diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java index 9ec40eb7254..5edacfafad4 100644 --- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java +++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java @@ -210,7 +210,7 @@ public abstract class BaseHapiFhirDao implements IDao { } catch (DataFormatException e) { throw new InvalidRequestException("Invalid resource reference found at path[" + nextPathsUnsplit + "] - Resource type is unknown or not supported on this server - " + nextValue.getReference().getValue()); } - + Class type = resourceDefinition.getImplementingClass(); String id = nextValue.getReference().getIdPart(); if (StringUtils.isBlank(id)) { @@ -271,6 +271,7 @@ public abstract class BaseHapiFhirDao implements IDao { protected List extractSearchParamUri(ResourceTable theEntity, IResource theResource) { return mySearchParamExtractor.extractSearchParamUri(theEntity, theResource); } + protected List extractSearchParamCoords(ResourceTable theEntity, IResource theResource) { return mySearchParamExtractor.extractSearchParamCoords(theEntity, theResource); } @@ -591,7 +592,7 @@ public abstract class BaseHapiFhirDao implements IDao { } Set allDefs = new HashSet(); - + TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource); if (tagList != null) { for (Tag next : tagList) { @@ -610,8 +611,8 @@ public abstract class BaseHapiFhirDao implements IDao { theEntity.addTag(tag); theEntity.setHasTags(true); } - } - + } + List profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource); if (profiles != null) { for (IIdType next : profiles) { @@ -621,18 +622,18 @@ public abstract class BaseHapiFhirDao implements IDao { theEntity.setHasTags(true); } } - - + for (ResourceTag next : new ArrayList(theEntity.getTags())) { TagDefinition nextDef = next.getTag(); if (!allDefs.contains(nextDef)) { - theEntity.getTags().remove(next); + if (shouldDroppedTagBeRemovedOnUpdate(theEntity, next)) { + theEntity.getTags().remove(next); + } } } if (theEntity.getTags().size() == 0) { theEntity.setHasTags(false); } - String title = ResourceMetadataKeyEnum.TITLE.get(theResource); if (title != null && title.length() > BaseHasResource.MAX_TITLE_LENGTH) { @@ -642,6 +643,29 @@ public abstract class BaseHapiFhirDao implements IDao { } + /** + * This method is called when an update to an existing resource detects that the resource supplied for update is + * missing a tag/profile/security label that the currently persisted resource holds. + *

+ * The default implementation removes any profile declarations, but leaves tags and security labels in place. + * Subclasses may choose to override and change this behaviour. + *

+ * + * @param theEntity + * The entity being updated (Do not modify the entity! Undefined behaviour will occur!) + * @param theTag + * The tag + * @return Retturns true if the tag should be removed + * @see Updates to Tags, Profiles, and Security + * Labels for a description of the logic that the default behaviour folows. + */ + protected boolean shouldDroppedTagBeRemovedOnUpdate(ResourceTable theEntity, ResourceTag theTag) { + if (theTag.getTag().getTagType() == TagTypeEnum.PROFILE) { + return true; + } + return false; + } + protected Set processMatchUrl(String theMatchUrl, Class theResourceType) { RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(theResourceType); @@ -1260,17 +1284,15 @@ public abstract class BaseHapiFhirDao implements IDao { } /** - * This method is invoked immediately before storing a new resource, or an - * update to an existing resource to allow the DAO to ensure that it is valid - * for persistence. By default, checks for the "subsetted" tag and rejects - * resources which have it. Subclasses should call the superclass implementation to - * preserve this check. + * This method is invoked immediately before storing a new resource, or an update to an existing resource to allow + * the DAO to ensure that it is valid for persistence. By default, checks for the "subsetted" tag and rejects + * resources which have it. Subclasses should call the superclass implementation to preserve this check. * * @param theResource * The resource that is about to be persisted */ protected void validateResourceForStorage(T theResource) { - IResource res = (IResource)theResource; + IResource res = (IResource) theResource; TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(res); if (tagList != null) { Tag tag = tagList.getTag(Constants.TAG_SUBSETTED_SYSTEM, Constants.TAG_SUBSETTED_CODE); diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2UpdateTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2UpdateTest.java index 230380c6821..22dce227967 100644 --- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2UpdateTest.java +++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2UpdateTest.java @@ -1,6 +1,7 @@ package ca.uhn.fhir.jpa.dao; import static org.hamcrest.Matchers.contains; +import static org.hamcrest.Matchers.containsInAnyOrder; import static org.hamcrest.Matchers.containsString; import static org.hamcrest.Matchers.endsWith; import static org.hamcrest.Matchers.not; @@ -17,9 +18,8 @@ import static org.mockito.Mockito.verify; import java.util.ArrayList; import java.util.Date; -import java.util.HashMap; +import java.util.HashSet; import java.util.List; -import java.util.Map; import java.util.Set; import org.hl7.fhir.instance.model.api.IBaseResource; @@ -27,10 +27,12 @@ import org.hl7.fhir.instance.model.api.IIdType; import org.junit.Test; import org.mockito.ArgumentCaptor; -import ca.uhn.fhir.model.api.IQueryParameterType; import ca.uhn.fhir.model.api.IResource; 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.base.composite.BaseCodingDt; +import ca.uhn.fhir.model.dstu2.composite.CodingDt; import ca.uhn.fhir.model.dstu2.resource.Organization; import ca.uhn.fhir.model.dstu2.resource.Patient; import ca.uhn.fhir.model.primitive.IdDt; @@ -166,6 +168,62 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test { myPatientDao.update(p); } + /** + * Per the spec, update should preserve tags and security labels but not profiles + */ + @Test + public void testUpdateMaintainsTagsAndSecurityLabels() throws InterruptedException { + String methodName = "testUpdateMaintainsTagsAndSecurityLabels"; + + IIdType p1id; + { + Patient p1 = new Patient(); + p1.addName().addFamily(methodName); + + TagList tagList = new TagList(); + tagList.addTag("tag_scheme1", "tag_term1"); + ResourceMetadataKeyEnum.TAG_LIST.put(p1, tagList); + List secList = new ArrayList(); + secList.add(new CodingDt("sec_scheme1", "sec_term1")); + ResourceMetadataKeyEnum.SECURITY_LABELS.put(p1, secList); + List profileList = new ArrayList(); + profileList.add(new IdDt("http://foo1")); + ResourceMetadataKeyEnum.PROFILES.put(p1, profileList); + + p1id = myPatientDao.create(p1).getId().toUnqualifiedVersionless(); + } + { + Patient p1 = new Patient(); + p1.setId(p1id); + p1.addName().addFamily(methodName); + + TagList tagList = new TagList(); + tagList.addTag("tag_scheme2", "tag_term2"); + ResourceMetadataKeyEnum.TAG_LIST.put(p1, tagList); + List secList = new ArrayList(); + secList.add(new CodingDt("sec_scheme2", "sec_term2")); + ResourceMetadataKeyEnum.SECURITY_LABELS.put(p1, secList); + List profileList = new ArrayList(); + profileList.add(new IdDt("http://foo2")); + ResourceMetadataKeyEnum.PROFILES.put(p1, profileList); + + myPatientDao.update(p1); + } + { + Patient p1 = myPatientDao.read(p1id); + TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(p1); + assertThat(tagList, containsInAnyOrder(new Tag("tag_scheme1", "tag_term1"), new Tag("tag_scheme2", "tag_term2"))); + List secList = ResourceMetadataKeyEnum.SECURITY_LABELS.get(p1); + Set secListValues = new HashSet(); + for (BaseCodingDt next : secList) { + secListValues.add(next.getSystemElement().getValue() + "|" + next.getCodeElement().getValue()); + } + assertThat(secListValues, containsInAnyOrder("sec_scheme1|sec_term1", "sec_scheme2|sec_term2")); + List profileList = ResourceMetadataKeyEnum.PROFILES.get(p1); + assertThat(profileList, contains(new IdDt("http://foo2"))); // no foo1 + } + } + @Test public void testUpdateMaintainsSearchParams() throws InterruptedException { Patient p1 = new Patient(); @@ -236,13 +294,13 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test { { Patient patient = new Patient(); patient.addName().addFamily(name); - + List tl = new ArrayList(); tl.add(new IdDt("http://foo/bar")); tl.add(new IdDt("http://foo/bar")); tl.add(new IdDt("http://foo/bar")); ResourceMetadataKeyEnum.PROFILES.put(patient, tl); - + id = myPatientDao.create(patient).getId().toUnqualifiedVersionless(); } @@ -255,7 +313,7 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test { } } - + @Test public void testUpdateModifiesProfiles() { String name = "testUpdateModifiesProfiles"; @@ -263,11 +321,11 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test { { Patient patient = new Patient(); patient.addName().addFamily(name); - + List tl = new ArrayList(); tl.add(new IdDt("http://foo/bar")); ResourceMetadataKeyEnum.PROFILES.put(patient, tl); - + id = myPatientDao.create(patient).getId().toUnqualifiedVersionless(); } @@ -284,11 +342,11 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test { Patient patient = new Patient(); patient.setId(id); patient.addName().addFamily(name); - + List tl = new ArrayList(); tl.add(new IdDt("http://foo/baz")); ResourceMetadataKeyEnum.PROFILES.put(patient, tl); - + id = myPatientDao.update(patient).getId().toUnqualifiedVersionless(); } @@ -300,11 +358,8 @@ public class FhirResourceDaoDstu2UpdateTest extends BaseJpaDstu2Test { assertEquals("http://foo/baz", tl.get(0).getValue()); } - } - - @Test public void testUpdateUnknownNumericIdFails() { Patient p = new Patient(); diff --git a/src/site/xdoc/doc_validation.xml b/src/site/xdoc/doc_validation.xml index b32e12539b3..1cbae15bd46 100644 --- a/src/site/xdoc/doc_validation.xml +++ b/src/site/xdoc/doc_validation.xml @@ -40,17 +40,18 @@

There are two implementations of IParserErrorHandler worth - mentioning. + mentioning. You can also supply your own implementation if you want.

    - -
      + logs any errors but does not abort parsing. By default this handler is used, and it + logs errors at "warning" level. It can also be configured to silently ignore issues. + +
    • StrictErrorHandler throws a DataFormatException if any errors are detected. -
    +

@@ -82,37 +83,39 @@ -

+

HAPI provides a built-in and configurable mechanism for validating resources. - This mechanism is called the FHIR Validator. + This mechanism is called the Resource Validator. +

+ +

+ FHIR resource definitions are distributed with a set of XML schema files (XSD) + as well as a set of XML Schematron (SCH) files. These two sets of files are + complimentary to each other, meaning that in order to claim compliance to the + FHIR specification, your resources must validate against both sets. +

+

+ The two sets of files are included with HAPI, and it uses them to perform + validation.

- - -

- FHIR resource definitions are distributed with a set of XML schema files (XSD) - as well as a set of XML Schematron (SCH) files. These two sets of files are - complimentary to each other, meaning that in order to claim compliance to the - FHIR specification, your resources must validate against both sets. -

-

- The two sets of files are included with HAPI, and it uses them to perform - validation. -

- - -

In order to use HAPI's Schematron support, a libaray called Phloc-Schematron - is used, so this library must be added to your classpath (or Maven pom file). - See Downloads for more information. + is used, so this library must be added to your classpath (or Maven POM file, Gradle + file, etc.) + Note that this library is specified as an optional dependency by HAPI FHIR + so you need to explicitly include it if you want to use this + functionality. +

+

+ See Downloads for more information on how + to add it.

- @@ -142,6 +145,46 @@ + +
+ +
+ +

+ As of HAPI FHIR 1.2, HAPI supports validation against StructureDefinition + resources. This functionality uses the HL7 "InstanceValidator", which is able + to check a resource for conformance to a given profile (StructureDefinition), + including validating codes for conformance to their given ValueSets. +

+

+ StructureDefinition validation can be used to validate a resource against the + official structure definitions (produced by HL7) as well as against custom + definitions provided either by HL7 or by the user. +

+ + + +

+ To use this functionality, you must add the following two dependencies + to your classpath (or Maven POM file, Gradle file, etc.): +

+
    +
  • + hapi-fhir-structures-hl7org-dstu2: This file contains the "reference implementation" + structures and tooling. You need to include it even if you are not using the RI model + (the StructureDefinition validation will work against HAPI structures as well) +
    • +
  • + hapi-fhir-validation-resources: This file contains the official FHIR + StructureDefinition files, and the ValueSets needed to support them. +
    • +
+

+ See the download page for more information. +

+ + +
diff --git a/src/site/xdoc/download.xml.vm b/src/site/xdoc/download.xml.vm index 788e85612e2..2c25c061cca 100644 --- a/src/site/xdoc/download.xml.vm +++ b/src/site/xdoc/download.xml.vm @@ -12,26 +12,38 @@ - - - + + + - + - + + + + + - + + + + + - + + + + +
HAPI Structure LibraryHAPI VersionFHIR Specification VersionHAPI Structure LibraryHAPI VersionFHIR Specification Version
hapi-fhir-structures-dstuhapi-fhir-structures-dstu 1.1 DSTU1 0.0.82
hapi-fhir-structures-dstu21.2DSTU1 0.0.82
hapi-fhir-structures-dstu2 1.1 DSTU2 0.5.0
hapi-fhir-structures-hl7org-dstu21.2DSTU2 1.0.0
hapi-fhir-structures-hl7org-dstu2 1.1DSTU2 Latest Dev (SVN 5843)DSTU2 0.5.0 Snapshot (SVN 5843)
1.2DSTU2 1.0.0
@@ -62,7 +74,7 @@

See using snapshot builds below to find out - how to get these builds.S + how to get these builds.

@@ -78,11 +90,10 @@

- At this time, the only official release of FHIR is the "DSTU1" release, - which is available by including the hapi-fhir-structures-dstu-[version].jar. - 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 hapi-fhir-structures-dstu-[version].jar.

If you use Maven, you can include these JARs with the following dependency tags @@ -137,6 +148,17 @@ ${hapi_stable_version} ]]> +

+ If you want to use HAPI's + StructureDefinition validation + you will also need to include the hapi-fhir-validation-resources-[version].jar: +

+ + ca.uhn.hapi.fhir + hapi-fhir-validation-resources + ${hapi_stable_version} +]]> +
@@ -153,10 +175,16 @@

- DSTU2: + DSTU2 (HAPI):

+

+ DSTU2 (RI): +

+