[Biojava-l] Bug fix for Biojava in regard to email with subject :( Hibernate Exception and suggestion for change in BioSqlSchema)
Andreas Prlic
andreas at sdsc.edu
Thu Mar 25 16:47:45 UTC 2010
Excellent, thanks Richard and Deepak!
Andreas
On Thu, Mar 25, 2010 at 9:27 AM, Richard Holland
<holland at eaglegenomics.com>wrote:
> Patched and in subversion on the head in the new Biojava 3 code. I modified
> the code slightly to simplify it. There were also parallel changes required
> over in SimpleDocRef itself to enable it to continue working without being
> connected to BioSQL.
>
> On 25 Mar 2010, at 01:19, Deepak Sheoran wrote:
>
> > I am writing this email again, I didn't get any response weather this
> bugs are patched or are they lost some where on mailing list. I am not sure
> that's why I am writing this back. I don't know how to apply this patch So I
> am counting on you guys to apply theses patch and reply me back so I know
> its fixed.
> >
> >
> >
> > Thanks
> > Deepak Sheoran
> >
> >
> > Hi
> > In response to bug fix suggested by Richard I have created some patches.
> We need to apply these to fix biojava from processing references from a
> genbank record in a wrong manner which cause more hibernate exceptions.
> After applying patch, reference resolution code will test pubmed or medline
> id, then if no match then test author/title/location, then if still no match
> create a new reference. I even tested it with GenbankRelease 175 and I
> gained almost 3159 more records in my database.
> >
> > Can somebody please have a look on second issue of it and fix it
> > "
> > 2. I think that's a bug (compound locations with null features) but not
> sure why. Could be that the process of constructing a CompoundRichLocation
> is somehow losing the feature reference from the original
> SimpleRichLocation. Again I can't investigate until March - can someone else
> take a look at the code? (A good starting point would be to look at how a
> CompoundRichLocation decides to select the feature from the
> SimpleRichLocations it is made up from).
> > "
> >
> > Also I am planning on making a bridge between biosql database loaded
> using bioperl and biojava, here is my some of the investigation can you guys
> suggest some direction on it.
> > Have a look on attached files
> > 1) Biojava_BioPerl_Diff.xls ==> it have view of tables where genbank
> record is stored in biosql instance by bioperl and biojava
> > 2) GenbankRecord.doc ==> its word document having a genbank showing
> where its information goes in biosql using bioperl and biojava
> > 3) BioSqlRichobjectBuilder.patch ==> patch needed for
> BioSqlRichObjectBuild.java class
> > 4) GenBankFormat.patch ==> patch needed for GenBankFormat.java class
> >
> >
> > Thanks
> > Deepak Sheoran
> >
> >
> >
> > -------- Original Message --------
> > Subject: Re: Hibernate Exception and suggestion for change in
> BioSqlSchema
> > Date: Tue, 9 Feb 2010 20:34:32 +1300
> > From: Richard Holland <holland at eaglegenomics.com>
> > To: Deepak Sheoran <sheoran143 at gmail.com>
> > CC: biojava-l at biojava.org
> >
> > Hi. It's possible that your original email didn't make it to the list
> because it is HTML format, and the list only accepts plain text.
> >
> > However, in answer to your two questions:
> >
> > 1. The code that does the resolution of references might be better if
> it looks up existing IDs rather than using author, title, location to
> identify existing records. I would suggest modifying it to a three-step
> process - test ID, then if no match then test author/title/location, then if
> still no match create a new reference. Could someone do that? (I'm unable to
> do anything until late March).
> >
> > 2. I think that's a bug (compound locations with null features) but not
> sure why. Could be that the process of constructing a CompoundRichLocation
> is somehow losing the feature reference from the original
> SimpleRichLocation. Again I can't investigate until March - can someone else
> take a look at the code? (A good starting point would be to look at how a
> CompoundRichLocation decides to select the feature from the
> SimpleRichLocations it is made up from).
> >
> > cheers,
> > Richard
> >
> > On 9 Feb 2010, at 20:21, Deepak Sheoran wrote:
> >
> > >
> > > Hi Richard
> > >
> > > Below is the email which I sent to Biojava-1 mailing list but it never
> get posted on the mailing list server neither do i got any response, so
> please have a look on this email and tell what can be the solution of the
> problem described in the message.
> > >
> > >
> > > Thanks
> > > Deepak Sheoran
> > > -------- Original Message --------
> > > Subject: Hibernate Exception and suggestion for change in
> BioSqlSchema
> > > Date: Wed, 03 Feb 2010 08:07:35 -0600
> > > From: Deepak Sheoran
> > <sheoran143 at gmail.com>
> >
> > > To:
> > biojava-l at lists.open-bio.org
> >
> > >
> > > Hi guys,
> > >
> > > A couple of days back I was having some problem with hibernate
> exception but that exception got resolved and the reference to that email
> is:
> >
> http://old.nabble.com/Hibernate-Exception-when-persisting-some-richsequence-object-to-biosql-schema-to27299245.html
> >
> > > On Richard suggestion in above link I am able to resolve some of
> issues but then, I got stuck in to some other error with hibernate and then
> decided to investigate the matter and below are some facts and information
> which I found and I guess it is going to affect all of us.
> > > • The "Reference" table in bioSql schema have unique constraint on
> "dbxref_id" column (CONSTRAINT reference_dbxref_id_key UNIQUE (dbxref_id)).
> Which mean only one entry in reference table can use on dbxref_id.
> > > This Works wells but in cases when you have little variation in value
> of following column "location", "title", "authors" and all these variation
> refers to same PUBMED_ID. Then we can't persist or create a richsequence
> object .
> > > Now when you tie RichObjectFactory to a active hibernate session then
> the class "BioSqlRichObjectBuilder" have method called "buildObject(Class
> clazz, List paramsList) " which is responsible for looking up details of
> object in the database and if it find one then it will return that object,
> else it will try to persist the new object into the database.
> > > But problem is with below part of that method:
> > > …..LineNumber: 114
> > > else if (SimpleDocRef.class.isAssignableFrom(clazz))
> > > { queryType = "DocRef";
> > > // convert List constructor to String representation
> for query
> > > ourParamsList.set(0,
> DocRefAuthor.Tools.generateAuthorString((List)ourParamsList.get(0), true));
> > > if (ourParamsList.size()<3) {
> > > queryText = "from DocRef as cr where cr.authors
> = ? and cr.location = ? and cr.title is null";
> > > } else {
> > > queryText = "from DocRef as cr where cr.authors
> = ? and cr.location = ? and cr.title = ?";
> > > }
> > > }
> > > ..LineNubmer: 123
> > > Now when hibernate search the database, it won't find any other record
> in "reference" table because those two record are different in string
> comparison, so it will return a new object back to "GenbankFormat" to
> following piece of code
> > > ….LineNumber: 447
> > > else {
> > > try {
> > > CrossRef cr =
> (CrossRef)RichObjectFactory.getObject(SimpleCrossRef.class,new
> Object[]{dbname, raccession, new Integer(0)});
> > > RankedCrossRef rcr = new
> SimpleRankedCrossRef(cr, ++rcrossrefCount);
> > >
> rlistener.getCurrentFeature().addRankedCrossRef(rcr);
> > > } catch (ChangeVetoException e)
> {
> > > throw new
> ParseException(e+", accession:"+accession);
> > > }
> > > }
> > > …..LineNumber:455
> > > Then we will add that object to rlistener. And move to next part of
> genbank record and then biojava search for a new crossref in database and it
> will try to persist the old one it get a hibernate exception regarding
> violation of "unique constraint on dbxref_id" column.
> > >
> > > The only way to get these record in database is:
> > > • The very easy solution and the way I did it for testing
> my theory is Change the bioSql schema so that it can allow many to one on
> relation between "reference" and "dbxref" table. Which even make sense
> because one paper can have many different variation of naming, and this
> change allow us to store that info too. But this is something BioSql people
> have decide and I don't know how to approach them.
> > > • Second solution is slightly difficult to implement, is to
> change the way "BioSqlRichObjectBuilder.buildObject(Class clazz,List
> paramsList)" make decision about weather a particular DocRef already exist
> in database or not. I am mean testing all possible string variations of
> authors, location, title of the docRef which we are searching. Which does
> have many complications and may slow down process of creating a richsequence
> object when link RichObjectFactory with a active hibernate session.
> > >
> > > Example:Below is a sample of what i have in my local biosql schema
> which has modification suggested by me. (dbxref_id column have Pubmed_id , I
> replaced the local dbxref_id which was present on this table in my database
> with pubmed_id stored in "dbxref" table, for easy reference with outside
> world in this email)
> > > Reference_id
> > > Dbxref_id
> > > Location
> > > Title
> > > Authors
> > > crc
> > > 216
> > > 18554304
> > > FEMS Microbiol. Ecol. 66 (3THEMATIC ISSUE: GUT MICROBIOLOGY), 528-536
> (2008)
> > > Isolation of lactate-utilizing butyrate-producing bacteria from human
> feces and in vivo administration of Anaerostipes caccae strain L2 and
> galacto-oligosaccharides in a rat model
> > > Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y.,
> Nomoto,K., Ito,M. and Sawada,H.
> > > 9E940E01F4BE3CD0
> > > 230
> > > 18554304
> > > FEMS Microbiol. Ecol. 66 (3), 528-536 (2008)
> > > Isolation of lactate-utilizing butyrate-producing bacteria from human
> feces and in vivo administration of Anaerostipes caccae strain L2 and
> galacto-oligosaccharides in a rat model
> > > Sato,T., Matsumoto,K., Okumura,T., Yokoi,W., Naito,E., Yoshida,Y.,
> Nomoto,K., Ito,M. and Sawada,H.
> > > D3BC0C17F3F786C9
> > > 415
> > > 16790744
> > > Infect. Immun. 74 (7), 3715-3726 (2006)
> > > Intrastrain Heterogeneity of the mgpB Gene in Mycoplasma genitalium Is
> Extensive In Vitro and In Vivo and Suggests that Variation Is Generated via
> Recombination with Repetitive Chromosomal Sequences
> > > Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and
> Totten,P.A.
> > > 60AEDFA0CEEACC38
> > > 969
> > > 16790744
> > > Infect. Immun. 74 (7), 3715-3726 (2006)
> > > Intrastrain heterogeneity of the mgpB gene in mycoplasma genitalium is
> extensive in vitro and in vivo and suggests that variation is generated via
> recombination with repetitive chromosomal sequences
> > > Iverson-Cabral,S.L., Astete,S.G., Cohen,C.R., Rocha,E.P. and
> Totten,P.A.
> > > 4B1232999F6E8130
> > > 929
> > > 8688087
> > > Science 273 (5278), 1058-1073 (1996)
> > > Complete genome sequence of the methanogenic archaeon, Methanococcus
> jannaschii
> > > Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
> Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D.,
> Kerlavage,A.R., Dougherty,B.A., Tomb,J.-F., Adams,M.D., Reich,C.I.,
> Overbeek,R., Kirkness,E.F., Weinstock,K.G., Merrick,J.M., Glodek,A.,
> Scott,J.L., Geoghagen,N.S.M., Weidman,J.F., Fuhrmann,J.L., Presley,E.A.,
> Nguyen,D., Utterback,T.R., Kelley,J.M., Peterson,J.D., Sadow,P.W.,
> Hanna,M.C., Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.P.,
> Borodovsky,M., Klenk,H.-P., Fraser,C.M., Smith,H.O., Woese,C.R. and
> Venter,J.C.
> > > 3E79B40DD2AAA2B7
> > > 932
> > > 8688087
> > > Science 273 (5278), 1058-1073 (1996)
> > > Complete genome sequence of the methanogenic archaeon, Methanococcus
> jannaschii
> > > Bult,C.J., White,O., Olsen,G.J., Zhou,L., Fleischmann,R.D.,
> Sutton,G.G., Blake,J.A., FitzGerald,L.M., Clayton,R.A., Gocayne,J.D.,
> Kerlavage,A.R., Dougherty,B.A., Tomb,J., Adams,M.D., Reich,C.I.,
> Overbeek,R., Kirkness,E.F., Weinstock,K.G., Merrick,J.M., Glodek,A.,
> Scott,J.D., Geoghagen,N.S., Weidman,J.F., Fuhrmann,J.L., Nguyen,D.T.,
> Utterback,T., Kelley,J.M., Peterson,J.D., Sadow,P.W., Hanna,M.C.,
> Cotton,M.D., Hurst,M.A., Roberts,K.M., Kaine,B.B., Borodovsky,M.,
> Klenk,H.P., Fraser,C.M., Smith,H.O., Woese,C.R. and Venter,J.C.
> > > 094EB3384F8D6DE8
> > > 1426
> > > 10684935
> > > Nucleic Acids Res. 28 (6), 1397-1406 (2000)
> > > Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae
> AR39
> > > Read,T.D., Brunham,R.C., Shen,C., Gill,S.R., Heidelberg,J.F., White,O.,
> Hickey,E.K., Peterson,J., Umayam,L.A., Utterback,T., Berry,K., Bass,S.,
> Linher,K., Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M.,
> Nelson,W., DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S.L., Eisen,J. and
> Fraser,C.M.
> > > 357648D8FD8C6C8A
> > > 1481
> > > 10684935
> > > Nucleic Acids Res. 28 (6), 1397-1406 (2000)
> > > Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae
> AR39
> > > Read,T., Brunham,R., Shen,C., Gill,S., Heidelberg,J., White,O.,
> Hickey,E., Peterson,J., Utterback,T., Berry,K., Bass,S., Linher,K.,
> Weidman,J., Khouri,H., Craven,B., Bowman,C., Dodson,R., Gwinn,M., Nelson,W.,
> DeBoy,R., Kolonay,J., McClarty,G., Salzberg,S., Eisen,J. and Fraser,C.
> > > 115411EB2DEE5654
> > > 1497
> > > 14689165
> > > Arch. Microbiol. 181 (2), 144-154 (2004)
> > > The effect of FITA mutations on the symbiotic properties of
> Sinorhizobium fredii varies in a chromosomal-background-dependent manner
> > > Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R.,
> del Rosario Espuny,M., Temprano,F., Romero,F., Krishnan,H.B., Pueppke,S.G.
> and Ruiz-Sainz,J.E.
> > > 4D5D376EECCD186B
> > > 1501
> > > 14689165
> > > Arch. Microbiol. 181 (2), 144-154 (2004)
> > > The effect of FITA mutations on the symbiotic properties of
> Sinorhizobium fredii varies in a chromosomal-background-dependent manner
> > > Vinardell,J.M., Lopez-Baena,F.J., Hidalgo,A., Ollero,F.J., Bellogin,R.,
> Del Rosario Espuny,M., Temprano,F., Romero,F., Krishnan,H.B., Pueppke,S.G.
> and Ruiz-Sainz,J.E.
> > > 4D57954EECDED66B
> > > 1556
> > > 18060065
> > > PLoS ONE 2 (12), E1271 (2007)
> > > Analysis of the Neurotoxin Complex Genes in Clostridium botulinum A1-A4
> and B1 Strains: BoNT/A3, /Ba4 and /B1 Clusters Are Located within Plasmids
> > > Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,A.C., Bruce,D.C.,
> Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.
> > > 698688FB6DB95247
> > > 1559
> > > 18060065
> > > PLoS ONE 2 (12), E1271 (2007)
> > > Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4
> and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids
> > > Smith,T.J., Hill,K.K., Foley,B.T., Detter,J.C., Munk,C.A., Bruce,D.C.,
> Doggett,N.A., Smith,L.A., Marks,J.D., Xie,G. and Brettin,T.S.
> > > E25E1BA99DB18F3D
> > >
> > > • The second kind of error which I got was :
> org.hibernate.PropertyValueException: not-null property references a null or
> transient value: Location.feature
> > > • Which means in richsequence object some feature have
> location object which have its feature set to null.
> > > • My Observation:
> > > • Usually occur when you try to persist a
> richsequence object to database, and occur to those features which have
> CompoundRichLocation usually "joins" and "complement" in cds region of a
> genbank record
> > > • After catching the hibernate exception I went
> through all the features and either biojava or hibernate changed the object
> type of a CompoundRichLocation to SimpleRichLocation and set the feature
> variable to null.
> > > • Below is the screen shot of one of my tests
> > > • Settings before trying to persits the
> richsequence object to database
> > >
> > > <Mail Attachment.png>
> > > •
> > > • After trying to persits the richsequence object to
> database and got in hibernate exception catch
> > >
> > > • <Mail Attachment.png>
> > >
> > > • So my question is why is this happening and how to stop
> or how to get these record into database, I have no clue why is this
> happening.
> > > • Some extra information to make things more clear to you
> guys.
> > > • Below are some Locus line from genbank record for
> which I know the error of location, I mean the cds region causing error, and
> array index in richsequence.feature arrayList object.
> > > • LOCUS AE001439 1643831
> bp DNA circular BCT 19-JAN-2006
> > > • richSequence.feature Index : 2540
> and line number in the genbank record : 22115
> > > • LOCUS CP001189 3887492
> bp DNA circular BCT 16-OCT-2008
> > > • richSequence.feature Index : 127
> and line number in the genbank record : 2137
> > > • LOCUS CP001292 328635
> bp DNA circular BCT 17-DEC-2008
> > > • richSequence.feature Index : 389
> and line number in the genbank record : 3632
> > > • LOCUS AM279694 238517
> bp DNA linear BCT 23-OCT-2008
> > > • richSequence.feature Index : 47
> and line number in the genbank record : 4841
> > > • LOCUS CR931663 18517
> bp DNA linear BCT 18-SEP-2008
> > > • richSequence.feature Index : 45
> and line number in the genbank record : 442
> > > • The complete exception msg :
> > > org.hibernate.PropertyValueException: not-null property references a
> null or transient value: Location.feature
> > > at
> org.hibernate.engine.Nullability.checkNullability(Nullability.java:72)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:290)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
> > > at
> org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
> > > at
> org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
> > > at
> org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
> > > at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
> > > at
> org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
> > > at
> org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> > > at
> org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
> > > at
> org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
> > > at
> org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
> > > at
> org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> > > at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:94)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
> > > at
> org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:507)
> > > at
> org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:499)
> > > at
> org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:218)
> > > at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:268)
> > > at
> org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:216)
> > > at
> org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> > > at
> org.hibernate.engine.Cascade.cascadeCollectionElements(Cascade.java:296)
> > > at
> org.hibernate.engine.Cascade.cascadeCollection(Cascade.java:242)
> > > at
> org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:219)
> > > at
> org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:169)
> > > at org.hibernate.engine.Cascade.cascade(Cascade.java:130)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.cascadeAfterSave(AbstractSaveEventListener.java:456)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:334)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:181)
> > > at
> org.hibernate.event.def.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:121)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:187)
> > > at
> org.hibernate.event.def.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:33)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:172)
> > > at
> org.hibernate.event.def.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:27)
> > > at
> org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:70)
> > > at
> org.hibernate.impl.SessionImpl.fireSave(SessionImpl.java:535)
> > > at org.hibernate.impl.SessionImpl.save(SessionImpl.java:523)
> > > at
> trashtesting.GenBankLoaderTesting.main(GenBankLoaderTesting.java:78)
> > >
> > >
> >
> > --
> > Richard Holland, BSc MBCS
> > Operations and Delivery Director, Eagle Genomics Ltd
> > T: +44 (0)1223 654481 ext 3 | E:
> > holland at eaglegenomics.com
> > http://www.eaglegenomics.com/
> >
> >
> >
> >
> <Biojava_BioPerl_diff.xls><BioSqlRichObjectBuilder.patch><GenbankFormat.patch><GenbankRecord.doc>
>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
More information about the Biojava-l
mailing list