/** @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);
}
@Test
public void evaluate_shouldReturnHivPatientsNotScreenedForTb() throws Exception {
// Get HIV Program and TB screening encounter type
Program hivProgram = MetadataUtils.getProgram(Metadata.HIV_PROGRAM);
EncounterType screeningEncType =
MetadataUtils.getEncounterType(Metadata.TB_SCREENING_ENCOUNTER_TYPE);
// Enroll patients #6 and #7
PatientService ps = Context.getPatientService();
TestUtils.enrollInProgram(ps.getPatient(6), hivProgram, TestUtils.date(2011, 1, 1));
TestUtils.enrollInProgram(ps.getPatient(7), hivProgram, TestUtils.date(2011, 1, 1));
// Screen patient #6 for TB a year later
TestUtils.saveEncounter(ps.getPatient(6), screeningEncType, TestUtils.date(2012, 1, 1));
Context.flushSession();
List<Integer> cohort = Arrays.asList(6, 7, 8);
CalculationResultMap resultMap =
Context.getService(PatientCalculationService.class)
.evaluate(cohort, new NeverScreenedForTbCalculation());
Assert.assertFalse((Boolean) resultMap.get(6).getValue());
Assert.assertTrue((Boolean) resultMap.get(7).getValue());
Assert.assertNull(resultMap.get(8)); // not in HIV program
}
@Test
public void test() throws Exception {
ReportDefinition rd = builder.build(report);
// Run report on all patients for June 2012
EvaluationContext context =
ReportingTestUtils.reportingContext(
Arrays.asList(2, 6, 7, 8, 999),
TestUtils.date(2012, 6, 1),
TestUtils.date(2012, 6, 30));
ReportData data = Context.getService(ReportDefinitionService.class).evaluate(rd, context);
// ReportingTestUtils.printReport(data);
Assert.assertThat(data.getDataSets().size(), is(1));
// Check that report definition can be serialized/de-serialized
Context.getService(ReportDefinitionService.class).saveDefinition(rd);
Context.getService(ReportDefinitionService.class).getDefinition(rd.getId());
}
/** @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);
}
/** Setup each test */
@Before
public void setup() throws Exception {
commonMetadata.install();
VisitType outpatient = MetadataUtils.getVisitType(CommonMetadata._VisitType.OUTPATIENT);
// Patient #7 has two visits on 1-Jan-2012 (from 9am to 10am and another from 11am to 12pm)
TestUtils.saveVisit(
TestUtils.getPatient(7),
outpatient,
TestUtils.date(2012, 1, 1, 9, 0, 0),
TestUtils.date(2012, 1, 1, 10, 0, 0));
TestUtils.saveVisit(
TestUtils.getPatient(7),
outpatient,
TestUtils.date(2012, 1, 1, 11, 0, 0),
TestUtils.date(2012, 1, 1, 12, 0, 0));
// Patient #8 has visit on 2-Jan-2012
TestUtils.saveVisit(
TestUtils.getPatient(8),
outpatient,
TestUtils.date(2012, 1, 2, 9, 0, 0),
TestUtils.date(2012, 1, 2, 10, 0, 0));
}
/**
* @see
* org.openmrs.module.kenyaemr.calculation.library.hiv.MissedAppointmentsOrDefaultedCalculation#evaluate(java.util.Collection,
* java.util.Map, org.openmrs.calculation.patient.PatientCalculationContext)
* @verifies determine whether patients have a Missed appointments or defaulted
*/
@Test
public void evaluate_shouldDetermineWhetherPatientsWhoMissedAppointmentsOrDefaulted()
throws Exception {
// Get HIV Program
Program hivProgram = MetadataUtils.getProgram(Metadata.HIV_PROGRAM);
// Enroll patients #6, #7, #8 in the HIV Program
PatientService ps = Context.getPatientService();
for (int i = 6; i <= 8; ++i) {
TestUtils.enrollInProgram(ps.getPatient(i), hivProgram, TestUtils.date(2011, 1, 1));
}
// Give patient #7 a return visit obs of 10 days ago
Concept returnVisit = Context.getConceptService().getConcept(5096);
Calendar calendar = Calendar.getInstance();
calendar.add(Calendar.DATE, -10);
TestUtils.saveObs(
Context.getPatientService().getPatient(7),
returnVisit,
calendar.getTime(),
calendar.getTime());
// Give patient #8 a return visit obs of 10 days in the future
calendar = Calendar.getInstance();
calendar.add(Calendar.DATE, 10);
TestUtils.saveObs(
Context.getPatientService().getPatient(8),
returnVisit,
calendar.getTime(),
calendar.getTime());
Context.flushSession();
List<Integer> ptIds = Arrays.asList(6, 7, 8, 9);
CalculationResultMap resultMap =
new MissedAppointmentsOrDefaultedCalculation()
.evaluate(
ptIds,
null,
Context.getService(PatientCalculationService.class).createCalculationContext());
Assert.assertFalse(
(Boolean) resultMap.get(6).getValue()); // patient in HIV program but no return visit obs
Assert.assertTrue((Boolean) resultMap.get(7).getValue()); // patient has missed visit
Assert.assertFalse(
(Boolean) resultMap.get(8).getValue()); // patient has future return visit date
Assert.assertFalse((Boolean) resultMap.get(9).getValue()); // patient not in HIV Program
}
/** @see EmrVisitAssignmentHandler#checkLocations(org.openmrs.Visit, org.openmrs.Encounter) */
@Test
public void checkLocations() {
Patient patient = TestUtils.getPatient(7);
Form moh257 = MetadataUtils.getForm(HivMetadata._Form.MOH_257_VISIT_SUMMARY);
VisitType outpatient = MetadataUtils.getVisitType(CommonMetadata._VisitType.OUTPATIENT);
// Save regular visit on Jan 1st at no specific location
Visit visit0 = TestUtils.saveVisit(patient, outpatient, TestUtils.date(2012, 1, 1), null);
// Save regular visit on Jan 1st at location #2
Visit visit1 = TestUtils.saveVisit(patient, outpatient, TestUtils.date(2012, 1, 1), null);
visit1.setLocation(Context.getLocationService().getLocation(1));
// Save regular visit on Jan 1st at location #2
Visit visit2 = TestUtils.saveVisit(patient, outpatient, TestUtils.date(2012, 1, 1), null);
visit2.setLocation(Context.getLocationService().getLocation(2));
// Save MOH257 for that day (will default to location #1)
Encounter encounter = TestUtils.saveEncounter(patient, moh257, TestUtils.date(2012, 1, 1));
Assert.assertThat(EmrVisitAssignmentHandler.checkLocations(visit0, encounter), is(true));
Assert.assertThat(EmrVisitAssignmentHandler.checkLocations(visit1, encounter), is(true));
Assert.assertThat(EmrVisitAssignmentHandler.checkLocations(visit2, encounter), is(false));
}
@Test
public void evaluate_shouldReturnTrueForAllAlivePatients() {
// Mark patient #8 as deceased on 1st Jan 2012
TestUtils.getPatient(8).setDead(true);
TestUtils.getPatient(8).setDeathDate(TestUtils.date(2012, 1, 1));
List<Integer> ptIds = Arrays.asList(2, 6, 7, 8);
CalculationResultMap resultMap =
Context.getService(PatientCalculationService.class)
.evaluate(ptIds, new EligibleForTbProgramCalculation());
Assert.assertTrue((Boolean) resultMap.get(2).getValue());
Assert.assertTrue((Boolean) resultMap.get(6).getValue());
Assert.assertTrue((Boolean) resultMap.get(7).getValue());
Assert.assertFalse((Boolean) resultMap.get(8).getValue()); // Deceased
}
/**
* @see VisitsOnDayCalculation#evaluate(java.util.Collection, java.util.Map,
* org.openmrs.calculation.patient.PatientCalculationContext)
*/
@Test
public void evaluate_shouldFetchAllPatientVisitsOnDate() throws Exception {
List<Integer> ptIds = Arrays.asList(7, 8);
Map<String, Object> paramValues = new HashMap<String, Object>();
paramValues.put("date", TestUtils.date(2012, 1, 1));
CalculationResultMap resultMap =
new VisitsOnDayCalculation()
.evaluate(
ptIds,
paramValues,
Context.getService(PatientCalculationService.class).createCalculationContext());
Assert.assertThat(((ListResult) resultMap.get(7)).getValues().size(), is(2)); // Has two visit
Assert.assertThat(resultMap.get(8).isEmpty(), is(true)); // No visits on that day
}
/**
* @see EligibleForArtTriggerCalculation#evaluate(java.util.Collection, java.util.Map,
* org.openmrs.calculation.patient.PatientCalculationContext)
* @verifies calculate the obs which triggered a patient to become eligible for ART
* @verifies return null for patients who have never been eligible for ART
*/
@Test
public void evaluate_shouldCalculateEligibilityTrigger() throws Exception {
PatientService ps = Context.getPatientService();
// Confirm patient #6 HIV+ when they're 1 year old and give them very low CD4 soon after
TestUtils.saveObs(
ps.getPatient(6),
Dictionary.getConcept(Dictionary.DATE_OF_HIV_DIAGNOSIS),
TestUtils.date(2008, 05, 27),
TestUtils.date(2010, 1, 1));
TestUtils.saveObs(
ps.getPatient(6),
Dictionary.getConcept(Dictionary.CD4_COUNT),
300.0,
TestUtils.date(2009, 1, 1));
// Give patient #7 low CD4 when they're 3 years old and very low CD4 after
TestUtils.saveObs(
ps.getPatient(7),
Dictionary.getConcept(Dictionary.CD4_COUNT),
900.0,
TestUtils.date(1979, 8, 25));
TestUtils.saveObs(
ps.getPatient(7),
Dictionary.getConcept(Dictionary.CD4_COUNT),
300.0,
TestUtils.date(2009, 1, 1));
// Give patient #8 WHO stage of 3
TestUtils.saveObs(
ps.getPatient(8),
Dictionary.getConcept(Dictionary.CURRENT_WHO_STAGE),
Dictionary.getConcept(Dictionary.WHO_STAGE_3_PEDS),
TestUtils.date(2009, 1, 1));
Context.flushSession();
List<Integer> cohort = Arrays.asList(6, 7, 8, 999);
CalculationResultMap resultMap =
new EligibleForArtTriggerCalculation()
.evaluate(
cohort,
null,
Context.getService(PatientCalculationService.class).createCalculationContext());
Obs patient6Trigger = (Obs) resultMap.get(6).getValue(); // Eligible through HIV confirmation
Assert.assertEquals(Dictionary.DATE_OF_HIV_DIAGNOSIS, patient6Trigger.getConcept().getUuid());
Assert.assertEquals(TestUtils.date(2008, 05, 27), patient6Trigger.getValueDate());
Obs patient7Trigger = (Obs) resultMap.get(7).getValue(); // Eligible through CD4 count
Assert.assertEquals(Dictionary.CD4_COUNT, patient7Trigger.getConcept().getUuid());
Assert.assertEquals(TestUtils.date(1979, 8, 25), patient7Trigger.getObsDatetime());
Obs patient8Trigger = (Obs) resultMap.get(8).getValue(); // Eligible through WHO stage
Assert.assertEquals(Dictionary.CURRENT_WHO_STAGE, patient8Trigger.getConcept().getUuid());
Assert.assertEquals(TestUtils.date(2009, 1, 1), patient8Trigger.getObsDatetime());
Assert.assertNull(resultMap.get(999)); // Was never eligible for ART
}
/** Tests for {@link Moh731CohortLibrary} */
public class Moh731CohortLibraryTest extends BaseModuleContextSensitiveTest {
@Autowired private CommonMetadata commonMetadata;
@Autowired private HivMetadata hivMetadata;
@Autowired private Moh731CohortLibrary moh731Cohorts;
private EvaluationContext context;
private static final Date PERIOD_START = TestUtils.date(2012, 6, 1),
PERIOD_END = TestUtils.date(2012, 6, 30);
/** Setup each test */
@Before
public void setup() throws Exception {
executeDataSet("dataset/test-concepts.xml");
commonMetadata.install();
hivMetadata.install();
List<Integer> cohort = Arrays.asList(2, 6, 7, 8, 999);
context = ReportingTestUtils.reportingContext(cohort, PERIOD_START, PERIOD_END);
}
/** @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);
}
/** @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);
}
}