honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Test fixes

This commit is contained in:
James Agnew 2019-09-19 09:45:07 -04:00
parent 170698562a
commit 2be63a1650
15 changed files with 157 additions and 41 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

39
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseElement.java
View File

@ -20,31 +20,29 @@ package ca.uhn.fhir.model.api;
* #L%
*/
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import java.util.*;
public abstract class BaseElement implements /*IElement, */ISupportsUndeclaredExtensions {
private static final long serialVersionUID = -3092659584634499332L;
private List<String> myFormatCommentsPost;
private List<String> myFormatCommentsPre;
private Map<String, Object> userData;
@Child(name = "extension", type = {ExtensionDt.class}, order=0, min=0, max=Child.MAX_UNLIMITED, modifier=false, summary=false)
@Description(shortDefinition="Additional Content defined by implementations", formalDefinition="May be used to represent additional information that is not part of the basic definition of the resource. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension." )
@Child(name = "extension", type = {ExtensionDt.class}, order = 0, min = 0, max = Child.MAX_UNLIMITED, modifier = false, summary = false)
@Description(shortDefinition = "Additional Content defined by implementations", formalDefinition = "May be used to represent additional information that is not part of the basic definition of the resource. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.")
private List<ExtensionDt> myUndeclaredExtensions;
/**
* May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.
*/
@Child(name = "modifierExtension", type = {ExtensionDt.class}, order=1, min=0, max=Child.MAX_UNLIMITED, modifier=true, summary=false)
@Description(shortDefinition="Extensions that cannot be ignored", formalDefinition="May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions." )
/**
* May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.
*/
@Child(name = "modifierExtension", type = {ExtensionDt.class}, order = 1, min = 0, max = Child.MAX_UNLIMITED, modifier = true, summary = false)
@Description(shortDefinition = "Extensions that cannot be ignored", formalDefinition = "May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.")
private List<ExtensionDt> myUndeclaredModifierExtensions;
@Override
@ -148,6 +146,21 @@ public abstract class BaseElement implements /*IElement, */ISupportsUndeclaredEx
return (myFormatCommentsPre != null && !myFormatCommentsPre.isEmpty()) || (myFormatCommentsPost != null && !myFormatCommentsPost.isEmpty());
}
@Override
public Object getUserData(String name) {
if (userData == null)
return null;
return userData.get(name);
}
@Override
public void setUserData(String name, Object value) {
if (userData == null) {
userData = new HashMap<>();
}
userData.put(name, value);
}
/**
* Intended to be called by extending classes {@link #isEmpty()} implementations, returns <code>true</code> if all
* content in this superclass instance is empty per the semantics of {@link #isEmpty()}.

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IElement.java
View File

@ -26,4 +26,5 @@ import org.hl7.fhir.instance.model.api.IBase;
public interface IElement extends IBase {
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/TagList.java
View File

@ -282,4 +282,14 @@ public class TagList implements Set<Tag>, Serializable, IBase {
throw new UnsupportedOperationException();
}
@Override
public Object getUserData(String theName) {
throw new UnsupportedOperationException();
}
@Override
public void setUserData(String theName, Object theValue) {
throw new UnsupportedOperationException();
}
}

10
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBase.java
View File

@ -61,4 +61,14 @@ public interface IBase extends Serializable {
*/
default String fhirType() { return null; }
/**
* Retrieves any user suplied data in this element
*/
Object getUserData(String theName);
/**
* Sets a user supplied data value in this element
*/
void setUserData(String theName, Object theValue);
}

4
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IBaseElement.java
View File

@ -26,4 +26,8 @@ public interface IBaseElement {
String getId();
Object getUserData(String theName);
void setUserData(String theName, Object theValue);
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/BinaryAccessProvider.java
View File

@ -201,6 +201,7 @@ public class BinaryAccessProvider {
IBaseExtension<?, ?> ext = target.getTarget().addExtension();
ext.setUrl(JpaConstants.EXT_EXTERNALIZED_BINARY_ID);
ext.setUserData(JpaConstants.EXTENSION_EXT_SYSTEMDEFINED, Boolean.TRUE);
IPrimitiveType<String> blobIdString = (IPrimitiveType<String>) myCtx.getElementDefinition("string").newInstance();
blobIdString.setValueAsString(blobId);
ext.setValue(blobIdString);

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/MemoryBinaryStorageSvcImpl.java
View File

@ -85,6 +85,7 @@ public class MemoryBinaryStorageSvcImpl extends BaseBinaryStorageSvcImpl impleme
public void expungeBlob(IIdType theResourceId, String theBlobId) {
String key = toKey(theResourceId, theBlobId);
myDataMap.remove(key);
myDetailsMap.remove(key);
}
private String toKey(IIdType theResourceId, String theBlobId) {

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -173,7 +173,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
private SearchBuilderFactory mySearchBuilderFactory;
private FhirContext myContext;
private ApplicationContext myApplicationContext;
private Class<? extends IPrimitiveType<byte[]>> myBase64Type;
@Override
public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
@ -1448,21 +1447,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
validateMetaCount(totalMetaCount);
List<? extends IPrimitiveType<byte[]>> base64fields = myContext.newTerser().getAllPopulatedChildElementsOfType(theResource, myBase64Type);
for (IPrimitiveType<byte[]> nextBase64 : base64fields) {
if (nextBase64 instanceof IBaseHasExtensions) {
boolean hasExternalizedBinaryReference = ((IBaseHasExtensions) nextBase64)
.getExtension()
.stream()
.anyMatch(t-> t.getUrl().equals(EXT_EXTERNALIZED_BINARY_ID));
if (hasExternalizedBinaryReference) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "externalizedBinaryStorageExtensionFoundInRequestBody", EXT_EXTERNALIZED_BINARY_ID);
throw new InvalidRequestException(msg);
}
}
}
}
@Override
@ -1470,10 +1454,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
return mySearchParamRegistry;
}
@SuppressWarnings("unchecked")
@PostConstruct
public void start() {
myBase64Type = (Class<? extends IPrimitiveType<byte[]>>) myContext.getElementDefinition("base64Binary").getImplementingClass();
// nothing yet
}
@SuppressWarnings("unchecked")

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -29,6 +29,7 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.delete.DeleteConflictList;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
import ca.uhn.fhir.jpa.search.PersistedJpaBundleProvider;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@ -75,6 +76,7 @@ import javax.validation.constraints.NotNull;
import java.io.IOException;
import java.util.*;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.EXT_EXTERNALIZED_BINARY_ID;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@Transactional(propagation = Propagation.REQUIRED)
@ -96,6 +98,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
private String myResourceName;
private Class<T> myResourceType;
private String mySecondaryPrimaryKeyParamName;
private Class<? extends IPrimitiveType<byte[]>> myBase64Type;
@Override
public void addTag(IIdType theId, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel, RequestDetails theRequest) {
@ -871,6 +874,25 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
/*
* Don't allow clients to submit resources with binary storage attachments present.
*/
List<? extends IPrimitiveType<byte[]>> base64fields = getContext().newTerser().getAllPopulatedChildElementsOfType(theResource, myBase64Type);
for (IPrimitiveType<byte[]> nextBase64 : base64fields) {
if (nextBase64 instanceof IBaseHasExtensions) {
boolean hasExternalizedBinaryReference = ((IBaseHasExtensions) nextBase64)
.getExtension()
.stream()
.filter(t-> t.getUserData(JpaConstants.EXTENSION_EXT_SYSTEMDEFINED) == null)
.anyMatch(t-> t.getUrl().equals(EXT_EXTERNALIZED_BINARY_ID));
if (hasExternalizedBinaryReference) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirDao.class, "externalizedBinaryStorageExtensionFoundInRequestBody", EXT_EXTERNALIZED_BINARY_ID);
throw new InvalidRequestException(msg);
}
}
}
}
@Override
@ -1178,6 +1200,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
public void start() {
super.start();
ourLog.debug("Starting resource DAO for type: {}", getResourceName());
myBase64Type = (Class<? extends IPrimitiveType<byte[]>>) getContext().getElementDefinition("base64Binary").getImplementingClass();
}
protected <MT extends IBaseMetaType> MT toMetaDt(Class<MT> theType, Collection<TagDefinition> tagDefinitions) {

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BinaryAccessProviderR4Test.java
View File

@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.provider.r4;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
@ -41,6 +42,8 @@ public class BinaryAccessProviderR4Test extends BaseResourceProviderR4Test {
@Autowired
private MemoryBinaryStorageSvcImpl myStorageSvc;
@Autowired
private IBinaryStorageSvc myBinaryStorageSvc;
@Override
@Before
@ -165,14 +168,38 @@ public class BinaryAccessProviderR4Test extends BaseResourceProviderR4Test {
public void testReadUnknownBlobId() throws IOException {
IIdType id = createDocumentReference(false);
DocumentReference dr = ourClient.read().resource(DocumentReference.class).withId(id).execute();
dr.getContentFirstRep()
.getAttachment()
.getDataElement()
.addExtension(JpaConstants.EXT_EXTERNALIZED_BINARY_ID, new StringType("AAAAA"));
ourClient.update().resource(dr).execute();
// Write a binary using the operation
String path = ourServerBase +
"/DocumentReference/" + id.getIdPart() + "/" +
JpaConstants.OPERATION_BINARY_ACCESS_WRITE +
"?path=DocumentReference.content.attachment";
HttpPost post = new HttpPost(path);
post.setEntity(new ByteArrayEntity(SOME_BYTES, ContentType.IMAGE_JPEG));
post.addHeader("Accept", "application/fhir+json; _pretty=true");
String attachmentId;
try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
assertEquals(200, resp.getStatusLine().getStatusCode());
assertThat(resp.getEntity().getContentType().getValue(), containsString("application/fhir+json"));
String response = IOUtils.toString(resp.getEntity().getContent(), Constants.CHARSET_UTF8);
ourLog.info("Response: {}", response);
DocumentReference ref = myFhirCtx.newJsonParser().parseResource(DocumentReference.class, response);
Attachment attachment = ref.getContentFirstRep().getAttachment();
assertEquals(ContentType.IMAGE_JPEG.getMimeType(), attachment.getContentType());
assertEquals(15, attachment.getSize());
assertEquals(null, attachment.getData());
assertEquals("2", ref.getMeta().getVersionId());
attachmentId = attachment.getDataElement().getExtensionString(JpaConstants.EXT_EXTERNALIZED_BINARY_ID);
assertThat(attachmentId, matchesPattern("[a-zA-Z0-9]{100}"));
}
myBinaryStorageSvc.expungeBlob(id, attachmentId);
path = ourServerBase +
"/DocumentReference/" + id.getIdPart() + "/" +
JpaConstants.OPERATION_BINARY_ACCESS_READ +
"?path=DocumentReference.content.attachment";

5
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/util/JpaConstants.java
View File

@ -238,6 +238,11 @@ public class JpaConstants {
*/
public static final String EXT_EXTERNALIZED_BINARY_ID = "http://hapifhir.io/fhir/StructureDefinition/externalized-binary-id";
/**
* Placed in system-generated extensions
*/
public static final String EXTENSION_EXT_SYSTEMDEFINED = JpaConstants.class.getName() + "_EXTENSION_EXT_SYSTEMDEFINED";
/**
* <p>
* This extension represents the equivalent of the

10
hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/model/dstu2/composite/ContainedDt.java
View File

@ -51,4 +51,14 @@ public class ContainedDt extends BaseContainedDt {
return myContainedResources == null || myContainedResources.size() == 0;
}
@Override
public Object getUserData(String theName) {
throw new UnsupportedOperationException();
}
@Override
public void setUserData(String theName, Object theValue) {
throw new UnsupportedOperationException();
}
}

10
hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/model/dstu2/resource/BaseResource.java
View File

@ -168,6 +168,16 @@ public abstract class BaseResource extends BaseElement implements IResource {
return Collections.emptyList();
}
@Override
public Object getUserData(String theName) {
throw new UnsupportedOperationException();
}
@Override
public void setUserData(String theName, Object theValue) {
throw new UnsupportedOperationException();
}
@Override
public List<String> getFormatCommentsPre() {
return Collections.emptyList();

10
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/client/GenericClientDstu2Test.java
View File

@ -1193,6 +1193,16 @@ public class GenericClientDstu2Test {
return null;
}
@Override
public Object getUserData(String theName) {
throw new UnsupportedOperationException();
}
@Override
public void setUserData(String theName, Object theValue) {
throw new UnsupportedOperationException();
}
@Override
public List<String> getFormatCommentsPre() {
return null;

8
src/changes/changes.xml
View File

@ -579,6 +579,14 @@
can now be used to upload custom vocabulary that has been converted into a standard file format
defined by HAPI FHIR. This is useful for uploading large organizational code systems.
</action>
<action type="change">
Two new operations,
<![CDATA[<code>$apply-codesystem-delta-add</code>]]>
and
<![CDATA[<code>$apply-codesystem-delta-remove</code>]]>
have been added to the terminology server. These methods allow
codes to be dynamically added and removed from external (notpresent) codesystems.
</action>
<action type="fix" issue="1404">
In the JAX-RS server, the resource type history and instance vread
operations had ambiguous paths that could lead to the wrong method