Merge pull request #1050 from anthonys123/master
Fixes for issue #1048. FhirInstanceValidator::validate() now looking…
This commit is contained in:
James Agnew
GitHub
commit
7b7f3c333b
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@ -4,23 +4,34 @@ import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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import java.io.IOException;
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import java.util.Arrays;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.*;
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import org.junit.Test;
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import ca.uhn.fhir.jpa.dao.DaoConfig;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.dstu2.resource.*;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
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import ca.uhn.fhir.model.dstu2.resource.Observation;
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import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
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import ca.uhn.fhir.model.dstu2.resource.Organization;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.dstu2.resource.StructureDefinition;
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import ca.uhn.fhir.model.dstu2.resource.ValueSet;
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import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.api.*;
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import ca.uhn.fhir.rest.server.exceptions.*;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.ValidationModeEnum;
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import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.TestUtil;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.After;
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import org.junit.AfterClass;
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import org.junit.Before;
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import org.junit.Test;
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import java.io.IOException;
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import java.util.Arrays;
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public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2ValidateTest.class);
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@ -122,7 +133,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
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String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
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Observation input = new Observation();
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String profileUri = "http://example.com/" + methodName;
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String profileUri = "http://example.com/StructureDefinition/" + methodName;
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ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(profileUri)));
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input.addIdentifier().setSystem("http://acme").setValue("12345");
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@ -1,5 +1,12 @@
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package ca.uhn.fhir.jpa.dao.dstu3;
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<<<<<<< master
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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=======
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>>>>>>> master
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.ValidationModeEnum;
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@ -9,9 +16,16 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.TestUtil;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.Bundle;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.IdType;
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import org.hl7.fhir.dstu3.model.Observation;
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import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
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import org.hl7.fhir.dstu3.model.OperationOutcome;
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import org.hl7.fhir.dstu3.model.Organization;
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import org.hl7.fhir.dstu3.model.Patient;
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import org.hl7.fhir.dstu3.model.StructureDefinition;
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import org.hl7.fhir.dstu3.model.ValueSet;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.AfterClass;
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@ -20,11 +34,14 @@ import org.junit.Test;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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<<<<<<< master
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=======
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import static ca.uhn.fhir.jpa.util.TestUtil.sleepAtLeast;
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import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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>>>>>>> master
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public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu3ValidateTest.class);
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@ -199,7 +216,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
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String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
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Observation input = new Observation();
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String profileUri = "http://example.com/" + methodName;
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String profileUri = "http://example.com/StructureDefinition/" + methodName;
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input.getMeta().getProfile().add(new IdType(profileUri));
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input.addIdentifier().setSystem("http://acme").setValue("12345");
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@ -4,21 +4,35 @@ import static org.hamcrest.Matchers.containsString;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.api.MethodOutcome;
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import ca.uhn.fhir.rest.api.ValidationModeEnum;
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import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.util.TestUtil;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.r4.model.*;
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import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.*;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.r4.model.CanonicalType;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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import org.hl7.fhir.r4.model.OperationOutcome;
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import org.hl7.fhir.r4.model.Organization;
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import org.hl7.fhir.r4.model.Patient;
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import org.hl7.fhir.r4.model.StructureDefinition;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.junit.AfterClass;
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import org.junit.Ignore;
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import org.junit.Test;
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import ca.uhn.fhir.util.StopWatch;
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import ca.uhn.fhir.rest.api.*;
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import ca.uhn.fhir.rest.server.exceptions.*;
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import ca.uhn.fhir.util.TestUtil;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
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@ -153,7 +167,7 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
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String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
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Observation input = new Observation();
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String profileUri = "http://example.com/" + methodName;
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String profileUri = "http://example.com/StructureDefinition/" + methodName;
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input.getMeta().getProfile().add(new CanonicalType(profileUri));
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input.addIdentifier().setSystem("http://acme").setValue("12345");
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@ -12,6 +12,8 @@ import com.github.benmanes.caffeine.cache.Caffeine;
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import com.github.benmanes.caffeine.cache.LoadingCache;
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import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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import org.apache.commons.lang3.Validate;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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@ -21,7 +23,12 @@ import org.fhir.ucum.UcumService;
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import org.hl7.fhir.convertors.VersionConvertor_30_40;
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import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
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import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
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import org.hl7.fhir.dstu3.model.*;
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import org.hl7.fhir.dstu3.model.CodeSystem;
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import org.hl7.fhir.dstu3.model.CodeableConcept;
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import org.hl7.fhir.dstu3.model.Coding;
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import org.hl7.fhir.dstu3.model.Questionnaire;
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import org.hl7.fhir.dstu3.model.StructureDefinition;
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import org.hl7.fhir.dstu3.model.ValueSet;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.TerminologyServiceException;
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import org.hl7.fhir.r4.context.IWorkerContext;
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@ -42,11 +49,18 @@ import org.w3c.dom.Element;
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import org.w3c.dom.NodeList;
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import org.xml.sax.InputSource;
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import java.io.StringReader;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.concurrent.TimeUnit;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import java.io.StringReader;
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import java.util.*;
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import java.util.concurrent.TimeUnit;
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public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
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@ -94,8 +108,48 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
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return root.getLocalName();
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}
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private ArrayList<String> determineIfProfilesSpecified(Document theDocument)
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{
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ArrayList<String> profileNames = new ArrayList<String>();
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NodeList list = theDocument.getChildNodes().item(0).getChildNodes();
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for (int i = 0; i < list.getLength(); i++) {
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if (list.item(i).getNodeName().compareToIgnoreCase("meta") == 0)
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{
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NodeList metaList = list.item(i).getChildNodes();
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for (int j = 0; j < metaList.getLength(); j++)
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{
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if (metaList.item(j).getNodeName().compareToIgnoreCase("profile") == 0)
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{
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profileNames.add(metaList.item(j).getAttributes().item(0).getNodeValue());
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}
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}
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break;
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}
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}
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return profileNames;
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}
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private StructureDefinition findStructureDefinitionForResourceName(final FhirContext theCtx, String resourceName) {
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String sdName = "http://hl7.org/fhir/StructureDefinition/" + resourceName;
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String sdName = null;
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try {
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// Test if a URL was passed in specifying the structure definition and test if "StructureDefinition" is part of the URL
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URL testIfUrl = new URL(resourceName);
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if (resourceName.toLowerCase().contains("structuredefinition"))
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{
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sdName = resourceName;
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}
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else
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{
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ourLog.error(String.format("Structure definition URL must contain the text, \"StructureDefinition\", URL=%s",
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resourceName));
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throw new InternalErrorException(String.format("Structure definition URL must contain the text, \"StructureDefinition\", URL=%s",
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resourceName));
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}
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}
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catch (MalformedURLException e)
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{
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sdName = "http://hl7.org/fhir/StructureDefinition/" + resourceName;
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}
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StructureDefinition profile = myStructureDefintion != null ? myStructureDefintion : myValidationSupport.fetchStructureDefinition(theCtx, sdName);
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return profile;
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}
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@ -227,27 +281,72 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
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return Collections.singletonList(m);
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}
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String resourceName = determineResourceName(document);
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StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
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if (profile != null) {
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try {
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v.validate(null, messages, document, profile.getUrl());
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} catch (Exception e) {
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ourLog.error("Failure during validation", e);
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throw new InternalErrorException("Unexpected failure while validating resource", e);
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// Determine if meta/profiles are present...
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ArrayList<String> resourceNames = determineIfProfilesSpecified(document);
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if (resourceNames.isEmpty())
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{
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resourceNames.add(determineResourceName(document));
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}
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for (String resourceName : resourceNames) {
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StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
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if (profile != null) {
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try {
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v.validate(null, messages, document, profile.getUrl());
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} catch (Exception e) {
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ourLog.error("Failure during validation", e);
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throw new InternalErrorException("Unexpected failure while validating resource", e);
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}
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}
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else
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{
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profile = findStructureDefinitionForResourceName(theCtx, determineResourceName(document));
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if (profile != null) {
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try {
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v.validate(null, messages, document, profile.getUrl());
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} catch (Exception e) {
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ourLog.error("Failure during validation", e);
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throw new InternalErrorException("Unexpected failure while validating resource", e);
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}
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}
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}
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}
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} else if (theEncoding == EncodingEnum.JSON) {
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Gson gson = new GsonBuilder().create();
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JsonObject json = gson.fromJson(theInput, JsonObject.class);
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String resourceName = json.get("resourceType").getAsString();
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StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
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if (profile != null) {
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try {
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v.validate(null, messages, json, profile.getUrl());
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} catch (Exception e) {
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throw new InternalErrorException("Unexpected failure while validating resource", e);
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ArrayList<String> resourceNames = new ArrayList<String>();
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JsonArray profiles = null;
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try {
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profiles = json.getAsJsonObject("meta").getAsJsonArray("profile");
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for (JsonElement element : profiles)
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{
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resourceNames.add(element.getAsString());
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}
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} catch (Exception e) {
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resourceNames.add(json.get("resourceType").getAsString());
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}
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for (String resourceName : resourceNames) {
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StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
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if (profile != null) {
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try {
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v.validate(null, messages, json, profile.getUrl());
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} catch (Exception e) {
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throw new InternalErrorException("Unexpected failure while validating resource", e);
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}
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}
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else
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{
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profile = findStructureDefinitionForResourceName(theCtx, json.get("resourceType").getAsString());
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if (profile != null) {
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try {
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v.validate(null, messages, json, profile.getUrl());
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} catch (Exception e) {
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ourLog.error("Failure during validation", e);
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throw new InternalErrorException("Unexpected failure while validating resource", e);
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}
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}
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}
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}
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} else {
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@ -1,6 +1,12 @@
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package org.hl7.fhir.instance.hapi.validation;
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import ca.uhn.fhir.context.*;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
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import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition;
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import ca.uhn.fhir.rest.api.EncodingEnum;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.validation.IValidationContext;
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@ -10,6 +16,8 @@ import com.github.benmanes.caffeine.cache.Caffeine;
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import com.github.benmanes.caffeine.cache.LoadingCache;
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import com.google.gson.Gson;
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import com.google.gson.GsonBuilder;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.Validate;
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@ -20,7 +28,12 @@ import org.hl7.fhir.convertors.VersionConvertorAdvisor40;
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import org.hl7.fhir.convertors.VersionConvertor_10_40;
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import org.hl7.fhir.exceptions.FHIRException;
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import org.hl7.fhir.exceptions.TerminologyServiceException;
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import org.hl7.fhir.instance.model.*;
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import org.hl7.fhir.instance.model.CodeableConcept;
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import org.hl7.fhir.instance.model.Coding;
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import org.hl7.fhir.instance.model.Questionnaire;
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import org.hl7.fhir.instance.model.Resource;
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import org.hl7.fhir.instance.model.StructureDefinition;
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import org.hl7.fhir.instance.model.ValueSet;
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import org.hl7.fhir.r4.context.IWorkerContext;
|
||||
import org.hl7.fhir.r4.formats.IParser;
|
||||
import org.hl7.fhir.r4.formats.ParserType;
|
||||
|
|
@ -40,15 +53,20 @@ import org.w3c.dom.Element;
|
|||
import org.w3c.dom.NodeList;
|
||||
import org.xml.sax.InputSource;
|
||||
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.io.StringReader;
|
||||
import java.util.*;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
|
||||
public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
|
||||
|
||||
|
|
@ -128,8 +146,48 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
return root.getLocalName();
|
||||
}
|
||||
|
||||
private ArrayList<String> determineIfProfilesSpecified(Document theDocument)
|
||||
{
|
||||
ArrayList<String> profileNames = new ArrayList<String>();
|
||||
NodeList list = theDocument.getChildNodes().item(0).getChildNodes();
|
||||
for (int i = 0; i < list.getLength(); i++) {
|
||||
if (list.item(i).getNodeName().compareToIgnoreCase("meta") == 0)
|
||||
{
|
||||
NodeList metaList = list.item(i).getChildNodes();
|
||||
for (int j = 0; j < metaList.getLength(); j++)
|
||||
{
|
||||
if (metaList.item(j).getNodeName().compareToIgnoreCase("profile") == 0)
|
||||
{
|
||||
profileNames.add(metaList.item(j).getAttributes().item(0).getNodeValue());
|
||||
}
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
return profileNames;
|
||||
}
|
||||
|
||||
private StructureDefinition findStructureDefinitionForResourceName(final FhirContext theCtx, String resourceName) {
|
||||
String sdName = "http://hl7.org/fhir/StructureDefinition/" + resourceName;
|
||||
String sdName = null;
|
||||
try {
|
||||
// Test if a URL was passed in specifying the structure definition and test if "StructureDefinition" is part of the URL
|
||||
URL testIfUrl = new URL(resourceName);
|
||||
if (resourceName.toLowerCase().contains("structuredefinition"))
|
||||
{
|
||||
sdName = resourceName;
|
||||
}
|
||||
else
|
||||
{
|
||||
ourLog.error(String.format("Structure definition URL must contain the text, \"StructureDefinition\", URL=%s",
|
||||
resourceName));
|
||||
throw new InternalErrorException(String.format("Structure definition URL must contain the text, \"StructureDefinition\", URL=%s",
|
||||
resourceName));
|
||||
}
|
||||
}
|
||||
catch (MalformedURLException e)
|
||||
{
|
||||
sdName = "http://hl7.org/fhir/StructureDefinition/" + resourceName;
|
||||
}
|
||||
StructureDefinition profile = myStructureDefintion != null ? myStructureDefintion : myValidationSupport.fetchResource(theCtx, StructureDefinition.class, sdName);
|
||||
return profile;
|
||||
}
|
||||
|
|
@ -257,27 +315,72 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
return Collections.singletonList(m);
|
||||
}
|
||||
|
||||
String resourceName = determineResourceName(document);
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, document, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
// Determine if meta/profiles are present...
|
||||
ArrayList<String> resourceNames = determineIfProfilesSpecified(document);
|
||||
if (resourceNames.isEmpty())
|
||||
{
|
||||
resourceNames.add(determineResourceName(document));
|
||||
}
|
||||
|
||||
for (String resourceName : resourceNames) {
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, document, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
profile = findStructureDefinitionForResourceName(theCtx, determineResourceName(document));
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, document, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
} else if (theEncoding == EncodingEnum.JSON) {
|
||||
Gson gson = new GsonBuilder().create();
|
||||
JsonObject json = gson.fromJson(theInput, JsonObject.class);
|
||||
|
||||
String resourceName = json.get("resourceType").getAsString();
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, json, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
ArrayList<String> resourceNames = new ArrayList<String>();
|
||||
JsonArray profiles = null;
|
||||
try {
|
||||
profiles = json.getAsJsonObject("meta").getAsJsonArray("profile");
|
||||
for (JsonElement element : profiles)
|
||||
{
|
||||
resourceNames.add(element.getAsString());
|
||||
}
|
||||
} catch (Exception e) {
|
||||
resourceNames.add(json.get("resourceType").getAsString());
|
||||
}
|
||||
|
||||
for (String resourceName : resourceNames) {
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, json, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
profile = findStructureDefinitionForResourceName(theCtx, json.get("resourceType").getAsString());
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, json, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
|
|
|
|||
|
|
@ -1,15 +1,24 @@
|
|||
package org.hl7.fhir.r4.hapi.validation;
|
||||
|
||||
import java.io.StringReader;
|
||||
import java.util.*;
|
||||
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
|
||||
import ca.uhn.fhir.context.ConfigurationException;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.validation.IValidationContext;
|
||||
import ca.uhn.fhir.validation.IValidatorModule;
|
||||
import com.google.gson.Gson;
|
||||
import com.google.gson.GsonBuilder;
|
||||
import com.google.gson.JsonArray;
|
||||
import com.google.gson.JsonElement;
|
||||
import com.google.gson.JsonObject;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.hl7.fhir.exceptions.PathEngineException;
|
||||
import org.hl7.fhir.r4.hapi.ctx.*;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
|
||||
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
|
||||
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
|
||||
import org.hl7.fhir.r4.model.Base;
|
||||
import org.hl7.fhir.r4.model.StructureDefinition;
|
||||
import org.hl7.fhir.r4.model.TypeDetails;
|
||||
import org.hl7.fhir.r4.utils.FHIRPathEngine.IEvaluationContext;
|
||||
import org.hl7.fhir.r4.utils.IResourceValidator.BestPracticeWarningLevel;
|
||||
import org.hl7.fhir.r4.utils.IResourceValidator.IdStatus;
|
||||
|
|
@ -21,14 +30,15 @@ import org.w3c.dom.Element;
|
|||
import org.w3c.dom.NodeList;
|
||||
import org.xml.sax.InputSource;
|
||||
|
||||
import com.google.gson.*;
|
||||
import java.io.StringReader;
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
|
||||
import ca.uhn.fhir.context.ConfigurationException;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.rest.api.EncodingEnum;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.validation.IValidationContext;
|
||||
import ca.uhn.fhir.validation.IValidatorModule;
|
||||
import javax.xml.parsers.DocumentBuilder;
|
||||
import javax.xml.parsers.DocumentBuilderFactory;
|
||||
|
||||
public class FhirInstanceValidator extends BaseValidatorBridge implements IValidatorModule {
|
||||
|
||||
|
|
@ -77,8 +87,48 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
return root.getLocalName();
|
||||
}
|
||||
|
||||
private ArrayList<String> determineIfProfilesSpecified(Document theDocument)
|
||||
{
|
||||
ArrayList<String> profileNames = new ArrayList<String>();
|
||||
NodeList list = theDocument.getChildNodes().item(0).getChildNodes();
|
||||
for (int i = 0; i < list.getLength(); i++) {
|
||||
if (list.item(i).getNodeName().compareToIgnoreCase("meta") == 0)
|
||||
{
|
||||
NodeList metaList = list.item(i).getChildNodes();
|
||||
for (int j = 0; j < metaList.getLength(); j++)
|
||||
{
|
||||
if (metaList.item(j).getNodeName().compareToIgnoreCase("profile") == 0)
|
||||
{
|
||||
profileNames.add(metaList.item(j).getAttributes().item(0).getNodeValue());
|
||||
}
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
return profileNames;
|
||||
}
|
||||
|
||||
private StructureDefinition findStructureDefinitionForResourceName(final FhirContext theCtx, String resourceName) {
|
||||
String sdName = "http://hl7.org/fhir/StructureDefinition/" + resourceName;
|
||||
String sdName = null;
|
||||
try {
|
||||
// Test if a URL was passed in specifying the structure definition and test if "StructureDefinition" is part of the URL
|
||||
URL testIfUrl = new URL(resourceName);
|
||||
if (resourceName.toLowerCase().contains("structuredefinition"))
|
||||
{
|
||||
sdName = resourceName;
|
||||
}
|
||||
else
|
||||
{
|
||||
ourLog.error(String.format("Structure definition URL must contain the text, \"StructureDefinition\", URL=%s",
|
||||
resourceName));
|
||||
throw new InternalErrorException(String.format("Structure definition URL must contain the text, \"StructureDefinition\", URL=%s",
|
||||
resourceName));
|
||||
}
|
||||
}
|
||||
catch (MalformedURLException e)
|
||||
{
|
||||
sdName = "http://hl7.org/fhir/StructureDefinition/" + resourceName;
|
||||
}
|
||||
StructureDefinition profile = myStructureDefintion != null ? myStructureDefintion : myValidationSupport.fetchStructureDefinition(theCtx, sdName);
|
||||
return profile;
|
||||
}
|
||||
|
|
@ -200,27 +250,72 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
|
|||
return Collections.singletonList(m);
|
||||
}
|
||||
|
||||
String resourceName = determineResourceName(document);
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, document, profile);
|
||||
} catch (Exception e) {
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
// Determine if meta/profiles are present...
|
||||
ArrayList<String> resourceNames = determineIfProfilesSpecified(document);
|
||||
if (resourceNames.isEmpty())
|
||||
{
|
||||
resourceNames.add(determineResourceName(document));
|
||||
}
|
||||
|
||||
for (String resourceName : resourceNames) {
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, document, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
profile = findStructureDefinitionForResourceName(theCtx, determineResourceName(document));
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, document, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
} else if (theEncoding == EncodingEnum.JSON) {
|
||||
Gson gson = new GsonBuilder().create();
|
||||
JsonObject json = gson.fromJson(theInput, JsonObject.class);
|
||||
|
||||
String resourceName = json.get("resourceType").getAsString();
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, json, profile);
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
ArrayList<String> resourceNames = new ArrayList<String>();
|
||||
JsonArray profiles = null;
|
||||
try {
|
||||
profiles = json.getAsJsonObject("meta").getAsJsonArray("profile");
|
||||
for (JsonElement element : profiles)
|
||||
{
|
||||
resourceNames.add(element.getAsString());
|
||||
}
|
||||
} catch (Exception e) {
|
||||
resourceNames.add(json.get("resourceType").getAsString());
|
||||
}
|
||||
|
||||
for (String resourceName : resourceNames) {
|
||||
StructureDefinition profile = findStructureDefinitionForResourceName(theCtx, resourceName);
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, json, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
profile = findStructureDefinitionForResourceName(theCtx, json.get("resourceType").getAsString());
|
||||
if (profile != null) {
|
||||
try {
|
||||
v.validate(null, messages, json, profile.getUrl());
|
||||
} catch (Exception e) {
|
||||
ourLog.error("Failure during validation", e);
|
||||
throw new InternalErrorException("Unexpected failure while validating resource", e);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
|
|
|
|||
|
|
@ -1,5 +1,20 @@
|
|||
package org.hl7.fhir.dstu3.hapi.validation;
|
||||
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.hamcrest.Matchers.greaterThan;
|
||||
import static org.hamcrest.Matchers.hasSize;
|
||||
import static org.hamcrest.Matchers.lessThan;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertFalse;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.assertTrue;
|
||||
import static org.mockito.ArgumentMatchers.nullable;
|
||||
import static org.mockito.Matchers.any;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
|
|
@ -11,19 +26,44 @@ import org.apache.commons.io.IOUtils;
|
|||
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
|
||||
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
|
||||
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport.CodeValidationResult;
|
||||
import org.hl7.fhir.dstu3.model.*;
|
||||
import org.hl7.fhir.dstu3.model.Base;
|
||||
import org.hl7.fhir.dstu3.model.BooleanType;
|
||||
import org.hl7.fhir.dstu3.model.Bundle;
|
||||
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.dstu3.model.CodeSystem;
|
||||
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.dstu3.model.CodeType;
|
||||
import org.hl7.fhir.dstu3.model.CodeableConcept;
|
||||
import org.hl7.fhir.dstu3.model.Coding;
|
||||
import org.hl7.fhir.dstu3.model.ContactPoint;
|
||||
import org.hl7.fhir.dstu3.model.DateTimeType;
|
||||
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
|
||||
import org.hl7.fhir.dstu3.model.Extension;
|
||||
import org.hl7.fhir.dstu3.model.Goal;
|
||||
import org.hl7.fhir.dstu3.model.ImagingStudy;
|
||||
import org.hl7.fhir.dstu3.model.Observation;
|
||||
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
|
||||
import org.hl7.fhir.dstu3.model.Patient;
|
||||
import org.hl7.fhir.dstu3.model.Period;
|
||||
import org.hl7.fhir.dstu3.model.Procedure;
|
||||
import org.hl7.fhir.dstu3.model.Questionnaire;
|
||||
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemComponent;
|
||||
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
|
||||
import org.hl7.fhir.dstu3.model.Reference;
|
||||
import org.hl7.fhir.dstu3.model.RelatedPerson;
|
||||
import org.hl7.fhir.dstu3.model.StringType;
|
||||
import org.hl7.fhir.dstu3.model.StructureDefinition;
|
||||
import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionKind;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
|
||||
import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.junit.*;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Before;
|
||||
import org.junit.Ignore;
|
||||
import org.junit.Rule;
|
||||
import org.junit.Test;
|
||||
import org.junit.rules.TestRule;
|
||||
import org.junit.rules.TestWatcher;
|
||||
import org.junit.runner.Description;
|
||||
|
|
@ -32,16 +72,15 @@ import org.mockito.stubbing.Answer;
|
|||
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.util.*;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.TreeSet;
|
||||
import java.util.zip.GZIPInputStream;
|
||||
|
||||
import static org.hamcrest.Matchers.*;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.mockito.ArgumentMatchers.nullable;
|
||||
import static org.mockito.Matchers.any;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
public class FhirInstanceValidatorDstu3Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorDstu3Test.class);
|
||||
|
|
@ -845,7 +884,7 @@ public class FhirInstanceValidatorDstu3Test {
|
|||
addValidConcept("http://loinc.org", "12345");
|
||||
|
||||
Observation input = new Observation();
|
||||
input.getMeta().addProfile("http://foo/myprofile");
|
||||
input.getMeta().addProfile("http://foo/structuredefinition/myprofile");
|
||||
|
||||
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
|
||||
input.setStatus(ObservationStatus.FINAL);
|
||||
|
|
@ -854,7 +893,7 @@ public class FhirInstanceValidatorDstu3Test {
|
|||
ValidationResult output = myVal.validateWithResult(input);
|
||||
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
|
||||
assertEquals(errors.toString(), 1, errors.size());
|
||||
assertEquals("StructureDefinition reference \"http://foo/myprofile\" could not be resolved", errors.get(0).getMessage());
|
||||
assertEquals("StructureDefinition reference \"http://foo/structuredefinition/myprofile\" could not be resolved", errors.get(0).getMessage());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -1,5 +1,20 @@
|
|||
package org.hl7.fhir.r4.validation;
|
||||
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.hamcrest.Matchers.greaterThan;
|
||||
import static org.hamcrest.Matchers.hasItem;
|
||||
import static org.hamcrest.Matchers.hasSize;
|
||||
import static org.hamcrest.Matchers.lessThan;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertFalse;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.assertTrue;
|
||||
import static org.mockito.ArgumentMatchers.nullable;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.util.TestUtil;
|
||||
|
|
@ -15,23 +30,53 @@ import org.hl7.fhir.exceptions.FHIRException;
|
|||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.r4.conformance.ProfileUtilities;
|
||||
import org.hl7.fhir.r4.context.IWorkerContext;
|
||||
import org.hl7.fhir.r4.hapi.ctx.*;
|
||||
import org.hl7.fhir.r4.hapi.ctx.DefaultProfileValidationSupport;
|
||||
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
|
||||
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
|
||||
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult;
|
||||
import org.hl7.fhir.r4.hapi.ctx.PrePopulatedValidationSupport;
|
||||
import org.hl7.fhir.r4.hapi.ctx.ValidationSupportChain;
|
||||
import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
|
||||
import org.hl7.fhir.r4.model.Base;
|
||||
import org.hl7.fhir.r4.model.Base64BinaryType;
|
||||
import org.hl7.fhir.r4.model.BooleanType;
|
||||
import org.hl7.fhir.r4.model.Bundle;
|
||||
import org.hl7.fhir.r4.hapi.validation.CachingValidationSupport;
|
||||
import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
|
||||
import org.hl7.fhir.r4.hapi.validation.PrePopulatedValidationSupport;
|
||||
import org.hl7.fhir.r4.hapi.validation.ValidationSupportChain;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
|
||||
import org.hl7.fhir.r4.model.CodeSystem;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.r4.model.CodeType;
|
||||
import org.hl7.fhir.r4.model.Consent;
|
||||
import org.hl7.fhir.r4.model.ContactPoint;
|
||||
import org.hl7.fhir.r4.model.DateTimeType;
|
||||
import org.hl7.fhir.r4.model.Extension;
|
||||
import org.hl7.fhir.r4.model.Media;
|
||||
import org.hl7.fhir.r4.model.Observation;
|
||||
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
import org.hl7.fhir.r4.model.Period;
|
||||
import org.hl7.fhir.r4.model.Practitioner;
|
||||
import org.hl7.fhir.r4.model.Procedure;
|
||||
import org.hl7.fhir.r4.model.QuestionnaireResponse;
|
||||
import org.hl7.fhir.r4.model.Reference;
|
||||
import org.hl7.fhir.r4.model.RelatedPerson;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.hl7.fhir.r4.model.StructureDefinition;
|
||||
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
|
||||
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
|
||||
import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent;
|
||||
import org.hl7.fhir.r4.utils.FHIRPathEngine;
|
||||
import org.hl7.fhir.r4.utils.IResourceValidator;
|
||||
import org.hl7.fhir.utilities.validation.ValidationMessage;
|
||||
import org.junit.*;
|
||||
import org.junit.AfterClass;
|
||||
import org.junit.Before;
|
||||
import org.junit.Ignore;
|
||||
import org.junit.Rule;
|
||||
import org.junit.Test;
|
||||
import org.junit.rules.TestRule;
|
||||
import org.junit.rules.TestWatcher;
|
||||
import org.junit.runner.Description;
|
||||
|
|
@ -40,17 +85,16 @@ import org.mockito.stubbing.Answer;
|
|||
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.util.*;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.TreeSet;
|
||||
import java.util.stream.Collectors;
|
||||
import java.util.zip.GZIPInputStream;
|
||||
|
||||
import static org.hamcrest.Matchers.*;
|
||||
import static org.junit.Assert.*;
|
||||
import static org.mockito.ArgumentMatchers.nullable;
|
||||
import static org.mockito.Matchers.any;
|
||||
import static org.mockito.Mockito.mock;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
public class FhirInstanceValidatorR4Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirInstanceValidatorR4Test.class);
|
||||
|
|
@ -912,7 +956,7 @@ public class FhirInstanceValidatorR4Test {
|
|||
addValidConcept("http://loinc.org", "12345");
|
||||
|
||||
Observation input = new Observation();
|
||||
input.getMeta().addProfile("http://foo/myprofile");
|
||||
input.getMeta().addProfile("http://foo/structuredefinition/myprofile");
|
||||
|
||||
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
|
||||
input.setStatus(ObservationStatus.FINAL);
|
||||
|
|
@ -921,7 +965,7 @@ public class FhirInstanceValidatorR4Test {
|
|||
ValidationResult output = myVal.validateWithResult(input);
|
||||
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
|
||||
assertEquals(errors.toString(), 1, errors.size());
|
||||
assertEquals("StructureDefinition reference \"http://foo/myprofile\" could not be resolved", errors.get(0).getMessage());
|
||||
assertEquals("StructureDefinition reference \"http://foo/structuredefinition/myprofile\" could not be resolved", errors.get(0).getMessage());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
Loading…
Reference in New Issue