sorry.. here is the stack trace if i don't call dc.commit() until after
looping through all the samples.
net.sf.basedb.core.BaseException: net.sf.basedb.core.data.ExtractData
at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1120)
at net.sf.basedb.core.Extract.countLabeledExtracts(Extract.java:250)
at edu.ucsd.basedb.plugins.AutoBuild.addLabeledExtract(AutoBuild.java:265)
at edu.ucsd.basedb.plugins.AutoBuild.run(AutoBuild.java:412)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:82)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
at java.lang.Thread.run(Thread.java:613)
Caused by: org.hibernate.TransientObjectException:
net.sf.basedb.core.data.ExtractData
at
org.hibernate.engine.ForeignKeys.getEntityIdentifierIfNotUnsaved(ForeignKeys.java:219)
at org.hibernate.type.EntityType.getIdentifier(EntityType.java:108)
at org.hibernate.type.ManyToOneType.nullSafeSet(ManyToOneType.java:87)
at
org.hibernate.loader.hql.QueryLoader.bindNamedParameters(QueryLoader.java:517)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1576)
at org.hibernate.loader.Loader.doQuery(Loader.java:661)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
at org.hibernate.loader.Loader.doList(Loader.java:2144)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2028)
at org.hibernate.loader.Loader.list(Loader.java:2023)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:393)
at
org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
at
org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
at net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1114)
... 6 more
thanks for any help.
-keith
Keith Ching wrote:
> Hi,
>
> I am trying to write a plugin to automatically make objects from sample
> -> rawbioassay.
> however, after you call dc.commit() it closes the connection. what is
> the normal way to
> re-establish a connection? dc.reconnect() does not seem to work.
> getting a new dc via
> dc = sc.newDbControl(); does not seem to work either.
>
> i need to commit the created objects between steps because subsequent
> objects do database
> lookups of previous objects to create themselves.
>
> here is my general outline.
>
> ArraySlide slide;
> for (Sample sourceObj : sources)
> {
> dc.reattachItem(sourceObj);
> /**
> * 1. get the slide
> */
> slideName = sourceObj.getName().split(" ")[0];
> slide = getSlideByName(dc, slideName);
>
> /**
> * 2. make chromatin input sample from pooled sample
> */
> Sample chromatinSample = getChromatinSample(dc, sourceObj);
> Extract chromatinExtract = addExtract(dc, chromatinSample);
> /**
> * 3. make the extract from the pooled sample
> */
> Extract pooledExtract = addExtract(dc, sourceObj);
> dc.commit();
>
> dc = sc.newDbControl();
> /**
> * 4. make the labelled extracts from extracts
> */
> LabeledExtract chromatinLabeledExtract =
> addLabeledExtract(dc, inputLabel, chromatinExtract);
> LabeledExtract pooledLabeledExtract =
> addLabeledExtract(dc, poolLabel, pooledExtract);
> dc.commit();
> dc = sc.newDbControl();
> /**
> * 5. make the hybridization from the matched pairs, add
> the slide
> */
> Hybridization hyb = addHybridization(dc,
> chromatinLabeledExtract, pooledLabeledExtract, slide);
> dc.commit();
> dc = sc.newDbControl();
> /**
> * 6. make the scan
> */
> Scan scan = addScan(dc, hyb);
> dc.commit();
> dc = sc.newDbControl();
> /**
> * 7. make the rawbioassay
> */
> String datatype = "GenePix";
> RawBioAssay myRawBioAssay = addRawBioAssay(dc, scan,
> RawDataTypes.getRawDataType(datatype) );
> dc.commit();
> dc = sc.newDbControl();
> // group into experiment ?
>
> fileNames = fileNames + " " +
> myRawBioAssay.getName();
> }
>
>
--
Keith Ching, Ph.D.
Bioinformatics, Laboratory of Gene Regulation
Ludwig Institute for Cancer Research
9500 Gilman Drive, #0653
CMM East, Room 3020
La Jolla, CA 92093-0653
[EMAIL PROTECTED]
858-822-5767
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys - and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
The BASE general discussion mailing list
[email protected]
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
