioSqlTest {
	
	String driver = "org.hsqldb.jdbcDriver" ;
	String user = "sa";
	String pass = "";
	String url = "jdbc:hsqldb:file:./database/biosqldb" ;

	public BioSqlTest() {
	}
	
	/**
	 * demonstrates the switch from between to range location after
persistence code
	 */
	public void generateFeaturePersistenceProblem() throws Exception
{
		BioSQLSequenceDB db1 = new BioSQLSequenceDB(driver, url,
user, pass
	
, "testbiosqldb_1", true);
		db1.addSequence(getSequence()) ;
		
		Sequence seq = db1.getSequence("test_seq") ;
		for (Iterator iter = seq.features(); iter.hasNext();) {
			StrandedFeature f = (StrandedFeature)
iter.next();
			Location loc = f.getLocation() ;
			
			/*
			 * ERROR: Location is now a RangeLocation and
not a BetweenLocation !
			 */
			
			if(loc instanceof BetweenLocation) {
				// ok
				System.out.println("[feature] location
is still a BetweenLocation: "
				+ loc.getClass().getName());
			}
			else {
				// problem
				System.out.println("[feature] location
is now an instance of: " 
							+
loc.getClass().getName());
			}
		}
	}
	
	public void generateOntolgyPersistenceProblem() throws Exception
{

		BioSQLSequenceDB db2 = new BioSQLSequenceDB(driver, url,
user, pass
	
, "testbiosqldb_2", true);
									
		/*
		 	EXCEPTION: the second addSequence will cause a
exception 
		 	in the ontology persistence code

			Caused by: java.sql.SQLException: Failed to
persist term: ATYPE from ontology: ontology: __biojava_guano with error:
-9 : 23000
				at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:5
06)
				at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
68)
				... 12 more
			Caused by: java.sql.SQLException: Violation of
unique index: SYS_IDX_SYS_CT_9_10 in statement [insert into term
(name, definition, ontology_id) values (?, ?, ?)]
				at
org.hsqldb.jdbcDriver.throwError(Unknown Source)
				at
org.hsqldb.jdbcPreparedStatement.executeUpdate(Unknown Source)
				at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delega
tingPreparedStatement.java:233)
				at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delega
tingPreparedStatement.java:233)
				at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:4
98)
				... 13 more
		 */
		
		db2.addSequence(getSequence()) ;
	}
	
	public static Sequence getSequence() throws Exception {
		SymbolList sl =
DNATools.createDNA("ACTGGTGTACCCCAATGGGAATATC") ;
		Sequence sequence = new SimpleSequence(sl, null,
"test_seq", null);
		sequence.createFeature(getFeature());
		return sequence ;
	}
	
	private static StrandedFeature.Template getFeature() throws
Exception {
		SimpleAnnotation annotation = new SimpleAnnotation();
		annotation.setProperty("Comment", "comment line");
		StrandedFeature.Template templ = new
StrandedFeature.Template();
		templ.annotation = annotation;
		templ.location = new BetweenLocation(new
RangeLocation(3,4));
		templ.strand = StrandedFeature.POSITIVE;
		templ.type = "ATYPE";
		templ.source = "ASRC";
		
		return templ ;
	}
	
	public static void main(String[] args) {
		BioSqlTest test = new BioSqlTest() ;
		try {
			test.generateFeaturePersistenceProblem() ;
		}
		catch(Throwable t) {
			t.printStackTrace();
		}

		try {
			//test.generateOntolgyPersistenceProblem() ;
		}
		catch(Throwable t) {
			t.printStackTrace();
		}
		finally {
			System.exit(0);
		}
	}
}

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