diff --git a/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/QualifierDetailsTest.java b/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/QualifierDetailsTest.java
new file mode 100644
index 00000000000..d63b545b74e
--- /dev/null
+++ b/hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/QualifierDetailsTest.java
@@ -0,0 +1,21 @@
+package ca.uhn.fhir.rest.param;
+
+import com.google.common.collect.Sets;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class QualifierDetailsTest {
+
+ @Test
+ public void testBlacklist() {
+
+ QualifierDetails details = new QualifierDetails();
+ details.setColonQualifier(":Patient");
+ assertFalse(details.passes(null, Sets.newHashSet(":Patient")));
+ assertTrue(details.passes(null, Sets.newHashSet(":Observation")));
+
+ }
+
+
+}
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-error-on-missing-profile-validation.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-error-on-missing-profile-validation.yaml
new file mode 100644
index 00000000000..c468181274e
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-error-on-missing-profile-validation.yaml
@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1742
+title: "When validating a resource, the validator will now report an error if the resource declares conformance
+ to an unknown or invalid profile URL via the `Resource.meta.profile` declaration. Previously this was a warning
+ and did not block successful validation."
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-limit-type-on-has.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-limit-type-on-has.yaml
new file mode 100644
index 00000000000..4397032c2aa
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-limit-type-on-has.yaml
@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 1742
+title: "When performing a search in the JPA server where the only parameter was a `_has` parameter,
+ the server did not respect the resource typename being searched for, causing false positive
+ search results. This has been corrected."
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-terminology-delta-defer.yaml b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-terminology-delta-defer.yaml
new file mode 100644
index 00000000000..bdc0dff48f5
--- /dev/null
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-terminology-delta-defer.yaml
@@ -0,0 +1,6 @@
+---
+type: add
+issue: 1742
+title: When performing a terminology delta ADD operation, if the number of codes being added is large
+ the codes will be added in small batches via an asynchronous scheduled task in order to avoid overwhelming
+ the database with a large operation.
diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
index 00fd60b7ff5..f085f2e4d45 100644
--- a/hapi-fhir-jpaserver-base/pom.xml
+++ b/hapi-fhir-jpaserver-base/pom.xml
@@ -48,6 +48,11 @@
commons-csv
+
+ co.elastic.apm
+ apm-agent-api
+
+
ca.uhn.hapi.fhir
hapi-fhir-base
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
index 6168d8fe5e4..57e8aa333a6 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
@@ -102,7 +102,7 @@ public class DaoConfig {
/**
* update setter javadoc if default changes
*/
- private int myDeferIndexingForCodesystemsOfSize = 2000;
+ private int myDeferIndexingForCodesystemsOfSize = 100;
private boolean myDeleteStaleSearches = true;
private boolean myEnforceReferentialIntegrityOnDelete = true;
private boolean myUniqueIndexesEnabled = true;
@@ -392,7 +392,7 @@ public class DaoConfig {
* the code system will be indexed later in an incremental process in order to
* avoid overwhelming Lucene with a huge number of codes in a single operation.
*
- * Defaults to 2000
+ * Defaults to 100
*
*/
public int getDeferIndexingForCodesystemsOfSize() {
@@ -404,7 +404,7 @@ public class DaoConfig {
* the code system will be indexed later in an incremental process in order to
* avoid overwhelming Lucene with a huge number of codes in a single operation.
*
- * Defaults to 2000
+ * Defaults to 100
*
*/
public void setDeferIndexingForCodesystemsOfSize(int theDeferIndexingForCodesystemsOfSize) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.java
index 6f367cefc91..5928bdc1354 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.java
@@ -50,4 +50,8 @@ public interface ITermConceptDao extends JpaRepository {
@Query("SELECT t FROM TermConcept t WHERE t.myIndexStatus = null")
Page findResourcesRequiringReindexing(Pageable thePageRequest);
+ @Modifying
+ @Query("DELETE FROM TermConcept t WHERE t.myId = :pid")
+ void deleteByPid(@Param("pid") Long theId);
+
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
index 37ba84a0aba..cf2dc290618 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
@@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@@ -39,4 +40,9 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository findIdsByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
+
+ @Modifying
+ @Query("DELETE FROM TermConceptParentChildLink t WHERE t.myChildPid = :pid OR t.myParentPid = :pid")
+ void deleteByConceptPid(@Param("pid") Long theId);
+
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
index 6077495a1c2..ca72f0a6f56 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
@@ -430,7 +430,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
break;
case Constants.PARAM_HAS:
- addPredicateHas(theAndOrParams, theRequest);
+ addPredicateHas(theResourceName, theAndOrParams, theRequest);
break;
case Constants.PARAM_TAG:
@@ -756,7 +756,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
return retVal;
}
- private void addPredicateHas(List> theHasParameters, RequestDetails theRequest) {
+ private void addPredicateHas(String theResourceType, List> theHasParameters, RequestDetails theRequest) {
for (List nextOrList : theHasParameters) {
@@ -811,8 +811,9 @@ class PredicateBuilderReference extends BasePredicateBuilder {
Join join = myQueryRoot.join("myResourceLinksAsTarget", JoinType.LEFT);
Predicate pathPredicate = myPredicateBuilder.createResourceLinkPathPredicate(targetResourceType, paramReference, join);
- Predicate pidPredicate = join.get("mySourceResourcePid").in(subQ);
- Predicate andPredicate = myBuilder.and(pathPredicate, pidPredicate);
+ Predicate sourceTypePredicate = myBuilder.equal(join.get("myTargetResourceType"), theResourceType);
+ Predicate sourcePidPredicate = join.get("mySourceResourcePid").in(subQ);
+ Predicate andPredicate = myBuilder.and(pathPredicate, sourcePidPredicate, sourceTypePredicate);
myQueryRoot.addPredicate(andPredicate);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
index 73abe091453..ce89811024b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
@@ -47,7 +47,7 @@ public class TermCodeSystem implements Serializable {
@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
private String myCodeSystemUri;
- @OneToOne()
+ @OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CURRENT_VERSION_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_CURVER"))
private TermCodeSystemVersion myCurrentVersion;
@Column(name = "CURRENT_VERSION_PID", nullable = true, insertable = false, updatable = false)
@@ -57,7 +57,7 @@ public class TermCodeSystem implements Serializable {
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODESYSTEM_PID")
@Column(name = "PID")
private Long myPid;
- @OneToOne()
+ @OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
private ResourceTable myResource;
@Column(name = "RES_ID", insertable = false, updatable = false)
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
index f92e421888a..c87f76e3d3e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
@@ -50,7 +50,7 @@ public class TermCodeSystemVersion implements Serializable {
@Column(name = "PID")
private Long myId;
- @OneToOne()
+ @OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
private ResourceTable myResource;
@@ -64,7 +64,7 @@ public class TermCodeSystemVersion implements Serializable {
* This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
* issued. It should be made non-nullable at some point.
*/
- @ManyToOne
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_CODESYSVER_CS_ID"))
private TermCodeSystem myCodeSystem;
@@ -72,7 +72,7 @@ public class TermCodeSystemVersion implements Serializable {
private Long myCodeSystemPid;
@SuppressWarnings("unused")
- @OneToOne(mappedBy = "myCurrentVersion", optional = true)
+ @OneToOne(mappedBy = "myCurrentVersion", optional = true, fetch = FetchType.LAZY)
private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
@Column(name = "CS_DISPLAY", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
index 1b6aa71b777..ab37618e3fa 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
@@ -65,7 +65,7 @@ public class TermConcept implements Serializable {
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "CONCEPT_UPDATED", nullable = true)
private Date myUpdated;
- @ManyToOne()
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
private TermCodeSystemVersion myCodeSystem;
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@@ -79,11 +79,11 @@ public class TermConcept implements Serializable {
@Field(name = "myDisplayPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
})
private String myDisplay;
- @OneToMany(mappedBy = "myConcept", orphanRemoval = false)
+ @OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
@Field(name = "PROPmyProperties", analyzer = @Analyzer(definition = "termConceptPropertyAnalyzer"))
@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
private Collection myProperties;
- @OneToMany(mappedBy = "myConcept", orphanRemoval = false)
+ @OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
private Collection myDesignations;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
index 58069ed8932..61cfcf80ee2 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
@@ -39,7 +39,7 @@ public class TermConceptDesignation implements Serializable {
public static final int MAX_LENGTH = 500;
public static final int MAX_VAL_LENGTH = 2000;
- @ManyToOne
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CONCEPT"))
private TermConcept myConcept;
@Id()
@@ -62,7 +62,7 @@ public class TermConceptDesignation implements Serializable {
*
* @since 3.5.0
*/
- @ManyToOne
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CS_VER_PID", nullable = true, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CSV"))
private TermCodeSystemVersion myCodeSystemVersion;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
index a75511c57ab..2ceceabe931 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
@@ -32,14 +32,14 @@ import java.io.Serializable;
public class TermConceptParentChildLink implements Serializable {
private static final long serialVersionUID = 1L;
- @ManyToOne()
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CHILD_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CHILD"))
private TermConcept myChild;
@Column(name = "CHILD_PID", insertable = false, updatable = false)
private Long myChildPid;
- @ManyToOne()
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
private TermCodeSystemVersion myCodeSystem;
@@ -47,7 +47,7 @@ public class TermConceptParentChildLink implements Serializable {
@Fields({@Field(name = "myCodeSystemVersionPid")})
private long myCodeSystemVersionPid;
- @ManyToOne(cascade = {})
+ @ManyToOne(fetch = FetchType.LAZY, cascade = {})
@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
private TermConcept myParent;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
index 7a59b5d3c3a..8bdbd909b24 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
@@ -44,7 +44,7 @@ public class TermConceptProperty implements Serializable {
private static final int MAX_LENGTH = 500;
static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
- @ManyToOne
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
private TermConcept myConcept;
/**
@@ -52,7 +52,7 @@ public class TermConceptProperty implements Serializable {
*
* @since 3.5.0
*/
- @ManyToOne
+ @ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CS_VER_PID", nullable = true, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CSV"))
private TermCodeSystemVersion myCodeSystemVersion;
@Id()
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
index 49ef70e13b6..7125a415277 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
@@ -56,6 +56,9 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
import ca.uhn.fhir.util.AsyncUtil;
import ca.uhn.fhir.util.StopWatch;
+import co.elastic.apm.api.ElasticApm;
+import co.elastic.apm.api.Span;
+import co.elastic.apm.api.Transaction;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.exception.ExceptionUtils;
@@ -601,7 +604,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
private List myPreviouslyAddedResourcePids;
private Integer myMaxResultsToFetch;
private SearchRuntimeDetails mySearchRuntimeDetails;
-
+ private Transaction myParentTransaction;
/**
* Constructor
*/
@@ -614,6 +617,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
mySearchRuntimeDetails = new SearchRuntimeDetails(theRequest, mySearch.getUuid());
mySearchRuntimeDetails.setQueryString(theParams.toNormalizedQueryString(theCallingDao.getContext()));
myRequest = theRequest;
+ myParentTransaction = ElasticApm.currentTransaction();
}
/**
@@ -841,7 +845,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
@Override
public Void call() {
StopWatch sw = new StopWatch();
-
+ Span span = myParentTransaction.startSpan("db", "query", "search");
+ span.setName("FHIR Database Search");
try {
// Create an initial search in the DB and give it an ID
saveSearch();
@@ -897,7 +902,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
ourLog.error("Failed during search loading after {}ms", sw.getMillis(), t);
}
myUnsyncedPids.clear();
-
Throwable rootCause = ExceptionUtils.getRootCause(t);
rootCause = defaultIfNull(rootCause, t);
@@ -924,12 +928,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_SEARCH_FAILED, params);
saveSearch();
-
+ span.captureException(t);
} finally {
myIdToSearchTask.remove(mySearch.getUuid());
myInitialCollectionLatch.countDown();
markComplete();
+ span.end();
}
return null;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
index 5a1ed416a51..f8175bf481e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
@@ -1246,6 +1246,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
return retVal;
}
+ @Transactional
@Override
public List findCodesAbove(String theSystem, String theCode) {
TermCodeSystem cs = getCodeSystem(theSystem);
@@ -1277,6 +1278,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
return retVal;
}
+ @Transactional
@Override
public List findCodesBelow(String theSystem, String theCode) {
TermCodeSystem cs = getCodeSystem(theSystem);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
index 94c5d7cd1a1..da22a1f823b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
@@ -223,7 +223,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
* save parent concepts first (it's way too slow to do that)
*/
if (theConcept.getId() == null) {
- retVal += ensureParentsSaved(theConcept.getParents());
+ boolean needToSaveParents = false;
+ for (TermConceptParentChildLink next : theConcept.getParents()) {
+ if (next.getParent().getId() == null) {
+ needToSaveParents = true;
+ }
+ }
+ if (needToSaveParents) {
+ retVal += ensureParentsSaved(theConcept.getParents());
+ }
}
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
@@ -485,7 +493,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
conceptToAdd.setCodeSystemVersion(theCsv);
if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
- conceptToAdd = myConceptDao.save(conceptToAdd);
+ saveConcept(conceptToAdd);
Long nextConceptPid = conceptToAdd.getId();
Validate.notNull(nextConceptPid);
} else {
@@ -508,7 +516,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
ourLog.info("Saving parent/child link - Parent[{}] Child[{}]", parentLink.getParent().getCode(), parentLink.getChild().getCode());
if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
- myConceptParentChildLinkDao.save(parentLink);
+ myConceptParentChildLinkDao.save(parentLink);
} else {
myDeferredStorageSvc.addConceptLinkToStorageQueue(parentLink);
}
@@ -655,12 +663,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
private void deleteConceptChildrenAndConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
deleteConceptChildrenAndConcept(nextChildLink.getChild(), theRemoveCounter);
- myConceptParentChildLinkDao.delete(nextChildLink);
}
+ myConceptParentChildLinkDao.deleteByConceptPid(theConcept.getId());
+
myConceptDesignationDao.deleteAll(theConcept.getDesignations());
myConceptPropertyDao.deleteAll(theConcept.getProperties());
- myConceptDao.delete(theConcept);
+
+ ourLog.info("Deleting concept {} - Code {}", theConcept.getId(), theConcept.getCode());
+ myConceptDao.deleteByPid(theConcept.getId());
theRemoveCounter.incrementAndGet();
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
index e262ef1cedb..09e7cc7e69b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
@@ -98,6 +98,13 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
myDeferredValueSets.addAll(theValueSets);
}
+ @Override
+ public void saveAllDeferred() {
+ while (!isStorageQueueEmpty()) {
+ saveDeferred();
+ }
+ }
+
@Override
public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
index 881ce14e7f6..2aff45f7fef 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
@@ -50,4 +50,9 @@ public interface ITermDeferredStorageSvc {
void addConceptMapsToStorageQueue(List theConceptMaps);
void addValueSetsToStorageQueue(List theValueSets);
+
+ /**
+ * This is mostly here for unit tests - Saves any and all deferred concepts and links
+ */
+ void saveAllDeferred();
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
index 4ba4f35f181..b85abe96435 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
@@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
+import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
@@ -134,8 +135,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
+
+ myTermDeferredStorageSvc.saveAllDeferred();
}
+ @Autowired
+ private ITermDeferredStorageSvc myTermDeferredStorageSvc;
+
private void createExternalCsAndLocalVs() {
CodeSystem codeSystem = createExternalCs();
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
index 7430378c272..55b8c5bf988 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
@@ -15,7 +15,6 @@ import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
-import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.utils.IResourceValidator;
@@ -323,11 +322,15 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
ValidationModeEnum mode = ValidationModeEnum.CREATE;
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
- MethodOutcome output = myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
- OperationOutcome oo = (OperationOutcome) output.getOperationOutcome();
- String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
- ourLog.info(outputString);
- assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
+ try {
+ myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
+ fail();
+ } catch (PreconditionFailedException e) {
+ OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
+ String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+ ourLog.info(outputString);
+ assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
+ }
}
@Test
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
index 91a5702e629..26f5bd9b4da 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
@@ -172,6 +172,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myDeviceDaoR4")
protected IFhirResourceDao myDeviceDao;
@Autowired
+ @Qualifier("myProvenanceDaoR4")
+ protected IFhirResourceDao myProvenanceDao;
+ @Autowired
@Qualifier("myDiagnosticReportDaoR4")
protected IFhirResourceDao myDiagnosticReportDao;
@Autowired
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
index db077f8bfd7..6c1a2f34aeb 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
@@ -589,6 +589,41 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
+ @Test
+ public void testHasLimitsByType() {
+
+ Patient patient = new Patient();
+ patient.setActive(true);
+ IIdType patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+ Encounter encounter = new Encounter();
+ encounter.setStatus(Encounter.EncounterStatus.ARRIVED);
+ IIdType encounterId = myEncounterDao.create(encounter).getId().toUnqualifiedVersionless();
+
+ Device device = new Device();
+ device.setManufacturer("Acme");
+ IIdType deviceId = myDeviceDao.create(device).getId().toUnqualifiedVersionless();
+
+ Provenance provenance = new Provenance();
+ provenance.addTarget().setReferenceElement(patientId);
+ provenance.addTarget().setReferenceElement(encounterId);
+ provenance.addAgent().setWho(new Reference(deviceId));
+ myProvenanceDao.create(provenance);
+
+ String criteria = "_has:Provenance:target:agent=" + deviceId.getValue();
+ SearchParameterMap map = myMatchUrlService.translateMatchUrl(criteria, myFhirCtx.getResourceDefinition(Encounter.class));
+
+ map.setLoadSynchronous(true);
+
+ myCaptureQueriesListener.clear();
+ IBundleProvider results = myEncounterDao.search(map);
+ myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
+
+ List ids = toUnqualifiedVersionlessIdValues(results);
+ assertThat(ids, containsInAnyOrder(encounterId.getValue()));
+
+ }
+
@Test
public void testHasParameter() {
IIdType pid0;
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
index 1b72bfc8f7e..1279ab11d4e 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
@@ -164,6 +164,8 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
}
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+
+ myTerminologyDeferredStorageSvc.saveAllDeferred();
}
private void createLocalCsAndVs() {
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
index 2351887144f..992eb5f3f83 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
@@ -147,6 +147,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
}
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://loinc.org", codesToAdd);
+ myTerminologyDeferredStorageSvc.saveAllDeferred();
+
// Create a valueset
ValueSet vs = new ValueSet();
vs.setUrl("http://example.com/fhir/ValueSet/observation-vitalsignresult");
@@ -395,12 +397,15 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
ValidationModeEnum mode = ValidationModeEnum.CREATE;
String encoded = myFhirCtx.newJsonParser().encodeResourceToString(input);
- MethodOutcome output = myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
- org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) output.getOperationOutcome();
- String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
- ourLog.info(outputString);
- assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
-
+ try {
+ myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
+ fail();
+ } catch (PreconditionFailedException e) {
+ org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) e.getOperationOutcome();
+ String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
+ ourLog.info(outputString);
+ assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
+ }
}
@Test
@@ -614,6 +619,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
upload("/r4/uscore/ValueSet-omb-race-category.json");
upload("/r4/uscore/ValueSet-us-core-usps-state.json");
+ myTerminologyDeferredStorageSvc.saveAllDeferred();
+
{
String resource = loadResource("/r4/uscore/patient-resource-badcode.json");
IBaseResource parsedResource = myFhirCtx.newJsonParser().parseResource(resource);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
index a8f485ba05d..186a023026c 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
@@ -15,6 +15,7 @@ import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.*;
+import ca.uhn.fhir.rest.client.apache.ResourceEntity;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
@@ -26,6 +27,9 @@ import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
+import ca.uhn.fhir.validation.ResultSeverityEnum;
+import ca.uhn.fhir.validation.SingleValidationMessage;
+import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
@@ -52,6 +56,7 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
+import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
@@ -2260,6 +2265,28 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
}
+
+ @Test
+ public void testValidateResourceContainingProfileDeclarationDoesntResolve() throws IOException {
+ Observation input = new Observation();
+ input.getText().setDiv(new XhtmlNode().setValue("AA
")).setStatus(Narrative.NarrativeStatus.GENERATED);
+ input.getMeta().addProfile("http://foo/structuredefinition/myprofile");
+
+ input.getCode().setText("Hello");
+ input.setStatus(ObservationStatus.FINAL);
+
+ HttpPost post = new HttpPost(ourServerBase + "/Observation/$validate?_pretty=true");
+ post.setEntity(new ResourceEntity(myFhirCtx, input));
+
+ try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
+ String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
+ ourLog.info(respString);
+ assertEquals(412, resp.getStatusLine().getStatusCode());
+ assertThat(respString, containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
+ }
+ }
+
+
@SuppressWarnings("unused")
@Test
public void testFullTextSearch() throws Exception {
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java
index 074f0d39ad6..5f89fb013a6 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java
@@ -31,8 +31,10 @@ import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
+import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.apache.commons.lang3.StringUtils.leftPad;
import static org.hamcrest.CoreMatchers.containsString;
+import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
@@ -126,17 +128,23 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
ourLog.info("All concepts: {}", myTermConceptDao.findAll());
});
+ myCaptureQueriesListener.clear();
+
delta = new CustomTerminologySet();
TermConcept root = delta.addRootConcept("RootA", "Root A");
root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAB").setDisplay("Child AB");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
+
+ myCaptureQueriesListener.logAllQueriesForCurrentThread();
+
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAB seq=1",
"RootB seq=0"
);
+
}
@Test
@@ -175,6 +183,12 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
);
assertEquals(2, outcome.getUpdatedConceptCount());
+ runInTransaction(() -> {
+ TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA").orElseThrow(() -> new IllegalStateException());
+ assertEquals(2, concept.getParents().size());
+ assertThat(concept.getParentPidsAsString(), matchesPattern("^[0-9]+ [0-9]+$"));
+ });
+
}
@Test
@@ -538,9 +552,15 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
assertEquals(true, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeAAA").isPresent()));
// Remove CodeA
- delta = new CustomTerminologySet();
- delta.addRootConcept("codeA");
- myTermCodeSystemStorageSvc.applyDeltaCodeSystemsRemove("http://foo/cs", delta);
+ myCaptureQueriesListener.clear();
+ runInTransaction(()->{
+ CustomTerminologySet delta2 = new CustomTerminologySet();
+ delta2.addRootConcept("codeA");
+ myTermCodeSystemStorageSvc.applyDeltaCodeSystemsRemove("http://foo/cs", delta2);
+ });
+ myCaptureQueriesListener.logAllQueriesForCurrentThread();
+
+ ourLog.info("*** Done removing");
assertEquals(false, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeB").isPresent()));
assertEquals(false, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeA").isPresent()));
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
index 3f2e784734a..7c3f2efaf78 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
@@ -100,6 +100,8 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), CS_URL, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
+ myTerminologyDeferredStorageSvc.saveAllDeferred();
+
return id;
}
diff --git a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java
index 37323be9e1c..717279b54c1 100644
--- a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java
+++ b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java
@@ -171,11 +171,18 @@ public class ValidatorWrapper {
for (int i = 0; i < messages.size(); i++) {
ValidationMessage next = messages.get(i);
String message = next.getMessage();
+
+ // TODO: are these still needed?
if ("Binding has no source, so can't be checked".equals(message) ||
"ValueSet http://hl7.org/fhir/ValueSet/mimetypes not found".equals(message)) {
messages.remove(i);
i--;
}
+
+ if (message.endsWith("' could not be resolved, so has not been checked") && next.getLevel() == ValidationMessage.IssueSeverity.WARNING) {
+ next.setLevel(ValidationMessage.IssueSeverity.ERROR);
+ }
+
}
return messages;
diff --git a/hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java b/hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
index fe617e9b955..d666335bed8 100644
--- a/hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
+++ b/hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
@@ -66,10 +66,13 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
-import static org.mockito.ArgumentMatchers.*;
+import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.*;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
public class FhirInstanceValidatorR4Test extends BaseTest {
@@ -280,6 +283,33 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
assertEquals("Primitive types must have a value that is not empty", all.get(0).getMessage());
}
+ /**
+ * See #1740
+ */
+ @Ignore
+ @Test
+ public void testValidateScalarInRepeatableField() {
+ String operationDefinition = "{\n" +
+ " \"resourceType\": \"OperationDefinition\",\n" +
+ " \"name\": \"Questionnaire\",\n" +
+ " \"status\": \"draft\",\n" +
+ " \"kind\" : \"operation\",\n" +
+ " \"code\": \"populate\",\n" +
+ " \"resource\": \"Patient\",\n" + // should be array
+ " \"system\": false,\n" + " " +
+ " \"type\": false,\n" +
+ " \"instance\": true\n" +
+ "}";
+
+ FhirValidator val = ourCtx.newValidator();
+ val.registerValidatorModule(new FhirInstanceValidator(myDefaultValidationSupport));
+
+ ValidationResult result = val.validateWithResult(operationDefinition);
+ List all = logResultsAndReturnAll(result);
+ assertFalse(result.isSuccessful());
+ assertEquals("Primitive types must have a value that is not empty", all.get(0).getMessage());
+ }
+
/**
* See #1676 - We should ignore schema location
*/
@@ -400,7 +430,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
List errors = logResultsAndReturnNonInformationalOnes(output);
errors = errors
.stream()
- .filter(t->t.getMessage().contains("Bundle entry missing fullUrl"))
+ .filter(t -> t.getMessage().contains("Bundle entry missing fullUrl"))
.collect(Collectors.toList());
assertEquals(5, errors.size());
}
@@ -658,7 +688,6 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
.setCode("acd");
-
// Should pass
ValidationResult output = val.validateWithResult(input);
List all = logResultsAndReturnErrorOnes(output);
@@ -1038,7 +1067,10 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
myInstanceVal.setValidationSupport(myMockSupport);
ValidationResult output = myVal.validateWithResult(input);
List errors = logResultsAndReturnNonInformationalOnes(output);
- assertThat(errors.toString(), containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
+
+ assertEquals(1, errors.size());
+ assertEquals("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked", errors.get(0).getMessage());
+ assertEquals(ResultSeverityEnum.ERROR, errors.get(0).getSeverity());
}
@Test
@@ -1094,7 +1126,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
@Ignore
public void testValidateDecimalWithTrailingDot() {
String input = "{" +
- " \"resourceType\": \"Observation\"," +
+ " \"resourceType\": \"Observation\"," +
" \"status\": \"final\"," +
" \"subject\": {\"reference\":\"Patient/123\"}," +
" \"code\": { \"coding\": [{ \"system\":\"http://foo\", \"code\":\"123\" }] }," +
@@ -1110,8 +1142,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
" },\n" +
" \"text\": \"210.0-925.\"\n" +
" }\n" +
- " ]"+
- "}";
+ " ]" +
+ "}";
ourLog.info(input);
ValidationResult output = myVal.validateWithResult(input);
logResultsAndReturnAll(output);
@@ -1263,7 +1295,7 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
String encoded = loadResource("/r4/r4-caredove-bundle.json");
IResourceValidator.IValidatorResourceFetcher resourceFetcher = mock(IResourceValidator.IValidatorResourceFetcher.class);
- when(resourceFetcher.validationPolicy(any(),anyString(), anyString())).thenReturn(IResourceValidator.ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
+ when(resourceFetcher.validationPolicy(any(), anyString(), anyString())).thenReturn(IResourceValidator.ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS);
myInstanceVal.setValidatorResourceFetcher(resourceFetcher);
myVal.validateWithResult(encoded);
diff --git a/pom.xml b/pom.xml
index ef8d1092440..8522fbdeed9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -679,6 +679,7 @@
UTF-8
1.0.1
+ 1.13.0
5.4.1
@@ -1036,6 +1037,11 @@
httpcore
${httpcore_version}
+
+ co.elastic.apm
+ apm-agent-api
+ ${elastic_apm_version}
+
org.apache.jena
apache-jena-libs