Examples with CodeType org.hl7.fhir.r4.model.CodeType used on opensource projects

Example 21 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project kindling by HL7.

the class ProfileGenerator method makeSearchParam.

public SearchParameter makeSearchParam(StructureDefinition p, String id, String rn, SearchParameterDefn spd, ResourceDefn rd) throws Exception {
    boolean shared;
    boolean created = true;
    SearchParameter sp;
    if (definitions.getCommonSearchParameters().containsKey(rn + "::" + spd.getCode())) {
        shared = true;
        CommonSearchParameter csp = definitions.getCommonSearchParameters().get(rn + "::" + spd.getCode());
        if (csp.getDefinition() == null) {
            sp = new SearchParameter();
            csp.setDefinition(sp);
            sp.setId(csp.getId());
        } else {
            created = false;
            sp = csp.getDefinition();
        }
    } else {
        shared = false;
        sp = new SearchParameter();
        sp.setId(id.replace("[", "").replace("]", ""));
    }
    spd.setCommonId(sp.getId());
    if (created) {
        sp.setUrl("http://hl7.org/fhir/SearchParameter/" + sp.getId());
        sp.setVersion(version.toCode());
        if (context.getSearchParameter(sp.getUrl()) != null)
            throw new Exception("Duplicated Search Parameter " + sp.getUrl());
        context.cacheResource(sp);
        spd.setResource(sp);
        definitions.addNs(sp.getUrl(), "Search Parameter: " + sp.getName(), rn.toLowerCase() + ".html#search");
        sp.setStatus(spd.getStandardsStatus() == StandardsStatus.NORMATIVE ? PublicationStatus.fromCode("active") : PublicationStatus.fromCode("draft"));
        StandardsStatus sst = ToolingExtensions.getStandardsStatus(sp);
        if (sst == null || (spd.getStandardsStatus() == null && spd.getStandardsStatus().isLowerThan(sst)))
            ToolingExtensions.setStandardsStatus(sp, spd.getStandardsStatus(), spd.getNormativeVersion());
        sp.setExperimental(p.getExperimental());
        sp.setName(spd.getCode());
        sp.setCode(spd.getCode());
        sp.setDate(genDate.getTime());
        sp.setPublisher(p.getPublisher());
        for (ContactDetail tc : p.getContact()) {
            ContactDetail t = sp.addContact();
            if (tc.hasNameElement())
                t.setNameElement(tc.getNameElement().copy());
            for (ContactPoint ts : tc.getTelecom()) t.getTelecom().add(ts.copy());
        }
        if (!definitions.hasResource(p.getType()) && !p.getType().equals("Resource") && !p.getType().equals("DomainResource"))
            throw new Exception("unknown resource type " + p.getType());
        sp.setType(getSearchParamType(spd.getType()));
        if (sp.getType() == SearchParamType.REFERENCE && spd.isHierarchy()) {
            sp.addModifier(SearchParameter.SearchModifierCode.BELOW);
            sp.addModifier(SearchParameter.SearchModifierCode.ABOVE);
        }
        if (shared) {
            sp.setDescription("Multiple Resources: \r\n\r\n* [" + rn + "](" + rn.toLowerCase() + ".html): " + spd.getDescription() + "\r\n");
        } else
            sp.setDescription(preProcessMarkdown(spd.getDescription(), "Search Description"));
        if (!Utilities.noString(spd.getExpression()))
            sp.setExpression(spd.getExpression());
        // addModifiers(sp);
        addComparators(sp);
        String xpath = Utilities.noString(spd.getXPath()) ? new XPathQueryGenerator(this.definitions, null, null).generateXpath(spd.getPaths(), rn) : spd.getXPath();
        if (xpath != null) {
            if (xpath.contains("[x]"))
                xpath = convertToXpath(xpath);
            sp.setXpath(xpath);
            sp.setXpathUsage(spd.getxPathUsage());
        }
        if (sp.getType() == SearchParamType.COMPOSITE) {
            for (CompositeDefinition cs : spd.getComposites()) {
                SearchParameterDefn cspd = findSearchParameter(rd, cs.getDefinition());
                if (cspd != null)
                    sp.addComponent().setExpression(cs.getExpression()).setDefinition(cspd.getUrl());
                else
                    sp.addComponent().setExpression(cs.getExpression()).setDefinition("http://hl7.org/fhir/SearchParameter/" + rn + "-" + cs.getDefinition());
            }
            sp.setMultipleOr(false);
        }
        sp.addBase(p.getType());
    } else {
        if (sp.getType() != getSearchParamType(spd.getType()))
            throw new FHIRException("Type mismatch on common parameter: expected " + sp.getType().toCode() + " but found " + getSearchParamType(spd.getType()).toCode());
        if (!sp.getDescription().contains("[" + rn + "](" + rn.toLowerCase() + ".html)"))
            sp.setDescription(sp.getDescription() + "* [" + rn + "](" + rn.toLowerCase() + ".html): " + spd.getDescription() + "\r\n");
        // ext.addExtension("description", new MarkdownType(spd.getDescription()));
        if (!Utilities.noString(spd.getExpression()) && !sp.getExpression().contains(spd.getExpression()))
            sp.setExpression(sp.getExpression() + " | " + spd.getExpression());
        String xpath = new XPathQueryGenerator(this.definitions, null, null).generateXpath(spd.getPaths(), rn);
        if (xpath != null) {
            if (xpath.contains("[x]"))
                xpath = convertToXpath(xpath);
            if (sp.getXpath() != null && !sp.getXpath().contains(xpath))
                sp.setXpath(sp.getXpath() + " | " + xpath);
            if (sp.getXpathUsage() != spd.getxPathUsage())
                throw new FHIRException("Usage mismatch on common parameter: expected " + sp.getXpathUsage().toCode() + " but found " + spd.getxPathUsage().toCode());
        }
        boolean found = false;
        for (CodeType ct : sp.getBase()) found = found || p.getType().equals(ct.asStringValue());
        if (!found)
            sp.addBase(p.getType());
    }
    spd.setUrl(sp.getUrl());
    for (String target : spd.getWorkingTargets()) {
        if ("Any".equals(target) == true) {
            for (String resourceName : definitions.sortedResourceNames()) {
                boolean found = false;
                for (CodeType st : sp.getTarget()) found = found || st.asStringValue().equals(resourceName);
                if (!found)
                    sp.addTarget(resourceName);
            }
        } else {
            boolean found = false;
            for (CodeType st : sp.getTarget()) found = found || st.asStringValue().equals(target);
            if (!found)
                sp.addTarget(target);
        }
    }
    return sp;
}

Example 22 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project quality-measure-and-cohort-service by Alvearie.

the class R4RestFhirTerminologyProvider method lookup.

/**
 * This is a small patch to the OSS implementation to use named-parameter lookup on
 * the operation response instead of just assuming a positional location.
 */
@Override
public Code lookup(Code code, CodeSystemInfo codeSystem) throws ResourceNotFoundException {
    Parameters respParam = fhirClient.operation().onType(CodeSystem.class).named("lookup").withParameter(Parameters.class, "code", new CodeType(code.getCode())).andParameter("system", new UriType(codeSystem.getId())).execute();
    StringType display = (StringType) respParam.getParameter("display");
    if (display != null) {
        code.withDisplay(display.getValue());
    }
    return code.withSystem(codeSystem.getId());
}

Example 23 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project quality-measure-and-cohort-service by Alvearie.

the class ValueSetUtilTest method testCorrectValidation.

@Test
public void testCorrectValidation() {
    ValueSetArtifact artifact = new ValueSetArtifact();
    artifact.setUrl("fakeUrl");
    ValueSet fakeValueSet = new ValueSet();
    fakeValueSet.setId("fakeId");
    fakeValueSet.setVersion("fakeVersion");
    ValueSet.ValueSetComposeComponent compose = new ValueSet.ValueSetComposeComponent();
    ValueSet.ConceptSetComponent component = new ValueSet.ConceptSetComponent();
    component.setConcept(Collections.singletonList(new ValueSet.ConceptReferenceComponent(new CodeType("fakeCode"))));
    compose.setInclude(Collections.singletonList(component));
    fakeValueSet.setCompose(compose);
    artifact.setFhirResource(fakeValueSet);
    ValueSetUtil.validateArtifact(artifact);
}

Example 24 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project elexis-server by elexis.

the class ObservationResourceProvider method filterCode.

private List<Observation> filterCode(List<Observation> observations, CodeType code) {
    ArrayList<Observation> ret = new ArrayList<>();
    String systemString = CodeTypeUtil.getSystem(code).orElse("");
    String codeString = CodeTypeUtil.getCode(code).orElse("");
    for (Observation observation : observations) {
        if (systemString.equals(CodingSystem.ELEXIS_LOCAL_LABORATORY_VITOLABKEY.getSystem())) {
            if (CodeTypeUtil.isVitoLabkey(modelService, observation, codeString)) {
                ret.add(observation);
            }
        } else if (CodeTypeUtil.isCodeInConcept(observation.getCode(), systemString, codeString)) {
            ret.add(observation);
        }
    }
    return ret;
}

Example 25 with CodeType

use of org.hl7.fhir.r4.model.CodeType in project elexis-server by elexis.

the class MedicationRequestTest method updateMedicationRequest.

@Test
public void updateMedicationRequest() {
    // load existing order
    Bundle results = client.search().forResource(MedicationRequest.class).where(MedicationRequest.PATIENT.hasId(patient.getId())).returnBundle(Bundle.class).execute();
    assertNotNull(results);
    List<BundleEntryComponent> entries = results.getEntry();
    assertFalse(entries.isEmpty());
    Optional<MedicationRequest> activeOrder = getActiveOrderWithDosage(entries);
    assertTrue(activeOrder.isPresent());
    MedicationRequest updateOrder = activeOrder.get();
    updateOrder.getDosageInstruction().get(0).setText("test");
    List<Extension> entryTypes = updateOrder.getExtensionsByUrl("www.elexis.info/extensions/prescription/entrytype");
    assertEquals(EntryType.FIXED_MEDICATION.name(), ((CodeType) entryTypes.get(0).getValue()).getValue());
    entryTypes.get(0).setValue(new CodeType(EntryType.SYMPTOMATIC_MEDICATION.name()));
    // update the medication
    MethodOutcome outcome = client.update().resource(updateOrder).execute();
    // read and validate change
    MedicationRequest oldOrder = client.read().resource(MedicationRequest.class).withId(activeOrder.get().getId()).execute();
    assertNotNull(oldOrder);
    MedicationRequest newOrder = client.read().resource(MedicationRequest.class).withId(outcome.getId()).execute();
    assertNotNull(newOrder);
    assertEquals(MedicationRequestStatus.COMPLETED, oldOrder.getStatus());
    assertEquals(MedicationRequestStatus.ACTIVE, newOrder.getStatus());
    assertEquals("test", newOrder.getDosageInstruction().get(0).getText());
    entryTypes = newOrder.getExtensionsByUrl("www.elexis.info/extensions/prescription/entrytype");
    assertEquals(EntryType.SYMPTOMATIC_MEDICATION.name(), ((CodeType) entryTypes.get(0).getValue()).getValue());
}