Version: Next

Useful ObjectStore properties

You can configure some parameters to update how queries are handled by setting these in your mine.properties file. If you do not, the default values will be used.

os.query.max-query-parse-time#

InterMine includes a cost-based query optimiser that attempts to rewrite SQL queries to make use of precomputed tables. This involved parsing SQL strings into a Java representation, which is normally very fast but if multiple OR constraints are found in large queries, can be slow.

There is a timeout to prevent query parsing from taking too long, if the time is exceeded a query will run as normal without possible optimisation. The default can be overridden by setting os.query.max-query-parse-time in *mine.properties to an integer value defining a number of milliseconds.

Used in QueryOptimiserContext.java.

os.query.max-time#

When the query is executed, via ObjectStoreInterMineImpl.executeWithConnection(), SQL EXPLAIN is run on the generated query. If the estimated time to complete the query is more than the max-time parameter set, the query will fail.

Defaults to 100000000 milliseconds.

os.query.max-limit#

When the query is executed, via ObjectStoreInterMineImpl.executeWithConnection(), SQL EXPLAIN is run on the generated query. If the estimated number of rows is more than the max-limit parameter set, the query will fail.

Note this relies on Postgres's statistics being up to date and correct, be sure to run ANALYSE.

Defaults to 100000000 rows.

os.query.max-offset#

Sets the maximum number of rows available to export.

If the offset for a query is greater than the os.query.max-offset, the query will fail to run. See TableExportAction.checkTable() for the exact ExportException used.

// exception thrown in TableExportAction.checkTable()
if (pt.getExactSize() > pt.getMaxRetrievableIndex()) {
    throw new ExportException("Result is too big for export. "
        + "Table for export can have at the most "
        + pt.getMaxRetrievableIndex() + " rows.");
}

Defaults to 100000000 rows.

os.queue-len#