Migration of rawbioassays fails due to NULL value

[Nicklas Nordborg]

The stacktrace:

Starting BASE. Please wait...
[0%]    Dry-run, changes will not be permanent
[2%]    Loaded 4 mappings from migrate_rba2dba_relax_test.txt
[5%]    Starting migration of 60119 raw bioassays...
[53%]   Migrated 37395 raw bioassays so far...

net.sf.basedb.core.BaseException: INSERT INTO "ParentDerivedBioAssays" (
                                "derivedbioassay_id", "parentbioassay_id"
                        ) VALUES (
                                ?, ?
                        )
        at net.sf.basedb.core.MigrateRbaToDba.flush(MigrateRbaToDba.java:528)
        at net.sf.basedb.core.MigrateRbaToDba.execute(MigrateRbaToDba.java:263)
        at org.hibernate.jdbc.WorkExecutor.executeWork(WorkExecutor.java:37)
        at org.hibernate.internal.AbstractSharedSessionContract.lambda$doWork$1(AbstractSharedSessionContract.java:1109)
        at org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.coordinateWork(JdbcCoordinatorImpl.java:308)
        at org.hibernate.internal.AbstractSharedSessionContract.doWork(AbstractSharedSessionContract.java:1125)
        at org.hibernate.internal.AbstractSharedSessionContract.doWork(AbstractSharedSessionContract.java:1112)
        at net.sf.basedb.core.hibernate.SessionWrapper.doWork(SessionWrapper.java:261)
        at net.sf.basedb.core.HibernateUtil.doWork(HibernateUtil.java:1387)
        at net.sf.basedb.core.MigrateRbaToDba.migrateAll(MigrateRbaToDba.java:66)
        at net.sf.basedb.install.OneTimeFix.main(OneTimeFix.java:151)
Caused by: java.sql.BatchUpdateException: Batch entry 44 INSERT INTO "ParentDerivedBioAssays" (
                                "derivedbioassay_id", "parentbioassay_id"
                        ) VALUES (
                                16384260, NULL
                        ) was aborted: FEL: null-värde i kolumn "parentbioassay_id" i relation "ParentDerivedBioAssays" bryter mot not-null-villkoret
  Detail: Misslyckande rad innehåller (16384260, null).  Call getNextException to see other errors in the batch.
        at org.postgresql.jdbc.BatchResultHandler.handleError(BatchResultHandler.java:165)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2367)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:560)
        at org.postgresql.jdbc.PgStatement.internalExecuteBatch(PgStatement.java:893)
        at org.postgresql.jdbc.PgStatement.executeBatch(PgStatement.java:916)
        at org.postgresql.jdbc.PgPreparedStatement.executeBatch(PgPreparedStatement.java:1684)
        at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:2544)
        at net.sf.basedb.core.AnnotationBatcher$UpdateBatcher.flush(AnnotationBatcher.java:1253)
        at net.sf.basedb.core.MigrateRbaToDba.flush(MigrateRbaToDba.java:523)
        ... 10 more
Caused by: org.postgresql.util.PSQLException: FEL: null-värde i kolumn "parentbioassay_id" i relation "ParentDerivedBioAssays" bryter mot not-null-villkoret
  Detail: Misslyckande rad innehåller (16384260, null).
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366)
        ... 17 more

The cause is most likely a raw bioassay that doesn't have any parent derived bioassay (we have that in the Relax server where OncoArray raw bioassays are linked directly to extracts).

[Nicklas Nordborg]

In 8222:

Fixes #2323: Migration of rawbioassays fails due to NULL value