Thanks Nicklas for the help with boolean queries. Now I'm confused by
something else also affy-related.
I'm trying to write code to lookup which ArrayDesigns a Reporter is on.
For non-Affy arrays this is easy (join via arrayDesignBlocks, features and
reporter).
For Affy arrays it looks like we have to use the CDF file through the Affy API
- get all the reporter ids (e.g. ProbeSetNames) and put them in a hash for
reverse lookup later.
Here's a code snippet to do some of that (see last email for the definition of
affyQuery). A lot of the code is taken directly from
net/sf/basedb/core/Affymetrix.java, which is used by the "Affymetrix CDF
probeset importer" plugin for Affy array design (see the "verify reporters"
link on any Affy ArrayDesign page). When I run this plugin as the same user
who runs the code below, it works fine. However I get a NullPointerException
with my code...
Hashtable affyProbeLookup = new Hashtable();
ItemResultList<ArrayDesign> affyList = affyQuery.list(dc);
for (ArrayDesign ad : affyList) {
int adId = ad.getId();
FusionCDFData cdf = Affymetrix.loadCdfFile(Affymetrix.getCdfFile(ad));
if (cdf == null) continue;
int numProbesets = cdf.getHeader().getNumProbeSets();
int index = 0;
while (index < numProbesets) {
String probesetId = cdf.getProbeSetName(index); // Line 96
affyProbeLookup.put(probesetId, adId);
index++;
}
}
Exception in thread "main" java.lang.NullPointerException
at affymetrix.gcos.cdf.CDFFileData.getProbeSetName(Unknown Source)
at affymetrix.fusion.cdf.FusionCDFData.getProbeSetName(Unknown Source)
at base_api_test.run_test(base_api_test.java:96)
at base_api_test.main(base_api_test.java:216)
note: the cdf object seems OK (numProbesets is set properly).
If anyone can point me in the right direction, it would be appreciated.
It's a bit difficult not having the Affy source and line numbers
(is that available?)
cheers,
Bob.
Nicklas Nordborg writes:
> Bob MacCallum wrote:
> > Hi all,
> >
> > The following works as expected:
> >
> > ItemQuery<ArrayDesign> affyQuery = ArrayDesign.getQuery();
> > affyQuery.include(Include.SHARED);
> > affyQuery.restrict(
> > Restrictions.eq(Hql.property("affyChip"),
> > Expressions.integer(1)
> > )
> > );
>
> I think this may depend on the database that is used. I am sure it works
> for MySQL since it uses a "bit"-column which can be either 0 or 1. I
> don't know how Postgres handles it or if maybe Hibernate is smart enough
> to fix any potential problems. I remember that our predefined queries
> that filtered on boolean columns had to come in two versions, one for
> MySQL and one for Postgres (see
> http://base.thep.lu.se/browser/trunk/config/dist/mysql-queries.xml). I
> think this has been fixed in Hibernate (or maybe in MySQL) some time
> ago, since it now works with true/false values instead of 1/0.
>
> Another possibility is to replace Expressions.integer(1) with
> Expressions.parameter("isAffy", true, Type.BOOLEAN). This should be safe
> with any database.
>
> > but I'm a bit puzzled why there is no "Expressions.boolean(true)" in the
> > API.
>
> Well, a lot of things get added when they are needed. I guess the reason
> is that we have not had any explicit need to filter on a boolean value
> before.
>
> > Not urgent!
>
> Ok. Considering potential database issues, I think it maybe is better to
> go for the Expresssion.parameter() in any case.
>
> /Nicklas
>
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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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