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
--
De Stasio Alessandro
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