Fix #124 - Resource references shouldn't include version when they are
encoded
This commit is contained in:
James Agnew
parent
ef88eb9a97
commit
c8a70c1904
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@ -21,6 +21,7 @@ package ca.uhn.fhir.parser;
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*/
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.io.IOException;
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import java.io.Reader;
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@ -65,6 +66,7 @@ public abstract class BaseParser implements IParser {
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private ContainedResources myContainedResources;
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private FhirContext myContext;
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private boolean mySuppressNarratives;
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private String myServerBaseUrl;
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public BaseParser(FhirContext theContext) {
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myContext = theContext;
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@ -163,8 +165,9 @@ public abstract class BaseParser implements IParser {
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}
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protected String determineReferenceText(BaseResourceReferenceDt theRef) {
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String reference = theRef.getReference().getValue();
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if (isBlank(reference)) {
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IdDt ref = theRef.getReference();
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if (isBlank(ref.getIdPart())) {
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String reference = ref.getValue();
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if (theRef.getResource() != null) {
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IdDt containedId = getContainedResources().getResourceId(theRef.getResource());
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if (containedId != null && !containedId.isEmpty()) {
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@ -177,8 +180,22 @@ public abstract class BaseParser implements IParser {
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reference = theRef.getResource().getId().getValue();
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}
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}
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return reference;
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} else {
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if (isNotBlank(myServerBaseUrl) && StringUtils.equals(myServerBaseUrl, ref.getBaseUrl())) {
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String reference = ref.toUnqualifiedVersionless().getValue();
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return reference;
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} else {
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String reference = ref.toVersionless().getValue();
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return reference;
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}
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}
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return reference;
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}
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@Override
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public IParser setServerBaseUrl(String theUrl) {
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myServerBaseUrl = isNotBlank(theUrl) ? theUrl : null;
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return this;
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}
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protected String determineResourceBaseUrl(String bundleBaseUrl, BundleEntry theEntry) {
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@ -32,7 +32,8 @@ import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.TagList;
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/**
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*
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* A parser, which can be used to convert between HAPI FHIR model/structure objects, and
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* their respective String wire formats, in either XML or JSON.
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* <p>
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* Thread safety: <b>Parsers are not guaranteed to be thread safe</b>. Create a new parser instance for every thread or every message being parsed/encoded.
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* </p>
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@ -66,10 +67,25 @@ public interface IParser {
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*/
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void encodeTagListToWriter(TagList theTagList, Writer theWriter) throws IOException;
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/**
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* Parse a DSTU1 style Atom Bundle. Note that as of DSTU2, Bundle is a resource so you
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* should use {@link #parseResource(Class, Reader)} with the Bundle class found in the
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* <code>ca.uhn.hapi.fhir.model.[version].resource</code> package instead.
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*/
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<T extends IBaseResource> Bundle parseBundle(Class<T> theResourceType, Reader theReader);
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/**
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* Parse a DSTU1 style Atom Bundle. Note that as of DSTU2, Bundle is a resource so you
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* should use {@link #parseResource(Class, Reader)} with the Bundle class found in the
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* <code>ca.uhn.hapi.fhir.model.[version].resource</code> package instead.
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*/
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Bundle parseBundle(Reader theReader);
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/**
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* Parse a DSTU1 style Atom Bundle. Note that as of DSTU2, Bundle is a resource so you
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* should use {@link #parseResource(Class, String)} with the Bundle class found in the
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* <code>ca.uhn.hapi.fhir.model.[version].resource</code> package instead.
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*/
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Bundle parseBundle(String theMessageString) throws ConfigurationException, DataFormatException;
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/**
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@ -143,7 +159,7 @@ public interface IParser {
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*
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* @param thePrettyPrint
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* The flag
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* @return Returns an instance of <code>this</code> parser so that method calls can be conveniently chained
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* @return Returns an instance of <code>this</code> parser so that method calls can be chained together
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*/
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IParser setPrettyPrint(boolean thePrettyPrint);
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@ -152,4 +168,14 @@ public interface IParser {
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*/
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IParser setSuppressNarratives(boolean theSuppressNarratives);
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/**
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* Sets the server's base URL used by this parser. If a value is set, resource references
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* will be turned into relative references if they are provided as absolute URLs but
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* have a base matching the given base.
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*
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* @param theUrl The base URL, e.g. "http://example.com/base"
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* @return Returns an instance of <code>this</code> parser so that method calls can be chained together
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*/
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IParser setServerBaseUrl(String theUrl);
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}
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@ -49,16 +49,13 @@ import javax.json.stream.JsonGenerator;
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import javax.json.stream.JsonGeneratorFactory;
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import javax.json.stream.JsonParsingException;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.primitive.*;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.Validate;
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import org.hl7.fhir.instance.model.IBase;
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import org.hl7.fhir.instance.model.IBaseResource;
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import org.hl7.fhir.instance.model.IPrimitiveType;
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import org.hl7.fhir.instance.model.api.IBaseBinary;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.hl7.fhir.instance.model.api.IBaseBinary;
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import org.hl7.fhir.instance.model.api.IBaseBooleanDatatype;
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import org.hl7.fhir.instance.model.api.IBaseDatatype;
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import org.hl7.fhir.instance.model.api.IBaseDecimalDatatype;
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@ -91,6 +88,7 @@ import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.api.Tag;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.model.api.annotation.Child;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.base.composite.BaseContainedDt;
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import ca.uhn.fhir.model.base.composite.BaseNarrativeDt;
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import ca.uhn.fhir.model.base.composite.BaseResourceReferenceDt;
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@ -147,7 +147,9 @@ public class RestfulServerUtils {
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if (theNarrativeMode == RestfulServer.NarrativeModeEnum.ONLY) {
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writer.append(theResource.getText().getDiv().getValueAsString());
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} else {
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getNewParser(theServer.getFhirContext(), responseEncoding, thePrettyPrint, theNarrativeMode).encodeResourceToWriter(theResource, writer);
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IParser parser = getNewParser(theServer.getFhirContext(), responseEncoding, thePrettyPrint, theNarrativeMode);
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parser.setServerBaseUrl(theServerBase);
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parser.encodeResourceToWriter(theResource, writer);
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}
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} finally {
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writer.close();
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@ -372,8 +374,9 @@ public class RestfulServerUtils {
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writer.append("<hr/>");
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}
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} else {
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IParser newParser = RestfulServerUtils.getNewParser(theServer.getFhirContext(), responseEncoding, thePrettyPrint, theNarrativeMode);
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newParser.encodeBundleToWriter(bundle, writer);
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IParser parser = RestfulServerUtils.getNewParser(theServer.getFhirContext(), responseEncoding, thePrettyPrint, theNarrativeMode);
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parser.setServerBaseUrl(theServerBase);
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parser.encodeBundleToWriter(bundle, writer);
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}
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} finally {
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writer.close();
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@ -1122,7 +1122,6 @@ public abstract class BaseFhirResourceDao<T extends IResource> extends BaseFhirD
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CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
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CriteriaQuery<ResourceTable> cq = builder.createQuery(ResourceTable.class);
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Root<ResourceTable> from = cq.from(ResourceTable.class);
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// cq.where(builder.equal(from.get("myResourceType"), getContext().getResourceDefinition(myResourceType).getName()));
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cq.where(from.get("myId").in(theIncludePids));
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TypedQuery<ResourceTable> q = myEntityManager.createQuery(cq);
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@ -101,6 +101,26 @@ public class JsonParserTest {
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}
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@Test
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public void testEncodeOmitsVersionAndBase() {
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Patient p = new Patient();
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p.getManagingOrganization().setReference("http://example.com/base/Patient/1/_history/2");
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String enc;
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enc = ourCtx.newJsonParser().encodeResourceToString(p);
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ourLog.info(enc);
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assertThat(enc, containsString("\"http://example.com/base/Patient/1\""));
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enc = ourCtx.newJsonParser().setServerBaseUrl("http://example.com/base").encodeResourceToString(p);
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ourLog.info(enc);
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assertThat(enc, containsString("\"Patient/1\""));
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enc = ourCtx.newJsonParser().setServerBaseUrl("http://example.com/base2").encodeResourceToString(p);
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ourLog.info(enc);
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assertThat(enc, containsString("\"http://example.com/base/Patient/1\""));
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}
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@Test
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public void testDecimalPrecisionPreserved() {
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String number = "52.3779939997090374535378485873776474764643249869328698436986235758587";
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@ -97,6 +97,26 @@ public class XmlParserTest {
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}
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@Test
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public void testEncodeOmitsVersionAndBase() {
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Patient p = new Patient();
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p.getManagingOrganization().setReference("http://example.com/base/Patient/1/_history/2");
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String enc;
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enc = ourCtx.newXmlParser().encodeResourceToString(p);
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ourLog.info(enc);
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assertThat(enc, containsString("\"http://example.com/base/Patient/1\""));
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enc = ourCtx.newXmlParser().setServerBaseUrl("http://example.com/base").encodeResourceToString(p);
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ourLog.info(enc);
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assertThat(enc, containsString("\"Patient/1\""));
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enc = ourCtx.newXmlParser().setServerBaseUrl("http://example.com/base2").encodeResourceToString(p);
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ourLog.info(enc);
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assertThat(enc, containsString("\"http://example.com/base/Patient/1\""));
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}
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@Test
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public void testDuplicateContainedResources() {
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@ -4,6 +4,7 @@ import static org.hamcrest.Matchers.not;
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import static org.hamcrest.Matchers.stringContainsInOrder;
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import static org.junit.Assert.*;
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import java.io.IOException;
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import java.net.URLEncoder;
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import java.util.concurrent.TimeUnit;
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@ -67,6 +68,19 @@ public class ReadTest {
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assertThat(responseContent, stringContainsInOrder("1", "\""));
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assertThat(responseContent, not(stringContainsInOrder("1", "\"", "1")));
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}
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@Test
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public void testEncodeConvertsReferencesToRelative() throws Exception {
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HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1?_format=xml");
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HttpResponse status = ourClient.execute(httpGet);
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String responseContent = IOUtils.toString(status.getEntity().getContent());
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IOUtils.closeQuietly(status.getEntity().getContent());
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ourLog.info(responseContent);
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assertEquals(200, status.getStatusLine().getStatusCode());
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String ref = ourCtx.newXmlParser().parseResource(Patient.class, responseContent).getManagingOrganization().getReference().getValue();
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assertEquals("Organization/555", ref);
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}
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@Test
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public void testReadJson() throws Exception {
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@ -216,6 +230,7 @@ public class ReadTest {
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Patient patient = new Patient();
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patient.addIdentifier(theId.getIdPart(), theId.getVersionIdPart());
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patient.setId("Patient/1/_history/1");
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patient.getManagingOrganization().setReference("http://localhost:" + ourPort + "/Organization/555/_history/666");
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return patient;
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}
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@ -41,6 +41,7 @@ import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
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import ca.uhn.fhir.rest.annotation.IdParam;
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import ca.uhn.fhir.rest.annotation.OptionalParam;
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import ca.uhn.fhir.rest.annotation.Read;
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import ca.uhn.fhir.rest.annotation.RequiredParam;
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import ca.uhn.fhir.rest.annotation.Search;
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import ca.uhn.fhir.rest.client.IGenericClient;
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@ -63,6 +64,20 @@ public class SearchTest {
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private static Server ourServer;
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@Test
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public void testEncodeConvertsReferencesToRelative() throws Exception {
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HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=searchWithRef");
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HttpResponse status = ourClient.execute(httpGet);
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String responseContent = IOUtils.toString(status.getEntity().getContent());
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IOUtils.closeQuietly(status.getEntity().getContent());
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ourLog.info(responseContent);
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assertEquals(200, status.getStatusLine().getStatusCode());
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Patient patient = (Patient) ourCtx.newXmlParser().parseBundle(responseContent).getEntries().get(0).getResource();
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String ref = patient.getManagingOrganization().getReference().getValue();
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assertEquals("Organization/555", ref);
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}
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@Test
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public void testOmitEmptyOptionalParam() throws Exception {
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HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_id=");
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@ -312,6 +327,15 @@ public class SearchTest {
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retVal.add(patient);
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return retVal;
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}
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@Search(queryName="searchWithRef")
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public Patient searchWithRef() {
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Patient patient = new Patient();
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patient.setId("Patient/1/_history/1");
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patient.getManagingOrganization().setReference("http://localhost:" + ourPort + "/Organization/555/_history/666");
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return patient;
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}
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@Search
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public List<Patient> findPatient(@RequiredParam(name = "_id") StringParam theParam) {
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@ -0,0 +1,105 @@
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package ca.uhn.fhir.rest.server;
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import static org.junit.Assert.assertEquals;
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import java.util.concurrent.TimeUnit;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.HttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClientBuilder;
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import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
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import org.eclipse.jetty.server.Server;
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import org.eclipse.jetty.servlet.ServletHandler;
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import org.eclipse.jetty.servlet.ServletHolder;
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import org.junit.AfterClass;
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import org.junit.BeforeClass;
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import org.junit.Test;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
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import ca.uhn.fhir.rest.annotation.Search;
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import ca.uhn.fhir.util.PortUtil;
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/**
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* Created by dsotnikov on 2/25/2014.
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*/
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public class SearchDstu2Test {
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private static CloseableHttpClient ourClient;
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private static FhirContext ourCtx = new FhirContext();
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchDstu2Test.class);
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private static int ourPort;
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private static Server ourServer;
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@Test
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public void testEncodeConvertsReferencesToRelative() throws Exception {
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HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?_query=searchWithRef");
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HttpResponse status = ourClient.execute(httpGet);
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String responseContent = IOUtils.toString(status.getEntity().getContent());
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IOUtils.closeQuietly(status.getEntity().getContent());
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ourLog.info(responseContent);
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assertEquals(200, status.getStatusLine().getStatusCode());
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Patient patient = (Patient) ourCtx.newXmlParser().parseResource(Bundle.class, responseContent).getEntry().get(0).getResource();
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String ref = patient.getManagingOrganization().getReference().getValue();
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assertEquals("Organization/555", ref);
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}
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@AfterClass
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public static void afterClass() throws Exception {
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ourServer.stop();
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}
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@BeforeClass
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public static void beforeClass() throws Exception {
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ourPort = PortUtil.findFreePort();
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ourServer = new Server(ourPort);
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DummyPatientResourceProvider patientProvider = new DummyPatientResourceProvider();
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ServletHandler proxyHandler = new ServletHandler();
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RestfulServer servlet = new RestfulServer();
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servlet.getFhirContext().setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
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servlet.setResourceProviders(patientProvider);
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ServletHolder servletHolder = new ServletHolder(servlet);
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proxyHandler.addServletWithMapping(servletHolder, "/*");
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ourServer.setHandler(proxyHandler);
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ourServer.start();
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PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
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HttpClientBuilder builder = HttpClientBuilder.create();
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builder.setConnectionManager(connectionManager);
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ourClient = builder.build();
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}
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/**
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* Created by dsotnikov on 2/25/2014.
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*/
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public static class DummyPatientResourceProvider implements IResourceProvider {
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@Search(queryName="searchWithRef")
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public Patient searchWithRef() {
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Patient patient = new Patient();
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patient.setId("Patient/1/_history/1");
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patient.getManagingOrganization().setReference("http://localhost:" + ourPort + "/Organization/555/_history/666");
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return patient;
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}
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@Override
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public Class<? extends IResource> getResourceType() {
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return Patient.class;
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}
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}
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}
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@ -4,17 +4,22 @@
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<properties>
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<author>James Agnew</author>
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||||
<title>HAPI FHIR Changelog</title>
|
||||
<!--
|
||||
com.phloc:phloc-commons ............................... 4.3.5 -> 4.3.6
|
||||
[INFO] org.apache.httpcomponents:httpclient .................... 4.3.6 -> 4.4
|
||||
[INFO] org.codehaus.woodstox:woodstox-core-asl ............... 4.4.0 -> 4.4.1
|
||||
[INFO] org.slf4j:jcl-over-slf4j ............................. 1.7.9 -> 1.7.10
|
||||
[INFO] org.slf4j:slf4j-api .................................. 1.7.9 -> 1.7.10
|
||||
[INFO] org.springframework:spring-beans ...... 4.1.3.RELEASE -> 4.1.5.RELEASE
|
||||
-->
|
||||
</properties>
|
||||
<body>
|
||||
<release version="1.0" date="TBA">
|
||||
<action type="add">
|
||||
Bump the version of a few dependencies to the
|
||||
latest versions:
|
||||
<![CDATA[
|
||||
<ul>
|
||||
<li>Phloc-commons (for schematron validation) 4.3.5 -> 4.3.6</li>
|
||||
<li>Apache HttpClient 4.3.6 -> 4.4</li>
|
||||
<li>Woodstox 4.4.0 -> 4.4.1</li>
|
||||
<li>SLF4j 1.7.9 -> 1.7.10</li>
|
||||
<li>Spring (used in hapi-fhir-jpaserver-base module) 4.1.3.RELEASE -> 4.1.5.RELEASE</li>
|
||||
</ul>
|
||||
]]>
|
||||
</action>
|
||||
<action type="add">
|
||||
Add support for "profile" and "tag" elements in the resource Meta block
|
||||
when parsing DSTU2 structures.
|
||||
|
|
@ -50,6 +55,15 @@
|
|||
the new syntax required in DSTU2: [resource name]:[search param NAME]
|
||||
insead of the DSTU1 style [resource name].[search param PATH]
|
||||
</action>
|
||||
<action type="add" fix="124">
|
||||
When encoding resources, the parser will now convert any resource
|
||||
references to versionless references automatically (i.e. it will
|
||||
omit the version part automatically if one is present in the reference)
|
||||
since references between resources must be versionless. Additionally,
|
||||
references in server responses will omit the server base URL part of the
|
||||
reference if the base matches the base for the server giving
|
||||
the response.
|
||||
</action>
|
||||
</release>
|
||||
<release version="0.9" date="2015-Mar-14">
|
||||
<action type="add">
|
||||
|
|
|
|||
Loading…
Reference in New Issue