[Biojava-l] BioSQL

[Yasumasa Shigemoto]

Thomas,

Thank you for your reply.

I specify the property and get the other Exception.

$ java -Djdbc.drivers=org.postgresql.Driver biosql.SeqDumper
"jdbc:postgresql:biosqldb" "postgres" "postgres" ""
Exception in thread "main" org.biojava.bio.BioException: Biodatabase  doesn't ex
ist
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceD
B.java:128)
        at biosql.SeqDumper.main(SeqDumper.java:26)

And I try once again specifying the last argument "biosqldb".
$ java -Djdbc.drivers=org.postgresql.Driver biosql.SeqDumper
"jdbc:postgresql:biosqldb" "postgres" "postgres" "biosqldb"
Exception in thread "main" org.biojava.bio.BioException: Biodatabase biosqldb do
esn't exist
        at org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceD
B.java:128)
        at biosql.SeqDumper.main(SeqDumper.java:26)

What should I specify last argument?


Thomas Down wrote:

> On Tue, Aug 27, 2002 at 04:38:29PM +0900, Yasumasa Shigemoto wrote:
> >
> > I'm trying BioSQL but I don't understand the following 'biodatabases'.
> >
> > public BioSQLSequenceDB(java.lang.String dbURL,
> >                         java.lang.String dbUser,
> >                         java.lang.String dbPass,
> >                         java.lang.String biodatabase,
> >                         boolean create)
> >
> > What is specified for the biodatabase for example?
> >
> > I try "SeqDumper.java" but I get the Exception.
> >
> > $ java biosql.SeqDumper "jdbc:postgresql:biosqldb" "postgres" "postgres"
> > ""
> > Exception in thread "main" java.sql.SQLException: No suitable driver
>
> Hi...
>
> This is a limitation in JDBC -- you need to explicitly load the database
> driver(s) you're using.  There are several ways to do this.  The one
> I tend to use is to set the "jdbc.drivers" system property.  For
> examples:
>
>      java -Djdbc.drivers=org.postgresql.Driver biosql.SeqDumper "jdbc:postgresql:biosqldb" "postgres" "postgres" ""
>
> Note that you still need to add the relevant JAR file as well.
>
> A lot of people have been having this problem.  Future versions
> may include code to test automatically for some common database
> drivers.  However, this isn't an ideal solution, since the BioSQL
> code tries to be database-independent.
>
> Hope this helps,
>
>      Thomas.
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