Examples with Package org.hl7.fhir.utilities.graphql.Package used on opensource projects

Example 36 with Package

use of org.hl7.fhir.utilities.graphql.Package in project redmatch by aehrc.

the class FhirExporter method getValue.

/**
 * Resolves a value.
 *
 * @param value The value specified in the transformation rules.
 * @param fhirType The type of the FHIR attribute where this value will be set.
 * @param vertex A vertex with patient data.
 * @param recordId The id of this record. Used to create the references to FHIR ids.
 * @param enumFactory If the type is an enumeration, this is the factory to create an instance.
 * @param fhirPackage The target FHIR package.
 * @return The value or null if the value cannot be determined. This can also be a list.
 */
private Base getValue(Value value, Class<?> fhirType, JsonObject vertex, String recordId, Class<?> enumFactory, VersionedFhirPackage fhirPackage) throws IOException {
    // If this is a field-based value then make sure that there is a value and if not return null
    if (value instanceof FieldBasedValue) {
        FieldBasedValue fbv = (FieldBasedValue) value;
        // Account for field ids of the form xx___y
        String fieldId = fbv.getFieldId();
        String shortFieldId = null;
        String regex = "(?<fieldId>.*)___\\d+$";
        Pattern pattern = Pattern.compile(regex);
        Matcher matcher = pattern.matcher(fieldId);
        if (matcher.find()) {
            shortFieldId = matcher.group("fieldId");
            log.debug("Transformed fieldId into '" + fieldId + "'");
        }
        boolean hasValue = false;
        JsonElement jsonElement = vertex.get(fieldId);
        if (jsonElement != null) {
            String rawValue = jsonElement.getAsString();
            if (!rawValue.isEmpty()) {
                hasValue = true;
            }
        }
        if (!hasValue && shortFieldId != null) {
            jsonElement = vertex.get(shortFieldId);
            if (jsonElement != null) {
                String rawValue = jsonElement.getAsString();
                if (!rawValue.isEmpty()) {
                    hasValue = true;
                }
            }
        }
        if (!hasValue) {
            return null;
        }
    }
    if (value instanceof BooleanValue) {
        return new BooleanType(((BooleanValue) value).getValue());
    } else if (value instanceof CodeLiteralValue) {
        String code = ((CodeLiteralValue) value).getCode();
        return getCode(code, enumFactory);
    } else if (value instanceof ConceptLiteralValue) {
        ConceptLiteralValue clv = (ConceptLiteralValue) value;
        String system = clv.getSystem();
        String code = clv.getCode();
        String display = clv.getDisplay() != null ? clv.getDisplay() : "";
        return getConcept(system, code, display, fhirType);
    } else if (value instanceof DoubleValue) {
        return new DecimalType(((DoubleValue) value).getValue());
    } else if (value instanceof IntegerValue) {
        return new IntegerType(((IntegerValue) value).getValue());
    } else if (value instanceof ReferenceValue) {
        ReferenceValue rv = (ReferenceValue) value;
        Reference ref = new Reference();
        String resourceType = rv.getResourceType();
        String resourceId = rv.getResourceId();
        boolean unique = uniqueIds.contains(resourceType + "<" + resourceId + ">");
        CodeInfo codeInfo = terminologyService.lookup(fhirPackage, resourceType);
        if (codeInfo.isProfile()) {
            resourceType = StringUtils.getLastPath(codeInfo.getBaseResource());
        }
        if (unique) {
            // This is a reference to a unique resource - no need to append row id
            if (fhirResourceMap.containsKey(resourceId)) {
                ref.setReference("/" + resourceType + "/" + resourceId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId);
            }
        } else {
            if (fhirResourceMap.containsKey(resourceId + "-" + recordId)) {
                ref.setReference("/" + resourceType + "/" + resourceId + "-" + recordId);
            } else {
                log.debug("Did not find resource " + resourceType + "/" + resourceId + "-" + recordId);
            }
        }
        return ref;
    } else if (value instanceof StringValue) {
        if (fhirType.equals(StringType.class)) {
            return new StringType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(MarkdownType.class)) {
            return new MarkdownType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(IdType.class)) {
            return new IdType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UriType.class)) {
            return new UriType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(OidType.class)) {
            return new OidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UuidType.class)) {
            return new UuidType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(CanonicalType.class)) {
            return new CanonicalType(((StringValue) value).getStringValue());
        } else if (fhirType.equals(UrlType.class)) {
            return new UrlType(((StringValue) value).getStringValue());
        } else {
            throw new TransformationException("Got StringValue for FHIR type " + fhirType.getName() + ". This should not happen!");
        }
    } else if (value instanceof CodeSelectedValue) {
        CodeSelectedValue csv = (CodeSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        return getTarget(m).getCodeElement();
    } else if (value instanceof ConceptSelectedValue) {
        ConceptSelectedValue csv = (ConceptSelectedValue) value;
        String fieldId = csv.getFieldId();
        Mapping m = getSelectedMapping(fieldId, vertex);
        if (m == null) {
            throw new TransformationException("Mapping for field " + fieldId + " is required but was not found.");
        }
        if (fhirType.isAssignableFrom(Coding.class)) {
            return getTarget(m);
        } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
            return new CodeableConcept().addCoding(getTarget(m));
        } else {
            throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT_SELECTED.");
        }
    } else if (value instanceof ConceptValue) {
        // Ontoserver REDCap plugin format: 74400008|Appendicitis|http://snomed.info/sct
        ConceptValue cv = (ConceptValue) value;
        String fieldId = cv.getFieldId();
        Mapping m = getMapping(fieldId);
        if (m != null) {
            if (fhirType.isAssignableFrom(Coding.class)) {
                return getTarget(m);
            } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                return new CodeableConcept().addCoding(getTarget(m));
            } else {
                throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
            }
        } else {
            au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
            Coding c = field.getCoding(vertex);
            if (c != null) {
                if (fhirType.isAssignableFrom(Coding.class)) {
                    return c;
                } else if (fhirType.isAssignableFrom(CodeableConcept.class)) {
                    return new CodeableConcept().addCoding(c);
                } else {
                    throw new TransformationException("FHIR type of field " + fieldId + " (" + fhirType + ") is incompatible with CONCEPT.");
                }
            }
        }
        throw new TransformationException("Could not get concept for field " + fieldId + ".");
    } else if (value instanceof FieldValue) {
        FieldValue fv = (FieldValue) value;
        String fieldId = fv.getFieldId();
        FieldValue.DatePrecision pr = fv.getDatePrecision();
        au.csiro.redmatch.model.Field field = doc.getSchema().getField(fieldId);
        return field.getValue(vertex, fhirType, pr);
    } else {
        throw new TransformationException("Unable to get VALUE for " + value);
    }
}

Example 37 with Package

use of org.hl7.fhir.utilities.graphql.Package in project bunsen by cerner.

the class AvroConverterTest method testCompile.

@Test
public void testCompile() throws IOException {
    List<Schema> schemas = AvroConverter.generateSchemas(FhirContexts.forStu3(), ImmutableMap.of(TestData.US_CORE_PATIENT, Collections.emptyList(), TestData.VALUE_SET, Collections.emptyList(), TestData.US_CORE_MEDICATION_REQUEST, ImmutableList.of(TestData.US_CORE_MEDICATION)));
    // Wrap the schemas in a protocol to simplify the invocation of the compiler.
    Protocol protocol = new Protocol("fhir-test", "FHIR Resources for Testing", null);
    protocol.setTypes(schemas);
    SpecificCompiler compiler = new SpecificCompiler(protocol);
    Path generatedCodePath = Files.createTempDirectory("generated_code");
    generatedCodePath.toFile().deleteOnExit();
    compiler.compileToDestination(null, generatedCodePath.toFile());
    // Check that java files were created as expected.
    Set<String> javaFiles = Files.find(generatedCodePath, 10, (path, basicFileAttributes) -> true).map(path -> generatedCodePath.relativize(path)).map(Object::toString).collect(Collectors.toSet());
    // Ensure common types were generated
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/Period.java"));
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/Coding.java"));
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/ValueSet.java"));
    // The specific profile should be created in the expected sub-package.
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/us/core/Patient.java"));
    // Check extension types.
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/us/core/UsCoreRace.java"));
    // Choice types include each choice that could be used.
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/ChoiceBooleanInteger.java"));
    // Contained types created.
    Assert.assertTrue(javaFiles.contains("com/cerner/bunsen/stu3/avro/us/core/MedicationRequestContained.java"));
}

Example 38 with Package

use of org.hl7.fhir.utilities.graphql.Package in project beneficiary-fhir-data by CMSgov.

the class SamhsaMatcherR4FromClaimTransformerV2Test method verifySamhsaMatcherForDiagnosisPackage.

/**
 * Verify SAMHSA matcher for package with the given system, code and if the expectation is that
 * there should be a match for this combination.
 *
 * @param system the system value
 * @param code the code
 * @param shouldMatch if the matcher should match on this combination
 */
private void verifySamhsaMatcherForDiagnosisPackage(String system, String code, boolean shouldMatch, ExplanationOfBenefit explanationOfBenefit) {
    ExplanationOfBenefit modifiedEob = explanationOfBenefit.copy();
    // Set diagnosis DRG
    for (ExplanationOfBenefit.DiagnosisComponent diagnosisComponent : modifiedEob.getDiagnosis()) {
        diagnosisComponent.getDiagnosisCodeableConcept().setCoding(new ArrayList<>());
        CodeableConcept codeableConcept = new CodeableConcept();
        Coding coding = new Coding(system, code, null);
        codeableConcept.setCoding(Collections.singletonList(coding));
        diagnosisComponent.setPackageCode(codeableConcept);
    }
    // Set procedure to empty so we dont check it for matches
    for (ExplanationOfBenefit.ProcedureComponent diagnosisComponent : modifiedEob.getProcedure()) {
        CodeableConcept codeableConcept = diagnosisComponent.getProcedureCodeableConcept();
        ArrayList<Coding> codingList = new ArrayList<>();
        codeableConcept.setCoding(codingList);
    }
    // Set item coding to non-SAMHSA so we dont check it for matches
    List<Coding> codings = new ArrayList<>();
    Coding coding = new Coding();
    coding.setSystem(TransformerConstants.CODING_SYSTEM_HCPCS);
    coding.setCode(NON_SAMHSA_HCPCS_CODE);
    codings.add(coding);
    modifiedEob.getItem().get(0).getProductOrService().setCoding(codings);
    assertEquals(shouldMatch, samhsaMatcherV2.test(modifiedEob));
}

Example 39 with Package

use of org.hl7.fhir.utilities.graphql.Package in project beneficiary-fhir-data by CMSgov.

the class SamhsaMatcherR4FromClaimTransformerV2Test method verifySamhsaMatcherForItemWithSingleCoding.

/**
 * Verify SAMHSA matcher for item with the given system, code and if the expectation is that there
 * should be a match for this combination.
 *
 * @param system the system value
 * @param code the code
 * @param shouldMatch if the matcher should match on this combination
 * @param explanationOfBenefit the explanation of benefit
 */
private void verifySamhsaMatcherForItemWithSingleCoding(String system, String code, boolean shouldMatch, ExplanationOfBenefit explanationOfBenefit) {
    ExplanationOfBenefit modifiedEob = explanationOfBenefit.copy();
    // Set Top level diagnosis and package code to null so we can test item logic
    for (ExplanationOfBenefit.DiagnosisComponent diagnosisComponent : modifiedEob.getDiagnosis()) {
        CodeableConcept codeableConcept = diagnosisComponent.getDiagnosisCodeableConcept();
        codeableConcept.setCoding(new ArrayList<>());
        diagnosisComponent.setPackageCode(null);
    }
    List<Coding> codings = new ArrayList<>();
    Coding coding = new Coding();
    coding.setSystem(system);
    coding.setCode(code);
    codings.add(coding);
    modifiedEob.getItem().get(0).getProductOrService().setCoding(codings);
    assertEquals(shouldMatch, samhsaMatcherV2.test(modifiedEob));
}

Example 40 with Package

use of org.hl7.fhir.utilities.graphql.Package in project beneficiary-fhir-data by CMSgov.

the class SamhsaMatcherFromClaimTransformerTest method verifySamhsaMatcherForItemWithMultiCoding.

/**
 * Verify SAMHSA matcher for item with the given system, code and if the expectation is that there
 * should be a match for this combination.
 *
 * @param system the system value of the first coding
 * @param code the code of the first coding
 * @param system2 the system value of the second coding
 * @param code2 the code of the second coding
 * @param shouldMatch if the matcher should match on this combination
 * @param explanationOfBenefit the explanation of benefit
 */
private void verifySamhsaMatcherForItemWithMultiCoding(String system, String code, String system2, String code2, boolean shouldMatch, ExplanationOfBenefit explanationOfBenefit) {
    ExplanationOfBenefit modifiedEob = explanationOfBenefit.copy();
    // Set Top level diagnosis and package code to null so we can test item logic
    for (ExplanationOfBenefit.DiagnosisComponent diagnosisComponent : modifiedEob.getDiagnosis()) {
        CodeableConcept codeableConcept = diagnosisComponent.getDiagnosisCodeableConcept();
        codeableConcept.setCoding(new ArrayList<>());
        diagnosisComponent.setPackageCode(null);
    }
    List<Coding> codings = new ArrayList<>();
    Coding coding = new Coding();
    coding.setSystem(system);
    coding.setCode(code);
    Coding coding2 = new Coding();
    coding2.setSystem(system2);
    coding2.setCode(code2);
    codings.add(coding);
    codings.add(coding2);
    modifiedEob.getItem().get(0).getService().setCoding(codings);
    assertEquals(shouldMatch, samhsaMatcher.test(modifiedEob));
}