@DocumentedDefinition(value = "exclude test patients")
public CohortDefinition getExcludeTestPatients() {
PersonAttributeCohortDefinition personAttributeCohortDefinition =
new PersonAttributeCohortDefinition();
personAttributeCohortDefinition.setAttributeType(
emrApiProperties.getTestPatientPersonAttributeType());
// the method add value has a bug, using set values for now
personAttributeCohortDefinition.setValues(Arrays.asList("true"));
CompositionCohortDefinition excludeTestPatientsCohortDefinition =
new CompositionCohortDefinition();
excludeTestPatientsCohortDefinition.addSearch(
"test", map((CohortDefinition) personAttributeCohortDefinition, ""));
excludeTestPatientsCohortDefinition.setCompositionString("NOT test");
return excludeTestPatientsCohortDefinition;
}
/**
* Patients who were enrolled on the given programs (excluding transfers) between ${onOrAfter} and
* ${onOrBefore}
*
* @param programs the programs
* @return the cohort definition
*/
public CohortDefinition enrolledExcludingTransfers(Program... programs) {
CompositionCohortDefinition cd = new CompositionCohortDefinition();
cd.setName("enrolled excluding transfers in program between dates");
cd.addParameter(new Parameter("onOrAfter", "After Date", Date.class));
cd.addParameter(new Parameter("onOrBefore", "Before Date", Date.class));
cd.addSearch(
"enrolled",
ReportUtils.map(
enrolled(programs), "enrolledOnOrAfter=${onOrAfter},enrolledOnOrBefore=${onOrBefore}"));
cd.addSearch("transferIn", ReportUtils.map(transferredIn(), "onOrBefore=${onOrBefore}"));
cd.addSearch(
"completeProgram", ReportUtils.map(compltedProgram(), "completedOnOrBefore=${onOrBefore}"));
cd.setCompositionString("enrolled AND NOT (transferIn OR completeProgram)");
return cd;
}
/**
* Patients who were enrolled on the given programs (excluding transfers) on ${onOrBefore}
*
* @param programs the programs
* @return the cohort definition
*/
public CohortDefinition enrolledExcludingTransfersOnDate(Program... programs) {
CompositionCohortDefinition cd = new CompositionCohortDefinition();
cd.setName("enrolled excluding transfers in program on date in this facility");
cd.addParameter(new Parameter("onOrBefore", "Before Date", Date.class));
cd.addSearch(
"enrolled", ReportUtils.map(enrolled(programs), "enrolledOnOrBefore=${onOrBefore}"));
cd.addSearch("transferIn", ReportUtils.map(transferredIn(), "onOrBefore=${onOrBefore}"));
cd.setCompositionString("enrolled AND NOT transferIn");
return cd;
}
/**
* Patients who are female and at least 18 years old on ${effectiveDate}
*
* @return the cohort definition
*/
public CohortDefinition femalesAgedAtLeast18() {
CompositionCohortDefinition cd = new CompositionCohortDefinition();
cd.setName("females aged at least 18");
cd.addParameter(new Parameter("effectiveDate", "Effective Date", Date.class));
cd.addSearch("females", ReportUtils.map(females()));
cd.addSearch(
"agedAtLeast18", ReportUtils.map(agedAtLeast(18), "effectiveDate=${effectiveDate}"));
cd.setCompositionString("females AND agedAtLeast18");
return cd;
}
public EvaluatedCohort evaluate(
final CohortDefinition cohortDefinition, final EvaluationContext evaluationContext)
throws EvaluationException {
MohCohortDefinition mohCohortDefinition = (MohCohortDefinition) cohortDefinition;
EncounterService service = Context.getEncounterService();
ConceptService conceptService = Context.getConceptService();
CohortDefinitionService definitionService = Context.getService(CohortDefinitionService.class);
// limit to people with adult initial or return encounters
EncounterCohortDefinition encounterCohortDefinition = new EncounterCohortDefinition();
encounterCohortDefinition.addEncounterType(
service.getEncounterType(ENCOUNTER_TYPE_ADULT_INITIAL));
encounterCohortDefinition.addEncounterType(
service.getEncounterType(ENCOUNTER_TYPE_ADULT_RETURN));
encounterCohortDefinition.setLocationList(mohCohortDefinition.getLocationList());
// find people who had adult encounters at this location
Cohort encounterCohort =
definitionService.evaluate(encounterCohortDefinition, evaluationContext);
// TODO set these with GPs and a settings page
Concept firstRapidConcept = conceptService.getConcept(FIRST_HIV_RAPID_TEST_QUALITATIVE_CONCEPT);
Concept secondRapidConcept =
conceptService.getConcept(SECOND_HIV_RAPID_TEST_QUALITATIVE_CONCEPT);
Concept positiveConcept = conceptService.getConcept(POSITIVE_CONCEPT);
// define search for all people who have rapid test positive results
CodedObsCohortDefinition firstRapidCohortDefinition = new CodedObsCohortDefinition();
firstRapidCohortDefinition.setTimeModifier(PatientSetService.TimeModifier.ANY);
firstRapidCohortDefinition.setLocationList(mohCohortDefinition.getLocationList());
firstRapidCohortDefinition.setQuestion(firstRapidConcept);
firstRapidCohortDefinition.setOperator(SetComparator.IN);
firstRapidCohortDefinition.setValueList(Arrays.asList(positiveConcept));
// define search all people who have rapid test 2 positive results
CodedObsCohortDefinition secondRapidCohortDefinition = new CodedObsCohortDefinition();
secondRapidCohortDefinition.setTimeModifier(PatientSetService.TimeModifier.ANY);
secondRapidCohortDefinition.setLocationList(mohCohortDefinition.getLocationList());
secondRapidCohortDefinition.setQuestion(secondRapidConcept);
secondRapidCohortDefinition.setOperator(SetComparator.IN);
secondRapidCohortDefinition.setValueList(Arrays.asList(positiveConcept));
// combine rapid test definitions
CompositionCohortDefinition rapidCompositionCohortDefinition =
new CompositionCohortDefinition();
rapidCompositionCohortDefinition.addSearch(
"PositiveFirstRapid", firstRapidCohortDefinition, null);
rapidCompositionCohortDefinition.addSearch(
"PositiveSecondRapid", secondRapidCohortDefinition, null);
rapidCompositionCohortDefinition.setCompositionString(
"PositiveFirstRapid OR PositiveSecondRapid");
Cohort rapidCompositionCohort =
definitionService.evaluate(rapidCompositionCohortDefinition, evaluationContext);
// set age limits
AgeCohortDefinition ageCohortDefinition = new AgeCohortDefinition();
ageCohortDefinition.setMinAge(18);
ageCohortDefinition.setMinAgeUnit(DurationUnit.MONTHS);
ageCohortDefinition.setMaxAge(14);
ageCohortDefinition.setMaxAgeUnit(DurationUnit.YEARS);
// TODO set this concept with a GP and settings page
Concept elisaConcept = conceptService.getConcept(HIV_ENZYME_IMMUNOASSAY_QUALITATIVE_CONCEPT);
// define search for all people with a positive elisa evaluation
CodedObsCohortDefinition elisaCohortDefinition = new CodedObsCohortDefinition();
elisaCohortDefinition.setTimeModifier(PatientSetService.TimeModifier.ANY);
elisaCohortDefinition.setLocationList(mohCohortDefinition.getLocationList());
elisaCohortDefinition.setQuestion(elisaConcept);
elisaCohortDefinition.setOperator(SetComparator.IN);
elisaCohortDefinition.setValueList(Arrays.asList(positiveConcept));
// find patients within age limits who had elisa positive results
CompositionCohortDefinition elisaCompositionCohortDefinition =
new CompositionCohortDefinition();
elisaCompositionCohortDefinition.addSearch("PaediatricAge", ageCohortDefinition, null);
elisaCompositionCohortDefinition.addSearch("PositiveElisa", elisaCohortDefinition, null);
elisaCompositionCohortDefinition.setCompositionString("PaediatricAge AND PositiveElisa");
Cohort elisaCompositionCohort =
definitionService.evaluate(elisaCompositionCohortDefinition, evaluationContext);
// Check for the elisa to make sure the elisa happened after 18 months
PersonAttributeCohortDefinition personAttributeCohortDefinition =
new PersonAttributeCohortDefinition();
personAttributeCohortDefinition.setAttributeType(
Context.getPersonService().getPersonAttributeTypeByName("Health Center"));
personAttributeCohortDefinition.setValueLocations(mohCohortDefinition.getLocationList());
// TODO use GPs and a settings page to configure these concepts
Concept transferConcept = conceptService.getConcept("TRANSFER CARE TO OTHER CENTER");
Concept withinConcept = conceptService.getConcept("AMPATH");
Concept missedVisitConcept = conceptService.getConcept("REASON FOR MISSED VISIT");
Concept transferVisitConcept = conceptService.getConcept("AMPATH CLINIC TRANSFER");
// define transfer specifications
CodedObsCohortDefinition transferCohortDefinition = new CodedObsCohortDefinition();
transferCohortDefinition.setTimeModifier(PatientSetService.TimeModifier.ANY);
transferCohortDefinition.setLocationList(mohCohortDefinition.getLocationList());
transferCohortDefinition.setQuestion(transferConcept);
transferCohortDefinition.setOperator(SetComparator.IN);
transferCohortDefinition.setValueList(Arrays.asList(withinConcept));
// find all people with proper health center location and a transfer
CompositionCohortDefinition transferCompositionCohortDefinition =
new CompositionCohortDefinition();
transferCompositionCohortDefinition.addSearch(
"HealthCenterAttribute", personAttributeCohortDefinition, null);
transferCompositionCohortDefinition.addSearch(
"TransferWithinAmpath", transferCohortDefinition, null);
transferCompositionCohortDefinition.setCompositionString(
"HealthCenterAttribute AND TransferWithinAmpath");
Cohort transferCompositionCohort =
definitionService.evaluate(transferCompositionCohortDefinition, evaluationContext);
// define missed visits at this location
CodedObsCohortDefinition missedVisitCohortDefinition = new CodedObsCohortDefinition();
missedVisitCohortDefinition.setTimeModifier(PatientSetService.TimeModifier.ANY);
missedVisitCohortDefinition.setLocationList(mohCohortDefinition.getLocationList());
missedVisitCohortDefinition.setQuestion(missedVisitConcept);
missedVisitCohortDefinition.setOperator(SetComparator.IN);
missedVisitCohortDefinition.setValueList(Arrays.asList(transferVisitConcept));
// find all people with defined health center and a missed visit
CompositionCohortDefinition missedVisitCompositionCohortDefinition =
new CompositionCohortDefinition();
missedVisitCompositionCohortDefinition.addSearch(
"HealthCenterAttribute", personAttributeCohortDefinition, null);
missedVisitCompositionCohortDefinition.addSearch(
"MissedVisitTransfer", missedVisitCohortDefinition, null);
missedVisitCompositionCohortDefinition.setCompositionString(
"HealthCenterAttribute AND MissedVisitTransfer");
Cohort missedVisitCompositionCohort =
definitionService.evaluate(missedVisitCompositionCohortDefinition, evaluationContext);
// build the patientIds by combining all found patients
Set<Integer> patientIds = new HashSet<Integer>();
patientIds.addAll(encounterCohort.getMemberIds());
patientIds.addAll(rapidCompositionCohort.getMemberIds());
patientIds.addAll(elisaCompositionCohort.getMemberIds());
patientIds.addAll(transferCompositionCohort.getMemberIds());
patientIds.addAll(missedVisitCompositionCohort.getMemberIds());
// find fake patients
PersonAttributeCohortDefinition fakePatientCohortDefinition =
new PersonAttributeCohortDefinition();
fakePatientCohortDefinition.setAttributeType(
Context.getPersonService().getPersonAttributeType(28));
fakePatientCohortDefinition.setValues(Collections.singletonList("true"));
Cohort fakePatientCohort =
definitionService.evaluate(fakePatientCohortDefinition, evaluationContext);
// remove fake patients from the list
patientIds.removeAll(fakePatientCohort.getMemberIds());
// build the cohort from the resulting list of patient ids
return new EvaluatedCohort(new Cohort(patientIds), cohortDefinition, evaluationContext);
}