I should add, I do realise that the preceding lines in the script are reassigning columns and data, so while I can check my table has no null values prior to the run, I don't know what's changed, as I assume it is rolling back everything that script does. My obvious course of action is to back up the db and run the script up to that line, so I can see what it's ACTUALLY complaining about.
Cheers Scott On Tuesday, September 11, 2018 at 11:28:13 AM UTC+1, Scott Renton wrote: > > 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 > -- All messages to this mailing list should adhere to the DuraSpace Code of Conduct: https://duraspace.org/about/policies/code-of-conduct/ --- You received this message because you are subscribed to the Google Groups "DSpace Technical Support" group. 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