Thanks for getting back to us.
Problem solved...
Nicklas Nordborg writes:
> This seems really strange. The only thing I can think of is that the
> data is coming from different databases. Are you really sure that both
> base.config files are the same?
yes the config files are the same:
diff -r /usr/local/base2dev/www/WEB-INF/classes
../../apache-tomcat-6.0.14/webapps/GEWebapp/WEB-INF/classes
[no output]
and we just have some extra jars in the webapp WEB-INF/lib directory:
bio-iisrv1 126% diff -r /usr/local/base2dev/www/WEB-INF/lib
../../apache-tomcat-6.0.14/webapps/GEWebapp/WEB-INF/lib
Only in ../../apache-tomcat-6.0.14/webapps/GEWebapp/WEB-INF/lib:
biojava-ensembl.jar biojava.jar bytecode.jar commons-collections-2.1.jar
commons-dbcp-1.1.jar commons-pool-1.1.jar gesol.jar GEWebapp.jar jstl.jar
mysql-connector-java-3.0.10-stable-bin.jar standard.jar
I figured out that
mysql-connector-java-3.0.10-stable-bin.jar
was both unnecessary and the **cause of this problem**
that's a relief!
> Do you get the same problem with other array designs?
Yes, sorry, I forgot to mention that we get this behaviour for all (e.g. affy
and non-affy) array designs:
commandline:
name = MMC1 for BASE2 v3
descr = made with a public GPR file
hasFeat = true
isAffy = false
tomcat logs:
name = MMC1 for BASE2 v3
descr = made with a public GPR file
hasFeat = false <<<!
isAffy = false
Here's a similar test for an Experiment object pulled out by getById().
Experiment ex = Experiment.getById(dc, 3);
System.out.println("\nname = " + ex.getName());
System.out.println("authors = " + ex.getAuthors());
System.out.println("bytes = " + ex.getBytes());
But it works fine (I was expecting failure for authors and bytes).
commandline:
name = Adult female tissues
authors = Koutsos AC, Blass C, ...
bytes = 23386272
tomcat logs:
name = Adult female tissues
authors = Koutsos AC, Blass C, ...
bytes = 23386272
Could it possibly be something to do with getXXXX() methods working
and isYYYY() or hasZZZZ() methods not?
Problem solved anyway, root cause not quite clear to me!
cheers,
Bob
>
> /Nicklas
>
> Bob MacCallum wrote:
> > Hi,
> >
> > This one is might odd. Before I send lines and lines of code and
> > stacktraces,
> > maybe someone has some intuition.
> >
> > Why would this code
> >
> > ArrayDesign ad = ArrayDesign.getById(dc, 14);
> > System.out.println("name = " + ad.getName());
> > System.out.println("descr = " + ad.getDescription());
> > System.out.println("hasFeat = " + ad.hasFeatures());
> > System.out.println("isAffy = " + ad.isAffyChip());
> >
> > print out the following from commandline testing:
> >
> > name = Affymetrix Plasmodium Anopheles
> > descr = Short description
> > hasFeat = true
> > isAffy = true
> >
> >
> > and the following from testing within a tomcat webapp:
> >
> > name = Affymetrix Plasmodium Anopheles
> > descr = Short description
> > hasFeat = false
> > isAffy = false
> >
> >
> > Needless to say, the former is correct, and the latter is causing major
> > headaches.
> >
> > It seems that the basic attributes (name, description) are being pulled
> > out of
> > the database OK, but the array-design-specific attributes is not.
> >
> > Some kind of conflict between hibernate and something in our servlet?
> > Will gladly send more details, but I'm not exactly sure where to start.
> >
> > Both are using an identical set of base config files and base jar files:
> >
> > the commandline version sets the class path to:
> > /usr/local/base2dev/www/WEB-INF/{lib,classes}
> >
> > the tomcat webapp has these copied over
> > (md5/diff says they are identical)
> >
> > many thanks,
> > Bob.
> >
>
>
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--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
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