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

Example 16 with ConceptSource

use of org.openmrs.ConceptSource in project openmrs-module-coreapps by openmrs.

the class DiagnosesFragmentController method searchNonCoded.

public List<SimpleObject> searchNonCoded(UiSessionContext context, UiUtils ui, @SpringBean("emrApiProperties") EmrApiProperties emrApiProperties, @SpringBean("emrConceptService") EmrConceptService emrConceptService, @RequestParam("term") String query, @RequestParam(value = "start", defaultValue = "0") Integer start, @RequestParam(value = "size", defaultValue = "50") Integer size) throws Exception {
    Collection<Concept> diagnosisSets = emrApiProperties.getDiagnosisSets();
    Locale locale = context.getLocale();
    List<ConceptSource> sources = emrApiProperties.getConceptSourcesForDiagnosisSearch();
    List<ConceptSearchResult> hits = emrConceptService.conceptSearch(query, locale, null, diagnosisSets, sources, null);
    List<SimpleObject> ret = new ArrayList<SimpleObject>();
    for (ConceptSearchResult hit : hits) {
        ret.add(simplify(hit, ui, locale));
    }
    return ret;
}

Example 17 with ConceptSource

use of org.openmrs.ConceptSource in project openmrs-module-coreapps by openmrs.

the class EncounterDiagnosesElement method generateHtml.

@Override
public String generateHtml(FormEntryContext context) {
    List<Diagnosis> existingDiagnoses = getExistingDiagnoses(context, emrApiProperties.getDiagnosisMetadata());
    if (FormEntryContext.Mode.VIEW == context.getMode()) {
        StringBuilder sb = new StringBuilder();
        if (existingDiagnoses != null) {
            List<ConceptSource> conceptSourcesForDiagnosisSearch = emrApiProperties.getConceptSourcesForDiagnosisSearch();
            for (Diagnosis diagnosis : existingDiagnoses) {
                sb.append("<p><small>");
                // question (e.g. "Primary diagnosis")
                sb.append(message("coreapps.patientDashBoard.diagnosisQuestion." + diagnosis.getOrder()));
                sb.append("</small><span>");
                // answer (e.g. "(Confirmed) Malaria [code]")
                sb.append("(" + message("coreapps.Diagnosis.Certainty." + diagnosis.getCertainty()) + ") ");
                sb.append(diagnosis.getDiagnosis().formatWithCode(getLocale(), conceptSourcesForDiagnosisSearch));
                sb.append("</span></p>");
            }
        }
        return sb.toString();
    } else {
        hiddenDiagnoses = new HiddenFieldWidget();
        errorWidget = new ErrorWidget();
        context.registerWidget(hiddenDiagnoses);
        context.registerErrorWidget(hiddenDiagnoses, errorWidget);
        try {
            Map<String, Object> fragmentConfig = new HashMap<String, Object>();
            fragmentConfig.put("formFieldName", "encounterDiagnoses");
            fragmentConfig.put("existingDiagnoses", existingDiagnoses);
            // add the prior diagnoses if requested
            if (FormEntryContext.Mode.ENTER == context.getMode() && dispositionTypeForPriorDiagnoses != null) {
                fragmentConfig.put("priorDiagnoses", getPriorDiagnoses(context, dispositionTypeForPriorDiagnoses));
            }
            try {
                StringBuilder output = new StringBuilder();
                output.append(errorWidget.generateHtml(context));
                output.append(uiUtils.includeFragment("coreapps", "diagnosis/encounterDiagnoses", fragmentConfig));
                if (selectedDiagnosesTarget != null) {
                    output.append("\n <script type=\"text/javascript\"> \n $(function() { $('#display-encounter-diagnoses-container').appendTo('" + selectedDiagnosesTarget + "'); }); \n </script>");
                }
                return output.toString();
            } catch (NullPointerException ex) {
                // (This is hacky, but I don't see a better way to do it.)
                return "Submitting the form, so we don't generate HTML";
            }
        } catch (PageAction pageAction) {
            throw new IllegalStateException("Included fragment threw a PageAction", pageAction);
        }
    }
}

Example 18 with ConceptSource

use of org.openmrs.ConceptSource in project openmrs-module-coreapps by openmrs.

the class DiagnosesFragmentController method search.

public List<SimpleObject> search(UiSessionContext context, UiUtils ui, @SpringBean("emrApiProperties") EmrApiProperties emrApiProperties, @SpringBean("emrConceptService") EmrConceptService emrConceptService, @RequestParam("term") String query, @RequestParam(value = "start", defaultValue = "0") Integer start, @RequestParam(value = "size", defaultValue = "50") Integer size) throws Exception {
    Collection<Concept> diagnosisSets = emrApiProperties.getDiagnosisSets();
    Locale locale = context.getLocale();
    List<ConceptSource> sources = emrApiProperties.getConceptSourcesForDiagnosisSearch();
    List<ConceptSearchResult> hits = emrConceptService.conceptSearch(query, locale, null, diagnosisSets, sources, null);
    List<SimpleObject> ret = new ArrayList<SimpleObject>();
    for (ConceptSearchResult hit : hits) {
        ret.add(simplify(hit, ui, locale));
    }
    return ret;
}

Example 19 with ConceptSource

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

the class FamilyHistoryRelativeCheckboxesTagHandlerTest 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);
    // standardTestDataset actually has "is-a" instead of narrower than. Hopefully this works for our test
    ConceptMapType narrowerThan = MetadataUtils.existing(ConceptMapType.class, "1ce7a784-7d8f-11e1-909d-c80aa9edcf4e");
    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 famHxDiagnosis = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.FAMILY_HISTORY_DIAGNOSIS).datatype(coded).conceptClass(// CIEL says Diagnosis, but this is wrong
    misc).name("109016BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Family history diagnosis", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).mapping(new ConceptMapBuilder("217715ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "160592").build()).build());
    // CIEL:1560 (Family Member) is both a question and an answer. At PIH we have two existing concepts for this purpose.
    // This one is only used as a question, so we mark it as NARROWER-THAN CIEL:1560. (And we want to test this here.)
    Concept famHxRelationship = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.FAMILY_HISTORY_RELATIONSHIP).datatype(coded).conceptClass(question).name("3e2256c6-26fe-102b-80cb-0017a47871b2", "RELATIONSHIP OF RELATIVE TO PATIENT", Locale.ENGLISH, // locale-preferred
    ConceptNameType.FULLY_SPECIFIED).name("93bc0d72-07d4-102c-b5fa-0017a47871b2", "CONTACT_REL", Locale.ENGLISH, ConceptNameType.SHORT).name("f672a35a-d5db-102d-ad2a-000c29c2a5d7", "RELATION DU PARENT PAR RAPPORT AU PATIENT", Locale.FRENCH, // locale-preferred
    null).description("ecf0bb66-07fe-102c-b5fa-0017a47871b2", "What is the relationship of this relative to this patient?", Locale.ENGLISH).mapping(new ConceptMapBuilder("e9335480-d593-11e4-9dcf-b36e1005e77b").type(narrowerThan).ensureTerm(ciel, "1560").build()).answers(// other options not needed for this test
    father).build());
    Concept famHxComment = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.FAMILY_HISTORY_COMMENT).datatype(text).conceptClass(question).name("109055BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Family history comment", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).mapping(new ConceptMapBuilder("217741ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "160618").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());
    Concept famHxConstruct = install(new ConceptBuilder(ClinicalConsultationConcepts.Concepts.FAMILY_HISTORY_CONSTRUCT).datatype(notApplicable).conceptClass(// CIEL says Finding but that's not necessary for the test
    misc).name("109017BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Patient's family history list", Locale.ENGLISH, ConceptNameType.FULLY_SPECIFIED).name("109019BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB", "Family history list", Locale.ENGLISH, null).setMembers(famHxDiagnosis, famHxRelationship, isSymptomPresent, famHxComment).mapping(new ConceptMapBuilder("217716ABBBBBBBBBBBBBBBBBBBBBBBBBBBBB").type(sameAs).ensureTerm(ciel, "160593").build()).build());
}

Example 20 with ConceptSource

use of org.openmrs.ConceptSource in project openmrs-core by openmrs.

the class AdministrationServiceImpl method setImplementationId.

/**
 * @see org.openmrs.api.AdministrationService#setImplementationId(org.openmrs.ImplementationId)
 */
@Override
public void setImplementationId(ImplementationId implementationId) throws APIException {
    if (implementationId == null) {
        return;
    }
    // check the validity of this implementation id with the server
    String description = implementationId.getDescription();
    try {
        // check that source id is valid
        description = checkImplementationIdValidity(implementationId.getImplementationId(), description, implementationId.getPassphrase());
        // save the server's description back to this concept source object
        implementationId.setDescription(description);
        boolean foundMatchingSource = false;
        // loop over the concept sources to make sure one exists for this hl7Code/implementationId
        List<ConceptSource> sources = Context.getConceptService().getAllConceptSources(false);
        if (sources != null) {
            for (ConceptSource source : sources) {
                if (implementationId.getImplementationId().equals(source.getHl7Code())) {
                    foundMatchingSource = true;
                }
            }
        }
        // as a new ConceptSource
        if (!foundMatchingSource) {
            ConceptSource newConceptSource = new ConceptSource();
            newConceptSource.setName(implementationId.getName());
            newConceptSource.setDescription(implementationId.getDescription());
            newConceptSource.setHl7Code(implementationId.getImplementationId());
            if (Context.getAuthenticatedUser() == null) {
                // (hackish)
                // fake the user because no one is logged in
                newConceptSource.setCreator(new User(1));
            }
            Context.getConceptService().saveConceptSource(newConceptSource);
        }
        // serialize and save the ImplementationId to the global properties table
        String value = Context.getSerializationService().getDefaultSerializer().serialize(implementationId);
        Context.getAdministrationService().saveGlobalProperty(new GlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_IMPLEMENTATION_ID, value));
    } catch (APIException e) {
        throw e;
    } catch (Exception e) {
        // pass any other exceptions on up the train
        throw new APIException(e);
    } finally {
    // save an empty concept source to the database when something fails?
    }
}