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Merge branch 'master' into ja_20200206_multitenancy

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This commit is contained in:
James Agnew 2020-03-03 09:25:19 -05:00
commit 4a160a2df3
182 changed files with 2318 additions and 712 deletions
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2
examples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

12
examples/src/main/java/example/ConverterExamples.java
View File

@ -1,7 +1,7 @@
package example;
import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.conv10_30.Observation10_30;
import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
import org.hl7.fhir.exceptions.FHIRException;
public class ConverterExamples {
@ -9,16 +9,12 @@ public class ConverterExamples {
@SuppressWarnings("unused")
public void c1020() throws FHIRException {
//START SNIPPET: 1020
// Create a converter
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
// Create an input resource to convert
org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
// Convert the resource
org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = Observation10_30.convertObservation(input);
String context = output.getContext().getReference();
//END SNIPPET: 1020
}
@ -31,7 +27,7 @@ public class ConverterExamples {
input.setTitle("My title");
// Convert the resource
org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
String context = output.getTitle();
//END SNIPPET: 1420
}

2
hapi-deployable-pom/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

23
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeElementDefinition.java
View File

@ -22,8 +22,11 @@ package ca.uhn.fhir.context;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import java.lang.reflect.Constructor;
import java.util.*;
@ -33,11 +36,11 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
private final Class<? extends T> myImplementingClass;
private final String myName;
private final boolean myStandardType;
private Map<Class<?>, Constructor<T>> myConstructors = Collections.synchronizedMap(new HashMap<Class<?>, Constructor<T>>());
private List<RuntimeChildDeclaredExtensionDefinition> myExtensions = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsModifier = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsNonModifier = new ArrayList<RuntimeChildDeclaredExtensionDefinition>();
private Map<String, RuntimeChildDeclaredExtensionDefinition> myUrlToExtension = new HashMap<String, RuntimeChildDeclaredExtensionDefinition>();
private Map<Class<?>, Constructor<T>> myConstructors = Collections.synchronizedMap(new HashMap<>());
private List<RuntimeChildDeclaredExtensionDefinition> myExtensions = new ArrayList<>();
private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsModifier = new ArrayList<>();
private List<RuntimeChildDeclaredExtensionDefinition> myExtensionsNonModifier = new ArrayList<>();
private Map<String, RuntimeChildDeclaredExtensionDefinition> myUrlToExtension = new HashMap<>();
private BaseRuntimeElementDefinition<?> myRootParentDefinition;
public BaseRuntimeElementDefinition(String theName, Class<? extends T> theImplementingClass, boolean theStandardType) {
@ -56,19 +59,17 @@ public abstract class BaseRuntimeElementDefinition<T extends IBase> {
myImplementingClass = theImplementingClass;
}
public void addExtension(RuntimeChildDeclaredExtensionDefinition theExtension) {
if (theExtension == null) {
throw new NullPointerException();
}
public void addExtension(@Nonnull RuntimeChildDeclaredExtensionDefinition theExtension) {
Validate.notNull(theExtension, "theExtension must not be null");
myExtensions.add(theExtension);
}
public abstract ChildTypeEnum getChildType();
@SuppressWarnings("unchecked")
private Constructor<T> getConstructor(Object theArgument) {
private Constructor<T> getConstructor(@Nullable Object theArgument) {
Class<? extends Object> argumentType;
Class<?> argumentType;
if (theArgument == null) {
argumentType = VOID_CLASS;
} else {

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/FhirContext.java
View File

@ -377,9 +377,8 @@ public class FhirContext {
*/
public RuntimeResourceDefinition getResourceDefinition(final Class<? extends IBaseResource> theResourceType) {
validateInitialized();
if (theResourceType == null) {
throw new NullPointerException("theResourceType can not be null");
}
Validate.notNull(theResourceType, "theResourceType can not be null");
if (Modifier.isAbstract(theResourceType.getModifiers())) {
throw new IllegalArgumentException("Can not scan abstract or interface class (resource definitions must be concrete classes): " + theResourceType.getName());
}

21
hapi-fhir-base/src/test/java/ca/uhn/fhir/rest/param/QualifierDetailsTest.java Normal file
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@ -0,0 +1,21 @@
package ca.uhn.fhir.rest.param;
import com.google.common.collect.Sets;
import org.junit.Test;
import static org.junit.Assert.*;
public class QualifierDetailsTest {
@Test
public void testBlacklist() {
QualifierDetails details = new QualifierDetails();
details.setColonQualifier(":Patient");
assertFalse(details.passes(null, Sets.newHashSet(":Patient")));
assertTrue(details.passes(null, Sets.newHashSet(":Observation")));
}
}

4
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ExportConceptMapToCsvCommand.java
View File

@ -26,7 +26,6 @@ import org.apache.commons.cli.Options;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVPrinter;
import org.apache.commons.csv.QuoteMode;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.ConceptMap;
@ -43,6 +42,7 @@ import java.util.List;
import java.util.concurrent.ExecutionException;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConceptMapCommand {
// TODO: Don't use qualified names for loggers in HAPI CLI.
@ -114,7 +114,7 @@ public class ExportConceptMapToCsvCommand extends AbstractImportExportCsvConcept
private void convertConceptMapToCsv(org.hl7.fhir.dstu3.model.ConceptMap theConceptMap) throws ExecutionException {
try {
convertConceptMapToCsv(VersionConvertor_30_40.convertConceptMap(theConceptMap));
convertConceptMapToCsv(convertConceptMap(theConceptMap));
} catch (FHIRException fe) {
throw new ExecutionException(fe);
}

10
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ImportCsvToConceptMapCommand.java
View File

@ -28,7 +28,6 @@ import org.apache.commons.cli.Options;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ConceptMap.ConceptMapGroupComponent;
@ -45,7 +44,10 @@ import java.util.Map;
import java.util.Set;
import java.util.concurrent.ExecutionException;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConceptMapCommand {
// TODO: Don't use qualified names for loggers in HAPI CLI.
@ -154,7 +156,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
private org.hl7.fhir.dstu3.model.ConceptMap convertCsvToConceptMapDstu3() throws ExecutionException {
try {
return VersionConvertor_30_40.convertConceptMap(convertCsvToConceptMapR4());
return convertConceptMap(convertCsvToConceptMapR4());
} catch (FHIRException fe) {
throw new ExecutionException(fe);
}
@ -174,7 +176,7 @@ public class ImportCsvToConceptMapCommand extends AbstractImportExportCsvConcept
.withFirstRecordAsHeader()
.withIgnoreHeaderCase()
.withIgnoreEmptyLines()
.withTrim());
.withTrim())
) {
retVal.setUrl(conceptMapUrl);

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

34
hapi-fhir-converter/src/main/java/ca/uhn/hapi/converters/server/VersionedApiConverterInterceptor.java
View File

@ -31,7 +31,11 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.interceptor.InterceptorAdapter;
import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
import org.hl7.fhir.converter.NullVersionConverterAdvisor40;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.VersionConvertorAdvisor30;
import org.hl7.fhir.convertors.VersionConvertorAdvisor40;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_10_40;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -40,7 +44,9 @@ import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.util.StringTokenizer;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* <b>This is an experimental interceptor! Use with caution as
@ -54,16 +60,12 @@ import static org.apache.commons.lang3.StringUtils.*;
public class VersionedApiConverterInterceptor extends InterceptorAdapter {
private final FhirContext myCtxDstu2;
private final FhirContext myCtxDstu2Hl7Org;
private VersionConvertor_30_40 myVersionConvertor_30_40;
private VersionConvertor_10_40 myVersionConvertor_10_40;
private VersionConvertor_10_30 myVersionConvertor_10_30;
private final NullVersionConverterAdvisor40 advisor40;
private final NullVersionConverterAdvisor30 advisor30;
public VersionedApiConverterInterceptor() {
myVersionConvertor_30_40 = new VersionConvertor_30_40();
VersionConvertorAdvisor40 advisor40 = new NullVersionConverterAdvisor40();
myVersionConvertor_10_40 = new VersionConvertor_10_40(advisor40);
VersionConvertorAdvisor30 advisor30 = new NullVersionConverterAdvisor30();
myVersionConvertor_10_30 = new VersionConvertor_10_30(advisor30);
advisor40 = new NullVersionConverterAdvisor40();
advisor30 = new NullVersionConverterAdvisor30();
myCtxDstu2 = FhirContext.forDstu2();
myCtxDstu2Hl7Org = FhirContext.forDstu2Hl7Org();
@ -104,17 +106,17 @@ public class VersionedApiConverterInterceptor extends InterceptorAdapter {
IBaseResource converted = null;
try {
if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU3) {
converted = myVersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
converted = VersionConvertor_30_40.convertResource(toDstu3(responseResource), true);
} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.R4) {
converted = myVersionConvertor_30_40.convertResource(toR4(responseResource), true);
converted = VersionConvertor_30_40.convertResource(toR4(responseResource), true);
} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.R4) {
converted = myVersionConvertor_10_40.convertResource(toR4(responseResource));
converted = VersionConvertor_10_40.convertResource(toR4(responseResource), advisor40);
} else if (wantVersion == FhirVersionEnum.R4 && haveVersion == FhirVersionEnum.DSTU2) {
converted = myVersionConvertor_10_40.convertResource(toDstu2(responseResource));
converted = VersionConvertor_10_40.convertResource(toDstu2(responseResource), advisor40);
} else if (wantVersion == FhirVersionEnum.DSTU2 && haveVersion == FhirVersionEnum.DSTU3) {
converted = myVersionConvertor_10_30.convertResource(toDstu3(responseResource));
converted = VersionConvertor_10_30.convertResource(toDstu3(responseResource), advisor30);
} else if (wantVersion == FhirVersionEnum.DSTU3 && haveVersion == FhirVersionEnum.DSTU2) {
converted = myVersionConvertor_10_30.convertResource(toDstu2(responseResource));
converted = VersionConvertor_10_30.convertResource(toDstu2(responseResource), advisor30);
}
} catch (FHIRException e) {
throw new InternalErrorException(e);

8
hapi-fhir-converter/src/main/java/org/hl7/fhir/converter/NullVersionConverterAdvisor50.java
View File

@ -27,8 +27,12 @@ import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ValueSet;
import java.util.IdentityHashMap;
public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50 {
private IdentityHashMap<ValueSet, CodeSystem> myCodeSystems = new IdentityHashMap<>();
@Override
public boolean ignoreEntry(Bundle.BundleEntryComponent src) {
return false;
@ -56,11 +60,11 @@ public class NullVersionConverterAdvisor50 implements VersionConvertorAdvisor50
@Override
public void handleCodeSystem(CodeSystem tgtcs, ValueSet source) throws FHIRException {
myCodeSystems.put(source, tgtcs);
}
@Override
public CodeSystem getCodeSystem(ValueSet src) throws FHIRException {
return null;
return myCodeSystems.get(src);
}
}

10
hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_10_30Test.java
View File

@ -16,13 +16,10 @@ public class VersionConvertor_10_30Test {
@Test
public void testConvert() throws FHIRException {
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = (Observation) VersionConvertor_10_30.convertResource(input);
String context = output.getContext().getReference();
assertEquals("Encounter/123", context);
@ -31,9 +28,6 @@ public class VersionConvertor_10_30Test {
@Test
public void testConvertSpecimen() throws FHIRException {
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
Specimen spec = new Specimen();
CodeableConcept cc = new CodeableConcept();
Coding coding = new Coding();
@ -58,7 +52,7 @@ public class VersionConvertor_10_30Test {
Specimen.SpecimenContainerComponent specimenContainerComponent = new Specimen.SpecimenContainerComponent();
specimenContainerComponent.getExtension().add(new Extension().setUrl("some_url").setValue(new StringType("some_value")));
spec.setContainer(Collections.singletonList(specimenContainerComponent));
Resource resource = converter.convertResource(spec);
Resource resource = VersionConvertor_10_30.convertResource(spec);
}

3
hapi-fhir-converter/src/test/java/org/hl7/fhir/converter/VersionConvertor_14_30Test.java
View File

@ -3,6 +3,7 @@ package org.hl7.fhir.converter;
import static org.junit.Assert.assertEquals;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.exceptions.FHIRException;
import org.junit.Test;
@ -14,7 +15,7 @@ public class VersionConvertor_14_30Test {
org.hl7.fhir.dstu2016may.model.Questionnaire input = new org.hl7.fhir.dstu2016may.model.Questionnaire();
input.setTitle("My title");
org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = (Questionnaire) VersionConvertor_14_30.convertResource(input);
String context = output.getTitle();
assertEquals("My title", context);

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

8
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -73,13 +73,13 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
@ -96,7 +96,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<classifier>classes</classifier>
</dependency>
<dependency>

13
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ConverterExamples.java
View File

@ -20,9 +20,8 @@ package ca.uhn.hapi.fhir.docs;
* #L%
*/
import org.hl7.fhir.converter.NullVersionConverterAdvisor30;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.convertors.conv10_30.Observation10_30;
import org.hl7.fhir.convertors.conv14_30.Questionnaire14_30;
import org.hl7.fhir.exceptions.FHIRException;
public class ConverterExamples {
@ -30,16 +29,12 @@ public class ConverterExamples {
@SuppressWarnings("unused")
public void c1020() throws FHIRException {
//START SNIPPET: 1020
// Create a converter
NullVersionConverterAdvisor30 advisor = new NullVersionConverterAdvisor30();
VersionConvertor_10_30 converter = new VersionConvertor_10_30(advisor);
// Create an input resource to convert
org.hl7.fhir.dstu2.model.Observation input = new org.hl7.fhir.dstu2.model.Observation();
input.setEncounter(new org.hl7.fhir.dstu2.model.Reference("Encounter/123"));
// Convert the resource
org.hl7.fhir.dstu3.model.Observation output = converter.convertObservation(input);
org.hl7.fhir.dstu3.model.Observation output = Observation10_30.convertObservation(input);
String context = output.getContext().getReference();
//END SNIPPET: 1020
}
@ -52,7 +47,7 @@ public class ConverterExamples {
input.setTitle("My title");
// Convert the resource
org.hl7.fhir.dstu3.model.Questionnaire output = VersionConvertor_14_30.convertQuestionnaire(input);
org.hl7.fhir.dstu3.model.Questionnaire output = Questionnaire14_30.convertQuestionnaire(input);
String context = output.getTitle();
//END SNIPPET: 1420
}

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_2_0/version.yaml
View File

@ -1,2 +1,3 @@
---
release-date: "TBD"
release-date: "2020-02-15"
codename: "Koala"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1693-forcedid-circular-dependency.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: change
issue: 1693
title: Adjusted schema definitions for Resource and Resource History tables to eliminate circular
dependencies with Forced ID table and to improve performance when expunging large numbers of resources.

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1702-includes-perf-fix.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: perf
issue: 1702
title: "Loading of _include and _revinclude values has been optimized to be slightly faster"

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1715-update-converters.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: change
issue: 1715
title: The version converters for all versions except R4/R5 have been reworked to be split into individual
classes per resource type (the R4/R5 converters were already organized this way). Thanks to Mark Iantorno
for a huge effort to write a Java source parser/serializer to acomplish this task.

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1717-avoid-multiterm-in-es.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1717
title: ValueSet expansions containing lists of terms did not correctly expand when backed by
ElasticSearch due to the use of a feature not supported in ES. Thanks to Jens Villadsen for
reporting!

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1721-dont-thrash-delta-links.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1721
title: When performing a terminology delta ADD operation, existing parent-child links were often
deleted and recrreated needlessly during operations, which could result in a deadlock. This has
been resolved.

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1726-collapse-date-joins.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: perf
issue: 1726
title: When performing date range searches in the JPA server, the server was generating extra
unneccessary joins in the generated SQL. This has been streamlined, which should result in
faster searches when performing date ranges.

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1728-index-canonical.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 1728
title: "Fields of type `canonical` were not previously indexed by the JPA server, meaning that some
default search parameters could not be honoured (e.g. StructureDefinition:valueset). This is now corrected."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1732-remove-deleted-from-results.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1732
title: In the JPA server, quickly deleting a resource and then performing a query that had recently returned that
search result could cause a cached stub resource (containing no data but with an ID and metadata populated) to
be returned. This has been corrected.

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1736-defer-large-terminology-delta-adds.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: add
issue: 1736
title: When performing large terminology concept additions via the delta addition service, concepts will
now be added via the deferred storage service, meaning that they will be added in small incremental batches
instead of as a part of one large transaction. This helps to avoid timeouts and memory issues when uploading
large collections of concepts.

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-error-on-missing-profile-validation.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1742
title: "When validating a resource, the validator will now report an error if the resource declares conformance
to an unknown or invalid profile URL via the `Resource.meta.profile` declaration. Previously this was a warning
and did not block successful validation."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-limit-type-on-has.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 1742
title: "When performing a search in the JPA server where the only parameter was a `_has` parameter,
the server did not respect the resource typename being searched for, causing false positive
search results. This has been corrected."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_3_0/1742-terminology-delta-defer.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: add
issue: 1742
title: When performing a terminology delta ADD operation, if the number of codes being added is large
the codes will be added in small batches via an asynchronous scheduled task in order to avoid overwhelming
the database with a large operation.

2
hapi-fhir-igpacks/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<artifactId>hapi-deployable-pom</artifactId>
<groupId>ca.uhn.hapi.fhir</groupId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-example/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

7
hapi-fhir-jpaserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>4.2.0-SNAPSHOT</version>
<version>4.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -48,6 +48,11 @@
<artifactId>commons-csv</artifactId>
</dependency>
<dependency>
<groupId>co.elastic.apm</groupId>
<artifactId>apm-agent-api</artifactId>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.jpa.subscription.dbmatcher.CompositeInMemoryDaoSubscriptionMa
import ca.uhn.fhir.jpa.subscription.dbmatcher.DaoSubscriptionMatcher;
import ca.uhn.fhir.jpa.subscription.module.cache.LinkedBlockingQueueSubscribableChannelFactory;
import ca.uhn.fhir.jpa.subscription.module.channel.ISubscribableChannelFactory;
import ca.uhn.fhir.jpa.subscription.module.channel.SubscriptionChannelFactory;
import ca.uhn.fhir.jpa.subscription.module.matcher.ISubscriptionMatcher;
import ca.uhn.fhir.jpa.subscription.module.matcher.InMemorySubscriptionMatcher;
import ca.uhn.fhir.rest.server.interceptor.consent.IConsentContextServices;
@ -204,10 +205,15 @@ public abstract class BaseConfig {
* Create a @Primary @Bean if you need a different implementation
*/
@Bean
public ISubscribableChannelFactory linkedBlockingQueueSubscribableChannelFactory() {
public ISubscribableChannelFactory subscribableChannelFactory() {
return new LinkedBlockingQueueSubscribableChannelFactory();
}
@Bean
public SubscriptionChannelFactory subscriptionChannelFactory() {
return new SubscriptionChannelFactory();
}
@Bean
@Primary
public ISubscriptionMatcher subscriptionMatcherCompositeInMemoryDatabase() {
@ -280,6 +286,4 @@ public abstract class BaseConfig {
private static HapiFhirHibernateJpaDialect hibernateJpaDialect(HapiLocalizer theLocalizer) {
return new HapiFhirHibernateJpaDialect(theLocalizer);
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -153,8 +153,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
@Autowired
protected ISearchCoordinatorSvc mySearchCoordinatorSvc;
@Autowired
protected ISearchParamRegistry mySerarchParamRegistry;
@Autowired
protected ITermReadSvc myTerminologySvc;
@Autowired
protected IResourceHistoryTableDao myResourceHistoryTableDao;
@ -162,8 +160,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
protected IResourceTableDao myResourceTableDao;
@Autowired
protected IResourceTagDao myResourceTagDao;
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
@Autowired
protected DeleteConflictService myDeleteConflictService;
@Autowired
@ -1550,4 +1547,5 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
"Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
}
}
}

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.delete.DeleteConflictList;
@ -39,16 +38,12 @@ import ca.uhn.fhir.jpa.util.ExpungeOutcome;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.*;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.QualifierDetails;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor.ActionRequestDetails;
import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.OperationOutcomeUtil;
@ -1164,38 +1159,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal;
}
@Transactional(propagation = Propagation.SUPPORTS)
@Override
public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
if (theSource == null || theSource.isEmpty()) {
return;
}
Map<String, RuntimeSearchParam> searchParams = mySerarchParamRegistry.getActiveSearchParams(getResourceName());
Set<String> paramNames = theSource.keySet();
for (String nextParamName : paramNames) {
QualifierDetails qualifiedParamName = SearchMethodBinding.extractQualifiersFromParameterName(nextParamName);
RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
if (param == null) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<>(searchParams.keySet()));
throw new InvalidRequestException(msg);
}
// Should not be null since the check above would have caught it
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(myResourceName);
RuntimeSearchParam paramDef = mySearchParamRegistry.getSearchParamByName(resourceDef, qualifiedParamName.getParamName());
for (String nextValue : theSource.get(nextParamName)) {
QualifiedParamList qualifiedParam = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifiedParamName.getWholeQualifier(), nextValue);
List<QualifiedParamList> paramList = Collections.singletonList(qualifiedParam);
IQueryParameterAnd<?> parsedParam = ParameterUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
theTarget.add(qualifiedParamName.getParamName(), parsedParam);
}
}
}
@Override
public DaoMethodOutcome update(T theResource) {
return update(theResource, null, null);

55
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseStorageDao.java
View File

@ -21,19 +21,24 @@ package ca.uhn.fhir.jpa.dao;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.IPreResourceShowDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.server.*;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.param.QualifierDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.method.SearchMethodBinding;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.FhirTerser;
@ -44,12 +49,14 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.InstantType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.validation.constraints.NotNull;
import java.util.List;
import java.util.Set;
import java.util.*;
import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_ERROR;
import static ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.OO_SEVERITY_INFO;
@ -57,6 +64,8 @@ import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseStorageDao {
@Autowired
protected ISearchParamRegistry mySearchParamRegistry;
/**
* May be overridden by subclasses to validate resources prior to storage
@ -206,4 +215,36 @@ public abstract class BaseStorageDao {
*/
protected abstract FhirContext getContext();
@Transactional(propagation = Propagation.SUPPORTS)
public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
if (theSource == null || theSource.isEmpty()) {
return;
}
Map<String, RuntimeSearchParam> searchParams = mySearchParamRegistry.getActiveSearchParams(getResourceName());
Set<String> paramNames = theSource.keySet();
for (String nextParamName : paramNames) {
QualifierDetails qualifiedParamName = SearchMethodBinding.extractQualifiersFromParameterName(nextParamName);
RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
if (param == null) {
String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<>(searchParams.keySet()));
throw new InvalidRequestException(msg);
}
// Should not be null since the check above would have caught it
RuntimeResourceDefinition resourceDef = getContext().getResourceDefinition(getResourceName());
RuntimeSearchParam paramDef = mySearchParamRegistry.getSearchParamByName(resourceDef, qualifiedParamName.getParamName());
for (String nextValue : theSource.get(nextParamName)) {
QualifiedParamList qualifiedParam = QualifiedParamList.splitQueryStringByCommasIgnoreEscape(qualifiedParamName.getWholeQualifier(), nextValue);
List<QualifiedParamList> paramList = Collections.singletonList(qualifiedParam);
IQueryParameterAnd<?> parsedParam = ParameterUtil.parseQueryParams(getContext(), paramDef, nextParamName, paramList);
theTarget.add(qualifiedParamName.getParamName(), parsedParam);
}
}
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/DaoConfig.java
View File

@ -102,7 +102,7 @@ public class DaoConfig {
/**
* update setter javadoc if default changes
*/
private int myDeferIndexingForCodesystemsOfSize = 2000;
private int myDeferIndexingForCodesystemsOfSize = 100;
private boolean myDeleteStaleSearches = true;
private boolean myEnforceReferentialIntegrityOnDelete = true;
private boolean myUniqueIndexesEnabled = true;
@ -397,7 +397,7 @@ public class DaoConfig {
* the code system will be indexed later in an incremental process in order to
* avoid overwhelming Lucene with a huge number of codes in a single operation.
* <p>
* Defaults to 2000
* Defaults to 100
* </p>
*/
public int getDeferIndexingForCodesystemsOfSize() {
@ -409,7 +409,7 @@ public class DaoConfig {
* the code system will be indexed later in an incremental process in order to
* avoid overwhelming Lucene with a huge number of codes in a single operation.
* <p>
* Defaults to 2000
* Defaults to 100
* </p>
*/
public void setDeferIndexingForCodesystemsOfSize(int theDeferIndexingForCodesystemsOfSize) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IResultIterator.java
View File

@ -29,4 +29,6 @@ public interface IResultIterator extends Iterator<ResourcePersistentId>, Closeab
int getSkippedCount();
int getNonSkippedCount();
}

145
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/SearchBuilder.java
View File

@ -29,17 +29,29 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchViewDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTagDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.predicate.*;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilder;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderFactory;
import ca.uhn.fhir.jpa.dao.predicate.QueryRoot;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinEnum;
import ca.uhn.fhir.jpa.dao.predicate.SearchBuilderJoinKey;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedCompositeStringUnique;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.jpa.util.*;
import ca.uhn.fhir.jpa.util.BaseIterator;
import ca.uhn.fhir.jpa.util.CurrentThreadCaptureQueriesListener;
import ca.uhn.fhir.jpa.util.JpaInterceptorBroadcaster;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.jpa.util.SqlQueryList;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.Include;
@ -80,10 +92,27 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.*;
import java.util.*;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.From;
import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import javax.persistence.criteria.Order;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.*;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* The SearchBuilder is responsible for actually forming the SQL query that handles
@ -103,8 +132,9 @@ public class SearchBuilder implements ISearchBuilder {
private static final List<ResourcePersistentId> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
private static ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
@Autowired
private DaoConfig myDaoConfig;
private final QueryRoot myQueryRoot = new QueryRoot();
private final String myResourceName;
private final Class<? extends IBaseResource> myResourceType;
@Autowired
protected IInterceptorBroadcaster myInterceptorBroadcaster;
@Autowired
@ -112,6 +142,8 @@ public class SearchBuilder implements ISearchBuilder {
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
private DaoConfig myDaoConfig;
@Autowired
private IResourceSearchViewDao myResourceSearchViewDao;
@Autowired
private FhirContext myContext;
@ -123,7 +155,6 @@ public class SearchBuilder implements ISearchBuilder {
private ISearchParamRegistry mySearchParamRegistry;
@Autowired
private PredicateBuilderFactory myPredicateBuilderFactory;
private List<ResourcePersistentId> myAlsoIncludePids;
private CriteriaBuilder myBuilder;
private IDao myCallingDao;
@ -133,9 +164,6 @@ public class SearchBuilder implements ISearchBuilder {
private Integer myMaxResultsToFetch;
private Set<ResourcePersistentId> myPidSet;
private PredicateBuilder myPredicateBuilder;
private final QueryRoot myQueryRoot = new QueryRoot();
private final String myResourceName;
private final Class<? extends IBaseResource> myResourceType;
/**
* Constructor
@ -254,7 +282,8 @@ public class SearchBuilder implements ISearchBuilder {
outerQuery.multiselect(myBuilder.countDistinct(myQueryRoot.getRoot()));
} else {
outerQuery.multiselect(myQueryRoot.get("myId").as(Long.class));
outerQuery.distinct(true);
// KHS This distinct call is causing performance issues in large installations
// outerQuery.distinct(true);
}
}
@ -475,6 +504,9 @@ public class SearchBuilder implements ISearchBuilder {
ResourcePersistentId resourceId;
for (ResourceSearchView next : resourceSearchViewList) {
if (next.getDeleted() != null) {
continue;
}
Class<? extends IBaseResource> resourceType = myContext.getResourceDefinition(next.getResourceType()).getImplementingClass();
@ -594,6 +626,7 @@ public class SearchBuilder implements ISearchBuilder {
return new HashSet<>();
}
String searchFieldName = theReverseMode ? "myTargetResourcePid" : "mySourceResourcePid";
String findFieldName = theReverseMode ? "mySourceResourcePid" : "myTargetResourcePid";
Collection<ResourcePersistentId> nextRoundMatches = theMatches;
HashSet<ResourcePersistentId> allAdded = new HashSet<>();
@ -618,17 +651,17 @@ public class SearchBuilder implements ISearchBuilder {
boolean matchAll = "*".equals(nextInclude.getValue());
if (matchAll) {
String sql;
sql = "SELECT r FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r." + searchFieldName + " IN (:target_pids) ";
List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
for (Collection<ResourcePersistentId> nextPartition : partitions) {
TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
TypedQuery<Long> q = theEntityManager.createQuery(sql, Long.class);
q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
List<ResourceLink> results = q.getResultList();
for (ResourceLink resourceLink : results) {
List<Long> results = q.getResultList();
for (Long resourceLink : results) {
if (theReverseMode) {
pidsToInclude.add(new ResourcePersistentId(resourceLink.getSourceResourcePid()));
pidsToInclude.add(new ResourcePersistentId(resourceLink));
} else {
pidsToInclude.add(new ResourcePersistentId(resourceLink.getTargetResourcePid()));
pidsToInclude.add(new ResourcePersistentId(resourceLink));
}
}
}
@ -665,16 +698,16 @@ public class SearchBuilder implements ISearchBuilder {
boolean haveTargetTypesDefinedByParam = param.hasTargets();
if (targetResourceType != null) {
sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType = :target_resource_type";
} else if (haveTargetTypesDefinedByParam) {
sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids) AND r.myTargetResourceType in (:target_resource_types)";
} else {
sql = "SELECT r FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
sql = "SELECT r." + findFieldName + " FROM ResourceLink r WHERE r.mySourcePath = :src_path AND r." + searchFieldName + " IN (:target_pids)";
}
List<Collection<ResourcePersistentId>> partitions = partition(nextRoundMatches, MAXIMUM_PAGE_SIZE);
for (Collection<ResourcePersistentId> nextPartition : partitions) {
TypedQuery<ResourceLink> q = theEntityManager.createQuery(sql, ResourceLink.class);
TypedQuery<Long> q = theEntityManager.createQuery(sql, Long.class);
q.setParameter("src_path", nextPath);
q.setParameter("target_pids", ResourcePersistentId.toLongList(nextPartition));
if (targetResourceType != null) {
@ -682,18 +715,10 @@ public class SearchBuilder implements ISearchBuilder {
} else if (haveTargetTypesDefinedByParam) {
q.setParameter("target_resource_types", param.getTargets());
}
List<ResourceLink> results = q.getResultList();
for (ResourceLink resourceLink : results) {
if (theReverseMode) {
Long pid = resourceLink.getSourceResourcePid();
if (pid != null) {
pidsToInclude.add(new ResourcePersistentId(pid));
}
} else {
Long pid = resourceLink.getTargetResourcePid();
if (pid != null) {
pidsToInclude.add(new ResourcePersistentId(pid));
}
List<Long> results = q.getResultList();
for (Long resourceLink : results) {
if (resourceLink != null) {
pidsToInclude.add(new ResourcePersistentId(resourceLink));
}
}
}
@ -965,6 +990,7 @@ public class SearchBuilder implements ISearchBuilder {
private SortSpec mySort;
private boolean myStillNeedToFetchIncludes;
private int mySkipCount = 0;
private int myNonSkipCount = 0;
private QueryIterator(SearchRuntimeDetails theSearchRuntimeDetails, RequestDetails theRequest) {
mySearchRuntimeDetails = theSearchRuntimeDetails;
@ -994,14 +1020,7 @@ public class SearchBuilder implements ISearchBuilder {
myMaxResultsToFetch = myDaoConfig.getFetchSizeDefaultMaximum();
}
final TypedQuery<Long> query = createQuery(mySort, myMaxResultsToFetch, false, myRequest);
mySearchRuntimeDetails.setQueryStopwatch(new StopWatch());
Query<Long> hibernateQuery = (Query<Long>) query;
hibernateQuery.setFetchSize(myFetchSize);
ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
myResultsIterator = new ScrollableResultsIterator<>(scroll);
initializeIteratorQuery(myMaxResultsToFetch);
// If the query resulted in extra results being requested
if (myAlsoIncludePids != null) {
@ -1036,11 +1055,32 @@ public class SearchBuilder implements ISearchBuilder {
ResourcePersistentId next = new ResourcePersistentId(nextLong);
if (myPidSet.add(next)) {
myNext = next;
myNonSkipCount++;
break;
} else {
mySkipCount++;
}
}
if (!myResultsIterator.hasNext()) {
if (myMaxResultsToFetch != null && (mySkipCount + myNonSkipCount == myMaxResultsToFetch)) {
if (mySkipCount > 0 && myNonSkipCount == 0) {
myMaxResultsToFetch += 1000;
StorageProcessingMessage message = new StorageProcessingMessage();
String msg = "Pass completed with no matching results. This indicates an inefficient query! Retrying with new max count of " + myMaxResultsToFetch;
ourLog.warn(msg);
message.setMessage(msg);
HookParams params = new HookParams()
.add(RequestDetails.class, myRequest)
.addIfMatchesType(ServletRequestDetails.class, myRequest)
.add(StorageProcessingMessage.class, message);
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_WARNING, params);
initializeIteratorQuery(myMaxResultsToFetch);
}
}
}
}
}
@ -1100,6 +1140,20 @@ public class SearchBuilder implements ISearchBuilder {
}
private void initializeIteratorQuery(Integer theMaxResultsToFetch) {
final TypedQuery<Long> query = createQuery(mySort, theMaxResultsToFetch, false, myRequest);
mySearchRuntimeDetails.setQueryStopwatch(new StopWatch());
Query<Long> hibernateQuery = (Query<Long>) query;
hibernateQuery.setFetchSize(myFetchSize);
ScrollableResults scroll = hibernateQuery.scroll(ScrollMode.FORWARD_ONLY);
myResultsIterator = new ScrollableResultsIterator<>(scroll);
mySkipCount = 0;
myNonSkipCount = 0;
}
@Override
public boolean hasNext() {
if (myNext == null) {
@ -1122,6 +1176,11 @@ public class SearchBuilder implements ISearchBuilder {
return mySkipCount;
}
@Override
public int getNonSkippedCount() {
return myNonSkipCount;
}
@Override
public void close() {
if (myResultsIterator != null) {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.java
View File

@ -50,4 +50,8 @@ public interface ITermConceptDao extends JpaRepository<TermConcept, Long> {
@Query("SELECT t FROM TermConcept t WHERE t.myIndexStatus = null")
Page<TermConcept> findResourcesRequiringReindexing(Pageable thePageRequest);
@Modifying
@Query("DELETE FROM TermConcept t WHERE t.myId = :pid")
void deleteByPid(@Param("pid") Long theId);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
View File

@ -4,6 +4,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@ -39,4 +40,9 @@ public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConcep
@Query("SELECT t.myPid FROM TermConceptParentChildLink t WHERE t.myCodeSystem.myId = :cs_pid")
Slice<Long> findIdsByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
@Modifying
@Query("DELETE FROM TermConceptParentChildLink t WHERE t.myChildPid = :pid OR t.myParentPid = :pid")
void deleteByConceptPid(@Param("pid") Long theId);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -24,10 +24,10 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IContextValidationSupport;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
@ -35,7 +35,6 @@ import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.validation.ValidationSupportChain;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
@ -53,6 +52,7 @@ import java.util.List;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
@Transactional
public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<CodeSystem> implements IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> {
@ -147,7 +147,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
CodeSystem csDstu3 = (CodeSystem) theResource;
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
org.hl7.fhir.r4.model.CodeSystem cs = convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, (ResourceTable) theEntity);

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
View File

@ -22,21 +22,24 @@ package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.TranslationMatch;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
@ -44,6 +47,8 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<ConceptMap> implements IFhirResourceDaoConceptMap<ConceptMap> {
@Autowired
private ITermReadSvc myHapiTerminologySvc;
@ -166,7 +171,7 @@ public class FhirResourceDaoConceptMapDstu3 extends BaseHapiFhirResourceDao<Conc
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
org.hl7.fhir.r4.model.ConceptMap converted = convertConceptMap(conceptMap);
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -33,12 +33,15 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
import org.apache.commons.codec.binary.StringUtils;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Enumerations.PublicationStatus;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetFilterComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
@ -51,7 +54,6 @@ import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import java.util.Collections;
import java.util.Date;
@ -59,6 +61,7 @@ import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueSet> implements IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> {
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoValueSetDstu3.class);
@ -420,7 +423,7 @@ public class FhirResourceDaoValueSetDstu3 extends BaseHapiFhirResourceDao<ValueS
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;
org.hl7.fhir.r4.model.ValueSet converted = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet converted = convertValueSet(valueSet);
myHapiTerminologySvc.storeTermValueSet(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/expunge/ExpungeEverythingService.java
View File

@ -78,8 +78,6 @@ public class ExpungeEverythingService {
ourLog.info("BEGINNING GLOBAL $expunge");
myTxTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
myTxTemplate.execute(t -> {
counter.addAndGet(doExpungeEverythingQuery("UPDATE " + ResourceHistoryTable.class.getSimpleName() + " d SET d.myForcedId = null"));
counter.addAndGet(doExpungeEverythingQuery("UPDATE " + ResourceTable.class.getSimpleName() + " d SET d.myForcedId = null"));
counter.addAndGet(doExpungeEverythingQuery("UPDATE " + TermCodeSystem.class.getSimpleName() + " d SET d.myCurrentVersion = null"));
return null;
});

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderDate.java
View File

@ -39,13 +39,17 @@ import javax.persistence.criteria.Join;
import javax.persistence.criteria.Predicate;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@Component
@Scope("prototype")
public class PredicateBuilderDate extends BasePredicateBuilder implements IPredicateBuilder {
private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderDate.class);
private Map<String, Join<ResourceTable, ResourceIndexedSearchParamDate>> myJoinMap;
PredicateBuilderDate(SearchBuilder theSearchBuilder) {
super(theSearchBuilder);
}
@ -56,7 +60,18 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
List<? extends IQueryParameterType> theList,
SearchFilterParser.CompareOperation operation) {
Join<ResourceTable, ResourceIndexedSearchParamDate> join = createJoin(SearchBuilderJoinEnum.DATE, theParamName);
boolean newJoin = false;
if (myJoinMap == null) {
myJoinMap = new HashMap<>();
}
String key = theResourceName + " " + theParamName;
Join<ResourceTable, ResourceIndexedSearchParamDate> join = myJoinMap.get(key);
if (join == null) {
join = createJoin(SearchBuilderJoinEnum.DATE, theParamName);
myJoinMap.put(key, join);
newJoin = true;
}
if (theList.get(0).getMissing() != null) {
Boolean missing = theList.get(0).getMissing();
@ -77,7 +92,14 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
}
Predicate orPredicates = myBuilder.or(toArray(codePredicates));
myQueryRoot.addPredicate(orPredicates);
if (newJoin) {
Predicate identityAndValuePredicate = combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, join, orPredicates);
myQueryRoot.addPredicate(identityAndValuePredicate);
} else {
myQueryRoot.addPredicate(orPredicates);
}
return orPredicates;
}
@ -86,12 +108,13 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
String theParamName,
CriteriaBuilder theBuilder,
From<?, ResourceIndexedSearchParamDate> theFrom) {
return createPredicateDate(theParam,
Predicate predicateDate = createPredicateDate(theParam,
theResourceName,
theParamName,
theBuilder,
theFrom,
null);
return combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, theFrom, predicateDate);
}
private Predicate createPredicateDate(IQueryParameterType theParam,
@ -99,7 +122,7 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
String theParamName,
CriteriaBuilder theBuilder,
From<?, ResourceIndexedSearchParamDate> theFrom,
SearchFilterParser.CompareOperation operation) {
SearchFilterParser.CompareOperation theOperation) {
Predicate p;
if (theParam instanceof DateParam) {
@ -109,7 +132,7 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
p = createPredicateDateFromRange(theBuilder,
theFrom,
range,
operation);
theOperation);
} else {
// TODO: handle missing date param?
p = null;
@ -119,12 +142,12 @@ public class PredicateBuilderDate extends BasePredicateBuilder implements IPredi
p = createPredicateDateFromRange(theBuilder,
theFrom,
range,
operation);
theOperation);
} else {
throw new IllegalArgumentException("Invalid token type: " + theParam.getClass());
}
return combineParamIndexPredicateWithParamNamePredicate(theResourceName, theParamName, theFrom, p);
return p;
}
private Predicate createPredicateDateFromRange(CriteriaBuilder theBuilder,

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
View File

@ -430,7 +430,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
break;
case Constants.PARAM_HAS:
addPredicateHas(theAndOrParams, theRequest);
addPredicateHas(theResourceName, theAndOrParams, theRequest);
break;
case Constants.PARAM_TAG:
@ -756,7 +756,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
return retVal;
}
private void addPredicateHas(List<List<IQueryParameterType>> theHasParameters, RequestDetails theRequest) {
private void addPredicateHas(String theResourceType, List<List<IQueryParameterType>> theHasParameters, RequestDetails theRequest) {
for (List<? extends IQueryParameterType> nextOrList : theHasParameters) {
@ -811,8 +811,9 @@ class PredicateBuilderReference extends BasePredicateBuilder {
Join<ResourceTable, ResourceLink> join = myQueryRoot.join("myResourceLinksAsTarget", JoinType.LEFT);
Predicate pathPredicate = myPredicateBuilder.createResourceLinkPathPredicate(targetResourceType, paramReference, join);
Predicate pidPredicate = join.get("mySourceResourcePid").in(subQ);
Predicate andPredicate = myBuilder.and(pathPredicate, pidPredicate);
Predicate sourceTypePredicate = myBuilder.equal(join.get("myTargetResourceType"), theResourceType);
Predicate sourcePidPredicate = join.get("mySourceResourcePid").in(subQ);
Predicate andPredicate = myBuilder.and(pathPredicate, sourcePidPredicate, sourceTypePredicate);
myQueryRoot.addPredicate(andPredicate);
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -148,7 +148,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), (ResourceTable) theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(cs), (ResourceTable) theEntity);
}
return retVal;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -166,7 +166,7 @@ public class FhirResourceDaoConceptMapR5 extends BaseHapiFhirResourceDao<Concept
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(conceptMap));
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -415,7 +415,7 @@ public class FhirResourceDaoValueSetR5 extends BaseHapiFhirResourceDao<ValueSet>
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSet));
} else {
myHapiTerminologySvc.deleteValueSetAndChildren(retVal);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystem.java
View File

@ -47,7 +47,7 @@ public class TermCodeSystem implements Serializable {
@Column(name = "CODE_SYSTEM_URI", nullable = false, length = MAX_URL_LENGTH)
private String myCodeSystemUri;
@OneToOne()
@OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CURRENT_VERSION_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_CURVER"))
private TermCodeSystemVersion myCurrentVersion;
@Column(name = "CURRENT_VERSION_PID", nullable = true, insertable = false, updatable = false)
@ -57,7 +57,7 @@ public class TermCodeSystem implements Serializable {
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODESYSTEM_PID")
@Column(name = "PID")
private Long myPid;
@OneToOne()
@OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_TRMCODESYSTEM_RES"))
private ResourceTable myResource;
@Column(name = "RES_ID", insertable = false, updatable = false)

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
View File

@ -50,7 +50,7 @@ public class TermCodeSystemVersion implements Serializable {
@Column(name = "PID")
private Long myId;
@OneToOne()
@OneToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CODESYSVER_RES_ID"))
private ResourceTable myResource;
@ -64,7 +64,7 @@ public class TermCodeSystemVersion implements Serializable {
* This was added in HAPI FHIR 3.3.0 and is nullable just to avoid migration
* issued. It should be made non-nullable at some point.
*/
@ManyToOne
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", nullable = true, foreignKey = @ForeignKey(name = "FK_CODESYSVER_CS_ID"))
private TermCodeSystem myCodeSystem;
@ -72,7 +72,7 @@ public class TermCodeSystemVersion implements Serializable {
private Long myCodeSystemPid;
@SuppressWarnings("unused")
@OneToOne(mappedBy = "myCurrentVersion", optional = true)
@OneToOne(mappedBy = "myCurrentVersion", optional = true, fetch = FetchType.LAZY)
private TermCodeSystem myCodeSystemHavingThisVersionAsCurrentVersionIfAny;
@Column(name = "CS_DISPLAY", nullable = true, updatable = false, length = MAX_VERSION_LENGTH)

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -65,7 +65,7 @@ public class TermConcept implements Serializable {
@Temporal(TemporalType.TIMESTAMP)
@Column(name = "CONCEPT_UPDATED", nullable = true)
private Date myUpdated;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
private TermCodeSystemVersion myCodeSystem;
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@ -79,11 +79,11 @@ public class TermConcept implements Serializable {
@Field(name = "myDisplayPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
})
private String myDisplay;
@OneToMany(mappedBy = "myConcept", orphanRemoval = false)
@OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
@Field(name = "PROPmyProperties", analyzer = @Analyzer(definition = "termConceptPropertyAnalyzer"))
@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
private Collection<TermConceptProperty> myProperties;
@OneToMany(mappedBy = "myConcept", orphanRemoval = false)
@OneToMany(mappedBy = "myConcept", orphanRemoval = false, fetch = FetchType.LAZY)
private Collection<TermConceptDesignation> myDesignations;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
View File

@ -39,7 +39,7 @@ public class TermConceptDesignation implements Serializable {
public static final int MAX_LENGTH = 500;
public static final int MAX_VAL_LENGTH = 2000;
@ManyToOne
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CONCEPT"))
private TermConcept myConcept;
@Id()
@ -62,7 +62,7 @@ public class TermConceptDesignation implements Serializable {
*
* @since 3.5.0
*/
@ManyToOne
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CS_VER_PID", nullable = true, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTDESIG_CSV"))
private TermCodeSystemVersion myCodeSystemVersion;

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -32,14 +32,14 @@ import java.io.Serializable;
public class TermConceptParentChildLink implements Serializable {
private static final long serialVersionUID = 1L;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CHILD_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CHILD"))
private TermConcept myChild;
@Column(name = "CHILD_PID", insertable = false, updatable = false)
private Long myChildPid;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CODESYSTEM_PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_CS"))
private TermCodeSystemVersion myCodeSystem;
@ -47,7 +47,7 @@ public class TermConceptParentChildLink implements Serializable {
@Fields({@Field(name = "myCodeSystemVersionPid")})
private long myCodeSystemVersionPid;
@ManyToOne(cascade = {})
@ManyToOne(fetch = FetchType.LAZY, cascade = {})
@JoinColumn(name = "PARENT_PID", nullable = false, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_TERM_CONCEPTPC_PARENT"))
private TermConcept myParent;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
View File

@ -44,7 +44,7 @@ public class TermConceptProperty implements Serializable {
private static final int MAX_LENGTH = 500;
static final int MAX_PROPTYPE_ENUM_LENGTH = 6;
@ManyToOne
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CONCEPT_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CONCEPT"))
private TermConcept myConcept;
/**
@ -52,7 +52,7 @@ public class TermConceptProperty implements Serializable {
*
* @since 3.5.0
*/
@ManyToOne
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "CS_VER_PID", nullable = true, referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPTPROP_CSV"))
private TermCodeSystemVersion myCodeSystemVersion;
@Id()

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/TerminologyUploaderProvider.java
View File

@ -39,7 +39,6 @@ import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.base.Charsets;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.Multimap;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.ICompositeType;
@ -61,6 +60,7 @@ import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
public class TerminologyUploaderProvider extends BaseJpaProvider {
@ -272,10 +272,10 @@ public class TerminologyUploaderProvider extends BaseJpaProvider {
CodeSystem nextCodeSystem;
switch (getContext().getVersion().getVersion()) {
case DSTU3:
nextCodeSystem = VersionConvertor_30_40.convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
nextCodeSystem = convertCodeSystem((org.hl7.fhir.dstu3.model.CodeSystem) theCodeSystem);
break;
case R5:
nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
nextCodeSystem = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem((org.hl7.fhir.r5.model.CodeSystem) theCodeSystem);
break;
default:
nextCodeSystem = (CodeSystem) theCodeSystem;

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderConceptMapDstu3.java
View File

@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.provider.dstu3;
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoConceptMap;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.term.TranslationRequest;
import ca.uhn.fhir.jpa.term.TranslationResult;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
@ -31,11 +31,21 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ConceptMap;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.exceptions.FHIRException;
import javax.servlet.http.HttpServletRequest;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderDstu3<ConceptMap> {
@Operation(name = JpaConstants.OPERATION_TRANSLATE, idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1, max = 1),
@ -129,7 +139,7 @@ public class BaseJpaResourceProviderConceptMapDstu3 extends JpaResourceProviderD
TranslationResult result = dao.translate(translationRequest, theRequestDetails);
// Convert from R4 to DSTU3
return VersionConvertor_30_40.convertParameters(result.toParameters());
return convertParameters(result.toParameters());
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
} finally {

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaResourceProviderDstu3.java
View File

@ -21,17 +21,28 @@ package ca.uhn.fhir.jpa.provider.dstu3;
*/
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.jpa.provider.BaseJpaResourceProvider;
import ca.uhn.fhir.rest.annotation.ConditionalUrlParam;
import ca.uhn.fhir.rest.annotation.Create;
import ca.uhn.fhir.rest.annotation.Delete;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.ResourceParam;
import ca.uhn.fhir.rest.annotation.Update;
import ca.uhn.fhir.rest.annotation.Validate;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.IdType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -41,6 +52,7 @@ import javax.servlet.http.HttpServletRequest;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_ADD;
import static ca.uhn.fhir.jpa.model.util.JpaConstants.OPERATION_META_DELETE;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaResourceProvider<T> {
@ -91,7 +103,7 @@ public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaRes
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -107,7 +119,7 @@ public class JpaResourceProviderDstu3<T extends IAnyResource> extends BaseJpaRes
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaSystemProviderDstu3.java
View File

@ -3,17 +3,26 @@ package ca.uhn.fhir.jpa.provider.dstu3;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl.Suggestion;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.provider.BaseJpaSystemProviderDstu2Plus;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.Transaction;
import ca.uhn.fhir.rest.annotation.TransactionParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IIdType;
@ -29,6 +38,7 @@ import java.util.TreeMap;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.hl7.fhir.convertors.conv30_40.Parameters30_40.convertParameters;
/*
* #%L
@ -72,7 +82,7 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -90,7 +100,7 @@ public class JpaSystemProviderDstu3 extends BaseJpaSystemProviderDstu2Plus<Bundl
) {
org.hl7.fhir.r4.model.Parameters retVal = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
try {
return VersionConvertor_30_40.convertParameters(retVal);
return convertParameters(retVal);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/BaseJpaResourceProviderConceptMapR5.java
View File

@ -122,7 +122,7 @@ public class BaseJpaResourceProviderConceptMapR5 extends JpaResourceProviderR5<C
IFhirResourceDaoConceptMap<ConceptMap> dao = (IFhirResourceDaoConceptMap<ConceptMap>) getDao();
TranslationResult result = dao.translate(translationRequest, theRequestDetails);
org.hl7.fhir.r4.model.Parameters parameters = result.toParameters();
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
} finally {
endRequest(theServletRequest);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaResourceProviderR5.java
View File

@ -86,7 +86,7 @@ public class JpaResourceProviderR5<T extends IAnyResource> extends BaseJpaResour
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theIdParam, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
@ -99,7 +99,7 @@ public class JpaResourceProviderR5<T extends IAnyResource> extends BaseJpaResour
@OperationParam(name = JpaConstants.OPERATION_EXPUNGE_PARAM_EXPUNGE_PREVIOUS_VERSIONS) BooleanType theExpungeOldVersions,
RequestDetails theRequest) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(null, theLimit, theExpungeDeletedResources, theExpungeOldVersions, null, theRequest);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
@Operation(name = OPERATION_META, idempotent = true, returnParameters = {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaSystemProviderR5.java
View File

@ -68,7 +68,7 @@ public class JpaSystemProviderR5 extends BaseJpaSystemProviderDstu2Plus<Bundle,
RequestDetails theRequestDetails
) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
@Operation(name = JpaConstants.OPERATION_EXPUNGE, idempotent = false, returnParameters = {
@ -82,7 +82,7 @@ public class JpaSystemProviderR5 extends BaseJpaSystemProviderDstu2Plus<Bundle,
RequestDetails theRequestDetails
) {
org.hl7.fhir.r4.model.Parameters parameters = super.doExpunge(theLimit, theExpungeDeletedResources, theExpungeOldVersions, theExpungeEverything, theRequestDetails);
return org.hl7.fhir.convertors.conv40_50.Parameters.convertParameters(parameters);
return org.hl7.fhir.convertors.conv40_50.Parameters40_50.convertParameters(parameters);
}
// This is generated by hand:

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
View File

@ -227,10 +227,14 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
template.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
ensureSearchEntityLoaded();
boolean entityLoaded = ensureSearchEntityLoaded();
assert entityLoaded;
}
});
assert mySearchEntity != null;
assert mySearchEntity.getSearchType() != null;
switch (mySearchEntity.getSearchType()) {
case HISTORY:
return template.execute(theStatus -> doHistoryInTransaction(theFromIndex, theToIndex));

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
View File

@ -56,6 +56,9 @@ import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.rest.server.util.ICachedSearchDetails;
import ca.uhn.fhir.util.AsyncUtil;
import ca.uhn.fhir.util.StopWatch;
import co.elastic.apm.api.ElasticApm;
import co.elastic.apm.api.Span;
import co.elastic.apm.api.Transaction;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.exception.ExceptionUtils;
@ -601,7 +604,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
private List<ResourcePersistentId> myPreviouslyAddedResourcePids;
private Integer myMaxResultsToFetch;
private SearchRuntimeDetails mySearchRuntimeDetails;
private Transaction myParentTransaction;
/**
* Constructor
*/
@ -614,6 +617,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
mySearchRuntimeDetails = new SearchRuntimeDetails(theRequest, mySearch.getUuid());
mySearchRuntimeDetails.setQueryString(theParams.toNormalizedQueryString(theCallingDao.getContext()));
myRequest = theRequest;
myParentTransaction = ElasticApm.currentTransaction();
}
/**
@ -774,10 +778,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
if (theResultIter.hasNext() == false) {
int skippedCount = theResultIter.getSkippedCount();
int nonSkippedCount = theResultIter.getNonSkippedCount();
int totalFetched = skippedCount + myCountSavedThisPass + myCountBlockedThisPass;
ourLog.trace("MaxToFetch[{}] SkippedCount[{}] CountSavedThisPass[{}] CountSavedThisTotal[{}] AdditionalPrefetchRemaining[{}]", myMaxResultsToFetch, skippedCount, myCountSavedThisPass, myCountSavedTotal, myAdditionalPrefetchThresholdsRemaining);
if (myMaxResultsToFetch != null && totalFetched < myMaxResultsToFetch) {
if (nonSkippedCount == 0 || (myMaxResultsToFetch != null && totalFetched < myMaxResultsToFetch)) {
ourLog.trace("Setting search status to FINISHED");
mySearch.setStatus(SearchStatusEnum.FINISHED);
mySearch.setTotalCount(myCountSavedTotal);
@ -840,7 +845,8 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
@Override
public Void call() {
StopWatch sw = new StopWatch();
Span span = myParentTransaction.startSpan("db", "query", "search");
span.setName("FHIR Database Search");
try {
// Create an initial search in the DB and give it an ID
saveSearch();
@ -896,7 +902,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
ourLog.error("Failed during search loading after {}ms", sw.getMillis(), t);
}
myUnsyncedPids.clear();
Throwable rootCause = ExceptionUtils.getRootCause(t);
rootCause = defaultIfNull(rootCause, t);
@ -923,12 +928,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
JpaInterceptorBroadcaster.doCallHooks(myInterceptorBroadcaster, myRequest, Pointcut.JPA_PERFTRACE_SEARCH_FAILED, params);
saveSearch();
span.captureException(t);
} finally {
myIdToSearchTask.remove(mySearch.getUuid());
myInitialCollectionLatch.countDown();
markComplete();
span.end();
}
return null;

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
View File

@ -66,6 +66,7 @@ import org.apache.lucene.search.BooleanQuery;
import org.apache.lucene.search.MultiPhraseQuery;
import org.apache.lucene.search.Query;
import org.apache.lucene.search.RegexpQuery;
import org.apache.lucene.search.TermQuery;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hibernate.search.jpa.FullTextEntityManager;
@ -600,11 +601,16 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
.map(t -> new Term("myCode", t))
.collect(Collectors.toList());
if (codes.size() > 0) {
MultiPhraseQuery query = new MultiPhraseQuery();
query.add(codes.toArray(new Term[0]));
BooleanQuery.Builder builder = new BooleanQuery.Builder();
builder.setMinimumNumberShouldMatch(1);
for (Term nextCode : codes) {
builder.add(new TermQuery(nextCode), BooleanClause.Occur.SHOULD);
}
luceneQuery = new BooleanQuery.Builder()
.add(luceneQuery, BooleanClause.Occur.MUST)
.add(query, BooleanClause.Occur.MUST)
.add(builder.build(), BooleanClause.Occur.MUST)
.build();
}
@ -1240,6 +1246,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
return retVal;
}
@Transactional
@Override
public List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode) {
TermCodeSystem cs = getCodeSystem(theSystem);
@ -1271,6 +1278,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc, ApplicationCo
return retVal;
}
@Transactional
@Override
public List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode) {
TermCodeSystem cs = getCodeSystem(theSystem);

115
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -45,7 +45,6 @@ import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.jpa.util.ScrollableResultsIterator;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -53,11 +52,7 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.apache.commons.lang3.Validate;
import org.hibernate.ScrollMode;
import org.hibernate.ScrollableResults;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
@ -78,11 +73,6 @@ import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import java.util.*;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
@ -165,11 +155,12 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
IIdType codeSystemId = cs.getResource().getIdDt();
UploadStatistics retVal = new UploadStatistics(codeSystemId);
HashMap<String, TermConcept> codeToConcept = new HashMap<>();
// Add root concepts
for (TermConcept nextRootConcept : theAdditions.getRootConcepts()) {
List<String> parentCodes = Collections.emptyList();
addConcept(csv, parentCodes, nextRootConcept, retVal, true, 0);
addConceptInHierarchy(csv, parentCodes, nextRootConcept, retVal, codeToConcept, 0);
}
return retVal;
@ -232,7 +223,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
* save parent concepts first (it's way too slow to do that)
*/
if (theConcept.getId() == null) {
retVal += ensureParentsSaved(theConcept.getParents());
boolean needToSaveParents = false;
for (TermConceptParentChildLink next : theConcept.getParents()) {
if (next.getParent().getId() == null) {
needToSaveParents = true;
}
}
if (needToSaveParents) {
retVal += ensureParentsSaved(theConcept.getParents());
}
}
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
@ -445,66 +444,68 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
Validate.isTrue(myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3), "Terminology operations only supported in DSTU3+ mode");
}
private void addConcept(TermCodeSystemVersion theCsv, Collection<String> theParentCodes, TermConcept theConceptToAdd, UploadStatistics theStatisticsTracker, boolean theRootConcept, int theSequence) {
private void addConceptInHierarchy(TermCodeSystemVersion theCsv, Collection<String> theParentCodes, TermConcept theConceptToAdd, UploadStatistics theStatisticsTracker, Map<String, TermConcept> theCodeToConcept, int theSequence) {
TermConcept conceptToAdd = theConceptToAdd;
List<TermConceptParentChildLink> childrenToAdd = theConceptToAdd.getChildren();
String nextCodeToAdd = conceptToAdd.getCode();
String parentDescription = "(root concept)";
Set<TermConcept> parentConcepts = new HashSet<>();
if (!theParentCodes.isEmpty()) {
parentDescription = "[" + String.join(", ", theParentCodes) + "]";
for (String nextParentCode : theParentCodes) {
Optional<TermConcept> nextParentOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextParentCode);
if (nextParentOpt.isPresent() == false) {
throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
}
parentConcepts.add(nextParentOpt.get());
}
}
ourLog.info("Saving concept {} with parent {}", theStatisticsTracker.getUpdatedConceptCount(), parentDescription);
Optional<TermConcept> existingCodeOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextCodeToAdd);
List<TermConceptParentChildLink> existingParentLinks;
if (existingCodeOpt.isPresent()) {
TermConcept existingCode = existingCodeOpt.get();
existingCode.setIndexStatus(null);
existingCode.setDisplay(conceptToAdd.getDisplay());
conceptToAdd = existingCode;
existingParentLinks = conceptToAdd.getParents();
} else {
existingParentLinks = Collections.emptyList();
}
Set<TermConcept> parentConceptsWeShouldLinkTo = new HashSet<>();
for (String nextParentCode : theParentCodes) {
// Don't add parent links that already exist for the code
if (existingParentLinks.stream().anyMatch(t -> t.getParent().getCode().equals(nextParentCode))) {
continue;
}
TermConcept nextParentOpt = theCodeToConcept.get(nextParentCode);
if (nextParentOpt == null) {
nextParentOpt = myConceptDao.findByCodeSystemAndCode(theCsv, nextParentCode).orElse(null);
}
if (nextParentOpt == null) {
throw new InvalidRequestException("Unable to add code \"" + nextCodeToAdd + "\" to unknown parent: " + nextParentCode);
}
parentConceptsWeShouldLinkTo.add(nextParentOpt);
}
if (conceptToAdd.getSequence() == null) {
conceptToAdd.setSequence(theSequence);
}
// Drop any old parent-child links if they aren't explicitly specified in the
// hierarchy being added
if (!theRootConcept) {
for (Iterator<TermConceptParentChildLink> iter = conceptToAdd.getParents().iterator(); iter.hasNext(); ) {
TermConceptParentChildLink nextLink = iter.next();
String parentCode = nextLink.getParent().getCode();
ourLog.info("Dropping existing parent/child link from {} -> {}", parentCode, nextCodeToAdd);
myConceptParentChildLinkDao.delete(nextLink);
iter.remove();
List<TermConceptParentChildLink> parentChildrenList = nextLink.getParent().getChildren();
parentChildrenList.remove(nextLink);
}
}
// Null out the hierarchy PIDs for this concept always. We do this because we're going to
// force a reindex, and it'll be regenerated then
conceptToAdd.setParentPids(null);
conceptToAdd.setCodeSystemVersion(theCsv);
conceptToAdd = myConceptDao.save(conceptToAdd);
Long nextConceptPid = conceptToAdd.getId();
Validate.notNull(nextConceptPid);
if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
saveConcept(conceptToAdd);
Long nextConceptPid = conceptToAdd.getId();
Validate.notNull(nextConceptPid);
} else {
myDeferredStorageSvc.addConceptToStorageQueue(conceptToAdd);
}
theCodeToConcept.put(conceptToAdd.getCode(), conceptToAdd);
theStatisticsTracker.incrementUpdatedConceptCount();
// Add link to new child to the parent
for (TermConcept nextParentConcept : parentConcepts) {
for (TermConcept nextParentConcept : parentConceptsWeShouldLinkTo) {
TermConceptParentChildLink parentLink = new TermConceptParentChildLink();
parentLink.setParent(nextParentConcept);
parentLink.setChild(conceptToAdd);
@ -513,7 +514,13 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
nextParentConcept.getChildren().add(parentLink);
conceptToAdd.getParents().add(parentLink);
ourLog.info("Saving parent/child link - Parent[{}] Child[{}]", parentLink.getParent().getCode(), parentLink.getChild().getCode());
myConceptParentChildLinkDao.save(parentLink);
if (theStatisticsTracker.getUpdatedConceptCount() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
myConceptParentChildLinkDao.save(parentLink);
} else {
myDeferredStorageSvc.addConceptLinkToStorageQueue(parentLink);
}
}
ourLog.trace("About to save parent-child links");
@ -527,13 +534,20 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
for (int i = 0; i < nextChild.getParents().size(); i++) {
if (nextChild.getParents().get(i).getId() == null) {
String parentCode = nextChild.getParents().get(i).getParent().getCode();
TermConcept parentConcept = myConceptDao.findByCodeSystemAndCode(theCsv, parentCode).orElseThrow(() -> new IllegalArgumentException("Unknown parent code: " + parentCode));
TermConcept parentConcept = theCodeToConcept.get(parentCode);
if (parentConcept == null) {
parentConcept = myConceptDao.findByCodeSystemAndCode(theCsv, parentCode).orElse(null);
}
if (parentConcept == null) {
throw new IllegalArgumentException("Unknown parent code: " + parentCode);
}
nextChild.getParents().get(i).setParent(parentConcept);
}
}
Collection<String> parentCodes = nextChild.getParents().stream().map(t -> t.getParent().getCode()).collect(Collectors.toList());
addConcept(theCsv, parentCodes, nextChild, theStatisticsTracker, false, childIndex);
addConceptInHierarchy(theCsv, parentCodes, nextChild, theStatisticsTracker, theCodeToConcept, childIndex);
childIndex++;
}
@ -649,12 +663,15 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
private void deleteConceptChildrenAndConcept(TermConcept theConcept, AtomicInteger theRemoveCounter) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
deleteConceptChildrenAndConcept(nextChildLink.getChild(), theRemoveCounter);
myConceptParentChildLinkDao.delete(nextChildLink);
}
myConceptParentChildLinkDao.deleteByConceptPid(theConcept.getId());
myConceptDesignationDao.deleteAll(theConcept.getDesignations());
myConceptPropertyDao.deleteAll(theConcept.getProperties());
myConceptDao.delete(theConcept);
ourLog.info("Deleting concept {} - Code {}", theConcept.getId(), theConcept.getCode());
myConceptDao.deleteByPid(theConcept.getId());
theRemoveCounter.incrementAndGet();
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
View File

@ -98,6 +98,13 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
myDeferredValueSets.addAll(theValueSets);
}
@Override
public void saveAllDeferred() {
while (!isStorageQueueEmpty()) {
saveDeferred();
}
}
@Override
public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred;

24
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcDstu3.java
View File

@ -9,10 +9,13 @@ import ca.uhn.fhir.jpa.term.api.ITermReadSvcDstu3;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.ValidateUtil;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.exceptions.FHIRException;
@ -31,6 +34,9 @@ import java.util.List;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSetExpansionComponent;
/*
* #%L
@ -104,7 +110,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent expandedR4 = super.expandValueSetInMemory(valueSetToExpandR4, null).getExpansion();
return VersionConvertor_30_40.convertValueSetExpansionComponent(expandedR4);
return convertValueSetExpansionComponent(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -118,7 +124,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(valueSetToExpandR4, null);
return VersionConvertor_30_40.convertValueSet(expandedR4);
return convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -127,7 +133,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws FHIRException {
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = VersionConvertor_30_40.convertValueSet((ValueSet) theValueSet);
valueSetToExpandR4 = convertValueSet((ValueSet) theValueSet);
return valueSetToExpandR4;
}
@ -139,7 +145,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
org.hl7.fhir.r4.model.ValueSet valueSetToExpandR4;
valueSetToExpandR4 = toCanonicalValueSet(valueSetToExpand);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSet(valueSetToExpandR4, theOffset, theCount);
return VersionConvertor_30_40.convertValueSet(expandedR4);
return convertValueSet(expandedR4);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -256,7 +262,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystem = myValidationSupport.fetchCodeSystem(myContext, theSystem);
try {
return VersionConvertor_30_40.convertCodeSystem(codeSystem);
return convertCodeSystem(codeSystem);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -323,7 +329,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public ValidateCodeResult validateCodeIsInPreExpandedValueSet(IBaseResource theValueSet, String theSystem, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
Coding coding = (Coding) theCoding;
org.hl7.fhir.r4.model.Coding codingR4 = null;
@ -347,7 +353,7 @@ public class TermReadSvcDstu3 extends BaseTermReadSvcImpl implements IValidation
public boolean isValueSetPreExpandedForCodeValidation(IBaseResource theValueSet) {
ValidateUtil.isNotNullOrThrowUnprocessableEntity(theValueSet, "ValueSet must not be null");
ValueSet valueSet = (ValueSet) theValueSet;
org.hl7.fhir.r4.model.ValueSet valueSetR4 = VersionConvertor_30_40.convertValueSet(valueSet);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = convertValueSet(valueSet);
return super.isValueSetPreExpandedForCodeValidation(valueSetR4);
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcR5.java
View File

@ -90,21 +90,21 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
super.throwInvalidValueSet(theValueSet);
}
return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5), null);
return expandValueSetAndReturnVersionIndependentConcepts(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5), null);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSetInMemory(valueSetToExpand, null);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
}
@Override
public IBaseResource expandValueSet(IBaseResource theInput, int theOffset, int theCount) {
org.hl7.fhir.r4.model.ValueSet valueSetToExpand = toCanonicalValueSet(theInput);
org.hl7.fhir.r4.model.ValueSet valueSetR4 = super.expandValueSet(valueSetToExpand, theOffset, theCount);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR4);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR4);
}
@Override
@ -117,8 +117,8 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
public ValueSetExpander.ValueSetExpansionOutcome expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
ValueSet valueSetToExpand = new ValueSet();
valueSetToExpand.getCompose().addInclude(theInclude);
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetToExpand), null);
return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(expandedR4));
org.hl7.fhir.r4.model.ValueSet expandedR4 = super.expandValueSetInMemory(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetToExpand), null);
return new ValueSetExpander.ValueSetExpansionOutcome(org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(expandedR4));
}
@Override
@ -199,13 +199,13 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
public org.hl7.fhir.r4.model.CodeSystem getCodeSystemFromContext(String theSystem) {
CodeSystem codeSystemR5 = myValidationSupport.fetchCodeSystem(myContext, theSystem);
return org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(codeSystemR5);
return org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(codeSystemR5);
}
@Override
protected org.hl7.fhir.r4.model.ValueSet getValueSetFromResourceTable(ResourceTable theResourceTable) {
ValueSet valueSetR5 = myValueSetResourceDao.toResource(ValueSet.class, theResourceTable, null, false);
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSetR5);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(valueSetR5);
}
@Override
@ -277,7 +277,7 @@ public class TermReadSvcR5 extends BaseTermReadSvcImpl implements IValidationSup
@Override
protected org.hl7.fhir.r4.model.ValueSet toCanonicalValueSet(IBaseResource theValueSet) throws org.hl7.fhir.exceptions.FHIRException {
return org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet((ValueSet) theValueSet);
return org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet((ValueSet) theValueSet);
}
@Override

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcDstu3.java
View File

@ -37,6 +37,9 @@ import org.springframework.context.event.ContextStartedEvent;
import org.springframework.context.event.EventListener;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.hl7.fhir.convertors.conv30_40.CodeSystem30_40.convertCodeSystem;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
import static org.hl7.fhir.convertors.conv30_40.ValueSet30_40.convertValueSet;
public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
@ -72,7 +75,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
CodeSystem resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertCodeSystem(theCodeSystemResource);
resourceToStore = convertCodeSystem(theCodeSystemResource);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -89,7 +92,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap resourceToStore;
try {
resourceToStore = VersionConvertor_30_40.convertConceptMap(theConceptMap);
resourceToStore = convertConceptMap(theConceptMap);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}
@ -105,7 +108,7 @@ public class TermVersionAdapterSvcDstu3 extends BaseTermVersionAdapterSvcImpl im
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetDstu3;
try {
valueSetDstu3 = VersionConvertor_30_40.convertValueSet(theValueSet);
valueSetDstu3 = convertValueSet(theValueSet);
} catch (FHIRException e) {
throw new InternalErrorException(e);
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR5.java
View File

@ -62,7 +62,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource) {
validateCodeSystemForStorage(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(theCodeSystemResource);
CodeSystem codeSystemR4 = org.hl7.fhir.convertors.conv40_50.CodeSystem40_50.convertCodeSystem(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(codeSystemR4, matchUrl).getId();
@ -74,7 +74,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
@Override
public void createOrUpdateConceptMap(org.hl7.fhir.r4.model.ConceptMap theConceptMap) {
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(theConceptMap);
ConceptMap conceptMapR4 = org.hl7.fhir.convertors.conv40_50.ConceptMap40_50.convertConceptMap(theConceptMap);
if (isBlank(theConceptMap.getIdElement().getIdPart())) {
String matchUrl = "ConceptMap?url=" + UrlUtil.escapeUrlParam(theConceptMap.getUrl());
@ -87,7 +87,7 @@ public class TermVersionAdapterSvcR5 extends BaseTermVersionAdapterSvcImpl imple
@Override
public void createOrUpdateValueSet(org.hl7.fhir.r4.model.ValueSet theValueSet) {
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(theValueSet);
ValueSet valueSetR4 = org.hl7.fhir.convertors.conv40_50.ValueSet40_50.convertValueSet(theValueSet);
if (isBlank(theValueSet.getIdElement().getIdPart())) {
String matchUrl = "ValueSet?url=" + UrlUtil.escapeUrlParam(theValueSet.getUrl());

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
View File

@ -50,4 +50,9 @@ public interface ITermDeferredStorageSvc {
void addConceptMapsToStorageQueue(List<ConceptMap> theConceptMaps);
void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
/**
* This is mostly here for unit tests - Saves any and all deferred concepts and links
*/
void saveAllDeferred();
}

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/SearchBuilderTest.java
View File

@ -39,11 +39,10 @@ public class SearchBuilderTest {
TypedQuery mockQuery = mock(TypedQuery.class);
when(mockEntityManager.createQuery(any(), any())).thenReturn(mockQuery);
List<ResourceLink> resultList = new ArrayList<>();
ResourceLink link = new ResourceLink();
List<Long> resultList = new ArrayList<>();
Long link = 1L;
ResourceTable target = new ResourceTable();
target.setId(1L);
link.setTargetResource(target);
resultList.add(link);
when(mockQuery.getResultList()).thenReturn(resultList);

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2ValidateTest.java
View File

@ -1,9 +1,5 @@
package ca.uhn.fhir.jpa.dao.dstu2;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@ -32,7 +28,11 @@ import org.junit.Before;
import org.junit.Test;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2ValidateTest.class);
@ -94,15 +94,14 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
myStructureDefinitionDao.create(sd, mySrd);
Observation input = new Observation();
ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(sd.getUrl())));
ResourceMetadataKeyEnum.PROFILES.put(input, Collections.singletonList(new IdDt(sd.getUrl())));
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getEncounter().setReference("http://foo.com/Encounter/9");
input.setStatus(ObservationStatusEnum.FINAL);
input.getCode().addCoding().setSystem("http://loinc.org").setCode("12345");
String encoded = null;
MethodOutcome outcome = null;
String encoded;
ValidationModeEnum mode = ValidationModeEnum.CREATE;
switch (enc) {
case JSON:
@ -130,12 +129,12 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
}
@Test
public void testValidateResourceContainingProfileDeclarationInvalid() throws Exception {
public void testValidateResourceContainingProfileDeclarationInvalid() {
String methodName = "testValidateResourceContainingProfileDeclarationInvalid";
Observation input = new Observation();
String profileUri = "http://example.com/StructureDefinition/" + methodName;
ResourceMetadataKeyEnum.PROFILES.put(input, Arrays.asList(new IdDt(profileUri)));
ResourceMetadataKeyEnum.PROFILES.put(input, Collections.singletonList(new IdDt(profileUri)));
input.addIdentifier().setSystem("http://acme").setValue("12345");
input.getEncounter().setReference("http://foo.com/Encounter/9");
@ -148,7 +147,7 @@ public class FhirResourceDaoDstu2ValidateTest extends BaseJpaDstu2Test {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(outcome.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
assertThat(ooString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -35,7 +35,6 @@ import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.Search;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.exceptions.FHIRException;
@ -60,6 +59,7 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import static org.hl7.fhir.convertors.conv30_40.ConceptMap30_40.convertConceptMap;
import static org.junit.Assert.fail;
@RunWith(SpringJUnit4ClassRunner.class)
@ -386,7 +386,7 @@ public abstract class BaseJpaDstu3Test extends BaseJpaTest {
*/
public static ConceptMap createConceptMap() {
try {
return VersionConvertor_30_40.convertConceptMap(BaseJpaR4Test.createConceptMap());
return convertConceptMap(BaseJpaR4Test.createConceptMap());
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -9,6 +9,7 @@ import ca.uhn.fhir.jpa.model.cross.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
@ -134,8 +135,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION" , cs, table);
myTermDeferredStorageSvc.saveAllDeferred();
}
@Autowired
private ITermDeferredStorageSvc myTermDeferredStorageSvc;
private void createExternalCsAndLocalVs() {
CodeSystem codeSystem = createExternalCs();

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValidateTest.java
View File

@ -99,7 +99,7 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
myValueSetDao.create(vs);
ValueSet expansion = myValueSetDao.expandByIdentifier("http://ccim.on.ca/fhir/iar/ValueSet/iar-citizenship-status", null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expansion));
// Questionnaire q = loadResourceFromClasspath(Questionnaire.class,"/dstu3/iar/Questionnaire-iar-test.xml" );
// myQuestionnaireDao.create(q);
@ -326,11 +326,11 @@ public class FhirResourceDaoDstu3ValidateTest extends BaseJpaDstu3Test {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
OperationOutcome oo = (OperationOutcome) e.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
}
}
@Test

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java
View File

@ -162,6 +162,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myConditionDaoR4")
protected IFhirResourceDao<Condition> myConditionDao;
@Autowired
@Qualifier("myEpisodeOfCareDaoR4")
protected IFhirResourceDao<EpisodeOfCare> myEpisodeOfCareDao;
@Autowired
protected DaoConfig myDaoConfig;
@Autowired
protected ModelConfig myModelConfig;
@ -169,6 +172,9 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
@Qualifier("myDeviceDaoR4")
protected IFhirResourceDao<Device> myDeviceDao;
@Autowired
@Qualifier("myProvenanceDaoR4")
protected IFhirResourceDao<Provenance> myProvenanceDao;
@Autowired
@Qualifier("myDiagnosticReportDaoR4")
protected IFhirResourceDao<DiagnosticReport> myDiagnosticReportDao;
@Autowired

32
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4QueryCountTest.java
View File

@ -133,6 +133,38 @@ public class FhirResourceDaoR4QueryCountTest extends BaseJpaR4Test {
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
@Test
public void testCreateWithClientAssignedId() {
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
runInTransaction(() -> {
Patient p = new Patient();
p.getMaritalStatus().setText("123");
return myPatientDao.create(p).getId().toUnqualified();
});
myCaptureQueriesListener.clear();
runInTransaction(() -> {
Patient p = new Patient();
p.setId("AAA");
p.getMaritalStatus().setText("123");
return myPatientDao.update(p).getId().toUnqualified();
});
myCaptureQueriesListener.logSelectQueriesForCurrentThread();
assertEquals(1, myCaptureQueriesListener.getSelectQueriesForCurrentThread().size());
myCaptureQueriesListener.logUpdateQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getUpdateQueriesForCurrentThread().size());
myCaptureQueriesListener.logInsertQueriesForCurrentThread();
assertEquals(4, myCaptureQueriesListener.getInsertQueriesForCurrentThread().size());
myCaptureQueriesListener.logDeleteQueriesForCurrentThread();
assertEquals(0, myCaptureQueriesListener.getDeleteQueriesForCurrentThread().size());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

233
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java
View File

@ -3,7 +3,14 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamDate;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamNumber;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap.EverythingModeEnum;
@ -33,7 +40,11 @@ import org.hl7.fhir.r4.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
import org.junit.*;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
@ -44,12 +55,30 @@ import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.Collections;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import java.util.stream.Collectors;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Mockito.mock;
@SuppressWarnings({"unchecked", "Duplicates"})
@ -73,6 +102,28 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
myDaoConfig.setReuseCachedSearchResultsForMillis(null);
}
@Test
public void testCanonicalReference() {
StructureDefinition sd = new StructureDefinition();
sd.getSnapshot().addElement().getBinding().setValueSet("http://foo");
String id = myStructureDefinitionDao.create(sd).getId().toUnqualifiedVersionless().getValue();
{
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo"));
List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
assertThat(ids, contains(id));
}
{
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);
map.add(StructureDefinition.SP_VALUESET, new ReferenceParam("http://foo2"));
List<String> ids = toUnqualifiedVersionlessIdValues(myStructureDefinitionDao.search(map));
assertThat(ids, empty());
}
}
@Test
public void testHasConditionAgeCompare() {
Patient patient = new Patient();
@ -569,6 +620,41 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
@Test
public void testHasLimitsByType() {
Patient patient = new Patient();
patient.setActive(true);
IIdType patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
Encounter encounter = new Encounter();
encounter.setStatus(Encounter.EncounterStatus.ARRIVED);
IIdType encounterId = myEncounterDao.create(encounter).getId().toUnqualifiedVersionless();
Device device = new Device();
device.setManufacturer("Acme");
IIdType deviceId = myDeviceDao.create(device).getId().toUnqualifiedVersionless();
Provenance provenance = new Provenance();
provenance.addTarget().setReferenceElement(patientId);
provenance.addTarget().setReferenceElement(encounterId);
provenance.addAgent().setWho(new Reference(deviceId));
myProvenanceDao.create(provenance);
String criteria = "_has:Provenance:target:agent=" + deviceId.getValue();
SearchParameterMap map = myMatchUrlService.translateMatchUrl(criteria, myFhirCtx.getResourceDefinition(Encounter.class));
map.setLoadSynchronous(true);
myCaptureQueriesListener.clear();
IBundleProvider results = myEncounterDao.search(map);
myCaptureQueriesListener.logSelectQueriesForCurrentThread(0);
List<String> ids = toUnqualifiedVersionlessIdValues(results);
assertThat(ids, containsInAnyOrder(encounterId.getValue()));
}
@Test
public void testHasParameter() {
IIdType pid0;
@ -3258,6 +3344,105 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testSearchWithDateAndReusesExistingJoin() {
// Add a search parameter to Observation.issued, so that between that one
// and the existing one on Observation.effective, we have 2 date search parameters
// on the same resource
{
SearchParameter sp = new SearchParameter();
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.addBase("Observation");
sp.setType(Enumerations.SearchParamType.DATE);
sp.setCode("issued");
sp.setExpression("Observation.issued");
mySearchParameterDao.create(sp);
mySearchParamRegistry.forceRefresh();
}
// Dates are reversed on these two observations
IIdType obsId1;
{
Observation obs = new Observation();
obs.setIssuedElement(new InstantType("2020-06-06T12:00:00Z"));
obs.setEffective(new InstantType("2019-06-06T12:00:00Z"));
obsId1 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
}
IIdType obsId2;
{
Observation obs = new Observation();
obs.setIssuedElement(new InstantType("2019-06-06T12:00:00Z"));
obs.setEffective(new InstantType("2020-06-06T12:00:00Z"));
obsId2 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
}
// Add two with a period
IIdType obsId3;
{
Observation obs = new Observation();
obs.setEffective(new Period().setStartElement(new DateTimeType("2000-06-06T12:00:00Z")).setEndElement(new DateTimeType("2001-06-06T12:00:00Z")));
obsId3 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
}
IIdType obsId4;
{
Observation obs = new Observation();
obs.setEffective(new Period().setStartElement(new DateTimeType("2001-01-01T12:00:00Z")).setEndElement(new DateTimeType("2002-01-01T12:00:00Z")));
obsId4 = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
}
// Two AND instances of 1 SP
{
myCaptureQueriesListener.clear();
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add("issued", new DateParam("ge2020-06-05"));
params.add("issued", new DateParam("lt2020-06-07"));
List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
assertThat(patients.toString(), patients, contains(obsId1));
String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
ourLog.info("Search query:\n{}", searchQuery);
assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "join"));
assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"));
assertEquals(searchQuery, 2, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"));
}
// Two AND instances of 1 SP and 1 instance of another
{
myCaptureQueriesListener.clear();
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add("issued", new DateParam("ge2020-06-05"));
params.add("issued", new DateParam("lt2020-06-07"));
params.add("date", new DateParam("gt2019-06-05"));
params.add("date", new DateParam("lt2019-06-07"));
List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
assertThat(patients.toString(), patients, contains(obsId1));
String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
ourLog.info("Search query:\n{}", searchQuery);
assertEquals(searchQuery, 2, StringUtils.countMatches(searchQuery.toLowerCase(), "join"));
assertEquals(searchQuery, 2, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"));
assertEquals(searchQuery, 4, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"));
}
// Period search
{
myCaptureQueriesListener.clear();
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.add("date", new DateParam("lt2002-01-01T12:00:00Z"));
List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
assertThat(patients.toString(), patients, containsInAnyOrder(obsId3, obsId4));
String searchQuery = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
ourLog.info("Search query:\n{}", searchQuery);
assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "join"));
assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "hash_identity"));
assertEquals(searchQuery, 1, StringUtils.countMatches(searchQuery.toLowerCase(), "sp_value_low"));
}
}
@Test
public void testSearchWithFetchSizeDefaultMaximum() {
myDaoConfig.setFetchSizeDefaultMaximum(5);
@ -4228,6 +4413,44 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
}
}
@Test
public void testCircularReferencesDontBreakRevIncludes() {
Patient p = new Patient();
p.setActive(true);
IIdType patientId = myPatientDao.create(p).getId().toUnqualifiedVersionless();
Encounter enc = new Encounter();
enc.setStatus(Encounter.EncounterStatus.ARRIVED);
enc.getSubject().setReference(patientId.getValue());
IIdType encId = myEncounterDao.create(enc).getId().toUnqualifiedVersionless();
Condition cond = new Condition();
cond.addIdentifier().setSystem("http://foo").setValue("123");
IIdType conditionId = myConditionDao.create(cond).getId().toUnqualifiedVersionless();
EpisodeOfCare ep = new EpisodeOfCare();
ep.setStatus(EpisodeOfCare.EpisodeOfCareStatus.ACTIVE);
IIdType epId = myEpisodeOfCareDao.create(ep).getId().toUnqualifiedVersionless();
enc.getEpisodeOfCareFirstRep().setReference(ep.getId());
myEncounterDao.update(enc);
cond.getEncounter().setReference(enc.getId());
myConditionDao.update(cond);
ep.getDiagnosisFirstRep().getCondition().setReference(cond.getId());
myEpisodeOfCareDao.update(ep);
// Search time
SearchParameterMap params = new SearchParameterMap();
params.setLoadSynchronous(true);
params.addRevInclude(new Include("*").setRecurse(true));
IBundleProvider results = myPatientDao.search(params);
List<String> values = toUnqualifiedVersionlessIdValues(results);
assertThat(values.toString(), values, containsInAnyOrder(patientId.getValue(), encId.getValue(), conditionId.getValue(), epId.getValue()));
}
private String toStringMultiline(List<?> theResults) {
StringBuilder b = new StringBuilder();
for (Object next : theResults) {

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java
View File

@ -30,7 +30,6 @@ import org.junit.Test;
import org.springframework.aop.framework.AopProxyUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.concurrent.ThreadPoolExecutorFactoryBean;
import org.springframework.test.context.TestPropertySource;
import java.util.ArrayList;
import java.util.Arrays;
@ -163,7 +162,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
}
@Test
public void testFetchTotalAccurateForSlowLoading() throws InterruptedException {
public void testFetchTotalAccurateForSlowLoading() {
create200Patients();
mySearchCoordinatorSvcImpl.setLoadingThrottleForUnitTests(25);
@ -836,8 +835,6 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
assertEquals(1, myCaptureQueriesListener.countSelectQueriesForCurrentThread());
assertEquals(4, myCaptureQueriesListener.countInsertQueriesForCurrentThread());
assertEquals(0, myCaptureQueriesListener.countDeleteQueriesForCurrentThread());
// Because of the forced ID's bidirectional link HFJ_RESOURCE <-> HFJ_FORCED_ID
assertEquals(1, myCaptureQueriesListener.countUpdateQueriesForCurrentThread());
runInTransaction(() -> {
assertEquals(1, myResourceTableDao.count());
assertEquals(1, myResourceHistoryTableDao.count());

50
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchTest.java
View File

@ -23,6 +23,7 @@ import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.util.TestUtil;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.ValidationResult;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
@ -37,8 +38,10 @@ import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.PlatformTransactionManager;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.assertEquals;
@ -146,6 +149,53 @@ public class FhirResourceDaoR4SearchWithElasticSearchTest extends BaseJpaTest {
}
@Test
public void testExpandVsWithMultiInclude_All() throws IOException {
CodeSystem cs = loadResource(myFhirCtx, CodeSystem.class, "/r4/expand-multi-cs.json");
myCodeSystemDao.update(cs);
ValueSet vs = loadResource(myFhirCtx, ValueSet.class, "/r4/expand-multi-vs-all.json");
ValueSet expanded = myValueSetDao.expand(vs, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
// All codes
List<String> codes = expanded
.getExpansion()
.getContains()
.stream()
.map(t -> t.getCode())
.sorted()
.collect(Collectors.toList());
assertThat(codes.toString(), codes, Matchers.contains("advice", "message", "note", "notification"));
}
@Test
public void testExpandVsWithMultiInclude_Some() throws IOException {
CodeSystem cs = loadResource(myFhirCtx, CodeSystem.class, "/r4/expand-multi-cs.json");
myCodeSystemDao.update(cs);
ValueSet vs = loadResource(myFhirCtx, ValueSet.class, "/r4/expand-multi-vs-all.json");
vs.getCompose().getInclude().get(0).getConcept().remove(0);
vs.getCompose().getInclude().get(0).getConcept().remove(0);
ValueSet expanded = myValueSetDao.expand(vs, null);
ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(expanded));
// All codes
List<String> codes = expanded
.getExpansion()
.getContains()
.stream()
.map(t -> t.getCode())
.sorted()
.collect(Collectors.toList());
assertThat(codes.toString(), codes, Matchers.contains("advice", "note"));
}
private CodeSystem createExternalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
View File

@ -164,6 +164,8 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
}
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(new ResourcePersistentId(table.getId()), URL_MY_CODE_SYSTEM, "SYSTEM NAME", "SYSTEM VERSION", cs, table);
myTerminologyDeferredStorageSvc.saveAllDeferred();
}
private void createLocalCsAndVs() {

13
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
View File

@ -147,6 +147,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
}
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://loinc.org", codesToAdd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
// Create a valueset
ValueSet vs = new ValueSet();
vs.setUrl("http://example.com/fhir/ValueSet/observation-vitalsignresult");
@ -399,12 +401,11 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
myObservationDao.validate(input, null, encoded, EncodingEnum.JSON, mode, null, mySrd);
fail();
} catch (PreconditionFailedException e) {
String ooString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(e.getOperationOutcome());
ourLog.info(ooString);
assertThat(ooString, containsString("StructureDefinition reference \\\"" + profileUri + "\\\" could not be resolved"));
org.hl7.fhir.r4.model.OperationOutcome oo = (org.hl7.fhir.r4.model.OperationOutcome) e.getOperationOutcome();
String outputString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo);
ourLog.info(outputString);
assertThat(outputString, containsString("Profile reference 'http://example.com/StructureDefinition/testValidateResourceContainingProfileDeclarationInvalid' could not be resolved, so has not been checked"));
}
}
@Test
@ -618,6 +619,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
upload("/r4/uscore/ValueSet-omb-race-category.json");
upload("/r4/uscore/ValueSet-us-core-usps-state.json");
myTerminologyDeferredStorageSvc.saveAllDeferred();
{
String resource = loadResource("/r4/uscore/patient-resource-badcode.json");
IBaseResource parsedResource = myFhirCtx.newJsonParser().parseResource(resource);

46
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4CacheTest.java
View File

@ -9,20 +9,29 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.client.interceptor.CapturingInterceptor;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Patient;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Date;
import static org.hamcrest.Matchers.*;
import static org.hamcrest.Matchers.blankOrNullString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.greaterThan;
import static org.hamcrest.Matchers.lessThan;
import static org.hamcrest.core.IsNot.not;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(ResourceProviderR4CacheTest.class);
private CapturingInterceptor myCapturingInterceptor;
@Autowired
private ISearchDao mySearchEntityDao;
@ -184,6 +193,39 @@ public class ResourceProviderR4CacheTest extends BaseResourceProviderR4Test {
assertEquals(results1.getId(), results2.getId());
}
@Test
public void testDeletedSearchResultsNotReturnedFromCache() {
Patient p = new Patient();
p.addName().setFamily("Foo");
String p1Id = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
p = new Patient();
p.addName().setFamily("Foo");
String p2Id = myPatientDao.create(p).getId().toUnqualifiedVersionless().getValue();
Bundle resp1 = ourClient
.search()
.forResource("Patient")
.where(Patient.NAME.matches().value("foo"))
.returnBundle(Bundle.class)
.execute();
assertEquals(2, resp1.getEntry().size());
ourClient.delete().resourceById(new IdType(p1Id)).execute();
Bundle resp2 = ourClient
.search()
.forResource("Patient")
.where(Patient.NAME.matches().value("foo"))
.returnBundle(Bundle.class)
.execute();
assertEquals(resp1.getId(), resp2.getId());
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp2));
assertEquals(1, resp2.getEntry().size());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

27
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -15,6 +15,7 @@ import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.client.apache.ResourceEntity;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
@ -26,6 +27,9 @@ import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.RequestValidatingInterceptor;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import ca.uhn.fhir.validation.ResultSeverityEnum;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
@ -52,6 +56,7 @@ import org.hl7.fhir.r4.model.Observation.ObservationStatus;
import org.hl7.fhir.r4.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionChannelType;
import org.hl7.fhir.r4.model.Subscription.SubscriptionStatus;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.util.AopTestUtils;
@ -2260,6 +2265,28 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
}
}
@Test
public void testValidateResourceContainingProfileDeclarationDoesntResolve() throws IOException {
Observation input = new Observation();
input.getText().setDiv(new XhtmlNode().setValue("<div>AA</div>")).setStatus(Narrative.NarrativeStatus.GENERATED);
input.getMeta().addProfile("http://foo/structuredefinition/myprofile");
input.getCode().setText("Hello");
input.setStatus(ObservationStatus.FINAL);
HttpPost post = new HttpPost(ourServerBase + "/Observation/$validate?_pretty=true");
post.setEntity(new ResourceEntity(myFhirCtx, input));
try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
ourLog.info(respString);
assertEquals(412, resp.getStatusLine().getStatusCode());
assertThat(respString, containsString("Profile reference 'http://foo/structuredefinition/myprofile' could not be resolved, so has not been checked"));
}
}
@SuppressWarnings("unused")
@Test
public void testFullTextSearch() throws Exception {

39
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java
View File

@ -182,33 +182,11 @@ public class SearchCoordinatorSvcImplTest {
when(mySearchBuilder.createQuery(any(), any(), any())).thenReturn(iter);
doAnswer(loadPids()).when(mySearchBuilder).loadResourcesByPid(any(Collection.class), any(Collection.class), any(List.class), anyBoolean(), any());
when(mySearchResultCacheSvc.fetchResultPids(any(), anyInt(), anyInt())).thenAnswer(t -> {
List<ResourcePersistentId> returnedValues = iter.getReturnedValues();
int offset = t.getArgument(1, Integer.class);
int end = t.getArgument(2, Integer.class);
end = Math.min(end, returnedValues.size());
offset = Math.min(offset, returnedValues.size());
ourLog.info("findWithSearchUuid {} - {} out of {} values", offset, end, returnedValues.size());
return returnedValues.subList(offset, end);
});
when(mySearchResultCacheSvc.fetchAllResultPids(any())).thenReturn(allResults);
when(mySearchCacheSvc.tryToMarkSearchAsInProgress(any())).thenAnswer(t->{
Search search = t.getArgument(0, Search.class);
assertEquals(SearchStatusEnum.PASSCMPLET, search.getStatus());
search.setStatus(SearchStatusEnum.LOADING);
return Optional.of(search);
});
when(mySearchCacheSvc.save(any())).thenAnswer(t -> {
Search search = t.getArgument(0, Search.class);
myCurrentSearch = search;
return search;
});
when(mySearchCacheSvc.fetchByUuid(any())).thenAnswer(t -> Optional.ofNullable(myCurrentSearch));
IFhirResourceDao dao = myCallingDao;
when(myDaoRegistry.getResourceDao(any(String.class))).thenReturn(dao);
IBundleProvider result = mySvc.registerSearch(myCallingDao, params, "Patient", new CacheControlDirective(), null);
assertNotNull(result.getUuid());
@ -602,6 +580,11 @@ public class SearchCoordinatorSvcImplTest {
return myWrap.getSkippedCount();
}
@Override
public int getNonSkippedCount() {
return myCount;
}
@Override
public void close() {
// nothing
@ -611,6 +594,7 @@ public class SearchCoordinatorSvcImplTest {
public static class ResultIterator extends BaseIterator<ResourcePersistentId> implements IResultIterator {
private final Iterator<ResourcePersistentId> myWrap;
private int myCount;
ResultIterator(Iterator<ResourcePersistentId> theWrap) {
myWrap = theWrap;
@ -623,6 +607,7 @@ public class SearchCoordinatorSvcImplTest {
@Override
public ResourcePersistentId next() {
myCount++;
return myWrap.next();
}
@ -631,6 +616,11 @@ public class SearchCoordinatorSvcImplTest {
return 0;
}
@Override
public int getNonSkippedCount() {
return myCount;
}
@Override
public void close() {
// nothing
@ -697,6 +687,11 @@ public class SearchCoordinatorSvcImplTest {
}
}
@Override
public int getNonSkippedCount() {
return 0;
}
@Override
public void close() {
// nothing

196
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcDeltaR4Test.java
View File

@ -1,10 +1,12 @@
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.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.UriParam;
@ -16,25 +18,36 @@ import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.apache.commons.lang3.StringUtils.leftPad;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.matchesPattern;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcDeltaR4Test.class);
@After
public void after() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
}
@Test
public void testAddRootConcepts() {
@ -115,17 +128,23 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
ourLog.info("All concepts: {}", myTermConceptDao.findAll());
});
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
TermConcept root = delta.addRootConcept("RootA", "Root A");
root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
root.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAB").setDisplay("Child AB");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
myCaptureQueriesListener.logAllQueriesForCurrentThread();
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAB seq=1",
"RootB seq=0"
);
}
@Test
@ -156,12 +175,86 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAAA seq=0",
"RootB seq=0",
" ChildAA seq=0",
" ChildAAA seq=0"
);
assertEquals(2, outcome.getUpdatedConceptCount());
runInTransaction(() -> {
TermConcept concept = myTermSvc.findCode("http://foo/cs", "ChildAA").orElseThrow(() -> new IllegalStateException());
assertEquals(2, concept.getParents().size());
assertThat(concept.getParentPidsAsString(), matchesPattern("^[0-9]+ [0-9]+$"));
});
}
@Test
public void testReAddingConceptsDoesntRecreateExistingLinks() {
createNotPresentCodeSystem();
assertHierarchyContains();
UploadStatistics outcome;
CustomTerminologySet delta;
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
delta.addRootConcept("RootA", "Root A")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0"
);
myCaptureQueriesListener.logDeleteQueries();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
myCaptureQueriesListener.logInsertQueries();
// 2 concepts, 1 link
assertEquals(3, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
delta.addRootConcept("RootA", "Root A")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAAA seq=0"
);
myCaptureQueriesListener.logDeleteQueries();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
myCaptureQueriesListener.logInsertQueries();
// 1 concept, 1 link
assertEquals(2, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.clear();
delta = new CustomTerminologySet();
delta.addRootConcept("RootA", "Root A")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAA").setDisplay("Child AA")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAA").setDisplay("Child AAA")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("ChildAAAA").setDisplay("Child AAAA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertHierarchyContains(
"RootA seq=0",
" ChildAA seq=0",
" ChildAAA seq=0",
" ChildAAAA seq=0"
);
myCaptureQueriesListener.logDeleteQueries();
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
myCaptureQueriesListener.logInsertQueries();
// 1 concept, 1 link
assertEquals(2, myCaptureQueriesListener.countInsertQueries());
myCaptureQueriesListener.clear();
}
@Test
@ -281,6 +374,49 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
}
@Test
public void testAddLargeHierarchy() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(5);
createNotPresentCodeSystem();
ValueSet vs;
vs = expandNotPresentCodeSystem();
assertEquals(0, vs.getExpansion().getContains().size());
CustomTerminologySet delta = new CustomTerminologySet();
// Create a nice deep hierarchy
TermConcept concept = delta.addRootConcept("Root", "Root");
int nestedDepth = 10;
for (int i = 0; i < nestedDepth; i++) {
String name = concept.getCode();
concept = concept.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode(name + "0").setDisplay(name + "0");
}
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertFalse(myTermDeferredStorageSvc.isStorageQueueEmpty());
while (!myTermDeferredStorageSvc.isStorageQueueEmpty()) {
myTermDeferredStorageSvc.saveDeferred();
}
List<String> expectedHierarchy = new ArrayList<>();
for (int i = 0; i < nestedDepth + 1; i++) {
String expected = leftPad("", i, " ") +
"Root" +
leftPad("", i, "0") +
" seq=0";
expectedHierarchy.add(expected);
}
assertHierarchyContains(expectedHierarchy.toArray(new String[0]));
}
@Autowired
private ITermDeferredStorageSvc myTermDeferredStorageSvc;
@Test
public void testAddModifiesExistingCodesInPlace() {
@ -307,54 +443,6 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
assertEquals("CODEA1", myTermSvc.lookupCode(myFhirCtx, "http://foo", "codea").getCodeDisplay());
}
@Test
public void testAddRelocateHierarchy() {
createNotPresentCodeSystem();
// Add code hierarchy
CustomTerminologySet delta = new CustomTerminologySet();
TermConcept codeA = delta.addRootConcept("CodeA", "Code A");
TermConcept codeAA = codeA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
codeAA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAAA").setDisplay("Code AAA");
codeAA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAAB").setDisplay("Code AAB");
TermConcept codeB = delta.addRootConcept("CodeB", "Code B");
TermConcept codeBA = codeB.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBA").setDisplay("Code BA");
codeBA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBAA").setDisplay("Code BAA");
codeBA.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeBAB").setDisplay("Code BAB");
UploadStatistics outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertEquals(8, outcome.getUpdatedConceptCount());
assertHierarchyContains(
"CodeA seq=0",
" CodeAA seq=0",
" CodeAAA seq=0",
" CodeAAB seq=1",
"CodeB seq=0",
" CodeBA seq=0",
" CodeBAA seq=0",
" CodeBAB seq=1"
);
// Move a single child code to a new spot and make sure the hierarchy comes along
// for the ride..
delta = new CustomTerminologySet();
delta
.addRootConcept("CodeB", "Code B")
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA).setCode("CodeAA").setDisplay("Code AA");
outcome = myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://foo/cs", delta);
assertEquals(2, outcome.getUpdatedConceptCount());
assertHierarchyContains(
"CodeA seq=0",
"CodeB seq=0",
" CodeBA seq=0",
" CodeBAA seq=0",
" CodeBAB seq=1",
" CodeAA seq=0", // <-- CodeAA got added here so it comes second
" CodeAAA seq=0",
" CodeAAB seq=1"
);
}
@Test
@Ignore
public void testAddWithPropertiesAndDesignations() {
@ -464,9 +552,15 @@ public class TerminologySvcDeltaR4Test extends BaseJpaR4Test {
assertEquals(true, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeAAA").isPresent()));
// Remove CodeA
delta = new CustomTerminologySet();
delta.addRootConcept("codeA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsRemove("http://foo/cs", delta);
myCaptureQueriesListener.clear();
runInTransaction(()->{
CustomTerminologySet delta2 = new CustomTerminologySet();
delta2.addRootConcept("codeA");
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsRemove("http://foo/cs", delta2);
});
myCaptureQueriesListener.logAllQueriesForCurrentThread();
ourLog.info("*** Done removing");
assertEquals(false, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeB").isPresent()));
assertEquals(false, runInTransaction(() -> myTermSvc.findCode("http://foo/cs", "codeA").isPresent()));

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