Prior to Virtuoso version 6.3, some RDF data in the quad store could be stored in a way that could break the sequence of an index, causing wrong results to be passed back.
To fix this, we have added an automated check to detect whether this condition is present, and to fix the index when needed.
When a DBA uses a Virtuoso 6.3 or later binary to start a database which was previously used only with Virtuoso 6.2 or earlier, the following text will appear in the virtuoso session log:
21:05:36 PL LOG: This database may contain RDF data that could cause indexing problems on previous versions of the server. 21:05:36 PL LOG: The content of the DB.DBA.RDF_QUAD table will be checked and an update may automatically be performed if 21:05:36 PL LOG: such data is found. 21:05:36 PL LOG: This check will take some time but is made only once.
As noted, this check may take some time, depending on the number of stored quads.
If the check finds no issues, the following message is entered in the log, and Virtuoso will flag the check as "done," so it will not affect subsequent restarts of the database server.
21:05:36 PL LOG: No need to update DB.DBA.RDF_QUAD
The database will continue to perform the usual startup routines and go into an online state.
If the problematic condition is detected, however, the following message will appear in the log, and the Virtuoso server will refuse to start until its instructions are followed --
21:05:36 PL LOG: An update is required. 21:05:36 PL LOG: 21:05:36 PL LOG: NOTICE: Before Virtuoso can continue fixing the DB.DBA.RDF_QUAD table and its indexes 21:05:36 PL LOG: the DB Administrator should check make sure that: 21:05:36 PL LOG: 21:05:36 PL LOG: * there is a recent backup of the database 21:05:36 PL LOG: * there is enough free disk space available to complete this conversion 21:05:36 PL LOG: * the database can be offline for the duration of this conversion 21:05:36 PL LOG: 21:05:36 PL LOG: Since the update can take a considerable amount of time on large databases 21:05:36 PL LOG: it is advisable to schedule this at an appropriate time. 21:05:36 PL LOG: 21:05:36 PL LOG: To continue the DBA must change the virtuoso.ini file and add the following flag: 21:05:36 PL LOG: 21:05:36 PL LOG: [Parameters] 21:05:36 PL LOG: AnalyzeFixQuadStore = 1 21:05:36 PL LOG: 21:05:36 PL LOG: For additional information please contact OpenLink Support <email@example.com> 21:05:36 PL LOG: This process will now exit.
Since the update may take a substantial amount of time and additional disk space (depending on the size of the quad store), we have decided not to automatically start the update process. Instead, we hand control back to the DBA and let them decide when to perform this update. If the DBA wants to delay the update until a more appropriate time, they should restart with the older binary as the newer binary will never start the database.
Once the DBA has checked the backups and disk space, and found an appropriate time-slot to run this update, they should edit the
virtuoso.ini file and add the following flag:
[Parameters] AnalyzeFixQuadStore = 1
Upon starting the Virtuoso server with this parameter setting, the following messages will appear in the
21:05:57 PL LOG: This database may contain RDF data that could cause indexing problems on previous versions of the server. 21:05:57 PL LOG: The content of the DB.DBA.RDF_QUAD table will be checked and an update may automatically be performed if 21:05:57 PL LOG: such data is found. 21:05:57 PL LOG: This check will take some time but is made only once. 21:05:57 PL LOG: 21:05:57 PL LOG: An update is required. 21:05:57 PL LOG: Please be patient. 21:05:57 PL LOG: The table DB.DBA.RDF_QUAD and two of its additional indexes will now be patched. 21:05:57 PL LOG: In case of an error during the operation, delete the transaction log before restarting the server. 21:05:57 Checkpoint started 21:05:57 Checkpoint finished, log off 21:05:57 PL LOG: Phase 1 of 9: Gathering statistics ... 21:05:58 PL LOG: * Index sizes before the processing: 002565531 RDF_QUAD, 002565531 POGS, 001171100 OP 21:05:58 PL LOG: Phase 2 of 9: Copying all quads to a temporary table ... 21:07:26 PL LOG: * Index sizes of temporary table: 001171100 OP 21:07:26 PL LOG: Phase 3 of 9: Cleaning the quad storage ... 21:07:51 PL LOG: Phase 4 of 9: Refilling the quad storage from the temporary table... 21:09:17 PL LOG: Phase 5 of 9: Cleaning the temporary table ... 21:09:41 PL LOG: Phase 6 of 9: Gathering statistics again ... 21:09:41 PL LOG: * Index sizes after the processing: 002565531 RDF_QUAD, 002565531 POGS, 001171100 OP 21:09:41 PL LOG: Phase 7 of 9: integrity check (completeness of index RDF_QUAD_POGS of DB.DBA.RDF_QUAD) ... 21:10:00 PL LOG: Phase 8 of 9: integrity check (completeness of primary key of DB.DBA.RDF_QUAD) ... 21:10:17 PL LOG: Phase 9 of 9: final checkpoint... 21:10:20 Checkpoint started 21:10:22 Checkpoint finished, log off 21:10:22 PL LOG: Update complete.
If the update process detects any problem, it will put some debug output into the
virtuoso.log and exit.
At this point, the DBA is advised to remove the
virtuoso.trx file and contact OpenLink Support.
After the update process has completed, the database will be left in an online state, as after a normal launch.