Examples with Concept org.openmrs.Concept used on opensource projects

Example 6 with Concept

use of org.openmrs.Concept in project openmrs-module-pihcore by PIH.

the class BaseEncounterDataSetManager method addObsColumn.

/**
 * Adds a column containing the value of an obs in the encounter, assuming a single observation exists for the given concept
 */
protected void addObsColumn(EncounterDataSetDefinition dsd, String columnName, String conceptLookup, DataConverter... converters) {
    Concept concept = Metadata.getConcept(conceptLookup);
    addColumn(dsd, columnName, pihEncounterData.getSingleObsInEncounter(concept), converters);
}

Example 7 with Concept

use of org.openmrs.Concept in project openmrs-module-pihcore by PIH.

the class BaseEncounterDataSetManager method addSymptomPresentOrAbsentColumn.

protected void addSymptomPresentOrAbsentColumn(EncounterDataSetDefinition dsd, String columnName, String symptomPresentQuestion, String symptomAbsentQuestion, String symptomAnswer, Object valueIfPresent, Object valueIfAbsent) {
    Concept presentConcept = Metadata.getConcept(symptomPresentQuestion);
    Concept absentConcept = Metadata.getConcept(symptomAbsentQuestion);
    Concept answerConcept = Metadata.getConcept(symptomAnswer);
    MultipleObsForEncounterDataDefinition d = new MultipleObsForEncounterDataDefinition();
    d.addQuestion(presentConcept);
    d.addQuestion(absentConcept);
    CodedObsConverter converter = new CodedObsConverter();
    converter.addOption(presentConcept.getUuid(), answerConcept.getUuid(), valueIfPresent);
    converter.addOption(absentConcept.getUuid(), answerConcept.getUuid(), valueIfAbsent);
    addColumn(dsd, columnName, d, converter);
}

Example 8 with Concept

use of org.openmrs.Concept in project openmrs-module-pihcore by PIH.

the class InpatientStatsDailyDataSetManager method constructDataSetDefinition.

@Override
public DataSetDefinition constructDataSetDefinition(DataSetDescriptor dataSetDescriptor, File file) {
    List<Location> inpatientLocations = adtService.getInpatientLocations();
    EncounterType admissionEncounterType = encounterService.getEncounterTypeByUuid(PihEmrConfigConstants.ENCOUNTERTYPE_ADMISSION_UUID);
    Concept dischargedDisposition = conceptService.getConceptByMapping("DISCHARGED", "PIH");
    Concept deathDisposition = conceptService.getConceptByMapping("DEATH", "PIH");
    Concept transferOutDisposition = conceptService.getConceptByMapping("Transfer out of hospital", "PIH");
    Concept leftWithoutCompletionOfTreatmentDisposition = conceptService.getConceptByMapping("Departed without medical discharge", "PIH");
    Concept leftWithoutSeeingClinicianDisposition = conceptService.getConceptByMapping("Left without seeing a clinician", "PIH");
    List<Concept> dispositionsToConsider = Arrays.asList(dischargedDisposition, deathDisposition, transferOutDisposition, leftWithoutCompletionOfTreatmentDisposition, leftWithoutSeeingClinicianDisposition);
    // Dispositions we're currently ignoring: "Transfer within hospital", "Admit to hospital", "Discharged", "Emergency Department observation", "Home"
    CohortIndicatorDataSetDefinition cohortDsd = new CohortIndicatorDataSetDefinition();
    cohortDsd.addParameter(getStartDateParameter());
    cohortDsd.addParameter(getEndDateParameter());
    DiedSoonAfterEncounterCohortDefinition diedSoonAfterAdmission = new DiedSoonAfterEncounterCohortDefinition();
    diedSoonAfterAdmission.setEncounterType(admissionEncounterType);
    diedSoonAfterAdmission.addParameter(new Parameter("diedOnOrAfter", "Died on or after", Date.class));
    diedSoonAfterAdmission.addParameter(new Parameter("diedOnOrBefore", "Died on or before", Date.class));
    for (Location location : inpatientLocations) {
        addIndicator(cohortDsd, "censusAtStart", "Census at start", location, Mapped.map(pihCohorts.getInpatientAtLocationOnDate(), "date=${startDate}"));
        addIndicator(cohortDsd, "censusAtEnd", "Census at end", location, Mapped.map(pihCohorts.getInpatientAtLocationOnDate(), "date=${endDate}"));
        addIndicator(cohortDsd, "admissions", "Admission", location, Mapped.mapStraightThrough(pihCohorts.getAdmissionAtLocationDuringPeriod()));
        addIndicator(cohortDsd, "transfersIn", "Transfer In", location, Mapped.mapStraightThrough(pihCohorts.getTransferInToLocationDuringPeriod()));
        addIndicator(cohortDsd, "transfersOut", "Transfer Out", location, Mapped.mapStraightThrough(pihCohorts.getTransferOutOfLocationDuringPeriod()));
        addIndicator(cohortDsd, "discharged", "Discharged", location, Mapped.mapStraightThrough(pihCohorts.getDischargeExitFromLocationDuringPeriod()));
        addIndicator(cohortDsd, "deathsWithin48", "Deaths within 48h", location, Mapped.mapStraightThrough(pihCohorts.getDiedExitFromLocationDuringPeriodSoonAfterAdmission()));
        addIndicator(cohortDsd, "deathsAfter48", "Deaths after 48h", location, Mapped.mapStraightThrough(pihCohorts.getDiedExitFromLocationDuringPeriodNotSoonAfterAdmission()));
        addIndicator(cohortDsd, "transfersOutOfHUM", "Transfer Outs", location, Mapped.mapStraightThrough(pihCohorts.getTransferOutOfHumExitFromLocationDuringPeriod()));
        // number left without completing treatment
        LastDispositionBeforeExitCohortDefinition leftWithoutCompletingTreatment = new LastDispositionBeforeExitCohortDefinition();
        leftWithoutCompletingTreatment.addParameter(new Parameter("exitOnOrAfter", "Exit on or after", Date.class));
        leftWithoutCompletingTreatment.addParameter(new Parameter("exitOnOrBefore", "Exit on or before", Date.class));
        leftWithoutCompletingTreatment.setExitFromWard(location);
        leftWithoutCompletingTreatment.setDispositionsToConsider(dispositionsToConsider);
        leftWithoutCompletingTreatment.addDisposition(leftWithoutCompletionOfTreatmentDisposition);
        addIndicator(cohortDsd, "leftWithoutCompletingTx", "Left Without Completing Treatment", location, Mapped.map(leftWithoutCompletingTreatment, "exitOnOrAfter=${startDate},exitOnOrBefore=${endDate}"));
        LastDispositionBeforeExitCohortDefinition leftWithoutSeeingClinician = new LastDispositionBeforeExitCohortDefinition();
        leftWithoutSeeingClinician.addParameter(new Parameter("exitOnOrAfter", "Exit on or after", Date.class));
        leftWithoutSeeingClinician.addParameter(new Parameter("exitOnOrBefore", "Exit on or before", Date.class));
        leftWithoutSeeingClinician.setExitFromWard(location);
        leftWithoutSeeingClinician.setDispositionsToConsider(dispositionsToConsider);
        leftWithoutSeeingClinician.addDisposition(leftWithoutSeeingClinicianDisposition);
        addIndicator(cohortDsd, "leftWithoutSeeingClinician", "Left Without Seeing Clinician", location, Mapped.map(leftWithoutSeeingClinician, "exitOnOrAfter=${startDate},exitOnOrBefore=${endDate}"));
    }
    // number of ED check-ins
    // TODO change this to count by visits or by encounters, instead of by patients
    EncounterCohortDefinition edCheckIn = new EncounterCohortDefinition();
    edCheckIn.addParameter(new Parameter("onOrAfter", "On or after", Date.class));
    edCheckIn.addParameter(new Parameter("onOrBefore", "On or before", Date.class));
    edCheckIn.addEncounterType(encounterService.getEncounterTypeByUuid(PihEmrConfigConstants.ENCOUNTERTYPE_CHECK_IN_UUID));
    edCheckIn.addLocation(locationService.getLocationByUuid(EMERGENCY_DEPARTMENT_UUID));
    edCheckIn.addLocation(locationService.getLocationByUuid(EMERGENCY_RECEPTION_UUID));
    addIndicator(cohortDsd, "edcheckin", "ED Check In", Mapped.map(edCheckIn, "onOrAfter=${startDate},onOrBefore=${endDate}"));
    // number of surgical op-notes entered
    EncounterCohortDefinition surgicalNotes = new EncounterCohortDefinition();
    surgicalNotes.addParameter(new Parameter("onOrAfter", "On or after", Date.class));
    surgicalNotes.addParameter(new Parameter("onOrBefore", "On or before", Date.class));
    surgicalNotes.addEncounterType(encounterService.getEncounterTypeByUuid(PihEmrConfigConstants.ENCOUNTERTYPE_POST_OPERATIVE_NOTE_UUID));
    addIndicator(cohortDsd, "orvolume", "OR Volume", Mapped.map(surgicalNotes, "onOrAfter=${startDate},onOrBefore=${endDate}"));
    // potential readmissions
    AdmissionSoonAfterExitCohortDefinition readmission = new AdmissionSoonAfterExitCohortDefinition();
    readmission.addParameter(new Parameter("onOrAfter", "On or after", Date.class));
    readmission.addParameter(new Parameter("onOrBefore", "On or before", Date.class));
    addIndicator(cohortDsd, "possiblereadmission", "Possible Readmission", Mapped.map(readmission, "onOrAfter=${startDate},onOrBefore=${endDate}"));
    return cohortDsd;
}

Example 9 with Concept

use of org.openmrs.Concept in project openmrs-module-pihcore by PIH.

the class BaseObsDataSetManager method addObsColumn.

/**
 * Adds a column containing the value of an obs in the encounter, assuming a single observation exists for the given concept
 */
protected void addObsColumn(ObsDataSetDefinition dsd, String columnName, String conceptLookup, DataConverter... converters) {
    Concept concept = Metadata.getConcept(conceptLookup);
    addColumn(dsd, columnName, pihObsData.getSingleObsInGroup(concept), converters);
}

Example 10 with Concept

use of org.openmrs.Concept in project openmrs-module-pihcore by PIH.

the class PastMedicalHistoryCheckboxTagHandlerTest method setupConcepts.

private void setupConcepts() throws Exception {
    // copied from some pihcore concept setup, but tweaked to work with standardTestDataset.xml
    ConceptDatatype coded = MetadataUtils.existing(ConceptDatatype.class, CoreConceptMetadataBundle.ConceptDatatypes.CODED);
    ConceptDatatype text = MetadataUtils.existing(ConceptDatatype.class, CoreConceptMetadataBundle.ConceptDatatypes.TEXT);
    ConceptDatatype notApplicable = MetadataUtils.existing(ConceptDatatype.class, CoreConceptMetadataBundle.ConceptDatatypes.N_A);
    ConceptClass diagnosis = MetadataUtils.existing(ConceptClass.class, "938834bf-a745-4dbd-b611-f06a9a5a3060");
    ConceptClass question = MetadataUtils.existing(ConceptClass.class, "a82ef63c-e4e4-48d6-988a-fdd74d7541a7");
    ConceptClass misc = MetadataUtils.existing(ConceptClass.class, "ecdee8a7-d741-4fe7-8e01-f79cacbe97bc");
    ConceptMapType sameAs = MetadataUtils.existing(ConceptMapType.class, CoreConceptMetadataBundle.ConceptMapTypes.SAME_AS);
    ConceptSource ciel = conceptSource("CIEL", "Columbia International eHealth Laboratory concept ID", null, CoreConceptMetadataBundle.ConceptSources.CIEL);
    conceptService.saveConceptSource(ciel);
    // these are in standardTestDataset.xml
    Concept no = conceptService.getConcept(8);
    Concept unknown = conceptService.getConcept(22);
    // need this to have a different UUID to match our dictionary
    yes = conceptService.getConcept(7);
    yes.setUuid(CommonConcepts.Concepts.YES);
    conceptService.saveConcept(yes);
    Concept pmhWhich = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.PAST_MEDICAL_HISTORY_FINDING).datatype(coded).conceptClass(diagnosis).name("1908BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Past medical history finding", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).description("1470FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF", "Coded list of past medical history problems but not procedures which are coded under Past Surgical History.", Locale.ENGLISH).mapping(new ConceptMapBuilder("171868ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "1628").build()).build());
    Concept isSymptomPresent = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.PAST_MEDICAL_HISTORY_PRESENCE).datatype(coded).conceptClass(diagnosis).name("2009BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Sign/symptom present", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).answers(yes, no, unknown).mapping(new ConceptMapBuilder("171968ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "1729").build()).build());
    // TODO waiting for confirmation from Andy that this is appropriate as comments
    Concept pmhComment = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.PAST_MEDICAL_HISTORY_COMMENT).datatype(text).conceptClass(question).name("108123BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Past medical history added (text)", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).mapping(new ConceptMapBuilder("217354ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "160221").build()).build());
    Concept pmhConstruct = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.PAST_MEDICAL_HISTORY_CONSTRUCT).datatype(notApplicable).conceptClass(misc).name("1913BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Past medical history", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).name("86916BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "PMH", Locale.ENGLISH, ConceptNameType.SHORT).setMembers(pmhWhich, isSymptomPresent, pmhComment).mapping(new ConceptMapBuilder("171873ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "1633").build()).build());
}