Batch API for annotation handling

[Nicklas Nordborg]

When updating a large number of annotation on a large number of items it easy to run into problems:

• The first-level cache in Hibernate can easily use up all available memory
• Dirty-checking and SQL execution by Hibernate takes a long time
• If the change history logging is enabled, this also takes a long time

The current annotation importer plug-in has been used as for testing. It was used to import values for 140+ different annotation types to 4900+ items (samples).

The data file is 4MB large. The work done by the annotation importer can be divided into the following steps. JConsole is used to check the memory usage and debug output to check the time.

Action	Time	Memory
Parse the file and find the item to update (loaded by ID)	7 sec	~500MB
Update annotations	5 min	~500MB -> 1.5GB
Commit - Hibernate	12 min	~1.5GB
Commit - Change log	13 min	~1.5GB -> 1.9GB

CPU usage may also be interesting. This is usually below 10% (less than a full single core). The CPU usage for Postgres is in the same range.

The main problems here are that the memory usage grows in the second step and that the last two steps takes a long time.

In theory it should be possible to improve the second step a lot since in this stage the annotation importer is only working with a single item at a time. We do not need Hibernate to keep things in the first-level cache. If we can manage this it may be that the Hibernate commit step is also automatically solved. The change log step may be harder, since we are already using the stateless session here. However, it is maybe possible to replace this with our own batch SQL implementation as we have done for reporters and raw data already.