Page type mismatch, expected 4/OID_INDEX (tx=0) but got 0, PageId=718102 about zoodb HOT 7 CLOSED

Thanks for figuring out the source of the problem!

I've already updated our code, but I cannot yet test the fix above as I now get a different issue when trying to reopen saved PeptideShaker projects. The below error occurs both with ZooDB 0.5.2 and 0.6.0.

Basically, we have the following HashMap

HashMap<String, HashSet<Long>> proteinMap = new HashMap<>();

which can be added to our ZooDB database without any issues (of course with content added first), but when trying to extract the map from the database (after saving the PeptideShaker project) I get the following error:

java.lang.RuntimeException: Field: class java.util.HashMap proteinMap
	at org.zoodb.internal.DataDeSerializer.deserializeFields2(DataDeSerializer.java:417)
	at org.zoodb.internal.DataDeSerializer.readObjPrivate(DataDeSerializer.java:304)
	at org.zoodb.internal.DataDeSerializer.readObject(DataDeSerializer.java:182)
	at org.zoodb.internal.server.index.ObjectPosIterator.findNext(ObjectPosIterator.java:64)
	at org.zoodb.internal.server.index.ObjectPosIterator.<init>(ObjectPosIterator.java:46)
	at org.zoodb.internal.server.DiskAccessOneFile.readAllObjects(DiskAccessOneFile.java:284)
	at org.zoodb.internal.model1p.Node1P.loadAllInstances(Node1P.java:136)
	at org.zoodb.internal.Session.loadAllInstances(Session.java:472)
	at org.zoodb.internal.Session.loadAllInstances(Session.java:477)
	at org.zoodb.internal.Session.loadAllInstances(Session.java:477)
	at org.zoodb.internal.Session.loadAllInstances(Session.java:455)
	at org.zoodb.internal.query.ClassExtent.iterator(ClassExtent.java:113)
	at org.zoodb.internal.query.QueryExecutor.applyQueryOnExtentV3(QueryExecutor.java:490)
	at org.zoodb.internal.query.QueryExecutor.runQueryV3(QueryExecutor.java:148)
	at org.zoodb.internal.query.QueryExecutor.runQuery(QueryExecutor.java:122)
	at org.zoodb.jdo.impl.QueryImpl.runQuery(QueryImpl.java:549)
	at org.zoodb.jdo.impl.QueryImpl.execute(QueryImpl.java:535)
	at com.compomics.util.db.object.ObjectsDB.establishConnection(ObjectsDB.java:916)
	at com.compomics.util.db.object.ObjectsDB.establishConnection(ObjectsDB.java:883)
	at com.compomics.util.db.object.ObjectsDB.<init>(ObjectsDB.java:131)
	at eu.isas.peptideshaker.utils.PsdbParent.loadPsdbFile(PsdbParent.java:220)
	at eu.isas.peptideshaker.gui.PeptideShakerGUI$104.run(PeptideShakerGUI.java:6563)
Caused by: java.lang.IllegalArgumentException: Can not set final java.util.HashMap field com.compomics.util.experiment.identification.IdentificationKeys.proteinMap to java.lang.Long
	at sun.reflect.UnsafeFieldAccessorImpl.throwSetIllegalArgumentException(UnsafeFieldAccessorImpl.java:167)
	at sun.reflect.UnsafeFieldAccessorImpl.throwSetIllegalArgumentException(UnsafeFieldAccessorImpl.java:171)
	at sun.reflect.UnsafeQualifiedObjectFieldAccessorImpl.set(UnsafeQualifiedObjectFieldAccessorImpl.java:83)
	at java.lang.reflect.Field.set(Field.java:764)
	at org.zoodb.internal.DataDeSerializer.deserializeFields2(DataDeSerializer.java:412)
	... 21 more

Do you have any idea what would cause such an issue? I have confirmed that the content of the map (upon database insertion) is correct.

If it can help to look at the PeptideShaker and utilities code please see the branches called new_backend, i.e. https://github.com/compomics/peptide-shaker/tree/new_backend and https://github.com/compomics/compomics-utilities/tree/new_backend.

I can of course also send you the data required to reproduce the error if that would help.

Thanks in advance!

from zoodb.

Hi, sorry, I only saw the issue today. I could import, save and load a large database fine with the version of new_backend that I checked out in February. May have something changed since then that affect this? I will try to have a look tomorrow and retry with the latest version.

from zoodb.

Thanks! Yes, it is most likely something that changed in our code, as I can no longer even reopen small projects. But I simply cannot figure out what change would result in the above IllegalArgumentException? Especially given that the object added to the database seems to be fine and the error only occurs when I later try to extract it?

from zoodb.

I checked out the latest version on new_branch, but I cannot reproduce the problem, instead the program just hangs at 8% when importing my example. Maybe you could send me a more recent example file(s)?

Having said that, it looks like a problem in ZooDB, I will have a look, maybe it is easy to find.

from zoodb.

Maybe you could send me a more recent example file(s)?

Of course, here's the SearchGUI output I've used in my recent testing: http://vedlegg.uib.no/?id=c3dfb40f94fe14ca2fa0b3cc49c8cff2

from zoodb.

I created a new issue for this: #128

Also, I added a question to the new Issue.

from zoodb.

I can confirm that (if loading with one thread, as suggested in #128) the "Page type mismatch" issue is resolved when reopening large saved PeptideShaker projets.

In other words, the issue was indeed due to the error in copying files larger 2GB. You may therefore close this issue. Thanks again for the help!

from zoodb.