This documentation relates to an old version of VIVO, version 1.8.x. Looking for another version? See all documentation.
The transition from release 1.5 to 1.6 was a major one. VIVO 1.6 included migration code that restructured existing data to match the new ontology. This restructuring meant that VIVO also had to recompute all of the inferences in the data and rebuild the search index. The process was time-comsuming and resource-intensive.
The good news is that VIVO 1.8 can make this transition more quickly. Improvements have been made in the migration code, the inferencing code, and the search index builder.
Sites will find it much easier to upgrade from release 1.5 to release 1.8 in a single operation.
Read the individual upgrade documents.
These instructions should be sufficient for a standard VIVO installation. You may need to take additional actions if your site has modified the VIVO code, Review the "Noteworthy Changes" section in each of these documents. They may help you to keep your local modifications working.
The standard release of VIVO will not perform a multi-step migration. You must remove the comment indicators from two lines in the file
productMods/WEB-INF/resources/startup_listeners.txt, in your VIVO distribution.
If your site uses a three-tier build, see "Auto-loaded RDF files move to the Home directory" in Upgrade instructions for VIVO release 1.6.2
See "Separate your existing deploy.properties file into two files" in Upgrade instructions for VIVO release 1.6.2
Run this as you usually would.
The section entitled "Run the RDB migration tool" in Upgrading VIVO to release 1.8.1 contains a full description of this tool and its options.
The bug that is described in that section has been fixed.
For most sites, simply go to the VIVO home directory and copy
If you are using an alternative triple store, find more information in the VIVO 1.8 Installation Instructions, under "Using a Different Data Store".
Start tomcat as you usually would.
The time required will depend on your hardware, and on the size and structure of your data. In our tests, migration of a small VIVO installation (25,000 individuals) took 25 minutes. Migration of a very large installation (1,500,000 individuals) took 26 hours.
These test migrations were performed on a MacBook Pro with 8 gigabytes of memory and a solid state drive. The
setenv.sh file in Tomcat was modified to allocate 6 gigabytes of memory to Tomcat.
When Tomcat is started, you can monitor the progress of the migration by watching the contents of
vivo.all.log. The log will contain a variety of messages, but these are the most prominent:
|Message content||The ontology files have changed dramatically from release 1.5 to 1.8. These messages describe the additions, deletions and changes.|
Updating /Users/jeb228/Testing/instances/florida_migration/vivo_home/rdf/abox/filegraph/academicDegree.rdf because graphs are not isomorphic
dbModel: 358 ; fileModel: 454
|Fraction of total time||< 1%|
|Message content||This is the actual migration code, adding and removing triples from the data store, according to the changes in the ontology.|
|Fraction of total time||40%|
Interspersed among the messages from
|Messages from|| |
|Message content||Because of the changes in the ontology, all inference triples must be recomputed.|
|Fraction of total time||50%|
|Message content||As a final step, the Solr search index must be rebuilt.|
|Fraction of total time||10%|
When the STOP_REBUILD message appears from IndexHistory, the migration is complete.