Alessandro De Stasio wrote:
> Hi,
> I'm writing a Fold Change Plugin. I need to extract all the Annotations
> from a list of BioAssay.
> So When I try:
>
> ...
> DbControl dc = sc.newDbControl();
> //From the input
> BioAssaySet source = getSourceBioAssaySet(dc);
> List<BioAssay> bioAssays = (List<BioAssay>)
> job.getValues("bioAssays");
> if(bioAssays!=null){
> Iterator it = bioAssays.iterator();
> while(it.hasNext()){
> BioAssay bassay = (BioAssay) it.next();
> AnnotationSet annSet = bassay.getAnnotationSet();
> ....
>
> On "bassay.getAnnotationSet()" call, I have this Exception:
>
> net.sf.basedb.core.ConnectionClosedException: The connection has been
> closed.
> at net.sf.basedb.core.DbControl.getItem(DbControl.java:718)
> at net.sf.basedb.core.BioAssay.getAnnotationSet(BioAssay.java:185)
> at
> foldchange.src.net.sf.basedb.foldchangePlugin.FoldChangePlugin.run(FoldChangePlugin.java:170)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:108)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:487)
> at java.lang.Thread.run(Thread.java:619)
>
> An idea? Thanks in advance
Yes, the DbControl that the 'bassay' object was loaded with is closed
before the run() method on your plug-in is invoked. I was pretty sure
that this was documented somewhere but I can't find anything except a
single code example on
http://base.thep.lu.se/chrome/site/latest/html/developerdoc/plugin_developer/plugin_developer.analyse.html
I guess this is something that should be clearly stated somewhere since
it is a very common mistake, even among experienced developers. In any
case, the solution is simpe. Just reload the 'bassay' object with the
new DbControl. The safest way is to use:
bassay = BioAssay.getById(dc, bassay.getId());
before the 'bassay' object is used.
In your case you should be able to do
(if you change the iterator to Iterator<BioAssay>)
BioAssay bassay = BioAssay.getById(dc, it.next().getId());
/Nicklas
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