/** @should return person data for each obs in the passed context */
@Override
public EvaluatedObsData evaluate(ObsDataDefinition definition, EvaluationContext context)
throws EvaluationException {
EvaluatedObsData c = new EvaluatedObsData(definition, context);
// create a map of obs ids -> patient ids
HqlQueryBuilder q = new HqlQueryBuilder();
q.select("o.obsId", "o.personId");
q.from(Obs.class, "o");
q.whereObsIn("o.obsId", context);
Map<Integer, Integer> convertedIds =
evaluationService.evaluateToMap(q, Integer.class, Integer.class, context);
if (!convertedIds.keySet().isEmpty()) {
// create a new (person) evaluation context using the retrieved ids
PersonEvaluationContext personEvaluationContext = new PersonEvaluationContext();
personEvaluationContext.setBasePersons(
new PersonIdSet(new HashSet<Integer>(convertedIds.values())));
// evaluate the joined definition via this person context
PersonToObsDataDefinition def = (PersonToObsDataDefinition) definition;
EvaluatedPersonData pd =
Context.getService(PersonDataService.class)
.evaluate(def.getJoinedDefinition(), personEvaluationContext);
// now create the result set by mapping the results in the person data set to obs ids
for (Integer obsId : convertedIds.keySet()) {
c.addData(obsId, pd.getData().get(convertedIds.get(obsId)));
}
}
return c;
}
/**
* @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 CohortDefinitionEvaluator#evaluate(CohortDefinition, EvaluationContext)
* @should return patients in the specified states before the start date
* @should return patients in the specified states after the start date
* @should return patients in the specified states before the end date
* @should return patients in the specified states after the end date
* @should find patients in specified states on the before start date if passed in time is at
* midnight
* @should find patients in specified states on the before end date if passed in time is at
* midnight
*/
public EvaluatedCohort evaluate(CohortDefinition cohortDefinition, EvaluationContext context) {
PatientStateCohortDefinition def = (PatientStateCohortDefinition) cohortDefinition;
HqlQueryBuilder qb = new HqlQueryBuilder();
qb.select("ps.patientProgram.patient.patientId");
qb.from(PatientState.class, "ps");
qb.whereIn("ps.state", def.getStates());
qb.whereGreaterOrEqualTo("ps.startDate", def.getStartedOnOrAfter());
qb.whereLessOrEqualTo("ps.startDate", def.getStartedOnOrBefore());
qb.whereGreaterOrEqualTo("ps.endDate", def.getEndedOnOrAfter());
qb.whereLessOrEqualTo("ps.endDate", def.getEndedOnOrBefore());
qb.whereIn("ps.patientProgram.location", def.getLocationList());
qb.wherePatientIn("ps.patientProgram.patient.patientId", context);
List<Integer> pIds = evaluationService.evaluateToList(qb, Integer.class, context);
return new EvaluatedCohort(new Cohort(pIds), cohortDefinition, context);
}
/**
* @see PersonDataEvaluator#evaluate(PersonDataDefinition, EvaluationContext)
* @should return the vital status by person
*/
public EvaluatedPersonData evaluate(PersonDataDefinition definition, EvaluationContext context)
throws EvaluationException {
EvaluatedPersonData c = new EvaluatedPersonData(definition, context);
HqlQueryBuilder q = new HqlQueryBuilder();
q.select("p.personId", "p.dead", "p.deathDate", "cod");
q.from(Person.class, "p");
q.leftOuterJoin("p.causeOfDeath", "cod");
q.wherePersonIn("p.personId", context);
List<Object[]> results = evaluationService.evaluateToList(q, context);
for (Object[] row : results) {
Integer pId = (Integer) row[0];
boolean dead = (row[1] == Boolean.TRUE);
Date deathDate = (dead ? (Date) row[2] : null);
Concept causeOfDeath = (dead ? (Concept) row[3] : null);
c.addData(pId, new VitalStatus(dead, deathDate, causeOfDeath));
}
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);
}
@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;
}
