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

This commit is contained in:
jamesagnew 2015-09-03 08:08:13 -04:00
parent 8b20f3a77d ae177b52e8
commit f3e44eea3b
10 changed files with 462 additions and 275 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -894,7 +894,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
}
}
protected MetaDt toMetaDt(List<TagDefinition> tagDefinitions) {
protected MetaDt toMetaDt(Collection<TagDefinition> tagDefinitions) {
MetaDt retVal = new MetaDt();
for (TagDefinition next : tagDefinitions) {
switch (next.getTagType()) {

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

@ -1733,9 +1733,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
}
myEntityManager.merge(entity);
myEntityManager.flush();
ourLog.info("Processed metaDeleteOperation on {} in {}ms", new Object[] { theResourceId.getValue(), w.getMillisAndRestart() });
return metaGetOperation(theResourceId);
}
@ -1761,16 +1762,16 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
ActionRequestDetails requestDetails = new ActionRequestDetails(theId, getResourceName());
notifyInterceptors(RestOperationTypeEnum.META, requestDetails);
Long pid = super.translateForcedIdToPid(theId);
String sql = "SELECT d FROM TagDefinition d WHERE d.myId IN (SELECT DISTINCT t.myTagId FROM ResourceTag t WHERE t.myResourceType = :res_type AND t.myResourceId = :res_id)";
TypedQuery<TagDefinition> q = myEntityManager.createQuery(sql, TagDefinition.class);
q.setParameter("res_type", myResourceName);
q.setParameter("res_id", pid);
List<TagDefinition> tagDefinitions = q.getResultList();
MetaDt retVal = super.toMetaDt(tagDefinitions);
Set<TagDefinition> tagDefs = new HashSet<TagDefinition>();
BaseHasResource entity = readEntity(theId);
for (BaseTag next : entity.getTags()) {
tagDefs.add(next.getTag());
}
MetaDt retVal = super.toMetaDt(tagDefs);
retVal.setLastUpdated(entity.getUpdated());
retVal.setVersionId(Long.toString(entity.getVersion()));
return retVal;
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTag.java
View File

@ -77,9 +77,10 @@ public class ResourceHistoryTag extends BaseTag implements Serializable {
public ResourceHistoryTag(ResourceHistoryTable theResourceHistoryTable, TagDefinition theTag) {
myResourceHistory=theResourceHistoryTable;
setTag(theTag);
setResource(theResourceHistoryTable);
setResourceId(theResourceHistoryTable.getResourceId());
setResourceType(theResourceHistoryTable.getResourceType());
}
public ResourceHistoryTable getResourceHistory() {

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

@ -143,7 +143,6 @@ public class ResourceTable extends BaseHasResource implements Serializable {
public ResourceTag addTag(TagDefinition theTag) {
ResourceTag tag = new ResourceTag(this, theTag);
tag.setResourceType(getResourceType());
getTags().add(tag);
return tag;
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTag.java
View File

@ -65,9 +65,10 @@ public class ResourceTag extends BaseTag {
}
public ResourceTag(ResourceTable theResourceTable, TagDefinition theTag) {
myResource = theResourceTable;
myResourceId = theResourceTable.getId();
setTag(theTag);
setResource(theResourceTable);
setResourceId(theResourceTable.getId());
setResourceType(theResourceTable.getResourceType());
}
public ResourceTable getResource() {

149
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2Test.java
View File

@ -230,8 +230,8 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
@Test
public void testCreateOperationOutcome() {
/*
* If any of this ever fails, it means that one of the OperationOutcome issue severity codes has changed code
* value across versions. We store the string as a constant, so something will need to be fixed.
* If any of this ever fails, it means that one of the OperationOutcome issue severity codes has changed code value across versions. We store the string as a constant, so something will need to
* be fixed.
*/
assertEquals(org.hl7.fhir.instance.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
assertEquals(ca.uhn.fhir.model.dstu.valueset.IssueSeverityEnum.ERROR.getCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
@ -311,7 +311,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
Patient p = new Patient();
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("Organization/");
try {
myPatientDao.create(p);
fail();
@ -325,7 +325,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
Patient p = new Patient();
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("Blah/123");
try {
myPatientDao.create(p);
fail();
@ -339,7 +339,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
Patient p = new Patient();
p.addName().addFamily("Hello");
p.getManagingOrganization().setReference("123");
try {
myPatientDao.create(p);
fail();
@ -348,8 +348,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
}
}
@Test
public void testCreateWithIfNoneExistBasic() {
String methodName = "testCreateWithIfNoneExistBasic";
@ -1108,6 +1106,141 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
}
@Test
public void testInstanceMetaOperations() {
String methodName = "testMetaRead";
IIdType id;
{
Patient patient = new Patient();
patient.addIdentifier().setSystem("urn:system").setValue(methodName);
TagList tagList = new TagList();
tagList.addTag("tag_scheme1", "tag_code1", "tag_display1");
tagList.addTag("tag_scheme2", "tag_code2", "tag_display2");
ResourceMetadataKeyEnum.TAG_LIST.put(patient, tagList);
List<BaseCodingDt> securityLabels = new ArrayList<BaseCodingDt>();
securityLabels.add(new CodingDt().setSystem("seclabel_sys1").setCode("seclabel_code1").setDisplay("seclabel_dis1"));
securityLabels.add(new CodingDt().setSystem("seclabel_sys2").setCode("seclabel_code2").setDisplay("seclabel_dis2"));
ResourceMetadataKeyEnum.SECURITY_LABELS.put(patient, securityLabels);
ArrayList<IdDt> profiles = new ArrayList<IdDt>();
profiles.add(new IdDt("http://profile/1"));
profiles.add(new IdDt("http://profile/2"));
ResourceMetadataKeyEnum.PROFILES.put(patient, profiles);
id = myPatientDao.create(patient).getId();
}
assertTrue(id.hasVersionIdPart());
/*
* Create a second version
*/
Patient pt = myPatientDao.read(id);
pt.addName().addFamily("anotherName");
myPatientDao.update(pt);
/*
* Meta-Delete on previous version
*/
MetaDt meta = new MetaDt();
meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
meta.addProfile("http://profile/1");
meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
MetaDt newMeta = myPatientDao.metaDeleteOperation(id.withVersion("1"), meta);
assertEquals(1, newMeta.getProfile().size());
assertEquals(1, newMeta.getSecurity().size());
assertEquals(1, newMeta.getTag().size());
assertEquals("tag_code2", newMeta.getTag().get(0).getCode());
assertEquals("http://profile/2", newMeta.getProfile().get(0).getValue());
assertEquals("seclabel_code2", newMeta.getSecurity().get(0).getCode());
/*
* Meta Read on Version
*/
meta = myPatientDao.metaGetOperation(id.withVersion("1"));
assertEquals(1, meta.getProfile().size());
assertEquals(1, meta.getSecurity().size());
assertEquals(1, meta.getTag().size());
assertEquals("tag_code2", meta.getTag().get(0).getCode());
assertEquals("http://profile/2", meta.getProfile().get(0).getValue());
assertEquals("seclabel_code2", meta.getSecurity().get(0).getCode());
/*
* Meta-read on Version 2
*/
meta = myPatientDao.metaGetOperation(id.withVersion("2"));
assertEquals(2, meta.getProfile().size());
assertEquals(2, meta.getSecurity().size());
assertEquals(2, meta.getTag().size());
/*
* Meta-read on latest version
*/
meta = myPatientDao.metaGetOperation(id.toVersionless());
assertEquals(2, meta.getProfile().size());
assertEquals(2, meta.getSecurity().size());
assertEquals(2, meta.getTag().size());
assertEquals("2", meta.getVersionId());
/*
* Meta-Add on previous version
*/
meta = new MetaDt();
meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
meta.addProfile("http://profile/1");
meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
newMeta = myPatientDao.metaAddOperation(id.withVersion("1"), meta);
assertEquals(2, newMeta.getProfile().size());
assertEquals(2, newMeta.getSecurity().size());
assertEquals(2, newMeta.getTag().size());
/*
* Meta Read on Version
*/
meta = myPatientDao.metaGetOperation(id.withVersion("1"));
assertEquals(2, meta.getProfile().size());
assertEquals(2, meta.getSecurity().size());
assertEquals(2, meta.getTag().size());
assertEquals("1", meta.getVersionId());
/*
* Meta delete on latest
*/
meta = new MetaDt();
meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
meta.addProfile("http://profile/1");
meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
newMeta = myPatientDao.metaDeleteOperation(id.toVersionless(), meta);
assertEquals(1, newMeta.getProfile().size());
assertEquals(1, newMeta.getSecurity().size());
assertEquals(1, newMeta.getTag().size());
assertEquals("tag_code2", newMeta.getTag().get(0).getCode());
assertEquals("http://profile/2", newMeta.getProfile().get(0).getValue());
assertEquals("seclabel_code2", newMeta.getSecurity().get(0).getCode());
/*
* Meta-Add on latest version
*/
meta = new MetaDt();
meta.addTag().setSystem("tag_scheme1").setCode("tag_code1");
meta.addProfile("http://profile/1");
meta.addSecurity().setSystem("seclabel_sys1").setCode("seclabel_code1");
newMeta = myPatientDao.metaAddOperation(id.toVersionless(), meta);
assertEquals(2, newMeta.getProfile().size());
assertEquals(2, newMeta.getSecurity().size());
assertEquals(2, newMeta.getTag().size());
assertEquals("2", newMeta.getVersionId());
}
@Test
public void testResourceInstanceMetaOperation() {
@ -1370,7 +1503,6 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
assertEquals(BundleEntrySearchModeEnum.INCLUDE, ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get((IResource) results.get(1)));
}
@Test
public void testSortByDate() {
Patient p = new Patient();
@ -1841,5 +1973,4 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
}
}
}

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
View File

@ -90,6 +90,7 @@ import ca.uhn.fhir.model.dstu2.valueset.AnswerFormatEnum;
import ca.uhn.fhir.model.dstu2.valueset.EncounterClassEnum;
import ca.uhn.fhir.model.dstu2.valueset.EncounterStateEnum;
import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
import ca.uhn.fhir.model.dstu2.valueset.SearchEntryModeEnum;
import ca.uhn.fhir.model.primitive.DateDt;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.IdDt;
@ -827,10 +828,21 @@ public class ResourceProviderDstu2Test extends BaseJpaTest {
p2.addName().addFamily("testSearchByIdentifierFamily01").addGiven("testSearchByIdentifierGiven02");
ourClient.create().resource(p2).execute().getId();
Bundle actual = ourClient.search().forResource(Patient.class).where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testSearchByIdentifier01")).encodedJson().prettyPrint().execute();
assertEquals(1, actual.size());
assertEquals(p1Id.getIdPart(), actual.getEntries().get(0).getResource().getId().getIdPart());
assertEquals(BundleEntrySearchModeEnum.MATCH, actual.getEntries().get(0).getSearchMode().getValueAsEnum());
//@formatter:off
ca.uhn.fhir.model.dstu2.resource.Bundle actual = ourClient
.search()
.forResource(Patient.class)
.where(Patient.IDENTIFIER.exactly().systemAndCode("urn:system", "testSearchByIdentifier01"))
.encodedJson()
.prettyPrint()
.returnBundle(ca.uhn.fhir.model.dstu2.resource.Bundle.class)
.execute();
//@formatter:on
assertEquals(1, actual.getEntry().size());
assertEquals(ourServerBase + "/Patient/" + p1Id.getIdPart(), actual.getEntry().get(0).getFullUrl());
assertEquals(p1Id.getIdPart(), actual.getEntry().get(0).getResource().getId().getIdPart());
assertEquals(SearchEntryModeEnum.MATCH, actual.getEntry().get(0).getSearch().getModeElement().getValueAsEnum());
}
@Test

25
hapi-fhir-structures-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2/Dstu2BundleFactory.java
View File

@ -69,6 +69,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(Dstu2BundleFactory.class);
private Bundle myBundle;
private FhirContext myContext;
private String myBase;
public Dstu2BundleFactory(FhirContext theContext) {
myContext = theContext;
@ -237,9 +238,7 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
} while (references.isEmpty() == false);
Entry entry = myBundle.addEntry().setResource(next);
if (next.getId().hasBaseUrl()) {
entry.setFullUrl(next.getId().getValue());
}
populateBundleEntryFullUrl(next, entry);
BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
if (searchMode != null) {
@ -253,16 +252,28 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
for (IResource next : includedResources) {
Entry entry = myBundle.addEntry();
entry.setResource(next).getSearch().setMode(SearchEntryModeEnum.INCLUDE);
if (next.getId().hasBaseUrl()) {
entry.setFullUrl(next.getId().getValue());
}
populateBundleEntryFullUrl(next, entry);
}
}
private void populateBundleEntryFullUrl(IResource next, Entry entry) {
if (next.getId().hasBaseUrl()) {
entry.setFullUrl(next.getId().toVersionless().getValue());
} else {
if (isNotBlank(myBase) && next.getId().hasIdPart()) {
IdDt id = next.getId().toVersionless();
id = id.withServerBase(myBase, myContext.getResourceDefinition(next).getName());
entry.setFullUrl(id.getValue());
}
}
}
@Override
public void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated) {
myBase = theServerBase;
if (myBundle.getId().isEmpty()) {
myBundle.setId(UUID.randomUUID().toString());
}
@ -306,6 +317,8 @@ public class Dstu2BundleFactory implements IVersionSpecificBundleFactory {
@Override
public void initializeBundleFromBundleProvider(RestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl,
boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
myBase = theServerBase;
int numToReturn;
String searchId = null;
List<IBaseResource> resourceList;

501
hapi-fhir-structures-hl7org-dstu2/src/main/java/ca/uhn/fhir/rest/server/provider/dstu2hl7org/Dstu2Hl7OrgBundleFactory.java
View File

@ -19,7 +19,8 @@ package ca.uhn.fhir.rest.server.provider.dstu2hl7org;
* limitations under the License.
* #L%
*/
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.Collections;
@ -64,15 +65,15 @@ import ca.uhn.fhir.util.ResourceReferenceInfo;
public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
private String myBase;
private Bundle myBundle;
private FhirContext myContext;
private String myBase;
private Bundle myBundle;
private FhirContext myContext;
public Dstu2Hl7OrgBundleFactory(FhirContext theContext) {
myContext = theContext;
}
public Dstu2Hl7OrgBundleFactory(FhirContext theContext) {
myContext = theContext;
}
private void addResourcesForSearch(List<? extends IBaseResource> theResult) {
private void addResourcesForSearch(List<? extends IBaseResource> theResult) {
List<IBaseResource> includedResources = new ArrayList<IBaseResource>();
Set<IIdType> addedResourceIds = new HashSet<IIdType>();
@ -131,290 +132,310 @@ public class Dstu2Hl7OrgBundleFactory implements IVersionSpecificBundleFactory {
} while (references.isEmpty() == false);
BundleEntryComponent entry = myBundle.addEntry().setResource((Resource) next);
IdType nextId = (IdType) next.getIdElement();
if (isNotBlank(myBase) && isNotBlank(nextId.getResourceType())) {
entry.setFullUrlElement(nextId.withServerBase(myBase, nextId.getResourceType()));
}
populateBundleEntryFullUrl(next, entry);
}
/*
* Actually add the resources to the bundle
*/
for (IBaseResource next : includedResources) {
myBundle.addEntry().setResource((Resource) next).getSearch().setMode(SearchEntryMode.INCLUDE);
BundleEntryComponent entry = myBundle.addEntry();
entry.setResource((Resource) next).getSearch().setMode(SearchEntryMode.INCLUDE);
populateBundleEntryFullUrl(next, entry);
}
}
@Override
public void addResourcesToBundle(List<IBaseResource> theResult, BundleTypeEnum theBundleType, String theServerBase, BundleInclusionRule theBundleInclusionRule, Set<Include> theIncludes) {
if (myBundle == null) {
myBundle = new Bundle();
}
private void populateBundleEntryFullUrl(IBaseResource next, BundleEntryComponent entry) {
if (next.getIdElement().hasBaseUrl()) {
entry.setFullUrl(next.getIdElement().toVersionless().getValue());
} else {
if (isNotBlank(myBase) && next.getIdElement().hasIdPart()) {
IIdType id = next.getIdElement().toVersionless();
id = id.withServerBase(myBase, myContext.getResourceDefinition(next).getName());
entry.setFullUrl(id.getValue());
}
}
}
List<IBaseResource> includedResources = new ArrayList<IBaseResource>();
Set<IIdType> addedResourceIds = new HashSet<IIdType>();
@Override
public void addResourcesToBundle(List<IBaseResource> theResult, BundleTypeEnum theBundleType, String theServerBase,
BundleInclusionRule theBundleInclusionRule, Set<Include> theIncludes) {
if (myBundle == null) {
myBundle = new Bundle();
}
for (IBaseResource next : theResult) {
if (next.getIdElement().isEmpty() == false) {
addedResourceIds.add(next.getIdElement());
}
}
List<IBaseResource> includedResources = new ArrayList<IBaseResource>();
Set<IIdType> addedResourceIds = new HashSet<IIdType>();
for (IBaseResource next : theResult) {
for (IBaseResource next : theResult) {
if (next.getIdElement().isEmpty() == false) {
addedResourceIds.add(next.getIdElement());
}
}
List<? extends IAnyResource> contained;
if (next instanceof IDomainResource) {
IDomainResource nextDomain = (IDomainResource) next;
contained = nextDomain.getContained();
} else {
contained = Collections.emptyList();
}
for (IBaseResource next : theResult) {
Set<String> containedIds = new HashSet<String>();
for (IAnyResource nextContained : contained) {
if (nextContained.getId().isEmpty() == false) {
containedIds.add(nextContained.getIdElement().getValue());
}
}
List<? extends IAnyResource> contained;
if (next instanceof IDomainResource) {
IDomainResource nextDomain = (IDomainResource) next;
contained = nextDomain.getContained();
} else {
contained = Collections.emptyList();
}
List<ResourceReferenceInfo> references = myContext.newTerser().getAllResourceReferences(next);
do {
List<IBaseResource> addedResourcesThisPass = new ArrayList<IBaseResource>();
Set<String> containedIds = new HashSet<String>();
for (IAnyResource nextContained : contained) {
if (nextContained.getId().isEmpty() == false) {
containedIds.add(nextContained.getIdElement().getValue());
}
}
for (ResourceReferenceInfo nextRefInfo : references) {
if (!theBundleInclusionRule.shouldIncludeReferencedResource(nextRefInfo, theIncludes))
continue;
List<ResourceReferenceInfo> references = myContext.newTerser().getAllResourceReferences(next);
do {
List<IBaseResource> addedResourcesThisPass = new ArrayList<IBaseResource>();
IBaseResource nextRes = (IBaseResource) nextRefInfo.getResourceReference().getResource();
if (nextRes != null) {
if (nextRes.getIdElement().hasIdPart()) {
if (containedIds.contains(nextRes.getIdElement().getValue())) {
// Don't add contained IDs as top level resources
continue;
}
for (ResourceReferenceInfo nextRefInfo : references) {
if (!theBundleInclusionRule.shouldIncludeReferencedResource(nextRefInfo, theIncludes))
continue;
IdType id = (IdType) nextRes.getIdElement();
if (id.hasResourceType() == false) {
String resName = myContext.getResourceDefinition(nextRes).getName();
id = id.withResourceType(resName);
}
IBaseResource nextRes = (IBaseResource) nextRefInfo.getResourceReference().getResource();
if (nextRes != null) {
if (nextRes.getIdElement().hasIdPart()) {
if (containedIds.contains(nextRes.getIdElement().getValue())) {
// Don't add contained IDs as top level resources
continue;
}
if (!addedResourceIds.contains(id)) {
addedResourceIds.add(id);
addedResourcesThisPass.add(nextRes);
}
IdType id = (IdType) nextRes.getIdElement();
if (id.hasResourceType() == false) {
String resName = myContext.getResourceDefinition(nextRes).getName();
id = id.withResourceType(resName);
}
}
}
}
if (!addedResourceIds.contains(id)) {
addedResourceIds.add(id);
addedResourcesThisPass.add(nextRes);
}
includedResources.addAll(addedResourcesThisPass);
}
}
}
// Linked resources may themselves have linked resources
references = new ArrayList<ResourceReferenceInfo>();
for (IBaseResource iResource : addedResourcesThisPass) {
List<ResourceReferenceInfo> newReferences = myContext.newTerser().getAllResourceReferences(iResource);
references.addAll(newReferences);
}
} while (references.isEmpty() == false);
includedResources.addAll(addedResourcesThisPass);
BundleEntryComponent entry = myBundle.addEntry().setResource((Resource) next);
// Linked resources may themselves have linked resources
references = new ArrayList<ResourceReferenceInfo>();
for (IBaseResource iResource : addedResourcesThisPass) {
List<ResourceReferenceInfo> newReferences = myContext.newTerser().getAllResourceReferences(iResource);
references.addAll(newReferences);
}
} while (references.isEmpty() == false);
// BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
// if (searchMode != null) {
// entry.getSearch().getModeElement().setValue(searchMode.getCode());
// }
}
BundleEntryComponent entry = myBundle.addEntry().setResource((Resource) next);
/*
* Actually add the resources to the bundle
*/
for (IBaseResource next : includedResources) {
myBundle.addEntry().setResource((Resource) next).getSearch().setMode(SearchEntryMode.INCLUDE);
}
// BundleEntrySearchModeEnum searchMode = ResourceMetadataKeyEnum.ENTRY_SEARCH_MODE.get(next);
// if (searchMode != null) {
// entry.getSearch().getModeElement().setValue(searchMode.getCode());
// }
}
}
/*
* Actually add the resources to the bundle
*/
for (IBaseResource next : includedResources) {
myBundle.addEntry().setResource((Resource) next).getSearch().setMode(SearchEntryMode.INCLUDE);
}
@Override
public void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl, Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated) {
}
if (isBlank(myBundle.getId())) {
myBundle.setId(UUID.randomUUID().toString());
}
@Override
public void addRootPropertiesToBundle(String theAuthor, String theServerBase, String theCompleteUrl,
Integer theTotalResults, BundleTypeEnum theBundleType, IPrimitiveType<Date> theLastUpdated) {
if (myBundle.getMeta().getLastUpdated() == null) {
InstantType instantType = new InstantType();
instantType.setValueAsString(theLastUpdated.getValueAsString());
myBundle.getMeta().setLastUpdatedElement(instantType);
}
if (isBlank(myBundle.getId())) {
myBundle.setId(UUID.randomUUID().toString());
}
if (!hasLink(Constants.LINK_SELF, myBundle) && isNotBlank(theCompleteUrl)) {
myBundle.addLink().setRelation("self").setUrl(theCompleteUrl);
}
if (myBundle.getMeta().getLastUpdated() == null) {
InstantType instantType = new InstantType();
instantType.setValueAsString(theLastUpdated.getValueAsString());
myBundle.getMeta().setLastUpdatedElement(instantType);
}
myBase = theServerBase;
if (!hasLink(Constants.LINK_SELF, myBundle) && isNotBlank(theCompleteUrl)) {
myBundle.addLink().setRelation("self").setUrl(theCompleteUrl);
}
if (myBundle.getTypeElement().isEmpty() && theBundleType != null) {
myBundle.getTypeElement().setValueAsString(theBundleType.getCode());
}
myBase = theServerBase;
if (myBundle.getTotalElement().isEmpty() && theTotalResults != null) {
myBundle.getTotalElement().setValue(theTotalResults);
}
}
if (myBundle.getTypeElement().isEmpty() && theBundleType != null) {
myBundle.getTypeElement().setValueAsString(theBundleType.getCode());
}
@Override
public ca.uhn.fhir.model.api.Bundle getDstu1Bundle() {
return null;
}
if (myBundle.getTotalElement().isEmpty() && theTotalResults != null) {
myBundle.getTotalElement().setValue(theTotalResults);
}
}
@Override
public IBaseResource getResourceBundle() {
return myBundle;
}
@Override
public ca.uhn.fhir.model.api.Bundle getDstu1Bundle() {
return null;
}
private boolean hasLink(String theLinkType, Bundle theBundle) {
for (BundleLinkComponent next : theBundle.getLink()) {
if (theLinkType.equals(next.getRelation())) {
return true;
}
}
return false;
}
@Override
public IBaseResource getResourceBundle() {
return myBundle;
}
@Override
public void initializeBundleFromBundleProvider(RestfulServer theServer, IBundleProvider theResult, EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint, int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType,
Set<Include> theIncludes) {
int numToReturn;
String searchId = null;
List<IBaseResource> resourceList;
if (theServer.getPagingProvider() == null) {
numToReturn = theResult.size();
if (numToReturn == 0) {
resourceList = Collections.emptyList();
} else {
resourceList = theResult.getResources(0, numToReturn);
RestfulServerUtils.validateResourceListNotNull(resourceList);
}
} else {
IPagingProvider pagingProvider = theServer.getPagingProvider();
if (theLimit == null) {
numToReturn = pagingProvider.getDefaultPageSize();
} else {
numToReturn = Math.min(pagingProvider.getMaximumPageSize(), theLimit);
}
private boolean hasLink(String theLinkType, Bundle theBundle) {
for (BundleLinkComponent next : theBundle.getLink()) {
if (theLinkType.equals(next.getRelation())) {
return true;
}
}
return false;
}
numToReturn = Math.min(numToReturn, theResult.size() - theOffset);
resourceList = theResult.getResources(theOffset, numToReturn + theOffset);
RestfulServerUtils.validateResourceListNotNull(resourceList);
@Override
public void initializeBundleFromBundleProvider(RestfulServer theServer, IBundleProvider theResult,
EncodingEnum theResponseEncoding, String theServerBase, String theCompleteUrl, boolean thePrettyPrint,
int theOffset, Integer theLimit, String theSearchId, BundleTypeEnum theBundleType, Set<Include> theIncludes) {
myBase = theServerBase;
int numToReturn;
String searchId = null;
List<IBaseResource> resourceList;
if (theServer.getPagingProvider() == null) {
numToReturn = theResult.size();
if (numToReturn == 0) {
resourceList = Collections.emptyList();
} else {
resourceList = theResult.getResources(0, numToReturn);
RestfulServerUtils.validateResourceListNotNull(resourceList);
}
} else {
IPagingProvider pagingProvider = theServer.getPagingProvider();
if (theLimit == null) {
numToReturn = pagingProvider.getDefaultPageSize();
} else {
numToReturn = Math.min(pagingProvider.getMaximumPageSize(), theLimit);
}
if (theSearchId != null) {
searchId = theSearchId;
} else {
if (theResult.size() > numToReturn) {
searchId = pagingProvider.storeResultList(theResult);
Validate.notNull(searchId, "Paging provider returned null searchId");
}
}
}
numToReturn = Math.min(numToReturn, theResult.size() - theOffset);
resourceList = theResult.getResources(theOffset, numToReturn + theOffset);
RestfulServerUtils.validateResourceListNotNull(resourceList);
for (IBaseResource next : resourceList) {
if (next.getIdElement() == null || next.getIdElement().isEmpty()) {
if (!(next instanceof OperationOutcome)) {
throw new InternalErrorException("Server method returned resource of type[" + next.getClass().getSimpleName() + "] with no ID specified (IBaseResource#setId(IdDt) must be called)");
}
}
}
if (theSearchId != null) {
searchId = theSearchId;
} else {
if (theResult.size() > numToReturn) {
searchId = pagingProvider.storeResultList(theResult);
Validate.notNull(searchId, "Paging provider returned null searchId");
}
}
}
if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
for (IBaseResource nextRes : resourceList) {
RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
RestfulServerUtils.addProfileToBundleEntry(theServer.getFhirContext(), nextRes, theServerBase);
}
}
}
for (IBaseResource next : resourceList) {
if (next.getIdElement() == null || next.getIdElement().isEmpty()) {
if (!(next instanceof OperationOutcome)) {
throw new InternalErrorException("Server method returned resource of type[" + next.getClass().getSimpleName()
+ "] with no ID specified (IBaseResource#setId(IdDt) must be called)");
}
}
}
addResourcesToBundle(resourceList, theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType, theResult.getPublished());
if (theServer.getAddProfileTag() != AddProfileTagEnum.NEVER) {
for (IBaseResource nextRes : resourceList) {
RuntimeResourceDefinition def = theServer.getFhirContext().getResourceDefinition(nextRes);
if (theServer.getAddProfileTag() == AddProfileTagEnum.ALWAYS || !def.isStandardProfile()) {
RestfulServerUtils.addProfileToBundleEntry(theServer.getFhirContext(), nextRes, theServerBase);
}
}
}
if (theServer.getPagingProvider() != null) {
int limit;
limit = theLimit != null ? theLimit : theServer.getPagingProvider().getDefaultPageSize();
limit = Math.min(limit, theServer.getPagingProvider().getMaximumPageSize());
addResourcesToBundle(resourceList, theBundleType, theServerBase, theServer.getBundleInclusionRule(), theIncludes);
addRootPropertiesToBundle(null, theServerBase, theCompleteUrl, theResult.size(), theBundleType,
theResult.getPublished());
if (searchId != null) {
if (theOffset + numToReturn < theResult.size()) {
myBundle.addLink().setRelation(Constants.LINK_NEXT).setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
}
if (theOffset > 0) {
int start = Math.max(0, theOffset - limit);
myBundle.addLink().setRelation(Constants.LINK_PREVIOUS).setUrl(RestfulServerUtils.createPagingLink(theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
}
}
}
}
if (theServer.getPagingProvider() != null) {
int limit;
limit = theLimit != null ? theLimit : theServer.getPagingProvider().getDefaultPageSize();
limit = Math.min(limit, theServer.getPagingProvider().getMaximumPageSize());
@Override
public void initializeBundleFromResourceList(String theAuthor, List<? extends IBaseResource> theResources, String theServerBase, String theCompleteUrl, int theTotalResults, BundleTypeEnum theBundleType) {
myBundle = new Bundle();
if (searchId != null) {
if (theOffset + numToReturn < theResult.size()) {
myBundle.addLink().setRelation(Constants.LINK_NEXT).setUrl(RestfulServerUtils.createPagingLink(theIncludes,
theServerBase, searchId, theOffset + numToReturn, numToReturn, theResponseEncoding, thePrettyPrint));
}
if (theOffset > 0) {
int start = Math.max(0, theOffset - limit);
myBundle.addLink().setRelation(Constants.LINK_PREVIOUS).setUrl(RestfulServerUtils.createPagingLink(
theIncludes, theServerBase, searchId, start, limit, theResponseEncoding, thePrettyPrint));
}
}
}
}
myBundle.setId(UUID.randomUUID().toString());
@Override
public void initializeBundleFromResourceList(String theAuthor, List<? extends IBaseResource> theResources,
String theServerBase, String theCompleteUrl, int theTotalResults, BundleTypeEnum theBundleType) {
myBundle = new Bundle();
myBundle.getMeta().setLastUpdatedElement(InstantType.withCurrentTime());
myBundle.setId(UUID.randomUUID().toString());
myBundle.addLink().setRelation(Constants.LINK_FHIR_BASE).setUrl(theServerBase);
myBundle.addLink().setRelation(Constants.LINK_SELF).setUrl(theCompleteUrl);
myBundle.getTypeElement().setValueAsString(theBundleType.getCode());
myBundle.getMeta().setLastUpdatedElement(InstantType.withCurrentTime());
if (theBundleType.equals(BundleTypeEnum.TRANSACTION)) {
for (IBaseResource nextBaseRes : theResources) {
IBaseResource next = (IBaseResource) nextBaseRes;
BundleEntryComponent nextEntry = myBundle.addEntry();
myBundle.addLink().setRelation(Constants.LINK_FHIR_BASE).setUrl(theServerBase);
myBundle.addLink().setRelation(Constants.LINK_SELF).setUrl(theCompleteUrl);
myBundle.getTypeElement().setValueAsString(theBundleType.getCode());
nextEntry.setResource((Resource) next);
if (next.getIdElement().isEmpty()) {
nextEntry.getRequest().setMethod(HTTPVerb.POST);
} else {
nextEntry.getRequest().setMethod(HTTPVerb.PUT);
if (next.getIdElement().isAbsolute()) {
nextEntry.getRequest().setUrl(next.getIdElement().getValue());
} else {
String resourceType = myContext.getResourceDefinition(next).getName();
nextEntry.getRequest().setUrl(new IdType(theServerBase, resourceType, next.getIdElement().getIdPart(), next.getIdElement().getVersionIdPart()).getValue());
}
}
}
} else {
addResourcesForSearch(theResources);
}
if (theBundleType.equals(BundleTypeEnum.TRANSACTION)) {
for (IBaseResource nextBaseRes : theResources) {
IBaseResource next = (IBaseResource) nextBaseRes;
BundleEntryComponent nextEntry = myBundle.addEntry();
myBundle.getTotalElement().setValue(theTotalResults);
}
nextEntry.setResource((Resource) next);
if (next.getIdElement().isEmpty()) {
nextEntry.getRequest().setMethod(HTTPVerb.POST);
} else {
nextEntry.getRequest().setMethod(HTTPVerb.PUT);
if (next.getIdElement().isAbsolute()) {
nextEntry.getRequest().setUrl(next.getIdElement().getValue());
} else {
String resourceType = myContext.getResourceDefinition(next).getName();
nextEntry.getRequest().setUrl(new IdType(theServerBase, resourceType, next.getIdElement().getIdPart(),
next.getIdElement().getVersionIdPart()).getValue());
}
}
}
} else {
addResourcesForSearch(theResources);
}
@Override
public void initializeWithBundleResource(IBaseResource theBundle) {
myBundle = (Bundle) theBundle;
}
myBundle.getTotalElement().setValue(theTotalResults);
}
@Override
public List<IBaseResource> toListOfResources() {
ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
for (BundleEntryComponent next : myBundle.getEntry()) {
if (next.getResource() != null) {
retVal.add(next.getResource());
} else if (next.getResponse().getLocationElement().isEmpty() == false) {
IdType id = new IdType(next.getResponse().getLocation());
String resourceType = id.getResourceType();
if (isNotBlank(resourceType)) {
IBaseResource res = (IBaseResource) myContext.getResourceDefinition(resourceType).newInstance();
res.setId(id);
retVal.add(res);
}
}
}
return retVal;
}
@Override
public void initializeWithBundleResource(IBaseResource theBundle) {
myBundle = (Bundle) theBundle;
}
@Override
public List<IBaseResource> toListOfResources() {
ArrayList<IBaseResource> retVal = new ArrayList<IBaseResource>();
for (BundleEntryComponent next : myBundle.getEntry()) {
if (next.getResource() != null) {
retVal.add(next.getResource());
} else if (next.getResponse().getLocationElement().isEmpty() == false) {
IdType id = new IdType(next.getResponse().getLocation());
String resourceType = id.getResourceType();
if (isNotBlank(resourceType)) {
IBaseResource res = (IBaseResource) myContext.getResourceDefinition(resourceType).newInstance();
res.setId(id);
retVal.add(res);
}
}
}
return retVal;
}
}

8
src/changes/changes.xml
View File

@ -151,6 +151,14 @@
security labels were not always properly removed by an update that
was trying to remove them. Also don't store duplicates.
</action>
<action type="fix">
Instance $meta operations on JPA server did not previously return the
resource version and lastUpdated time
</action>
<action type="fix">
Server responses populate Bundle.entry.fullUrl if possible. Thanks
to Bill de Beaubien for reporting!
</action>
</release>
<release version="1.1" date="2015-07-13">
<action type="add">