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My code basically is doing this: // Connecting to the BioSQL DB SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass, biodatabase, create); // Reading a GeneBank flat file SequenceIterator iter = (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br); while (iter.hasNext()) { Sequence seq = iter.nextSequence(); try { db.addSequence(seq); } catch (Exception e) { e.printStackTrace(); } ... } It progresses a little ways and I get the following error stack: [java] Caused by: java.sql.SQLException: Couldn't create term 'ORGANISM' for 'ORGANISM' in legacy ontology namespace [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe quenceDB.java:942) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ LSequenceDB.java:894) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB .java:485) [java] ... 2 more [java] Caused by: org.biojava.bio.BioRuntimeException: Error commiting to BioSQL tables (rolled back successfully) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:536) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java:61) [java] at org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(Ontolog ySQL.java:503) [java] at org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java:338) [java] at org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349) [java] at org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe quenceDB.java:938) [java] ... 4 more [java] Caused by: java.sql.SQLException: Failed to persist term: ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : 23000 [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:562) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:524) [java] ... 10 more [java] Caused by: java.sql.SQLException: Duplicate key or integrity constraint violation, message from server: "Duplicate entry 'ORGANISM-5' for key 2" [java] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977) [java] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163) [java] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272) [java] at com.mysql.jdbc.Connection.execSQL(Connection.java:2236) [java] at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741) [java] at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588) [java] at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating PreparedStatement.java:233) [java] at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating PreparedStatement.java:233) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:554) [java] ... 11 more [java] Exception in thread "main" org.biojava.bio.BioError: Error looking up biosqlized ID for ORGANISM [java] at org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe quenceDB.java:927) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ LSequenceDB.java:894) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB .java:485) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. java:365) [java] at com.gts.genebank.GeneralReader.main(GeneralReader.java:64) [java] Caused by: java.lang.NullPointerException [java] at org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682) [java] ... 5 more [java] Java Result: 1 What am I doing wrong? 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In-Reply-To: Message-ID: It appears you have data problems, might you be able to select * from ontology_term; from your biosql database and send the result? michael On Tue, 3 Aug 2004, Michael Griffith wrote: > Hi, > > I am trying to use the BioJava 1.4 nightly build (8.3.2004) to read a > GeneBank File and insert it into a BIOSQL/MySQL db. > > My code basically is doing this: > > // Connecting to the BioSQL DB > SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass, > biodatabase, create); > > // Reading a GeneBank flat file > SequenceIterator iter = (SequenceIterator)SeqIOTools.fileToBiojava(format, > alpha, br); > while (iter.hasNext()) { > > Sequence seq = iter.nextSequence(); > > try { > db.addSequence(seq); > } > catch (Exception e) { > e.printStackTrace(); > } > ... > } > > It progresses a little ways and I get the following error stack: > > [java] Caused by: java.sql.SQLException: Couldn't create term 'ORGANISM' > for 'ORGANISM' in legacy ontology namespace > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe > quenceDB.java:942) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ > LSequenceDB.java:894) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB > .java:485) > [java] ... 2 more > [java] Caused by: org.biojava.bio.BioRuntimeException: Error commiting > to BioSQL tables (rolled back successfully) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:536) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java:61) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(Ontolog > ySQL.java:503) > [java] at > org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java:338) > [java] at > org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349) > [java] at > org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe > quenceDB.java:938) > [java] ... 4 more > [java] Caused by: java.sql.SQLException: Failed to persist term: > ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : 23000 > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:562) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:524) > [java] ... 10 more > [java] Caused by: java.sql.SQLException: Duplicate key or integrity > constraint violation, message from server: "Duplicate entry 'ORGANISM-5' > for key 2" > [java] at > com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977) > [java] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163) > [java] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272) > [java] at com.mysql.jdbc.Connection.execSQL(Connection.java:2236) > [java] at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741) > [java] at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588) > [java] at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating > PreparedStatement.java:233) > [java] at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating > PreparedStatement.java:233) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:554) > [java] ... 11 more > [java] Exception in thread "main" org.biojava.bio.BioError: Error > looking up biosqlized ID for ORGANISM > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe > quenceDB.java:927) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ > LSequenceDB.java:894) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB > .java:485) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. > java:365) > [java] at > com.gts.genebank.GeneralReader.main(GeneralReader.java:64) > [java] Caused by: java.lang.NullPointerException > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682) > [java] ... 5 more > [java] Java Result: 1 > > > What am I doing wrong? Any help would be greatly appreciated! > > MG > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From mg at guerrilla-tech.com Tue Aug 3 13:20:17 2004 From: mg at guerrilla-tech.com (Michael Griffith) Date: Tue Aug 3 13:23:55 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: Message-ID: Michael, Well, that could be the problem? I don't have a table called ontology_term. I do have a table called ontology that looks like this: 4 __core_ontology BioSQL core ontology (imported by BioJava) 5 __biojava_guano Namespace for old, but still useful, shit imported from ontology-less BioJava data models The version of my schema was created from: biosql-schema/sql/biosqldb-mysql.sql Version 1.38. Is this correct? Cheers! MG On 8/3/04 12:18 PM, "Michael Heuer" wrote: > > It appears you have data problems, might you be able to > > select * from ontology_term; > > from your biosql database and send the result? > > michael > > > On Tue, 3 Aug 2004, Michael Griffith wrote: > >> Hi, >> >> I am trying to use the BioJava 1.4 nightly build (8.3.2004) to read a >> GeneBank File and insert it into a BIOSQL/MySQL db. >> >> My code basically is doing this: >> >> // Connecting to the BioSQL DB >> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass, >> biodatabase, create); >> >> // Reading a GeneBank flat file >> SequenceIterator iter = (SequenceIterator)SeqIOTools.fileToBiojava(format, >> alpha, br); >> while (iter.hasNext()) { >> >> Sequence seq = iter.nextSequence(); >> >> try { >> db.addSequence(seq); >> } >> catch (Exception e) { >> e.printStackTrace(); >> } >> ... >> } >> >> It progresses a little ways and I get the following error stack: >> >> [java] Caused by: java.sql.SQLException: Couldn't create term 'ORGANISM' >> for 'ORGANISM' in legacy ontology namespace >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe >> quenceDB.java:942) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ >> LSequenceDB.java:894) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB >> .java:485) >> [java] ... 2 more >> [java] Caused by: org.biojava.bio.BioRuntimeException: Error commiting >> to BioSQL tables (rolled back successfully) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:536) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java:61) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(Ontolog >> ySQL.java:503) >> [java] at >> org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java:338) >> [java] at >> org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349) >> [java] at >> org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe >> quenceDB.java:938) >> [java] ... 4 more >> [java] Caused by: java.sql.SQLException: Failed to persist term: >> ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : 23000 >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:562) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:524) >> [java] ... 10 more >> [java] Caused by: java.sql.SQLException: Duplicate key or integrity >> constraint violation, message from server: "Duplicate entry 'ORGANISM-5' >> for key 2" >> [java] at >> com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977) >> [java] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163) >> [java] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272) >> [java] at com.mysql.jdbc.Connection.execSQL(Connection.java:2236) >> [java] at >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741) >> [java] at >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588) >> [java] at >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating >> PreparedStatement.java:233) >> [java] at >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating >> PreparedStatement.java:233) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:554) >> [java] ... 11 more >> [java] Exception in thread "main" org.biojava.bio.BioError: Error >> looking up biosqlized ID for ORGANISM >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe >> quenceDB.java:927) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ >> LSequenceDB.java:894) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB >> .java:485) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. >> java:365) >> [java] at >> com.gts.genebank.GeneralReader.main(GeneralReader.java:64) >> [java] Caused by: java.lang.NullPointerException >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682) >> [java] ... 5 more >> [java] Java Result: 1 >> >> >> What am I doing wrong? Any help would be greatly appreciated! >> >> MG >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev@biojava.org >> http://biojava.org/mailman/listinfo/biojava-dev >> > > From td2 at sanger.ac.uk Tue Aug 3 13:37:39 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Aug 3 13:38:59 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: References: Message-ID: On 3 Aug 2004, at 18:20, Michael Griffith wrote: > Michael, > > Well, that could be the problem? I don't have a table called > ontology_term. > I do have a table called ontology that looks like this: > > 4 __core_ontology BioSQL core ontology (imported by BioJava) > 5 __biojava_guano Namespace for old, but still useful, shit > imported > from ontology-less BioJava data models > > The version of my schema was created from: > biosql-schema/sql/biosqldb-mysql.sql Version 1.38. Is this correct? The table formerly known as ontology_term is now just called "term" -- could you take a look at that? Thomas. From mg at base-pair.com Tue Aug 3 13:42:28 2004 From: mg at base-pair.com (Michael Griffith) Date: Tue Aug 3 13:46:07 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: Message-ID: Thomas, Thanks for the reply. Since the original post, I tried the older schema, but of course it didn't work. I got this message: org.biojava.bio.BioException: This database appears to be an old (pre-Singapore) BioSQL. If you need to access it, try an older BioJava snapshot (1.3pre1 or earlier). So I recreated the schema with the latest from CVS, version 1.38 and tried to re-run my load. It failed in the same spot with the same error stack. Any help is GREATLY appreciated! Cheers! MG Here is the contents of my term table: 1 triple (null) (null) 1 2 any (null) (null) 1 3 has-a (null) (null) 1 4 has-a(triple, any) (null) (null) 1 5 3 (null) (null) 1 6 size (null) (null) 1 7 size(has-a(triple, any), 3) (null) (null) 1 8 injective (null) (null) 1 9 relation (null) (null) 1 10 is-a (null) (null) 1 11 is-a(injective, relation) (null) (null) 1 12 source (null) (null) 1 13 symmetric (null) (null) 1 14 is-a(symmetric, relation) (null) (null) 1 15 is-a(triple, any) (null) (null) 1 16 partial-order (null) (null) 1 17 is-a(is-a, partial-order) (null) (null) 1 18 is-a(is-a, relation) (null) (null) 1 19 anti-symmetric (null) (null) 1 20 is-a(partial-order, anti-symmetric) (null) (null) 1 21 aTriple (null) (null) 1 22 remote-term (null) (null) 1 23 disjoint (null) (null) 1 24 inverse (null) (null) 1 25 remoteTerm (null) (null) 1 26 equivalence (null) (null) 1 27 transitive (null) (null) 1 28 is-a(transitive, relation) (null) (null) 1 29 1 (null) (null) 1 30 is-a(partial-order, any) (null) (null) 1 31 is-a(has-a, relation) (null) (null) 1 32 reflexive (null) (null) 1 33 none (null) (null) 1 34 disjoint(none, any) (null) (null) 1 35 is-a(any, any) (null) (null) 1 36 positive-integer (null) (null) 1 37 is-a(equivalence, transitive) (null) (null) 1 38 is-a(disjoint, relation) (null) (null) 1 39 has-a(triple, source) (null) (null) 1 40 is-a(relation, any) (null) (null) 1 41 object (null) (null) 1 42 has-a(triple, object) (null) (null) 1 43 has-a(relation, size) (null) (null) 1 44 is-a(aTriple, has-a) (null) (null) 1 45 identity (null) (null) 1 46 is-a(identity, equivalence) (null) (null) 1 47 size(is-a(partial-order, any), 3) (null) (null) 1 48 has-a(triple, relation) (null) (null) 1 49 remoteTerm(remote-term, any) (null) (null) 1 50 size(remoteTerm(remote-term, any), 1) (null) (null) 1 51 is-a(reflexive, relation) (null) (null) 1 52 is-a(equivalence, symmetric) (null) (null) 1 53 is-a(equivalence, any) (null) (null) 1 54 is-a(remote-term, any) (null) (null) 1 55 triple-term (null) (null) 1 56 is-a(equivalence, reflexive) (null) (null) 1 57 is-a(remoteTerm, has-a) (null) (null) 1 58 size(is-a(equivalence, any), 3) (null) (null) 1 59 is-a(partial-order, reflexive) (null) (null) 1 60 is-a(partial-order, transitive) (null) (null) 1 61 aTriple(triple-term, triple) (null) (null) 1 62 size(aTriple(triple-term, triple), 1) (null) (null) 1 63 is-a(triple-term, any) (null) (null) 1 64 part-of (null) (null) 1 65 inverse(part-of, has-a) (null) (null) 1 66 is-a(size, positive-integer) (null) (null) 1 67 source (null) (null) 2 68 GenBank (null) (null) 2 69 sex (null) (null) 2 70 dev_stage (null) (null) 2 71 organism (null) (null) 2 72 db_xref (null) (null) 2 73 lab_host (null) (null) 2 74 mol_type (null) (null) 2 75 clone (null) (null) 2 76 note (null) (null) 2 77 clone_lib (null) (null) 2 78 TYPE (null) (null) 2 79 ACCESSION (null) (null) 2 80 genbank_accessions (null) (null) 2 81 tissue_type (null) (null) 2 82 strain (null) (null) 2 83 KEYWORDS (null) (null) 2 Here is the stack trace: [java] *** Importing a core ontology -- hope this is okay [java] *** Importing terms [java] /*--------------------------------------*/ [java] Trying to add: AA000001 to the database [java] org.biojava.bio.BioRuntimeException: Error adding sequence: AA000001 (rolled back successfully) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB .java:498) [java] /*--------------------------------------*/ [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. java:365) [java] at com.gts.genebank.GeneralReader.main(GeneralReader.java:66) [java] /*--------------------------------------*/ [java] Trying to add: AA000002 to the database [java] Caused by: java.sql.SQLException: Couldn't create term 'ORGANISM' for 'ORGANISM' in legacy ontology namespace [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe quenceDB.java:942) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ LSequenceDB.java:894) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB .java:485) [java] ... 2 more [java] Caused by: org.biojava.bio.BioRuntimeException: Error commiting to BioSQL tables (rolled back successfully) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:536) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java:61) [java] at org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(Ontolog ySQL.java:503) [java] at org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java:338) [java] at org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349) [java] at org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe quenceDB.java:938) [java] ... 4 more [java] Caused by: java.sql.SQLException: Failed to persist term: ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : 23000 [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:562) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:524) [java] ... 10 more [java] Caused by: java.sql.SQLException: Duplicate key or integrity constraint violation, message from server: "Duplicate entry 'ORGANISM-2' for key 2" [java] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977) [java] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163) [java] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272) [java] at com.mysql.jdbc.Connection.execSQL(Connection.java:2236) [java] at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741) [java] at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588) [java] at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating PreparedStatement.java:233) [java] at org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Delegating PreparedStatement.java:233) [java] at org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java:554) [java] ... 11 more [java] Exception in thread "main" org.biojava.bio.BioError: Error looking up biosqlized ID for ORGANISM [java] at org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(BioSQLSe quenceDB.java:927) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty(BioSQ LSequenceDB.java:894) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB .java:485) [java] at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. java:365) [java] at com.gts.genebank.GeneralReader.main(GeneralReader.java:66) [java] Caused by: java.lang.NullPointerException [java] at org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682) [java] ... 5 more [java] Java Result: 1 On 8/3/04 12:37 PM, "Thomas Down" wrote: > > On 3 Aug 2004, at 18:20, Michael Griffith wrote: > >> Michael, >> >> Well, that could be the problem? I don't have a table called >> ontology_term. >> I do have a table called ontology that looks like this: >> >> 4 __core_ontology BioSQL core ontology (imported by BioJava) >> 5 __biojava_guano Namespace for old, but still useful, shit >> imported >> from ontology-less BioJava data models >> >> The version of my schema was created from: >> biosql-schema/sql/biosqldb-mysql.sql Version 1.38. Is this correct? > > The table formerly known as ontology_term is now just called "term" -- > could you take a look at that? > > Thomas. > > From td2 at sanger.ac.uk Tue Aug 3 13:49:01 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Aug 3 13:50:21 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: References: Message-ID: <67105644-E575-11D8-A15D-000A95C8B056@sanger.ac.uk> Hi Michael, I think I've found the problem -- it's actually documented in a comment in BioSQLSequenceDB.intern_ontology_term method, but probably ought to be somewhere more obvious... The issue seems to be that MySQL ignores the case of strings when enforcing uniqueness constraint, but Genbank files contain the key ORGANISM in both upper- and lower-case variants, so when BioJava tries to store both of these in the term table it runs into trouble. The solution seems to be to create the term.name field as BINARY rather than VARCHAR. If you make this change to your schema and recreate the database, everything should be fine. Presumably this issue has come up before (although I can't remember it myself, I always used PostgreSQL in my BioSQL days). Has anyone tried to feed this change back into the official mysql schema? Thomas. On 3 Aug 2004, at 18:07, Michael Griffith wrote: > Hi, > > I am trying to use the BioJava 1.4 nightly build (8.3.2004) to read a > GeneBank File and insert it into a BIOSQL/MySQL db. > > My code basically is doing this: > > // Connecting to the BioSQL DB > SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass, > biodatabase, create); > > // Reading a GeneBank flat file > SequenceIterator iter = > (SequenceIterator)SeqIOTools.fileToBiojava(format, > alpha, br); > while (iter.hasNext()) { > > Sequence seq = iter.nextSequence(); > > try { > db.addSequence(seq); > } > catch (Exception e) { > e.printStackTrace(); > } > ... > } > > It progresses a little ways and I get the following error stack: > > [java] Caused by: java.sql.SQLException: Couldn't create term > 'ORGANISM' > for 'ORGANISM' in legacy ontology namespace > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(Bio > SQLSe > quenceDB.java:942) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty( > BioSQ > LSequenceDB.java:894) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque > nceDB > .java:485) > [java] ... 2 more > [java] Caused by: org.biojava.bio.BioRuntimeException: Error > commiting > to BioSQL tables (rolled back successfully) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: > 536) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java: > 61) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(On > tolog > ySQL.java:503) > [java] at > org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java: > 338) > [java] at > org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349) > [java] at > org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(Bio > SQLSe > quenceDB.java:938) > [java] ... 4 more > [java] Caused by: java.sql.SQLException: Failed to persist term: > ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : > 23000 > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: > 562) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: > 524) > [java] ... 10 more > [java] Caused by: java.sql.SQLException: Duplicate key or > integrity > constraint violation, message from server: "Duplicate entry > 'ORGANISM-5' > for key 2" > [java] at > com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977) > [java] at > com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163) > [java] at > com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272) > [java] at > com.mysql.jdbc.Connection.execSQL(Connection.java:2236) > [java] at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java: > 1741) > [java] at > com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java: > 1588) > [java] at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg > ating > PreparedStatement.java:233) > [java] at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg > ating > PreparedStatement.java:233) > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: > 554) > [java] ... 11 more > [java] Exception in thread "main" org.biojava.bio.BioError: Error > looking up biosqlized ID for ORGANISM > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(Bio > SQLSe > quenceDB.java:927) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty( > BioSQ > LSequenceDB.java:894) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque > nceDB > .java:485) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequen > ceDB. > java:365) > [java] at > com.gts.genebank.GeneralReader.main(GeneralReader.java:64) > [java] Caused by: java.lang.NullPointerException > [java] at > org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682) > [java] ... 5 more > [java] Java Result: 1 > > > What am I doing wrong? Any help would be greatly appreciated! > > MG > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From mg at guerrilla-tech.com Tue Aug 3 13:56:11 2004 From: mg at guerrilla-tech.com (Michael Griffith) Date: Tue Aug 3 13:59:48 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: <67105644-E575-11D8-A15D-000A95C8B056@sanger.ac.uk> Message-ID: Thomas, Thanks! Not being an expert with mySQL -- how do you change the field def? I added [BINARY] after the Varchar def and tried creating the field as Binary. How should it be defined? Again, thanks! MG On 8/3/04 12:49 PM, "Thomas Down" wrote: > Hi Michael, > > I think I've found the problem -- it's actually documented in a comment > in BioSQLSequenceDB.intern_ontology_term method, but probably ought to > be somewhere more obvious... > > The issue seems to be that MySQL ignores the case of strings when > enforcing uniqueness constraint, but Genbank files contain the key > ORGANISM in both upper- and lower-case variants, so when BioJava tries > to store both of these in the term table it runs into trouble. > > The solution seems to be to create the term.name field as BINARY rather > than VARCHAR. If you make this change to your schema and recreate the > database, everything should be fine. > > Presumably this issue has come up before (although I can't remember it > myself, I always used PostgreSQL in my BioSQL days). Has anyone tried > to feed this change back into the official mysql schema? > > Thomas. > > On 3 Aug 2004, at 18:07, Michael Griffith wrote: > >> Hi, >> >> I am trying to use the BioJava 1.4 nightly build (8.3.2004) to read a >> GeneBank File and insert it into a BIOSQL/MySQL db. >> >> My code basically is doing this: >> >> // Connecting to the BioSQL DB >> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass, >> biodatabase, create); >> >> // Reading a GeneBank flat file >> SequenceIterator iter = >> (SequenceIterator)SeqIOTools.fileToBiojava(format, >> alpha, br); >> while (iter.hasNext()) { >> >> Sequence seq = iter.nextSequence(); >> >> try { >> db.addSequence(seq); >> } >> catch (Exception e) { >> e.printStackTrace(); >> } >> ... >> } >> >> It progresses a little ways and I get the following error stack: >> >> [java] Caused by: java.sql.SQLException: Couldn't create term >> 'ORGANISM' >> for 'ORGANISM' in legacy ontology namespace >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(Bio >> SQLSe >> quenceDB.java:942) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty( >> BioSQ >> LSequenceDB.java:894) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque >> nceDB >> .java:485) >> [java] ... 2 more >> [java] Caused by: org.biojava.bio.BioRuntimeException: Error >> commiting >> to BioSQL tables (rolled back successfully) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: >> 536) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.access$200(OntologySQL.java: >> 61) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL$OntologyMonitor.postChange(On >> tolog >> ySQL.java:503) >> [java] at >> org.biojava.utils.ChangeSupport.firePostChangeEvent(ChangeSupport.java: >> 338) >> [java] at >> org.biojava.ontology.Ontology$Impl.addTerm(Ontology.java:349) >> [java] at >> org.biojava.ontology.Ontology$Impl.createTerm(Ontology.java:358) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(Bio >> SQLSe >> quenceDB.java:938) >> [java] ... 4 more >> [java] Caused by: java.sql.SQLException: Failed to persist term: >> ORGANISM from ontology: ontology: __biojava_guano with error: 1062 : >> 23000 >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: >> 562) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: >> 524) >> [java] ... 10 more >> [java] Caused by: java.sql.SQLException: Duplicate key or >> integrity >> constraint violation, message from server: "Duplicate entry >> 'ORGANISM-5' >> for key 2" >> [java] at >> com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977) >> [java] at >> com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163) >> [java] at >> com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272) >> [java] at >> com.mysql.jdbc.Connection.execSQL(Connection.java:2236) >> [java] at >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java: >> 1741) >> [java] at >> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java: >> 1588) >> [java] at >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg >> ating >> PreparedStatement.java:233) >> [java] at >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg >> ating >> PreparedStatement.java:233) >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.persistTerm(OntologySQL.java: >> 554) >> [java] ... 11 more >> [java] Exception in thread "main" org.biojava.bio.BioError: Error >> looking up biosqlized ID for ORGANISM >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:684) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.intern_ontology_term(Bio >> SQLSe >> quenceDB.java:927) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.persistBioentryProperty( >> BioSQ >> LSequenceDB.java:894) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque >> nceDB >> .java:485) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequen >> ceDB. >> java:365) >> [java] at >> com.gts.genebank.GeneralReader.main(GeneralReader.java:64) >> [java] Caused by: java.lang.NullPointerException >> [java] at >> org.biojava.bio.seq.db.biosql.OntologySQL.termID(OntologySQL.java:682) >> [java] ... 5 more >> [java] Java Result: 1 >> >> >> What am I doing wrong? Any help would be greatly appreciated! >> >> MG >> >> _______________________________________________ >> biojava-dev mailing list >> biojava-dev@biojava.org >> http://biojava.org/mailman/listinfo/biojava-dev >> > > From td2 at sanger.ac.uk Tue Aug 3 14:09:03 2004 From: td2 at sanger.ac.uk (Thomas Down) Date: Tue Aug 3 14:10:26 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: References: Message-ID: <33FE1F54-E578-11D8-A15D-000A95C8B056@sanger.ac.uk> On 3 Aug 2004, at 18:56, Michael Griffith wrote: > Thomas, > > Thanks! Not being an expert with mySQL -- how do you change the field > def? > I added [BINARY] after the Varchar def and tried creating the field as > Binary. How should it be defined? Actually, it looks like the solution to this may depend on the version of MySQL you're using. See: http://dev.mysql.com/doc/mysql/en/CHAR.html But on the version I'm running (4.0.17 I think), the following seems to work: CREATE TABLE term ( term_id INT(10) UNSIGNED NOT NULL auto_increment, name VARCHAR(255) BINARY NOT NULL, definition TEXT, identifier VARCHAR(40), is_obsolete CHAR(1), ontology_id INT(10) UNSIGNED NOT NULL, PRIMARY KEY (term_id), UNIQUE (name,ontology_id), UNIQUE (identifier) ) TYPE=INNODB; Hope this works for you, Thomas. From mg at base-pair.com Tue Aug 3 14:19:23 2004 From: mg at base-pair.com (Michael Griffith) Date: Tue Aug 3 14:23:10 2004 Subject: [Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem... In-Reply-To: <33FE1F54-E578-11D8-A15D-000A95C8B056@sanger.ac.uk> Message-ID: Wonderful! It works! Thanks to everyone! As an aside there seems to be a table definition missing from the schema: CREATE TABLE term_relationship_term ( term_relationship_id INTEGER NOT NULL, term_id INTEGER NOT NULL, PRIMARY KEY ( term_relationship_id, term_id ), UNIQUE ( term_relationship_id ), UNIQUE ( term_id ) ); Cheers! MG On 8/3/04 1:09 PM, "Thomas Down" wrote: > > On 3 Aug 2004, at 18:56, Michael Griffith wrote: > >> Thomas, >> >> Thanks! Not being an expert with mySQL -- how do you change the field >> def? >> I added [BINARY] after the Varchar def and tried creating the field as >> Binary. How should it be defined? > > Actually, it looks like the solution to this may depend on the version > of MySQL you're using. See: > > http://dev.mysql.com/doc/mysql/en/CHAR.html > > But on the version I'm running (4.0.17 I think), the following seems to > work: > > CREATE TABLE term ( > term_id INT(10) UNSIGNED NOT NULL auto_increment, > name VARCHAR(255) BINARY NOT NULL, > definition TEXT, > identifier VARCHAR(40), > is_obsolete CHAR(1), > ontology_id INT(10) UNSIGNED NOT NULL, > PRIMARY KEY (term_id), > UNIQUE (name,ontology_id), > UNIQUE (identifier) > ) TYPE=INNODB; > > > Hope this works for you, > > Thomas. > > _______________________________________________ > biojava-dev mailing list > biojava-dev@biojava.org > http://biojava.org/mailman/listinfo/biojava-dev > From crollinsep at ub.umu.se Tue Aug 3 22:35:14 2004 From: crollinsep at ub.umu.se (Cheryl Rollins) Date: Tue Aug 3 22:52:07 2004 Subject: [Biojava-dev] Buy cheap Viagra through us. Message-ID: Hi, We have a new offer for you. 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Are you by any chance trying to communicate with a 9i+ database using an 8i driver? -hilmar On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: > Hi, > > I have been trying to get the latest BioSQL (Oracle) and BioJava to > play > nicely -- and I feel that I am close, but I am still getting errors. > I am > trying to read a GenBank file to the Oracle BioSQL schema with the > following > code: > > SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass > biodatabase, create); > > SequenceIterator iter = > (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, > br); > int counter= 0; > > while (iter.hasNext()) { > > Sequence seq = iter.nextSequence(); > > try { > db.addSequence(seq); > } > catch (Exception e) { > e.printStackTrace(); > } > ... > } > > This code works perfectly well with the mySQL version of the bio-sql > schema, > however with the oracle version, I get the following SQLException > stack. > > The loop loads about 65 of the first 70 records, and hangs on record > #71, > every time. What is puzzling, is I have never had any sort of these > kinds > of errors with any other Java/Oracle application. > > [java] org.biojava.bio.BioRuntimeException: Error adding sequence: > NM_019764 > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque > nceDB > .java:498) > [java] Trying to add: NM_021274 to the database -- insert attemp > #:71 > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequen > ceDB. > java:365) > [java] at > com.gts.genebank.GeneralReader.main(GeneralReader.java:74) > [java] Caused by: java.sql.SQLException: No more data to read from > socket > [java] at > oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) > [java] at > oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) > [java] at > oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) > [java] at > oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) > [java] at > oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) > [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) > [java] at > oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) > [java] at > oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java:1093) > [java] at > oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement.java > :2047 > ) > [java] at > oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.java: > 1940) > [java] at > oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement > .java > :2709) > [java] at > oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrepared > State > ment.java:589) > [java] at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg > ating > PreparedStatement.java:233) > [java] at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg > ating > PreparedStatement.java:233) > [java] at > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque > nceDB > .java:455) > [java] ... 2 more > > Any help would be greatly appreciated! > > Cheers! > > MG > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From swooten_sm at travelmarket.no Mon Aug 9 13:07:14 2004 From: swooten_sm at travelmarket.no (Stacy Wooten) Date: Mon Aug 9 13:05:46 2004 Subject: [Biojava-dev] Buy cheap Viagra through us. 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MG On 8/9/04 11:25 AM, "Hilmar Lapp" wrote: > This smells like a problem with one of the LOB columns, which is > Anncomment.Comment_Text and Biosequence.Seq, and the stack trace looks > like it's the Seq column (which holds the sequence). > > LOB columns in Oracle need to be streamed if they are over 4000 chars > (otherwise the server can do the conversion). I believe the more recent > versions of the Oracle JDBC driver do that transparently behind the > scenes if you call {set,get}String() on a column that in reality is a > LOB. > > Are you by any chance trying to communicate with a 9i+ database using > an 8i driver? > > -hilmar > > On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: > >> Hi, >> >> I have been trying to get the latest BioSQL (Oracle) and BioJava to >> play >> nicely -- and I feel that I am close, but I am still getting errors. >> I am >> trying to read a GenBank file to the Oracle BioSQL schema with the >> following >> code: >> >> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass >> biodatabase, create); >> >> SequenceIterator iter = >> (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, >> br); >> int counter= 0; >> >> while (iter.hasNext()) { >> >> Sequence seq = iter.nextSequence(); >> >> try { >> db.addSequence(seq); >> } >> catch (Exception e) { >> e.printStackTrace(); >> } >> ... >> } >> >> This code works perfectly well with the mySQL version of the bio-sql >> schema, >> however with the oracle version, I get the following SQLException >> stack. >> >> The loop loads about 65 of the first 70 records, and hangs on record >> #71, >> every time. What is puzzling, is I have never had any sort of these >> kinds >> of errors with any other Java/Oracle application. >> >> [java] org.biojava.bio.BioRuntimeException: Error adding sequence: >> NM_019764 >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque >> nceDB >> .java:498) >> [java] Trying to add: NM_021274 to the database -- insert attemp >> #:71 >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequen >> ceDB. >> java:365) >> [java] at >> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) >> [java] Caused by: java.sql.SQLException: No more data to read from >> socket >> [java] at >> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) >> [java] at >> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) >> [java] at >> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) >> [java] at >> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) >> [java] at >> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) >> [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) >> [java] at >> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) >> [java] at >> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java:1093) >> [java] at >> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement.java >> :2047 >> ) >> [java] at >> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.java: >> 1940) >> [java] at >> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement >> .java >> :2709) >> [java] at >> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrepared >> State >> ment.java:589) >> [java] at >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg >> ating >> PreparedStatement.java:233) >> [java] at >> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Deleg >> ating >> PreparedStatement.java:233) >> [java] at >> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeque >> nceDB >> .java:455) >> [java] ... 2 more >> >> Any help would be greatly appreciated! >> >> Cheers! >> >> MG >> >> From kdj at sanger.ac.uk Mon Aug 9 13:21:20 2004 From: kdj at sanger.ac.uk (Keith James) Date: Mon Aug 9 13:22:25 2004 Subject: [Biojava-dev] MORE Oracle BioSQL & BioJava problems In-Reply-To: References: Message-ID: >>>>> "Michael" == Michael Griffith writes: [...] Michael> The loop loads about 65 of the first 70 records, and Michael> hangs on record #71, every time. What is puzzling, is I Michael> have never had any sort of these kinds of errors with any Michael> other Java/Oracle application. Michael> [java] org.biojava.bio.BioRuntimeException: Error adding Michael> sequence: NM_019764 [java] at Michael> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB Michael> .java:498) [java] Trying to add: NM_021274 to the Michael> database -- insert attemp #:71 [java] at Michael> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. Michael> java:365) [java] at Michael> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) Michael> [java] Caused by: java.sql.SQLException: No more data to Michael> read from socket [java] at Michael> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) Firstly, IANABU (I am not a BioSQL user), but here's some things to try anyway, What version of Oracle and drivers? What DBCP version? It looks like the BioSQL code is using streams for the sequence, so it shouldn't be a data size problem. It looks like your connection may be getting closed too early. This could be a bad interaction with the the Oracle driver or it could be DBCP which in its 1.1 incarnation is quite flaky and prone to allowing shared connections. Is autocommit getting turned on accidentally? Anywhere a LOB gets populated it must be off in case multiple reads/writes are required (again this could be a symptom of a shared connection). Try a more recent DBCP. Use P6Spy (http://www.p6spy.com) to get the exact insert statements sent to the server and post them to the list. Keith -- - Keith James Microarray Facility, Team 65 - - The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK - From hlapp at gnf.org Mon Aug 9 15:28:57 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Aug 9 15:30:16 2004 Subject: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems In-Reply-To: References: Message-ID: <5BC16838-EA3A-11D8-A842-000A95AE92B0@gnf.org> Which rel. is the target Oracle DB? What is the length of the sequence string causing trouble? If it is indeed longer than 4000 chars, does the problem disappear when you make the sequence shorter than 4000 chars? Which JDBC API call is used to set the sequence string in the biojava language binding? If it is indeed setString(), what happens if you change that to the streaming API? -hilmar On Aug 9, 2004, at 10:08 AM, Michael Griffith wrote: > Hilmar, > > Thanks for the reply. > > Just to make sure I had the latest and greatest JDBC driver, I > downloaded > 9.2.0.3 from Oracle's web site. I got the same exact error, in the > same > exact order. > > I am still puzzled as to what is going on. > > MG > > > On 8/9/04 11:25 AM, "Hilmar Lapp" wrote: > >> This smells like a problem with one of the LOB columns, which is >> Anncomment.Comment_Text and Biosequence.Seq, and the stack trace looks >> like it's the Seq column (which holds the sequence). >> >> LOB columns in Oracle need to be streamed if they are over 4000 chars >> (otherwise the server can do the conversion). I believe the more >> recent >> versions of the Oracle JDBC driver do that transparently behind the >> scenes if you call {set,get}String() on a column that in reality is a >> LOB. >> >> Are you by any chance trying to communicate with a 9i+ database using >> an 8i driver? >> >> -hilmar >> >> On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: >> >>> Hi, >>> >>> I have been trying to get the latest BioSQL (Oracle) and BioJava to >>> play >>> nicely -- and I feel that I am close, but I am still getting errors. >>> I am >>> trying to read a GenBank file to the Oracle BioSQL schema with the >>> following >>> code: >>> >>> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass >>> biodatabase, create); >>> >>> SequenceIterator iter = >>> (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, >>> br); >>> int counter= 0; >>> >>> while (iter.hasNext()) { >>> >>> Sequence seq = iter.nextSequence(); >>> >>> try { >>> db.addSequence(seq); >>> } >>> catch (Exception e) { >>> e.printStackTrace(); >>> } >>> ... >>> } >>> >>> This code works perfectly well with the mySQL version of the bio-sql >>> schema, >>> however with the oracle version, I get the following SQLException >>> stack. >>> >>> The loop loads about 65 of the first 70 records, and hangs on record >>> #71, >>> every time. What is puzzling, is I have never had any sort of these >>> kinds >>> of errors with any other Java/Oracle application. >>> >>> [java] org.biojava.bio.BioRuntimeException: Error adding sequence: >>> NM_019764 >>> [java] at >>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeq >>> ue >>> nceDB >>> .java:498) >>> [java] Trying to add: NM_021274 to the database -- insert attemp >>> #:71 >>> [java] at >>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequ >>> en >>> ceDB. >>> java:365) >>> [java] at >>> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) >>> [java] Caused by: java.sql.SQLException: No more data to read >>> from >>> socket >>> [java] at >>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) >>> [java] at >>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) >>> [java] at >>> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) >>> [java] at >>> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) >>> [java] at >>> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) >>> [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) >>> [java] at >>> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) >>> [java] at >>> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java: >>> 1093) >>> [java] at >>> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement.ja >>> va >>> :2047 >>> ) >>> [java] at >>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.jav >>> a: >>> 1940) >>> [java] at >>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStateme >>> nt >>> .java >>> :2709) >>> [java] at >>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrepar >>> ed >>> State >>> ment.java:589) >>> [java] at >>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Del >>> eg >>> ating >>> PreparedStatement.java:233) >>> [java] at >>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Del >>> eg >>> ating >>> PreparedStatement.java:233) >>> [java] at >>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeq >>> ue >>> nceDB >>> .java:455) >>> [java] ... 2 more >>> >>> Any help would be greatly appreciated! >>> >>> Cheers! >>> >>> MG >>> >>> > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From mg at base-pair.com Mon Aug 9 15:28:40 2004 From: mg at base-pair.com (Michael Griffith) Date: Mon Aug 9 15:32:09 2004 Subject: [Biojava-dev] MORE Oracle BioSQL & BioJava problems In-Reply-To: Message-ID: Keith, Thanks for the reply. Oracle Server is 9.2.0.4 running on Suse Linux JDBC Client is 9.2.0.3 running on OSX I've tried DBCP 1.1 and 1.2 According to what I've been able to trace to the source, autocommit is off. I've never seen P6spy before -- so it will take some time to figure out how it works. Once I have the SQL Statements, I'll post them to this thread. Thanks for your suggestions -- any other help is greatly appreciated! MG On 8/9/04 12:21 PM, "Keith James" wrote: >>>>>> "Michael" == Michael Griffith writes: > > [...] > > Michael> The loop loads about 65 of the first 70 records, and > Michael> hangs on record #71, every time. What is puzzling, is I > Michael> have never had any sort of these kinds of errors with any > Michael> other Java/Oracle application. > > Michael> [java] org.biojava.bio.BioRuntimeException: Error adding > Michael> sequence: NM_019764 [java] at > Michael> > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSequenceDB > Michael> .java:498) [java] Trying to add: NM_021274 to the > Michael> database -- insert attemp #:71 [java] at > Michael> > org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequenceDB. > Michael> java:365) [java] at > Michael> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) > Michael> [java] Caused by: java.sql.SQLException: No more data to > Michael> read from socket [java] at > Michael> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) > > Firstly, IANABU (I am not a BioSQL user), but here's some things to > try anyway, > > What version of Oracle and drivers? What DBCP version? > > It looks like the BioSQL code is using streams for the sequence, so it > shouldn't be a data size problem. > > It looks like your connection may be getting closed too early. This > could be a bad interaction with the the Oracle driver or it could be > DBCP which in its 1.1 incarnation is quite flaky and prone to allowing > shared connections. Is autocommit getting turned on accidentally? > Anywhere a LOB gets populated it must be off in case multiple > reads/writes are required (again this could be a symptom of a shared > connection). > > Try a more recent DBCP. > > Use P6Spy (http://www.p6spy.com) to get the exact insert statements > sent to the server and post them to the list. > > Keith From fbowlingxl at edcgi.ro Mon Aug 9 21:02:10 2004 From: fbowlingxl at edcgi.ro (Fannie Bowling) Date: Mon Aug 9 21:02:05 2004 Subject: [Biojava-dev] We give you $200 bonus at Casino Zeal! 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The offending Java code appears to be: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values (?, ?, ?, ?, ?)"); String seqstr = seqToke.tokenizeSymbolList(seq); create_biosequence.setCharacterStream(4, new StringReader(seqstr), seqstr.length()); In all Java/Oracle applications we've developed, we've always inserted an empty_clob(), and then updated the clob separately using the record locator. I am a little apprehensive to hack the Opensource code, just because I want to stay in sync with the BioJava releases... Has anyone else using BioJava/BioSQL in Oracle run into this problem? Thanks in advance! MG On 8/9/04 2:28 PM, "Hilmar Lapp" wrote: > Which rel. is the target Oracle DB? > > What is the length of the sequence string causing trouble? If it is > indeed longer than 4000 chars, does the problem disappear when you make > the sequence shorter than 4000 chars? Which JDBC API call is used to > set the sequence string in the biojava language binding? If it is > indeed setString(), what happens if you change that to the streaming > API? > > -hilmar > > On Aug 9, 2004, at 10:08 AM, Michael Griffith wrote: > >> Hilmar, >> >> Thanks for the reply. >> >> Just to make sure I had the latest and greatest JDBC driver, I >> downloaded >> 9.2.0.3 from Oracle's web site. I got the same exact error, in the >> same >> exact order. >> >> I am still puzzled as to what is going on. >> >> MG >> >> >> On 8/9/04 11:25 AM, "Hilmar Lapp" wrote: >> >>> This smells like a problem with one of the LOB columns, which is >>> Anncomment.Comment_Text and Biosequence.Seq, and the stack trace looks >>> like it's the Seq column (which holds the sequence). >>> >>> LOB columns in Oracle need to be streamed if they are over 4000 chars >>> (otherwise the server can do the conversion). I believe the more >>> recent >>> versions of the Oracle JDBC driver do that transparently behind the >>> scenes if you call {set,get}String() on a column that in reality is a >>> LOB. >>> >>> Are you by any chance trying to communicate with a 9i+ database using >>> an 8i driver? >>> >>> -hilmar >>> >>> On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: >>> >>>> Hi, >>>> >>>> I have been trying to get the latest BioSQL (Oracle) and BioJava to >>>> play >>>> nicely -- and I feel that I am close, but I am still getting errors. >>>> I am >>>> trying to read a GenBank file to the Oracle BioSQL schema with the >>>> following >>>> code: >>>> >>>> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, dbPass >>>> biodatabase, create); >>>> >>>> SequenceIterator iter = >>>> (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, >>>> br); >>>> int counter= 0; >>>> >>>> while (iter.hasNext()) { >>>> >>>> Sequence seq = iter.nextSequence(); >>>> >>>> try { >>>> db.addSequence(seq); >>>> } >>>> catch (Exception e) { >>>> e.printStackTrace(); >>>> } >>>> ... >>>> } >>>> >>>> This code works perfectly well with the mySQL version of the bio-sql >>>> schema, >>>> however with the oracle version, I get the following SQLException >>>> stack. >>>> >>>> The loop loads about 65 of the first 70 records, and hangs on record >>>> #71, >>>> every time. What is puzzling, is I have never had any sort of these >>>> kinds >>>> of errors with any other Java/Oracle application. >>>> >>>> [java] org.biojava.bio.BioRuntimeException: Error adding sequence: >>>> NM_019764 >>>> [java] at >>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeq >>>> ue >>>> nceDB >>>> .java:498) >>>> [java] Trying to add: NM_021274 to the database -- insert attemp >>>> #:71 >>>> [java] at >>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSequ >>>> en >>>> ceDB. >>>> java:365) >>>> [java] at >>>> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) >>>> [java] Caused by: java.sql.SQLException: No more data to read >>>> from >>>> socket >>>> [java] at >>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) >>>> [java] at >>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) >>>> [java] at >>>> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) >>>> [java] at >>>> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) >>>> [java] at >>>> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) >>>> [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) >>>> [java] at >>>> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) >>>> [java] at >>>> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java: >>>> 1093) >>>> [java] at >>>> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement.ja >>>> va >>>> :2047 >>>> ) >>>> [java] at >>>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.jav >>>> a: >>>> 1940) >>>> [java] at >>>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStateme >>>> nt >>>> .java >>>> :2709) >>>> [java] at >>>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrepar >>>> ed >>>> State >>>> ment.java:589) >>>> [java] at >>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Del >>>> eg >>>> ating >>>> PreparedStatement.java:233) >>>> [java] at >>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(Del >>>> eg >>>> ating >>>> PreparedStatement.java:233) >>>> [java] at >>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLSeq >>>> ue >>>> nceDB >>>> .java:455) >>>> [java] ... 2 more >>>> >>>> Any help would be greatly appreciated! >>>> >>>> Cheers! >>>> >>>> MG >>>> >>>> >> >> From sblountpf at abaceeli.am Tue Aug 10 16:46:40 2004 From: sblountpf at abaceeli.am (Sasha Blount) Date: Tue Aug 10 16:46:50 2004 Subject: [Biojava-dev] Buy cheap Viagra through us. 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To exclude that possibility, do the following: SQL> DROP VIEW biosequence; SQL> RENAME SG_Biosequence TO biosequence; SQL> ALTER TABLE biosequence RENAME ent_oid TO bioentry_id; and then try again the offending sequence. (I don't give this a high likelihood though. What you describe as the way to insert LOBs is e.g. the same way Tim Bunce wrote it for DBD::Oracle, so chances are this is where the problem is.) -hilm On Aug 10, 2004, at 1:29 PM, Michael Griffith wrote: > Hi Hilmar, > > The DB target is Oracle 9i (9.2.0.4) running on SUSE Linux 9x. > > I do believe the problem occurs on sequences that are > 4000 chars. > > The offending Java code appears to be: > > PreparedStatement create_biosequence = conn.prepareStatement("insert > into > biosequence " + "(bioentry_id, version, length, seq, alphabet) " + > "values > (?, ?, ?, ?, ?)"); > > String seqstr = seqToke.tokenizeSymbolList(seq); > create_biosequence.setCharacterStream(4, new StringReader(seqstr), > seqstr.length()); > > In all Java/Oracle applications we've developed, we've always inserted > an > empty_clob(), and then updated the clob separately using the record > locator. > > I am a little apprehensive to hack the Opensource code, just because I > want > to stay in sync with the BioJava releases... > > Has anyone else using BioJava/BioSQL in Oracle run into this problem? > > Thanks in advance! > > MG > > > > On 8/9/04 2:28 PM, "Hilmar Lapp" wrote: > >> Which rel. is the target Oracle DB? >> >> What is the length of the sequence string causing trouble? If it is >> indeed longer than 4000 chars, does the problem disappear when you >> make >> the sequence shorter than 4000 chars? Which JDBC API call is used to >> set the sequence string in the biojava language binding? If it is >> indeed setString(), what happens if you change that to the streaming >> API? >> >> -hilmar >> >> On Aug 9, 2004, at 10:08 AM, Michael Griffith wrote: >> >>> Hilmar, >>> >>> Thanks for the reply. >>> >>> Just to make sure I had the latest and greatest JDBC driver, I >>> downloaded >>> 9.2.0.3 from Oracle's web site. I got the same exact error, in the >>> same >>> exact order. >>> >>> I am still puzzled as to what is going on. >>> >>> MG >>> >>> >>> On 8/9/04 11:25 AM, "Hilmar Lapp" wrote: >>> >>>> This smells like a problem with one of the LOB columns, which is >>>> Anncomment.Comment_Text and Biosequence.Seq, and the stack trace >>>> looks >>>> like it's the Seq column (which holds the sequence). >>>> >>>> LOB columns in Oracle need to be streamed if they are over 4000 >>>> chars >>>> (otherwise the server can do the conversion). I believe the more >>>> recent >>>> versions of the Oracle JDBC driver do that transparently behind the >>>> scenes if you call {set,get}String() on a column that in reality is >>>> a >>>> LOB. >>>> >>>> Are you by any chance trying to communicate with a 9i+ database >>>> using >>>> an 8i driver? >>>> >>>> -hilmar >>>> >>>> On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: >>>> >>>>> Hi, >>>>> >>>>> I have been trying to get the latest BioSQL (Oracle) and BioJava to >>>>> play >>>>> nicely -- and I feel that I am close, but I am still getting >>>>> errors. >>>>> I am >>>>> trying to read a GenBank file to the Oracle BioSQL schema with the >>>>> following >>>>> code: >>>>> >>>>> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, >>>>> dbPass >>>>> biodatabase, create); >>>>> >>>>> SequenceIterator iter = >>>>> (SequenceIterator)SeqIOTools.fileToBiojava(format, >>>>> alpha, >>>>> br); >>>>> int counter= 0; >>>>> >>>>> while (iter.hasNext()) { >>>>> >>>>> Sequence seq = iter.nextSequence(); >>>>> >>>>> try { >>>>> db.addSequence(seq); >>>>> } >>>>> catch (Exception e) { >>>>> e.printStackTrace(); >>>>> } >>>>> ... >>>>> } >>>>> >>>>> This code works perfectly well with the mySQL version of the >>>>> bio-sql >>>>> schema, >>>>> however with the oracle version, I get the following SQLException >>>>> stack. >>>>> >>>>> The loop loads about 65 of the first 70 records, and hangs on >>>>> record >>>>> #71, >>>>> every time. What is puzzling, is I have never had any sort of >>>>> these >>>>> kinds >>>>> of errors with any other Java/Oracle application. >>>>> >>>>> [java] org.biojava.bio.BioRuntimeException: Error adding sequence: >>>>> NM_019764 >>>>> [java] at >>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLS >>>>> eq >>>>> ue >>>>> nceDB >>>>> .java:498) >>>>> [java] Trying to add: NM_021274 to the database -- insert >>>>> attemp >>>>> #:71 >>>>> [java] at >>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSe >>>>> qu >>>>> en >>>>> ceDB. >>>>> java:365) >>>>> [java] at >>>>> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) >>>>> [java] Caused by: java.sql.SQLException: No more data to read >>>>> from >>>>> socket >>>>> [java] at >>>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) >>>>> [java] at >>>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) >>>>> [java] at >>>>> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) >>>>> [java] at >>>>> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) >>>>> [java] at >>>>> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) >>>>> [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) >>>>> [java] at >>>>> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) >>>>> [java] at >>>>> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java: >>>>> 1093) >>>>> [java] at >>>>> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement. >>>>> ja >>>>> va >>>>> :2047 >>>>> ) >>>>> [java] at >>>>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.j >>>>> av >>>>> a: >>>>> 1940) >>>>> [java] at >>>>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleState >>>>> me >>>>> nt >>>>> .java >>>>> :2709) >>>>> [java] at >>>>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrep >>>>> ar >>>>> ed >>>>> State >>>>> ment.java:589) >>>>> [java] at >>>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(D >>>>> el >>>>> eg >>>>> ating >>>>> PreparedStatement.java:233) >>>>> [java] at >>>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(D >>>>> el >>>>> eg >>>>> ating >>>>> PreparedStatement.java:233) >>>>> [java] at >>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLS >>>>> eq >>>>> ue >>>>> nceDB >>>>> .java:455) >>>>> [java] ... 2 more >>>>> >>>>> Any help would be greatly appreciated! >>>>> >>>>> Cheers! >>>>> >>>>> MG >>>>> >>>>> >>> >>> > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From autobuilder at derkholm.net Wed Aug 11 00:11:01 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Aug 10 23:48:42 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1092197461537.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040811 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From vicki_cook_fz at adlikon.ch Wed Aug 11 04:48:44 2004 From: vicki_cook_fz at adlikon.ch (vicki_cook_fz@adlikon.ch) Date: Wed Aug 11 04:51:06 2004 Subject: [Biojava-dev] Make $314 Message-ID: <0f9601c47f80$5c19141a$2aada544@humberc.on.ca> Hello, We sent you an email a while ago, because you now qualify for a new mortgage. 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It's main goal is the easy import of structured text files like microarray experiment results. To show it's functions i added three jpegs showing the three user interface steps the tool exists of. Step1 : let the user choose a filename and some file specific elements like tab or comma separated Step2 : here one can select the cols and rows needed Step3 : now the labelling of the remaining cols is done manually and a mapping to a string for the spotid is choosen My former tutor told me that this little tool could be of interest to BioJava. Sincerely yours, Jan Taubert -------------- next part -------------- A non-text attachment was scrubbed... Name: step1.JPG Type: image/jpeg Size: 70122 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/biojava-dev/attachments/20040810/315e51be/step1-0001.jpg -------------- next part -------------- A non-text attachment was scrubbed... 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More generally we need to improve some areas of the protein I/O. Notably the EmblLikeFormat doesn't really work too well for SwissProt. There are just too many subtle differences between the two. - Mark Matthew Pocock Sent by: biojava-dev-bounces@portal.open-bio.org 08/05/2004 09:06 PM To: Biojava-dev cc: Subject: [Biojava-dev] [Fwd: [Biojava-l] failed to read genbank peptide file] This looks like it may be a real bug. Does anyone have time to look into this? Matthew (feeling wasted after ISMB) ----- Message from Hongyu Zhang on Thu, 29 Jul 2004 22:41:02 -0700 ----- To: biojava-l@biojava.org Subject: [Biojava-l] failed to read genbank peptide file I am new to biojava. After being very happy with bioperl, I am glad to start my biojava adventure. But it looks like something is still not quite mature in biojava right now. I've used the example in "biojava in anger" to successfully read Genbank nucleotide files, but when reading peptide files I got constant errors. I did change the read function from readGenbank() to readGenpept(), but it didn't help :( . Is anyone aware of the problems when reading Genbank formatted peptide files? I put three sections below 1) the Java code 2) the command line and input file to this code 3) error message 1) First is my code, which is copied and revised from "biojava in anger": import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*; import java.io.*; import org.biojava.bio.*; import java.util.*; public class ReadGB { public static void main(String[] args) { BufferedReader br = null; try { //create a buffered reader to read the sequence file specified by args[0] br = new BufferedReader(new FileReader(args[0])); } catch (FileNotFoundException ex) { //can't find the file specified by args[0] ex.printStackTrace(); System.exit(-1); } //read the GenBank File SequenceIterator sequences = SeqIOTools.readGenpept(br); //iterate through the sequences while(sequences.hasNext()){ try { Sequence seq = sequences.nextSequence(); //do stuff with the sequence } catch (BioException ex) { //not in GenBank format ex.printStackTrace(); }catch (NoSuchElementException ex) { //request for more sequence when there isn't any ex.printStackTrace(); } } } } 2) After I successfully compiled the java code, I ran it in unix shell window like this: $ java ReadGB input_file where the input_file is copied from the followin NCBI link: http://www.ncbi.nih.gov/entrez/batchseq.cgi?txt=on&list_uids=7288210 3) And then I got this error message org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:175) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:103) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: org.biojava.bio.BioError: Could not initialize OntoTools at org.biojava.ontology.OntoTools.(OntoTools.java:106) at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:392) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:274) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more Caused by: java.lang.NullPointerException at java.io.Reader.(Reader.java:61) at java.io.InputStreamReader.(InputStreamReader.java:55) at org.biojava.ontology.OntoTools.(OntoTools.java:61) ... 15 more org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:175) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:103) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:392) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:274) at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:141) ... 8 more org.biojava.bio.BioException: Couldn't realize feature at org.biojava.bio.seq.SimpleFeatureRealizer$TemplateImpl.realize(SimpleFeatureRealizer.java:147) at org.biojava.bio.seq.SimpleFeatureRealizer.realizeFeature(SimpleFeatureRealizer.java:97) at org.biojava.bio.seq.impl.SimpleSequence.realizeFeature(SimpleSequence.java:217) at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:223) at org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence(SequenceBuilderBase.java:175) at org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence(SmartSequenceBuilder.java:103) at org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence(SequenceBuilderFilter.java:99) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:102) at ReadGB.main(ReadGB.java:30) Caused by: java.lang.NoClassDefFoundError at org.biojava.bio.seq.impl.SimpleFeature.(SimpleFeature.java:392) at org.biojava.bio.seq.impl.SimpleStrandedFeature.(SimpleStrandedFeature.java:97) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:274) at 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I adjusted the schema with the sql statements below, and ran the test. It made no difference. I think my only hope of getting this to work is if the BioJava group recognizes this as a bug and changes the code to first insert an empty_clob(), then to update the clob using the record locator. MG On 8/10/04 3:48 PM, "Hilmar Lapp" wrote: > Can you reduce this to a simple test case using a dummy table with e.g. > a single column of type CLOB, and then try to insert a value > 4000 > chars through the JDBC driver? > > There's a remote possibility that the driver is trying to do behind the > scenes what you describe if it determines the target column to be of a > LOB type, and it may fail to determine that when the table is in fact a > view (which it is here). To exclude that possibility, do the following: > > SQL> DROP VIEW biosequence; > SQL> RENAME SG_Biosequence TO biosequence; > SQL> ALTER TABLE biosequence RENAME ent_oid TO bioentry_id; > > and then try again the offending sequence. (I don't give this a high > likelihood though. What you describe as the way to insert LOBs is e.g. > the same way Tim Bunce wrote it for DBD::Oracle, so chances are this is > where the problem is.) > > -hilm > > On Aug 10, 2004, at 1:29 PM, Michael Griffith wrote: > >> Hi Hilmar, >> >> The DB target is Oracle 9i (9.2.0.4) running on SUSE Linux 9x. >> >> I do believe the problem occurs on sequences that are > 4000 chars. >> >> The offending Java code appears to be: >> >> PreparedStatement create_biosequence = conn.prepareStatement("insert >> into >> biosequence " + "(bioentry_id, version, length, seq, alphabet) " + >> "values >> (?, ?, ?, ?, ?)"); >> >> String seqstr = seqToke.tokenizeSymbolList(seq); >> create_biosequence.setCharacterStream(4, new StringReader(seqstr), >> seqstr.length()); >> >> In all Java/Oracle applications we've developed, we've always inserted >> an >> empty_clob(), and then updated the clob separately using the record >> locator. >> >> I am a little apprehensive to hack the Opensource code, just because I >> want >> to stay in sync with the BioJava releases... >> >> Has anyone else using BioJava/BioSQL in Oracle run into this problem? >> >> Thanks in advance! >> >> MG >> >> >> >> On 8/9/04 2:28 PM, "Hilmar Lapp" wrote: >> >>> Which rel. is the target Oracle DB? >>> >>> What is the length of the sequence string causing trouble? If it is >>> indeed longer than 4000 chars, does the problem disappear when you >>> make >>> the sequence shorter than 4000 chars? Which JDBC API call is used to >>> set the sequence string in the biojava language binding? If it is >>> indeed setString(), what happens if you change that to the streaming >>> API? >>> >>> -hilmar >>> >>> On Aug 9, 2004, at 10:08 AM, Michael Griffith wrote: >>> >>>> Hilmar, >>>> >>>> Thanks for the reply. >>>> >>>> Just to make sure I had the latest and greatest JDBC driver, I >>>> downloaded >>>> 9.2.0.3 from Oracle's web site. I got the same exact error, in the >>>> same >>>> exact order. >>>> >>>> I am still puzzled as to what is going on. >>>> >>>> MG >>>> >>>> >>>> On 8/9/04 11:25 AM, "Hilmar Lapp" wrote: >>>> >>>>> This smells like a problem with one of the LOB columns, which is >>>>> Anncomment.Comment_Text and Biosequence.Seq, and the stack trace >>>>> looks >>>>> like it's the Seq column (which holds the sequence). >>>>> >>>>> LOB columns in Oracle need to be streamed if they are over 4000 >>>>> chars >>>>> (otherwise the server can do the conversion). I believe the more >>>>> recent >>>>> versions of the Oracle JDBC driver do that transparently behind the >>>>> scenes if you call {set,get}String() on a column that in reality is >>>>> a >>>>> LOB. >>>>> >>>>> Are you by any chance trying to communicate with a 9i+ database >>>>> using >>>>> an 8i driver? >>>>> >>>>> -hilmar >>>>> >>>>> On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I have been trying to get the latest BioSQL (Oracle) and BioJava to >>>>>> play >>>>>> nicely -- and I feel that I am close, but I am still getting >>>>>> errors. >>>>>> I am >>>>>> trying to read a GenBank file to the Oracle BioSQL schema with the >>>>>> following >>>>>> code: >>>>>> >>>>>> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, >>>>>> dbPass >>>>>> biodatabase, create); >>>>>> >>>>>> SequenceIterator iter = >>>>>> (SequenceIterator)SeqIOTools.fileToBiojava(format, >>>>>> alpha, >>>>>> br); >>>>>> int counter= 0; >>>>>> >>>>>> while (iter.hasNext()) { >>>>>> >>>>>> Sequence seq = iter.nextSequence(); >>>>>> >>>>>> try { >>>>>> db.addSequence(seq); >>>>>> } >>>>>> catch (Exception e) { >>>>>> e.printStackTrace(); >>>>>> } >>>>>> ... >>>>>> } >>>>>> >>>>>> This code works perfectly well with the mySQL version of the >>>>>> bio-sql >>>>>> schema, >>>>>> however with the oracle version, I get the following SQLException >>>>>> stack. >>>>>> >>>>>> The loop loads about 65 of the first 70 records, and hangs on >>>>>> record >>>>>> #71, >>>>>> every time. What is puzzling, is I have never had any sort of >>>>>> these >>>>>> kinds >>>>>> of errors with any other Java/Oracle application. >>>>>> >>>>>> [java] org.biojava.bio.BioRuntimeException: Error adding sequence: >>>>>> NM_019764 >>>>>> [java] at >>>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLS >>>>>> eq >>>>>> ue >>>>>> nceDB >>>>>> .java:498) >>>>>> [java] Trying to add: NM_021274 to the database -- insert >>>>>> attemp >>>>>> #:71 >>>>>> [java] at >>>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQLSe >>>>>> qu >>>>>> en >>>>>> ceDB. >>>>>> java:365) >>>>>> [java] at >>>>>> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) >>>>>> [java] Caused by: java.sql.SQLException: No more data to read >>>>>> from >>>>>> socket >>>>>> [java] at >>>>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) >>>>>> [java] at >>>>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) >>>>>> [java] at >>>>>> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) >>>>>> [java] at >>>>>> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) >>>>>> [java] at >>>>>> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) >>>>>> [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) >>>>>> [java] at >>>>>> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) >>>>>> [java] at >>>>>> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java: >>>>>> 1093) >>>>>> [java] at >>>>>> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatement. >>>>>> ja >>>>>> va >>>>>> :2047 >>>>>> ) >>>>>> [java] at >>>>>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement.j >>>>>> av >>>>>> a: >>>>>> 1940) >>>>>> [java] at >>>>>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleState >>>>>> me >>>>>> nt >>>>>> .java >>>>>> :2709) >>>>>> [java] at >>>>>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePrep >>>>>> ar >>>>>> ed >>>>>> State >>>>>> ment.java:589) >>>>>> [java] at >>>>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(D >>>>>> el >>>>>> eg >>>>>> ating >>>>>> PreparedStatement.java:233) >>>>>> [java] at >>>>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(D >>>>>> el >>>>>> eg >>>>>> ating >>>>>> PreparedStatement.java:233) >>>>>> [java] at >>>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQLS >>>>>> eq >>>>>> ue >>>>>> nceDB >>>>>> .java:455) >>>>>> [java] ... 2 more >>>>>> >>>>>> Any help would be greatly appreciated! >>>>>> >>>>>> Cheers! >>>>>> >>>>>> MG >>>>>> >>>>>> >>>> >>>> >> >> From hlapp at gnf.org Tue Aug 17 12:07:24 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Aug 17 12:08:45 2004 Subject: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems In-Reply-To: Message-ID: <874AC3D7-F067-11D8-8FB9-000A959EB4C4@gnf.org> I can imagine that the biojava folks will be very appreciative if you can submit a patch, also given that you successfully solved this very problem before :-) I believe the biojava folks don't have a notion of different driver code for different RDBMSs, so that fix may need to be enclosed in something that tests for Oracle being the JDBC driver. -hilmar On Tuesday, August 17, 2004, at 08:39 AM, Michael Griffith wrote: > Hilmar, > > > The problem is definitely related to clob handling. I adjusted the > schema > with the sql statements below, and ran the test. It made no difference. > > I think my only hope of getting this to work is if the BioJava group > recognizes this as a bug and changes the code to first insert an > empty_clob(), then to update the clob using the record locator. > > MG > > > On 8/10/04 3:48 PM, "Hilmar Lapp" wrote: > >> Can you reduce this to a simple test case using a dummy table with >> e.g. >> a single column of type CLOB, and then try to insert a value > 4000 >> chars through the JDBC driver? >> >> There's a remote possibility that the driver is trying to do behind >> the >> scenes what you describe if it determines the target column to be of a >> LOB type, and it may fail to determine that when the table is in fact >> a >> view (which it is here). To exclude that possibility, do the >> following: >> >> SQL> DROP VIEW biosequence; >> SQL> RENAME SG_Biosequence TO biosequence; >> SQL> ALTER TABLE biosequence RENAME ent_oid TO bioentry_id; >> >> and then try again the offending sequence. (I don't give this a high >> likelihood though. What you describe as the way to insert LOBs is e.g. >> the same way Tim Bunce wrote it for DBD::Oracle, so chances are this >> is >> where the problem is.) >> >> -hilm >> >> On Aug 10, 2004, at 1:29 PM, Michael Griffith wrote: >> >>> Hi Hilmar, >>> >>> The DB target is Oracle 9i (9.2.0.4) running on SUSE Linux 9x. >>> >>> I do believe the problem occurs on sequences that are > 4000 chars. >>> >>> The offending Java code appears to be: >>> >>> PreparedStatement create_biosequence = conn.prepareStatement("insert >>> into >>> biosequence " + "(bioentry_id, version, length, seq, alphabet) " + >>> "values >>> (?, ?, ?, ?, ?)"); >>> >>> String seqstr = seqToke.tokenizeSymbolList(seq); >>> create_biosequence.setCharacterStream(4, new StringReader(seqstr), >>> seqstr.length()); >>> >>> In all Java/Oracle applications we've developed, we've always >>> inserted >>> an >>> empty_clob(), and then updated the clob separately using the record >>> locator. >>> >>> I am a little apprehensive to hack the Opensource code, just because >>> I >>> want >>> to stay in sync with the BioJava releases... >>> >>> Has anyone else using BioJava/BioSQL in Oracle run into this problem? >>> >>> Thanks in advance! >>> >>> MG >>> >>> >>> >>> On 8/9/04 2:28 PM, "Hilmar Lapp" wrote: >>> >>>> Which rel. is the target Oracle DB? >>>> >>>> What is the length of the sequence string causing trouble? If it is >>>> indeed longer than 4000 chars, does the problem disappear when you >>>> make >>>> the sequence shorter than 4000 chars? Which JDBC API call is used to >>>> set the sequence string in the biojava language binding? If it is >>>> indeed setString(), what happens if you change that to the streaming >>>> API? >>>> >>>> -hilmar >>>> >>>> On Aug 9, 2004, at 10:08 AM, Michael Griffith wrote: >>>> >>>>> Hilmar, >>>>> >>>>> Thanks for the reply. >>>>> >>>>> Just to make sure I had the latest and greatest JDBC driver, I >>>>> downloaded >>>>> 9.2.0.3 from Oracle's web site. I got the same exact error, in the >>>>> same >>>>> exact order. >>>>> >>>>> I am still puzzled as to what is going on. >>>>> >>>>> MG >>>>> >>>>> >>>>> On 8/9/04 11:25 AM, "Hilmar Lapp" wrote: >>>>> >>>>>> This smells like a problem with one of the LOB columns, which is >>>>>> Anncomment.Comment_Text and Biosequence.Seq, and the stack trace >>>>>> looks >>>>>> like it's the Seq column (which holds the sequence). >>>>>> >>>>>> LOB columns in Oracle need to be streamed if they are over 4000 >>>>>> chars >>>>>> (otherwise the server can do the conversion). I believe the more >>>>>> recent >>>>>> versions of the Oracle JDBC driver do that transparently behind >>>>>> the >>>>>> scenes if you call {set,get}String() on a column that in reality >>>>>> is >>>>>> a >>>>>> LOB. >>>>>> >>>>>> Are you by any chance trying to communicate with a 9i+ database >>>>>> using >>>>>> an 8i driver? >>>>>> >>>>>> -hilmar >>>>>> >>>>>> On Monday, August 9, 2004, at 09:03 AM, Michael Griffith wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I have been trying to get the latest BioSQL (Oracle) and BioJava >>>>>>> to >>>>>>> play >>>>>>> nicely -- and I feel that I am close, but I am still getting >>>>>>> errors. >>>>>>> I am >>>>>>> trying to read a GenBank file to the Oracle BioSQL schema with >>>>>>> the >>>>>>> following >>>>>>> code: >>>>>>> >>>>>>> SequenceDB db = new BioSQLSequenceDB(dbDriver, dbURL, dbUser, >>>>>>> dbPass >>>>>>> biodatabase, create); >>>>>>> >>>>>>> SequenceIterator iter = >>>>>>> (SequenceIterator)SeqIOTools.fileToBiojava(format, >>>>>>> alpha, >>>>>>> br); >>>>>>> int counter= 0; >>>>>>> >>>>>>> while (iter.hasNext()) { >>>>>>> >>>>>>> Sequence seq = iter.nextSequence(); >>>>>>> >>>>>>> try { >>>>>>> db.addSequence(seq); >>>>>>> } >>>>>>> catch (Exception e) { >>>>>>> e.printStackTrace(); >>>>>>> } >>>>>>> ... >>>>>>> } >>>>>>> >>>>>>> This code works perfectly well with the mySQL version of the >>>>>>> bio-sql >>>>>>> schema, >>>>>>> however with the oracle version, I get the following SQLException >>>>>>> stack. >>>>>>> >>>>>>> The loop loads about 65 of the first 70 records, and hangs on >>>>>>> record >>>>>>> #71, >>>>>>> every time. What is puzzling, is I have never had any sort of >>>>>>> these >>>>>>> kinds >>>>>>> of errors with any other Java/Oracle application. >>>>>>> >>>>>>> [java] org.biojava.bio.BioRuntimeException: Error adding >>>>>>> sequence: >>>>>>> NM_019764 >>>>>>> [java] at >>>>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQ >>>>>>> LS >>>>>>> eq >>>>>>> ue >>>>>>> nceDB >>>>>>> .java:498) >>>>>>> [java] Trying to add: NM_021274 to the database -- insert >>>>>>> attemp >>>>>>> #:71 >>>>>>> [java] at >>>>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.addSequence(BioSQL >>>>>>> Se >>>>>>> qu >>>>>>> en >>>>>>> ceDB. >>>>>>> java:365) >>>>>>> [java] at >>>>>>> com.gts.genebank.GeneralReader.main(GeneralReader.java:74) >>>>>>> [java] Caused by: java.sql.SQLException: No more data to >>>>>>> read >>>>>>> from >>>>>>> socket >>>>>>> [java] at >>>>>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:134) >>>>>>> [java] at >>>>>>> oracle.jdbc.dbaccess.DBError.throwSqlException(DBError.java:179) >>>>>>> [java] at >>>>>>> oracle.jdbc.dbaccess.DBError.check_error(DBError.java:1160) >>>>>>> [java] at >>>>>>> oracle.jdbc.ttc7.MAREngine.unmarshalUB1(MAREngine.java:963) >>>>>>> [java] at >>>>>>> oracle.jdbc.ttc7.MAREngine.unmarshalSB1(MAREngine.java:893) >>>>>>> [java] at oracle.jdbc.ttc7.Oall7.receive(Oall7.java:369) >>>>>>> [java] at >>>>>>> oracle.jdbc.ttc7.TTC7Protocol.doOall7(TTC7Protocol.java:1891) >>>>>>> [java] at >>>>>>> oracle.jdbc.ttc7.TTC7Protocol.parseExecuteFetch(TTC7Protocol.java >>>>>>> : >>>>>>> 1093) >>>>>>> [java] at >>>>>>> oracle.jdbc.driver.OracleStatement.executeNonQuery(OracleStatemen >>>>>>> t. >>>>>>> ja >>>>>>> va >>>>>>> :2047 >>>>>>> ) >>>>>>> [java] at >>>>>>> oracle.jdbc.driver.OracleStatement.doExecuteOther(OracleStatement >>>>>>> .j >>>>>>> av >>>>>>> a: >>>>>>> 1940) >>>>>>> [java] at >>>>>>> oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleSta >>>>>>> te >>>>>>> me >>>>>>> nt >>>>>>> .java >>>>>>> :2709) >>>>>>> [java] at >>>>>>> oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePr >>>>>>> ep >>>>>>> ar >>>>>>> ed >>>>>>> State >>>>>>> ment.java:589) >>>>>>> [java] at >>>>>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate >>>>>>> (D >>>>>>> el >>>>>>> eg >>>>>>> ating >>>>>>> PreparedStatement.java:233) >>>>>>> [java] at >>>>>>> org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate >>>>>>> (D >>>>>>> el >>>>>>> eg >>>>>>> ating >>>>>>> PreparedStatement.java:233) >>>>>>> [java] at >>>>>>> org.biojava.bio.seq.db.biosql.BioSQLSequenceDB._addSequence(BioSQ >>>>>>> LS >>>>>>> eq >>>>>>> ue >>>>>>> nceDB >>>>>>> .java:455) >>>>>>> [java] ... 2 more >>>>>>> >>>>>>> Any help would be greatly appreciated! >>>>>>> >>>>>>> Cheers! >>>>>>> >>>>>>> MG >>>>>>> >>>>>>> >>>>> >>>>> >>> >>> > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From jwk2004 at gmail.com Tue Aug 17 13:57:52 2004 From: jwk2004 at gmail.com (James) Date: Tue Aug 17 13:58:44 2004 Subject: [Biojava-dev] Error in generating docbook Message-ID: y0! I tried building all the docs for BioJava from cvs I checked out. All the docs built except for the docbook, in which the infamous "Fatal error during transformation" spewd on my console. After digging around BioJava, I figured out the problem. The problem lies in the biojava-doc-main.xml inside the folder /biojava-live/docs. The first line which is: Well, I was playing around with BioSQL/HSQLDB and BioJava. I didn't have much success with the biosqldb-hsqldb.sql from BioJava's CVS. That sql file did load into my hsqldb 1.7.2 just fine except I had problems loading genbank files using the UploadFlat.java from CVS. So I downloaded and modified the original biosqldb-mysql.sql from BioSQL's CVS to valid hsqldb syntax (Even though the schema didn't change, just the syntax changed). And it worked! Problem is that when I load genbank files, I get this error: This database appears to be an old (pre-Singapore) BioSQL. If you need to access it, try an older BioJava snapshot (1.3pre1 or earlier) Any assistance would be greatly appreciated! =) I included my modified files below. =============================================================== Filename: biosqldb-hsqldb_modified.sql =============================================================== CREATE TABLE biodatabase ( biodatabase_id INT NOT NULL IDENTITY, name VARCHAR(128) NOT NULL, authority VARCHAR(128), description LONGVARCHAR, PRIMARY KEY (biodatabase_id), UNIQUE (name) ); CREATE INDEX db_auth on biodatabase(authority); CREATE TABLE taxon ( taxon_id INT NOT NULL IDENTITY, ncbi_taxon_id INT, parent_taxon_id INT, node_rank VARCHAR(32), genetic_code TINYINT, mito_genetic_code TINYINT, left_value INT, right_value INT, PRIMARY KEY (taxon_id), UNIQUE (ncbi_taxon_id), UNIQUE (left_value), UNIQUE (right_value) ); -- HSQLDB 1.7.1 UNIQUE BUG -- UNIQUE (left_value), -- UNIQUE (right_value) CREATE INDEX taxparent ON taxon(parent_taxon_id); CREATE TABLE taxon_name ( taxon_id INT NOT NULL, name VARCHAR(255) NOT NULL, name_class VARCHAR(32) NOT NULL, UNIQUE (taxon_id,name,name_class) ); CREATE INDEX taxnametaxonid ON taxon_name(taxon_id); CREATE INDEX taxnamename ON taxon_name(name); CREATE TABLE ontology ( ontology_id INT NOT NULL IDENTITY, name VARCHAR(32) NOT NULL, definition LONGVARCHAR, PRIMARY KEY (ontology_id), UNIQUE (name) ); CREATE TABLE term ( term_id INT NOT NULL IDENTITY, name VARCHAR(255) NOT NULL, definition LONGVARCHAR, identifier VARCHAR(40), is_obsolete CHAR(1), ontology_id INT NOT NULL, PRIMARY KEY (term_id), UNIQUE (name,ontology_id), UNIQUE (identifier) ); -- HSQLDB 1.7.1 UNIQUE BUG -- UNIQUE (identifier) CREATE INDEX term_ont ON term(ontology_id); -- We use the field name "name" instead of "synonym" (which is a reserved word in some RDBMS) CREATE TABLE term_synonym ( synonym VARCHAR(255) NOT NULL, term_id INT NOT NULL, PRIMARY KEY (term_id,synonym) ); CREATE TABLE term_dbxref ( term_id INT NOT NULL, dbxref_id INT NOT NULL, rank SMALLINT, PRIMARY KEY (term_id, dbxref_id) ); CREATE INDEX trmdbxref_dbxrefid ON term_dbxref(dbxref_id); CREATE TABLE term_relationship ( term_relationship_id INT NOT NULL IDENTITY, subject_term_id INT NOT NULL, predicate_term_id INT NOT NULL, object_term_id INT NOT NULL, ontology_id INT NOT NULL, PRIMARY KEY (term_relationship_id), UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id) ); CREATE INDEX trmrel_predicateid ON term_relationship(predicate_term_id); CREATE INDEX trmrel_objectid ON term_relationship(object_term_id); CREATE INDEX trmrel_ontid ON term_relationship(ontology_id); CREATE TABLE term_path ( term_path_id INT NOT NULL IDENTITY, subject_term_id INT NOT NULL, predicate_term_id INT NOT NULL, object_term_id INT NOT NULL, ontology_id INT NOT NULL, distance INT, PRIMARY KEY (term_path_id), UNIQUE (subject_term_id,predicate_term_id,object_term_id,ontology_id,distance) ); CREATE INDEX trmpath_predicateid ON term_path(predicate_term_id); CREATE INDEX trmpath_objectid ON term_path(object_term_id); CREATE INDEX trmpath_ontid ON term_path(ontology_id); CREATE TABLE bioentry ( bioentry_id INT NOT NULL IDENTITY, biodatabase_id INT NOT NULL, taxon_id INT, name VARCHAR(40) NOT NULL, accession VARCHAR(40) NOT NULL, identifier VARCHAR(40), division VARCHAR(6), description LONGVARCHAR, version SMALLINT NOT NULL, PRIMARY KEY (bioentry_id), UNIQUE (accession,biodatabase_id,version), UNIQUE (identifier) ); -- HSQLDB 1.7.1 UNIQUE BUG -- UNIQUE (identifier) CREATE INDEX bioentry_name ON bioentry(name); CREATE INDEX bioentry_db ON bioentry(biodatabase_id); CREATE INDEX bioentry_tax ON bioentry(taxon_id); -- BioJava addition. Not currently in main BioSQL CREATE TABLE term_relationship_term ( term_relationship_id int DEFAULT 0 NOT NULL, term_id int DEFAULT 0 NOT NULL, PRIMARY KEY (term_relationship_id,term_id), UNIQUE (term_relationship_id), UNIQUE (term_id) ); CREATE TABLE bioentry_relationship ( bioentry_relationship_id INT NOT NULL IDENTITY, object_bioentry_id INT NOT NULL, subject_bioentry_id INT NOT NULL, term_id INT NOT NULL, rank INT, PRIMARY KEY (bioentry_relationship_id), UNIQUE (object_bioentry_id,subject_bioentry_id,term_id) ); CREATE INDEX bioentryrel_trm ON bioentry_relationship(term_id); CREATE INDEX bioentryrel_child ON bioentry_relationship(subject_bioentry_id); CREATE TABLE bioentry_path ( object_bioentry_id INT NOT NULL, subject_bioentry_id INT NOT NULL, term_id INT NOT NULL, distance INT, UNIQUE (object_bioentry_id,subject_bioentry_id,term_id,distance) ); CREATE INDEX bioentrypath_trm ON bioentry_path(term_id); CREATE INDEX bioentrypath_child ON bioentry_path(subject_bioentry_id); CREATE TABLE biosequence ( bioentry_id INT NOT NULL, version SMALLINT, length INT, alphabet VARCHAR(10), seq LONGVARCHAR, PRIMARY KEY (bioentry_id) ); -- add these only if you want them: -- ALTER TABLE biosequence ADD COLUMN ( isoelec_pt NUMERIC(4,2) ); -- ALTER TABLE biosequence ADD COLUMN ( mol_wgt DOUBLE PRECISION ); -- ALTER TABLE biosequence ADD COLUMN ( perc_gc DOUBLE PRECISION ); CREATE TABLE dbxref ( dbxref_id INT NOT NULL IDENTITY, dbname VARCHAR(40) NOT NULL, accession VARCHAR(40) NOT NULL, version SMALLINT NOT NULL, PRIMARY KEY (dbxref_id), UNIQUE(accession, dbname, version) ); CREATE INDEX dbxref_db ON dbxref(dbname); CREATE TABLE dbxref_qualifier_value ( dbxref_id INT NOT NULL, term_id INT NOT NULL, rank SMALLINT DEFAULT 0 NOT NULL, value LONGVARCHAR, PRIMARY KEY (dbxref_id,term_id,rank) ); CREATE INDEX dbxrefqual_dbx ON dbxref_qualifier_value(dbxref_id); CREATE INDEX dbxrefqual_trm ON dbxref_qualifier_value(term_id); CREATE TABLE bioentry_dbxref ( bioentry_id INT NOT NULL, dbxref_id INT NOT NULL, rank SMALLINT, PRIMARY KEY (bioentry_id,dbxref_id) ); CREATE INDEX dblink_dbx ON bioentry_dbxref(dbxref_id); CREATE TABLE reference ( reference_id INT NOT NULL IDENTITY, dbxref_id INT, location LONGVARCHAR NOT NULL, title LONGVARCHAR, authors LONGVARCHAR NOT NULL, crc VARCHAR(32), PRIMARY KEY (reference_id), UNIQUE (dbxref_id), UNIQUE (crc) ); CREATE TABLE bioentry_reference ( bioentry_id INT NOT NULL, reference_id INT NOT NULL, start_pos INT, end_pos INT, rank SMALLINT DEFAULT 0 NOT NULL, PRIMARY KEY(bioentry_id,reference_id,rank) ); CREATE INDEX bioentryref_ref ON bioentry_reference(reference_id); -- We use the table name "anncomment" instead of "comment" (which is a reserved word in some RDBMS) CREATE TABLE comment ( comment_id INT NOT NULL IDENTITY, bioentry_id INT NOT NULL, comment_text LONGVARCHAR NOT NULL, rank SMALLINT DEFAULT 0 NOT NULL, PRIMARY KEY (comment_id), UNIQUE(bioentry_id, rank) ); CREATE TABLE bioentry_qualifier_value ( bioentry_id INT NOT NULL, term_id INT NOT NULL, value LONGVARCHAR, rank INT DEFAULT 0 NOT NULL, UNIQUE (bioentry_id,term_id,rank) ); CREATE INDEX bioentryqual_trm ON bioentry_qualifier_value(term_id); CREATE TABLE seqfeature ( seqfeature_id INT NOT NULL IDENTITY, bioentry_id INT NOT NULL, type_term_id INT NOT NULL, source_term_id INT NOT NULL, display_name VARCHAR(64), rank SMALLINT DEFAULT 0 NOT NULL, PRIMARY KEY (seqfeature_id), UNIQUE (bioentry_id,type_term_id,source_term_id,rank) ); CREATE INDEX seqfeature_trm ON seqfeature(type_term_id); CREATE INDEX seqfeature_fsrc ON seqfeature(source_term_id); CREATE TABLE seqfeature_relationship ( seqfeature_relationship_id INT NOT NULL IDENTITY, object_seqfeature_id INT NOT NULL, subject_seqfeature_id INT NOT NULL, term_id INT NOT NULL, rank INT, PRIMARY KEY (seqfeature_relationship_id), UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id) ); CREATE INDEX seqfeaturerel_trm ON seqfeature_relationship(term_id); CREATE INDEX seqfeaturerel_child ON seqfeature_relationship(subject_seqfeature_id); CREATE TABLE seqfeature_path ( object_seqfeature_id INT NOT NULL, subject_seqfeature_id INT NOT NULL, term_id INT NOT NULL, distance INT, UNIQUE (object_seqfeature_id,subject_seqfeature_id,term_id,distance) ); CREATE INDEX seqfeaturepath_trm ON seqfeature_path(term_id); CREATE INDEX seqfeaturepath_child ON seqfeature_path(subject_seqfeature_id); CREATE TABLE seqfeature_qualifier_value ( seqfeature_id INT NOT NULL, term_id INT NOT NULL, rank SMALLINT DEFAULT 0 NOT NULL, value LONGVARCHAR NOT NULL, PRIMARY KEY (seqfeature_id,term_id,rank) ); CREATE INDEX seqfeaturequal_trm ON seqfeature_qualifier_value(term_id); CREATE TABLE seqfeature_dbxref ( seqfeature_id INT NOT NULL, dbxref_id INT NOT NULL, rank SMALLINT, PRIMARY KEY (seqfeature_id,dbxref_id) ); CREATE INDEX feadblink_dbx ON seqfeature_dbxref(dbxref_id); CREATE TABLE location ( location_id INT NOT NULL IDENTITY, seqfeature_id INT NOT NULL, dbxref_id INT, term_id INT, start_pos INT, end_pos INT, strand TINYINT NOT NULL, rank SMALLINT DEFAULT 0 NOT NULL, PRIMARY KEY (location_id), UNIQUE (seqfeature_id, rank) ); CREATE INDEX seqfeatureloc_start ON location(start_pos, end_pos); CREATE INDEX seqfeatureloc_dbx ON location(dbxref_id); CREATE INDEX seqfeatureloc_trm ON location(term_id); CREATE TABLE location_qualifier_value ( location_id INT NOT NULL, term_id INT NOT NULL, value VARCHAR(255) NOT NULL, int_value INT, PRIMARY KEY (location_id,term_id) ); CREATE INDEX locationqual_trm ON location_qualifier_value(term_id); -- -- Create the foreign key constraints -- -- ontology term ALTER TABLE term ADD CONSTRAINT FKont_term FOREIGN KEY (ontology_id) REFERENCES ontology(ontology_id) ON DELETE CASCADE; -- term synonyms ALTER TABLE term_synonym ADD CONSTRAINT FKterm_syn FOREIGN KEY (term_id) REFERENCES term(term_id) ON DELETE CASCADE; -- term_dbxref ALTER TABLE term_dbxref ADD CONSTRAINT FKdbxref_trmdbxref FOREIGN KEY (dbxref_id) REFERENCES dbxref(dbxref_id) ON DELETE CASCADE; ALTER TABLE term_dbxref ADD CONSTRAINT FKterm_trmdbxref FOREIGN KEY (term_id) REFERENCES term(term_id) ON DELETE CASCADE; -- term_relationship ALTER TABLE term_relationship ADD CONSTRAINT FKtrmsubject_trmrel FOREIGN KEY (subject_term_id) REFERENCES term(term_id) ON DELETE CASCADE; ALTER TABLE term_relationship ADD CONSTRAINT FKtrmpredicate_trmrel FOREIGN KEY (predicate_term_id) REFERENCES term(term_id) ON DELETE CASCADE; ALTER TABLE term_relationship ADD CONSTRAINT FKtrmobject_trmrel FOREIGN KEY (object_term_id) REFERENCES term(term_id) ON DELETE CASCADE; ALTER TABLE term_relationship ADD CONSTRAINT FKterm_trmrel FOREIGN KEY (ontology_id) REFERENCES ontology(ontology_id) ON DELETE CASCADE; -- term_path ALTER TABLE term_path ADD CONSTRAINT FKtrmsubject_trmpath FOREIGN KEY (subject_term_id) REFERENCES term(term_id) ON DELETE CASCADE; ALTER TABLE term_path ADD CONSTRAINT FKtrmpredicate_trmpath FOREIGN KEY (predicate_term_id) REFERENCES term(term_id) ON DELETE CASCADE; ALTER TABLE term_path ADD CONSTRAINT FKtrmobject_trmpath FOREIGN KEY (object_term_id) REFERENCES term(term_id) ON DELETE CASCADE; ALTER TABLE term_path ADD CONSTRAINT FKontology_trmpath FOREIGN KEY (ontology_id) REFERENCES ontology(ontology_id) ON DELETE CASCADE; -- taxon, taxon_name -- unfortunately, we can't constrain parent_taxon_id as it is violated -- occasionally by the downloads available from NCBI -- ALTER TABLE taxon ADD CONSTRAINT FKtaxon_taxon -- FOREIGN KEY (parent_taxon_id) REFERENCES taxon(taxon_id); ALTER TABLE taxon_name ADD CONSTRAINT FKtaxon_taxonname FOREIGN KEY (taxon_id) REFERENCES taxon(taxon_id) ON DELETE CASCADE; -- bioentry ALTER TABLE bioentry ADD CONSTRAINT FKtaxon_bioentry FOREIGN KEY (taxon_id) REFERENCES taxon(taxon_id); ALTER TABLE bioentry ADD CONSTRAINT FKbiodatabase_bioentry FOREIGN KEY (biodatabase_id) REFERENCES biodatabase(biodatabase_id); -- bioentry_relationship ALTER TABLE bioentry_relationship ADD CONSTRAINT FKterm_bioentryrel FOREIGN KEY (term_id) REFERENCES term(term_id); ALTER TABLE bioentry_relationship ADD CONSTRAINT FKparentent_bioentryrel FOREIGN KEY (object_bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; ALTER TABLE bioentry_relationship ADD CONSTRAINT FKchildent_bioentryrel FOREIGN KEY (subject_bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; -- bioentry_path ALTER TABLE bioentry_path ADD CONSTRAINT FKterm_bioentrypath FOREIGN KEY (term_id) REFERENCES term(term_id); ALTER TABLE bioentry_path ADD CONSTRAINT FKparentent_bioentrypath FOREIGN KEY (object_bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; ALTER TABLE bioentry_path ADD CONSTRAINT FKchildent_bioentrypath FOREIGN KEY (subject_bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; -- biosequence ALTER TABLE biosequence ADD CONSTRAINT FKbioentry_bioseq FOREIGN KEY (bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; -- comment ALTER TABLE comment ADD CONSTRAINT FKbioentry_comment FOREIGN KEY(bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; -- bioentry_dbxref ALTER TABLE bioentry_dbxref ADD CONSTRAINT FKbioentry_dblink FOREIGN KEY (bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; ALTER TABLE bioentry_dbxref ADD CONSTRAINT FKdbxref_dblink FOREIGN KEY (dbxref_id) REFERENCES dbxref(dbxref_id) ON DELETE CASCADE; -- dbxref_qualifier_value ALTER TABLE dbxref_qualifier_value ADD CONSTRAINT FKtrm_dbxrefqual FOREIGN KEY (term_id) REFERENCES term(term_id); ALTER TABLE dbxref_qualifier_value ADD CONSTRAINT FKdbxref_dbxrefqual FOREIGN KEY (dbxref_id) REFERENCES dbxref(dbxref_id) ON DELETE CASCADE; -- bioentry_reference ALTER TABLE bioentry_reference ADD CONSTRAINT FKbioentry_entryref FOREIGN KEY (bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; ALTER TABLE bioentry_reference ADD CONSTRAINT FKreference_entryref FOREIGN KEY (reference_id) REFERENCES reference(reference_id) ON DELETE CASCADE; -- bioentry_qualifier_value ALTER TABLE bioentry_qualifier_value ADD CONSTRAINT FKbioentry_entqual FOREIGN KEY (bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; ALTER TABLE bioentry_qualifier_value ADD CONSTRAINT FKterm_entqual FOREIGN KEY (term_id) REFERENCES term(term_id); -- reference ALTER TABLE reference ADD CONSTRAINT FKdbxref_reference FOREIGN KEY ( dbxref_id ) REFERENCES dbxref ( dbxref_id ) ; -- seqfeature ALTER TABLE seqfeature ADD CONSTRAINT FKterm_seqfeature FOREIGN KEY (type_term_id) REFERENCES term(term_id); ALTER TABLE seqfeature ADD CONSTRAINT FKsourceterm_seqfeature FOREIGN KEY (source_term_id) REFERENCES term(term_id); ALTER TABLE seqfeature ADD CONSTRAINT FKbioentry_seqfeature FOREIGN KEY (bioentry_id) REFERENCES bioentry(bioentry_id) ON DELETE CASCADE; -- seqfeature_relationship ALTER TABLE seqfeature_relationship ADD CONSTRAINT FKterm_seqfeatrel FOREIGN KEY (term_id) REFERENCES term(term_id); ALTER TABLE seqfeature_relationship ADD CONSTRAINT FKparentfeat_seqfeatrel FOREIGN KEY (object_seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; ALTER TABLE seqfeature_relationship ADD CONSTRAINT FKchildfeat_seqfeatrel FOREIGN KEY (subject_seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; -- seqfeature_path ALTER TABLE seqfeature_path ADD CONSTRAINT FKterm_seqfeatpath FOREIGN KEY (term_id) REFERENCES term(term_id); ALTER TABLE seqfeature_path ADD CONSTRAINT FKparentfeat_seqfeatpath FOREIGN KEY (object_seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; ALTER TABLE seqfeature_path ADD CONSTRAINT FKchildfeat_seqfeatpath FOREIGN KEY (subject_seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; -- seqfeature_qualifier_value ALTER TABLE seqfeature_qualifier_value ADD CONSTRAINT FKterm_featqual FOREIGN KEY (term_id) REFERENCES term(term_id); ALTER TABLE seqfeature_qualifier_value ADD CONSTRAINT FKseqfeature_featqual FOREIGN KEY (seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; -- seqfeature_dbxref ALTER TABLE seqfeature_dbxref ADD CONSTRAINT FKseqfeature_feadblink FOREIGN KEY (seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; ALTER TABLE seqfeature_dbxref ADD CONSTRAINT FKdbxref_feadblink FOREIGN KEY (dbxref_id) REFERENCES dbxref(dbxref_id) ON DELETE CASCADE; -- location ALTER TABLE location ADD CONSTRAINT FKseqfeature_location FOREIGN KEY (seqfeature_id) REFERENCES seqfeature(seqfeature_id) ON DELETE CASCADE; ALTER TABLE location ADD CONSTRAINT FKdbxref_location FOREIGN KEY (dbxref_id) REFERENCES dbxref(dbxref_id); ALTER TABLE location ADD CONSTRAINT FKterm_featloc FOREIGN KEY (term_id) REFERENCES term(term_id); -- location_qualifier_value ALTER TABLE location_qualifier_value ADD CONSTRAINT FKfeatloc_locqual FOREIGN KEY (location_id) REFERENCES location(location_id) ON DELETE CASCADE; ALTER TABLE location_qualifier_value ADD CONSTRAINT FKterm_locqual FOREIGN KEY (term_id) REFERENCES term(term_id); =============================================================== Filename: Testhsqldb.java (modified from UploadFlat.java from CVS) =============================================================== import java.sql.Connection; 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Message-ID: <3b3501c4899c$325c351f$21d1f37b@vgh.bwl.de> Hi, We have a new offer for you. Buy cheap Viagra through our online store. - Private online ordering - No prescription required - World wide shipping Order your drugs offshore and save over 70%! Click here: http://therxshop.net/meds/ Best regards, Donald Cunfingham No thanks: http://therxshop.net/rm.html From mg at base-pair.com Tue Aug 24 10:55:43 2004 From: mg at base-pair.com (Michael Griffith) Date: Tue Aug 24 10:59:07 2004 Subject: FW: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems In-Reply-To: Message-ID: Hello all, For some reason this message was rejected by the moderator of the bio-sql mail list. I believe it may because I had a zip file attachment of the bio-sql/oracle scripts attached. I was asked by the moderator to resend it. I am doing so, and posting to the bioJava group as well. I would like to help Shepard this problem to resolution, but have had no real experience working on Open source projects to make fixes, etc. Please let me know what else I may do. Cheers! MG ------ Forwarded Message From: Michael Griffith Date: Thu, 19 Aug 2004 16:00:02 -0500 To: Michael Heuer Cc: , Subject: Re: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems Michael, The BioSQL DDL is the current version that is in the CVS for bio-sql project. It is also attached here as a zip file. In the create objects section there is a missing table that needs to get created after all the other objects are created: CREATE TABLE term_relationship_term ( term_relationship_id int NOT NULL, term_id int NOT NULL ) In the class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.java, at line 446, the Prepare statement reads: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values(?, ?, ?, ?, ?)"); I think it should be something like: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values(?, ?, ?, empty_clob(), ?)"); Then -- I think you can do this with the JDBC clob classes, but I have always used the Oracle JDBC/CLOB classes. I would think you'd want to keep all the oracle stuff segregated out... After your insert is successful in biosequence, you'll want to update the clob table. You have to select the record for update using the newly inserted id. String sqlLock= "SELECT seq FROM biosequence WHERE bioentry_id = ? FOR UPDATE"; String sqlUpdate="UPDATE biosequence SET seq=? where bioentry_id=?"; try { // First get the locator (necessary for Oracle) // // Get newly created record from DB stNew = conn.prepareStatement(sqlLock); stNew.setInt(1, bioentry_id); rsNew = stNew.executeQuery(); rsNew.next(); oracle.sql.CLOB dbClob = (oracle.sql.CLOB) rsNew.getClob(1); pst = conn.prepareStatement(sqlUpdate); dbClob.putString(1, seqstr); pst.setClob(1, dbClob); pst.setInt(2, bioentry_id); result = pst.executeUpdate(); if (result < 0) { conn.rollback(); } else { conn.commit(); } } catch (Exception e) { // Log the error... } finally { try { // Close all resources... // } catch (Exception e) { // Log any errors } } } On 8/18/04 2:49 PM, "Michael Heuer" wrote: > Hello Michael, > > I found a couple of instances of Oracle on which to test, 8.1.7.4.0 on > Solaris and 9.2.0.1.0 on Solaris. > > If you could send me your version of the biosql DDL and a source code > example of what you mean by > >> In all Java/Oracle applications we've developed, we've always inserted >> an empty_clob(), and then updated the clob separately using the record >> locator. > > then I'll give it a go. > > Or alternatively, if you know what changes need to be made to the biojava > codebase, then you just need to do > > $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login > (when prompted, the password is 'cvs') > > $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava co > biojava-live > $ cd biojava-live > > (make changes to source code) > > $ ant > (to make sure it builds properly) > > $ cvs diff -u . > patch.txt > (to generate the patch) > > michael > > ------ End of Forwarded Message From marabestgo at certto.com.br Tue Aug 24 11:14:57 2004 From: marabestgo at certto.com.br (Mara Best) Date: Tue Aug 24 11:12:29 2004 Subject: [Biojava-dev] Try CortiZyte, a revolutionary weightloss product. Message-ID: <58be01c489ed$47977a95$ece8019c@crans.ens-cachan.fr> Try CortiZyte! With our pharmaceutical grade all-natural weight-loss formula, you will: - Lose pounds and inches like crazy - Jump start your metabolism - Boost your energy level - Lose your appetite and feel satisfied - Reduce cholesterol levels - Eliminate cellulite and excess fat pockets - Stimulate your body's natural fat-burning ability Most Important: You Will Keep The Weight Off! Get the facts about all-natural CortiZyte: http://www.diet34.com/ From mg at base-pair.com Thu Aug 19 17:00:02 2004 From: mg at base-pair.com (Michael Griffith) Date: Tue Aug 24 19:39:41 2004 Subject: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems In-Reply-To: Message-ID: Michael, The BioSQL DDL is the current version that is in the CVS for bio-sql project. It is also attached here as a zip file. In the create objects section there is a missing table that needs to get created after all the other objects are created: CREATE TABLE term_relationship_term ( term_relationship_id int NOT NULL, term_id int NOT NULL ) In the class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.java, at line 446, the Prepare statement reads: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values(?, ?, ?, ?, ?)"); I think it should be something like: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values(?, ?, ?, empty_clob(), ?)"); Then -- I think you can do this with the JDBC clob classes, but I have always used the Oracle JDBC/CLOB classes. I would think you'd want to keep all the oracle stuff segregated out... After your insert is successful in biosequence, you'll want to update the clob table. You have to select the record for update using the newly inserted id. String sqlLock= "SELECT seq FROM biosequence WHERE bioentry_id = ? FOR UPDATE"; String sqlUpdate="UPDATE biosequence SET seq=? where bioentry_id=?"; try { // First get the locator (necessary for Oracle) // // Get newly created record from DB stNew = conn.prepareStatement(sqlLock); stNew.setInt(1, bioentry_id); rsNew = stNew.executeQuery(); rsNew.next(); oracle.sql.CLOB dbClob = (oracle.sql.CLOB) rsNew.getClob(1); pst = conn.prepareStatement(sqlUpdate); dbClob.putString(1, seqstr); pst.setClob(1, dbClob); pst.setInt(2, bioentry_id); result = pst.executeUpdate(); if (result < 0) { conn.rollback(); } else { conn.commit(); } } catch (Exception e) { // Log the error... } finally { try { // Close all resources... // } catch (Exception e) { // Log any errors } } } On 8/18/04 2:49 PM, "Michael Heuer" wrote: > Hello Michael, > > I found a couple of instances of Oracle on which to test, 8.1.7.4.0 on > Solaris and 9.2.0.1.0 on Solaris. > > If you could send me your version of the biosql DDL and a source code > example of what you mean by > >> In all Java/Oracle applications we've developed, we've always inserted >> an empty_clob(), and then updated the clob separately using the record >> locator. > > then I'll give it a go. > > Or alternatively, if you know what changes need to be made to the biojava > codebase, then you just need to do > > $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login > (when prompted, the password is 'cvs') > > $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava co > biojava-live > $ cd biojava-live > > (make changes to source code) > > $ ant > (to make sure it builds properly) > > $ cvs diff -u . > patch.txt > (to generate the patch) > > michael > > -------------- next part -------------- A non-text attachment was scrubbed... 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I would like to help Shepard this problem to resolution, but have had no real experience working on Open source projects to make fixes, etc. Please let me know what else I may do. Cheers! MG ------ Forwarded Message From: Michael Griffith Date: Thu, 19 Aug 2004 16:00:02 -0500 To: Michael Heuer Cc: , Subject: Re: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems Michael, The BioSQL DDL is the current version that is in the CVS for bio-sql project. It is also attached here as a zip file. In the create objects section there is a missing table that needs to get created after all the other objects are created: CREATE TABLE term_relationship_term ( term_relationship_id int NOT NULL, term_id int NOT NULL ) In the class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.java, at line 446, the Prepare statement reads: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values(?, ?, ?, ?, ?)"); I think it should be something like: PreparedStatement create_biosequence = conn.prepareStatement("insert into biosequence " + "(bioentry_id, version, length, seq, alphabet) " + "values(?, ?, ?, empty_clob(), ?)"); Then -- I think you can do this with the JDBC clob classes, but I have always used the Oracle JDBC/CLOB classes. I would think you'd want to keep all the oracle stuff segregated out... After your insert is successful in biosequence, you'll want to update the clob table. You have to select the record for update using the newly inserted id. String sqlLock= "SELECT seq FROM biosequence WHERE bioentry_id = ? FOR UPDATE"; String sqlUpdate="UPDATE biosequence SET seq=? where bioentry_id=?"; try { // First get the locator (necessary for Oracle) // // Get newly created record from DB stNew = conn.prepareStatement(sqlLock); stNew.setInt(1, bioentry_id); rsNew = stNew.executeQuery(); rsNew.next(); oracle.sql.CLOB dbClob = (oracle.sql.CLOB) rsNew.getClob(1); pst = conn.prepareStatement(sqlUpdate); dbClob.putString(1, seqstr); pst.setClob(1, dbClob); pst.setInt(2, bioentry_id); result = pst.executeUpdate(); if (result < 0) { conn.rollback(); } else { conn.commit(); } } catch (Exception e) { // Log the error... } finally { try { // Close all resources... // } catch (Exception e) { // Log any errors } } } On 8/18/04 2:49 PM, "Michael Heuer" wrote: > Hello Michael, > > I found a couple of instances of Oracle on which to test, 8.1.7.4.0 on > Solaris and 9.2.0.1.0 on Solaris. > > If you could send me your version of the biosql DDL and a source code > example of what you mean by > >> In all Java/Oracle applications we've developed, we've always inserted >> an empty_clob(), and then updated the clob separately using the record >> locator. > > then I'll give it a go. > > Or alternatively, if you know what changes need to be made to the biojava > codebase, then you just need to do > > $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login > (when prompted, the password is 'cvs') > > $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava co > biojava-live > $ cd biojava-live > > (make changes to source code) > > $ ant > (to make sure it builds properly) > > $ cvs diff -u . > patch.txt > (to generate the patch) > > michael > > ------ End of Forwarded Message _______________________________________________ biojava-dev mailing list biojava-dev@biojava.org http://biojava.org/mailman/listinfo/biojava-dev From autobuilder at derkholm.net Wed Aug 25 00:10:43 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Tue Aug 24 23:45:27 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1093407043664.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040825 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From matthew at ujsa.com Wed Aug 25 01:19:45 2004 From: matthew at ujsa.com (=?Windows-1251?B?0OXq6+Ds7e7lIO/w5eTr7ubl7ejl?=) Date: Wed Aug 25 01:38:40 2004 Subject: [Biojava-dev] =?windows-1251?b?0OXq6+Ds4DogyNLAy8jfISEh7vLk+/Ug?= =?windows-1251?b?7eAg7O7w5SDoIO/u5+3g4uDy5ev87fvlIPLz8PshISE=?= Message-ID: <117014540.20040825052445@> ??????!!! ????? ?? ???? ? ?????????????? ????!!! ???????????? ????? ?? ????!!! ??????????? ????????? - ????????? ???????!!! ???????? ?????, ????????!!! 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I would like > to > help Shepard this problem to resolution, but have had no real > experience > working on Open source projects to make fixes, etc. Please let me > know what > else I may do. > > Cheers! > > MG > ------ Forwarded Message > From: Michael Griffith > Date: Thu, 19 Aug 2004 16:00:02 -0500 > To: Michael Heuer > Cc: , > Subject: Re: [Biojava-dev] Re: MORE Oracle BioSQL & BioJava problems > > Michael, > > The BioSQL DDL is the current version that is in the CVS for bio-sql > project. It is also attached here as a zip file. In the create objects > section there is a missing table that needs to get created after all > the > other objects are created: > > CREATE TABLE term_relationship_term ( > term_relationship_id int NOT NULL, > term_id int NOT NULL > ) > > In the class org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.java, at > line > 446, the Prepare statement reads: > > PreparedStatement create_biosequence = conn.prepareStatement("insert > into > biosequence " + "(bioentry_id, version, length, seq, alphabet) " + > "values(?, ?, ?, ?, ?)"); > > I think it should be something like: > > PreparedStatement create_biosequence = conn.prepareStatement("insert > into > biosequence " + "(bioentry_id, version, length, seq, alphabet) " + > "values(?, ?, ?, empty_clob(), ?)"); > > Then -- I think you can do this with the JDBC clob classes, but I have > always used the Oracle JDBC/CLOB classes. I would think you'd want to > keep > all the oracle stuff segregated out... > > After your insert is successful in biosequence, you'll want to update > the > clob table. You have to select the record for update using the newly > inserted id. > > String sqlLock= "SELECT seq FROM biosequence WHERE bioentry_id = ? > FOR > UPDATE"; > String sqlUpdate="UPDATE biosequence SET seq=? where > bioentry_id=?"; > try { > // First get the locator (necessary for Oracle) > // > // Get newly created record from DB > stNew = conn.prepareStatement(sqlLock); > stNew.setInt(1, bioentry_id); > rsNew = stNew.executeQuery(); > rsNew.next(); > > oracle.sql.CLOB dbClob = (oracle.sql.CLOB) > rsNew.getClob(1); > pst = conn.prepareStatement(sqlUpdate); > dbClob.putString(1, seqstr); > pst.setClob(1, dbClob); > pst.setInt(2, bioentry_id); > result = pst.executeUpdate(); > if (result < 0) { > conn.rollback(); > } else { > conn.commit(); > } > } catch (Exception e) { > // Log the error... > } finally { > try { > // Close all resources... > // > } > catch (Exception e) { > // Log any errors > } > } > > } > > > On 8/18/04 2:49 PM, "Michael Heuer" wrote: > >> Hello Michael, >> >> I found a couple of instances of Oracle on which to test, 8.1.7.4.0 on >> Solaris and 9.2.0.1.0 on Solaris. >> >> If you could send me your version of the biosql DDL and a source code >> example of what you mean by >> >>> In all Java/Oracle applications we've developed, we've always >>> inserted >>> an empty_clob(), and then updated the clob separately using the >>> record >>> locator. >> >> then I'll give it a go. >> >> Or alternatively, if you know what changes need to be made to the >> biojava >> codebase, then you just need to do >> >> $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava login >> (when prompted, the password is 'cvs') >> >> $ cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/biojava co >> biojava-live >> $ cd biojava-live >> >> (make changes to source code) >> >> $ ant >> (to make sure it builds properly) >> >> $ cvs diff -u . > patch.txt >> (to generate the patch) >> >> michael >> >> > > ------ End of Forwarded Message > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From autobuilder at derkholm.net Fri Aug 27 00:10:46 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Thu Aug 26 23:45:04 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: <31156635.1093579846514.JavaMail.thomas@calette.derkholm.net> BioJava automatic build system, run 20040827 Binary build: OK Javadocs build: OK Core test suite: OK A snapshot release has been made at: http://www.derkholm.net/autobuild/ No changes were made in the last 24 hours. -- BioJava Autobuilder, maintained by Thomas Down If you notice any problems, contact autobuilder@derkholm.net From lcochranzj at vs.co.nz Thu Aug 26 23:56:42 2004 From: lcochranzj at vs.co.nz (Lidia A. 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HPUfFmFhejkYMi8x/hpwxvh1eoznlguW46xq4sfPflOlbCQbYVpG6UJWWAgAaUUXSUZM6yFC HgNA/5aUKCkRx1Z4Uq/aS2W7Rn89SpVcRMCgVfHc9XiY0szttoRb5QYVoqp6rfyk/esVW64N HdMNZjbatqNW6Hve0s0dypWGs3mG8aL2zDbQVP9y75TVU130whDz0lQIzkoBVPhC11EEAiUu KyBEBbpmPCpz8YEMfh8CHX+ynWEbMOy2Yj201Q8DqFABN92Dmhs3nVYZpxYcViaJbn7yrWRn nZHIrZ8VgVkvr2AizbCg4eW6BSu5gFHQxJDqBOGA+Q+f/Zznn7uEexA+wVyO2Cr8Hbfsdqn0 zMevKWXedwaxzIK4ePX0yfyx6qt04VQVGrDrogcHAD+C+p/kCWvjHgocgMAKFAYBdAdSHctz LWhyQAUGDwlkIgUQDdEMBHByOHp6zHVnxyZ0Hgk2DAv6oIQ6NUffuRVrkJxDZVOvddgAokS+ iYj1r3eohZxCJZmwEDC/tYqN5Sqp4ttFfYvJEYyCf6oimtYSnxr0hBXz69Wu/iOYg/r17e3k vLrVuvNQ19vTlVrnxI0f7f6kBuMgheCw5vQ68BtiziuLVDYiJK5V7ecuv95FFhIRfFgADxQc DQ8WBHMQZ/JgrLamxvqbq3wHMB1XfqCEUmRAU0NdREhXAHFMPkFEMEExOTIsNM3I6m0Ay7q+ 2s+2zMQG38HArq8a3usxAN+iopi4qoyx49W9o7y8rrZG9PWcppWuqVHoifzvd5357UGO9T8e qKrd1Mr1ZejKCyG11hDTeMJ/ya4FGVEXaCQaA2QJr3Cn0zZaAAD9ZRJRUk+Q7jUKwwsWwTxD GJAGVZFKQxB5ZgVqBHlBgii1gu1PizACRRB2Xamxqn3AP/5hQcwScRIxNfE7xGU1yCAyigsm nQSDIIqydwsgfLJxCyBGslsLML/kv9O+TTxTgWZutKBxmg2EUmbJjois48bT+XgcjqZ1tJ0/ sdjqX2MUyXWmLE6acGlHkqwtTVSMO2Nj3MkmplwvmhxpMKYsXJnUfiRl0/xNbsQ08MlwfSz7 fz49BPhyFfXx9qQMSPiIZRqfZ8XE3TF6BMh1doIETVQqNQGEvUIJFEfBeRRsFn547B1OZY/x xFE54uglgybqlwj1svdOgrfzuO0VD956k8kDfS4OFv14//p9CPtKxSwqAtjS1+j+RTV9MoAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ------=_NextPart_000_0008_0000167B.000000F2-- From autobuilder at derkholm.net Mon Aug 30 00:10:56 2004 From: autobuilder at derkholm.net (autobuilder@derkholm.net) Date: Sun Aug 29 23:44:36 2004 Subject: [Biojava-dev] [biojava-builder] BioJava nightly build report Message-ID: 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