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hapi-fhir
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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
James 2016-12-04 21:09:48 -05:00
parent ccfe74ba38 bf05dd86f8
commit fd26f074e5
13 changed files with 2935 additions and 204 deletions
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3
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
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@ -244,6 +244,9 @@ public abstract class BaseParser implements IParser {
continue;
}
theContained.addContained(resource);
if (resource.getIdElement().isLocal() && existingIdToContainedResource != null) {
existingIdToContainedResource.remove(resource.getIdElement().getValue());
}
} else {
continue;
}

12
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/client/RestfulClientFactory.java
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@ -287,7 +287,17 @@ public abstract class RestfulClientFactory implements IRestfulClientFactory {
}
@SuppressWarnings("rawtypes")
Class implementingClass = myContext.getResourceDefinition(capabilityStatementResourceName).getImplementingClass();
Class implementingClass;
try {
implementingClass = myContext.getResourceDefinition(capabilityStatementResourceName).getImplementingClass();
} catch (DataFormatException e) {
if (!myContext.getVersion().getVersion().isOlderThan(FhirVersionEnum.DSTU3)) {
capabilityStatementResourceName = "Conformance";
implementingClass = myContext.getResourceDefinition(capabilityStatementResourceName).getImplementingClass();
} else {
throw e;
}
}
try {
conformance = (IBaseResource) client.fetchConformance().ofType(implementingClass).execute();
} catch (FhirClientConnectionException e) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
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@ -2209,15 +2209,19 @@ public class SearchBuilder {
for (ResourceLink resourceLink : results) {
if (theReverseMode) {
Long pid = resourceLink.getSourceResourcePid();
if (pid != null) {
pidsToInclude.add(pid);
}
} else {
Long pid = resourceLink.getTargetResourcePid();
if (pid != null) {
pidsToInclude.add(pid);
}
}
}
}
}
}
if (theLastUpdated != null && (theLastUpdated.getLowerBoundAsInstant() != null || theLastUpdated.getUpperBoundAsInstant() != null)) {
pidsToInclude = new HashSet<Long>(filterResourceIdsByLastUpdated(theEntityManager, theLastUpdated, pidsToInclude));

104
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
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@ -22,91 +22,40 @@ import static org.mockito.Mockito.reset;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.verifyNoMoreInteractions;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.nio.charset.StandardCharsets;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.RandomStringUtils;
import org.hamcrest.Matchers;
import org.hamcrest.core.StringContains;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
import org.mockito.ArgumentCaptor;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.FhirResourceDaoDstu2;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3Test;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.api.Tag;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.base.composite.BaseCodingDt;
import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
import ca.uhn.fhir.model.dstu2.composite.IdentifierDt;
import ca.uhn.fhir.model.dstu2.composite.MetaDt;
import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.resource.BaseResource;
import ca.uhn.fhir.model.dstu2.composite.*;
import ca.uhn.fhir.model.dstu2.resource.*;
import ca.uhn.fhir.model.dstu2.resource.Bundle;
import ca.uhn.fhir.model.dstu2.resource.ConceptMap;
import ca.uhn.fhir.model.dstu2.resource.Device;
import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu2.resource.Encounter;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.resource.Organization;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.resource.Questionnaire;
import ca.uhn.fhir.model.dstu2.valueset.AdministrativeGenderEnum;
import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
import ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum;
import ca.uhn.fhir.model.dstu2.valueset.IssueTypeEnum;
import ca.uhn.fhir.model.dstu2.valueset.QuantityComparatorEnum;
import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.model.dstu2.valueset.*;
import ca.uhn.fhir.model.primitive.*;
import ca.uhn.fhir.model.valueset.BundleEntrySearchModeEnum;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.QuantityParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.util.TestUtil;
@ -130,6 +79,31 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
}
}
@After
public final void after() {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Test
public void testValidateAgainstDstu2Profile() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
String stream = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_structuredefinition_dstu2.xml"), StandardCharsets.UTF_8);
StructureDefinition sd = myFhirCtx.newXmlParser().parseResource(StructureDefinition.class, stream);
myStructureDefinitionDao.create(sd, mySrd);
String rawResource = IOUtils.toString(getClass().getResourceAsStream("/binu_testpatient_resource.json"), StandardCharsets.UTF_8);
try {
myValueSetDao.validate(null, null, rawResource, EncodingEnum.JSON, ValidationModeEnum.UPDATE, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome()));
}
}
@Test
public void testCreateBundleAllowsDocumentAndCollection() {
String methodName = "testCreateBundleAllowsDocumentAndCollection";

95
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
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@ -29,13 +29,7 @@ import java.net.Socket;
import java.net.SocketTimeoutException;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
@ -43,79 +37,31 @@ import org.apache.commons.lang3.Validate;
import org.apache.http.NameValuePair;
import org.apache.http.client.ClientProtocolException;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpDelete;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPatch;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.methods.*;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.apache.http.message.BasicNameValuePair;
import org.hl7.fhir.dstu3.model.AuditEvent;
import org.hl7.fhir.dstu3.model.BaseResource;
import org.hl7.fhir.dstu3.model.Basic;
import org.hl7.fhir.dstu3.model.Bundle;
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.Bundle.HTTPVerb;
import org.hl7.fhir.dstu3.model.Bundle.SearchEntryMode;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Condition;
import org.hl7.fhir.dstu3.model.DateTimeType;
import org.hl7.fhir.dstu3.model.DateType;
import org.hl7.fhir.dstu3.model.Device;
import org.hl7.fhir.dstu3.model.DiagnosticRequest;
import org.hl7.fhir.dstu3.model.DocumentManifest;
import org.hl7.fhir.dstu3.model.DocumentReference;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.Encounter.EncounterLocationComponent;
import org.hl7.fhir.dstu3.model.Encounter.EncounterStatus;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.ImagingStudy;
import org.hl7.fhir.dstu3.model.InstantType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Location;
import org.hl7.fhir.dstu3.model.Medication;
import org.hl7.fhir.dstu3.model.MedicationAdministration;
import org.hl7.fhir.dstu3.model.MedicationRequest;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Period;
import org.hl7.fhir.dstu3.model.Practitioner;
import org.hl7.fhir.dstu3.model.Quantity;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.dstu3.model.QuestionnaireResponse;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.Subscription;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.dstu3.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.dstu3.model.TemporalPrecisionEnum;
import org.hl7.fhir.dstu3.model.UnsignedIntType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import com.google.common.collect.Lists;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.parser.IParser;
@ -124,11 +70,7 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.SummaryEnum;
import ca.uhn.fhir.rest.client.IGenericClient;
import ca.uhn.fhir.rest.gclient.StringClientParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
import ca.uhn.fhir.rest.param.StringAndListParam;
import ca.uhn.fhir.rest.param.StringOrListParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.server.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@ -148,6 +90,29 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
myDaoConfig.setAllowMultipleDelete(true);
}
@Override
@After
public void after() throws Exception {
super.after();
myDaoConfig.setAllowMultipleDelete(new DaoConfig().isAllowMultipleDelete());
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
}
@Test
public void testIncludeWithExternalReferences() {
myDaoConfig.setAllowExternalReferences(true);
Patient p = new Patient();
p.getManagingOrganization().setReference("http://example.com/Organization/123");
ourClient.create().resource(p).execute();
Bundle b = ourClient.search().forResource("Patient").include(Patient.INCLUDE_ORGANIZATION).returnBundle(Bundle.class).execute();
assertEquals(1, b.getEntry().size());
}
private void checkParamMissing(String paramName) throws IOException, ClientProtocolException {
HttpGet get = new HttpGet(ourServerBase + "/Observation?" + paramName + ":missing=false");
CloseableHttpResponse resp = ourHttpClient.execute(get);

40
hapi-fhir-jpaserver-base/src/test/resources/binu_testpatient_resource.json Normal file
View File

@ -0,0 +1,40 @@
{
"resourceType": "Patient",
"id": "67.20068.14731",
"meta": {
"versionId": "1",
"lastUpdated": "2016-11-30T02:18:24.929-05:00",
"profile": [
"http://example.org/fhir/StructureDefinition/DutchPatient"
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"> GHASIYA <b>AL WAHEIBI </b></div><table class=\"hapiPropertyTable\"><tbody><tr><td>Identifier</td><td>14731</td></tr><tr><td>Address</td><td></td></tr><tr><td>Date of birth</td><td><span>01 January 1981</span></td></tr></tbody></table></div>"
},
"identifier": [{
"value": "14731",
"period": {
"start": "2005-03-15"
}
}],
"active": false,
"name": [{
"family": [
"AL WAHEIBI"
],
"given": [
"GHASIYA"
]
}],
"gender": "female",
"birthDate": "1981-01-01",
"deceasedBoolean": true,
"address": {
"use": "home"
},
"placeOfBirth": {
"url": "http://hl7.org/fhir/StructureDefinition/birthPlace",
"valueString": "Narakal"
}
}

2531
hapi-fhir-jpaserver-base/src/test/resources/binu_testpatient_structuredefinition_dstu2.xml Normal file
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File diff suppressed because it is too large Load Diff

13
hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java
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@ -11,14 +11,10 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.StringReader;
import java.io.*;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.nio.charset.StandardCharsets;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.hamcrest.core.IsNot;
@ -84,7 +80,7 @@ public class JsonParserTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserTest.class);
private void parseAndEncode(String name) throws IOException {
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream(name));
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream(name), StandardCharsets.UTF_8);
// ourLog.info(msg);
msg = msg.replace("\"div\": \"<div>", "\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">");
@ -107,6 +103,7 @@ public class JsonParserTest {
assertEquals(exp, act);
}
@Test
public void testDecimalPrecisionPreserved() {
String number = "52.3779939997090374535378485873776474764643249869328698436986235758587";

75
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/RestfulClientFactoryDstu2Test.java Normal file
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@ -0,0 +1,75 @@
package ca.uhn.fhir.rest.client;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.util.List;
import java.util.Map;
import org.junit.AfterClass;
import org.junit.Test;
import org.mockito.Mockito;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.model.dstu2.resource.Conformance;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.client.apache.ApacheRestfulClientFactory;
import ca.uhn.fhir.rest.client.api.IHttpClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TestUtil;
public class RestfulClientFactoryDstu2Test {
private static FhirContext ourCtx = FhirContext.forDstu2();
/**
* See #518
*/
@SuppressWarnings({ "unchecked", "cast" })
@Test
public void testMissingCapabilityStatementDstu2() throws Exception {
FhirContext ctx = mock(FhirContext.class);
IRestfulClientFactory restfulClientFactory = mock(IRestfulClientFactory.class);
IHttpClient httpClient = mock(IHttpClient.class);
when(ctx.getResourceDefinition(Mockito.eq("CapabilityStatement"))).thenThrow(new DataFormatException());
when(ctx.getResourceDefinition(Mockito.eq("Conformance"))).thenReturn(ourCtx.getResourceDefinition("Conformance"));
when(ctx.getResourceDefinition(Conformance.class)).thenReturn(ourCtx.getResourceDefinition("Conformance"));
when(ctx.getVersion()).thenReturn(FhirVersionEnum.DSTU2.getVersionImplementation());
when(ctx.getRestfulClientFactory()).thenReturn(restfulClientFactory);
when(restfulClientFactory.getHttpClient(any(StringBuilder.class), (Map<String, List<String>>)any(Map.class), any(String.class), any(RequestTypeEnum.class), any(List.class))).thenReturn(httpClient);
IHttpRequest httpRequest = mock(IHttpRequest.class);
when(httpClient.createGetRequest(any(FhirContext.class), any(EncodingEnum.class))).thenReturn(httpRequest);
IHttpResponse httpResponse = mock(IHttpResponse.class);
when(httpRequest.execute()).thenReturn(httpResponse);
when(httpResponse.getStatus()).thenReturn(404);
ApacheRestfulClientFactory cf = new ApacheRestfulClientFactory(ctx);
IHttpClient client = mock(IHttpClient.class);
BaseClient baseClient = mock(BaseClient.class);
try {
cf.validateServerBase("http://localhost:9999", client, baseClient);
fail();
} catch (ResourceNotFoundException e) {
// ok
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

50
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.parser;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
@ -17,7 +18,9 @@ import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.*;
@ -36,6 +39,7 @@ import org.hl7.fhir.dstu3.model.Enumeration;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.*;
import org.mockito.ArgumentCaptor;
@ -66,6 +70,32 @@ public class JsonParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
/**
* See #276
*/
@Test
public void testDoubleEncodingContainedResources() throws Exception {
Patient patient = new Patient();
patient.setId("#patient-1");
patient.setActive(true);
Coverage coverage = new Coverage();
coverage.setId("#coverage-1");
coverage.getBeneficiary().setResource(patient);
Claim resource = new Claim();
resource.getContained().add(patient);
resource.getContained().add(coverage);
resource.getPatient().setReference("#patient-1");
resource.addCoverage().getCoverage().setReference("#coverage-1");
IParser p = ourCtx.newJsonParser().setPrettyPrint(true);
String encoded = p.encodeResourceToString(resource);
ourLog.info(encoded);
assertEquals(3, countMatches(encoded, "resourceType"));
}
/**
* #480
*/
@ -124,17 +154,16 @@ public class JsonParserDstu3Test {
ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
ArgumentCaptor<ValueType> actual = ArgumentCaptor.forClass(ValueType.class);
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),elementName.capture(), expected.capture(), actual.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), elementName.capture(), expected.capture(), actual.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
assertEquals("_id", elementName.getAllValues().get(0));
assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
assertEquals(ValueType.SCALAR, actual.getAllValues().get(0));
}
@Test
public void testEncodeAndParseExtensions() throws Exception {
@ -221,7 +250,6 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeAndParseMetaProfileAndTags() {
Patient p = new Patient();
@ -300,7 +328,6 @@ public class JsonParserDstu3Test {
assertEquals("sec_label2", tagList.get(1).getDisplay());
}
/**
* See #336
*/
@ -355,7 +382,6 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeAndParseSecurityLabels() {
Patient p = new Patient();
@ -434,8 +460,6 @@ public class JsonParserDstu3Test {
}
/**
* See #326
*/
@ -504,7 +528,6 @@ public class JsonParserDstu3Test {
assertThat(encoded, not(containsString("tag")));
}
/**
* #158
*/
@ -750,12 +773,12 @@ public class JsonParserDstu3Test {
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setDontStripVersionsFromReferencesAtPaths((String[])null);
parser.setDontStripVersionsFromReferencesAtPaths((String[]) null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setDontStripVersionsFromReferencesAtPaths((List<String>)null);
parser.setDontStripVersionsFromReferencesAtPaths((List<String>) null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
@ -1752,7 +1775,6 @@ public class JsonParserDstu3Test {
assertEquals(1, rp.getName().size());
assertEquals("Doe", rp.getName().get(0).getFamilyAsSingleString());
}
/**

76
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/rest/client/RestfulClientFactoryTest.java Normal file
View File

@ -0,0 +1,76 @@
package ca.uhn.fhir.rest.client;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.dstu3.model.Conformance;
import org.junit.AfterClass;
import org.junit.Test;
import org.mockito.Mockito;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.client.apache.ApacheRestfulClientFactory;
import ca.uhn.fhir.rest.client.api.IHttpClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TestUtil;
@SuppressWarnings("deprecation")
public class RestfulClientFactoryTest {
private static FhirContext ourCtx = FhirContext.forDstu3();
/**
* See #518
*/
@SuppressWarnings({ "unchecked", "cast" })
@Test
public void testMissingCapabilityStatement() throws Exception {
FhirContext ctx = mock(FhirContext.class);
IRestfulClientFactory restfulClientFactory = mock(IRestfulClientFactory.class);
IHttpClient httpClient = mock(IHttpClient.class);
when(ctx.getResourceDefinition(Mockito.eq("CapabilityStatement"))).thenThrow(new DataFormatException());
when(ctx.getResourceDefinition(Mockito.eq("Conformance"))).thenReturn(ourCtx.getResourceDefinition("Conformance"));
when(ctx.getResourceDefinition(Conformance.class)).thenReturn(ourCtx.getResourceDefinition("Conformance"));
when(ctx.getVersion()).thenReturn(FhirVersionEnum.DSTU3.getVersionImplementation());
when(ctx.getRestfulClientFactory()).thenReturn(restfulClientFactory);
when(restfulClientFactory.getHttpClient(any(StringBuilder.class), (Map<String, List<String>>)any(Map.class), any(String.class), any(RequestTypeEnum.class), any(List.class))).thenReturn(httpClient);
IHttpRequest httpRequest = mock(IHttpRequest.class);
when(httpClient.createGetRequest(any(FhirContext.class), any(EncodingEnum.class))).thenReturn(httpRequest);
IHttpResponse httpResponse = mock(IHttpResponse.class);
when(httpRequest.execute()).thenReturn(httpResponse);
when(httpResponse.getStatus()).thenReturn(404);
ApacheRestfulClientFactory cf = new ApacheRestfulClientFactory(ctx);
IHttpClient client = mock(IHttpClient.class);
BaseClient baseClient = mock(BaseClient.class);
try {
cf.validateServerBase("http://localhost:9999", client, baseClient);
fail();
} catch (ResourceNotFoundException e) {
// ok
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

7
pom.xml
View File

@ -274,6 +274,11 @@
<id>vadi2</id>
<name>Vadim Peretokin</name>
</developer>
<developer>
<id>lawley</id>
<name>Michael Lawley</name>
<organization>CSIRO</organization>
</developer>
</developers>
<licenses>
@ -307,7 +312,7 @@
<maven_source_plugin_version>2.4</maven_source_plugin_version>
<phloc_schematron_version>2.7.1</phloc_schematron_version>
<phloc_commons_version>4.4.5</phloc_commons_version>
<spring_version>4.3.1.RELEASE</spring_version>
<spring_version>4.3.4.RELEASE</spring_version>
<thymeleaf-version>3.0.1.RELEASE</thymeleaf-version>
<xmlunit_version>1.6</xmlunit_version>

29
src/changes/changes.xml
View File

@ -7,6 +7,15 @@
</properties>
<body>
<release version="2.2" date="TBD">
<action type="add">
Bump the version of a few dependencies to the
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>spring (JPA): 4.3.1 -&gt; 4.3.4</li>
</ul>
]]>
</action>
<action type="fix">
Fix issue in AuthorizationIntetceptor where
transactions are blocked even when they
@ -46,6 +55,26 @@
or log a warning depending on the configured
error handler.
</action>
<action type="fix" issue="276">
Fix issue when serializing resources that have
contained resources which are referred to
from multiple places. Sometimes when serializing
these resources the contained resource section
would contain duplicates. Thanks to Hugo Soares
and Stefan Evinance for reporting and providing
a test case!
</action>
<action type="add" issue="518">
Allow client to gracefully handle running in DSTU3 mode
but with a structures JAR that does not contain a
CapabilityStatement resource. Thanks to Michael Lawley
for the pull request!
</action>
<action type="fix">
Fix a crash in JPA server when searching using an _include if _include targets are
external references (and therefore can't be loaded
by the server). Thanks to Hannes Ulrich for reporting!
</action>
</release>
<release version="2.1" date="2016-11-11">
<action type="add">