Hi folks
I know there have been a few of these- I've hit upon one now. I'm migrating
a v5.6 database to v6, and getting the following error:
./dspace database migrate
Database URL: jdbc:postgresql://localhost:5432/dspace
Migrating database to latest version... (Check dspace logs for details)
Migration exception:
java.sql.SQLException: Flyway migration error occurred
at
org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:673)
at
org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:576)
at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:221)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
Caused by: org.flywaydb.core.internal.dbsupport.FlywaySqlScriptException:
Migration V6.0_2015.03.07__DS-2701_Hibernate_migration.sql failed
-----------------------------------------------------------------
SQL State : 23502
Error Code : 0
Message : ERROR: column "bitstream_id" contains null values
Location :
org/dspace/storage/rdbms/sqlmigration/postgres/V6.0_2015.03.07__DS-2701_Hibernate_migration.sql
(/home/lib/dspace/dspace/bin/file:/home/lib/dspace/dspace/lib/dspace-api-6.3.jar!/org/dspace/storage/rdbms/sqlmigration/postgres/V6.0_2015.03.07__DS-2701_Hibernate_migration.sql)
Line : 236
Statement : ALTER TABLE bundle2bitstream ALTER COLUMN bitstream_id SET NOT
NULL
at
org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlScript.java:117)
at
org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:71)
at
org.flywaydb.core.internal.command.DbMigrate.doMigrate(DbMigrate.java:352)
at
org.flywaydb.core.internal.command.DbMigrate.access$1100(DbMigrate.java:47)
at
org.flywaydb.core.internal.command.DbMigrate$4.doInTransaction(DbMigrate.java:308)
at
org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
at
org.flywaydb.core.internal.command.DbMigrate.applyMigration(DbMigrate.java:305)
at
org.flywaydb.core.internal.command.DbMigrate.access$1000(DbMigrate.java:47)
at
org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:230)
at
org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:173)
at
org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:173)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
at
org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:662)
... 8 more
Caused by: org.postgresql.util.PSQLException: ERROR: column "bitstream_id"
contains null values
at
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2422)
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2167)
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:306)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:441)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:365)
at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:307)
at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:293)
at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:270)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:266)
at
org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:291)
at
org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:291)
at
org.flywaydb.core.internal.dbsupport.JdbcTemplate.executeStatement(JdbcTemplate.java:238)
at
org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlScript.java:114)
... 24 more
I definitely have no null values in the offending column:
dspace=> select * from bundle2bitstream where bitstream_id is null;
id | bundle_id | bitstream_id | bitstream_order
----+-----------+--------------+-----------------
(0 rows)
I know the processing in the script prior to this is complicated, so there
may be something else it's not doing- I don't know if it rolls back to the
beginning of the script, but just wondering if anyone has any ideas to
what's actually going on here! I have installed the pgcrypto for v6 as per
the installation instructions, so I think my database should be ready.
It did 5.7 and the first 6 migration ok:
+----------------+-----------------------------------------------------+---------------------+---------+
| Version | Description |
Installed on | State |
+----------------+-----------------------------------------------------+---------------------+---------+
| 1.1 | Initial DSpace 1.1 database schema |
| <Baseln |
| 1.2 | Upgrade to DSpace 1.2 schema |
| <Baseln |
| 1.3 | Upgrade to DSpace 1.3 schema |
| <Baseln |
| 1.3.9 | Drop constraint for DSpace 1 4 schema |
| <Baseln |
| 1.4 | Upgrade to DSpace 1.4 schema |
| <Baseln |
| 1.5 | Upgrade to DSpace 1.5 schema |
| <Baseln |
| 1.5.9 | Drop constraint for DSpace 1 6 schema |
| <Baseln |
| 1.6 | Upgrade to DSpace 1.6 schema |
| <Baseln |
| 1.7 | Upgrade to DSpace 1.7 schema |
| <Baseln |
| 1.8 | Upgrade to DSpace 1.8 schema |
| <Baseln |
| 3.0 | Upgrade to DSpace 3.x schema |
| <Baseln |
| 4.0 | Initializing from DSpace 4.0 database schema |
2018-01-25 16:34:33 | Success |
| 4.9.2015.10.26 | DS-2818 registry update |
| Ignored |
| 5.0.2014.08.08 | DS-1945 Helpdesk Request a Copy |
2018-01-25 16:34:33 | Success |
| 5.0.2014.09.25 | DS 1582 Metadata For All Objects drop constraint |
2018-01-25 16:34:34 | Success |
| 5.0.2014.09.26 | DS-1582 Metadata For All Objects |
2018-02-01 12:23:35 | Success |
| 5.6.2016.08.23 | DS-3097 |
2018-02-01 12:23:37 | Success |
| 5.7.2017.04.11 | DS-3563 Index metadatavalue resource type id column |
2018-09-06 11:11:16 | Success |
| 5.7.2017.05.05 | DS 3431 Add Policies for BasicWorkflow |
2018-09-06 11:11:16 | Success |
| 6.0.2015.03.06 | DS 2701 Dso Uuid Migration |
2018-09-06 11:11:17 | Success |
| 6.0.2015.03.07 | DS-2701 Hibernate migration |
| Pending |
| 6.0.2015.08.31 | DS 2701 Hibernate Workflow Migration |
| Pending |
| 6.0.2016.01.03 | DS-3024 |
| Pending |
| 6.0.2016.01.26 | DS 2188 Remove DBMS Browse Tables |
| Pending |
| 6.0.2016.02.25 | DS-3004-slow-searching-as-admin |
| Pending |
| 6.0.2016.04.01 | DS-1955 Increase embargo reason |
| Pending |
| 6.0.2016.04.04 | DS-3086-OAI-Performance-fix |
| Pending |
| 6.0.2016.04.14 | DS-3125-fix-bundle-bitstream-delete-rights |
| Pending |
| 6.0.2016.05.10 | DS-3168-fix-requestitem item id column |
| Pending |
| 6.0.2016.07.21 | DS-2775 |
| Pending |
| 6.0.2016.07.26 | DS-3277 fix handle assignment |
| Pending |
| 6.0.2016.08.23 | DS-3097 |
| Pending |
| 6.0.2017.02.14 | statistics-harvester |
| Pending |
| 6.1.2017.01.03 | DS 3431 Add Policies for BasicWorkflow |
| Pending |
+----------------+-----------------------------------------------------+---------------------+---------+
Cheers
Scott
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