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I am migrating old server which is running dspace 6.0 to new server which
is running CRIS dspace 6.0
So far I have done "mvn package" and "ant fresh_install" successfully.
After that, I backup database from the old server use pg_dump and restore
it in a new server using psql -f backupfile command.
And then, I started the tomcat9 service and it is failed to start service I
guess this is database problem.
I stopped tomcat9 service and try to run command "[dspace]/bin/dspace
database info" and I got the following result.
+----------------+-----------------------------------------------------+---------------------+---------+
| 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 |
2017-07-05 15:39:55 | Success |
| 1.7 | Upgrade to DSpace 1.7 schema |
2017-07-05 15:39:55 | Success |
| 1.8 | Upgrade to DSpace 1.8 schema |
2017-07-05 15:39:55 | Success |
| 1.8.2.0 | DSpaceCRIS-crismodule database schema |
2017-07-05 15:39:56 | Success |
| 1.8.2.1 | DSpaceCRIS-crispubmed database schema |
2017-07-05 15:39:58 | Success |
| 1.8.2.2 | DSpaceCRIS-subscription database schema |
2017-07-05 15:39:58 | Success |
| 3.0 | Upgrade to DSpace 3.x schema |
2017-07-05 15:39:58 | Success |
| 3.2.1.0 | DSpaceCRIS-Upgrade-crismodule 182 to 321 |
2017-07-05 15:39:58 | Success |
| 4.0 | Upgrade to DSpace 4.x schema |
2017-07-05 15:39:58 | Success |
| 4.1.0.0 | DSpaceCRIS-Upgrade-crismodule 321 to 4 |
2017-07-05 15:39:59 | Success |
| 4.3.0.0 | DSpaceCRIS-Upgrade-crismodule 4 to 43 |
2017-07-05 15:39:59 | Success |
| 4.9.2015.10.26 | DS-2818 registry update |
2017-07-05 15:39:59 | Success |
| 5.0.2014.08.08 | DS-1945 Helpdesk Request a Copy |
2017-07-05 15:39:59 | Success |
| 5.0.2014.09.25 | DS 1582 Metadata For All Objects drop constraint |
2017-07-05 15:39:59 | Success |
| 5.0.2014.09.26 | DS-1582 Metadata For All Objects |
2017-07-05 15:39:59 | Success |
| 5.3.0.0 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:07 | Success |
| 5.3.0.1 | FIX-SNAPSHOT-DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:07 | Success |
| 5.3.0.2 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:07 | Success |
| 5.3.0.3 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:07 | Success |
| 5.3.0.4 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:07 | Success |
| 5.3.0.5 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:07 | Success |
| 5.3.0.6 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:08 | Success |
| 5.3.1.0 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:08 | Success |
| 5.3.1.1 | DSpaceCRIS-Upgrade-crismodule 5 to 53 |
2017-07-05 15:40:08 | Success |
| 5.4.0.0 | DSpaceCRIS-Upgrade-crismodule 5 to 54 |
2017-07-05 15:40:08 | Success |
| 5.4.0.1 | DSpaceCRIS-Upgrade-crismodule 5 to 54 |
2017-07-05 15:40:08 | Success |
| 5.5.0.1 | DSpaceCRIS-Upgrade-crismodule 5 to 55 |
2017-07-05 15:40:08 | Success |
| 5.5.1.0 | DSpaceCRIS-Upgrade-crismodule 5 to 55 |
2017-07-05 15:40:08 | Success |
| 5.5.1.1 | DSpaceCRIS-Upgrade-crismodule 5 to 55 |
2017-07-05 15:40:08 | Success |
| 5.5.1.2 | DSpaceCRIS-Upgrade-crismodule 5 to 55 |
2017-07-05 15:40:08 | Success |
| 5.5.1.3 | DSpaceCRIS-Upgrade-crismodule 5 to 55 |
2017-07-05 15:40:08 | Success |
| 5.5.1.4 | DSpaceCRIS-Upgrade-crismodule 5 to 55 |
2017-07-05 15:40:08 | Success |
| 5.6.0.0 | DSpaceCRIS-Upgrade-crismodule 5 to 56 |
2017-07-05 15:40:08 | Success |
| 5.6.0.1 | DSpaceCRIS-Upgrade-crismodule 5 to 56 |
2017-07-05 15:40:08 | Success |
| 5.6.2.0 | DSpaceCRIS-Upgrade-crismodule 5 to 56 |
2017-07-05 15:40:09 | Success |
| 5.6.2016.08.23 | DS-3097 |
2017-07-05 15:40:09 | Success |
| 5.7.2017.04.11 | DS-3563 Index metadatavalue resource type id column |
2017-07-05 15:40:09 | Success |
| 6.0.2015.03.06 | DS 2701 Dso Uuid Migration |
2017-07-05 15:40:09 | 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 |
| 6.0.2017.05.04 | D4CRIS-2 |
| Pending |
| 6.0.2017.06.15 | D4CRIS-2 |
| Pending |
| 6.0.2017.06.16 | D4CRIS-2 |
| Pending |
| 6.0.2017.06.26 | D4CRIS-2 |
| Pending |
+----------------+-----------------------------------------------------+---------------------+---------+
So I guess some are succeed maybe the database tried to migrated to new
server when i start tomcat service.
Now I run command "[dspace]/bin/dspace database migerate" and got the
following error message, which showing there is duplicated keys so it can't
create primary key on the column.
PS C:\dspace\bin> ./dspace database migrate
Using DSpace installation in: C:\dspace
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option
MaxPermSize=2048m; support was removed in 8.0
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:669)
at
org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:577)
at
org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:224)
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(ScriptLauncher.java:230)
at
org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:82)
Caused by: org.flywaydb.core.internal.dbsupport.FlywaySqlScriptException:
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 "group2group_pkey"
Detail: Key (parent_id, child_id)=(a393424d-eb09-4a5c-bb6d-f226f0a27637,
70e3dd59-cbc2-4c21-94a6-b11928b2bac7) is duplicated.
Location :
org/dspace/storage/rdbms/sqlmigration/postgres/V6.0_2015.03.07__DS-2701_Hibernate_migration.sql
(C:\dspace\file:\C:\dspace\lib\dspace-api-CRIS-6.0.0-SNAPSHOT.jar!\org\dspace\storage\rdbms\sqlmigration\postgres\V6.0_2015.03.07__DS-2701_Hibernate_migration.sql)
Line : 130
Statement : ALTER TABLE Group2Group add primary key (parent_id,child_id)
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:658)
... 8 more
Caused by: org.postgresql.util.PSQLException: ERROR: could not create
unique index "group2group_pkey"
Detail: Key (parent_id, child_id)=(a393424d-eb09-4a5c-bb6d-f226f0a27637,
70e3dd59-cbc2-4c21-94a6-b11928b2bac7) is duplicated.
at
org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2458)
at
org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2158)
at
org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.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(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 have noticed the group2group table has ID, parent_id, child_id and "ID"
column doesn't have any duplicated keys but 'parent_id' and "child_id" are
duplicated same as picture below.
<https://lh3.googleusercontent.com/-sZfiIoGopEc/WVyakWGEksI/AAAAAAAAGnY/Gsfs-8P4JK0zHTYyph9T4Nh1batqK_v1ACLcBGAs/s1600/Untitled.png>
Of course I can run query which can delete the duplicated rows. However, I
want to know what is table 'group2group' and how this work in dspace. If I
remove duplicated parent_id and child_id column, there will be empty ID
keys as you can see in the picture. Assume we remove ID 100 because of
duplicated keys of parent_id and child_id, there will be no 100 between id
999 and id 101.
I am waiting your guys suggestion how to solve this database problem and
please give me some idea :(
I asked the student who handled old dspace server before and he said he did
some modification to do certain tasks. I think this is the main cause of
the problem that "dspace database migration" failed.
Please save me. Thanks in advance...
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