/** @should return patient data for each obs in the passed context */
@Override
public EvaluatedObsData evaluate(
ObsDataDefinition definition, EvaluationContext obsEvaluationContext)
throws EvaluationException {
DataSetQueryService dqs = Context.getService(DataSetQueryService.class);
EvaluatedObsData c = new EvaluatedObsData(definition, obsEvaluationContext);
// create a map of obs ids -> patient ids (note assumption that personId = patientId)
Set<Integer> obsIds = ObsDataUtil.getObsIdsForContext(obsEvaluationContext, true);
Map<Integer, Integer> convertedIds =
dqs.convertData(Person.class, "personId", null, Obs.class, "person.personId", obsIds);
// create a new (patient) evaluation context using the retrieved ids
EvaluationContext patientEvaluationContext = new EvaluationContext();
patientEvaluationContext.setBaseCohort(new Cohort(convertedIds.values()));
// evaluate the joined definition via this patient context
PatientToObsDataDefinition def = (PatientToObsDataDefinition) definition;
EvaluatedPatientData pd =
Context.getService(PatientDataService.class)
.evaluate(def.getJoinedDefinition(), patientEvaluationContext);
// now create the result set by mapping the results in the patient data set to obs ids
for (Integer obsId : obsIds) {
c.addData(obsId, pd.getData().get(convertedIds.get(obsId)));
}
return c;
}
@RequestMapping(method = RequestMethod.POST)
public void process(
final @RequestParam(required = false, value = "cohort") Integer cohortId,
final @RequestParam(required = true, value = "template") MultipartFile template,
final HttpServletResponse response)
throws IOException, EvaluationException {
EvaluationContext context = new EvaluationContext();
context.addParameterValue("currentDate", new Date());
if (cohortId != null) {
context.setBaseCohort(Context.getCohortService().getCohort(cohortId));
}
PatientDataSetDefinition definition = new PatientDataSetDefinition();
definition.addColumn(
"id", new PatientIdDataDefinition(), StringUtils.EMPTY, new ObjectFormatter());
ListConverter listConverter = new ListConverter();
listConverter.setMaxNumberOfItems(1);
PatientIdentifierDataDefinition preferredIdentifier = new PatientIdentifierDataDefinition();
preferredIdentifier.addType(Context.getPatientService().getPatientIdentifierType(1));
definition.addColumn("identifier", preferredIdentifier, StringUtils.EMPTY, listConverter);
definition.addColumn(
"name",
new PreferredNameDataDefinition(),
StringUtils.EMPTY,
new ObjectFormatter("{familyName}, {givenName}"));
AgeDataDefinition ageOnDate = new AgeDataDefinition();
ageOnDate.addParameter(new Parameter("effectiveDate", "effective date", Date.class));
definition.addColumn("age", ageOnDate, "effectiveDate=${currentDate}", new AgeConverter());
definition.addColumn(
"birthdate",
new BirthdateDataDefinition(),
StringUtils.EMPTY,
new BirthdateConverter("dd-MMM-yyyy"));
definition.addColumn(
"gender", new GenderDataDefinition(), StringUtils.EMPTY, new ObjectFormatter());
ReportDefinition reportDefinition = new ReportDefinition();
reportDefinition.setName("Test Report");
reportDefinition.addDataSetDefinition("PatientDataSetDefinition", definition, null);
final ReportDesign design = new ReportDesign();
design.setName("Test Report Design With Excel Template Renderer");
design.setReportDefinition(reportDefinition);
design.setRendererType(ExcelTemplateRenderer.class);
Properties properties = new Properties();
properties.put("repeatingSections", "sheet:1,dataset:PatientDataSetDefinition");
design.setProperties(properties);
ReportDesignResource resource = new ReportDesignResource();
resource.setName("excel-template.xls");
InputStream inputStream = template.getInputStream();
resource.setContents(IOUtils.toByteArray(inputStream));
IOUtils.closeQuietly(inputStream);
design.addResource(resource);
ExcelTemplateRenderer renderer =
new ExcelTemplateRenderer() {
public ReportDesign getDesign(String argument) {
return design;
}
};
ReportDefinitionService rs = Context.getService(ReportDefinitionService.class);
ReportData data = rs.evaluate(reportDefinition, context);
CsvReportRenderer csvReportRenderer = new CsvReportRenderer();
csvReportRenderer.render(data, "output:csv", System.out);
File file = File.createTempFile("excel", "summary");
BufferedOutputStream bufferedOutputStream =
new BufferedOutputStream(new FileOutputStream(file));
renderer.render(data, "output:xls", bufferedOutputStream);
bufferedOutputStream.close();
response.setHeader("Content-Disposition", "attachment; filename=patient-summary.xls");
response.setContentType("application/vnd.ms-excel");
response.setContentLength((int) file.length());
FileCopyUtils.copy(new FileInputStream(file), response.getOutputStream());
if (file.delete()) log.info("Temporary file deleted!");
}
/** @see DataSetEvaluator#evaluate(DataSetDefinition, EvaluationContext) */
@SuppressWarnings("unchecked")
public DataSet evaluate(DataSetDefinition dataSetDefinition, EvaluationContext context)
throws EvaluationException {
PatientDataSetDefinition dsd = (PatientDataSetDefinition) dataSetDefinition;
context = ObjectUtil.nvl(context, new EvaluationContext());
SimpleDataSet dataSet = new SimpleDataSet(dsd, context);
dataSet.setSortCriteria(dsd.getSortCriteria());
// Construct a new EvaluationContext based on the passed filters
Cohort c = context.getBaseCohort();
if (dsd.getRowFilters() != null) {
for (Mapped<? extends CohortDefinition> q : dsd.getRowFilters()) {
Cohort s = Context.getService(CohortDefinitionService.class).evaluate(q, context);
c = CohortUtil.intersectNonNull(c, s);
}
}
if (c == null) {
c =
Context.getService(CohortDefinitionService.class)
.evaluate(new AllPatientsCohortDefinition(), context);
}
EvaluationContext ec = context.shallowCopy();
if (!CohortUtil.areEqual(ec.getBaseCohort(), c)) {
ec.setBaseCohort(c);
}
// Evaluate each specified ColumnDefinition for all of the included rows and add these to the
// dataset
for (RowPerObjectColumnDefinition cd : dsd.getColumnDefinitions()) {
if (log.isDebugEnabled()) {
log.debug("Evaluating column: " + cd.getName());
log.debug(
"With Data Definition: "
+ DefinitionUtil.format(cd.getDataDefinition().getParameterizable()));
log.debug("With Mappings: " + cd.getDataDefinition().getParameterMappings());
log.debug("With Parameters: " + ec.getParameterValues());
}
StopWatch sw = new StopWatch();
sw.start();
MappedData<? extends PatientDataDefinition> dataDef =
(MappedData<? extends PatientDataDefinition>) cd.getDataDefinition();
EvaluatedPatientData data =
Context.getService(PatientDataService.class).evaluate(dataDef, ec);
for (Integer id : c.getMemberIds()) {
for (DataSetColumn column : cd.getDataSetColumns()) {
Object val = data.getData().get(id);
val = DataUtil.convertData(val, dataDef.getConverters());
dataSet.addColumnValue(id, column, val);
}
}
sw.stop();
if (log.isDebugEnabled()) {
log.debug("Evaluated column. Duration: " + sw.toString());
}
}
return dataSet;
}