Hey Fabrice,
I'll take a look at the changes and incorporate them and cut a new
release sometime next week.
Cheers,
Ed
On Thu, 1 Oct 2009, Fabrice Legeai wrote:
Hi,
I've finally corrected this by modifying few lines of the addSequenceEdit()
method of apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter
I've replaced :
ChadoFeature srcFeature = new ChadoFeature(seqEdit.getRefFeature("exon"),
this.jdbcAdapter.getConnectionUsedForLastTransaction());
by
ChadoFeature srcFeature = new ChadoFeature(seqEdit,
this.jdbcAdapter.getConnectionUsedForLastTransaction());
And add few tests before the insertion stuff :
if (uniquename == null) {
uniquename=seqEdit.getEditType() + seqEdit.getRefSequence().getName()
+ "_" + seqEdit.getPosition() + seqEdit.getResidues();
}
if (name == null) {
name=uniquename;
}
if (date == null) {
date = new Date();
}
I am not really sure that it is the best thing to do, but it works. Would you
please integrate this (or a better solution) in a next release of Apollo ?
Cheers,
Fabrice
Fabrice Legeai wrote:
Hi,
I am having trouble while saving gameXML files that includes SequenceEdit
into my chadoDB (I've attached an example). It looks like that Apollo is
looking for a refFeature, by instance an exon, but can find anything then
crash with a null pointer exception :
Exception in thread "Thread-5" java.lang.NullPointerException
at
apollo.dataadapter.chado.jdbc.ChadoFeature.<init>(ChadoFeature.java:67)
at
apollo.dataadapter.chado.jdbc.PureJDBCTransactionWriter.addSequenceEdit(PureJDBCTransactionWriter.java:1421)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.addSequenceEdit(JdbcChadoWriter.java:800)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.addSequenceEdit(JdbcChadoWriter.java:382)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.processSequenceEdits(JdbcChadoWriter.java:714)
at
apollo.dataadapter.chado.jdbc.JdbcChadoWriter.write(JdbcChadoWriter.java:111)
at
apollo.dataadapter.chado.ChadoAdapter.commitChanges(ChadoAdapter.java:288)
at
apollo.dataadapter.AbstractApolloAdapter.commitChanges(AbstractApolloAdapter.java:324)
at
apollo.dataadapter.chado.ChadoAdapterGUI.doOperation(ChadoAdapterGUI.java:301)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:361)
at
org.bdgp.swing.widget.DataAdapterChooser.doCommit(DataAdapterChooser.java:414)
at
apollo.main.DataLoader$SaveAdapterChooser.doCommit(DataLoader.java:776)
at
org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)
at java.lang.Thread.run(Thread.java:619)
Any help is welcome.
Thanks,
Fabrice
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--
Fabrice Legeai
INRA UMR Bio3P IRISA Equipe Symbiose
IRISA-INRIA, Campus de Beaulieu, 35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 71 18
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