Examples with SingleValidationMessage ca.uhn.fhir.validation.SingleValidationMessage used on opensource projects

Example 1 with SingleValidationMessage

use of ca.uhn.fhir.validation.SingleValidationMessage in project synthea by synthetichealth.

the class FHIRR4ExporterTest method testFHIRR4Export.

@Test
public void testFHIRR4Export() throws Exception {
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());
    FhirContext ctx = FhirR4.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    ValidationResources validator = new ValidationResources();
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        TestHelper.exportOff();
        FhirR4.TRANSACTION_BUNDLE = person.randBoolean();
        FhirR4.USE_US_CORE_IG = person.randBoolean();
        FhirR4.USE_SHR_EXTENSIONS = false;
        String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
        // (these should have been converted into URIs)
        if (fhirJson.contains("SNOMED-CT")) {
            validationErrors.add("JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
        }
        // Let's crack open the Bundle and validate
        // each individual entry.resource to get context-sensitive error
        // messages...
        // IMPORTANT: this approach significantly reduces memory usage when compared to
        // validating the entire bundle at a time, but means that validating references
        // is impossible.
        // As of 2021-01-05, validating the bundle didn't validate references anyway,
        // but at some point we may want to do that.
        Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
        for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
            ValidationResult eresult = validator.validateR4(entry.getResource());
            if (!eresult.isSuccessful()) {
                for (SingleValidationMessage emessage : eresult.getMessages()) {
                    boolean valid = false;
                    if (emessage.getSeverity() == ResultSeverityEnum.INFORMATION || emessage.getSeverity() == ResultSeverityEnum.WARNING) {
                        /*
               * Ignore warnings.
               */
                        valid = true;
                    } else if (emessage.getMessage().contains("us-core-documentreference-type")) {
                        /*
               * The instance validator does not expand intentional value sets like this one.
               */
                        valid = true;
                    } else if (emessage.getMessage().contains("@ AllergyIntolerance ait-2")) {
                        /*
               * The ait-2 invariant:
               * Description:
               * AllergyIntolerance.clinicalStatus SHALL NOT be present
               * if verification Status is entered-in-error
               * Expression:
               * verificationStatus!='entered-in-error' or clinicalStatus.empty()
               */
                        valid = true;
                    } else if (emessage.getMessage().contains("@ ExplanationOfBenefit dom-3")) {
                        /*
               * For some reason, it doesn't like the contained ServiceRequest and contained
               * Coverage resources in the ExplanationOfBenefit, both of which are
               * properly referenced. Running $validate on test servers finds this valid...
               */
                        valid = true;
                    } else if (emessage.getMessage().contains("per-1: If present, start SHALL have a lower value than end")) {
                        /*
               * The per-1 invariant does not account for daylight savings time... so, if the
               * daylight savings switch happens between the start and end, the validation
               * fails, even if it is valid.
               */
                        // ignore this error
                        valid = true;
                    } else if (emessage.getMessage().contains("Unknown extension http://hl7.org/fhir/us/core") || emessage.getMessage().contains("Unknown extension http://synthetichealth") || emessage.getMessage().contains("not be resolved, so has not been checked")) {
                        /*
               * Despite setting instanceValidator.setAnyExtensionsAllowed(true) and
               * instanceValidator.setErrorForUnknownProfiles(false), the FHIR validator still
               * reports these as errors
               */
                        // ignore this error
                        valid = true;
                    }
                    if (!valid) {
                        System.out.println(parser.encodeResourceToString(entry.getResource()));
                        System.out.println("ERROR: " + emessage.getMessage());
                        validationErrors.add(emessage.getMessage());
                    }
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            Exporter.export(person, System.currentTimeMillis());
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 2 with SingleValidationMessage

use of ca.uhn.fhir.validation.SingleValidationMessage in project synthea by synthetichealth.

the class HospitalExporterTestStu3 method testFHIRExport.

@Test
public void testFHIRExport() throws Exception {
    FhirContext ctx = FhirStu3.getContext();
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    File tempOutputFolder = tempFolder.newFolder();
    Config.set("exporter.baseDirectory", tempOutputFolder.toString());
    Config.set("exporter.hospital.fhir_stu3.export", "true");
    Config.set("exporter.fhir.transaction_bundle", "true");
    // set this manually, in case it has already been loaded.
    FhirStu3.TRANSACTION_BUNDLE = true;
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Location location = new Location(Generator.DEFAULT_STATE, null);
    Provider.clear();
    Provider.loadProviders(location, 1L);
    assertNotNull(Provider.getProviderList());
    assertFalse(Provider.getProviderList().isEmpty());
    Provider.getProviderList().get(0).incrementEncounters(EncounterType.WELLNESS, 0);
    HospitalExporterStu3.export(0L);
    File expectedExportFolder = tempOutputFolder.toPath().resolve("fhir_stu3").toFile();
    assertTrue(expectedExportFolder.exists() && expectedExportFolder.isDirectory());
    File expectedExportFile = expectedExportFolder.toPath().resolve("hospitalInformation0.json").toFile();
    assertTrue(expectedExportFile.exists() && expectedExportFile.isFile());
    FileReader fileReader = new FileReader(expectedExportFile.getPath());
    BufferedReader bufferedReader = new BufferedReader(fileReader);
    StringBuilder fhirJson = new StringBuilder();
    String line = null;
    while ((line = bufferedReader.readLine()) != null) {
        fhirJson.append(line);
    }
    bufferedReader.close();
    IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson.toString());
    ValidationResult result = validator.validateWithResult(resource);
    if (result.isSuccessful() == false) {
        for (SingleValidationMessage message : result.getMessages()) {
            System.out.println(message.getSeverity().toString() + ": " + message.getMessage());
        }
    }
    assertTrue(result.isSuccessful());
}

Example 3 with SingleValidationMessage

use of ca.uhn.fhir.validation.SingleValidationMessage in project synthea by synthetichealth.

the class FHIRDSTU2ExporterTest method testFHIRDSTU2Export.

@Test
public void testFHIRDSTU2Export() throws Exception {
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());
    FhirContext ctx = FhirDstu2.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        Config.set("exporter.fhir_dstu2.export", "true");
        FhirDstu2.TRANSACTION_BUNDLE = person.randBoolean();
        String fhirJson = FhirDstu2.convertToFHIRJson(person, System.currentTimeMillis());
        // (these should have been converted into URIs)
        if (fhirJson.contains("SNOMED-CT")) {
            validationErrors.add("JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
        }
        // let's crack open the Bundle and validate
        // each individual entry.resource to get context-sensitive error
        // messages...
        Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
        for (Entry entry : bundle.getEntry()) {
            ValidationResult eresult = validator.validateWithResult(entry.getResource());
            if (!eresult.isSuccessful()) {
                for (SingleValidationMessage emessage : eresult.getMessages()) {
                    if (emessage.getMessage().contains("start SHALL have a lower value than end")) {
                        continue;
                    }
                    System.out.println(parser.encodeResourceToString(entry.getResource()));
                    System.out.println("ERROR: " + emessage.getMessage());
                    validationErrors.add(emessage.getMessage());
                }
            }
            if (entry.getResource() instanceof DiagnosticReport) {
                DiagnosticReport report = (DiagnosticReport) entry.getResource();
                if (report.getPerformer().isEmpty()) {
                    validationErrors.add("Performer is a required field on DiagnosticReport!");
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            Exporter.export(person, System.currentTimeMillis());
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 4 with SingleValidationMessage

use of ca.uhn.fhir.validation.SingleValidationMessage in project synthea by synthetichealth.

the class FHIRSTU3ExporterTest method testFHIRSTU3Export.

@Test
public void testFHIRSTU3Export() throws Exception {
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());
    FhirContext ctx = FhirStu3.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    ValidationResources validationResources = new ValidationResources();
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        TestHelper.exportOff();
        Config.set("exporter.fhir_stu3.export", "true");
        Config.set("exporter.fhir.use_shr_extensions", "true");
        FhirStu3.TRANSACTION_BUNDLE = person.randBoolean();
        String fhirJson = FhirStu3.convertToFHIRJson(person, System.currentTimeMillis());
        // (these should have been converted into URIs)
        if (fhirJson.contains("SNOMED-CT")) {
            validationErrors.add("JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
        }
        // let's crack open the Bundle and validate
        // each individual entry.resource to get context-sensitive error
        // messages...
        Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            ValidationResult eresult = validator.validateWithResult(entry.getResource());
            if (!eresult.isSuccessful()) {
                for (SingleValidationMessage emessage : eresult.getMessages()) {
                    boolean valid = false;
                    if (emessage.getMessage().contains("@ Observation obs-7")) {
                        /*
               * The obs-7 invariant basically says that Observations should have values, unless
               * they are made of components. This test replaces an invalid XPath expression
               * that was causing correct instances to fail validation.
               */
                        valid = validateObs7((Observation) entry.getResource());
                    } else if (emessage.getMessage().contains("@ Condition con-4")) {
                        /*
               * The con-4 invariant says "If condition is abated, then clinicalStatus must be
               * either inactive, resolved, or remission" which is very clear and sensical.
               * However, the XPath expression does not evaluate correctly for valid instances,
               * so we must manually validate.
               */
                        valid = validateCon4((Condition) entry.getResource());
                    } else if (emessage.getMessage().contains("@ MedicationRequest mps-1")) {
                        /*
               * The mps-1 invariant says MedicationRequest.requester.onBehalfOf can only be
               * specified if MedicationRequest.requester.agent is practitioner or device.
               * But the invariant is poorly written and does not correctly handle references
               * starting with "urn:uuid"
               */
                        // ignore this error
                        valid = true;
                    } else if (emessage.getMessage().contains("per-1: If present, start SHALL have a lower value than end")) {
                        /*
               * The per-1 invariant does not account for daylight savings time... so, if the
               * daylight savings switch happens between the start and end, the validation
               * fails, even if it is valid.
               */
                        // ignore this error
                        valid = true;
                    }
                    if (!valid) {
                        System.out.println(parser.encodeResourceToString(entry.getResource()));
                        System.out.println("ERROR: " + emessage.getMessage());
                        validationErrors.add(emessage.getMessage());
                    }
                }
            }
            // Check ExplanationOfBenefit Resources against BlueButton
            if (entry.getResource().fhirType().equals("ExplanationOfBenefit")) {
                ValidationResult bbResult = validationResources.validateSTU3(entry.getResource());
                for (SingleValidationMessage message : bbResult.getMessages()) {
                    if (message.getMessage().contains("extension https://bluebutton.cms.gov/assets")) {
                        /*
               * The instance validator complains about the BlueButton extensions, ignore
               */
                        continue;
                    } else if (message.getSeverity() == ResultSeverityEnum.ERROR) {
                        if (!(message.getMessage().contains("Element 'ExplanationOfBenefit.id': minimum required = 1, but only found 0") || message.getMessage().contains("Could not verify slice for profile"))) {
                            // For some reason the validator is not detecting the IDs on the resources,
                            // even though they appear to be present while debugging and during normal
                            // operations.
                            System.out.println(message.getSeverity() + ": " + message.getMessage());
                            Assert.fail(message.getSeverity() + ": " + message.getMessage());
                        }
                    }
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            Exporter.export(person, System.currentTimeMillis());
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 5 with SingleValidationMessage

use of ca.uhn.fhir.validation.SingleValidationMessage in project synthea by synthetichealth.

the class HospitalExporterTestR4 method testFHIRExport.

@Test
public void testFHIRExport() throws Exception {
    FhirContext ctx = FhirR4.getContext();
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    File tempOutputFolder = tempFolder.newFolder();
    Config.set("exporter.baseDirectory", tempOutputFolder.toString());
    Config.set("exporter.hospital.fhir.export", "true");
    Config.set("exporter.fhir.transaction_bundle", "true");
    // set this manually, in case it has already been loaded.
    FhirR4.TRANSACTION_BUNDLE = true;
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Location location = new Location(Generator.DEFAULT_STATE, null);
    Provider.clear();
    Provider.loadProviders(location, 1L);
    assertNotNull(Provider.getProviderList());
    assertFalse(Provider.getProviderList().isEmpty());
    Provider.getProviderList().get(0).incrementEncounters(EncounterType.WELLNESS, 0);
    HospitalExporterR4.export(new Generator(), 0L);
    File expectedExportFolder = tempOutputFolder.toPath().resolve("fhir").toFile();
    assertTrue(expectedExportFolder.exists() && expectedExportFolder.isDirectory());
    File expectedExportFile = expectedExportFolder.toPath().resolve("hospitalInformation0.json").toFile();
    assertTrue(expectedExportFile.exists() && expectedExportFile.isFile());
    FileReader fileReader = new FileReader(expectedExportFile.getPath());
    BufferedReader bufferedReader = new BufferedReader(fileReader);
    StringBuilder fhirJson = new StringBuilder();
    String line = null;
    while ((line = bufferedReader.readLine()) != null) {
        fhirJson.append(line);
    }
    bufferedReader.close();
    IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson.toString());
    ValidationResult result = validator.validateWithResult(resource);
    if (result.isSuccessful() == false) {
        for (SingleValidationMessage message : result.getMessages()) {
            System.out.println(message.getSeverity().toString() + ": " + message.getMessage());
        }
    }
    assertTrue(result.isSuccessful());
}