org.javassist
javassist
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 18ae898014a..7a7f588a72f 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
@@ -152,6 +152,18 @@ public class DaoConfig {
private boolean myPreExpandValueSetsExperimental = false;
private boolean myFilterParameterEnabled = false;
private StoreMetaSourceInformation myStoreMetaSourceInformation = StoreMetaSourceInformation.SOURCE_URI_AND_REQUEST_ID;
+ /**
+ * EXPERIMENTAL - Do not use in production! Do not change default of {@code 0}!
+ */
+ private int myPreExpandValueSetsDefaultOffsetExperimental = 0;
+ /**
+ * EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
+ */
+ private int myPreExpandValueSetsDefaultCountExperimental = 1000;
+ /**
+ * EXPERIMENTAL - Do not use in production! Do not change default of {@code 1000}!
+ */
+ private int myPreExpandValueSetsMaxCountExperimental = 1000;
/**
* Constructor
@@ -1707,6 +1719,86 @@ public class DaoConfig {
}
}
+ /**
+ * EXPERIMENTAL - Do not use in production!
+ *
+ * This is the default value of {@code offset} parameter for the ValueSet {@code $expand} operation when
+ * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+ *
+ *
+ * The default value for this setting is {@code 0}.
+ *
+ */
+ public int getPreExpandValueSetsDefaultOffsetExperimental() {
+ return myPreExpandValueSetsDefaultOffsetExperimental;
+ }
+
+ /**
+ * EXPERIMENTAL - Do not use in production!
+ *
+ * This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
+ * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+ *
+ *
+ * The default value for this setting is {@code 1000}.
+ *
+ */
+ public int getPreExpandValueSetsDefaultCountExperimental() {
+ return myPreExpandValueSetsDefaultCountExperimental;
+ }
+
+ /**
+ * EXPERIMENTAL - Do not use in production!
+ *
+ * This is the default value of {@code count} parameter for the ValueSet {@code $expand} operation when
+ * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+ *
+ *
+ * If {@code thePreExpandValueSetsDefaultCountExperimental} is greater than
+ * {@link DaoConfig#getPreExpandValueSetsMaxCountExperimental()}, the lesser value is used.
+ *
+ *
+ * The default value for this setting is {@code 1000}.
+ *
+ */
+ public void setPreExpandValueSetsDefaultCountExperimental(int thePreExpandValueSetsDefaultCountExperimental) {
+ myPreExpandValueSetsDefaultCountExperimental = Math.min(thePreExpandValueSetsDefaultCountExperimental, getPreExpandValueSetsMaxCountExperimental());
+ }
+
+ /**
+ * EXPERIMENTAL - Do not use in production!
+ *
+ * This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
+ * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+ *
+ *
+ * The default value for this setting is {@code 1000}.
+ *
+ */
+ public int getPreExpandValueSetsMaxCountExperimental() {
+ return myPreExpandValueSetsMaxCountExperimental;
+ }
+
+ /**
+ * EXPERIMENTAL - Do not use in production!
+ *
+ * This is the max value of {@code count} parameter for the ValueSet {@code $expand} operation when
+ * {@link DaoConfig#isPreExpandValueSetsExperimental()} returns {@code true}.
+ *
+ *
+ * If {@code thePreExpandValueSetsMaxCountExperimental} is lesser than
+ * {@link DaoConfig#getPreExpandValueSetsDefaultCountExperimental()}, the default {@code count} is lowered to the
+ * new max {@code count}.
+ *
+ *
+ * The default value for this setting is {@code 1000}.
+ *
+ */
+ public void setPreExpandValueSetsMaxCountExperimental(int thePreExpandValueSetsMaxCountExperimental) {
+ myPreExpandValueSetsMaxCountExperimental = thePreExpandValueSetsMaxCountExperimental;
+ setPreExpandValueSetsDefaultCountExperimental(Math.min(getPreExpandValueSetsDefaultCountExperimental(), getPreExpandValueSetsMaxCountExperimental()));
+ }
+
public enum IndexEnabledEnum {
ENABLED,
DISABLED
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
index 45148a1d9d5..1db5197f8f7 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
@@ -20,15 +20,25 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
-import static org.apache.commons.lang3.StringUtils.isBlank;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.util.*;
-
-import javax.annotation.PostConstruct;
-
+import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IContextValidationSupport;
+import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
+import ca.uhn.fhir.model.dstu2.composite.CodingDt;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet.CodeSystemConcept;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeInclude;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet.ComposeIncludeConcept;
+import ca.uhn.fhir.model.dstu2.resource.ValueSet.ExpansionContains;
+import ca.uhn.fhir.model.primitive.DateTimeDt;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.UriParam;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.instance.hapi.validation.CachingValidationSupport;
import org.hl7.fhir.instance.hapi.validation.DefaultProfileValidationSupport;
@@ -38,20 +48,14 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
-import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
-import ca.uhn.fhir.model.dstu2.composite.CodingDt;
-import ca.uhn.fhir.model.dstu2.resource.ValueSet;
-import ca.uhn.fhir.model.dstu2.resource.ValueSet.*;
-import ca.uhn.fhir.model.primitive.DateTimeDt;
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.rest.api.server.IBundleProvider;
-import ca.uhn.fhir.rest.api.server.RequestDetails;
-import ca.uhn.fhir.rest.param.TokenParam;
-import ca.uhn.fhir.rest.param.UriParam;
-import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import javax.annotation.PostConstruct;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import java.util.Set;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2
implements IFhirResourceDaoValueSet, IFhirResourceDaoCodeSystem {
@@ -95,7 +99,11 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2
public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequest) {
ValueSet source = loadValueSetForExpansion(theId, theRequest);
return expand(source, theFilter);
+ }
+ @Override
+ public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequest) {
+ throw new UnsupportedOperationException();
}
@Override
@@ -131,6 +139,11 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2
return retVal;
}
+ @Override
+ public ValueSet expand(ValueSet source, String theFilter, int theOffset, int theCount) {
+ throw new UnsupportedOperationException();
+ }
+
@Override
public ValueSet expandByIdentifier(String theUri, String theFilter) {
if (isBlank(theUri)) {
@@ -153,7 +166,11 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2
}
return expand(source, theFilter);
+ }
+ @Override
+ public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
+ throw new UnsupportedOperationException();
}
@Override
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java
index 1659463242f..3131726b20f 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java
@@ -27,15 +27,21 @@ public interface IFhirResourceDaoValueSet exten
T expand(IIdType theId, String theFilter, RequestDetails theRequestDetails);
+ T expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails);
+
T expand(T theSource, String theFilter);
+ T expand(T theSource, String theFilter, int theOffset, int theCount);
+
T expandByIdentifier(String theUri, String theFilter);
+ T expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount);
+
void purgeCaches();
ValidateCodeResult validateCode(IPrimitiveType theValueSetIdentifier, IIdType theId, IPrimitiveType theCode, IPrimitiveType theSystem, IPrimitiveType theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
- public class ValidateCodeResult {
+ class ValidateCodeResult {
private String myDisplay;
private String myMessage;
private boolean myResult;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
index 9577c47b842..dca653b2058 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDao.java
@@ -21,20 +21,34 @@ package ca.uhn.fhir.jpa.dao.data;
*/
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
+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;
+import java.util.List;
import java.util.Optional;
public interface ITermValueSetConceptDao extends JpaRepository {
+ @Query("SELECT COUNT(*) FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
+ Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
+
@Query("DELETE FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
@Modifying
void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
- @Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
- Optional findByValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
+ @Query("SELECT vsc from TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid")
+ Slice findByTermValueSetId(Pageable thePage, @Param("pid") Long theValueSetId);
+ @Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myId = :pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
+ Optional findByTermValueSetIdSystemAndCode(@Param("pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
+
+ @Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.myCode = :codeval")
+ List findOneByValueSetIdAndCode(@Param("resource_pid") Long theValueSetId, @Param("codeval") String theCode);
+
+ @Query("SELECT vsc FROM TermValueSetConcept vsc WHERE vsc.myValueSet.myResourcePid = :resource_pid AND vsc.mySystem = :system_url AND vsc.myCode = :codeval")
+ List findOneByValueSetIdSystemAndCode(@Param("resource_pid") Long theValueSetId, @Param("system_url") String theSystem, @Param("codeval") String theCode);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDesignationDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDesignationDao.java
index 1a0875b5a2f..1792b8496e0 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDesignationDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptDesignationDao.java
@@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.dao.data;
*/
import ca.uhn.fhir.jpa.entity.TermValueSetConceptDesignation;
+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;
@@ -28,8 +30,13 @@ import org.springframework.data.repository.query.Param;
public interface ITermValueSetConceptDesignationDao extends JpaRepository {
- @Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myValueSet.myId = :pid")
+ @Query("SELECT COUNT(vscd) FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
+ Integer countByTermValueSetId(@Param("pid") Long theValueSetId);
+
+ @Query("DELETE FROM TermValueSetConceptDesignation vscd WHERE vscd.myValueSet.myId = :pid")
@Modifying
void deleteByTermValueSetId(@Param("pid") Long theValueSetId);
+ @Query("SELECT vscd FROM TermValueSetConceptDesignation vscd WHERE vscd.myConcept.myId = :pid")
+ Slice findByTermValueSetConceptId(Pageable thePage, @Param("pid") Long theValueSetConceptId);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
index d04cf883041..86053789288 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
@@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.dao.data;
*/
import ca.uhn.fhir.jpa.entity.TermValueSet;
-import ca.uhn.fhir.jpa.entity.TermValueSetExpansionStatusEnum;
-import org.springframework.data.domain.Page;
+import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
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;
@@ -44,6 +44,6 @@ public interface ITermValueSetDao extends JpaRepository {
Optional findByUrl(@Param("url") String theUrl);
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myExpansionStatus = :expansion_status")
- Page findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetExpansionStatusEnum theExpansionStatus);
+ Slice findByExpansionStatus(Pageable pageable, @Param("expansion_status") TermValueSetPreExpansionStatusEnum theExpansionStatus);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
index 282b1ab5a19..3e5d9f89445 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
@@ -75,6 +75,12 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
return expand(source, theFilter);
}
+ @Override
+ public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
+ ValueSet source = read(theId, theRequestDetails);
+ return expand(source, theFilter, theOffset, theCount);
+ }
+
private ValueSet doExpand(ValueSet theSource) {
validateIncludes("include", theSource.getCompose().getInclude());
@@ -105,7 +111,38 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
ValueSet retVal = outcome.getValueset();
retVal.setStatus(PublicationStatus.ACTIVE);
return retVal;
+ }
+ private ValueSet doExpand(ValueSet theSource, int theOffset, int theCount) {
+
+ validateIncludes("include", theSource.getCompose().getInclude());
+ validateIncludes("exclude", theSource.getCompose().getExclude());
+
+ /*
+ * If all of the code systems are supported by the HAPI FHIR terminology service, let's
+ * use that as it's more efficient.
+ */
+
+ boolean allSystemsAreSuppportedByTerminologyService = true;
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
+ if (!myTerminologySvc.supportsSystem(next.getSystem())) {
+ allSystemsAreSuppportedByTerminologyService = false;
+ }
+ }
+ for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
+ if (!myTerminologySvc.supportsSystem(next.getSystem())) {
+ allSystemsAreSuppportedByTerminologyService = false;
+ }
+ }
+ if (allSystemsAreSuppportedByTerminologyService) {
+ return (ValueSet) myTerminologySvc.expandValueSet(theSource, theOffset, theCount);
+ }
+
+ HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
+ ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
+ ValueSet retVal = outcome.getValueset();
+ retVal.setStatus(PublicationStatus.ACTIVE);
+ return retVal;
}
private void validateIncludes(String name, List listToValidate) {
@@ -148,20 +185,42 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
// }
//
// return expand(defaultValueSet, theFilter);
-
}
@Override
- public ValueSet expand(ValueSet source, String theFilter) {
+ public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
+ if (isBlank(theUri)) {
+ throw new InvalidRequestException("URI must not be blank or missing");
+ }
+
+ ValueSet source = new ValueSet();
+ source.setUrl(theUri);
+
+ source.getCompose().addInclude().addValueSet(theUri);
+
+ if (isNotBlank(theFilter)) {
+ ConceptSetComponent include = source.getCompose().addInclude();
+ ConceptSetFilterComponent filter = include.addFilter();
+ filter.setProperty("display");
+ filter.setOp(FilterOperator.EQUAL);
+ filter.setValue(theFilter);
+ }
+
+ ValueSet retVal = doExpand(source, theOffset, theCount);
+ return retVal;
+ }
+
+ @Override
+ public ValueSet expand(ValueSet theSource, String theFilter) {
ValueSet toExpand = new ValueSet();
- // for (UriType next : source.getCompose().getInclude()) {
+ // for (UriType next : theSource.getCompose().getInclude()) {
// ConceptSetComponent include = toExpand.getCompose().addInclude();
// include.setSystem(next.getValue());
// addFilterIfPresent(theFilter, include);
// }
- for (ConceptSetComponent next : source.getCompose().getInclude()) {
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
@@ -170,7 +229,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
- toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
+ toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
@@ -179,7 +238,32 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
}
return retVal;
+ }
+ @Override
+ public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
+ ValueSet toExpand = new ValueSet();
+ toExpand.setId(theSource.getId());
+ toExpand.setUrl(theSource.getUrl());
+
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
+ toExpand.getCompose().addInclude(next);
+ addFilterIfPresent(theFilter, next);
+ }
+
+ if (toExpand.getCompose().isEmpty()) {
+ throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
+ }
+
+ toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
+
+ ValueSet retVal = doExpand(toExpand, theOffset, theCount);
+
+ if (isNotBlank(theFilter)) {
+ applyFilter(retVal.getExpansion().getTotalElement(), retVal.getExpansion().getContains(), theFilter);
+ }
+
+ return retVal;
}
private void applyFilter(IntegerType theTotalElement, List theContains, String theFilter) {
@@ -246,10 +330,14 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
}
if (vs != null) {
- ValueSet expansion = doExpand(vs);
- List contains = expansion.getExpansion().getContains();
-
- ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
+ ValidateCodeResult result;
+ if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+ result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
+ } else {
+ ValueSet expansion = doExpand(vs);
+ List contains = expansion.getExpansion().getContains();
+ result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
+ }
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
@@ -269,7 +357,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3
}
private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(List contains, String theSystem, String theCode,
- Coding theCoding, CodeableConcept theCodeableConcept) {
+ Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/TransactionProcessorVersionAdapterDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/TransactionProcessorVersionAdapterDstu3.java
index 3398660898e..413f6e262ce 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/TransactionProcessorVersionAdapterDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/TransactionProcessorVersionAdapterDstu3.java
@@ -21,19 +21,24 @@ package ca.uhn.fhir.jpa.dao.dstu3;
*/
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.OperationOutcome;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.codesystems.IssueType;
import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.Date;
import java.util.List;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
public class TransactionProcessorVersionAdapterDstu3 implements TransactionProcessor.ITransactionProcessorVersionAdapter {
@Override
public void setResponseStatus(Bundle.BundleEntryComponent theBundleEntry, String theStatus) {
@@ -106,6 +111,22 @@ public class TransactionProcessorVersionAdapterDstu3 implements TransactionProce
if (value != null) {
retVal = value.toCode();
}
+
+ /*
+ * This is a workaround for the fact that PATCH isn't a valid constant for
+ * DSTU3 Bundle.entry.request.method (it was added in R4)
+ */
+ if (isBlank(retVal)) {
+ if (theEntry.getResource() instanceof IBaseBinary) {
+ String contentType = ((IBaseBinary) theEntry.getResource()).getContentType();
+ try {
+ PatchTypeEnum.forContentTypeOrThrowInvalidRequestException(contentType);
+ retVal = "PATCH";
+ } catch (InvalidRequestException e) {
+ // ignore
+ }
+ }
+ }
return retVal;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
index 0663d8cd3f7..aa719557794 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
@@ -70,6 +70,12 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
return expand(source, theFilter);
}
+ @Override
+ public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
+ ValueSet source = read(theId, theRequestDetails);
+ return expand(source, theFilter, theOffset, theCount);
+ }
+
private ValueSet doExpand(ValueSet theSource) {
/*
@@ -109,6 +115,32 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
// return retVal;
}
+ private ValueSet doExpand(ValueSet theSource, int theOffset, int theCount) {
+ boolean allSystemsAreSuppportedByTerminologyService = true;
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
+ if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
+ allSystemsAreSuppportedByTerminologyService = false;
+ }
+ }
+ for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
+ if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
+ allSystemsAreSuppportedByTerminologyService = false;
+ }
+ }
+ if (allSystemsAreSuppportedByTerminologyService) {
+ return myTerminologySvc.expandValueSet(theSource, theOffset, theCount);
+ }
+
+ HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
+
+ ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
+
+ ValueSet retVal = outcome.getValueset();
+ retVal.setStatus(PublicationStatus.ACTIVE);
+
+ return retVal;
+ }
+
private void validateIncludes(String name, List listToValidate) {
for (ConceptSetComponent nextExclude : listToValidate) {
if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
@@ -149,20 +181,42 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
// }
//
// return expand(defaultValueSet, theFilter);
-
}
@Override
- public ValueSet expand(ValueSet source, String theFilter) {
+ public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
+ if (isBlank(theUri)) {
+ throw new InvalidRequestException("URI must not be blank or missing");
+ }
+
+ ValueSet source = new ValueSet();
+ source.setUrl(theUri);
+
+ source.getCompose().addInclude().addValueSet(theUri);
+
+ if (isNotBlank(theFilter)) {
+ ConceptSetComponent include = source.getCompose().addInclude();
+ ConceptSetFilterComponent filter = include.addFilter();
+ filter.setProperty("display");
+ filter.setOp(FilterOperator.EQUAL);
+ filter.setValue(theFilter);
+ }
+
+ ValueSet retVal = doExpand(source, theOffset, theCount);
+ return retVal;
+ }
+
+ @Override
+ public ValueSet expand(ValueSet theSource, String theFilter) {
ValueSet toExpand = new ValueSet();
- // for (UriType next : source.getCompose().getInclude()) {
+ // for (UriType next : theSource.getCompose().getInclude()) {
// ConceptSetComponent include = toExpand.getCompose().addInclude();
// include.setSystem(next.getValue());
// addFilterIfPresent(theFilter, include);
// }
- for (ConceptSetComponent next : source.getCompose().getInclude()) {
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
@@ -171,7 +225,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
- toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
+ toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
@@ -180,7 +234,32 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
}
return retVal;
+ }
+ @Override
+ public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
+ ValueSet toExpand = new ValueSet();
+ toExpand.setId(theSource.getId());
+ toExpand.setUrl(theSource.getUrl());
+
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
+ toExpand.getCompose().addInclude(next);
+ addFilterIfPresent(theFilter, next);
+ }
+
+ if (toExpand.getCompose().isEmpty()) {
+ throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
+ }
+
+ toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
+
+ ValueSet retVal = doExpand(toExpand, theOffset, theCount);
+
+ if (isNotBlank(theFilter)) {
+ applyFilter(retVal.getExpansion().getTotalElement(), retVal.getExpansion().getContains(), theFilter);
+ }
+
+ return retVal;
}
private void applyFilter(IntegerType theTotalElement, List theContains, String theFilter) {
@@ -207,15 +286,15 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
}
@Override
- public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType theValueSetIdentifier, IIdType theId, IPrimitiveType theCode,
+ public ValidateCodeResult validateCode(IPrimitiveType theValueSetIdentifier, IIdType theId, IPrimitiveType theCode,
IPrimitiveType theSystem, IPrimitiveType theDisplay, Coding theCoding,
CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List valueSetIds = Collections.emptyList();
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
- boolean haveCoding = theCoding != null && theCoding.isEmpty() == false;
- boolean haveCode = theCode != null && theCode.isEmpty() == false;
+ boolean haveCoding = theCoding != null && !theCoding.isEmpty();
+ boolean haveCode = theCode != null && !theCode.isEmpty();
if (!haveCodeableConcept && !haveCoding && !haveCode) {
throw new InvalidRequestException("No code, coding, or codeableConcept provided to validate");
@@ -224,7 +303,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
throw new InvalidRequestException("$validate-code can only validate (system AND code) OR (coding) OR (codeableConcept)");
}
- boolean haveIdentifierParam = theValueSetIdentifier != null && theValueSetIdentifier.isEmpty() == false;
+ boolean haveIdentifierParam = theValueSetIdentifier != null && !theValueSetIdentifier.isEmpty();
ValueSet vs = null;
if (theId != null) {
vs = read(theId, theRequestDetails);
@@ -241,15 +320,20 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
// String system = toStringOrNull(theSystem);
IContextValidationSupport.LookupCodeResult result = myCodeSystemDao.lookupCode(theCode, theSystem, null, null);
if (result.isFound()) {
- ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
+ ValidateCodeResult retVal = new ValidateCodeResult(true, "Found code", result.getCodeDisplay());
return retVal;
}
}
if (vs != null) {
- ValueSet expansion = doExpand(vs);
- List contains = expansion.getExpansion().getContains();
- ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
+ ValidateCodeResult result;
+ if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+ result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
+ } else {
+ ValueSet expansion = doExpand(vs);
+ List contains = expansion.getExpansion().getContains();
+ result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
+ }
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
@@ -268,10 +352,10 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4 imple
return thePrimitive != null ? thePrimitive.getValue() : null;
}
- private ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCodeIsInContains(List contains, String theSystem, String theCode,
+ private ValidateCodeResult validateCodeIsInContains(List contains, String theSystem, String theCode,
Coding theCoding, CodeableConcept theCodeableConcept) {
for (ValueSetExpansionContainsComponent nextCode : contains) {
- ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
+ ValidateCodeResult result = validateCodeIsInContains(nextCode.getContains(), theSystem, theCode, theCoding, theCodeableConcept);
if (result != null) {
return result;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
index 12be4a64a15..f0bb1ed9b12 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
@@ -70,6 +70,12 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5 imple
return expand(source, theFilter);
}
+ @Override
+ public ValueSet expand(IIdType theId, String theFilter, int theOffset, int theCount, RequestDetails theRequestDetails) {
+ ValueSet source = read(theId, theRequestDetails);
+ return expand(source, theFilter, theOffset, theCount);
+ }
+
private ValueSet doExpand(ValueSet theSource) {
/*
@@ -109,6 +115,38 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5 imple
// return retVal;
}
+ private ValueSet doExpand(ValueSet theSource, int theOffset, int theCount) {
+
+ /*
+ * If all of the code systems are supported by the HAPI FHIR terminology service, let's
+ * use that as it's more efficient.
+ */
+
+ boolean allSystemsAreSuppportedByTerminologyService = true;
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
+ if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
+ allSystemsAreSuppportedByTerminologyService = false;
+ }
+ }
+ for (ConceptSetComponent next : theSource.getCompose().getExclude()) {
+ if (!isBlank(next.getSystem()) && !myTerminologySvc.supportsSystem(next.getSystem())) {
+ allSystemsAreSuppportedByTerminologyService = false;
+ }
+ }
+ if (allSystemsAreSuppportedByTerminologyService) {
+ return (ValueSet) myTerminologySvc.expandValueSet(theSource, theOffset, theCount);
+ }
+
+ HapiWorkerContext workerContext = new HapiWorkerContext(getContext(), myValidationSupport);
+
+ ValueSetExpansionOutcome outcome = workerContext.expand(theSource, null);
+
+ ValueSet retVal = outcome.getValueset();
+ retVal.setStatus(PublicationStatus.ACTIVE);
+
+ return retVal;
+ }
+
private void validateIncludes(String name, List listToValidate) {
for (ConceptSetComponent nextExclude : listToValidate) {
if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
@@ -149,20 +187,42 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5 imple
// }
//
// return expand(defaultValueSet, theFilter);
-
}
@Override
- public ValueSet expand(ValueSet source, String theFilter) {
+ public ValueSet expandByIdentifier(String theUri, String theFilter, int theOffset, int theCount) {
+ if (isBlank(theUri)) {
+ throw new InvalidRequestException("URI must not be blank or missing");
+ }
+
+ ValueSet source = new ValueSet();
+ source.setUrl(theUri);
+
+ source.getCompose().addInclude().addValueSet(theUri);
+
+ if (isNotBlank(theFilter)) {
+ ConceptSetComponent include = source.getCompose().addInclude();
+ ConceptSetFilterComponent filter = include.addFilter();
+ filter.setProperty("display");
+ filter.setOp(FilterOperator.EQUAL);
+ filter.setValue(theFilter);
+ }
+
+ ValueSet retVal = doExpand(source, theOffset, theCount);
+ return retVal;
+ }
+
+ @Override
+ public ValueSet expand(ValueSet theSource, String theFilter) {
ValueSet toExpand = new ValueSet();
- // for (UriType next : source.getCompose().getInclude()) {
+ // for (UriType next : theSource.getCompose().getInclude()) {
// ConceptSetComponent include = toExpand.getCompose().addInclude();
// include.setSystem(next.getValue());
// addFilterIfPresent(theFilter, include);
// }
- for (ConceptSetComponent next : source.getCompose().getInclude()) {
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
toExpand.getCompose().addInclude(next);
addFilterIfPresent(theFilter, next);
}
@@ -171,7 +231,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5 imple
throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
}
- toExpand.getCompose().getExclude().addAll(source.getCompose().getExclude());
+ toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
ValueSet retVal = doExpand(toExpand);
@@ -180,7 +240,32 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5 imple
}
return retVal;
+ }
+ @Override
+ public ValueSet expand(ValueSet theSource, String theFilter, int theOffset, int theCount) {
+ ValueSet toExpand = new ValueSet();
+ toExpand.setId(theSource.getId());
+ toExpand.setUrl(theSource.getUrl());
+
+ for (ConceptSetComponent next : theSource.getCompose().getInclude()) {
+ toExpand.getCompose().addInclude(next);
+ addFilterIfPresent(theFilter, next);
+ }
+
+ if (toExpand.getCompose().isEmpty()) {
+ throw new InvalidRequestException("ValueSet does not have any compose.include or compose.import values, can not expand");
+ }
+
+ toExpand.getCompose().getExclude().addAll(theSource.getCompose().getExclude());
+
+ ValueSet retVal = doExpand(toExpand, theOffset, theCount);
+
+ if (isNotBlank(theFilter)) {
+ applyFilter(retVal.getExpansion().getTotalElement(), retVal.getExpansion().getContains(), theFilter);
+ }
+
+ return retVal;
}
private void applyFilter(IntegerType theTotalElement, List theContains, String theFilter) {
@@ -247,9 +332,14 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5 imple
}
if (vs != null) {
- ValueSet expansion = doExpand(vs);
- List contains = expansion.getExpansion().getContains();
- ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
+ ValidateCodeResult result;
+ if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+ result = myTerminologySvc.validateCodeIsInPreExpandedValueSet(vs, toStringOrNull(theSystem), toStringOrNull(theCode), toStringOrNull(theDisplay), theCoding, theCodeableConcept);
+ } else {
+ ValueSet expansion = doExpand(vs);
+ List contains = expansion.getExpansion().getContains();
+ result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
+ }
if (result != null) {
if (theDisplay != null && isNotBlank(theDisplay.getValue()) && isNotBlank(result.getDisplay())) {
if (!theDisplay.getValue().equals(result.getDisplay())) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
index 28a60a1fef8..0ba562efe79 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
@@ -71,11 +71,11 @@ public class TermValueSet implements Serializable {
@Enumerated(EnumType.STRING)
@Column(name = "EXPANSION_STATUS", nullable = false, length = MAX_EXPANSION_STATUS_LENGTH)
- private TermValueSetExpansionStatusEnum myExpansionStatus;
+ private TermValueSetPreExpansionStatusEnum myExpansionStatus;
public TermValueSet() {
super();
- myExpansionStatus = TermValueSetExpansionStatusEnum.NOT_EXPANDED;
+ myExpansionStatus = TermValueSetPreExpansionStatusEnum.NOT_EXPANDED;
}
public Long getId() {
@@ -120,11 +120,11 @@ public class TermValueSet implements Serializable {
return myConcepts;
}
- public TermValueSetExpansionStatusEnum getExpansionStatus() {
+ public TermValueSetPreExpansionStatusEnum getExpansionStatus() {
return myExpansionStatus;
}
- public void setExpansionStatus(TermValueSetExpansionStatusEnum theExpansionStatus) {
+ public void setExpansionStatus(TermValueSetPreExpansionStatusEnum theExpansionStatus) {
myExpansionStatus = theExpansionStatus;
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
index b1ab2cff713..e3aa0c5196a 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
@@ -52,6 +52,16 @@ public class TermValueSetConceptDesignation implements Serializable {
@JoinColumn(name = "VALUESET_CONCEPT_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_CONCEPT_PID"))
private TermValueSetConcept myConcept;
+ @ManyToOne()
+ @JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VSCD_VS_PID"))
+ private TermValueSet myValueSet;
+
+ @Transient
+ private String myValueSetUrl;
+
+ @Transient
+ private String myValueSetName;
+
@Column(name = "LANG", nullable = true, length = MAX_LENGTH)
private String myLanguage;
@@ -80,6 +90,31 @@ public class TermValueSetConceptDesignation implements Serializable {
return this;
}
+ public TermValueSet getValueSet() {
+ return myValueSet;
+ }
+
+ public TermValueSetConceptDesignation setValueSet(TermValueSet theValueSet) {
+ myValueSet = theValueSet;
+ return this;
+ }
+
+ public String getValueSetUrl() {
+ if (myValueSetUrl == null) {
+ myValueSetUrl = getValueSet().getUrl();
+ }
+
+ return myValueSetUrl;
+ }
+
+ public String getValueSetName() {
+ if (myValueSetName == null) {
+ myValueSetName = getValueSet().getName();
+ }
+
+ return myValueSetName;
+ }
+
public String getLanguage() {
return myLanguage;
}
@@ -167,6 +202,9 @@ public class TermValueSetConceptDesignation implements Serializable {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConcept != null ? ("myConcept - id=" + myConcept.getId()) : ("myConcept=(null)"))
+ .append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
+ .append("myValueSetUrl", this.getValueSetUrl())
+ .append("myValueSetName", this.getValueSetName())
.append("myLanguage", myLanguage)
.append("myUseSystem", myUseSystem)
.append("myUseCode", myUseCode)
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetExpansionStatusEnum.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetExpansionStatusEnum.java
deleted file mode 100644
index 33cb4301097..00000000000
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetExpansionStatusEnum.java
+++ /dev/null
@@ -1,42 +0,0 @@
-package ca.uhn.fhir.jpa.entity;
-
-/*
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-/**
- * This enum is used to indicate the expansion status of a given ValueSet in the terminology tables. In this context,
- * an expanded ValueSet has its included concepts stored in the terminology tables as well.
- */
-public enum TermValueSetExpansionStatusEnum {
-
- /**
- * This status indicates the ValueSet is waiting to be picked up and expanded by a scheduled task.
- */
- NOT_EXPANDED,
- /**
- * This status indicates the ValueSet has been picked up by a scheduled task and is mid-expansion.
- */
- EXPANSION_IN_PROGRESS,
- /**
- * This status indicates the ValueSet has been picked up by a scheduled task and expansion is complete.
- */
- EXPANDED
-
-}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnum.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnum.java
new file mode 100644
index 00000000000..83e1e0af62e
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnum.java
@@ -0,0 +1,71 @@
+package ca.uhn.fhir.jpa.entity;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * This enum is used to indicate the pre-expansion status of a given ValueSet in the terminology tables. In this context,
+ * an expanded ValueSet has its included concepts stored in the terminology tables as well.
+ */
+public enum TermValueSetPreExpansionStatusEnum {
+ /**
+ * Sorting agnostic.
+ */
+
+ NOT_EXPANDED("notExpanded"),
+ EXPANSION_IN_PROGRESS("expansionInProgress"),
+ EXPANDED("expanded"),
+ FAILED_TO_EXPAND("failedToExpand");
+
+ private static Map ourValues;
+ private String myCode;
+
+ TermValueSetPreExpansionStatusEnum(String theCode) {
+ myCode = theCode;
+ }
+
+ public String getCode() {
+ return myCode;
+ }
+
+ public static TermValueSetPreExpansionStatusEnum fromCode(String theCode) {
+ if (ourValues == null) {
+ HashMap values = new HashMap();
+ for (TermValueSetPreExpansionStatusEnum next : values()) {
+ values.put(next.getCode(), next);
+ }
+ ourValues = Collections.unmodifiableMap(values);
+ }
+ return ourValues.get(theCode);
+ }
+
+ /**
+ * Convert from Enum ordinal to Enum type.
+ *
+ * Usage:
+ *
+ * TermValueSetExpansionStatusEnum termValueSetExpansionStatusEnum = TermValueSetExpansionStatusEnum.values[ordinal];
+ */
+ public static final TermValueSetPreExpansionStatusEnum values[] = values();
+}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java
index e0ce7b36245..464adce1f57 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaProvider.java
@@ -1,9 +1,10 @@
package ca.uhn.fhir.jpa.provider;
import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.util.ExpungeOptions;
import ca.uhn.fhir.jpa.util.ExpungeOutcome;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@@ -12,6 +13,7 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.jboss.logging.MDC;
+import org.springframework.beans.factory.annotation.Autowired;
import javax.servlet.http.HttpServletRequest;
import java.util.Date;
@@ -42,6 +44,10 @@ import java.util.TreeSet;
public class BaseJpaProvider {
public static final String REMOTE_ADDR = "req.remoteAddr";
public static final String REMOTE_UA = "req.userAgent";
+
+ @Autowired
+ protected DaoConfig myDaoConfig;
+
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaProvider.class);
private FhirContext myContext;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
index e55de8b4a51..884941f053c 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
@@ -35,6 +35,7 @@ import javax.servlet.http.HttpServletRequest;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDstu3 {
+ private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetDstu3.class);
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
public ValueSet expand(
@@ -46,6 +47,8 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
@OperationParam(name = "url", min = 0, max = 1) UriType theUrl,
@OperationParam(name = "identifier", min = 0, max = 1) UriType theIdentifier,
@OperationParam(name = "filter", min = 0, max = 1) StringType theFilter,
+ @OperationParam(name = "offset", min = 0, max = 1) IntegerType theOffset,
+ @OperationParam(name = "count", min = 0, max = 1) IntegerType theCount,
RequestDetails theRequestDetails) {
boolean haveId = theId != null && theId.hasIdPart();
@@ -55,27 +58,59 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
}
boolean haveIdentifier = url != null && isNotBlank(url.getValue());
- boolean haveValueSet = theValueSet != null && theValueSet.isEmpty() == false;
+ boolean haveValueSet = theValueSet != null && !theValueSet.isEmpty();
if (!haveId && !haveIdentifier && !haveValueSet) {
- throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request");
+ throw new InvalidRequestException("$expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request.");
}
if (moreThanOneTrue(haveId, haveIdentifier, haveValueSet)) {
throw new InvalidRequestException("$expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.");
}
+ int offset = myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental();
+ if (theOffset != null && theOffset.hasValue()) {
+ if (theOffset.getValue() >= 0) {
+ offset = theOffset.getValue();
+ } else {
+ throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
+ }
+ }
+
+ int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
+ if (theCount != null && theCount.hasValue()) {
+ if (theCount.getValue() >= 0) {
+ count = theCount.getValue();
+ } else {
+ throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
+ }
+ }
+ int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
+ if (count > countMax) {
+ ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
+ count = countMax;
+ }
+
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet dao = (IFhirResourceDaoValueSet) getDao();
- if (haveId) {
- return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
- } else if (haveIdentifier) {
- return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
+ if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+ if (haveId) {
+ return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
+ } else if (haveIdentifier) {
+ return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter), offset, count);
+ } else {
+ return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
+ }
} else {
- return dao.expand(theValueSet, toFilterString(theFilter));
+ if (haveId) {
+ return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
+ } else if (haveIdentifier) {
+ return dao.expandByIdentifier(url.getValue(), toFilterString(theFilter));
+ } else {
+ return dao.expand(theValueSet, toFilterString(theFilter));
+ }
}
-
} finally {
endRequest(theServletRequest);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderConceptMapR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderConceptMapR4.java
index e13582a995e..544670c2a5b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderConceptMapR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderConceptMapR4.java
@@ -62,7 +62,7 @@ public class BaseJpaResourceProviderConceptMapR4 extends JpaResourceProviderR4 {
+ private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetR4.class);
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
public ValueSet expand(
@@ -43,31 +44,65 @@ public class BaseJpaResourceProviderValueSetR4 extends JpaResourceProviderR4= 0) {
+ offset = theOffset.getValue();
+ } else {
+ throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
+ }
+ }
+
+ int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
+ if (theCount != null && theCount.hasValue()) {
+ if (theCount.getValue() >= 0) {
+ count = theCount.getValue();
+ } else {
+ throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
+ }
+ }
+ int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
+ if (count > countMax) {
+ ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
+ count = countMax;
+ }
+
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet dao = (IFhirResourceDaoValueSet) getDao();
- if (haveId) {
- return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
- } else if (haveIdentifier) {
- return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
+ if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+ if (haveId) {
+ return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
+ } else if (haveIdentifier) {
+ return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
+ } else {
+ return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
+ }
} else {
- return dao.expand(theValueSet, toFilterString(theFilter));
+ if (haveId) {
+ return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
+ } else if (haveIdentifier) {
+ return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
+ } else {
+ return dao.expand(theValueSet, toFilterString(theFilter));
+ }
}
-
} finally {
endRequest(theServletRequest);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
index 65522e01231..f05a8f4cdaa 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderValueSetR5.java
@@ -35,6 +35,7 @@ import javax.servlet.http.HttpServletRequest;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5 {
+ private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseJpaResourceProviderValueSetR5.class);
@Operation(name = JpaConstants.OPERATION_EXPAND, idempotent = true)
public ValueSet expand(
@@ -43,31 +44,65 @@ public class BaseJpaResourceProviderValueSetR5 extends JpaResourceProviderR5= 0) {
+ offset = theOffset.getValue();
+ } else {
+ throw new InvalidRequestException("offset parameter for $expand operation must be >= 0 when specified. offset: " + theOffset.getValue());
+ }
+ }
+
+ int count = myDaoConfig.getPreExpandValueSetsDefaultCountExperimental();
+ if (theCount != null && theCount.hasValue()) {
+ if (theCount.getValue() >= 0) {
+ count = theCount.getValue();
+ } else {
+ throw new InvalidRequestException("count parameter for $expand operation must be >= 0 when specified. count: " + theCount.getValue());
+ }
+ }
+ int countMax = myDaoConfig.getPreExpandValueSetsMaxCountExperimental();
+ if (count > countMax) {
+ ourLog.warn("count parameter for $expand operation of {} exceeds maximum value of {}; using maximum value.", count, countMax);
+ count = countMax;
+ }
+
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet dao = (IFhirResourceDaoValueSet) getDao();
- if (haveId) {
- return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
- } else if (haveIdentifier) {
- return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
+ if (myDaoConfig.isPreExpandValueSetsExperimental()) {
+ if (haveId) {
+ return dao.expand(theId, toFilterString(theFilter), offset, count, theRequestDetails);
+ } else if (haveIdentifier) {
+ return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter), offset, count);
+ } else {
+ return dao.expand(theValueSet, toFilterString(theFilter), offset, count);
+ }
} else {
- return dao.expand(theValueSet, toFilterString(theFilter));
+ if (haveId) {
+ return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
+ } else if (haveIdentifier) {
+ return dao.expandByIdentifier(theUrl.getValue(), toFilterString(theFilter));
+ } else {
+ return dao.expand(theValueSet, toFilterString(theFilter));
+ }
}
-
} finally {
endRequest(theServletRequest);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
index c574f84a122..2e3324b8719 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.*;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
@@ -351,7 +352,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (optionalExistingTermConceptMapById.isPresent()) {
TermConceptMap existingTermConceptMap = optionalExistingTermConceptMapById.get();
- ourLog.info("Deleting existing TermConceptMap {} and its children...", existingTermConceptMap.getId());
+ ourLog.info("Deleting existing TermConceptMap[{}] and its children...", existingTermConceptMap.getId());
for (TermConceptMapGroup group : existingTermConceptMap.getConceptMapGroups()) {
for (TermConceptMapGroupElement element : group.getConceptMapGroupElements()) {
@@ -368,7 +369,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
myConceptMapDao.deleteTermConceptMapById(existingTermConceptMap.getId());
- ourLog.info("Done deleting existing TermConceptMap {} and its children.", existingTermConceptMap.getId());
+ ourLog.info("Done deleting existing TermConceptMap[{}] and its children.", existingTermConceptMap.getId());
ourLog.info("Flushing...");
myConceptMapGroupElementTargetDao.flush();
@@ -392,11 +393,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (optionalExistingTermValueSetById.isPresent()) {
TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
- ourLog.info("Deleting existing TermValueSet {} and its children...", existingTermValueSet.getId());
+ ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
myValueSetConceptDesignationDao.deleteByTermValueSetId(existingTermValueSet.getId());
myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
myValueSetDao.deleteByTermValueSetId(existingTermValueSet.getId());
- ourLog.info("Done deleting existing TermValueSet {} and its children.", existingTermValueSet.getId());
+ ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
ourLog.info("Flushing...");
myValueSetConceptDesignationDao.flush();
@@ -420,7 +421,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
count = 0;
while (true) {
Slice link = theLoader.get();
- if (link.hasContent() == false) {
+ if (!link.hasContent()) {
break;
}
@@ -478,28 +479,221 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return valueSet;
}
+ @Override
+ @Transactional(propagation = Propagation.REQUIRED)
+ public ValueSet expandValueSet(ValueSet theValueSetToExpand, int theOffset, int theCount) {
+ ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSetToExpand, "ValueSet to expand can not be null");
+
+ Optional optionalTermValueSet;
+ if (theValueSetToExpand.hasId()) {
+ optionalTermValueSet = myValueSetDao.findByResourcePid(theValueSetToExpand.getIdElement().getIdPartAsLong());
+ } else if (theValueSetToExpand.hasUrl()) {
+ optionalTermValueSet = myValueSetDao.findByUrl(theValueSetToExpand.getUrl());
+ } else {
+ throw new UnprocessableEntityException("ValueSet to be expanded must provide either ValueSet.id or ValueSet.url");
+ }
+
+ if (!optionalTermValueSet.isPresent()) {
+ throw new InvalidRequestException("ValueSet is not present in terminology tables: " + theValueSetToExpand.getUrl());
+ }
+
+ TermValueSet termValueSet = optionalTermValueSet.get();
+
+ validatePreExpansionStatusOfValueSetOrThrowException(termValueSet.getExpansionStatus());
+
+ ValueSet.ValueSetExpansionComponent expansionComponent = new ValueSet.ValueSetExpansionComponent();
+ expansionComponent.setIdentifier(UUID.randomUUID().toString());
+ expansionComponent.setTimestamp(new Date());
+
+ populateExpansionComponent(expansionComponent, termValueSet, theOffset, theCount);
+
+ ValueSet valueSet = new ValueSet();
+ valueSet.setStatus(Enumerations.PublicationStatus.ACTIVE);
+ valueSet.setCompose(theValueSetToExpand.getCompose());
+ valueSet.setExpansion(expansionComponent);
+ return valueSet;
+ }
+
+ private void validatePreExpansionStatusOfValueSetOrThrowException(TermValueSetPreExpansionStatusEnum thePreExpansionStatus) {
+ if (TermValueSetPreExpansionStatusEnum.EXPANDED != thePreExpansionStatus) {
+ String statusMsg = myContext.getLocalizer().getMessage(
+ TermValueSetPreExpansionStatusEnum.class,
+ thePreExpansionStatus.getCode());
+ String msg = myContext.getLocalizer().getMessage(
+ BaseHapiTerminologySvcImpl.class,
+ "valueSetNotReadyForExpand",
+ thePreExpansionStatus.name(),
+ statusMsg);
+ throw new UnprocessableEntityException(msg);
+ }
+ }
+
+ private void populateExpansionComponent(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
+ int total = myValueSetConceptDao.countByTermValueSetId(theTermValueSet.getId());
+ theExpansionComponent.setTotal(total);
+ theExpansionComponent.setOffset(theOffset);
+ theExpansionComponent.addParameter().setName("offset").setValue(new IntegerType(theOffset));
+ theExpansionComponent.addParameter().setName("count").setValue(new IntegerType(theCount));
+
+ if (theCount == 0 || total == 0) {
+ return;
+ }
+
+ expandConcepts(theExpansionComponent, theTermValueSet, theOffset, theCount);
+ }
+
+ private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
+ int conceptsExpanded = 0;
+ for (int i = theOffset; i < (theOffset + theCount); i++) {
+ final int page = i;
+ Supplier> loader = () -> myValueSetConceptDao.findByTermValueSetId(PageRequest.of(page, 1), theTermValueSet.getId());
+
+ Slice slice = loader.get();
+ if (!slice.hasContent()) {
+ break;
+ }
+
+ for (TermValueSetConcept concept : slice.getContent()) {
+ ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
+ containsComponent.setSystem(concept.getSystem());
+ containsComponent.setCode(concept.getCode());
+ containsComponent.setDisplay(concept.getDisplay());
+
+ // TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
+ expandDesignations(theTermValueSet, concept, containsComponent);
+
+ if (++conceptsExpanded % 250 == 0) {
+ ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
+ }
+ }
+
+ if (!slice.hasNext()) {
+ break;
+ }
+ }
+
+ if (conceptsExpanded > 0) {
+ ourLog.info("Have expanded {} concepts in ValueSet[{}]", conceptsExpanded, theTermValueSet.getUrl());
+ }
+ }
+
+ private void expandDesignations(TermValueSet theValueSet, TermValueSetConcept theConcept, ValueSet.ValueSetExpansionContainsComponent theContainsComponent) {
+ int designationsExpanded = 0;
+ int index = 0;
+ while (true) {
+ final int page = index++;
+ Supplier> loader = () -> myValueSetConceptDesignationDao.findByTermValueSetConceptId(PageRequest.of(page, 1000), theConcept.getId());
+
+ Slice slice = loader.get();
+ if (!slice.hasContent()) {
+ break;
+ }
+
+ for (TermValueSetConceptDesignation designation : slice.getContent()) {
+ ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
+ designationComponent.setLanguage(designation.getLanguage());
+ designationComponent.setUse(new Coding(
+ designation.getUseSystem(),
+ designation.getUseCode(),
+ designation.getUseDisplay()));
+ designationComponent.setValue(designation.getValue());
+
+ if (++designationsExpanded % 250 == 0) {
+ ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
+ }
+ }
+
+ if (!slice.hasNext()) {
+ break;
+ }
+ }
+
+ if (designationsExpanded > 0) {
+ ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", designationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
+ }
+ }
+
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
expandValueSet(theValueSetToExpand, theValueSetCodeAccumulator, new AtomicInteger(0));
}
+ @SuppressWarnings("ConstantConditions")
private void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator, AtomicInteger theCodeCounter) {
Set addedCodes = new HashSet<>();
+ StopWatch sw = new StopWatch();
+ String valueSetInfo = getValueSetInfo(theValueSetToExpand);
+ ourLog.info("Working with {}", valueSetInfo);
+
// Handle includes
ourLog.debug("Handling includes");
for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getInclude()) {
- boolean add = true;
- expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
+ for (int i = 0; ; i++) {
+ int finalI = i;
+ Boolean shouldContinue = myTxTemplate.execute(t -> {
+ boolean add = true;
+ return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter, finalI);
+ });
+ if (!shouldContinue) {
+ break;
+ }
+ }
}
// Handle excludes
ourLog.debug("Handling excludes");
- for (ValueSet.ConceptSetComponent include : theValueSetToExpand.getCompose().getExclude()) {
- boolean add = false;
- expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, include, add, theCodeCounter);
+ for (ValueSet.ConceptSetComponent exclude : theValueSetToExpand.getCompose().getExclude()) {
+ for (int i = 0; ; i++) {
+ int finalI = i;
+ Boolean shouldContinue = myTxTemplate.execute(t -> {
+ boolean add = false;
+ return expandValueSetHandleIncludeOrExclude(theValueSetCodeAccumulator, addedCodes, exclude, add, theCodeCounter, finalI);
+ });
+ if (!shouldContinue) {
+ break;
+ }
+ }
}
+
+ ourLog.info("Done working with {} in {}ms", valueSetInfo, sw.getMillis());
+ }
+
+ private String getValueSetInfo(ValueSet theValueSet) {
+ StringBuilder sb = new StringBuilder();
+ boolean isIdentified = false;
+ sb
+ .append("ValueSet:");
+ if (theValueSet.hasId()) {
+ isIdentified = true;
+ sb
+ .append(" ValueSet.id[")
+ .append(theValueSet.getId())
+ .append("]");
+ }
+ if (theValueSet.hasUrl()) {
+ isIdentified = true;
+ sb
+ .append(" ValueSet.url[")
+ .append(theValueSet.getUrl())
+ .append("]");
+ }
+ if (theValueSet.hasIdentifier()) {
+ isIdentified = true;
+ sb
+ .append(" ValueSet.identifier[")
+ .append(theValueSet.getIdentifierFirstRep().getSystem())
+ .append("|")
+ .append(theValueSet.getIdentifierFirstRep().getValue())
+ .append("]");
+ }
+
+ if (!isIdentified) {
+ sb.append(" None of ValueSet.id, ValueSet.url, and ValueSet.identifier are provided.");
+ }
+
+ return sb.toString();
}
protected List expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.r4.model.ValueSet theValueSetToExpandR4) {
@@ -513,16 +707,21 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
return retVal;
}
- private void expandValueSetHandleIncludeOrExclude(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter) {
+ /**
+ * @return Returns true if there are potentially more results to process.
+ */
+ private Boolean expandValueSetHandleIncludeOrExclude(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set theAddedCodes, ValueSet.ConceptSetComponent theInclude, boolean theAdd, AtomicInteger theCodeCounter, int theQueryIndex) {
+
String system = theInclude.getSystem();
boolean hasSystem = isNotBlank(system);
boolean hasValueSet = theInclude.getValueSet().size() > 0;
if (hasSystem) {
- ourLog.info("Starting {} expansion around code system: {}", (theAdd ? "inclusion" : "exclusion"), system);
+ ourLog.info("Starting {} expansion around CodeSystem: {}", (theAdd ? "inclusion" : "exclusion"), system);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
if (cs != null) {
+
TermCodeSystemVersion csv = cs.getCurrentVersion();
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
@@ -532,7 +731,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
if (myFulltextSearchSvc == null) {
expandWithoutHibernateSearch(theValueSetCodeAccumulator, theAddedCodes, theInclude, system, theAdd, theCodeCounter);
- return;
+ return false;
}
/*
@@ -592,10 +791,10 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
String value = nextFilter.getValue();
if (value.endsWith("$")) {
value = value.substring(0, value.length() - 1);
- } else if (value.endsWith(".*") == false) {
+ } else if (!value.endsWith(".*")) {
value = value + ".*";
}
- if (value.startsWith("^") == false && value.startsWith(".*") == false) {
+ if (!value.startsWith("^") && !value.startsWith(".*")) {
value = ".*" + value;
} else if (value.startsWith("^")) {
value = value.substring(1);
@@ -646,25 +845,43 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
- int maxResult = 50000;
- jpaQuery.setMaxResults(maxResult);
+ /*
+ * DM 2019-08-21 - Processing slows after any ValueSets with many codes explicitly identified. This might
+ * be due to the dark arts that is memory management. Will monitor but not do anything about this right now.
+ */
+ BooleanQuery.setMaxClauseCount(10000);
StopWatch sw = new StopWatch();
AtomicInteger count = new AtomicInteger(0);
- for (Object next : jpaQuery.getResultList()) {
+ int maxResultsPerBatch = 10000;
+ jpaQuery.setMaxResults(maxResultsPerBatch);
+ jpaQuery.setFirstResult(theQueryIndex * maxResultsPerBatch);
+
+ ourLog.info("Beginning batch expansion for {} with max results per batch: {}", (theAdd ? "inclusion" : "exclusion"), maxResultsPerBatch);
+
+ StopWatch swForBatch = new StopWatch();
+ AtomicInteger countForBatch = new AtomicInteger(0);
+
+ List resultList = jpaQuery.getResultList();
+ int resultsInBatch = resultList.size();
+ int firstResult = jpaQuery.getFirstResult();
+ for (Object next : resultList) {
count.incrementAndGet();
+ countForBatch.incrementAndGet();
TermConcept concept = (TermConcept) next;
addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, concept, theAdd, theCodeCounter);
}
+ ourLog.info("Batch expansion for {} with starting index of {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), firstResult, countForBatch, swForBatch.getMillis());
- if (maxResult == count.get()) {
- throw new InternalErrorException("Expansion fragment produced too many (>= " + maxResult + ") results");
+ if (resultsInBatch < maxResultsPerBatch) {
+ ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
+ return false;
+ } else {
+ return true;
}
- ourLog.info("Expansion for {} produced {} results in {}ms", (theAdd ? "inclusion" : "exclusion"), count, sw.getMillis());
-
} else {
// No codesystem matching the URL found in the database
@@ -673,7 +890,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
throw new InvalidRequestException("Unknown code system: " + system);
}
- if (theInclude.getConcept().isEmpty() == false) {
+ if (!theInclude.getConcept().isEmpty()) {
for (ValueSet.ConceptReferenceComponent next : theInclude.getConcept()) {
String nextCode = next.getCode();
if (isNoneBlank(system, nextCode) && !theAddedCodes.contains(system + "|" + nextCode)) {
@@ -693,10 +910,12 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
addConceptsToList(theValueSetCodeAccumulator, theAddedCodes, system, concept, theAdd);
}
+ return false;
}
} else if (hasValueSet) {
+
for (CanonicalType nextValueSet : theInclude.getValueSet()) {
- ourLog.info("Starting {} expansion around ValueSet URI: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
+ ourLog.info("Starting {} expansion around ValueSet: {}", (theAdd ? "inclusion" : "exclusion"), nextValueSet.getValueAsString());
List expanded = expandValueSet(nextValueSet.getValueAsString());
for (VersionIndependentConcept nextConcept : expanded) {
@@ -715,9 +934,14 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
+
+ return false;
+
} else {
throw new InvalidRequestException("ValueSet contains " + (theAdd ? "include" : "exclude") + " criteria with no system defined");
}
+
+
}
private void expandWithoutHibernateSearch(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, AtomicInteger theCodeCounter) {
@@ -736,6 +960,48 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
+ protected ValidateCodeResult validateCodeIsInPreExpandedValueSet(
+ ValueSet theValueSet, String theSystem, String theCode, String theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
+
+ ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet.hasId(), "ValueSet.id is required");
+
+ Long valueSetId = theValueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong();
+
+ List concepts = new ArrayList<>();
+ if (isNotBlank(theCode)) {
+ if (isNotBlank(theSystem)) {
+ concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theSystem, theCode);
+ } else {
+ concepts = myValueSetConceptDao.findOneByValueSetIdAndCode(valueSetId, theCode);
+ }
+ } else if (theCoding != null) {
+ if (theCoding.hasSystem() && theCoding.hasCode()) {
+ concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, theCoding.getSystem(), theCoding.getCode());
+ }
+ } else if (theCodeableConcept != null){
+ for (Coding coding : theCodeableConcept.getCoding()) {
+ if (coding.hasSystem() && coding.hasCode()) {
+ concepts = myValueSetConceptDao.findOneByValueSetIdSystemAndCode(valueSetId, coding.getSystem(), coding.getCode());
+ if (!concepts.isEmpty()) {
+ break;
+ }
+ }
+ }
+ }
+
+ for (TermValueSetConcept concept : concepts) {
+ if (isNotBlank(theDisplay) && theDisplay.equals(concept.getDisplay())) {
+ return new ValidateCodeResult(true, "Validation succeeded", concept.getDisplay());
+ }
+ }
+
+ if (!concepts.isEmpty()) {
+ return new ValidateCodeResult(true, "Validation succeeded", concepts.get(0).getDisplay());
+ }
+
+ return null;
+ }
+
private void fetchChildren(TermConcept theConcept, Set theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
@@ -781,7 +1047,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
*/
TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_MANDATORY);
- return txTemplate.execute(t->{
+ return txTemplate.execute(t -> {
TermCodeSystemVersion csv = findCurrentCodeSystemVersionForSystem(theCodeSystem);
return myConceptDao.findByCodeSystemAndCode(csv, theCode);
});
@@ -798,7 +1064,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
StopWatch stopwatch = new StopWatch();
Optional concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
- if (concept.isPresent() == false) {
+ if (!concept.isPresent()) {
return Collections.emptySet();
}
@@ -829,7 +1095,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
Stopwatch stopwatch = Stopwatch.createStarted();
Optional concept = fetchLoadedCode(theCodeSystemResourcePid, theCode);
- if (concept.isPresent() == false) {
+ if (!concept.isPresent()) {
return Collections.emptySet();
}
@@ -1014,8 +1280,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
- Page concepts = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
- if (concepts.hasContent() == false) {
+ Page concepts = myConceptDao.findResourcesRequiringReindexing(PageRequest.of(0, maxResult));
+ if (!concepts.hasContent()) {
if (myChildToParentPidCache != null) {
ourLog.info("Clearing parent concept cache");
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
@@ -1076,7 +1342,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
} else {
return saveConcept(theConcept);
}
-
+
}
/**
@@ -1122,28 +1388,28 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Transactional(propagation = Propagation.NEVER)
@Override
public synchronized void saveDeferred() {
- if (!myProcessDeferred) {
+ if (isProcessDeferredPaused()) {
return;
- } else if (myDeferredConcepts.isEmpty() && myConceptLinksToSaveLater.isEmpty()) {
+ } else if (isNoDeferredConceptsAndNoConceptLinksToSaveLater()) {
processReindexing();
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
- if (!myDeferredConcepts.isEmpty() || !myConceptLinksToSaveLater.isEmpty()) {
+ if (isDeferredConceptsOrConceptLinksToSaveLater()) {
tt.execute(t -> {
processDeferredConcepts();
return null;
});
}
- if (myDeferredValueSets.size() > 0) {
+ if (isDeferredValueSets()) {
tt.execute(t -> {
processDeferredValueSets();
return null;
});
}
- if (myDeferredConceptMaps.size() > 0) {
+ if (isDeferredConceptMaps()) {
tt.execute(t -> {
processDeferredConceptMaps();
return null;
@@ -1152,6 +1418,42 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
+ private boolean isProcessDeferredPaused() {
+ return !myProcessDeferred;
+ }
+
+ private boolean isNoDeferredConceptsAndNoConceptLinksToSaveLater() {
+ return isNoDeferredConcepts() && isNoConceptLinksToSaveLater();
+ }
+
+ private boolean isDeferredConceptsOrConceptLinksToSaveLater() {
+ return isDeferredConcepts() || isConceptLinksToSaveLater();
+ }
+
+ private boolean isDeferredConcepts() {
+ return !myDeferredConcepts.isEmpty();
+ }
+
+ private boolean isNoDeferredConcepts() {
+ return myDeferredConcepts.isEmpty();
+ }
+
+ private boolean isConceptLinksToSaveLater() {
+ return !myConceptLinksToSaveLater.isEmpty();
+ }
+
+ private boolean isNoConceptLinksToSaveLater() {
+ return myConceptLinksToSaveLater.isEmpty();
+ }
+
+ private boolean isDeferredValueSets() {
+ return !myDeferredValueSets.isEmpty();
+ }
+
+ private boolean isDeferredConceptMaps() {
+ return !myDeferredConceptMaps.isEmpty();
+ }
+
@Override
public void setApplicationContext(ApplicationContext theApplicationContext) throws BeansException {
myApplicationContext = theApplicationContext;
@@ -1498,31 +1800,86 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
@Scheduled(fixedDelay = 600000) // 10 minutes.
@Override
public synchronized void preExpandValueSetToTerminologyTables() {
- new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
- @Override
- protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+ if (isNotSafeToPreExpandValueSets()) {
+ ourLog.info("Skipping scheduled pre-expansion of ValueSets while deferred entities are being loaded.");
+ return;
+ }
+ TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
+
+ while (true) {
+ TermValueSet valueSetToExpand = txTemplate.execute(t -> {
Optional optionalTermValueSet = getNextTermValueSetNotExpanded();
- if (optionalTermValueSet.isPresent()) {
- TermValueSet termValueSet = optionalTermValueSet.get();
- termValueSet.setExpansionStatus(TermValueSetExpansionStatusEnum.EXPANSION_IN_PROGRESS);
- myValueSetDao.saveAndFlush(termValueSet);
-
- ValueSet valueSet = getValueSetFromResourceTable(termValueSet.getResource());
-
- expandValueSet(valueSet, new ValueSetConceptAccumulator(termValueSet, myValueSetConceptDao, myValueSetConceptDesignationDao));
-
- termValueSet.setExpansionStatus(TermValueSetExpansionStatusEnum.EXPANDED);
- myValueSetDao.saveAndFlush(termValueSet);
+ if (!optionalTermValueSet.isPresent()) {
+ return null;
}
+
+ TermValueSet termValueSet = optionalTermValueSet.get();
+ termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
+ return myValueSetDao.saveAndFlush(termValueSet);
+ });
+ if (valueSetToExpand == null) {
+ return;
}
- });
+
+ // We have a ValueSet to pre-expand.
+ try {
+ ValueSet valueSet = txTemplate.execute(t -> {
+ TermValueSet refreshedValueSetToExpand = myValueSetDao.findById(valueSetToExpand.getId()).get();
+ return getValueSetFromResourceTable(refreshedValueSetToExpand.getResource());
+ });
+ expandValueSet(valueSet, new ValueSetConceptAccumulator(valueSetToExpand, myValueSetConceptDao, myValueSetConceptDesignationDao));
+
+ // We are done with this ValueSet.
+ txTemplate.execute(t -> {
+ valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANDED);
+ myValueSetDao.saveAndFlush(valueSetToExpand);
+ return null;
+ });
+
+ } catch (Exception e) {
+ ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
+ txTemplate.execute(t -> {
+ valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
+ myValueSetDao.saveAndFlush(valueSetToExpand);
+ return null;
+ });
+ }
+ }
+ }
+
+ private boolean isNotSafeToPreExpandValueSets() {
+ return !isSafeToPreExpandValueSets();
+ }
+
+ private boolean isSafeToPreExpandValueSets() {
+ if (isProcessDeferredPaused()) {
+ return false;
+ }
+
+ if (isDeferredConcepts()) {
+ return false;
+ }
+
+ if (isConceptLinksToSaveLater()) {
+ return false;
+ }
+
+ if (isDeferredValueSets()) {
+ return false;
+ }
+
+ if (isDeferredConceptMaps()) {
+ return false;
+ }
+
+ return true;
}
protected abstract ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable);
private Optional getNextTermValueSetNotExpanded() {
Optional retVal = Optional.empty();
- Page page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetExpansionStatusEnum.NOT_EXPANDED);
+ Slice page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
if (!page.getContent().isEmpty()) {
retVal = Optional.of(page.getContent().get(0));
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
index 498f25dfe94..eb9b7c7e96e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
@@ -20,13 +20,13 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.*;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
@@ -92,6 +92,11 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
throw new UnsupportedOperationException();
}
+ @Override
+ public IBaseResource expandValueSet(IBaseResource theValueSetToExpand, int theOffset, int theCount) {
+ throw new UnsupportedOperationException();
+ }
+
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
throw new UnsupportedOperationException();
@@ -144,4 +149,8 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvcImpl {
return retVal;
}
+ @Override
+ public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
+ throw new UnsupportedOperationException();
+ }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
index da83782a810..09f17ea98bf 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@@ -15,6 +16,7 @@ import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@@ -29,7 +31,8 @@ import java.util.Collections;
import java.util.List;
import java.util.Optional;
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
* #%L
@@ -177,6 +180,20 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
}
}
+ @Override
+ public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
+ ValueSet valueSetToExpand = (ValueSet) theInput;
+
+ try {
+ org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
+ valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet(valueSetToExpand);
+ org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4, theOffset, theCount);
+ return VersionConvertor_30_40.convertValueSet(expandedR4);
+ } catch (FHIRException e) {
+ throw new InternalErrorException(e);
+ }
+ }
+
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
@@ -345,5 +362,26 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvcImpl implemen
return null;
}
+ @Override
+ public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
+ ValueSet valueSet = (ValueSet) theValueSet;
+ Coding coding = (Coding) theCoding;
+ CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
+ try {
+ org.hl7.fhir.r4.model.ValueSet valueSetR4;
+ valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
+
+ org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
+
+ org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
+ for (Coding nestedCoding : codeableConcept.getCoding()) {
+ codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
+ }
+
+ return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
+ } catch (FHIRException e) {
+ throw new InternalErrorException(e);
+ }
+ }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
index b764fcf5ee8..a27afaccd49 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
@@ -2,18 +2,17 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
-import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
-import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.StructureDefinition;
-import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r4.terminologies.ValueSetExpander;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
@@ -137,6 +136,12 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
return super.expandValueSet(valueSetToExpand);
}
+ @Override
+ public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
+ ValueSet valueSetToExpand = (ValueSet) theInput;
+ return super.expandValueSet(valueSetToExpand, theOffset, theCount);
+ }
+
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
ValueSet valueSetToExpand = (ValueSet) theValueSetToExpand;
@@ -272,4 +277,11 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvcImpl implements
return super.lookupCode(theContext, theSystem, theCode);
}
+ @Override
+ public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
+ ValueSet valueSet = (ValueSet) theValueSet;
+ Coding coding = (Coding) theCoding;
+ CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
+ return super.validateCodeIsInPreExpandedValueSet(valueSet, theSystem, theCode, theDisplay, coding, codeableConcept);
+ }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
index 2f27d7b1761..b828627e94e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java
@@ -2,14 +2,16 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.UrlUtil;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.*;
+import org.hl7.fhir.r5.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander;
@@ -143,6 +145,13 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
}
+ @Override
+ public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
+ org.hl7.fhir.r4.model.ValueSet valueSetToExpand = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theInput);
+ org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(valueSetToExpand, theOffset, theCount);
+ return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
+ }
+
@Override
public void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSetToExpand);
@@ -280,4 +289,19 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
return super.lookupCode(theContext, theSystem, theCode);
}
+ @Override
+ public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
+ org.hl7.fhir.r4.model.ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet);
+
+ Coding coding = (Coding) theCoding;
+ org.hl7.fhir.r4.model.Coding codingR4 = new org.hl7.fhir.r4.model.Coding(coding.getSystem(), coding.getCode(), coding.getDisplay());
+
+ CodeableConcept codeableConcept = (CodeableConcept) theCodeableConcept;
+ org.hl7.fhir.r4.model.CodeableConcept codeableConceptR4 = new org.hl7.fhir.r4.model.CodeableConcept();
+ for (Coding nestedCoding : codeableConcept.getCoding()) {
+ codeableConceptR4.addCoding(new org.hl7.fhir.r4.model.Coding(nestedCoding.getSystem(), nestedCoding.getCode(), nestedCoding.getDisplay()));
+ }
+
+ return super.validateCodeIsInPreExpandedValueSet(valueSetR4, theSystem, theCode, theDisplay, codingR4, codeableConceptR4);
+ }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
index 5faf0f72320..8675d594205 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
@@ -1,16 +1,12 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
-import org.hl7.fhir.instance.model.api.IBaseCoding;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.instance.model.api.IPrimitiveType;
-import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.ConceptMap;
-import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.instance.model.api.*;
+import org.hl7.fhir.r4.model.*;
import javax.annotation.Nullable;
import java.util.List;
@@ -44,6 +40,8 @@ public interface IHapiTerminologySvc {
ValueSet expandValueSet(ValueSet theValueSetToExpand);
+ ValueSet expandValueSet(ValueSet theValueSetToExpand, int theOffset, int theCount);
+
void expandValueSet(ValueSet theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
/**
@@ -51,6 +49,11 @@ public interface IHapiTerminologySvc {
*/
IBaseResource expandValueSet(IBaseResource theValueSetToExpand);
+ /**
+ * Version independent
+ */
+ IBaseResource expandValueSet(IBaseResource theValueSetToExpand, int theOffset, int theCount);
+
void expandValueSet(IBaseResource theValueSetToExpand, IValueSetConceptAccumulator theValueSetCodeAccumulator);
List expandValueSet(String theValueSet);
@@ -109,4 +112,9 @@ public interface IHapiTerminologySvc {
AtomicInteger applyDeltaCodesystemsRemove(String theSystem, CodeSystem theDelta);
void preExpandValueSetToTerminologyTables();
+
+ /**
+ * Version independent
+ */
+ ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
index 5c3ec5d20a8..f719c98b37d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcImpl.java
@@ -32,7 +32,9 @@ import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
+import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
+import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.*;
@@ -41,6 +43,7 @@ import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@@ -67,26 +70,10 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
+
public static final String IMGTHLA_HLA_NOM_TXT = "hla_nom.txt";
public static final String IMGTHLA_HLA_XML = "hla.xml";
- public static final String LOINC_ANSWERLIST_FILE = "AnswerList.csv";
- public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink.csv";
- public static final String LOINC_DOCUMENT_ONTOLOGY_FILE = "DocumentOntology.csv";
- public static final String LOINC_UPLOAD_PROPERTIES_FILE = "loincupload.properties";
- public static final String LOINC_FILE = "LoincTable/Loinc.csv";
- public static final String LOINC_HIERARCHY_FILE = "MultiAxialHierarchy.csv";
- public static final String LOINC_PART_FILE = "Part.csv";
- public static final String LOINC_PART_LINK_FILE = "LoincPartLink.csv";
- public static final String LOINC_PART_RELATED_CODE_MAPPING_FILE = "PartRelatedCodeMapping.csv";
- public static final String LOINC_RSNA_PLAYBOOK_FILE = "LoincRsnaRadiologyPlaybook.csv";
- public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE = "Top2000CommonLabResultsUs.csv";
- public static final String LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE = "Top2000CommonLabResultsSi.csv";
- public static final String LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE = "LoincUniversalLabOrdersValueSet.csv";
- public static final String LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV = "LoincIeeeMedicalDeviceCodeMappingTable.csv";
- public static final String LOINC_IMAGING_DOCUMENT_CODES_FILE = "ImagingDocumentCodes.csv";
- public static final String LOINC_GROUP_FILE = "Group.csv";
- public static final String LOINC_GROUP_TERMS_FILE = "GroupLoincTerms.csv";
- public static final String LOINC_PARENT_GROUP_FILE = "ParentGroup.csv";
+
public static final String CUSTOM_CONCEPTS_FILE = "concepts.csv";
public static final String CUSTOM_HIERARCHY_FILE = "hierarchy.csv";
public static final String CUSTOM_CODESYSTEM_JSON = "codesystem.json";
@@ -219,35 +206,61 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
@Override
public UploadStatistics loadLoinc(List theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
+ List loincUploadPropertiesFragment = Arrays.asList(
+ LOINC_UPLOAD_PROPERTIES_FILE.getCode()
+ );
+ descriptors.verifyMandatoryFilesExist(loincUploadPropertiesFragment);
+
+ Properties uploadProperties = getProperties(descriptors, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+
List mandatoryFilenameFragments = Arrays.asList(
- LOINC_FILE,
- LOINC_HIERARCHY_FILE,
- LOINC_UPLOAD_PROPERTIES_FILE,
- LOINC_ANSWERLIST_FILE,
- LOINC_ANSWERLIST_LINK_FILE,
- LOINC_PART_FILE,
- LOINC_PART_LINK_FILE,
- LOINC_PART_RELATED_CODE_MAPPING_FILE,
- LOINC_DOCUMENT_ONTOLOGY_FILE,
- LOINC_RSNA_PLAYBOOK_FILE,
- LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE,
- LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE,
- LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE,
- LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV,
- LOINC_IMAGING_DOCUMENT_CODES_FILE
+ uploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_DOCUMENT_ONTOLOGY_FILE.getCode(), LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_HIERARCHY_FILE.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE.getCode(), LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode())
);
descriptors.verifyMandatoryFilesExist(mandatoryFilenameFragments);
List optionalFilenameFragments = Arrays.asList(
+ uploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()),
+ uploadProperties.getProperty(LOINC_PARENT_GROUP_FILE.getCode(), LOINC_PARENT_GROUP_FILE_DEFAULT.getCode())
);
descriptors.verifyOptionalFilesExist(optionalFilenameFragments);
ourLog.info("Beginning LOINC processing");
- return processLoincFiles(descriptors, theRequestDetails);
+ return processLoincFiles(descriptors, theRequestDetails, uploadProperties);
}
}
+ @NotNull
+ private Properties getProperties(LoadedFileDescriptors theDescriptors, String thePropertiesFile) {
+ Properties retVal = new Properties();
+ for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
+ if (next.getFilename().endsWith(thePropertiesFile)) {
+ try {
+ try (InputStream inputStream = next.getInputStream()) {
+ retVal.load(inputStream);
+ }
+ } catch (IOException e) {
+ throw new InternalErrorException("Failed to read " + thePropertiesFile, e);
+ }
+ }
+ }
+ return retVal;
+ }
+
@Override
public UploadStatistics loadSnomedCt(List theFiles, RequestDetails theRequestDetails) {
try (LoadedFileDescriptors descriptors = new LoadedFileDescriptors(theFiles)) {
@@ -444,7 +457,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
// return new UploadStatistics(conceptCount, target);
}
- UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
+ UploadStatistics processLoincFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails, Properties theUploadProperties) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map code2concept = new HashMap<>();
final List valueSets = new ArrayList<>();
@@ -469,93 +482,82 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
IRecordHandler handler;
- Properties uploadProperties = new Properties();
- for (FileDescriptor next : theDescriptors.getUncompressedFileDescriptors()) {
- if (next.getFilename().endsWith("loincupload.properties")) {
- try {
- try (InputStream inputStream = next.getInputStream()) {
- uploadProperties.load(inputStream);
- }
- } catch (IOException e) {
- throw new InternalErrorException("Failed to read loincupload.properties", e);
- }
- }
- }
-
- // Part file
+ // Part
handler = new LoincPartHandler(codeSystemVersion, code2concept);
- iterateOverZipFile(theDescriptors, LOINC_PART_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_FILE.getCode(), LOINC_PART_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
Map partTypeAndPartNameToPartNumber = ((LoincPartHandler) handler).getPartTypeAndPartNameToPartNumber();
- // Loinc Codes
+ // LOINC codes
handler = new LoincHandler(codeSystemVersion, code2concept, propertyNamesToTypes, partTypeAndPartNameToPartNumber);
- iterateOverZipFile(theDescriptors, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_FILE.getCode(), LOINC_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Loinc Hierarchy
+ // LOINC hierarchy
handler = new LoincHierarchyHandler(codeSystemVersion, code2concept);
- iterateOverZipFile(theDescriptors, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_HIERARCHY_FILE.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Answer lists (ValueSets of potential answers/values for loinc "questions")
- handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Answer lists (ValueSets of potential answers/values for LOINC "questions")
+ handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_ANSWERLIST_FILE.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Answer list links (connects loinc observation codes to answerlist codes)
+ // Answer list links (connects LOINC observation codes to answer list codes)
handler = new LoincAnswerListLinkHandler(code2concept, valueSets);
- iterateOverZipFile(theDescriptors, LOINC_ANSWERLIST_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_ANSWERLIST_LINK_FILE.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // RSNA Playbook file
+ // RSNA playbook
// Note that this should come before the "Part Related Code Mapping"
// file because there are some duplicate mappings between these
// two files, and the RSNA Playbook file has more metadata
- handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_RSNA_PLAYBOOK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ handler = new LoincRsnaPlaybookHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_RSNA_PLAYBOOK_FILE.getCode(), LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Part link file
+ // Part link
handler = new LoincPartLinkHandler(codeSystemVersion, code2concept);
- iterateOverZipFile(theDescriptors, LOINC_PART_LINK_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_LINK_FILE.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
// Part related code mapping
- handler = new LoincPartRelatedCodeMappingHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_PART_RELATED_CODE_MAPPING_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ handler = new LoincPartRelatedCodeMappingHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PART_RELATED_CODE_MAPPING_FILE.getCode(), LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Document Ontology File
- handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_DOCUMENT_ONTOLOGY_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Document ontology
+ handler = new LoincDocumentOntologyHandler(code2concept, propertyNamesToTypes, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_DOCUMENT_ONTOLOGY_FILE.getCode(), LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Top 2000 Codes - US
- handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Top 2000 codes - US
+ handler = new LoincTop2000LabResultsUsHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Top 2000 Codes - SI
- handler = new LoincTop2000LabResultsSiHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Top 2000 codes - SI
+ handler = new LoincTop2000LabResultsSiHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE.getCode(), LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Universal Lab Order ValueSet
- handler = new LoincUniversalOrderSetHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Universal lab order ValueSet
+ handler = new LoincUniversalOrderSetHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE.getCode(), LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // IEEE Medical Device Codes
- handler = new LoincIeeeMedicalDeviceCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // IEEE medical device codes
+ handler = new LoincIeeeMedicalDeviceCodeHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE.getCode(), LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Imaging Document Codes
- handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_IMAGING_DOCUMENT_CODES_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Imaging document codes
+ handler = new LoincImagingDocumentCodeHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_IMAGING_DOCUMENT_CODES_FILE.getCode(), LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Group File
- handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Group
+ handler = new LoincGroupFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_GROUP_FILE.getCode(), LOINC_GROUP_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Group Terms File
- handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_GROUP_TERMS_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Group terms
+ handler = new LoincGroupTermsFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_GROUP_TERMS_FILE.getCode(), LOINC_GROUP_TERMS_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
- // Parent Group File
- handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, uploadProperties);
- iterateOverZipFile(theDescriptors, LOINC_PARENT_GROUP_FILE, handler, ',', QuoteMode.NON_NUMERIC, false);
+ // Parent group
+ handler = new LoincParentGroupFileHandler(code2concept, valueSets, conceptMaps, theUploadProperties);
+ iterateOverZipFile(theDescriptors, theUploadProperties.getProperty(LOINC_PARENT_GROUP_FILE.getCode(), LOINC_PARENT_GROUP_FILE_DEFAULT.getCode()), handler, ',', QuoteMode.NON_NUMERIC, false);
IOUtils.closeQuietly(theDescriptors);
+ valueSets.add(getValueSetLoincAll());
+
for (Entry next : code2concept.entrySet()) {
TermConcept nextConcept = next.getValue();
if (nextConcept.getParents().isEmpty()) {
@@ -573,6 +575,23 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
return new UploadStatistics(conceptCount, target);
}
+ private ValueSet getValueSetLoincAll() {
+ ValueSet retVal = new ValueSet();
+
+ retVal.setId("loinc-all");
+ retVal.setUrl("http://loinc.org/vs");
+ retVal.setVersion("1.0.0");
+ retVal.setName("All LOINC codes");
+ retVal.setStatus(Enumerations.PublicationStatus.ACTIVE);
+ retVal.setDate(new Date());
+ retVal.setPublisher("Regenstrief Institute, Inc.");
+ retVal.setDescription("A value set that includes all LOINC codes");
+ retVal.setCopyright("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/");
+ retVal.getCompose().addInclude().setSystem(IHapiTerminologyLoaderSvc.LOINC_URI);
+
+ return retVal;
+ }
+
private UploadStatistics processSnomedCtFiles(LoadedFileDescriptors theDescriptors, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map id2concept = new HashMap<>();
@@ -732,7 +751,7 @@ public class TerminologyLoaderSvcImpl implements IHapiTerminologyLoaderSvc {
private void verifyOptionalFilesExist(List theExpectedFilenameFragments) {
List notFound = notFound(theExpectedFilenameFragments);
if (!notFound.isEmpty()) {
- ourLog.warn("Could not find the following optional file: " + notFound);
+ ourLog.warn("Could not find the following optional files: " + notFound);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
index 4e2e5b92ec2..9c3f6a0a3f3 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetConceptAccumulator.java
@@ -71,7 +71,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
// Get existing entity so it can be deleted.
- Optional optionalConcept = myValueSetConceptDao.findByValueSetIdSystemAndCode(myTermValueSet.getId(), theSystem, theCode);
+ Optional optionalConcept = myValueSetConceptDao.findByTermValueSetIdSystemAndCode(myTermValueSet.getId(), theSystem, theCode);
if (optionalConcept.isPresent()) {
TermValueSetConcept concept = optionalConcept.get();
@@ -103,9 +103,8 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
}
myValueSetConceptDao.save(concept);
- if (myConceptsSaved++ % 250 == 0) {
+ if (myConceptsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
ourLog.info("Have pre-expanded {} concepts in ValueSet[{}]", myConceptsSaved, myTermValueSet.getUrl());
- myValueSetConceptDao.flush();
}
return concept;
@@ -116,6 +115,7 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
TermValueSetConceptDesignation designation = new TermValueSetConceptDesignation();
designation.setConcept(theConcept);
+ designation.setValueSet(myTermValueSet);
designation.setLanguage(theDesignation.getLanguage());
if (isNoneBlank(theDesignation.getUseSystem(), theDesignation.getUseCode())) {
designation.setUseSystem(theDesignation.getUseSystem());
@@ -127,9 +127,8 @@ public class ValueSetConceptAccumulator implements IValueSetConceptAccumulator {
designation.setValue(theDesignation.getValue());
myValueSetConceptDesignationDao.save(designation);
- if (myDesignationsSaved++ % 250 == 0) {
- ourLog.info("Have pre-expanded {} designations in ValueSet[{}]", myDesignationsSaved, myTermValueSet.getUrl());
- myValueSetConceptDesignationDao.flush();
+ if (myDesignationsSaved++ % 250 == 0) { // TODO: DM 2019-08-23 - This message never appears in the log. Fix it!
+ ourLog.info("Have pre-expanded {} designations for Concept[{}|{}] in ValueSet[{}]", myDesignationsSaved, theConcept.getSystem(), theConcept.getCode(), myTermValueSet.getUrl());
}
return designation;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java
index 5aa95013365..3104b452c6e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/ValueSetExpansionComponentWithConceptAccumulator.java
@@ -22,15 +22,23 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import ca.uhn.fhir.model.api.annotation.Block;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.Collection;
@Block()
public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.ValueSetExpansionComponent implements IValueSetConceptAccumulator {
+ private final int myMaxResults = 50000;
+ private int myConceptsCount;
+
+ public ValueSetExpansionComponentWithConceptAccumulator() {
+ myConceptsCount = 0;
+ }
@Override
public void includeConcept(String theSystem, String theCode, String theDisplay) {
+ incrementConceptsCount();
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
contains.setSystem(theSystem);
contains.setCode(theCode);
@@ -39,6 +47,7 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
@Override
public void includeConceptWithDesignations(String theSystem, String theCode, String theDisplay, Collection theDesignations) {
+ incrementConceptsCount();
ValueSet.ValueSetExpansionContainsComponent contains = this.addContains();
contains.setSystem(theSystem);
contains.setCode(theCode);
@@ -65,4 +74,10 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
theSystem.equals(t.getSystem()) &&
theCode.equals(t.getCode()));
}
+
+ private void incrementConceptsCount() {
+ if (++myConceptsCount > myMaxResults) {
+ throw new InternalErrorException("Expansion produced too many (>= " + myMaxResults + ") results");
+ }
+ }
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
index 57ca69fd2d8..a2e2b7a43c6 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/BaseLoincHandler.java
@@ -34,6 +34,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.apache.commons.lang3.StringUtils.*;
public abstract class BaseLoincHandler implements IRecordHandler {
@@ -114,7 +115,7 @@ public abstract class BaseLoincHandler implements IRecordHandler {
conceptMap.setId(theMapping.getConceptMapId());
conceptMap.setUrl(theMapping.getConceptMapUri());
conceptMap.setName(theMapping.getConceptMapName());
- conceptMap.setVersion(myUploadProperties.getProperty("conceptmap.version"));
+ conceptMap.setVersion(myUploadProperties.getProperty(LOINC_CONCEPTMAP_VERSION.getCode()));
conceptMap.setPublisher(REGENSTRIEF_INSTITUTE_INC);
conceptMap.addContact()
.setName(REGENSTRIEF_INSTITUTE_INC)
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
index b8e7dc20166..5e6700da2cd 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java
@@ -31,7 +31,9 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
-import static org.apache.commons.lang3.StringUtils.*;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.trim;
public class LoincAnswerListHandler extends BaseLoincHandler {
@@ -72,7 +74,7 @@ public class LoincAnswerListHandler extends BaseLoincHandler {
}
// Answer list ValueSet
- ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, "answerlist.version");
+ ValueSet vs = getValueSet(answerListId, "http://loinc.org/vs/" + answerListId, answerListName, LOINC_ANSWERLIST_VERSION.getCode());
if (vs.getIdentifier().isEmpty()) {
vs.addIdentifier()
.setSystem("urn:ietf:rfc:3986")
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java
index 0ece9206e5c..b5474f283eb 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java
@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
@@ -52,6 +53,18 @@ public class LoincHierarchyHandler implements IRecordHandler {
TermConcept child = getOrCreate(childCode, childCodeText);
parent.addChild(child, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
+
+ parent.addPropertyCoding(
+ "child",
+ IHapiTerminologyLoaderSvc.LOINC_URI,
+ child.getCode(),
+ child.getDisplay());
+
+ child.addPropertyCoding(
+ "parent",
+ IHapiTerminologyLoaderSvc.LOINC_URI,
+ parent.getCode(),
+ parent.getDisplay());
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
new file mode 100644
index 00000000000..aa2656cdea3
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
@@ -0,0 +1,142 @@
+package ca.uhn.fhir.jpa.term.loinc;
+
+/*
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * This enum is used to facilitate configurable filenames when uploading LOINC.
+ */
+public enum LoincUploadPropertiesEnum {
+ /**
+ * Sorting agnostic.
+ */
+
+ LOINC_UPLOAD_PROPERTIES_FILE("loincupload.properties"),
+
+ /*
+ * MANDATORY
+ */
+ // Answer lists (ValueSets of potential answers/values for LOINC "questions")
+ LOINC_ANSWERLIST_FILE("loinc.answerlist.file"),
+ LOINC_ANSWERLIST_FILE_DEFAULT("AnswerList.csv"),
+ // Answer list links (connects LOINC observation codes to answer list codes)
+ LOINC_ANSWERLIST_LINK_FILE("loinc.answerlist.link.file"),
+ LOINC_ANSWERLIST_LINK_FILE_DEFAULT("LoincAnswerListLink.csv"),
+
+ // Document ontology
+ LOINC_DOCUMENT_ONTOLOGY_FILE("loinc.document.ontology.file"),
+ LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT("DocumentOntology.csv"),
+
+ // LOINC codes
+ LOINC_FILE("loinc.file"),
+ LOINC_FILE_DEFAULT("LoincTable/Loinc.csv"),
+
+ // LOINC hierarchy
+ LOINC_HIERARCHY_FILE("loinc.hierarchy.file"),
+ LOINC_HIERARCHY_FILE_DEFAULT("MultiAxialHierarchy.csv"),
+
+ // IEEE medical device codes
+ LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE("loinc.ieee.medical.device.code.mapping.table.file"),
+ LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT("LoincIeeeMedicalDeviceCodeMappingTable.csv"),
+
+ // Imaging document codes
+ LOINC_IMAGING_DOCUMENT_CODES_FILE("loinc.imaging.document.codes.file"),
+ LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT("ImagingDocumentCodes.csv"),
+
+ // Part
+ LOINC_PART_FILE("loinc.part.file"),
+ LOINC_PART_FILE_DEFAULT("Part.csv"),
+ // Part link
+ LOINC_PART_LINK_FILE("loinc.part.link.file"),
+ LOINC_PART_LINK_FILE_DEFAULT("LoincPartLink.csv"),
+ // Part related code mapping
+ LOINC_PART_RELATED_CODE_MAPPING_FILE("loinc.part.related.code.mapping.file"),
+ LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT("PartRelatedCodeMapping.csv"),
+
+ // RSNA playbook
+ LOINC_RSNA_PLAYBOOK_FILE("loinc.rsna.playbook.file"),
+ LOINC_RSNA_PLAYBOOK_FILE_DEFAULT("LoincRsnaRadiologyPlaybook.csv"),
+
+ // Top 2000 codes - SI
+ LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE("loinc.top2000.common.lab.results.si.file"),
+ LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT("Top2000CommonLabResultsSi.csv"),
+ // Top 2000 codes - US
+ LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE("loinc.top2000.common.lab.results.us.file"),
+ LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT("Top2000CommonLabResultsUs.csv"),
+
+ // Universal lab order ValueSet
+ LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE("loinc.universal.lab.order.valueset.file"),
+ LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT("LoincUniversalLabOrdersValueSet.csv"),
+
+ /*
+ * OPTIONAL
+ */
+ // This is the version identifier for the answer list file
+ LOINC_ANSWERLIST_VERSION("loinc.answerlist.version"),
+
+ // This is the version identifier for uploaded ConceptMap resources
+ LOINC_CONCEPTMAP_VERSION("loinc.conceptmap.version"),
+
+ // Group
+ LOINC_GROUP_FILE("loinc.group.file"),
+ LOINC_GROUP_FILE_DEFAULT("Group.csv"),
+ // Group terms
+ LOINC_GROUP_TERMS_FILE("loinc.group.terms.file"),
+ LOINC_GROUP_TERMS_FILE_DEFAULT("GroupLoincTerms.csv"),
+
+ // Parent group
+ LOINC_PARENT_GROUP_FILE("loinc.parent.group.file"),
+ LOINC_PARENT_GROUP_FILE_DEFAULT("ParentGroup.csv");
+
+ private static Map ourValues;
+ private String myCode;
+
+ LoincUploadPropertiesEnum(String theCode) {
+ myCode = theCode;
+ }
+
+ public String getCode() {
+ return myCode;
+ }
+
+ public static LoincUploadPropertiesEnum fromCode(String theCode) {
+ if (ourValues == null) {
+ HashMap values = new HashMap();
+ for (LoincUploadPropertiesEnum next : values()) {
+ values.put(next.getCode(), next);
+ }
+ ourValues = Collections.unmodifiableMap(values);
+ }
+ return ourValues.get(theCode);
+ }
+
+ /**
+ * Convert from Enum ordinal to Enum type.
+ *
+ * Usage:
+ *
+ * LoincUploadPropertiesEnum loincUploadPropertiesEnum = LoincUploadPropertiesEnum.values[ordinal];
+ */
+ public static final LoincUploadPropertiesEnum values[] = values();
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnumTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnumTest.java
new file mode 100644
index 00000000000..a9b8f365ca4
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/entity/TermValueSetPreExpansionStatusEnumTest.java
@@ -0,0 +1,21 @@
+package ca.uhn.fhir.jpa.entity;
+
+import ca.uhn.fhir.i18n.HapiLocalizer;
+import org.junit.Test;
+
+import static org.junit.Assert.fail;
+
+public class TermValueSetPreExpansionStatusEnumTest {
+ @Test
+ public void testHaveDescriptions() {
+ HapiLocalizer localizer = new HapiLocalizer();
+
+ for (TermValueSetPreExpansionStatusEnum next : TermValueSetPreExpansionStatusEnum.values()) {
+ String key = "ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum." + next.getCode();
+ String msg = localizer.getMessage(key);
+ if (msg.equals(HapiLocalizer.UNKNOWN_I18N_KEY_MESSAGE)) {
+ fail("No value for key: " + key);
+ }
+ }
+ }
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
index af7fcd14fac..c789f0a82b9 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
@@ -397,7 +397,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
@Test
public void testExpandInvalidParams() throws IOException {
- //@formatter:off
try {
ourClient
.operation()
@@ -407,11 +406,9 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
.execute();
fail();
} catch (InvalidRequestException e) {
- assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request", e.getMessage());
+ assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires an identifier or a valueSet as a part of the request.", e.getMessage());
}
- //@formatter:on
- //@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-dstu3.xml");
ourClient
@@ -425,9 +422,7 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
- //@formatter:on
- //@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/extensional-case-dstu3.xml");
ourClient
@@ -441,8 +436,30 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have an identifier specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
- //@formatter:on
+ try {
+ ourClient
+ .operation()
+ .onInstance(myExtensionalVsId)
+ .named("expand")
+ .withParameter(Parameters.class, "offset", new IntegerType(-1))
+ .execute();
+ fail();
+ } catch (InvalidRequestException e) {
+ assertEquals("HTTP 400 Bad Request: offset parameter for $expand operation must be >= 0 when specified. offset: -1", e.getMessage());
+ }
+
+ try {
+ ourClient
+ .operation()
+ .onInstance(myExtensionalVsId)
+ .named("expand")
+ .withParameter(Parameters.class, "count", new IntegerType(-1))
+ .execute();
+ fail();
+ } catch (InvalidRequestException e) {
+ assertEquals("HTTP 400 Bad Request: count parameter for $expand operation must be >= 0 when specified. count: -1", e.getMessage());
+ }
}
@Test
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java
index 2e6d360908b..2b84ec5ed5c 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderTransactionSearchDstu3Test.java
@@ -4,11 +4,19 @@ import static org.hamcrest.Matchers.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
+import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.concurrent.TimeUnit;
+import ca.uhn.fhir.rest.api.Constants;
+import com.google.common.base.Charsets;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.entity.ContentType;
+import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
@@ -180,6 +188,50 @@ public class SystemProviderTransactionSearchDstu3Test extends BaseJpaDstu3Test {
assertThat(actualIds, contains(ids.subList(5, 10).toArray(new String[0])));
}
+
+ @Test
+ public void testPatchUsingJsonPatch_Transaction() throws Exception {
+ String methodName = "testPatchUsingJsonPatch_Transaction";
+ IIdType pid1;
+ {
+ Patient patient = new Patient();
+ patient.setActive(true);
+ patient.addIdentifier().setSystem("urn:system").setValue("0");
+ patient.addName().setFamily(methodName).addGiven("Joe");
+ pid1 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+ }
+
+ String patchString = "[ { \"op\":\"replace\", \"path\":\"/active\", \"value\":false } ]";
+ Binary patch = new Binary();
+ patch.setContentType(ca.uhn.fhir.rest.api.Constants.CT_JSON_PATCH);
+ patch.setContent(patchString.getBytes(Charsets.UTF_8));
+
+ // Note that we don't set the type
+ Bundle input = new Bundle();
+ input.setType(Bundle.BundleType.TRANSACTION);
+ input.addEntry()
+ .setFullUrl(pid1.getValue())
+ .setResource(patch)
+ .getRequest().setUrl(pid1.getValue());
+
+ HttpPost post = new HttpPost(ourServerBase);
+ String encodedRequest = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(input);
+ ourLog.info("Requet:\n{}", encodedRequest);
+ post.setEntity(new StringEntity(encodedRequest, ContentType.parse(ca.uhn.fhir.rest.api.Constants.CT_FHIR_JSON_NEW+ Constants.CHARSET_UTF8_CTSUFFIX)));
+ try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
+ String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+ ourLog.info(responseString);
+ assertEquals(200, response.getStatusLine().getStatusCode());
+ assertThat(responseString, containsString("\"resourceType\":\"Bundle\""));
+ }
+
+ Patient newPt = ourClient.read().resource(Patient.class).withId(pid1.getIdPart()).execute();
+ assertEquals("2", newPt.getIdElement().getVersionIdPart());
+ assertEquals(false, newPt.getActive());
+ }
+
+
+
@Test
public void testTransactionWithGetHardLimitLargeSynchronous() {
List ids = create20Patients();
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
index b792a29aa06..007e9f63b22 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/TerminologyUploaderProviderDstu3Test.java
@@ -1,8 +1,6 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvcImpl;
-import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
@@ -20,6 +18,7 @@ import java.util.List;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*;
@@ -37,24 +36,24 @@ public class TerminologyUploaderProviderDstu3Test extends BaseResourceProviderDs
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
- addFile(zos, "loincupload.properties");
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
- addFile(zos, TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
+ addFile(zos, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+ addFile(zos, LOINC_PART_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_HIERARCHY_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_GROUP_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_PART_LINK_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
+ addFile(zos, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
zos.close();
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
index a6e1011f511..7a69fd83b55 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
@@ -264,7 +264,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
@Test
public void testExpandInvalidParams() throws IOException {
- //@formatter:off
try {
ourClient
.operation()
@@ -274,11 +273,9 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
.execute();
fail();
} catch (InvalidRequestException e) {
- assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request", e.getMessage());
+ assertEquals("HTTP 400 Bad Request: $expand operation at the type level (no ID specified) requires a url or a valueSet as a part of the request.", e.getMessage());
}
- //@formatter:on
- //@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/r4/extensional-case-r4.xml");
ourClient
@@ -292,9 +289,7 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
- //@formatter:on
- //@formatter:off
try {
ValueSet toExpand = loadResourceFromClasspath(ValueSet.class, "/r4/extensional-case.xml");
ourClient
@@ -308,8 +303,30 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: $expand must EITHER be invoked at the instance level, or have a url specified, or have a ValueSet specified. Can not combine these options.", e.getMessage());
}
- //@formatter:on
+ try {
+ ourClient
+ .operation()
+ .onInstance(myExtensionalVsId)
+ .named("expand")
+ .withParameter(Parameters.class, "offset", new IntegerType(-1))
+ .execute();
+ fail();
+ } catch (InvalidRequestException e) {
+ assertEquals("HTTP 400 Bad Request: offset parameter for $expand operation must be >= 0 when specified. offset: -1", e.getMessage());
+ }
+
+ try {
+ ourClient
+ .operation()
+ .onInstance(myExtensionalVsId)
+ .named("expand")
+ .withParameter(Parameters.class, "count", new IntegerType(-1))
+ .execute();
+ fail();
+ } catch (InvalidRequestException e) {
+ assertEquals("HTTP 400 Bad Request: count parameter for $expand operation must be >= 0 when specified. count: -1", e.getMessage());
+ }
}
@Test
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
index ecd67f4a724..a6ca90547bc 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import ca.uhn.fhir.jpa.term.loinc.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -19,8 +20,11 @@ import org.mockito.Captor;
import org.mockito.Mock;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Map;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.*;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.ArgumentMatchers.any;
@@ -252,6 +256,22 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
assertEquals("42176-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
assertEquals("1,3 beta glucan [Mass/volume] in Serum", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
+ // All LOINC codes
+ assertTrue(valueSets.containsKey("loinc-all"));
+ vs = valueSets.get("loinc-all");
+ assertEquals("http://loinc.org/vs", vs.getUrl());
+ assertEquals("1.0.0", vs.getVersion());
+ assertEquals("All LOINC codes", vs.getName());
+ assertEquals(Enumerations.PublicationStatus.ACTIVE, vs.getStatus());
+ assertTrue(vs.hasDate());
+ assertEquals("Regenstrief Institute, Inc.", vs.getPublisher());
+ assertEquals("A value set that includes all LOINC codes", vs.getDescription());
+ assertEquals("This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at https://loinc.org/license/", vs.getCopyright());
+ assertTrue(vs.hasCompose());
+ assertTrue(vs.getCompose().hasInclude());
+ assertEquals(1, vs.getCompose().getInclude().size());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, vs.getCompose().getInclude().get(0).getSystem());
+
// IEEE Medical Device Codes
conceptMap = conceptMaps.get(LoincIeeeMedicalDeviceCodeHandler.LOINC_IEEE_CM_ID);
ourLog.debug(FhirContext.forR4().newXmlParser().setPrettyPrint(true).encodeResourceToString(conceptMap));
@@ -322,8 +342,8 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
@Test
public void testLoadLoincMissingMandatoryFiles() throws IOException {
- myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
- myFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
+ myFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+ myFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
// Actually do the load
try {
@@ -336,26 +356,129 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
}
}
-
public static void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles) throws IOException {
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UPLOAD_PROPERTIES_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_GROUP_TERMS_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PARENT_GROUP_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_FILE, TerminologyLoaderSvcImpl.LOINC_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE, TerminologyLoaderSvcImpl.LOINC_HIERARCHY_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_ANSWERLIST_LINK_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_FILE, TerminologyLoaderSvcImpl.LOINC_PART_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE, TerminologyLoaderSvcImpl.LOINC_PART_LINK_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_PART_RELATED_CODE_MAPPING_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_DOCUMENT_ONTOLOGY_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_RSNA_PLAYBOOK_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_CSV);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_IMAGING_DOCUMENT_CODES_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE);
- theFiles.addFileZip("/loinc/", TerminologyLoaderSvcImpl.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE);
+ theFiles.addFileZip("/loinc/", LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_GROUP_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_FILE_DEFAULT.getCode(), LOINC_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_HIERARCHY_FILE_DEFAULT.getCode(), LOINC_HIERARCHY_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_FILE_DEFAULT.getCode(), LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode(), LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_PART_FILE_DEFAULT.getCode(), LOINC_PART_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_PART_LINK_FILE_DEFAULT.getCode(), LOINC_PART_LINK_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
+ theFiles.addFileZip("/loinc/", LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
+ }
+
+ @Test
+ public void testLoadLoincMultiaxialHierarchySupport() throws Exception {
+ addLoincMandatoryFilesToZip(myFiles);
+
+ // Actually do the load
+ mySvc.loadLoinc(myFiles.getFiles(), mySrd);
+
+ verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture(), myConceptMapCaptor.capture());
+ Map concepts = extractConcepts();
+ Map valueSets = extractValueSets();
+ Map conceptMaps = extractConceptMaps();
+
+ ConceptMap conceptMap;
+ TermConcept code;
+ ValueSet vs;
+ ConceptMap.ConceptMapGroupComponent group;
+
+ // Normal loinc code
+ code = concepts.get("10013-1");
+ assertEquals("10013-1", code.getCode());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, code.getCodingProperties("PROPERTY").get(0).getSystem());
+ assertEquals("LP6802-5", code.getCodingProperties("PROPERTY").get(0).getCode());
+ assertEquals("Elpot", code.getCodingProperties("PROPERTY").get(0).getDisplay());
+ assertEquals("EKG.MEAS", code.getStringProperty("CLASS"));
+ assertEquals("R' wave amplitude in lead I", code.getDisplay());
+
+ // Codes with parent and child properties
+ code = concepts.get("LP31755-9");
+ assertEquals("LP31755-9", code.getCode());
+ List properties = new ArrayList<>(code.getProperties());
+ assertEquals(1, properties.size());
+ assertEquals("child", properties.get(0).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
+ assertEquals("LP14559-6", properties.get(0).getValue());
+ assertEquals("Microorganism", properties.get(0).getDisplay());
+ assertEquals(0, code.getParents().size());
+ assertEquals(1, code.getChildren().size());
+
+ TermConcept childCode = code.getChildren().get(0).getChild();
+ assertEquals("LP14559-6", childCode.getCode());
+ assertEquals("Microorganism", childCode.getDisplay());
+
+ properties = new ArrayList<>(childCode.getProperties());
+ assertEquals(2, properties.size());
+ assertEquals("parent", properties.get(0).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
+ assertEquals(code.getCode(), properties.get(0).getValue());
+ assertEquals(code.getDisplay(), properties.get(0).getDisplay());
+ assertEquals("child", properties.get(1).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
+ assertEquals("LP98185-9", properties.get(1).getValue());
+ assertEquals("Bacteria", properties.get(1).getDisplay());
+ assertEquals(1, childCode.getParents().size());
+ assertEquals(1, childCode.getChildren().size());
+ assertEquals(code.getCode(), new ArrayList<>(childCode.getParents()).get(0).getParent().getCode());
+
+ TermConcept nestedChildCode = childCode.getChildren().get(0).getChild();
+ assertEquals("LP98185-9", nestedChildCode.getCode());
+ assertEquals("Bacteria", nestedChildCode.getDisplay());
+
+ properties = new ArrayList<>(nestedChildCode.getProperties());
+ assertEquals(2, properties.size());
+ assertEquals("parent", properties.get(0).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
+ assertEquals(childCode.getCode(), properties.get(0).getValue());
+ assertEquals(childCode.getDisplay(), properties.get(0).getDisplay());
+ assertEquals("child", properties.get(1).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
+ assertEquals("LP14082-9", properties.get(1).getValue());
+ assertEquals("Bacteria", properties.get(1).getDisplay());
+ assertEquals(1, nestedChildCode.getParents().size());
+ assertEquals(1, nestedChildCode.getChildren().size());
+ assertEquals(childCode.getCode(), new ArrayList<>(nestedChildCode.getParents()).get(0).getParent().getCode());
+
+ TermConcept doublyNestedChildCode = nestedChildCode.getChildren().get(0).getChild();
+ assertEquals("LP14082-9", doublyNestedChildCode.getCode());
+ assertEquals("Bacteria", doublyNestedChildCode.getDisplay());
+
+ properties = new ArrayList<>(doublyNestedChildCode.getProperties());
+ assertEquals(4, properties.size());
+ assertEquals("parent", properties.get(0).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(0).getCodeSystem());
+ assertEquals(nestedChildCode.getCode(), properties.get(0).getValue());
+ assertEquals(nestedChildCode.getDisplay(), properties.get(0).getDisplay());
+ assertEquals("child", properties.get(1).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(1).getCodeSystem());
+ assertEquals("LP52258-8", properties.get(1).getValue());
+ assertEquals("Bacteria | Body Fluid", properties.get(1).getDisplay());
+ assertEquals("child", properties.get(2).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(2).getCodeSystem());
+ assertEquals("LP52260-4", properties.get(2).getValue());
+ assertEquals("Bacteria | Cerebral spinal fluid", properties.get(2).getDisplay());
+ assertEquals("child", properties.get(3).getKey());
+ assertEquals(IHapiTerminologyLoaderSvc.LOINC_URI, properties.get(3).getCodeSystem());
+ assertEquals("LP52960-9", properties.get(3).getValue());
+ assertEquals("Bacteria | Cervix", properties.get(3).getDisplay());
+ assertEquals(1, doublyNestedChildCode.getParents().size());
+ assertEquals(3, doublyNestedChildCode.getChildren().size());
+ assertEquals(nestedChildCode.getCode(), new ArrayList<>(doublyNestedChildCode.getParents()).get(0).getParent().getCode());
+ assertEquals("LP52258-8", doublyNestedChildCode.getChildren().get(0).getChild().getCode());
+ assertEquals("LP52260-4", doublyNestedChildCode.getChildren().get(1).getChild().getCode());
+ assertEquals("LP52960-9", doublyNestedChildCode.getChildren().get(2).getChild().getCode());
}
@AfterClass
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
index fef85b39cc8..a5998ad8b4a 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -13,7 +14,7 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
+import org.hl7.fhir.r4.hapi.ctx.IValidationSupport.CodeValidationResult;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
@@ -562,6 +563,40 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
}
+ @Test
+ public void testDeleteValueSet() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
+ ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+
+ Long termValueSetId = myTermValueSetDao.findByResourcePid(valueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong()).get().getId();
+ assertEquals(3, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
+ assertEquals(24, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
+
+ new TransactionTemplate(myTxManager).execute(new TransactionCallbackWithoutResult() {
+ @Override
+ protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
+ myTermValueSetConceptDesignationDao.deleteByTermValueSetId(termValueSetId);
+ assertEquals(0, myTermValueSetConceptDesignationDao.countByTermValueSetId(termValueSetId).intValue());
+ myTermValueSetConceptDao.deleteByTermValueSetId(termValueSetId);
+ assertEquals(0, myTermValueSetConceptDao.countByTermValueSetId(termValueSetId).intValue());
+ myTermValueSetDao.deleteByTermValueSetId(termValueSetId);
+ assertFalse(myTermValueSetDao.findByResourcePid(valueSet.getIdElement().toUnqualifiedVersionless().getIdPartAsLong()).isPresent());
+ }
+ });
+ }
+
@Test
public void testDuplicateCodeSystemUrls() throws Exception {
loadAndPersistCodeSystem();
@@ -595,6 +630,294 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
loadAndPersistValueSet();
}
+ @Test
+ public void testExpandTermValueSetAndChildren() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
+ ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+
+ assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
+ assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
+ assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
+ assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
+ assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
+ assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
+ assertEquals(1000, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
+
+ assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getContains().size());
+
+ ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8450-9", containsComponent.getCode());
+ assertEquals("Systolic blood pressure--expiration", containsComponent.getDisplay());
+ assertEquals(2, containsComponent.getDesignation().size());
+
+ ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
+ assertEquals("nl", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systolische bloeddruk - expiratie", designationComponent.getValue());
+
+ designationComponent = containsComponent.getDesignation().get(1);
+ assertEquals("sv", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systoliskt blodtryck - utgång", designationComponent.getValue());
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(1);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("11378-7", containsComponent.getCode());
+ assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+
+ // ...
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(22);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8491-3", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
+ assertEquals(1, containsComponent.getDesignation().size());
+
+ designationComponent = containsComponent.getDesignation().get(0);
+ assertEquals("nl", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(23);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8492-1", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 8 hour minimum", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+ }
+
+ @Test
+ public void testExpandTermValueSetAndChildrenWithCount() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 23);
+ ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+
+ assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
+ assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
+ assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
+ assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
+ assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
+ assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
+ assertEquals(23, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
+
+ assertEquals(23, expandedValueSet.getExpansion().getContains().size());
+
+ ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8450-9", containsComponent.getCode());
+ assertEquals("Systolic blood pressure--expiration", containsComponent.getDisplay());
+ assertEquals(2, containsComponent.getDesignation().size());
+
+ ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
+ assertEquals("nl", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systolische bloeddruk - expiratie", designationComponent.getValue());
+
+ designationComponent = containsComponent.getDesignation().get(1);
+ assertEquals("sv", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systoliskt blodtryck - utgång", designationComponent.getValue());
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(1);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("11378-7", containsComponent.getCode());
+ assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+
+ // ...
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(22);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8491-3", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
+ assertEquals(1, containsComponent.getDesignation().size());
+
+ designationComponent = containsComponent.getDesignation().get(0);
+ assertEquals("nl", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
+ }
+
+ @Test
+ public void testExpandTermValueSetAndChildrenWithCountOfZero() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), 0);
+ ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+
+ assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
+ assertEquals(myDaoConfig.getPreExpandValueSetsDefaultOffsetExperimental(), expandedValueSet.getExpansion().getOffset());
+ assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
+ assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
+ assertEquals(0, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
+ assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
+ assertEquals(0, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
+
+ assertFalse(expandedValueSet.getExpansion().hasContains());
+ }
+
+ @Test
+ public void testExpandTermValueSetAndChildrenWithOffset() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, myDaoConfig.getPreExpandValueSetsDefaultCountExperimental());
+ ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+
+ assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
+ assertEquals(1, expandedValueSet.getExpansion().getOffset());
+ assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
+ assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
+ assertEquals(1, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
+ assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
+ assertEquals(1000, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
+
+ assertEquals(codeSystem.getConcept().size() - expandedValueSet.getExpansion().getOffset(), expandedValueSet.getExpansion().getContains().size());
+
+ ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("11378-7", containsComponent.getCode());
+ assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(1);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8493-9", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 10 hour minimum", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+
+ // ...
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(21);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8491-3", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
+ assertEquals(1, containsComponent.getDesignation().size());
+
+ ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
+ assertEquals("nl", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(22);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8492-1", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 8 hour minimum", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+ }
+
+ @Test
+ public void testExpandTermValueSetAndChildrenWithOffsetAndCount() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValueSet expandedValueSet = myTermSvc.expandValueSet(valueSet, 1, 22);
+ ourLog.info("Expanded ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expandedValueSet));
+
+ assertEquals(codeSystem.getConcept().size(), expandedValueSet.getExpansion().getTotal());
+ assertEquals(1, expandedValueSet.getExpansion().getOffset());
+ assertEquals(2, expandedValueSet.getExpansion().getParameter().size());
+ assertEquals("offset", expandedValueSet.getExpansion().getParameter().get(0).getName());
+ assertEquals(1, expandedValueSet.getExpansion().getParameter().get(0).getValueIntegerType().getValue().intValue());
+ assertEquals("count", expandedValueSet.getExpansion().getParameter().get(1).getName());
+ assertEquals(22, expandedValueSet.getExpansion().getParameter().get(1).getValueIntegerType().getValue().intValue());
+
+ assertEquals(22, expandedValueSet.getExpansion().getContains().size());
+
+ ValueSet.ValueSetExpansionContainsComponent containsComponent = expandedValueSet.getExpansion().getContains().get(0);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("11378-7", containsComponent.getCode());
+ assertEquals("Systolic blood pressure at First encounter", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(1);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8493-9", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 10 hour minimum", containsComponent.getDisplay());
+ assertFalse(containsComponent.hasDesignation());
+
+ // ...
+
+ containsComponent = expandedValueSet.getExpansion().getContains().get(21);
+ assertEquals("http://acme.org", containsComponent.getSystem());
+ assertEquals("8491-3", containsComponent.getCode());
+ assertEquals("Systolic blood pressure 1 hour minimum", containsComponent.getDisplay());
+ assertEquals(1, containsComponent.getDesignation().size());
+
+ ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.getDesignation().get(0);
+ assertEquals("nl", designationComponent.getLanguage());
+ assertEquals("http://snomed.info/sct", designationComponent.getUse().getSystem());
+ assertEquals("900000000000013009", designationComponent.getUse().getCode());
+ assertEquals("Synonym", designationComponent.getUse().getDisplay());
+ assertEquals("Systolische bloeddruk minimaal 1 uur", designationComponent.getValue());
+ }
+
@Test
public void testExpandValueSetWithValueSetCodeAccumulator() {
createCodeSystem();
@@ -607,17 +930,6 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
verify(myValueSetCodeAccumulator, times(9)).includeConceptWithDesignations(anyString(), anyString(), nullable(String.class), anyCollection());
}
- @Test
- public void testValidateCode() {
- createCodeSystem();
-
- IValidationSupport.CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
- assertEquals(true, validation.isOk());
-
- validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
- assertEquals(false, validation.isOk());
- }
-
@Test
public void testStoreTermCodeSystemAndChildren() throws Exception {
loadAndPersistCodeSystemWithDesignations();
@@ -985,7 +1297,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(0, termValueSet.getConcepts().size());
- assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
+ assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
});
myTermSvc.preExpandValueSetToTerminologyTables();
@@ -1003,7 +1315,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(codeSystem.getConcept().size(), termValueSet.getConcepts().size());
- assertEquals(TermValueSetExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
+ assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
ourLog.info("Code:\n" + concept.toString());
@@ -1083,7 +1395,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(0, termValueSet.getConcepts().size());
- assertEquals(TermValueSetExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
+ assertEquals(TermValueSetPreExpansionStatusEnum.NOT_EXPANDED, termValueSet.getExpansionStatus());
});
myTermSvc.preExpandValueSetToTerminologyTables();
@@ -1101,7 +1413,7 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
assertEquals("http://www.healthintersections.com.au/fhir/ValueSet/extensional-case-2", termValueSet.getUrl());
assertEquals("Terminology Services Connectation #1 Extensional case #2", termValueSet.getName());
assertEquals(codeSystem.getConcept().size() - 2, termValueSet.getConcepts().size());
- assertEquals(TermValueSetExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
+ assertEquals(TermValueSetPreExpansionStatusEnum.EXPANDED, termValueSet.getExpansionStatus());
TermValueSetConcept concept = termValueSet.getConcepts().get(0);
ourLog.info("Code:\n" + concept.toString());
@@ -2291,6 +2603,67 @@ public class TerminologySvcImplR4Test extends BaseJpaR4Test {
});
}
+ @Test
+ public void testValidateCode() {
+ createCodeSystem();
+
+ CodeValidationResult validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ParentWithNoChildrenA", null);
+ assertEquals(true, validation.isOk());
+
+ validation = myTermSvc.validateCode(myFhirCtx, CS_URL, "ZZZZZZZ", null);
+ assertEquals(false, validation.isOk());
+ }
+
+ @Test
+ public void testValidateCodeIsInPreExpandedValueSet() throws Exception {
+ myDaoConfig.setPreExpandValueSetsExperimental(true);
+
+ loadAndPersistCodeSystemAndValueSetWithDesignations();
+
+ CodeSystem codeSystem = myCodeSystemDao.read(myExtensionalCsId);
+ ourLog.info("CodeSystem:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem));
+
+ ValueSet valueSet = myValueSetDao.read(myExtensionalVsId);
+ ourLog.info("ValueSet:\n" + myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(valueSet));
+
+ myTermSvc.preExpandValueSetToTerminologyTables();
+
+ ValidateCodeResult result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, null, null, null, null);
+ assertNull(result);
+
+ result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, "BOGUS", null, null, null);
+ assertNull(result);
+
+ result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, "11378-7", null, null, null);
+ assertTrue(result.isResult());
+ assertEquals("Validation succeeded", result.getMessage());
+ assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
+
+ result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, "11378-7", "Systolic blood pressure at First encounter", null, null);
+ assertTrue(result.isResult());
+ assertEquals("Validation succeeded", result.getMessage());
+ assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
+
+ result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, "http://acme.org", "11378-7", null, null, null);
+ assertTrue(result.isResult());
+ assertEquals("Validation succeeded", result.getMessage());
+ assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
+
+ Coding coding = new Coding("http://acme.org", "11378-7", "Systolic blood pressure at First encounter");
+ result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, null, null, coding, null);
+ assertTrue(result.isResult());
+ assertEquals("Validation succeeded", result.getMessage());
+ assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
+
+ CodeableConcept codeableConcept = new CodeableConcept();
+ codeableConcept.addCoding(new Coding("BOGUS", "BOGUS", "BOGUS"));
+ codeableConcept.addCoding(coding);
+ result = myTermSvc.validateCodeIsInPreExpandedValueSet(valueSet, null, null, null, null, codeableConcept);
+ assertTrue(result.isResult());
+ assertEquals("Validation succeeded", result.getMessage());
+ assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
+ }
+
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc/loincupload.properties b/hapi-fhir-jpaserver-base/src/test/resources/loinc/loincupload.properties
index 7a7aab2ab36..8ecefb96c4e 100644
--- a/hapi-fhir-jpaserver-base/src/test/resources/loinc/loincupload.properties
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc/loincupload.properties
@@ -1,7 +1,95 @@
+#################
+### MANDATORY ###
+#################
-# This is the version identifier for the AnswerList file
-answerlist.version=Beta.1
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## Default value if key not provided: AnswerList.csv
+## File must be present
+loinc.answerlist.file=AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## Default value if key not provided: LoincAnswerListLink.csv
+## File must be present
+loinc.answerlist.link.file=LoincAnswerListLink.csv
+
+# Document ontology
+## Default value if key not provided: DocumentOntology.csv
+## File must be present
+loinc.document.ontology.file=DocumentOntology.csv
+
+# LOINC codes
+## Default value if key not provided: LoincTable/Loinc.csv
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## Default value if key not provided: MultiAxialHierarchy.csv
+## File must be present
+loinc.hierarchy.file=MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## Default value if key not provided: LoincIeeeMedicalDeviceCodeMappingTable.csv
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## Default value if key not provided: ImagingDocumentCodes.csv
+## File must be present
+loinc.imaging.document.codes.file=ImagingDocumentCodes.csv
+
+# Part
+## Default value if key not provided: Part.csv
+## File must be present
+loinc.part.file=Part.csv
+# Part link
+## Default value if key not provided: LoincPartLink.csv
+## File must be present
+loinc.part.link.file=LoincPartLink.csv
+# Part related code mapping
+## Default value if key not provided: PartRelatedCodeMapping.csv
+## File must be present
+loinc.part.related.code.mapping.file=PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## Default value if key not provided: LoincRsnaRadiologyPlaybook.csv
+## File must be present
+loinc.rsna.playbook.file=LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## Default value if key not provided: Top2000CommonLabResultsSi.csv
+## File must be present
+loinc.top2000.common.lab.results.si.file=Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## Default value if key not provided: Top2000CommonLabResultsUs.csv
+## File must be present
+loinc.top2000.common.lab.results.us.file=Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## Default value if key not provided: LoincUniversalLabOrdersValueSet.csv
+## File must be present
+loinc.universal.lab.order.valueset.file=LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
# This is the version identifier for uploaded ConceptMap resources
-conceptmap.version=Beta.1
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+# Group
+## Default value if key not provided: Group.csv
+## File may be omitted
+loinc.group.file=Group.csv
+# Group terms
+## Default value if key not provided: GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=GroupLoincTerms.csv
+
+# Parent group
+## Default value if key not provided: ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=ParentGroup.csv
diff --git a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
index cec3133a85a..d95169ad6b5 100644
--- a/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
+++ b/hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
@@ -79,6 +79,14 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks {
resVerProv.addIndex("IDX_RESVERPROV_SOURCEURI").unique(false).withColumns("SOURCE_URI");
resVerProv.addIndex("IDX_RESVERPROV_REQUESTID").unique(false).withColumns("REQUEST_ID");
+ // TermValueSetConceptDesignation
+ version.startSectionWithMessage("Processing table: TRM_VALUESET_C_DESIGNATION");
+ Builder.BuilderWithTableName termValueSetConceptDesignationTable = version.onTable("TRM_VALUESET_C_DESIGNATION");
+ termValueSetConceptDesignationTable.addColumn("VALUESET_PID").nonNullable().type(BaseTableColumnTypeTask.ColumnTypeEnum.LONG);
+ termValueSetConceptDesignationTable
+ .addForeignKey("FK_TRM_VSCD_VS_PID")
+ .toColumn("VALUESET_PID")
+ .references("TRM_VALUESET", "PID");
// Drop HFJ_SEARCH_RESULT foreign keys
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_RES");
version.onTable("HFJ_SEARCH_RESULT").dropForeignKey("FK_SEARCHRES_SEARCH");
diff --git a/hapi-fhir-structures-dstu2/pom.xml b/hapi-fhir-structures-dstu2/pom.xml
index 0604b84fd02..b16cd0536cd 100644
--- a/hapi-fhir-structures-dstu2/pom.xml
+++ b/hapi-fhir-structures-dstu2/pom.xml
@@ -216,6 +216,11 @@
${project.version}
test
+