Examples with DataRequirement org.hl7.fhir.r5.model.DataRequirement used on opensource projects

Example 16 with DataRequirement

use of org.hl7.fhir.r5.model.DataRequirement in project org.hl7.fhir.core by hapifhir.

the class ProfileDrivenRenderer method renderLeaf.

private void renderLeaf(ResourceWrapper res, BaseWrapper ew, ElementDefinition defn, XhtmlNode parent, XhtmlNode x, boolean title, boolean showCodeDetails, Map<String, String> displayHints, String path, int indent) throws FHIRException, UnsupportedEncodingException, IOException, EOperationOutcome {
    if (ew == null)
        return;
    Base e = ew.getBase();
    if (e instanceof StringType)
        x.addText(((StringType) e).getValue());
    else if (e instanceof CodeType)
        x.addText(((CodeType) e).getValue());
    else if (e instanceof IdType)
        x.addText(((IdType) e).getValue());
    else if (e instanceof Extension)
        return;
    else if (e instanceof InstantType)
        x.addText(((InstantType) e).toHumanDisplay());
    else if (e instanceof DateTimeType) {
        renderDateTime(x, e);
    } else if (e instanceof Base64BinaryType)
        x.addText(new Base64().encodeAsString(((Base64BinaryType) e).getValue()));
    else if (e instanceof org.hl7.fhir.r5.model.DateType) {
        org.hl7.fhir.r5.model.DateType dt = ((org.hl7.fhir.r5.model.DateType) e);
        renderDate(x, dt);
    } else if (e instanceof Enumeration) {
        Object ev = ((Enumeration<?>) e).getValue();
        // todo: look up a display name if there is one
        x.addText(ev == null ? "" : ev.toString());
    } else if (e instanceof BooleanType) {
        x.addText(((BooleanType) e).getValue().toString());
    } else if (e instanceof CodeableConcept) {
        renderCodeableConcept(x, (CodeableConcept) e, showCodeDetails);
    } else if (e instanceof Coding) {
        renderCoding(x, (Coding) e, showCodeDetails);
    } else if (e instanceof CodeableReference) {
        renderCodeableReference(x, (CodeableReference) e, showCodeDetails);
    } else if (e instanceof Annotation) {
        renderAnnotation(x, (Annotation) e);
    } else if (e instanceof Identifier) {
        renderIdentifier(x, (Identifier) e);
    } else if (e instanceof org.hl7.fhir.r5.model.IntegerType) {
        if (((org.hl7.fhir.r5.model.IntegerType) e).hasValue()) {
            x.addText(Integer.toString(((org.hl7.fhir.r5.model.IntegerType) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.Integer64Type) {
        if (((org.hl7.fhir.r5.model.Integer64Type) e).hasValue()) {
            x.addText(Long.toString(((org.hl7.fhir.r5.model.Integer64Type) e).getValue()));
        } else {
            x.addText("??");
        }
    } else if (e instanceof org.hl7.fhir.r5.model.DecimalType) {
        x.addText(((org.hl7.fhir.r5.model.DecimalType) e).getValue().toString());
    } else if (e instanceof HumanName) {
        renderHumanName(x, (HumanName) e);
    } else if (e instanceof SampledData) {
        renderSampledData(x, (SampledData) e);
    } else if (e instanceof Address) {
        renderAddress(x, (Address) e);
    } else if (e instanceof ContactPoint) {
        renderContactPoint(x, (ContactPoint) e);
    } else if (e instanceof Expression) {
        renderExpression(x, (Expression) e);
    } else if (e instanceof Money) {
        renderMoney(x, (Money) e);
    } else if (e instanceof ContactDetail) {
        ContactDetail cd = (ContactDetail) e;
        if (cd.hasName()) {
            x.tx(cd.getName() + ": ");
        }
        boolean first = true;
        for (ContactPoint c : cd.getTelecom()) {
            if (first)
                first = false;
            else
                x.tx(",");
            renderContactPoint(x, c);
        }
    } else if (e instanceof UriType) {
        renderUri(x, (UriType) e, defn.getPath(), rcontext != null && rcontext.getResourceResource() != null ? rcontext.getResourceResource().getId() : null);
    } else if (e instanceof Timing) {
        renderTiming(x, (Timing) e);
    } else if (e instanceof Range) {
        renderRange(x, (Range) e);
    } else if (e instanceof Quantity) {
        renderQuantity(x, (Quantity) e, showCodeDetails);
    } else if (e instanceof Ratio) {
        renderQuantity(x, ((Ratio) e).getNumerator(), showCodeDetails);
        x.tx("/");
        renderQuantity(x, ((Ratio) e).getDenominator(), showCodeDetails);
    } else if (e instanceof Period) {
        Period p = (Period) e;
        renderPeriod(x, p);
    } else if (e instanceof Reference) {
        Reference r = (Reference) e;
        if (r.getReference() != null && r.getReference().contains("#")) {
            if (containedIds.contains(r.getReference().substring(1))) {
                x.ah(r.getReference()).tx("See " + r.getReference());
            } else {
                // in this case, we render the resource in line
                ResourceWrapper rw = null;
                for (ResourceWrapper t : res.getContained()) {
                    if (r.getReference().substring(1).equals(t.getId())) {
                        rw = t;
                    }
                }
                if (rw == null) {
                    renderReference(res, x, r);
                } else {
                    x.an(rw.getId());
                    ResourceRenderer rr = RendererFactory.factory(rw, context.copy().setAddGeneratedNarrativeHeader(false));
                    rr.render(parent.blockquote(), rw);
                }
            }
        } else {
            renderReference(res, x, r);
        }
    } else if (e instanceof Resource) {
        return;
    } else if (e instanceof DataRequirement) {
        DataRequirement p = (DataRequirement) e;
        renderDataRequirement(x, p);
    } else if (e instanceof PrimitiveType) {
        x.tx(((PrimitiveType) e).primitiveValue());
    } else if (e instanceof ElementDefinition) {
        x.tx("todo-bundle");
    } else if (e != null && !(e instanceof Attachment) && !(e instanceof Narrative) && !(e instanceof Meta)) {
        throw new NotImplementedException("type " + e.getClass().getName() + " not handled - should not be here");
    }
}

Example 17 with DataRequirement

use of org.hl7.fhir.r5.model.DataRequirement in project eCRNow by drajer-health.

the class PlanDefinitionProcessor method processTriggerDefinitions.

private void processTriggerDefinitions(List<TriggerDefinition> tdlist, AbstractAction act) {
    if (tdlist != null && !tdlist.isEmpty()) {
        for (TriggerDefinition triggerDefinition : tdlist) {
            if (triggerDefinition.getType() != TriggerType.NAMEDEVENT && triggerDefinition.getType() != TriggerType.PERIODIC && triggerDefinition.hasData()) {
                logger.info(" Identified Data Trigger for Act {}", act.getActionId());
                List<DataRequirement> dr = triggerDefinition.getData();
                for (DataRequirement d : dr) {
                    // Create ActionData object
                    ActionData ad = new ActionData();
                    ad.setTriggerType(triggerDefinition.getType());
                    ad.setFhirDataType(FHIRAllTypes.valueOf(d.getType().toUpperCase()));
                    if (d.hasProfile())
                        ad.setProfiles(d.getProfile());
                    if (d.hasCodeFilter()) {
                        DataRequirementCodeFilterComponent cf = d.getCodeFilterFirstRep();
                        if (cf.hasPath()) {
                            ad.setPath(d.getType() + "." + cf.getPath());
                            logger.info(" Evaluation Path = {}", ad.getPath());
                        }
                        if (cf.hasValueSet())
                            ad.setValueSet(cf.getValueSetElement());
                    }
                    act.addActionData(ad);
                }
            } else if (triggerDefinition.getType() == TriggerType.PERIODIC) {
                if (triggerDefinition.hasTimingTiming()) {
                    Timing t = triggerDefinition.getTimingTiming();
                    if (t.hasRepeat()) {
                        TimingSchedule ts = getTimingSchedule(t, triggerDefinition.getType());
                        if (ts != null) {
                            act.addTimingData(ts);
                        }
                    }
                } else {
                // Not handling the others for eCR
                }
            } else {
            // Ignore other types for eCR
            }
        }
    }
}

Example 18 with DataRequirement

use of org.hl7.fhir.r5.model.DataRequirement in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestDataRequirementsProcessorWithExpressions.

@Test
public void TestDataRequirementsProcessorWithExpressions() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    try {
        Set<String> expressions = new HashSet<>();
        // TODO - add expressions to expressions
        // Active Ambulatory Opioid Rx");
        expressions.add("Conditions Indicating End of Life or With Limited Life Expectancy");
        CqlTranslator translator = createTranslator("OpioidCDS/cql/OpioidCDSCommon.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, expressions, false);
        assertTrue(moduleDefinitionLibrary.getType().getCode("http://terminology.hl7.org/CodeSystem/library-type").equalsIgnoreCase("module-definition"));
        List<Extension> directReferenceCodes = moduleDefinitionLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode");
        assertTrue(directReferenceCodes.size() == 4);
        Extension directReferenceCode = directReferenceCodes.get(0);
        Coding coding = directReferenceCode.getValueCoding();
        assertEquals("http://hl7.org/fhir/condition-category", coding.getSystem());
        assertEquals("encounter-diagnosis", coding.getCode());
        assertEquals("Encounter Diagnosis", coding.getDisplay());
        assertTrue(moduleDefinitionLibrary.getRelatedArtifact().size() == 6);
        RelatedArtifact conditionCategoryCodes = null;
        for (RelatedArtifact relatedArtifact : moduleDefinitionLibrary.getRelatedArtifact()) {
            if (relatedArtifact.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON && relatedArtifact.getResource() != null && relatedArtifact.getResource().equals("http://hl7.org/fhir/condition-category")) {
                conditionCategoryCodes = relatedArtifact;
                break;
            }
        }
        assertTrue(conditionCategoryCodes != null);
        assertTrue(moduleDefinitionLibrary.getParameter().size() == 1);
        ParameterDefinition conditionsIndicatingEndOfLife = null;
        for (ParameterDefinition parameter : moduleDefinitionLibrary.getParameter()) {
            if (parameter.getName().equals("Conditions Indicating End of Life or With Limited Life Expectancy")) {
                conditionsIndicatingEndOfLife = parameter;
                break;
            }
        }
        assertTrue(conditionsIndicatingEndOfLife != null);
        assertTrue(moduleDefinitionLibrary.getDataRequirement().size() == 3);
        DataRequirement diagnosisRequirement = null;
        for (DataRequirement requirement : moduleDefinitionLibrary.getDataRequirement()) {
            if (requirement.getType() == Enumerations.FHIRAllTypes.CONDITION && requirement.getCodeFilter().size() == 1) {
                DataRequirement.DataRequirementCodeFilterComponent cfc = requirement.getCodeFilterFirstRep();
                if (cfc.hasPath() && cfc.getPath().equals("category") && cfc.getCode().size() == 1 && cfc.getCodeFirstRep().hasCode() && cfc.getCodeFirstRep().getCode().equals("encounter-diagnosis")) {
                    diagnosisRequirement = requirement;
                    break;
                }
            }
        }
        assertTrue(diagnosisRequirement != null);
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 19 with DataRequirement

use of org.hl7.fhir.r5.model.DataRequirement in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestLibraryDataRequirements.

@Test
public void TestLibraryDataRequirements() {
    CqlTranslatorOptions cqlTranslatorOptions = new CqlTranslatorOptions();
    cqlTranslatorOptions.getFormats().add(CqlTranslator.Format.JSON);
    try {
        // CqlTranslator translator = createTranslator("/ecqm/resources/library-EXM506-2.2.000.json", cqlTranslatorOptions);
        CqlTranslator translator = createTranslator("CompositeMeasures/cql/BCSComponent.cql", cqlTranslatorOptions);
        translator.toELM();
        assertTrue(translator.getErrors().isEmpty());
        libraryManager.cacheLibrary(translator.getTranslatedLibrary());
        DataRequirementsProcessor dqReqTrans = new DataRequirementsProcessor();
        org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, translator.getTranslatedLibrary(), cqlTranslatorOptions, null, false);
        assertTrue(moduleDefinitionLibrary.getType().getCode("http://terminology.hl7.org/CodeSystem/library-type").equalsIgnoreCase("module-definition"));
        List<Extension> directReferenceCodes = moduleDefinitionLibrary.getExtensionsByUrl("http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-directReferenceCode");
        assertTrue(directReferenceCodes.size() == 5);
        Extension directReferenceCode = directReferenceCodes.get(0);
        Coding coding = directReferenceCode.getValueCoding();
        assertEquals("http://loinc.org", coding.getSystem());
        assertEquals("21112-8", coding.getCode());
        assertEquals("Birth date", coding.getDisplay());
        assertTrue(moduleDefinitionLibrary.getRelatedArtifact().size() >= 45);
        RelatedArtifact loincCodeSystem = null;
        for (RelatedArtifact relatedArtifact : moduleDefinitionLibrary.getRelatedArtifact()) {
            if (relatedArtifact.getType() == RelatedArtifact.RelatedArtifactType.DEPENDSON && relatedArtifact.getResource() != null && relatedArtifact.getResource().equals("http://loinc.org")) {
                loincCodeSystem = relatedArtifact;
                break;
            }
        }
        assertTrue(loincCodeSystem != null);
        assertTrue(moduleDefinitionLibrary.getParameter().size() >= 16);
        ParameterDefinition measurementPeriod = null;
        for (ParameterDefinition parameter : moduleDefinitionLibrary.getParameter()) {
            if (parameter.getName().equals("Measurement Period")) {
                measurementPeriod = parameter;
                break;
            }
        }
        assertTrue(measurementPeriod != null);
        assertTrue(moduleDefinitionLibrary.getDataRequirement().size() >= 15);
        DataRequirement diagnosisRequirement = null;
        for (DataRequirement requirement : moduleDefinitionLibrary.getDataRequirement()) {
            if (requirement.getType() == Enumerations.FHIRAllTypes.CONDITION && requirement.getCodeFilter().size() == 1) {
                DataRequirement.DataRequirementCodeFilterComponent cfc = requirement.getCodeFilterFirstRep();
                if (cfc.hasPath() && cfc.getPath().equals("code") && cfc.hasValueSet() && cfc.getValueSet().equals("http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.464.1003.198.12.1071")) {
                    diagnosisRequirement = requirement;
                    break;
                }
            }
        }
        assertTrue(diagnosisRequirement != null);
        FhirContext context = getFhirContext();
        IParser parser = context.newJsonParser();
        String moduleDefString = parser.setPrettyPrint(true).encodeResourceToString(moduleDefinitionLibrary);
        logger.debug(moduleDefString);
    } catch (IOException ioException) {
        ioException.printStackTrace();
    }
}

Example 20 with DataRequirement

use of org.hl7.fhir.r5.model.DataRequirement in project clinical_quality_language by cqframework.

the class DataRequirementsProcessorTest method TestDataRequirementsAnalysisCase10a.

@Test
public void TestDataRequirementsAnalysisCase10a() throws IOException {
    CqlTranslatorOptions translatorOptions = getTranslatorOptions();
    CqlTranslator translator = setupDataRequirementsAnalysis("TestCases/TestCase10a.cql", translatorOptions);
    org.hl7.fhir.r5.model.Library moduleDefinitionLibrary = getModuleDefinitionLibrary(translator, translatorOptions);
    /*
        Element that is a dateTime, referenced in a date comparison

        define "ESRD Observations":
          [Observation: "ESRD Diagnosis"] O
            where O.instant same day or after @2022-02-15

        {
            type: Observation
            mustSupport: [ 'code', 'issued' ]
            codeFilter: {
                path: 'code',
                valueSet: 'http://fakeurl.com/ersd-diagnosis'
            },
            dateFilter: {
                path: 'issued',
                valuePeriod: {
                    low: @2022-02-15
                }
            }
        }
        */
    // Validate the ELM is correct
    ExpressionDef ed = translator.getTranslatedLibrary().resolveExpressionRef("ESRD Observations");
    assertTrue(ed.getExpression() instanceof Query);
    Query q = (Query) ed.getExpression();
    assertTrue(q.getSource() != null && q.getSource().size() == 1);
    AliasedQuerySource source = q.getSource().get(0);
    assertTrue(source.getExpression() instanceof Retrieve);
    Retrieve r = (Retrieve) source.getExpression();
    assertTrue(r.getDataType().getLocalPart().equals("Observation"));
    // Validate the data requirement is reported in the module definition library
    DataRequirement expectedDataRequirement = null;
    for (DataRequirement dr : moduleDefinitionLibrary.getDataRequirement()) {
        if (dr.getType() == Enumerations.FHIRAllTypes.OBSERVATION) {
            expectedDataRequirement = dr;
        }
    }
    assertTrue(expectedDataRequirement != null);
    assertTrue(expectedDataRequirement.getMustSupport().size() == 2);
    boolean hasCode = false;
    assertTrue(expectedDataRequirement.getMustSupport().stream().filter(s -> s.getValue().equals("code")).count() == 1);
    assertTrue(expectedDataRequirement.getMustSupport().stream().filter(s -> s.getValue().equals("issued")).count() == 1);
    assertTrue(expectedDataRequirement.getCodeFilter().size() == 1);
    DataRequirement.DataRequirementCodeFilterComponent drcfc = expectedDataRequirement.getCodeFilter().get(0);
    assertTrue(drcfc.getPath().equals("code"));
    assertTrue(drcfc.getValueSet().equals("http://fakeurl.com/ersd-diagnosis"));
    assertTrue(expectedDataRequirement.getDateFilter().size() == 1);
    DataRequirement.DataRequirementDateFilterComponent drdfc = expectedDataRequirement.getDateFilter().get(0);
    LocalDate ld = LocalDate.of(2022, 2, 15);
    assertTrue(drdfc.getValuePeriod().getStart().compareTo(Date.from(ld.atStartOfDay(ZoneId.systemDefault()).toInstant())) == 0);
// outputModuleDefinitionLibrary(moduleDefinitionLibrary);
}