Merge branch 'master' of https://github.com/jamesagnew/hapi-fhir
This commit is contained in:
de Beaubien, Bill
commit
6139e498be
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@ -7,7 +7,7 @@ HAPI FHIR - Java API for HL7 FHIR Clients and Servers
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[](https://coveralls.io/github/jamesagnew/hapi-fhir?branch=master)
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[](http://search.maven.org/#search|ga|1|ca.uhn.hapi.fhir)
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[](https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e)
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[](https://github.com/jamesagnew/hapi-fhir/blob/master/LICENSE.txt)
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[](http://jamesagnew.github.io/hapi-fhir/license.html)
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Complete project documentation is available here:
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http://jamesagnew.github.io/hapi-fhir/
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@ -152,7 +152,7 @@ public class LoggingInterceptor implements IClientInterceptor {
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throw new InternalErrorException(e);
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}
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myLog.info("Client response body:\n{}", new String(bytes));
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myLog.info("Client response body:\n{}", new String(bytes, "UTF-8"));
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theResponse.setEntity(new MyEntityWrapper(respEntity, bytes));
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} else {
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myLog.info("Client response body: (none)");
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@ -50,7 +50,6 @@ import org.codehaus.stax2.XMLOutputFactory2;
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import org.codehaus.stax2.io.EscapingWriterFactory;
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import com.ctc.wstx.api.WstxInputProperties;
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import com.ctc.wstx.stax.WstxInputFactory;
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import com.ctc.wstx.stax.WstxOutputFactory;
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/**
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@ -1550,6 +1549,7 @@ public class XmlUtil {
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if (ourInputFactory == null) {
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try {
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// Detect if we're running with the Android lib, and force repackaged Woodstox to be used
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Class.forName("ca.uhn.fhir.repackage.javax.xml.stream.XMLInputFactory");
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System.setProperty("javax.xml.stream.XMLInputFactory", "com.ctc.wstx.stax.WstxInputFactory");
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} catch (ClassNotFoundException e) {
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@ -1589,6 +1589,7 @@ public class XmlUtil {
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if (ourOutputFactory == null) {
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try {
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// Detect if we're running with the Android lib, and force repackaged Woodstox to be used
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Class.forName("ca.uhn.fhir.repackage.javax.xml.stream.XMLOutputFactory");
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System.setProperty("javax.xml.stream.XMLOutputFactory", "com.ctc.wstx.stax.WstxOutputFactory");
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} catch (ClassNotFoundException e) {
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@ -1708,7 +1709,7 @@ public class XmlUtil {
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@Override
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public Writer createEscapingWriterFor(OutputStream theOut, String theEnc) throws UnsupportedEncodingException {
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return createEscapingWriterFor(new OutputStreamWriter(theOut), theEnc);
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return createEscapingWriterFor(new OutputStreamWriter(theOut, theEnc), theEnc);
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}
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@Override
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@ -38,6 +38,7 @@ import javax.xml.validation.Schema;
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import javax.xml.validation.SchemaFactory;
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import javax.xml.validation.Validator;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.input.BOMInputStream;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.w3c.dom.ls.LSInput;
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@ -203,6 +204,7 @@ class SchemaBaseValidator implements IValidatorModule {
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InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
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if (baseIs == null) {
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IOUtils.closeQuietly(baseIs);
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throw new InternalErrorException("Schema file not found: " + pathToBase);
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}
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@ -28,6 +28,7 @@ import java.util.Map;
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import javax.xml.transform.stream.StreamSource;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.oclc.purl.dsdl.svrl.SchematronOutputType;
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@ -120,12 +121,14 @@ public class SchematronBaseValidator implements IValidatorModule {
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return retVal;
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}
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String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase()
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+ ".sch";
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String pathToBase = myCtx.getVersion().getPathToSchemaDefinitions() + '/' + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getName().toLowerCase() + ".sch";
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InputStream baseIs = FhirValidator.class.getResourceAsStream(pathToBase);
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if (baseIs == null) {
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throw new InternalErrorException("No schematron found for resource type: "
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+ theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getImplementingClass().getCanonicalName());
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try {
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if (baseIs == null) {
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throw new InternalErrorException("No schematron found for resource type: " + theCtx.getFhirContext().getResourceDefinition(theCtx.getResource()).getBaseDefinition().getImplementingClass().getCanonicalName());
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}
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} finally {
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IOUtils.closeQuietly(baseIs);
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}
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retVal = SchematronResourceSCH.fromClassPath(pathToBase);
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@ -160,7 +160,7 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
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retVal.setPublisher(myPublisher);
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retVal.setDate(DateTimeDt.withCurrentTime());
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retVal.setFhirVersion("0.5.0"); // TODO: pull from model
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retVal.setFhirVersion("1.0.0"); // TODO: pull from model
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retVal.setAcceptUnknown(UnknownContentCodeEnum.UNKNOWN_EXTENSIONS); // TODO: make this configurable - this is a fairly big effort since the parser
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// needs to be modified to actually allow it
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@ -166,7 +166,7 @@ public class ServerConformanceProvider implements IServerConformanceProvider<Con
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retVal.setPublisher(myPublisher);
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retVal.setDate(new Date());
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retVal.setFhirVersion("0.5.0"); // TODO: pull from model
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retVal.setFhirVersion("1.0.0"); // TODO: pull from model
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retVal.setAcceptUnknown(UnknownContentCode.EXTENSIONS); // TODO: make this configurable - this is a fairly big effort since the parser
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// needs to be modified to actually allow it
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@ -890,7 +890,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
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String p = stack.addToLiteralPath("meta", "profile", ":"+Integer.toString(i));
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if (rule(errors, IssueType.INVALID, element.line(), element.col(), p, !Utilities.noString(ref), "StructureDefinition reference invalid")) {
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StructureDefinition pr = context.fetchResource(StructureDefinition.class, ref);
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if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference could not be resolved")) {
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if (warning(errors, IssueType.INVALID, element.line(), element.col(), p, pr != null, "StructureDefinition reference \"{0}\" could not be resolved", ref)) {
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if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), p, pr.hasSnapshot(), "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) {
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validateElement(errors, pr, pr.getSnapshot().getElement().get(0), null, null, element, element.getName(), stack);
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}
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@ -1,5 +1,6 @@
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package ca.uhn.fhir.validation;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.greaterThan;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertThat;
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@ -8,6 +9,7 @@ import static org.mockito.Mockito.mock;
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import static org.mockito.Mockito.when;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import org.hl7.fhir.instance.model.CodeType;
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@ -23,6 +25,8 @@ import org.mockito.invocation.InvocationOnMock;
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import org.mockito.stubbing.Answer;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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public class FhirInstanceValidatorTest {
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@ -120,20 +124,29 @@ public class FhirInstanceValidatorTest {
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}
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@Test
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public void testValidateJsonResource() {
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// @formatter:off
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String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"" + "}";
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// @formatter:on
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public void testValidateRawJsonResource() {
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//@formatter:off
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String input =
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"{" +
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"\"resourceType\":\"Patient\"," +
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"\"id\":\"123\"" +
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"}";
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//@formatter:on
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ValidationResult output = myVal.validateWithResult(input);
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assertEquals(output.toString(), 0, output.getMessages().size());
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}
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@Test
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public void testValidateJsonResourceBadAttributes() {
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// @formatter:off
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String input = "{" + "\"resourceType\":\"Patient\"," + "\"id\":\"123\"," + "\"foo\":\"123\"" + "}";
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// @formatter:on
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public void testValidateRawJsonResourceBadAttributes() {
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//@formatter:off
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String input =
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"{" +
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"\"resourceType\":\"Patient\"," +
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"\"id\":\"123\"," +
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"\"foo\":\"123\"" +
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"}";
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//@formatter:on
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ValidationResult output = myVal.validateWithResult(input);
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assertEquals(output.toString(), 1, output.getMessages().size());
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@ -143,6 +156,34 @@ public class FhirInstanceValidatorTest {
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assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
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}
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@Test
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public void testValidateRawXmlResource() {
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//@formatter:off
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String input =
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"<Patient xmlns=\"http://hl7.org/fhir\">" +
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"<id value=\"123\"/>" +
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"</Patient>";
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//@formatter:on
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ValidationResult output = myVal.validateWithResult(input);
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assertEquals(output.toString(), 0, output.getMessages().size());
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}
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@Test
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public void testValidateRawXmlResourceBadAttributes() {
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// @formatter:off
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String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "<foo value=\"222\"/>"
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+ "</Patient>";
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// @formatter:on
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ValidationResult output = myVal.validateWithResult(input);
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assertEquals(output.toString(), 1, output.getMessages().size());
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ourLog.info(output.getMessages().get(0).getLocationString());
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ourLog.info(output.getMessages().get(0).getMessage());
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assertEquals("/f:Patient/f:foo", output.getMessages().get(0).getLocationString());
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assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
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}
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@Test
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public void testValidateResourceFailingInvariant() {
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Observation input = new Observation();
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@ -158,6 +199,68 @@ public class FhirInstanceValidatorTest {
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}
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@Test
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public void testValidateResourceContainingProfileDeclarationDoesntResolve() {
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addValidConcept("http://loinc.org", "12345");
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Observation input = new Observation();
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input.getMeta().addProfile("http://foo/myprofile");
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input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
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input.setStatus(ObservationStatus.FINAL);
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myInstanceVal.setValidationSupport(myMockSupport);
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ValidationResult output = myVal.validateWithResult(input);
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List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
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assertEquals(errors.toString(), 1, errors.size());
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assertEquals("StructureDefinition reference \"http://foo/myprofile\" could not be resolved", errors.get(0).getMessage());
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}
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@Test
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public void testValidateResourceContainingProfileDeclaration() {
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addValidConcept("http://loinc.org", "12345");
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Observation input = new Observation();
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input.getMeta().addProfile("http://hl7.org/fhir/StructureDefinition/devicemetricobservation");
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input.addIdentifier().setSystem("http://acme").setValue("12345");
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input.getEncounter().setReference("http://foo.com/Encounter/9");
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input.setStatus(ObservationStatus.FINAL);
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input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
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myInstanceVal.setValidationSupport(myMockSupport);
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ValidationResult output = myVal.validateWithResult(input);
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List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
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assertThat(errors.toString(), containsString("Element '/f:Observation.subject': minimum required = 1, but only found 0"));
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assertThat(errors.toString(), containsString("Element encounter @ /f:Observation: max allowed = 0, but found 1"));
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assertThat(errors.toString(), containsString("Element '/f:Observation.device': minimum required = 1, but only found 0"));
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assertThat(errors.toString(), containsString(""));
|
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}
|
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|
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@Test
|
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public void testValidateResourceWithDefaultValueset() {
|
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Observation input = new Observation();
|
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|
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input.setStatus(ObservationStatus.FINAL);
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input.getCode().setText("No code here!");
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|
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ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input));
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.getMessages().size(), 0);
|
||||
}
|
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|
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@Test
|
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public void testValidateResourceWithDefaultValuesetBadCode() {
|
||||
String input = "<Observation xmlns=\"http://hl7.org/fhir\">\n" + " <status value=\"notvalidcode\"/>\n"
|
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+ " <code>\n" + " <text value=\"No code here!\"/>\n" + " </code>\n" + "</Observation>";
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(
|
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"Coded value notvalidcode is not in value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status)",
|
||||
output.getMessages().get(0).getMessage());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
|
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Observation input = new Observation();
|
||||
|
|
@ -188,52 +291,4 @@ public class FhirInstanceValidatorTest {
|
|||
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
|
||||
assertEquals(errors.toString(), 0, errors.size());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateResourceWithDefaultValueset() {
|
||||
Observation input = new Observation();
|
||||
|
||||
input.setStatus(ObservationStatus.FINAL);
|
||||
input.getCode().setText("No code here!");
|
||||
|
||||
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(input));
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.getMessages().size(), 0);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateResourceWithDefaultValuesetBadCode() {
|
||||
String input = "<Observation xmlns=\"http://hl7.org/fhir\">\n" + " <status value=\"notvalidcode\"/>\n"
|
||||
+ " <code>\n" + " <text value=\"No code here!\"/>\n" + " </code>\n" + "</Observation>";
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(
|
||||
"Coded value notvalidcode is not in value set http://hl7.org/fhir/ValueSet/observation-status (http://hl7.org/fhir/ValueSet/observation-status)",
|
||||
output.getMessages().get(0).getMessage());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateXmlResource() {
|
||||
// @formatter:off
|
||||
String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "</Patient>";
|
||||
// @formatter:on
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.toString(), 0, output.getMessages().size());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateXmlResourceBadAttributes() {
|
||||
// @formatter:off
|
||||
String input = "<Patient xmlns=\"http://hl7.org/fhir\">" + "<id value=\"123\"/>" + "<foo value=\"222\"/>"
|
||||
+ "</Patient>";
|
||||
// @formatter:on
|
||||
|
||||
ValidationResult output = myVal.validateWithResult(input);
|
||||
assertEquals(output.toString(), 1, output.getMessages().size());
|
||||
ourLog.info(output.getMessages().get(0).getLocationString());
|
||||
ourLog.info(output.getMessages().get(0).getMessage());
|
||||
assertEquals("/f:Patient/f:foo", output.getMessages().get(0).getLocationString());
|
||||
assertEquals("Element is unknown or does not match any slice", output.getMessages().get(0).getMessage());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
4
pom.xml
4
pom.xml
|
|
@ -783,9 +783,11 @@
|
|||
<copy todir="target/site/xref-base">
|
||||
<fileset dir="hapi-fhir-base/target/site/xref" />
|
||||
</copy>
|
||||
<!--
|
||||
<copy todir="target/site/cobertura">
|
||||
<fileset dir="hapi-fhir-cobertura/target/site/cobertura" />
|
||||
</copy>
|
||||
-->
|
||||
<copy todir="target/site">
|
||||
<fileset dir="hapi-fhir-base/target/site" includes="checkstyle.*" />
|
||||
</copy>
|
||||
|
|
@ -1164,7 +1166,9 @@
|
|||
<module>hapi-fhir-structures-dstu2</module>
|
||||
<module>hapi-fhir-structures-hl7org-dstu2</module>
|
||||
<module>hapi-fhir-jpaserver-base</module>
|
||||
<!--
|
||||
<module>hapi-fhir-cobertura</module>
|
||||
-->
|
||||
<module>examples</module>
|
||||
</modules>
|
||||
<reporting>
|
||||
|
|
|
|||
|
|
@ -137,10 +137,9 @@
|
|||
</menu>
|
||||
|
||||
|
||||
<menu name="Maven Reports" inherit="bottom">
|
||||
<menu name="Reports" inherit="bottom">
|
||||
<item name="Project Developers" href="team-list.html" />
|
||||
<item name="Cobertura (Test Coverage)" href="cobertura/index.html" />
|
||||
<item name="Surefire (Test Status)" href="surefire-report.html" />
|
||||
<item name="Coveralls (Test Coverage)" href="https://coveralls.io/github/jamesagnew/hapi-fhir" />
|
||||
<item name="FindBugs" href="findbugs.html" />
|
||||
<item name="Checkstyle" href="checkstyle.html" />
|
||||
</menu>
|
||||
|
|
|
|||
|
|
@ -24,6 +24,8 @@
|
|||
<a href="https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg"><img src="https://maven-badges.herokuapp.com/maven-central/ca.uhn.hapi.fhir/hapi-fhir-base/badge.svg" alt="Maven Central"/></a>
|
||||
<br/>
|
||||
<a href="https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e"><img src="https://www.versioneye.com/user/projects/55e1d0d9c6d8f2001c00043e/badge.svg?style=flat" alt="VersionEye"/></a>
|
||||
<br/>
|
||||
<a href="http://jamesagnew.github.io/hapi-fhir/license.html"><img src="https://img.shields.io/badge/license-apache%202.0-ff69b4.svg" alt="Apache 2.0 Licensed"/></a>
|
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</p>
|
||||
|
||||
<p>
|
||||
|
|
|
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Reference in New Issue