[Biojava-dev] BioSQLSequenceDB Create Behavior

[Simon Foote]

Hi Kevin,

I think the thought behind that is, in order to create a new biodatabase 
you have to provide a name, so it would be redundant.  Unless it is 
required lower down in the code somewhere, although I haven't seen a 
case of this yet.
Also of note, one can't currently set the authority or version for a 
biodatabase during a create or retrieve them for an existing 
biodatabase.  I do have the retrieve ability in my local copy, but 
haven't committed it in yet.

Simon

-- 
Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca


Kevin Fowler wrote:

> Hi,
>
>
> I notice that org.biojava.bio.seq.db.biosql.BioSQLSequenceDB doesn't 
> set the biodatabase name on create.
>
> for example:
>
>
>         db = new BioSQLSequenceDB(myDataSource,"MyName",true);
>
>         assert(db.getName()==null); // true if the DB was created, 
> false if it already existed.
>
>
>
> Is this a bug or a feature?
>
>
> --Kevin Fowler
>
>
>
>
> * **void* initDb(String biodatabase,* boolean* create)
>
> ...
>
> PreparedStatement getID = conn.prepareStatement(*"select * from 
> biodatabase where name = ?"*);
>
> getID.setString(1, biodatabase);
>
> ResultSet rs = getID.executeQuery();
>
> * if* (rs.next()) {
>
> dbid = rs.getInt(1);
>
> name = rs.getString(2);
>
> rs.close();
>
> getID.close();
>
> conn.close();
>
> * return*;
>
> }* else* {
>
> rs.close();
>
> getID.close();
>
> }
>
>
> * if* (create) {
>
> PreparedStatement createdb = conn.prepareStatement(*"insert into 
> biodatabase (name) values ( ? )"*);
>
> createdb.setString(1, biodatabase);
>
> createdb.executeUpdate();
>
> conn.commit();
>
> createdb.close();
>
>
> dbid = getDBHelper().getInsertID(conn,* "biodatabase"*,* 
> "biodatabase_id"*);
>
> }* else* {
>
> ...
>
>------------------------------------------------------------------------
>
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>

-- 
Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca