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Fixes

This commit is contained in:
James Agnew 2024-11-07 11:11:35 -05:00
parent e3270af4a9
commit 215cbaa80c
16 changed files with 2196 additions and 18 deletions
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12
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/HistorySearchDateRangeParam.java
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@ -22,6 +22,18 @@ package ca.uhn.fhir.rest.param;
import java.util.Map;
public class HistorySearchDateRangeParam extends DateRangeParam {
/**
* Constructor
*
* @since 8.0.0
*/
public HistorySearchDateRangeParam() {
this(Map.of(), new DateRangeParam(), null);
}
/**
* Constructor
*/
public HistorySearchDateRangeParam(
Map<String, String[]> theParameters, DateRangeParam theDateRange, Integer theOffset) {
super(theDateRange);

2
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/FileUtil.java
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@ -29,7 +29,7 @@ public class FileUtil {
if (theBytes <= 0) {
return "0 " + UNITS[0];
}
int digitGroups = (int) (Math.log10(theBytes) / Math.log10(1024));
int digitGroups = (int) (Math.log10((double)theBytes) / Math.log10(1024));
digitGroups = Math.min(digitGroups, UNITS.length - 1);
return new DecimalFormat("###0.#").format(theBytes / Math.pow(1024, digitGroups)) + " " + UNITS[digitGroups];
}

12
hapi-fhir-jpaserver-test-r5/pom.xml
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@ -47,6 +47,18 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-test</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.github.jsqlparser</groupId>
<artifactId>jsqlparser</artifactId>
<scope>test</scope>
</dependency>
</dependencies>

18
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
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@ -19,6 +19,7 @@ import ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor;
import ca.uhn.fhir.jpa.binary.provider.BinaryAccessProvider;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportJobSchedulingHelper;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.TestDaoSearch;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryProvenanceDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTagDao;
@ -142,7 +143,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.Mockito.mock;
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {TestR5Config.class})
@ContextConfiguration(classes = {TestR5Config.class, TestDaoSearch.Config.class})
public abstract class BaseJpaR5Test extends BaseJpaTest implements ITestDataBuilder {
@Autowired
protected IJobCoordinator myJobCoordinator;
@ -421,12 +422,15 @@ public abstract class BaseJpaR5Test extends BaseJpaTest implements ITestDataBuil
@AfterEach()
public void afterCleanupDao() {
myStorageSettings.setExpireSearchResults(new JpaStorageSettings().isExpireSearchResults());
myStorageSettings.setEnforceReferentialIntegrityOnDelete(new JpaStorageSettings().isEnforceReferentialIntegrityOnDelete());
myStorageSettings.setExpireSearchResultsAfterMillis(new JpaStorageSettings().getExpireSearchResultsAfterMillis());
myStorageSettings.setReuseCachedSearchResultsForMillis(new JpaStorageSettings().getReuseCachedSearchResultsForMillis());
myStorageSettings.setSuppressUpdatesWithNoChange(new JpaStorageSettings().isSuppressUpdatesWithNoChange());
myStorageSettings.setAllowContainsSearches(new JpaStorageSettings().isAllowContainsSearches());
JpaStorageSettings defaults = new JpaStorageSettings();
myStorageSettings.setAccessMetaSourceInformationFromProvenanceTable(defaults.isAccessMetaSourceInformationFromProvenanceTable());
myStorageSettings.setAllowContainsSearches(defaults.isAllowContainsSearches());
myStorageSettings.setEnforceReferentialIntegrityOnDelete(defaults.isEnforceReferentialIntegrityOnDelete());
myStorageSettings.setExpireSearchResults(defaults.isExpireSearchResults());
myStorageSettings.setExpireSearchResultsAfterMillis(defaults.getExpireSearchResultsAfterMillis());
myStorageSettings.setReuseCachedSearchResultsForMillis(defaults.getReuseCachedSearchResultsForMillis());
myStorageSettings.setSuppressUpdatesWithNoChange(defaults.isSuppressUpdatesWithNoChange());
myStorageSettings.setAutoCreatePlaceholderReferenceTargets(defaults.isAutoCreatePlaceholderReferenceTargets());
myPagingProvider.setDefaultPageSize(BasePagingProvider.DEFAULT_DEFAULT_PAGE_SIZE);
myPagingProvider.setMaximumPageSize(BasePagingProvider.DEFAULT_MAX_PAGE_SIZE);

47
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/dbpartitionmode/BaseDbpmJpaR5Test.java Normal file
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@ -0,0 +1,47 @@
package ca.uhn.fhir.jpa.dao.r5.dbpartitionmode;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.r5.BaseJpaR5Test;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.partition.IPartitionLookupSvc;
import ca.uhn.fhir.jpa.util.TestPartitionSelectorInterceptor;
import org.junit.jupiter.api.AfterEach;
import org.springframework.beans.factory.annotation.Autowired;
import static org.junit.jupiter.api.Assertions.assertFalse;
public class BaseDbpmJpaR5Test extends BaseJpaR5Test {
public static final String PARTITION_NAME_1 = "Partition_1";
public static final String PARTITION_NAME_2 = "Partition_2";
public static final int PARTITION_1 = 1;
public static final int PARTITION_2 = 2;
protected final TestPartitionSelectorInterceptor myPartitionSelectorInterceptor = new TestPartitionSelectorInterceptor();
@Autowired
private IPartitionLookupSvc myPartitionConfigSvc;
@Override
@AfterEach
protected void afterResetInterceptors() {
super.afterResetInterceptors();
myPartitionSettings.setPartitioningEnabled(false);
myInterceptorRegistry.unregisterInterceptor(myPartitionSelectorInterceptor);
}
protected void registerPartitionInterceptorAndCreatePartitions() {
assertFalse(myInterceptorRegistry.hasHooks(Pointcut.STORAGE_PARTITION_IDENTIFY_READ), ()->myInterceptorRegistry.getAllRegisteredInterceptors().toString());
myInterceptorRegistry.registerInterceptor(myPartitionSelectorInterceptor);
myPartitionConfigSvc.createPartition(new PartitionEntity().setId(PARTITION_1).setName(PARTITION_NAME_1), null);
myPartitionConfigSvc.createPartition(new PartitionEntity().setId(PARTITION_2).setName(PARTITION_NAME_2), null);
// Load to pre-cache and avoid adding SQL queries
myPartitionConfigSvc.getPartitionById(PARTITION_1);
myPartitionConfigSvc.getPartitionById(PARTITION_2);
myPartitionConfigSvc.getPartitionByName(PARTITION_NAME_1);
myPartitionConfigSvc.getPartitionByName(PARTITION_NAME_2);
}
}

19
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/dbpartitionmode/DbpmDisabledPartitioningDisabledTest.java Normal file
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@ -0,0 +1,19 @@
package ca.uhn.fhir.jpa.dao.r5.dbpartitionmode;
import ca.uhn.fhir.jpa.util.TestPartitionSelectorInterceptor;
import org.junit.jupiter.api.Nested;
/**
* This is a test verifying that we emit the right SQL for HAPI FHIR running in
* full legacy mode - No partitioning, no partition IDs in PKs.
*/
public class DbpmDisabledPartitioningDisabledTest extends BaseDbpmJpaR5Test {
@Nested
public class MyTestDefinitions extends TestDefinitions {
MyTestDefinitions() {
super(DbpmDisabledPartitioningDisabledTest.this, new TestPartitionSelectorInterceptor(), false, false);
}
}
}

32
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/dbpartitionmode/DbpmDisabledPartitioningEnabledNullDefaultPartitionTest.java Normal file
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@ -0,0 +1,32 @@
package ca.uhn.fhir.jpa.dao.r5.dbpartitionmode;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
/**
* This is a test verifying that we emit the right SQL when running in
* legacy partition mode with DEFAULT partition value of null (the default if
* not configured otherwise) - Partition IDs are in use, but they aren't
* included in primary keys or joins.
*/
public class DbpmDisabledPartitioningEnabledNullDefaultPartitionTest extends BaseDbpmJpaR5Test {
@Override
@BeforeEach
public void before() throws Exception {
super.before();
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setDefaultPartitionId(null);
registerPartitionInterceptorAndCreatePartitions();
}
@Nested
public class MyTestDefinitions extends TestDefinitions {
MyTestDefinitions() {
super(DbpmDisabledPartitioningEnabledNullDefaultPartitionTest.this, myPartitionSelectorInterceptor, true, false);
}
}
}

31
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/dbpartitionmode/DbpmDisabledPartitioningEnabledTest.java Normal file
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@ -0,0 +1,31 @@
package ca.uhn.fhir.jpa.dao.r5.dbpartitionmode;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
/**
* This is a test verifying that we emit the right SQL when running in
* legacy partition mode - Partition IDs are in use, but they aren't
* included in primary keys or joins.
*/
public class DbpmDisabledPartitioningEnabledTest extends BaseDbpmJpaR5Test {
@Override
@BeforeEach
public void before() throws Exception {
super.before();
myPartitionSettings.setPartitioningEnabled(true);
myPartitionSettings.setDefaultPartitionId(0);
registerPartitionInterceptorAndCreatePartitions();
}
@Nested
public class MyTestDefinitions extends TestDefinitions {
MyTestDefinitions() {
super(DbpmDisabledPartitioningEnabledTest.this, myPartitionSelectorInterceptor, true, false);
}
}
}

1929
hapi-fhir-jpaserver-test-r5/src/test/java/ca/uhn/fhir/jpa/dao/r5/dbpartitionmode/TestDefinitions.java Normal file
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File diff suppressed because it is too large Load Diff

1
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaTest.java
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@ -413,6 +413,7 @@ public abstract class BaseJpaTest extends BaseTest {
PartitionSettings defaultPartConfig = new PartitionSettings();
myPartitionSettings.setIncludePartitionInSearchHashes(defaultPartConfig.isIncludePartitionInSearchHashes());
myPartitionSettings.setAllowReferencesAcrossPartitions(defaultPartConfig.getAllowReferencesAcrossPartitions());
}
@AfterEach

11
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/util/DatabaseSupportUtil.java
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@ -19,9 +19,12 @@
*/
package ca.uhn.fhir.jpa.util;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.SystemUtils;
import java.util.UUID;
public final class DatabaseSupportUtil {
private DatabaseSupportUtil() {}
@ -50,4 +53,12 @@ public final class DatabaseSupportUtil {
&& StringUtils.isNotBlank(System.getenv("DOCKER_HOST"))
&& System.getenv("DOCKER_HOST").contains("colima");
}
/**
* Create a new connection to a randomized H2 database for testing
*/
public static DriverTypeEnum.ConnectionProperties newConnection() {
String url = "jdbc:h2:mem:test_migration-" + UUID.randomUUID() + ";CASE_INSENSITIVE_IDENTIFIERS=TRUE;";
return DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(url, "SA", "SA");
}
}

52
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/util/TestPartitionSelectorInterceptor.java Normal file
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@ -0,0 +1,52 @@
package ca.uhn.fhir.jpa.util;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.Hook;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.interceptor.model.ReadPartitionIdRequestDetails;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.partition.BaseRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.partition.RequestPartitionHelperSvc;
import jakarta.annotation.Nonnull;
import org.hl7.fhir.instance.model.api.IBaseResource;
public class TestPartitionSelectorInterceptor {
private RequestPartitionId myNextPartition;
private BaseRequestPartitionHelperSvc myHelperSvc = new RequestPartitionHelperSvc();
/**
* Constructor
*/
public TestPartitionSelectorInterceptor() {
super();
}
public void setNextPartitionId(Integer theNextPartitionId) {
myNextPartition = RequestPartitionId.fromPartitionId(theNextPartitionId);
}
public void setNextPartition(RequestPartitionId theNextPartition) {
myNextPartition = theNextPartition;
}
@Hook(Pointcut.STORAGE_PARTITION_IDENTIFY_CREATE)
public RequestPartitionId selectPartitionCreate(IBaseResource theResource) {
String resourceType = FhirContext.forR5Cached().getResourceType(theResource);
return selectPartition(resourceType);
}
@Hook(Pointcut.STORAGE_PARTITION_IDENTIFY_READ)
public RequestPartitionId selectPartitionRead(ReadPartitionIdRequestDetails theDetails) {
return selectPartition(theDetails.getResourceType());
}
@Nonnull
private RequestPartitionId selectPartition(String theResourceType) {
if (!myHelperSvc.isResourcePartitionable(theResourceType)) {
return RequestPartitionId.defaultPartition();
}
assert myNextPartition != null;
return myNextPartition;
}
}

16
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/util/BaseCaptureQueriesListener.java
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@ -28,11 +28,11 @@ import net.ttddyy.dsproxy.listener.MethodExecutionContext;
import net.ttddyy.dsproxy.proxy.ParameterSetOperation;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Queue;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.trim;
@ -85,10 +85,16 @@ public abstract class BaseCaptureQueriesListener
&& next.getParametersList().get(0).size() > 0) {
size = next.getParametersList().size();
List<ParameterSetOperation> values = next.getParametersList().get(0);
params = values.stream()
.map(t -> t.getArgs()[1])
.map(t -> t != null ? t.toString() : "NULL")
.collect(Collectors.toList());
params = new ArrayList<>();
for (ParameterSetOperation t : values) {
if (t.getMethod().getName().equals("setNull")) {
params.add(null);
} else {
Object arg = t.getArgs()[1];
String s = arg != null ? arg.toString() : null;
params.add(s);
}
}
} else {
params = Collections.emptyList();
size = next.getParametersList().size();

11
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/util/SqlQuery.java
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@ -138,10 +138,15 @@ public class SqlQuery {
break;
}
String nextParamValue = nextParams.remove(0);
if (theSanitizeParams) {
nextParamValue = UrlUtil.sanitizeUrlPart(nextParamValue);
String nextSubstitution;
if (nextParamValue != null) {
if (theSanitizeParams) {
nextParamValue = UrlUtil.sanitizeUrlPart(nextParamValue);
}
nextSubstitution = "'" + nextParamValue + "'";
} else {
nextSubstitution = "NULL";
}
String nextSubstitution = "'" + nextParamValue + "'";
retVal = retVal.substring(0, idx) + nextSubstitution + retVal.substring(idx + 1);
idx += nextSubstitution.length();
}

14
hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/ITestDataBuilder.java
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@ -21,6 +21,7 @@ package ca.uhn.fhir.test.utilities;
import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.util.FhirTerser;
@ -87,6 +88,13 @@ public interface ITestDataBuilder {
return t -> __setPrimitiveChild(getFhirContext(), t, "language", "string", theLanguage);
}
/**
* List.entry.item
*/
default ICreationArgument withListItem(IIdType theReference) {
return withElementAt("entry", withReference("item", theReference));
}
/**
* Set Patient.gender
*/
@ -233,6 +241,10 @@ public interface ITestDataBuilder {
return buildResource("Patient", theModifiers);
}
default IIdType createList(ICreationArgument... theModifiers) {
return createResource("List", theModifiers);
}
default IIdType createPatient(ICreationArgument... theModifiers) {
return createResource("Patient", theModifiers);
}
@ -315,7 +327,7 @@ public interface ITestDataBuilder {
IBaseReference reference = (IBaseReference) getFhirContext().getElementDefinition("Reference").newInstance();
reference.setReference(theReferenceValue.getValue());
RuntimeResourceDefinition resourceDef = getFhirContext().getResourceDefinition((IBaseResource) t);
BaseRuntimeElementDefinition<?> resourceDef = getFhirContext().getElementDefinition(t.getClass());
resourceDef.getChildByName(theReferenceName).getMutator().addValue(t, reference);
}
};

7
pom.xml
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@ -1164,6 +1164,11 @@
<artifactId>caffeine</artifactId>
<version>${caffeine_version}</version>
</dependency>
<dependency>
<groupId>com.github.jsqlparser</groupId>
<artifactId>jsqlparser</artifactId>
<version>5.0</version>
</dependency>
<dependency>
<groupId>com.googlecode.owasp-java-html-sanitizer</groupId>
<artifactId>owasp-java-html-sanitizer</artifactId>
@ -1355,7 +1360,7 @@
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
<version>23.0.0</version>
<version>24.0.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>