You can compile the subreport like the simple report - with help of JasperCompileManager.compileReport(java.lang.String sourceFileName) method, for example.
After that you can pass the compiled subreport as parameter to the master report.
The sample:
JasperReport jasperMasterReport = JasperCompileManager.compileReport(masterReportSource);
JasperReport jasperSubReport = JasperCompileManager.compileReport(subReportSource);
Map<String, Object> parameters = new HashMap()<String, Object>;
parameters.put("subreportParameter", jasperSubReport);
JasperFillManager.fillReportToFile(jasperMasterReport, parameters, outputFileName, connection);
The snippet from the master report's jrxml file (sample):
<parameter name="subreportParameter" class="net.sf.jasperreports.engine.JasperReport"/>
...
<detail>
<band height="50">
...
<subreport>
<reportElement isPrintRepeatedValues="false" x="5" y="25" width="325" height="20" isRemoveLineWhenBlank="true" backcolor="#ffcc99"/>
<subreportParameter name="City">
<subreportParameterExpression><![CDATA[$F{City}]]></subreportParameterExpression>
</subreportParameter>
<connectionExpression><![CDATA[$P{REPORT_CONNECTION}]]></connectionExpression>
<returnValue subreportVariable="PriceSum" toVariable="ProductTotalPrice" calculation="Sum"/>
<subreportExpression class="net.sf.jasperreports.engine.JasperReport"><![CDATA[$P{subreportParameter}]]></subreportExpression>
</subreport>
Notes
I mentioned an old API for generating result:
JasperFillManager.fillReportToFile(JasperReport, String, Map,
java.sql.Connection)
In case using JasperReports 6.x it is better to use exporters (concrete implementation of net.sf.jasperreports.export.Exporter interface, for example JRPdfExporter) for generating output file
The example how to use Exporter right can be found here
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