This issue should be logged as a bug in DSpace Jira since others may encounter the issue in the future.
As a work around, you could run the following SQL to identify the records in error. select eperson_group_id,eperson_id, count(*) from epersongroup2eperson group by eperson_group_id, eperson_id having count(*)>1; If the number of records in error is small, you could clean them up in the database. On Wed, Nov 9, 2016 at 6:18 AM, euler <[email protected]> wrote: > Hi Bruno, > > Running "ant update" worked flawlessly for me too. It's just that > automatic migration did not worked for me as shown when I run "dspace > database info". Also, this did not happen in another dspace instance that > I'm maintaining. The error that caught my attention is "ERROR: could not > create unique index "epersongroup2eperson_pkey" > > So I'm hoping if someone can help me on how to resolve this problem. > > Thanks > > On Wednesday, November 9, 2016 at 10:08:58 PM UTC+8, Bruno Nocera Zanette > wrote: >> >> Euler, >> How are you trying to do this? Which commands? >> For me, every time i've tried to update a version with "ant update" >> worked flawlessly. You seem to have compile, installed the files and then >> using "./bin/dspace database migrate" to do the migration. I've never tried >> to do it, so i don't know if there's any problem in it. >> >> Em qua, 9 de nov de 2016 às 10:55, euler <[email protected]> >> escreveu: >> >>> Dear All, >>> >>> I'm on the process of upgrading a dspace instance from 5.4 to 6.0. All >>> went well but I noticed in my log file this error: >>> >>> 2016-11-09 20:36:42,308 FATAL org.dspace.core.Context @ Cannot obtain >>> the bean which provides a database connection. Check previous entries in >>> the dspace.log to find why the db failed to initialize. >>> >>> and the page is just blank. >>> >>> When I run dspace database info, here's the result: >>> >>> Database Software: PostgreSQL version 9.5.1 >>> Database Driver: PostgreSQL Native Driver version PostgreSQL >>> 9.4.1211.jre7 >>> PostgreSQL 'pgcrypto' extension installed/up-to-date? true (version=1.2) >>> >>> +----------------+------------------------------------------ >>> --------+---------------------+---------+ >>> | 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 | Initializing from DSpace 1.6 database schema | >>> 2015-09-26 17:28:42 | Success | >>> | 1.7 | Upgrade to DSpace 1.7 schema | >>> 2015-09-26 17:28:43 | Success | >>> | 1.8 | Upgrade to DSpace 1.8 schema | >>> 2015-09-26 17:28:46 | Success | >>> | 3.0 | Upgrade to DSpace 3.x schema | >>> 2015-09-26 17:28:52 | Success | >>> | 4.0 | Upgrade to DSpace 4.x schema | >>> 2015-09-26 17:28:53 | Success | >>> | 4.9.2015.10.26 | DS-2818 registry update | >>> | Ignored | >>> | 5.0.2014.08.08 | DS-1945 Helpdesk Request a Copy | >>> 2015-09-26 17:28:53 | Success | >>> | 5.0.2014.09.25 | DS 1582 Metadata For All Objects drop constraint | >>> 2015-09-26 17:28:54 | Success | >>> | 5.0.2014.09.26 | DS-1582 Metadata For All Objects | >>> 2015-09-26 17:30:31 | Success | >>> | 5.6.2016.08.23 | DS-3097 | >>> 2016-11-09 17:59:33 | Success | >>> | 6.0.2015.03.06 | DS 2701 Dso Uuid Migration | >>> 2016-11-09 17:59:34 | 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 | >>> +----------------+------------------------------------------ >>> --------+---------------------+---------+ >>> >>> So I tried to run dspace database migrate and I received this error: >>> >>> 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(Databa >>> seUtils.java:666) >>> at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(Databa >>> seUtils.java:574) >>> at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils. >>> java:222) >>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >>> at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) >>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown >>> Source) >>> at java.lang.reflect.Method.invoke(Unknown Source) >>> at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptL >>> auncher.java:229) >>> at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher. >>> java:81) >>> Caused by: org.flywaydb.core.internal.dbsupport.FlywaySqlScriptExceptio >>> n: >>> Migration V6.0_2015.03.07__DS-2701_Hibernate_migration.sql failed >>> ----------------------------------------------------------------- >>> SQL State : 23505 >>> Error Code : 0 >>> Message : ERROR: could not create unique index >>> "epersongroup2eperson_pkey" >>> Detail: Key (eperson_group_id, >>> eperson_id)=(550bb4c5-7f50-4db7-89ad-e7d6b11ab3c1, >>> 505e83c3-1a4f-446e-9934-f5fcba38a76c) is duplicated. >>> Location : org/dspace/storage/rdbms/sqlmi >>> gration/postgres/V6.0_2015.03.07__DS-2701_Hibernate_migration.sql >>> ([dspace]\lib\dspace-api-6.0.jar!\org\dspace\storage\rdbms\s >>> qlmigration\postgres\V6.0_2015.03.07__DS-2701_Hibernate_migration.sql >>> ) >>> Line : 114 >>> Statement : ALTER TABLE EPersonGroup2EPerson add primary key >>> (eperson_group_id,eperson_id) >>> >>> at org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlSc >>> ript.java:117) >>> at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor >>> .execute(SqlMigrationExecutor.java:71) >>> at org.flywaydb.core.internal.command.DbMigrate.doMigrate(DbMig >>> rate.java:352) >>> at org.flywaydb.core.internal.command.DbMigrate.access$1100(DbM >>> igrate.java:47) >>> at org.flywaydb.core.internal.command.DbMigrate$4.doInTransacti >>> on(DbMigrate.java:308) >>> at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.exe >>> cute(TransactionTemplate.java:72) >>> at org.flywaydb.core.internal.command.DbMigrate.applyMigration( >>> DbMigrate.java:305) >>> at org.flywaydb.core.internal.command.DbMigrate.access$1000(DbM >>> igrate.java:47) >>> at org.flywaydb.core.internal.command.DbMigrate$2.doInTransacti >>> on(DbMigrate.java:230) >>> at org.flywaydb.core.internal.command.DbMigrate$2.doInTransacti >>> on(DbMigrate.java:173) >>> at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.exe >>> cute(TransactionTemplate.java:72) >>> at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigra >>> te.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(Databa >>> seUtils.java:655) >>> ... 8 more >>> Caused by: org.postgresql.util.PSQLException: ERROR: could not create >>> unique index "epersongroup2eperson_pkey" >>> Detail: Key (eperson_group_id, >>> eperson_id)=(550bb4c5-7f50-4db7-89ad-e7d6b11ab3c1, >>> 505e83c3-1a4f-446e-9934-f5fcba38a76c) is duplicated. >>> at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorRespons >>> e(QueryExecutorImpl.java:2458) >>> at org.postgresql.core.v3.QueryExecutorImpl.processResults(Quer >>> yExecutorImpl.java:2158) >>> at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecut >>> orImpl.java:291) >>> at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement. >>> java:432) >>> at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:358) >>> at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement >>> .java:305) >>> at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement >>> .java:291) >>> at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement >>> .java:269) >>> at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:265) >>> at org.apache.commons.dbcp2.DelegatingStatement.execute(Delegat >>> ingStatement.java:291) >>> at org.apache.commons.dbcp2.DelegatingStatement.execute(Delegat >>> ingStatement.java:291) >>> at org.flywaydb.core.internal.dbsupport.JdbcTemplate.executeSta >>> tement(JdbcTemplate.java:238) >>> at org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlSc >>> ript.java:114) >>> ... 24 more >>> >>> >>> Please help on how to resolve this error. >>> >>> Thanks in advance. >>> >>> euler >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "DSpace Technical Support" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/dspace-tech. >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> Bruno Nocera Zanette >> +55 41 9992-2508 >> > -- > You received this message because you are subscribed to the Google Groups > "DSpace Technical Support" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/dspace-tech. > For more options, visit https://groups.google.com/d/optout. > -- Terry Brady Applications Programmer Analyst Georgetown University Library Information Technology http://georgetown-university-libraries.github.io/ <https://www.library.georgetown.edu/lit/code> 425-298-5498 (Seattle, WA) -- You received this message because you are subscribed to the Google Groups "DSpace Technical Support" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/dspace-tech. For more options, visit https://groups.google.com/d/optout.
