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Fix #750 - Elements are not preserved in page requests

This commit is contained in:
James Agnew 2017-11-06 19:49:50 -05:00
parent 2b4a492870
commit 59f4177a59
9 changed files with 1148 additions and 999 deletions
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23
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
View File

@ -43,7 +43,7 @@ public abstract class BaseParser implements IParser {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseParser.class);
private ContainedResources myContainedResources;
private boolean myEncodeElementsAppliesToChildResourcesOnly;
private FhirContext myContext;
private Set<String> myDontEncodeElements;
private boolean myDontEncodeElementsIncludesStars;
@ -556,6 +556,16 @@ public abstract class BaseParser implements IParser {
&& theIncludedResource == false;
}
@Override
public boolean isEncodeElementsAppliesToChildResourcesOnly() {
return myEncodeElementsAppliesToChildResourcesOnly;
}
@Override
public void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly) {
myEncodeElementsAppliesToChildResourcesOnly = theEncodeElementsAppliesToChildResourcesOnly;
}
@Override
public boolean isOmitResourceId() {
return myOmitResourceId;
@ -1039,7 +1049,13 @@ public abstract class BaseParser implements IParser {
}
private boolean checkIfParentShouldBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, myEncodeElements, true);
Set<String> encodeElements = myEncodeElements;
if (encodeElements != null && encodeElements.isEmpty() == false) {
if (isEncodeElementsAppliesToChildResourcesOnly() && !mySubResource) {
encodeElements = null;
}
}
return checkIfPathMatchesForEncoding(thePathBuilder, theStarPass, myEncodeElementsAppliesToResourceTypes, encodeElements, true);
}
private boolean checkIfParentShouldNotBeEncodedAndBuildPath(StringBuilder thePathBuilder, boolean theStarPass) {
@ -1058,6 +1074,9 @@ public abstract class BaseParser implements IParser {
} else {
thePathBuilder.append(myResDef.getName());
}
if (theElements == null) {
return true;
}
if (theElements.contains(thePathBuilder.toString())) {
return true;
}

16
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/IParser.java
View File

@ -206,6 +206,22 @@ public interface IParser {
*/
void setEncodeElements(Set<String> theEncodeElements);
/**
* If set to <code>true</code> (default is false), the values supplied
* to {@link #setEncodeElements(Set)} will not be applied to the root
* resource (typically a Bundle), but will be applied to any sub-resources
* contained within it (i.e. search result resources in that bundle)
*/
void setEncodeElementsAppliesToChildResourcesOnly(boolean theEncodeElementsAppliesToChildResourcesOnly);
/**
* If set to <code>true</code> (default is false), the values supplied
* to {@link #setEncodeElements(Set)} will not be applied to the root
* resource (typically a Bundle), but will be applied to any sub-resources
* contained within it (i.e. search result resources in that bundle)
*/
boolean isEncodeElementsAppliesToChildResourcesOnly();
/**
* If provided, tells the parse which resource types to apply {@link #setEncodeElements(Set) encode elements} to. Any
* resource types not specified here will be encoded completely, with no elements excluded.

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BinaryUtil.java
View File

@ -19,12 +19,13 @@ public class BinaryUtil {
public static IBaseReference getSecurityContext(FhirContext theCtx, IBaseBinary theBinary) {
RuntimeResourceDefinition def = theCtx.getResourceDefinition("Binary");
BaseRuntimeChildDefinition child = def.getChildByName("securityContext");
List<IBase> values = child.getAccessor().getValues(theBinary);
IBaseReference retVal = null;
if (child != null) {
List<IBase> values = child.getAccessor().getValues(theBinary);
if (values.size() > 0) {
retVal = (IBaseReference) values.get(0);
}
}
return retVal;
}

48
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServerUtils.java
View File

@ -86,10 +86,41 @@ public class RestfulServerUtils {
}
}
if (elements != null && elements.size() > 0) {
Set<String> newElements = new HashSet<String>();
Set<String> newElements = new HashSet<>();
for (String next : elements) {
newElements.add("*." + next);
}
/*
* We try to be smart about what the user is asking for
* when they include an _elements parameter. If we're responding
* to something that returns a Bundle (e.g. a search) we assume
* the elements don't apply to the Bundle itself, unless
* the client has explicitly scoped the Bundle
* (i.e. with Bundle.total or something like that)
*/
switch (theRequestDetails.getRestOperationType()) {
case SEARCH_SYSTEM:
case SEARCH_TYPE:
case HISTORY_SYSTEM:
case HISTORY_TYPE:
case HISTORY_INSTANCE:
case GET_PAGE:
boolean haveExplicitBundleElement = false;
for (String next : newElements) {
if (next.startsWith("Bundle.")) {
haveExplicitBundleElement = true;
break;
}
}
if (!haveExplicitBundleElement) {
parser.setEncodeElementsAppliesToChildResourcesOnly(true);
}
break;
default:
break;
}
parser.setEncodeElements(newElements);
parser.setEncodeElementsAppliesToResourceTypes(elementsAppliesTo);
}
@ -147,6 +178,19 @@ public class RestfulServerUtils {
b.append(theBundleType.getCode());
}
String paramName = Constants.PARAM_ELEMENTS;
String[] params = theRequestParameters.get(paramName);
if (params != null) {
for (String nextValue : params) {
if (isNotBlank(nextValue)) {
b.append('&');
b.append(paramName);
b.append('=');
b.append(UrlUtil.escape(nextValue));
}
}
}
return b.toString();
} catch (UnsupportedEncodingException e) {
throw new Error("UTF-8 not supported", e);// should not happen
@ -587,10 +631,12 @@ public class RestfulServerUtils {
response.addHeader(Constants.HEADER_CONTENT_DISPOSITION, "Attachment;");
IBaseReference securityContext = BinaryUtil.getSecurityContext(theServer.getFhirContext(), bin);
if (securityContext != null) {
String securityContextRef = securityContext.getReferenceElement().getValue();
if (isNotBlank(securityContextRef)) {
response.addHeader(Constants.HEADER_X_SECURITY_CONTEXT, securityContextRef);
}
}
return response.sendAttachmentResponse(bin, theStausCode, contentType);
}

2
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseResourceReturningMethodBinding.java
View File

@ -332,7 +332,7 @@ public abstract class BaseResourceReturningMethodBinding extends BaseMethodBindi
}
bundleFactory.addRootPropertiesToBundle(theResult.getUuid(), serverBase, theLinkSelf, linkPrev, linkNext, theResult.size(), theBundleType, theResult.getPublished());
bundleFactory.addResourcesToBundle(new ArrayList<IBaseResource>(resourceList), theBundleType, serverBase, theServer.getBundleInclusionRule(), theIncludes);
bundleFactory.addResourcesToBundle(new ArrayList<>(resourceList), theBundleType, serverBase, theServer.getBundleInclusionRule(), theIncludes);
if (theServer.getPagingProvider() != null) {
int limit;

2
hapi-fhir-structures-dstu2.1/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2_1Test.java
View File

@ -1499,7 +1499,7 @@ public class JsonParserDstu2_1Test {
String val = ourCtx.newJsonParser().encodeResourceToString(patient);
String expected = "{\"resourceType\":\"Binary\",\"id\":\"11\",\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}";
String expected = "{\"resourceType\":\"Binary\",\"id\":\"11\",\"meta\":{\"versionId\":\"22\"},\"contentType\":\"foo\",\"content\":\"AQIDBA==\"}";
ourLog.info("Expected: {}", expected);
ourLog.info("Actual : {}", val);
assertEquals(expected, val);

321
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/XmlParserDstu3Test.java
View File

@ -1,41 +1,26 @@
package ca.uhn.fhir.parser;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.startsWith;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import java.io.IOException;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.text.SimpleDateFormat;
import java.util.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.parser.FooMessageHeaderWithExplicitField.FooMessageSourceComponent;
import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
import ca.uhn.fhir.parser.PatientWithCustomCompositeExtension.FooParentExtension;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Sets;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
import org.hamcrest.collection.IsEmptyCollection;
import org.hamcrest.core.StringContains;
import org.hamcrest.text.StringContainsInOrder;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Address.AddressUse;
import org.hl7.fhir.dstu3.model.Address.AddressUseEnumFactory;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleLinkComponent;
import org.hl7.fhir.dstu3.model.Bundle.BundleType;
import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;
import org.hl7.fhir.dstu3.model.DiagnosticReport.DiagnosticReportStatus;
import org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionBindingComponent;
@ -52,27 +37,27 @@ import org.junit.*;
import org.mockito.ArgumentCaptor;
import org.xmlunit.builder.DiffBuilder;
import org.xmlunit.builder.Input;
import org.xmlunit.diff.*;
import org.xmlunit.diff.ComparisonControllers;
import org.xmlunit.diff.DefaultNodeMatcher;
import org.xmlunit.diff.Diff;
import org.xmlunit.diff.ElementSelectors;
import com.google.common.collect.Sets;
import java.io.IOException;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.text.SimpleDateFormat;
import java.util.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
import ca.uhn.fhir.parser.FooMessageHeaderWithExplicitField.FooMessageSourceComponent;
import ca.uhn.fhir.parser.IParserErrorHandler.IParseLocation;
import ca.uhn.fhir.parser.PatientWithCustomCompositeExtension.FooParentExtension;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.IValidationContext;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationContext;
import ca.uhn.fhir.validation.ValidationResult;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.*;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.*;
public class XmlParserDstu3Test {
private static FhirContext ourCtx = FhirContext.forDstu3();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu3Test.class);
private static FhirContext ourCtx = FhirContext.forDstu3();
@After
public void after() {
@ -83,21 +68,24 @@ public class XmlParserDstu3Test {
}
@Test
public void testEncodeBinaryWithSecurityContext() {
Binary bin = new Binary();
bin.setContentType("text/plain");
bin.setContent("Now is the time".getBytes());
Reference securityContext = new Reference();
securityContext.setReference("DiagnosticReport/1");
bin.setSecurityContext(securityContext);
String encoded = ourCtx.newXmlParser().encodeResourceToString(bin);
ourLog.info(encoded);
assertThat(encoded, containsString("Binary"));
assertThat(encoded, containsString("<contentType value=\"text/plain\"/>"));
assertThat(encoded, containsString("<securityContext><reference value=\"DiagnosticReport/1\"/></securityContext>"));
assertThat(encoded, containsString("<content value=\"Tm93IGlzIHRoZSB0aW1l\"/>"));
}
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar";
Patient fhirPat = new Patient();
fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
IParser parser = ourCtx.newXmlParser();
String output = parser.encodeResourceToString(fhirPat);
System.out.println("output: " + output);
// Deserialize then check that valueReference value is still correct
fhirPat = parser.parseResource(Patient.class, output);
List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
Assert.assertEquals(1, extlst.size());
Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
}
/**
* See #544
@ -153,7 +141,7 @@ public class XmlParserDstu3Test {
assertEquals(1, b.getEntry().size());
Binary bin = (Binary) b.getEntry().get(0).getResource();
assertArrayEquals(new byte[] { 1, 2, 3, 4 }, bin.getContent());
assertArrayEquals(new byte[]{1, 2, 3, 4}, bin.getContent());
}
@ -969,7 +957,7 @@ public class XmlParserDstu3Test {
@Test
public void testEncodeBinaryWithNoContentType() {
Binary b = new Binary();
b.setContent(new byte[] { 1, 2, 3, 4 });
b.setContent(new byte[]{1, 2, 3, 4});
String output = ourCtx.newXmlParser().encodeResourceToString(b);
ourLog.info(output);
@ -977,6 +965,22 @@ public class XmlParserDstu3Test {
assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"><content value=\"AQIDBA==\"/></Binary>", output);
}
@Test
public void testEncodeBinaryWithSecurityContext() {
Binary bin = new Binary();
bin.setContentType("text/plain");
bin.setContent("Now is the time".getBytes());
Reference securityContext = new Reference();
securityContext.setReference("DiagnosticReport/1");
bin.setSecurityContext(securityContext);
String encoded = ourCtx.newXmlParser().encodeResourceToString(bin);
ourLog.info(encoded);
assertThat(encoded, containsString("Binary"));
assertThat(encoded, containsString("<contentType value=\"text/plain\"/>"));
assertThat(encoded, containsString("<securityContext><reference value=\"DiagnosticReport/1\"/></securityContext>"));
assertThat(encoded, containsString("<content value=\"Tm93IGlzIHRoZSB0aW1l\"/>"));
}
@Test
public void testEncodeBundleWithContained() {
DiagnosticReport rpt = new DiagnosticReport();
@ -1872,7 +1876,7 @@ public class XmlParserDstu3Test {
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name", "Bundle.entry")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
@ -1908,6 +1912,31 @@ public class XmlParserDstu3Test {
}
@Test
public void testEncodeWithEncodeElementsAppliesToChildResourcesOnly() throws Exception {
Patient patient = new Patient();
patient.getMeta().addProfile("http://profile");
patient.addName().setFamily("FAMILY");
patient.addAddress().addLine("LINE1");
Bundle bundle = new Bundle();
bundle.setTotal(100);
bundle.addEntry().setResource(patient);
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<>(Arrays.asList("Patient.name")));
p.setEncodeElementsAppliesToChildResourcesOnly(true);
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, containsString("total"));
assertThat(out, containsString("Patient"));
assertThat(out, containsString("name"));
assertThat(out, not(containsString("address")));
}
}
@Test
public void testEncodeWithNarrative() {
Patient p = new Patient();
@ -2779,7 +2808,7 @@ public class XmlParserDstu3Test {
*/
@Test
public void testParseContainedBinaryResource() {
byte[] bin = new byte[] { 0, 1, 2, 3, 4 };
byte[] bin = new byte[]{0, 1, 2, 3, 4};
final Binary binary = new Binary();
binary.setContentType("PatientConsent").setContent(bin);
@ -2835,7 +2864,7 @@ public class XmlParserDstu3Test {
/**
* See #426
*
* <p>
* Value type of FOO isn't a valid datatype
*/
@Test
@ -2934,6 +2963,30 @@ public class XmlParserDstu3Test {
assertEquals("value", capt.getValue());
}
@Test
public void testParseMetaUpdatedDate() {
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
" <id value=\"e2ee823b-ee4d-472d-b79d-495c23f16b99\"/>\n" +
" <meta>\n" +
" <lastUpdated value=\"2015-06-22T15:48:57.554-04:00\"/>\n" +
" </meta>\n" +
" <type value=\"searchset\"/>\n" +
" <base value=\"http://localhost:58109/fhir/context\"/>\n" +
" <total value=\"0\"/>\n" +
" <link>\n" +
" <relation value=\"self\"/>\n" +
" <url value=\"http://localhost:58109/fhir/context/Patient?_pretty=true\"/>\n" +
" </link>\n" +
"</Bundle>";
Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, input);
InstantType updated = b.getMeta().getLastUpdatedElement();
assertEquals("2015-06-22T15:48:57.554-04:00", updated.getValueAsString());
}
@Test
public void testParseMetadata() throws Exception {
@ -2987,43 +3040,6 @@ public class XmlParserDstu3Test {
}
public static void compareXml(String content, String reEncoded) {
Diff d = DiffBuilder.compare(Input.fromString(content))
.withTest(Input.fromString(reEncoded))
.withNodeMatcher(new DefaultNodeMatcher(ElementSelectors.byNameAndText))
.checkForSimilar()
.ignoreWhitespace() // this is working with newest Saxon 9.8.0-2 (not worked with 9.7.0-15
.ignoreComments() // this is not working even with newest Saxon 9.8.0-2
.withComparisonController(ComparisonControllers.Default)
.build();
assertTrue(d.toString(), !d.hasDifferences());
}
@Test
public void testParseMetaUpdatedDate() {
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
" <id value=\"e2ee823b-ee4d-472d-b79d-495c23f16b99\"/>\n" +
" <meta>\n" +
" <lastUpdated value=\"2015-06-22T15:48:57.554-04:00\"/>\n" +
" </meta>\n" +
" <type value=\"searchset\"/>\n" +
" <base value=\"http://localhost:58109/fhir/context\"/>\n" +
" <total value=\"0\"/>\n" +
" <link>\n" +
" <relation value=\"self\"/>\n" +
" <url value=\"http://localhost:58109/fhir/context/Patient?_pretty=true\"/>\n" +
" </link>\n" +
"</Bundle>";
Bundle b = ourCtx.newXmlParser().parseResource(Bundle.class, input);
InstantType updated = b.getMeta().getLastUpdatedElement();
assertEquals("2015-06-22T15:48:57.554-04:00", updated.getValueAsString());
}
// TODO: this should work
@Test
@Ignore
@ -3094,40 +3110,6 @@ public class XmlParserDstu3Test {
assertEquals("Patient", reincarnatedPatient.getIdElement().getResourceType());
}
/**
* See #344
*/
@Test
public void testParserIsCaseSensitive() {
Observation obs = new Observation();
SampledData data = new SampledData();
data.setData("1 2 3");
data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
data.setPeriod(1000L);
obs.setValue(data);
IParser p = ourCtx.newXmlParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
String encoded = p.encodeResourceToString(obs);
ourLog.info(encoded);
p.parseResource(encoded);
try {
p.parseResource(encoded.replace("Observation", "observation"));
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [1,1]]: Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'",
e.getMessage());
}
try {
p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Unknown element 'valueSampleddata' found during parse", e.getMessage());
}
}
@Test(expected = DataFormatException.class)
public void testParseWithInvalidLocalRef() throws IOException {
String string = IOUtils.toString(getClass().getResourceAsStream("/bundle_with_invalid_contained_ref.xml"), StandardCharsets.UTF_8);
@ -3226,6 +3208,40 @@ public class XmlParserDstu3Test {
}
/**
* See #344
*/
@Test
public void testParserIsCaseSensitive() {
Observation obs = new Observation();
SampledData data = new SampledData();
data.setData("1 2 3");
data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
data.setPeriod(1000L);
obs.setValue(data);
IParser p = ourCtx.newXmlParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
String encoded = p.encodeResourceToString(obs);
ourLog.info(encoded);
p.parseResource(encoded);
try {
p.parseResource(encoded.replace("Observation", "observation"));
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [1,1]]: Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'",
e.getMessage());
}
try {
p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
fail();
} catch (DataFormatException e) {
assertEquals("DataFormatException at [[row,col {unknown-source}]: [2,4]]: Unknown element 'valueSampleddata' found during parse", e.getMessage());
}
}
/**
* See #551
*/
@ -3245,7 +3261,7 @@ public class XmlParserDstu3Test {
/**
* See #339
*
* <p>
* https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
*/
@Test
@ -3275,35 +3291,22 @@ public class XmlParserDstu3Test {
}
@Test
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar";
Patient fhirPat = new Patient();
fhirPat.addExtension().setUrl("x1").setValue(new Reference(refVal));
IParser parser = ourCtx.newXmlParser();
String output = parser.encodeResourceToString(fhirPat);
System.out.println("output: " + output);
// Deserialize then check that valueReference value is still correct
fhirPat = parser.parseResource(Patient.class, output);
List<Extension> extlst = fhirPat.getExtensionsByUrl("x1");
Assert.assertEquals(1, extlst.size());
Assert.assertEquals(refVal, ((Reference) extlst.get(0).getValue()).getReference());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
public static void main(String[] args) {
IGenericClient c = ourCtx.newRestfulGenericClient("http://fhir-dev.healthintersections.com.au/open");
// c.registerInterceptor(new LoggingInterceptor(true));
c.read().resource("Patient").withId("324").execute();
public static void compareXml(String content, String reEncoded) {
Diff d = DiffBuilder.compare(Input.fromString(content))
.withTest(Input.fromString(reEncoded))
.withNodeMatcher(new DefaultNodeMatcher(ElementSelectors.byNameAndText))
.checkForSimilar()
.ignoreWhitespace() // this is working with newest Saxon 9.8.0-2 (not worked with 9.7.0-15
.ignoreComments() // this is not working even with newest Saxon 9.8.0-2
.withComparisonController(ComparisonControllers.Default)
.build();
assertTrue(d.toString(), !d.hasDifferences());
}
@ResourceDef(name = "Patient")

217
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/SearchR4Test.java
View File

@ -1,32 +1,5 @@
package ca.uhn.fhir.rest.server;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.junit.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
@ -38,15 +11,46 @@ import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.*;
import ca.uhn.fhir.util.PortUtil;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Patient;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.*;
public class SearchR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchR4Test.class);
private static CloseableHttpClient ourClient;
private static FhirContext ourCtx = FhirContext.forR4();
private static TokenAndListParam ourIdentifiers;
private static String ourLastMethod;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchR4Test.class);
private static int ourPort;
private static Server ourServer;
@ -57,74 +61,63 @@ public class SearchR4Test {
ourIdentifiers = null;
}
@Test
public void testSearchNormal() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar");
private Bundle executeAndReturnLinkNext(HttpGet httpGet, EncodingEnum theExpectEncoding) throws IOException, ClientProtocolException {
CloseableHttpResponse status = ourClient.execute(httpGet);
Bundle bundle;
try {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
assertEquals("search", ourLastMethod);
assertEquals("foo", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getSystem());
assertEquals("bar", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
EncodingEnum ct = EncodingEnum.forContentType(status.getEntity().getContentType().getValue().replaceAll(";.*", "").trim());
assertEquals(theExpectEncoding, ct);
bundle = ct.newParser(ourCtx).parseResource(Bundle.class, responseContent);
assertEquals(10, bundle.getEntry().size());
String linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertNotNull(linkNext);
} finally {
IOUtils.closeQuietly(status.getEntity().getContent());
}
return bundle;
}
@Test
public void testSearchWithInvalidChain() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier.chain=foo%7Cbar");
CloseableHttpResponse status = ourClient.execute(httpGet);
try {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
assertEquals(400, status.getStatusLine().getStatusCode());
OperationOutcome oo = (OperationOutcome) ourCtx.newJsonParser().parseResource(responseContent);
assertEquals(
"Invalid search parameter \"identifier.chain\". Parameter contains a chain (.chain) and chains are not supported for this parameter (chaining is only allowed on reference parameters)",
oo.getIssueFirstRep().getDiagnostics());
} finally {
IOUtils.closeQuietly(status.getEntity().getContent());
}
}
@Test
public void testPagingPreservesEncodingJson() throws Exception {
public void testPagingPreservesElements() throws Exception {
HttpGet httpGet;
String linkNext;
Bundle bundle;
String linkSelf;
// Initial search
httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=json");
httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_elements=name");
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
assertThat(toJson(bundle), not(containsString("active")));
linkSelf = bundle.getLink(Constants.LINK_SELF).getUrl();
assertThat(linkSelf, containsString("_elements=name"));
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=json"));
assertThat(linkNext, containsString("_elements=name"));
ourLog.info(toJson(bundle));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
assertThat(toJson(bundle), not(containsString("active")));
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=json"));
assertThat(linkNext, containsString("_elements=name"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
assertThat(toJson(bundle), not(containsString("active")));
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=json"));
assertThat(linkNext, containsString("_elements=name"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
assertThat(toJson(bundle), not(containsString("active")));
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=json"));
assertThat(linkNext, containsString("_elements=name"));
}
@ -161,34 +154,35 @@ public class SearchR4Test {
}
@Test
public void testPagingPreservesEncodingXml() throws Exception {
public void testPagingPreservesEncodingJson() throws Exception {
HttpGet httpGet;
String linkNext;
Bundle bundle;
// Initial search
httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=xml");
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=json");
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
assertThat(toJson(bundle), containsString("active"));
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
assertThat(linkNext, containsString("_format=json"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
assertThat(linkNext, containsString("_format=json"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
assertThat(linkNext, containsString("_format=json"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.JSON);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
assertThat(linkNext, containsString("_format=json"));
}
@ -260,25 +254,75 @@ public class SearchR4Test {
}
private Bundle executeAndReturnLinkNext(HttpGet httpGet, EncodingEnum theExpectEncoding) throws IOException, ClientProtocolException {
CloseableHttpResponse status = ourClient.execute(httpGet);
@Test
public void testPagingPreservesEncodingXml() throws Exception {
HttpGet httpGet;
String linkNext;
Bundle bundle;
// Initial search
httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar&_format=xml");
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
// Fetch the next page
httpGet = new HttpGet(linkNext);
bundle = executeAndReturnLinkNext(httpGet, EncodingEnum.XML);
linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertThat(linkNext, containsString("_format=xml"));
}
@Test
public void testSearchNormal() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier=foo%7Cbar");
CloseableHttpResponse status = ourClient.execute(httpGet);
try {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
EncodingEnum ct = EncodingEnum.forContentType(status.getEntity().getContentType().getValue().replaceAll(";.*", "").trim());
assertEquals(theExpectEncoding, ct);
bundle = ct.newParser(ourCtx).parseResource(Bundle.class, responseContent);
assertEquals(10, bundle.getEntry().size());
String linkNext = bundle.getLink(Constants.LINK_NEXT).getUrl();
assertNotNull(linkNext);
assertEquals("search", ourLastMethod);
assertEquals("foo", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getSystem());
assertEquals("bar", ourIdentifiers.getValuesAsQueryTokens().get(0).getValuesAsQueryTokens().get(0).getValue());
} finally {
IOUtils.closeQuietly(status.getEntity().getContent());
}
return bundle;
}
@Test
public void testSearchWithInvalidChain() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?identifier.chain=foo%7Cbar");
CloseableHttpResponse status = ourClient.execute(httpGet);
try {
String responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(responseContent);
assertEquals(400, status.getStatusLine().getStatusCode());
OperationOutcome oo = (OperationOutcome) ourCtx.newJsonParser().parseResource(responseContent);
assertEquals(
"Invalid search parameter \"identifier.chain\". Parameter contains a chain (.chain) and chains are not supported for this parameter (chaining is only allowed on reference parameters)",
oo.getIssueFirstRep().getDiagnostics());
} finally {
IOUtils.closeQuietly(status.getEntity().getContent());
}
}
@Test
public void testSearchWithPostAndInvalidParameters() throws Exception {
@ -308,6 +352,10 @@ public class SearchR4Test {
}
private String toJson(Bundle theBundle) {
return ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(theBundle);
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
@ -357,8 +405,9 @@ public class SearchR4Test {
for (int i = 0; i < 200; i++) {
Patient patient = new Patient();
patient.addName(new HumanName().setFamily("FAMILY"));
patient.setActive(true);
patient.getIdElement().setValue("Patient/" + i);
retVal.add((Patient) patient);
retVal.add(patient);
}
return retVal;
}

15
src/changes/changes.xml
View File

@ -175,11 +175,26 @@
was not encoded correctly. Thanks to Malcolm McRoberts for the pull
request with fix and test case!
</action>
<action type="add">
Bundle resources did not have their version encoded when serializing
in FHIR resource (XML/JSON) format.
</action>
<action type="add">
The Binary resource endpoint now supports the `X-Security-Context` header when
reading or writing Binary contents using their native Content-Type (i.e exchanging
the raw binary with the server, as opposed to exchanging a FHIR resource).
</action>
<action type="fix">
When paging through multiple pages of search results, if the
client had requested a subset of resources to be returned using the
<![CDATA[<code>_elements</code>]]> parameter, the elements list
was lost after the first page of results.
In addition, elements will not remove elements from
search/history Bundles (i.e. elements from the Bundle itself, as opposed
to elements in the entry resources) unless the Bundle elements are
explicitly listed, e.g. <![CDATA[<code>_include=Bundle.total</code>]]>.
Thanks to @parisni for reporting!
</action>
</release>
<release version="3.0.0" date="2017-09-27">
<action type="add">