[Biojava-l] Ontology and BioSQL
Richard HOLLAND
hollandr at gis.a-star.edu.sg
Thu Dec 2 05:05:15 EST 2004
That'd be nice but unfortunately Oracle is case-sensitive. However I
think I just got what was causing it, see my post of 5 seconds ago. I'm
not sure why it hasn't broken for other people though.
cheers,
Richard
Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: Thomas Down [mailto:td2 at sanger.ac.uk]
> Sent: Thursday, December 02, 2004 6:03 PM
> To: Richard HOLLAND
> Cc: mark.schreiber at group.novartis.com; biojava-l at biojava.org
> Subject: Re: [Biojava-l] Ontology and BioSQL
>
>
> Hi Richard,
>
> We've had a problem very much like this when using BioSQL
> with a MySQL
> database -- the issue occurs when you have two "ontology
> terms" (which
> are used for a number of different purposes -- feature types,
> annotation keys, etc) which differ only by name. For example
> "organism" and "ORGANISM". There's was a discussion of this issue in
> MySQL here:
>
>
> http://www.biojava.org/pipermail/biojava-dev/2004-August/001857.html
>
> From your stacktraces, it looks like you're actually using
> Oracle -- I
> don't use Oracle myself so can't confirm that this is the
> same problem,
> but it looks very similar.
>
> Is there a way to enforce uniqueness in a case-sensitive way
> in Oracle?
>
> Thomas.
>
>
> On 2 Dec 2004, at 08:52, Richard HOLLAND wrote:
>
> > Yup, this problem happened since the very first time I ran it on an
> > empty database. The terms get created in term, the term
> representing
> > the triple gets created in term, but it does not create the
> > relationship in term_relationship.
> >
> > The exception is being thrown by the persistTerm call on the very
> > first line of persistTriple.
> >
> > I'm thinking that this is something to do with the OntologyMonitor?
> > That
> > it is seeing the Triple get created, but
> > because the Triple is an instanceof Term it is firing two
> change events
> > - one for the Term representation, the
> > other for the Triple representation? That's the only way I
> can see the
> > Triple being created in the term table but
> > not in the term_relationship table, as otherwise we'd be getting
> > exceptions halfway through persistTriple way after that call to
> > persistTerm at the beginning, which we're not.
> >
> > In other words, the Triple already exists in the term table
> _before_
> > persistTriple is getting called. Why? How? Hmm.
> >
> > cheers,
> > Richard
> >
> > Richard Holland
> > Bioinformatics Specialist
> > GIS extension 8199
> >
> > ---------------------------------------------
> > This email is confidential and may be privileged. If you
> are not the
> > intended recipient, please delete it and notify us
> immediately. Please
> > do not copy or use it for any purpose, or disclose its
> content to any
> > other person. Thank you.
> > ---------------------------------------------
> >
> >
> >> -----Original Message-----
> >> From: mark.schreiber at group.novartis.com
> >> [mailto:mark.schreiber at group.novartis.com]
> >> Sent: Thursday, December 02, 2004 4:18 PM
> >> To: Richard HOLLAND
> >> Cc: biojava-l at biojava.org; biojava-l-bounces at portal.open-bio.org
> >> Subject: Re: [Biojava-l] Ontology and BioSQL
> >>
> >>
> >> Hi -
> >>
> >> The code responsible for the insert is:
> >>
> >> private void persistTriple(Connection conn, Ontology ont, Triple
> >> triple)
> >> throws SQLException
> >> {
> >> persistTerm(conn, triple);
> >>
> >> PreparedStatement import_trip = conn.prepareStatement(
> >> "insert into term_relationship " +
> >> " (subject_term_id, predicate_term_id,
> >> object_term_id,
> >> ontology_id) " +
> >> "values (?, ?, ?, ?)"
> >> );
> >> import_trip.setInt(1, termID(triple.getSubject()));
> >> import_trip.setInt(2, termID(triple.getPredicate()));
> >> import_trip.setInt(3, termID(triple.getObject()));
> >> import_trip.setInt(4, ontologyID(ont));
> >> import_trip.executeUpdate();
> >> import_trip.close();
> >> int tripID = dbHelper.getInsertID(conn, "term_relationship",
> >> "term_relationship_id");
> >>
> >> PreparedStatement link_trip_to_term = conn.prepareStatement(
> >> "insert into term_relationship_term " +
> >> " (term_relationship_id, term_id) " +
> >> "values (?, ?)" );
> >> link_trip_to_term.setInt(1, tripID);
> >> link_trip_to_term.setInt(2, termID(triple));
> >> link_trip_to_term.executeUpdate();
> >> link_trip_to_term.close();
> >>
> >> //System.err.println("Persisted triple: " + triple);
> >> }
> >>
> >> I can't immediately see any attempt to write it twice. Are you
> >> removing the old triples before running the program again?
> >>
> >> - Mark
> >>
> >>
> >>
> >>
> >>
> >> "Richard HOLLAND" <hollandr at gis.a-star.edu.sg>
> >> Sent by: biojava-l-bounces at portal.open-bio.org
> >> 12/02/2004 02:16 PM
> >>
> >>
> >> To: <biojava-l at biojava.org>
> >> cc: (bcc: Mark Schreiber/GP/Novartis)
> >> Subject: [Biojava-l] Ontology and BioSQL
> >>
> >>
> >> Hi all,
> >>
> >> I am trying to use the Ontology class in Biojava 1.4rc1 to create
> >> terms and triples, which are automatically persisted using
> the BioSQL
> >> links in BioJava. Here is my code:
> >>
> >> BioSQLSequenceDB db = new BioSQLSequenceDB(dbURL,
> >> dbUser,
> >> dbPass,
> >> biodatabase,
> >> createIfMissing);
> >>
> >> Ontology o = db.createOntology("MyOntology","An
> >> ontology"); // Use getOntology to update
> >> Term MyGroup = o.createTerm("MyGroup","My
> favourite terms.");
> >> Term Boo = o.createTerm("Boo","A fright");
> >> Term ISA = o.createTerm("ISA","Is a");
> >> Term Joke = o.createTerm("Joke","Something funny");
> >> o.createTriple(Boo,Joke,ISA,null,null);
> >>
> >> I get the following exception (NB. the ontology does not exist yet
> >> but the database connection is just fine):
> >>
> >> Exception in thread "main"
> >> org.biojava.bio.BioRuntimeException: Error removing from BioSQL
> >> tables (rolled back successfully) at
> >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(Ontolo
> >> gySQL.java
> >> :588)
> >> at org.biojava.bio.seq.db.biosql.OntologySQL.access$300(OntologyS
> >> QL.java:61
> >> )
> >> at
> >> org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.post
> >> Change(Ont
> >> ologySQL.java:512)
> >> at
> >> org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupp
> >> ort.java:3
> >> 38)
> >> at
> org.biojava.ontology.Ontology$Impl.createTriple(Ontology.java:497)
> >> at testapp.LoadOntology.main(LoadOntology.java:61)
> >> Caused by: java.sql.SQLException: Failed to persist term:
> >> ISA(Boo, Joke) from ontology: ontology: MyOntology with
> >> error: 1 : 23000 at
> >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(Ontology
> >> SQL.java:5
> >> 62)
> >> at
> >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(Ontolo
> >> gySQL.java
> >> :595)
> >> at
> >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(Ontolo
> >> gySQL.java
> >> :576)
> >> ... 5 more
> >> Caused by: java.sql.SQLException: ORA-00001: unique constraint
> >> (BIOSQL_OWNER.XAK1TERM) violated
> >> at
> >> oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseErr
> >> or.java:12
> >> 5)
> >> at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:305)
> >> at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:272)
> >> at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:623)
> >> at
> >> oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedSta
> >> tement.jav
> >> a:181)
> >> at
> >> oracle.jdbc.driver.T4CPreparedStatement.execute_for_rows(T4CPr
> >> eparedStat
> >> ement.java:543)
> >> at
> >> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(Oracle
> >> Statement.
> >> java:1028)
> >> at
> >> oracle.jdbc.driver.OraclePreparedStatement.executeInternal(Ora
> >> clePrepare
> >> dStatement.java:2888)
> >> at
> >> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(Oracl
> >> ePreparedS
> >> tatement.java:2960)
> >> at
> >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpd
> >> ate(Delega
> >> tingPreparedStatement.java:101)
> >> at
> >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpd
> >> ate(Delega
> >> tingPreparedStatement.java:101)
> >> at
> >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(Ontology
> >> SQL.java:5
> >> 54)
> >> ... 7 more
> >> Java Result: 1
> >>
> >> When I check in the database, I find that the ontology has been
> >> created, and entries made in term for each of the terms,
> and also an
> >> entry has been made in term for the triple itself. So why the
> >> exception? Is it trying to insert the triple twice?
> >>
> >> cheers,
> >> Richard
> >>
> >> Richard Holland
> >> Bioinformatics Specialist
> >> Genome Institute of Singapore
> >> 60 Biopolis Street, #02-01 Genome, Singapore 138672
> >> Tel: (65) 6478 8000 DID: (65) 6478 8199
> >> Email: hollandr at gis.a-star.edu.sg
> >>
> >> ---------------------------------------------
> >> This email is confidential and may be privileged. If you
> are not the
> >> intended recipient, please delete it and notify us immediately.
> >> Please do not copy or use it for any purpose, or disclose
> its content
> >> to any other person. Thank you.
> >> ---------------------------------------------
> >>
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> >>
> >>
> >>
> >>
> >
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