Correct tag handling for DSTU2
This commit is contained in:
jamesagnew
parent
517222d183
commit
875ad3b5f9
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@ -210,7 +210,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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} catch (DataFormatException e) {
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throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Resource type is unknown or not supported on this server - " + nextValue.getReference().getValue());
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}
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Class<? extends IBaseResource> type = resourceDefinition.getImplementingClass();
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String id = nextValue.getReference().getIdPart();
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if (StringUtils.isBlank(id)) {
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@ -271,6 +271,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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protected List<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IResource theResource) {
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return mySearchParamExtractor.extractSearchParamUri(theEntity, theResource);
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}
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protected List<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IResource theResource) {
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return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource);
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}
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@ -591,7 +592,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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}
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Set<TagDefinition> allDefs = new HashSet<TagDefinition>();
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TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource);
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if (tagList != null) {
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for (Tag next : tagList) {
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@ -610,8 +611,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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theEntity.addTag(tag);
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theEntity.setHasTags(true);
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}
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}
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}
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List<IdDt> profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource);
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if (profiles != null) {
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for (IIdType next : profiles) {
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@ -621,18 +622,18 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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theEntity.setHasTags(true);
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}
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}
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for (ResourceTag next : new ArrayList<ResourceTag>(theEntity.getTags())) {
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TagDefinition nextDef = next.getTag();
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if (!allDefs.contains(nextDef)) {
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theEntity.getTags().remove(next);
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if (shouldDroppedTagBeRemovedOnUpdate(theEntity, next)) {
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theEntity.getTags().remove(next);
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}
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}
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}
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if (theEntity.getTags().size() == 0) {
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theEntity.setHasTags(false);
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}
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String title = ResourceMetadataKeyEnum.TITLE.get(theResource);
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if (title != null && title.length() > BaseHasResource.MAX_TITLE_LENGTH) {
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@ -642,6 +643,29 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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}
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/**
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* This method is called when an update to an existing resource detects that the resource supplied for update is
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* missing a tag/profile/security label that the currently persisted resource holds.
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* <p>
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* The default implementation removes any profile declarations, but leaves tags and security labels in place.
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* Subclasses may choose to override and change this behaviour.
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* </p>
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*
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* @param theEntity
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* The entity being updated (Do not modify the entity! Undefined behaviour will occur!)
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* @param theTag
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* The tag
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* @return Retturns <code>true</code> if the tag should be removed
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* @see <a href="http://hl7.org/fhir/2015Sep/resource.html#1.11.3.7">Updates to Tags, Profiles, and Security
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* Labels</a> for a description of the logic that the default behaviour folows.
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*/
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protected boolean shouldDroppedTagBeRemovedOnUpdate(ResourceTable theEntity, ResourceTag theTag) {
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if (theTag.getTag().getTagType() == TagTypeEnum.PROFILE) {
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return true;
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}
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return false;
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}
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protected <R extends IResource> Set<Long> processMatchUrl(String theMatchUrl, Class<R> theResourceType) {
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RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType);
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@ -1260,17 +1284,15 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
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}
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/**
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* This method is invoked immediately before storing a new resource, or an
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* update to an existing resource to allow the DAO to ensure that it is valid
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* for persistence. By default, checks for the "subsetted" tag and rejects
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* resources which have it. Subclasses should call the superclass implementation to
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* preserve this check.
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* This method is invoked immediately before storing a new resource, or an update to an existing resource to allow
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* the DAO to ensure that it is valid for persistence. By default, checks for the "subsetted" tag and rejects
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* resources which have it. Subclasses should call the superclass implementation to preserve this check.
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*
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* @param theResource
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* The resource that is about to be persisted
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*/
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protected void validateResourceForStorage(T theResource) {
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IResource res = (IResource)theResource;
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IResource res = (IResource) theResource;
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TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res);
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if (tagList != null) {
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Tag tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE);
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@ -1,6 +1,7 @@
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package ca.uhn.fhir.jpa.dao;
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import static org.hamcrest.Matchers.contains;
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import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.endsWith;
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import static org.hamcrest.Matchers.not;
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@ -17,9 +18,8 @@ import static org.mockito.Mockito.verify;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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@ -27,10 +27,12 @@ import org.hl7.fhir.instance.model.api.IIdType;
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import org.junit.Test;
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import org.mockito.ArgumentCaptor;
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import ca.uhn.fhir.model.api.IQueryParameterType;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
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import ca.uhn.fhir.model.api.Tag;
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import ca.uhn.fhir.model.api.TagList;
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import ca.uhn.fhir.model.base.composite.BaseCodingDt;
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import ca.uhn.fhir.model.dstu2.composite.CodingDt;
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import ca.uhn.fhir.model.dstu2.resource.Organization;
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import ca.uhn.fhir.model.dstu2.resource.Patient;
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import ca.uhn.fhir.model.primitive.IdDt;
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@ -166,6 +168,62 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
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myPatientDao.update(p);
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}
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/**
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* Per the spec, update should preserve tags and security labels but not profiles
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*/
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@Test
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public void testUpdateMaintainsTagsAndSecurityLabels() throws InterruptedException {
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String methodName = "testUpdateMaintainsTagsAndSecurityLabels";
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IIdType p1id;
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{
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Patient p1 = new Patient();
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p1.addName().addFamily(methodName);
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TagList tagList = new TagList();
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tagList.addTag("tag_scheme1", "tag_term1");
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ResourceMetadataKeyEnum.TAG_LIST.put(p1, tagList);
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List<BaseCodingDt> secList = new ArrayList<BaseCodingDt>();
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secList.add(new CodingDt("sec_scheme1", "sec_term1"));
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ResourceMetadataKeyEnum.SECURITY_LABELS.put(p1, secList);
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List<IdDt> profileList = new ArrayList<IdDt>();
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profileList.add(new IdDt("http://foo1"));
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ResourceMetadataKeyEnum.PROFILES.put(p1, profileList);
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p1id = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
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}
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{
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Patient p1 = new Patient();
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p1.setId(p1id);
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p1.addName().addFamily(methodName);
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TagList tagList = new TagList();
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tagList.addTag("tag_scheme2", "tag_term2");
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ResourceMetadataKeyEnum.TAG_LIST.put(p1, tagList);
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List<BaseCodingDt> secList = new ArrayList<BaseCodingDt>();
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secList.add(new CodingDt("sec_scheme2", "sec_term2"));
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ResourceMetadataKeyEnum.SECURITY_LABELS.put(p1, secList);
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List<IdDt> profileList = new ArrayList<IdDt>();
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profileList.add(new IdDt("http://foo2"));
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ResourceMetadataKeyEnum.PROFILES.put(p1, profileList);
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myPatientDao.update(p1);
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}
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{
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Patient p1 = myPatientDao.read(p1id);
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TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(p1);
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assertThat(tagList, containsInAnyOrder(new Tag("tag_scheme1", "tag_term1"), new Tag("tag_scheme2", "tag_term2")));
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List<BaseCodingDt> secList = ResourceMetadataKeyEnum.SECURITY_LABELS.get(p1);
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Set<String> secListValues = new HashSet<String>();
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for (BaseCodingDt next : secList) {
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secListValues.add(next.getSystemElement().getValue() + "|" + next.getCodeElement().getValue());
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}
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assertThat(secListValues, containsInAnyOrder("sec_scheme1|sec_term1", "sec_scheme2|sec_term2"));
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List<IdDt> profileList = ResourceMetadataKeyEnum.PROFILES.get(p1);
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assertThat(profileList, contains(new IdDt("http://foo2"))); // no foo1
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}
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}
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@Test
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public void testUpdateMaintainsSearchParams() throws InterruptedException {
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Patient p1 = new Patient();
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@ -236,13 +294,13 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
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{
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Patient patient = new Patient();
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patient.addName().addFamily(name);
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List<IdDt> tl = new ArrayList<IdDt>();
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tl.add(new IdDt("http://foo/bar"));
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tl.add(new IdDt("http://foo/bar"));
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tl.add(new IdDt("http://foo/bar"));
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ResourceMetadataKeyEnum.PROFILES.put(patient, tl);
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id = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
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}
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@ -255,7 +313,7 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
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}
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}
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@Test
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public void testUpdateModifiesProfiles() {
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String name = "testUpdateModifiesProfiles";
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@ -263,11 +321,11 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
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{
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Patient patient = new Patient();
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patient.addName().addFamily(name);
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List<IdDt> tl = new ArrayList<IdDt>();
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tl.add(new IdDt("http://foo/bar"));
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ResourceMetadataKeyEnum.PROFILES.put(patient, tl);
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id = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
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}
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@ -284,11 +342,11 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
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Patient patient = new Patient();
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patient.setId(id);
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patient.addName().addFamily(name);
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List<IdDt> tl = new ArrayList<IdDt>();
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tl.add(new IdDt("http://foo/baz"));
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ResourceMetadataKeyEnum.PROFILES.put(patient, tl);
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id = myPatientDao.update(patient).getId().toUnqualifiedVersionless();
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}
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@ -300,11 +358,8 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test {
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assertEquals("http://foo/baz", tl.get(0).getValue());
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}
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}
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@Test
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public void testUpdateUnknownNumericIdFails() {
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Patient p = new Patient();
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@ -40,17 +40,18 @@
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</p>
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<p>
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There are two implementations of <code>IParserErrorHandler</code> worth
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mentioning.
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mentioning. You can also supply your own implementation if you want.
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</p>
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<ul>
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<ul>
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<li>
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<a href="./apidocs/ca/uhn/fhir/parser/LenientErrorHandler.html">LenientErrorHandler</a>
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logs any errors but does not abort parsing. This is the default.
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</ul>
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<ul>
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logs any errors but does not abort parsing. By default this handler is used, and it
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logs errors at "warning" level. It can also be configured to silently ignore issues.
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</li>
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<li>
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<a href="./apidocs/ca/uhn/fhir/parser/StrictErrorHandler.html">StrictErrorHandler</a>
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throws a <code>DataFormatException</code> if any errors are detected.
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</ul>
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</li>
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</ul>
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<p>
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@ -82,37 +83,39 @@
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<!-- RESOURCE VALIDATION -->
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<section name="Resource Validation">
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<section name="Resource Validation (Schema/Schematron)">
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<p>
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HAPI provides a built-in and configurable mechanism for validating resources.
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This mechanism is called the <i>FHIR Validator</i>.
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This mechanism is called the <i>Resource Validator</i>.
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</p>
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<p>
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FHIR resource definitions are distributed with a set of XML schema files (XSD)
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as well as a set of XML Schematron (SCH) files. These two sets of files are
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complimentary to each other, meaning that in order to claim compliance to the
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FHIR specification, your resources must validate against both sets.
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</p>
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<p>
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The two sets of files are included with HAPI, and it uses them to perform
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validation.
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</p>
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<subsection name="Background">
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<p>
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FHIR resource definitions are distributed with a set of XML schema files (XSD)
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as well as a set of XML Schematron (SCH) files. These two sets of files are
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complimentary to each other, meaning that in order to claim compliance to the
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FHIR specification, your resources must validate against both sets.
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</p>
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<p>
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The two sets of files are included with HAPI, and it uses them to perform
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validation.
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</p>
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</subsection>
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<subsection name="Preparation">
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<p>
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In order to use HAPI's Schematron support, a libaray called
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<a href="https://code.google.com/p/phloc-schematron/">Phloc-Schematron</a>
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is used, so this library must be added to your classpath (or Maven pom file).
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See <a href="./download.html">Downloads</a> for more information.
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is used, so this library must be added to your classpath (or Maven POM file, Gradle
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file, etc.)
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Note that this library is specified as an optional dependency by HAPI FHIR
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so you need to explicitly include it if you want to use this
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functionality.
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</p>
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<p>
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See <a href="./download.html">Downloads</a> for more information on how
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to add it.
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</p>
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</subsection>
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<subsection name="Validating a Resource">
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@ -142,6 +145,46 @@
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</subsection>
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<a name="structure_definition_validation"/>
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</section>
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<section name="Resource Validation (StructureDefinition / ValueSet)">
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<p>
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As of HAPI FHIR 1.2, HAPI supports validation against StructureDefinition
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resources. This functionality uses the HL7 "InstanceValidator", which is able
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to check a resource for conformance to a given profile (StructureDefinition),
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including validating codes for conformance to their given ValueSets.
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</p>
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<p>
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StructureDefinition validation can be used to validate a resource against the
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official structure definitions (produced by HL7) as well as against custom
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definitions provided either by HL7 or by the user.
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</p>
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<subsection name="Preparation">
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<p>
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To use this functionality, you must add the following two dependencies
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to your classpath (or Maven POM file, Gradle file, etc.):
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</p>
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<ul>
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<li>
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<b>hapi-fhir-structures-hl7org-dstu2</b>: This file contains the "reference implementation"
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structures and tooling. You need to include it even if you are not using the RI model
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(the StructureDefinition validation will work against HAPI structures as well)
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</li>
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<li>
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<b>hapi-fhir-validation-resources</b>: This file contains the official FHIR
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StructureDefinition files, and the ValueSets needed to support them.
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</li>
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</ul>
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<p>
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See the <a href="./download.html">download page</a> for more information.
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</p>
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</subsection>
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</section>
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</body>
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@ -12,26 +12,38 @@
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<table>
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<thead>
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<tr>
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<td>HAPI Structure Library</td>
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<td>HAPI Version</td>
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<td>FHIR Specification Version</td>
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<td><b>HAPI Structure Library</b></td>
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<td><b>HAPI Version</b></td>
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<td><b>FHIR Specification Version</b></td>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>hapi-fhir-structures-dstu</td>
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<td rowspan="2">hapi-fhir-structures-dstu</td>
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<td>1.1</td>
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<td><a href="http://www.hl7.org/fhir/DSTU1/index.html">DSTU1 0.0.82</a></td>
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</tr>
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<tr>
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<td>hapi-fhir-structures-dstu2</td>
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<td>1.2</td>
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<td><a href="http://www.hl7.org/fhir/DSTU1/index.html">DSTU1 0.0.82</a></td>
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</tr>
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<tr>
|
||||
<td rowspan="2">hapi-fhir-structures-dstu2</td>
|
||||
<td>1.1</td>
|
||||
<td><a href="http://www.hl7.org/fhir/2015May/index.html">DSTU2 0.5.0</a></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>hapi-fhir-structures-hl7org-dstu2</td>
|
||||
<td>1.2</td>
|
||||
<td><a href="http://hl7.org/fhir/2015Sep/index.html">DSTU2 1.0.0</a></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td rowspan="2">hapi-fhir-structures-hl7org-dstu2</td>
|
||||
<td>1.1</td>
|
||||
<td><a href="http://hl7-fhir.github.io/">DSTU2 Latest Dev</a> (SVN 5843)</td>
|
||||
<td><a href="http://hl7-fhir.github.io/">DSTU2 0.5.0 Snapshot</a> (SVN 5843)</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td>1.2</td>
|
||||
<td><a href="http://hl7.org/fhir/2015Sep/index.html">DSTU2 1.0.0</a></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
|
@ -62,7 +74,7 @@
|
|||
</p>
|
||||
<p>
|
||||
See <a href="#Using_Snapshot_Builds">using snapshot builds</a> below to find out
|
||||
how to get these builds.S
|
||||
how to get these builds.
|
||||
</p>
|
||||
</subsection>
|
||||
|
||||
|
|
@ -78,11 +90,10 @@
|
|||
|
||||
<subsection name="DSTU1 Resources - HAPI Structures">
|
||||
<p>
|
||||
At this time, the only official release of FHIR is the "DSTU1" release,
|
||||
which is available by including the <code>hapi-fhir-structures-dstu-[version].jar</code>.
|
||||
Note that the ballot process for the next release (DSTU2) has not yet been
|
||||
completed, but many users are already targeting it for new development as it
|
||||
is likely to be approved without significant changes.
|
||||
HAPI supports multiple versions of the FHIR specification. Code which
|
||||
needs to interact with or implement the DSTU1 specification (which is
|
||||
now gradually beginning to be replaced by newer specifications) can do
|
||||
so using <code>hapi-fhir-structures-dstu-[version].jar</code>.
|
||||
</p>
|
||||
<p>
|
||||
If you use Maven, you can include these JARs with the following dependency tags
|
||||
|
|
@ -137,6 +148,17 @@
|
|||
<version>${hapi_stable_version}</version>
|
||||
</dependency>]]></source>
|
||||
|
||||
<p>
|
||||
If you want to use HAPI's
|
||||
<a href="./doc_validation.html#structure_definition_validation">StructureDefinition validation</a>
|
||||
you will also need to include the <code>hapi-fhir-validation-resources-[version].jar</code>:
|
||||
</p>
|
||||
<source><![CDATA[<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-fhir-validation-resources</artifactId>
|
||||
<version>${hapi_stable_version}</version>
|
||||
</dependency>]]></source>
|
||||
|
||||
</subsection>
|
||||
|
||||
</section>
|
||||
|
|
@ -153,10 +175,16 @@
|
|||
<source><![CDATA[compile 'ca.uhn.hapi.fhir:hapi-fhir-base:${hapi_stable_version}'
|
||||
compile 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu:${hapi_stable_version}']]></source>
|
||||
<p>
|
||||
DSTU2:
|
||||
DSTU2 (HAPI):
|
||||
</p>
|
||||
<source><![CDATA[compile 'ca.uhn.hapi.fhir:hapi-fhir-base:${hapi_stable_version}'
|
||||
compile 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:${hapi_stable_version}']]></source>
|
||||
<p>
|
||||
DSTU2 (RI):
|
||||
</p>
|
||||
<source><![CDATA[compile 'ca.uhn.hapi.fhir:hapi-fhir-base:${hapi_stable_version}'
|
||||
compile 'ca.uhn.hapi.fhir:hapi-fhir-structures-hl7org-dstu2:${hapi_stable_version}'
|
||||
compile 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources:${hapi_stable_version}']]></source>
|
||||
</section>
|
||||
|
||||
<section name="Using Snapshot Builds">
|
||||
|
|
|
|||
Loading…
Reference in New Issue