[Biojava-l] Problem: BioSQL-cvs and/or RichSequence-Annotation

[mark.schreiber at novartis.com]

Wow, that tutorial is out of date!

The assembly sql is not required any longer. It was specifically put in by 
David Huen (I think) to allow him to store assembly data in biosql. Can 
anyone comment on the need for the accelerators?

As for you second point I would discourage the use of the enrich method 
whenever possible. It does the best it can but cannot work miracles. If 
you get a new download of CVS RichSequence.Tools has several 
createRichSequence methods to avoid the use of this 'anti-pattern'.

RichSequence seq = 
(SimpleRichSequence)RichSequence.Tools.enrich(DNATools.createDNASequence("gattacagattaca","urn:local:seq"));

As an aside there is no need to cast the return of enrich if you are 
assining it to a RichSequence pointer.

Hope this helps,

- Mark





Felix Dreher <dreher at mpiib-berlin.mpg.de>
Sent by: biojava-l-bounces at portal.open-bio.org
02/15/2006 10:49 PM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Problem: BioSQL-cvs and/or RichSequence-Annotation


Hello,

I have a question regarding the BioSQL-schema-scripts.
The tutorial on installing BioSQL 
(http://www.biojava.org/tutorials/biosql.html) says that three scripts 
are required:

biosqldb-pg.sql
biosql-accelerators-pg.sql
biosqldb-assembly-pg.sql

However, the 'assembly'-script can not be found on the CVS-server. 
Instead there is another script called 'biosqldb-views-pg.sql'.
So I would like to know which scripts should be used.


Furthermore I have a problem with adding an annotation (or also a 
feature) to a RichSequence.
As it seems to be a problem with Hibernate and/or the BioSQL-schemas: I 
use BioJava-live (CVS) from 2 weeks ago and the latest CVS-BioSQL-scripts.

When I try the following code, the following Exceptions are thrown 
(while the execution of line 2).

1        RichSequence seq =  (SimpleRichSequence) 
RichSequence.Tools.enrich(DNATools.createDNASequence("gattacagattaca","urn:local:seq"));
2        ComparableTerm ct = 
RichObjectFactory.getDefaultOntology().getOrCreateTerm("projectname");
3        seq.getAnnotation().setProperty(ct, "project_25");




Exception in thread "main" java.lang.RuntimeException: Error while 
trying to call new class 
org.biojavax.ontology.SimpleComparableOntology(class java.lang.String)
        at 
org.biojavax.bio.db.HibernateRichObjectBuilder.buildObject(HibernateRichObjectBuilder.java:154)
        at 
org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:97)
        at 
org.biojavax.RichObjectFactory.getDefaultOntology(RichObjectFactory.java:178)
        at hibernatetest.Main.main(Main.java:246)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at 
org.biojavax.bio.db.HibernateRichObjectBuilder.buildObject(HibernateRichObjectBuilder.java:138)
        ... 3 more
Caused by: org.hibernate.exception.SQLGrammarException: could not 
insert: [Ontology]
        at 
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:65)
        at 
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
        at 
org.hibernate.id.AbstractPostInsertGenerator.getGenerated(AbstractPostInsertGenerator.java:56)
        at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:1994)
        at 
org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:2405)
        at 
org.hibernate.action.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:37)
        at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:243)
        at 
org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:269)
        at 
org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:167)
        at 
org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:101)
        at 
org.hibernate.event.def.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:131)
        at 
org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:87)
        at 
org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:38)
        at 
org.hibernate.impl.SessionImpl.firePersist(SessionImpl.java:642)
        at org.hibernate.impl.SessionImpl.persist(SessionImpl.java:616)
        ... 8 more
Caused by: org.postgresql.util.PSQLException: ERROR: relation 
"ontology_ontology_id_seq" does not exist
        at 
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512)
        at 
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297)
        at 
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
        at 
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:430)
        at 
org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:346)
        at 
org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:250)
        at 
org.hibernate.id.AbstractPostInsertGenerator.getGenerated(AbstractPostInsertGenerator.java:42)
        ... 20 more



Thanks in advance!

Greetings,
Felix







-- 
Felix Dreher
Max-Planck-Institute for Infection Biology
Campus Charité Mitte
Department of Immunology
Mailing address: Schumannstraße 21/22
Visitors: Virchowweg 12
10117 Berlin
Germany
Tel.: +49 (0)30 28460-254 / -494
Mobile: +49 (0)163 7542426

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