Can anyone tell me why I'm getting the following error? The error I get with the current CVS build and the 1.1.4b build is different, but either way, I still don't understand what the problem is.
Current CVS build:
Hibernate: SELECT Refer0.referenceSequenceId, Pharm1.pharmgkbAccessionId AS pharmgkbAccessionId0, Pharm1.pharmgkbObjTypeId AS pharmgkbObjTypeId0, Pharm1.name AS name0, Pharm1.projectId AS projectId0,
Pharm1.modified_timestamp AS modified_timestamp0, Refer2.referenceSequenceId AS referenceSequenceId1, Refer2.start_gene AS start_gene1, Refer2.stop_gene AS stop_gene1, Refer2.sequence AS sequence1, Proje3.projectId AS projectId2, Proje3.projectName AS projectName2 FROM ReferenceSequenceGeneAssoc Refer0, PharmGKBObjects Pharm1, ReferenceSequences Refer2, Projects Proje3 WHERE Refer0.geneId = ? AND
Refer0.referenceSequenceId=Pharm1.pharmgkbAccessionId(+) AND Pharm1.pharmgkbAccessionId=Refer2.referenceSequenceId(+) AND Pharm1.projectId=Proje3.projectId(+)
02:18:59,772 ERROR PersistentCollection:87 - Failed to lazily initialize a collection
java.lang.NullPointerException
at cirrus.hibernate.LockMode.greaterThan(LockMode.java:30)
at cirrus.hibernate.impl.SessionImpl.lock(SessionImpl.java:1121)
at cirrus.hibernate.impl.SessionImpl.doLoad(SessionImpl.java:1412)
at cirrus.hibernate.impl.SessionImpl.doLoadByClass(SessionImpl.java:1314)
at cirrus.hibernate.impl.SessionImpl.internalLoadOneToOne(SessionImpl.java:1273)
at cirrus.hibernate.type.OneToOneType.resolveIdentifier(OneToOneType.java:68)
at cirrus.hibernate.impl.SessionImpl.initializeEntity(SessionImpl.java:1456)
at cirrus.hibernate.loader.Loader.doFind(Loader.java:144)
at cirrus.hibernate.loader.Loader.loadCollection(Loader.java:448)
at cirrus.hibernate.loader.CollectionLoader.initialize(CollectionLoader.java:67)
at cirrus.hibernate.impl.SessionImpl.initialize(SessionImpl.java:2222)
at cirrus.hibernate.collections.PersistentCollection.initialize(PersistentCollection.java:83)
at cirrus.hibernate.collections.PersistentCollection.read(PersistentCollection.java:53)
at cirrus.hibernate.collections.Set.iterator(Set.java:134)
at org.pharmgen.db.DbDocumentRoot.addAccessionObject(DbDocumentRoot.java:166)
at org.pharmgen.xml.ParserEventHandler.startElement(ParserEventHandler.java:282)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at org.pharmgen.xml.Parser.parse(Parser.java:126)
at test.XmlParser.main(XmlParser.java:44)
1.1.4b build:
Hibernate: SELECT Refer0.referenceSequenceId, Pharm1.pharmgkbAccessionId AS pharmgkbAccessionId0, Pharm1.pharmgkbObjTypeId AS pharmgkbObjTypeId0, Pharm1.name AS name0, Pharm1.projectId AS projectId0,
Pharm1.modified_timestamp AS modified_timestamp0, Refer2.referenceSequenceId AS referenceSequenceId1, Refer2.start_gene AS start_gene1, Refer2.stop_gene AS stop_gene1, Refer2.sequence AS sequence1, Proje3.projectId AS projectId2, Proje3.projectName AS projectName2 FROM ReferenceSequenceGeneAssoc Refer0, PharmGKBObjects Pharm1, ReferenceSequences Refer2, Projects Proje3 WHERE Refer0.geneId = ? AND
Refer0.referenceSequenceId=Pharm1.pharmgkbAccessionId(+) AND Pharm1.pharmgkbAccessionId=Refer2.referenceSequenceId(+) AND Pharm1.projectId=Proje3.projectId(+)
02:30:50,484 ERROR PersistentCollection:87 - Failed to lazily initialize a collection
cirrus.hibernate.TransientObjectException: You tried to lock a transient instance
at cirrus.hibernate.impl.SessionImpl.lock(SessionImpl.java:1113)
at cirrus.hibernate.impl.SessionImpl.doLoad(SessionImpl.java:1404)
at cirrus.hibernate.impl.SessionImpl.doLoadByClass(SessionImpl.java:1306)
at cirrus.hibernate.impl.SessionImpl.internalLoadOneToOne(SessionImpl.java:1265)
at cirrus.hibernate.type.OneToOneType.resolveIdentifier(OneToOneType.java:68)
at cirrus.hibernate.impl.SessionImpl.initializeEntity(SessionImpl.java:1448)
at cirrus.hibernate.loader.Loader.doFind(Loader.java:144)
at cirrus.hibernate.loader.Loader.loadCollection(Loader.java:448)
at cirrus.hibernate.loader.CollectionLoader.initialize(CollectionLoader.java:67)
at cirrus.hibernate.impl.SessionImpl.initialize(SessionImpl.java:2213)
at cirrus.hibernate.collections.PersistentCollection.initialize(PersistentCollection.java:83)
at cirrus.hibernate.collections.PersistentCollection.read(PersistentCollection.java:53)
at cirrus.hibernate.collections.Set.iterator(Set.java:134)
at org.pharmgen.db.DbDocumentRoot.addAccessionObject(DbDocumentRoot.java:166)
at org.pharmgen.xml.ParserEventHandler.startElement(ParserEventHandler.java:282)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at org.pharmgen.xml.Parser.parse(Parser.java:126)
at test.XmlParser.main(XmlParser.java:44)
Thanks, -Mark
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