/**
* @see
* PatientDataEvaluator#evaluate(org.openmrs.module.reporting.data.patient.definition.PatientDataDefinition,
* org.openmrs.module.reporting.evaluation.EvaluationContext)
*/
public EvaluatedPatientData evaluate(PatientDataDefinition definition, EvaluationContext context)
throws EvaluationException {
CalculationDataDefinition def = (CalculationDataDefinition) definition;
EvaluatedPatientData c = new EvaluatedPatientData(def, context);
// return right away if there is nothing to evaluate
if (context.getBaseCohort() != null && context.getBaseCohort().isEmpty()) {
return c;
}
// evaluate the calculation
PatientCalculationService service = Context.getService(PatientCalculationService.class);
CalculationResultMap resultMap =
service.evaluate(
context.getBaseCohort().getMemberIds(),
def.getCalculation(),
def.getCalculationParameters(),
context);
// move data into return object
for (Map.Entry<Integer, CalculationResult> entry : resultMap.entrySet()) {
c.addData(entry.getKey(), entry.getValue());
}
return c;
}
/** @see Moh731CohortLibrary#revisitsArt() */
@Test
public void revisitsArt() throws Exception {
EncounterType hivConsult =
MetadataUtils.getEncounterType(HivMetadata._EncounterType.HIV_CONSULTATION);
Concept stavudine = Context.getConceptService().getConcept(84309);
// Start patient #6 this month and give them a visit in the reporting period + 2 months
TestUtils.saveDrugOrder(TestUtils.getPatient(6), stavudine, TestUtils.date(2012, 6, 10), null);
TestUtils.saveEncounter(TestUtils.getPatient(6), hivConsult, TestUtils.date(2012, 6, 20));
// Start patient #7 in previous month and give them a visit in the reporting period + 2 months
TestUtils.saveDrugOrder(TestUtils.getPatient(7), stavudine, TestUtils.date(2012, 5, 10), null);
TestUtils.saveEncounter(TestUtils.getPatient(7), hivConsult, TestUtils.date(2012, 6, 20));
// Start patient #8 and give them visit outside of reporting period + 2 month window
TestUtils.saveDrugOrder(TestUtils.getPatient(8), stavudine, TestUtils.date(2012, 1, 10), null);
TestUtils.saveEncounter(TestUtils.getPatient(8), hivConsult, TestUtils.date(2012, 1, 20));
CohortDefinition cd = moh731Cohorts.revisitsArt();
context.addParameterValue("fromDate", PERIOD_START);
context.addParameterValue("toDate", PERIOD_END);
EvaluatedCohort evaluated =
Context.getService(CohortDefinitionService.class).evaluate(cd, context);
ReportingTestUtils.assertCohortEquals(Arrays.asList(7), evaluated);
}
/** @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;
}
/**
* @see
* org.openmrs.module.reporting.definition.service.DefinitionService#evaluate(org.openmrs.module.reporting.evaluation.Definition,
* org.openmrs.module.reporting.evaluation.EvaluationContext)
* @should evaluate a Appointment data definition
*/
@Transactional(readOnly = true)
public EvaluatedAppointmentData evaluate(
AppointmentDataDefinition definition, EvaluationContext context) throws EvaluationException {
if (context.getBaseCohort() != null && context.getBaseCohort().isEmpty()) {
return new EvaluatedAppointmentData(definition, context);
}
return (EvaluatedAppointmentData) super.evaluate(definition, context);
}
/**
* @see CohortDefinitionEvaluator#evaluateCohort(CohortDefinition, EvaluationContext)
* @should support integer parameter
* @should support string parameter
* @should support patient parameter
* @should support integer list parameter
* @should support patient list parameter
* @should support cohort parameter
* @should support date parameter
* @should should protect SQL Query Against database modifications
*/
public EvaluatedCohort evaluate(CohortDefinition cohortDefinition, EvaluationContext context) {
SqlCohortDefinition sqlCohortDefinition = (SqlCohortDefinition) cohortDefinition;
CohortQueryService cqs = Context.getService(CohortQueryService.class);
String sql = SqlScriptParser.parse(new StringReader(sqlCohortDefinition.getQuery()))[0];
Cohort c = cqs.executeSqlQuery(sql, context.getParameterValues());
if (context.getBaseCohort() != null) {
c = Cohort.intersect(c, context.getBaseCohort());
}
return new EvaluatedCohort(c, cohortDefinition, context);
}
@Override
public EncounterQueryResult evaluate(EncounterQuery definition, EvaluationContext context)
throws EvaluationException {
context = ObjectUtil.nvl(context, new EvaluationContext());
BasicEncounterQuery query = (BasicEncounterQuery) definition;
EncounterQueryResult result = new EncounterQueryResult(query, context);
if (context.getBaseCohort() != null && context.getBaseCohort().isEmpty()) {
return result;
}
if (context instanceof EncounterEvaluationContext) {
EncounterIdSet baseEncounters = ((EncounterEvaluationContext) context).getBaseEncounters();
if (baseEncounters != null && baseEncounters.getMemberIds().isEmpty()) {
return result;
}
}
HqlQueryBuilder q = new HqlQueryBuilder();
q.select("e.encounterId");
q.from(Encounter.class, "e");
q.whereIn("e.encounterType", query.getEncounterTypes());
q.whereIn("e.form", query.getForms());
q.whereGreaterOrEqualTo("e.encounterDatetime", query.getOnOrAfter());
q.whereLessOrEqualTo("e.encounterDatetime", query.getOnOrBefore());
q.whereIn("e.location", query.getLocationList());
q.whereEncounterIn("e.encounterId", context);
if (query.getWhich() == null || query.getWhich() == TimeQualifier.ANY) {
List<Integer> results = evaluationService.evaluateToList(q, Integer.class);
result.getMemberIds().addAll(results);
} else {
q.innerJoin("e.patient", "p");
q.select("p.patientId");
if (query.getWhich() == TimeQualifier.LAST) {
q.orderDesc("e.encounterDatetime");
} else {
q.orderAsc("e.encounterDatetime");
}
ListMap<Integer, Integer> foundEncountersForPatients = new ListMap<Integer, Integer>();
int maxNumPerPatient = ObjectUtil.nvl(query.getWhichNumber(), 1);
for (Object[] row : evaluationService.evaluateToList(q)) {
Integer encounterId = (Integer) row[0];
Integer patientId = (Integer) row[1];
foundEncountersForPatients.putInList(patientId, encounterId);
if (foundEncountersForPatients.get(patientId).size() <= maxNumPerPatient) {
result.add(encounterId);
}
}
}
return result;
}
@Override
public EvaluatedPersonData evaluate(PersonDataDefinition definition, EvaluationContext context)
throws EvaluationException {
FirstEncounterAtFacilityDataDefinition def =
(FirstEncounterAtFacilityDataDefinition) definition;
EvaluatedPersonData c = new EvaluatedPersonData(def, context);
if (context.getBaseCohort() == null || context.getBaseCohort().isEmpty()) {
return c;
}
// find the facility number
MOHFacility facility = (MOHFacility) context.getParameterValue("facility");
// fail quickly if the facility does not exist
if (facility == null) {
log.warn("No facility provided; returning empty data.");
return c;
}
// use HQL to do our bidding
String hql =
"from Encounter"
+ " where voided=false"
+ " and patientId in (:patientIds)"
+ " and location in (:locationList)"
+ " and encounterDatetime <= :onOrBefore"
+ " order by encounterDatetime asc";
Map<String, Object> m = new HashMap<String, Object>();
m.put("patientIds", context.getBaseCohort());
m.put("locationList", facility.getLocations());
m.put("onOrBefore", context.getEvaluationDate());
DataSetQueryService qs = Context.getService(DataSetQueryService.class);
List<Object> queryResult = qs.executeHqlQuery(hql, m);
ListMap<Integer, Encounter> encForPatients = new ListMap<Integer, Encounter>();
for (Object o : queryResult) {
Encounter enc = (Encounter) o;
encForPatients.putInList(enc.getPatientId(), enc);
}
for (Integer pId : encForPatients.keySet()) {
List<Encounter> l = encForPatients.get(pId);
c.addData(pId, l.get(0));
}
return c;
}
/** @see Moh731CohortLibrary#currentlyInCare() */
@Test
public void currentlyInCare() throws Exception {
EncounterType triage = MetadataUtils.getEncounterType(CommonMetadata._EncounterType.TRIAGE);
EncounterType hivConsult =
MetadataUtils.getEncounterType(HivMetadata._EncounterType.HIV_CONSULTATION);
// Give patient #2 irrelevant encounter during 90 day window
TestUtils.saveEncounter(TestUtils.getPatient(2), triage, TestUtils.date(2012, 6, 15));
// Give patient #6 relevant encounter before and after 90 day window
TestUtils.saveEncounter(TestUtils.getPatient(6), hivConsult, TestUtils.date(2012, 3, 31));
TestUtils.saveEncounter(TestUtils.getPatient(6), hivConsult, TestUtils.date(2012, 7, 1));
// Give patient #7 relevant encounter at start of 90 day window
TestUtils.saveEncounter(TestUtils.getPatient(7), hivConsult, TestUtils.date(2012, 4, 1));
// Give patient #8 relevant encounter at end of 90 day window
TestUtils.saveEncounter(TestUtils.getPatient(8), hivConsult, TestUtils.date(2012, 6, 30));
CohortDefinition cd = moh731Cohorts.currentlyInCare();
context.addParameterValue("onDate", PERIOD_END);
EvaluatedCohort evaluated =
Context.getService(CohortDefinitionService.class).evaluate(cd, context);
ReportingTestUtils.assertCohortEquals(Arrays.asList(7, 8), evaluated);
}
/**
* @should start on PCP_PROPHYLAXIS_STARTED with not null answer
* @should not start on PCP_PROPHYLAXIS_STARTED with null answer
* @should stop on REASON_PCP_PROPHYLAXIS_STOPPED with not null answer
* @should not stop on REASON_PCP_PROPHYLAXIS_STOPPED with null answer
* @should start on CURRENT_MEDICATIONS equal to TRIMETHOPRIM_AND_SULFAMETHOXAZOLE
* @should not start on CURRENT_MEDICATIONS equal to something other than
* TRIMETHOPRIM_AND_SULFAMETHOXAZOLE
* @should start on PATIENT_REPORTED_CURRENT_PCP_PROPHYLAXIS equal to
* TRIMETHOPRIM_AND_SULFAMETHOXAZOLE
* @should not start on PATIENT_REPORTED_CURRENT_PCP_PROPHYLAXIS equal to something other than
* TRIMETHOPRIM_AND_SULFAMETHOXAZOLE
*/
@Override
public EvaluatedPersonData evaluate(
final PersonDataDefinition definition, final EvaluationContext context)
throws EvaluationException {
EvaluatedPersonData data = new EvaluatedPersonData(definition, context);
if (context.getBaseCohort().isEmpty()) return data;
Map<String, Object> m = new HashMap<String, Object>();
m.put("personIds", context.getBaseCohort());
String sql =
"select person_id, obs_datetime"
+ " from obs"
+ " where"
+ " person_id in (:personIds)"
+ " and ("
+ " (concept_id = 1263 and value_coded is not null) "
+ " or (concept_id in (1193, 1109) and value_coded = 916) "
+ " )"
+ " and voided = 0";
ListMap<Integer, Date> mappedStartDates = makeDatesMapFromSQL(sql, m);
sql =
"select person_id, obs_datetime"
+ " from obs"
+ " where"
+ " person_id in (:personIds)"
+ " and ("
+ " (concept_id in (1262, 1925) and value_coded is not null) "
+ " or (concept_id = 1261 and value_coded = 1260) "
+ " )"
+ " and voided = 0";
ListMap<Integer, Date> mappedStopDates = makeDatesMapFromSQL(sql, m);
for (Integer memberId : context.getBaseCohort().getMemberIds()) {
Set<Date> stopDates = safeFind(mappedStopDates, memberId);
Set<Date> startDates = safeFind(mappedStartDates, memberId);
String rangeInformation =
buildRangeInformation(startDates, stopDates, context.getEvaluationDate());
data.addData(memberId, rangeInformation);
}
return data;
}
@Override
protected Map<String, Object> getSubstitutions(EvaluationContext context) {
Map<String, Object> m = new HashMap<String, Object>();
m.put("encounterTypeIds", Arrays.asList(1, 2, 3, 4, 13));
m.put("onOrBefore", context.getEvaluationDate());
return m;
}
@Override
public EncounterQueryResult evaluate(EncounterQuery definition, EvaluationContext context)
throws EvaluationException {
context = ObjectUtil.nvl(context, new EvaluationContext());
BasicEncounterQuery query = (BasicEncounterQuery) definition;
EncounterQueryResult result = new EncounterQueryResult(query, context);
Criteria criteria = sessionFactory.getCurrentSession().createCriteria(Encounter.class);
criteria.setProjection(Projections.id());
criteria.add(Restrictions.eq("voided", false));
if (query.getOnOrAfter() != null) {
criteria.add(Restrictions.ge("encounterDatetime", query.getOnOrAfter()));
}
if (query.getOnOrBefore() != null) {
criteria.add(
Restrictions.le(
"encounterDatetime", DateUtil.getEndOfDayIfTimeExcluded(query.getOnOrBefore())));
}
if (context.getBaseCohort() != null) {
if (context.getBaseCohort().size() == 0) {
return result;
} else {
criteria.add(Restrictions.in("patient.id", context.getBaseCohort().getMemberIds()));
}
}
if (context instanceof EncounterEvaluationContext) {
EncounterIdSet baseEncounters = ((EncounterEvaluationContext) context).getBaseEncounters();
if (baseEncounters != null) {
if (baseEncounters.getSize() == 0) {
return result;
} else {
criteria.add(Restrictions.in("id", baseEncounters.getMemberIds()));
}
}
}
for (Integer encounterId : ((List<Integer>) criteria.list())) {
result.add(encounterId);
}
return result;
}
/**
* @see PersonDataEvaluator#evaluate(PersonDataDefinition, EvaluationContext)
* @should return the most preferred name for each person in the passed context
* @should return empty result set for an empty base cohort
* @should return the preferred name for all persons
*/
public EvaluatedPersonData evaluate(PersonDataDefinition definition, EvaluationContext context)
throws EvaluationException {
EvaluatedPersonData c = new EvaluatedPersonData(definition, context);
if (context.getBaseCohort() != null && context.getBaseCohort().isEmpty()) {
return c;
}
HqlQueryBuilder q = new HqlQueryBuilder();
q.select("pn.person.personId", "pn");
q.from(PersonName.class, "pn");
q.wherePersonIn("pn.person.personId", context);
q.orderAsc("pn.preferred");
Map<Integer, Object> data = evaluationService.evaluateToMap(q, Integer.class, Object.class);
c.setData(data);
return c;
}
/**
* @see DataSetEvaluator#evaluate(DataSetDefinition, EvaluationContext)
* @should evaluate an EncounterAndObsDataSetDefinition
*/
public DataSet evaluate(DataSetDefinition dataSetDefinition, EvaluationContext context)
throws EvaluationException {
EncounterAndObsDataSetDefinition definition =
(EncounterAndObsDataSetDefinition) dataSetDefinition;
SimpleDataSet dataSet = new SimpleDataSet(dataSetDefinition, context);
context = ObjectUtil.nvl(context, new EvaluationContext());
Cohort cohort = context.getBaseCohort();
if (context.getLimit() != null) {
CohortUtil.limitCohort(cohort, context.getLimit());
}
// Retrieve the rows for the dataset
BasicEncounterQuery encounterQuery = new BasicEncounterQuery();
encounterQuery.setWhich(definition.getWhichEncounterQualifier());
encounterQuery.setWhichNumber(definition.getQuantity());
encounterQuery.setEncounterTypes(definition.getEncounterTypes());
encounterQuery.setForms(definition.getForms());
encounterQuery.setOnOrBefore(definition.getEncounterDatetimeOnOrBefore());
encounterQuery.setOnOrAfter(definition.getEncounterDatetimeOnOrAfter());
EncounterQueryResult encounterIdRows = encounterQueryService.evaluate(encounterQuery, context);
HqlQueryBuilder q = new HqlQueryBuilder();
EncounterEvaluationContext eec = new EncounterEvaluationContext();
eec.setBaseEncounters(encounterIdRows);
q.from(Encounter.class, "e").whereEncounterIn("e.encounterId", eec);
List<Encounter> encounters = evaluationService.evaluateToList(q, Encounter.class);
// Determine what columns to display in the dataset
List<EncounterAndObsDataSetDefinition.ObsOptionalColumn> optionalColumns =
definition.getOptionalColumns();
List<PatientIdentifierType> patientIdentifierTypes = definition.getPatientIdentifierTypes();
List<EncounterAndObsDataSetDefinition.ColumnDisplayFormat> columnDisplayFormat =
definition.getColumnDisplayFormat();
Integer maxColumnHeaderWidth = definition.getMaxColumnHeaderWidth();
if (patientIdentifierTypes == null) {
patientIdentifierTypes = new ArrayList<PatientIdentifierType>();
}
if (columnDisplayFormat == null) {
columnDisplayFormat = new ArrayList<ColumnDisplayFormat>();
}
if (columnDisplayFormat.size() == 0) {
columnDisplayFormat.add(EncounterAndObsDataSetDefinition.ColumnDisplayFormat.ID);
}
// section index should be added here
// Store all encounters within a data structure that keeps track of obs, obs groups, and their
// occurrences
// in order that column headers are unique and children obs are grouped by their parent
Map<Encounter, Map<ObsColumnDescriptor, Obs>> populatedFieldMap = populateFieldMap(encounters);
// Keeps track of the column headers for all obs-related columns
Set<ObsColumnDescriptor> allColumns = new TreeSet<ObsColumnDescriptor>();
for (Encounter encounter : encounters) {
Map<ObsColumnDescriptor, Obs> obsInEncounter = populatedFieldMap.get(encounter);
// Not all encounters will have data for all columns but
// each encounter row should have all column headers
// so encounters line up properly under a common set of column headers
allColumns.addAll(obsInEncounter.keySet());
}
// add the data to the DataSet
return addData(
dataSet,
encounters,
patientIdentifierTypes,
optionalColumns,
columnDisplayFormat,
maxColumnHeaderWidth,
allColumns,
populatedFieldMap);
}
@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;
}
public PatientDataResult calculateResult(
List<PatientDataResult> results, EvaluationContext context) {
PatientAttributeResult alert = new PatientAttributeResult(null, null);
ProgramWorkflowState state = (ProgramWorkflowState) context.getParameterValue("state");
StringBuffer alerts = new StringBuffer();
double height = 0;
double weight = 0;
for (PatientDataResult result : results) {
if (result.getName().equals("CD4Test")) {
AllObservationValuesResult cd4 = (AllObservationValuesResult) result;
if (cd4.getValue() != null) {
int decline = calculateDecline(cd4.getValue());
if (decline > 50
&& (state.toString().contains("GROUP") || state.toString().contains("FOLLOWING"))) {
alerts.append("CD4 decline(");
alerts.append(decline);
alerts.append(").\n");
}
Obs lastCd4 = null;
if (cd4.getValue().size() > 0) {
lastCd4 = cd4.getValue().get(cd4.getValue().size() - 1);
}
if (lastCd4 == null) {
alerts.append("No CD4 recorded.\n");
} else {
Date dateCd4 = lastCd4.getObsDatetime();
Date date = Calendar.getInstance().getTime();
int diff = calculateMonthsDifference(date, dateCd4);
if (diff > 12) {
alerts.append("Very late CD4(" + diff + " months ago).\n");
} else if ((diff > 6) && state.toString().contains("FOLLOWING")) {
alerts.append("Late CD4(" + diff + " months ago).\n");
}
if (state.toString().contains("FOLLOWING")
&& lastCd4.getValueNumeric() != null
&& lastCd4.getValueNumeric() < 500) {
alerts.append("Eligible for Treatment.\n");
}
}
}
}
if (result.getName().equals("viralLoadTest")) {
AllObservationValuesResult viraload = (AllObservationValuesResult) result;
if (viraload.getValue() != null) {
Obs lastviraload = null;
if (viraload.getValue().size() > 0) {
lastviraload = viraload.getValue().get(viraload.getValue().size() - 1);
}
if (state.toString().contains("GROUP") && (lastviraload == null)) {
alerts.append("No VL recorded.\n");
} else {
try {
Date dateVl = lastviraload.getObsDatetime();
Date date = Calendar.getInstance().getTime();
int diff = calculateMonthsDifference(date, dateVl);
if (state.toString().contains("GROUP")) {
if (diff > 12) {
alerts.append("Late VL(" + diff + " months ago).\n");
}
if (lastviraload.getValueNumeric() != null
&& lastviraload.getValueNumeric() > 1000) {
alerts.append("VL Failure " + lastviraload.getValueNumeric() + ".\n");
}
}
} catch (Exception e) {
}
}
}
}
if (result.getName().equals("weightObs")) {
AllObservationValuesResult wt = (AllObservationValuesResult) result;
if (wt.getValue() != null) {
int decline = calculatePercentageDecline(wt.getValue());
if (decline > 5) {
alerts.append("WT decline(");
alerts.append(decline);
alerts.append("%, ");
int kilosLost = calculateDecline(wt.getValue());
alerts.append(kilosLost);
alerts.append("kg)\n");
}
if (wt.getValue().size() > 0) {
weight = wt.getValue().get(wt.getValue().size() - 1).getValueNumeric();
}
}
if (wt.getValue() == null || wt.getValue().size() == 0) {
alerts.append("No weight recorded.\n");
}
}
if (result.getName().equals("RecentHeight")) {
ObservationResult heightOb = (ObservationResult) result;
if (heightOb.getValue() == null || heightOb.getValue().trim().length() == 0) {
alerts.append("No height recorded.\n");
} else {
height = Double.parseDouble(heightOb.getValue());
}
}
if (result.getName().equals("lastEncInMonth")) {
DateValueResult encinmonths = (DateValueResult) result;
if (encinmonths.getValue() != null) {
Date dateVl = encinmonths.getDateOfObservation();
Date date = Calendar.getInstance().getTime();
int diff = calculateMonthsDifference(date, dateVl);
if (diff > 12) {
alerts.append("LTFU determine status.\n");
}
}
}
if (result.getName().equals("IO") && result.getValue() != null) {
alerts.append("OI reported last visit: " + result.getValue() + "\n");
}
if (result.getName().equals("SideEffects") && result.getValue() != null) {
alerts.append("Side effects reported last visit: " + result.getValue() + "\n");
}
}
if (height > 0 && weight > 0) {
double bmi = weight / (height / 100 * height / 100);
int decimalPlace = 1;
BigDecimal bd = new BigDecimal(Double.toString(bmi));
bd = bd.setScale(decimalPlace, BigDecimal.ROUND_HALF_UP);
if (bmi < 16) {
alerts.append("Very low BMI (" + bd.doubleValue() + ").\n");
} else if (bmi < 18.5) {
alerts.append("Low BMI (" + bd.doubleValue() + ").\n");
}
}
alert.setValue(alerts.toString().trim());
return alert;
}