[Biojava-dev] BioJava Nightly Build + BioSQL/MySQL problem...
Michael Griffith
mg at base-pair.com
Tue Aug 3 13:42:28 EDT 2004
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" <td2 at sanger.ac.uk> 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.
>
>
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