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Fix nonnull annotations

This commit is contained in:
jamesagnew 2021-01-21 08:47:44 -05:00
parent 14b0688f69
commit 078a94f1a6
11 changed files with 52 additions and 78 deletions
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2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/FilesystemBinaryStorageSvcImpl.java
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@ -32,11 +32,11 @@ import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.CountingInputStream;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.Nullable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import java.io.*;
import java.util.Date;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -103,8 +103,6 @@ import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Required;
import org.springframework.data.domain.SliceImpl;
@ -539,7 +537,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return myDeleteExpungeService.expungeByResourcePids(theUrl, myResourceName, new SliceImpl<>(ResourcePersistentId.toLongList(theResourceIds)), theTheRequest);
}
@NotNull
@Nonnull
@Override
public DeleteMethodOutcome deletePidList(String theUrl, Collection<ResourcePersistentId> theResourceIds, DeleteConflictList theDeleteConflicts, RequestDetails theRequest) {
StopWatch w = new StopWatch();

74
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
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@ -20,54 +20,34 @@ package ca.uhn.fhir.jpa.dao;
* #L%
*/
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.TokenStream;
import org.apache.lucene.search.highlight.Formatter;
import org.apache.lucene.search.highlight.Highlighter;
import org.apache.lucene.search.highlight.Scorer;
import org.apache.lucene.search.highlight.TextFragment;
import org.apache.lucene.search.highlight.TokenGroup;
import org.hibernate.search.backend.lucene.index.LuceneIndexManager;
import org.hibernate.search.engine.search.predicate.dsl.BooleanPredicateClausesStep;
import org.hibernate.search.engine.search.predicate.dsl.SearchPredicateFactory;
import org.hibernate.search.engine.search.query.SearchQuery;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.mapping.SearchMapping;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionTemplate;
import javax.annotation.Nonnull;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
@ -76,20 +56,20 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FulltextSearchSvcImpl.class);
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
protected IForcedIdDao myForcedIdDao;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
private EntityManager myEntityManager;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private IdHelperService myIdHelperService;
private Boolean ourDisabled;
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
/**
* Constructor
@ -98,28 +78,28 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
super();
}
private void addTextSearch(SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, List<List<IQueryParameterType>> theTerms, String theFieldName, String theFieldNameEdgeNGram, String theFieldNameTextNGram){
private void addTextSearch(SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, List<List<IQueryParameterType>> theTerms, String theFieldName, String theFieldNameEdgeNGram, String theFieldNameTextNGram) {
if (theTerms == null) {
return;
}
for (List<? extends IQueryParameterType> nextAnd : theTerms) {
Set<String> terms = extractOrStringParams(nextAnd);
if (terms.size() == 1) {
b.must(f.phrase()
.field(theFieldName)
.boost(4.0f)
.matching(terms.iterator().next().toLowerCase())
.slop(2));
} else if (terms.size() > 1){
String joinedTerms = StringUtils.join(terms, ' ');
b.must(f.match().field(theFieldName).matching(joinedTerms));
} else {
ourLog.debug("No Terms found in query parameter {}", nextAnd);
}
if (terms.size() == 1) {
b.must(f.phrase()
.field(theFieldName)
.boost(4.0f)
.matching(terms.iterator().next().toLowerCase())
.slop(2));
} else if (terms.size() > 1) {
String joinedTerms = StringUtils.join(terms, ' ');
b.must(f.match().field(theFieldName).matching(joinedTerms));
} else {
ourLog.debug("No Terms found in query parameter {}", nextAnd);
}
}
}
@NotNull
@Nonnull
private Set<String> extractOrStringParams(List<? extends IQueryParameterType> nextAnd) {
Set<String> terms = new HashSet<>();
for (IQueryParameterType nextOr : nextAnd) {
@ -229,10 +209,4 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
return doSearch(theResourceName, theParams, null);
}
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
@Autowired
private PartitionSettings myPartitionSettings;
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/PartitionManagementProvider.java
View File

@ -29,9 +29,10 @@ import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import static ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.validatePartitionIdSupplied;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.instance.model.api.IPrimitiveType.toValueOrNull;
@ -151,7 +152,7 @@ public class PartitionManagementProvider {
return retVal;
}
@NotNull
@Nonnull
private PartitionEntity parseInput(@OperationParam(name = ProviderConstants.PARTITION_MANAGEMENT_PARTITION_ID, min = 1, max = 1, typeName = "integer") IPrimitiveType<Integer> thePartitionId, @OperationParam(name = ProviderConstants.PARTITION_MANAGEMENT_PARTITION_NAME, min = 1, max = 1, typeName = "code") IPrimitiveType<String> thePartitionName, @OperationParam(name = ProviderConstants.PARTITION_MANAGEMENT_PARTITION_DESC, min = 0, max = 1, typeName = "string") IPrimitiveType<String> thePartitionDescription) {
PartitionEntity input = new PartitionEntity();
if (thePartitionId != null) {

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/PersistedJpaBundleProvider.java
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@ -52,7 +52,6 @@ import ca.uhn.fhir.rest.api.server.SimplePreResourceShowDetails;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -191,7 +190,7 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
return retVal;
}
@NotNull
@Nonnull
private RequestPartitionId getRequestPartitionId() {
if (myRequestPartitionId == null) {
if (mySearchEntity.getResourceId() != null) {

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImpl.java
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@ -576,7 +576,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
return null;
}
@org.jetbrains.annotations.Nullable
@Nullable
private Integer getLoadSynchronousUpToOrNull(CacheControlDirective theCacheControlDirective) {
final Integer loadSynchronousUpTo;
if (theCacheControlDirective != null && theCacheControlDirective.isNoStore()) {

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/partition/PartitionManagementProviderTest.java
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@ -12,7 +12,6 @@ import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.IntegerType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
@ -28,6 +27,8 @@ import org.springframework.context.annotation.Configuration;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import javax.annotation.Nonnull;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
@ -87,7 +88,7 @@ public class PartitionManagementProviderTest {
assertEquals("a description", ((StringType) response.getParameter(ProviderConstants.PARTITION_MANAGEMENT_PARTITION_DESC)).getValue());
}
@NotNull
@Nonnull
private Parameters createInputPartition() {
Parameters input = new Parameters();
input.addParameter(ProviderConstants.PARTITION_MANAGEMENT_PARTITION_ID, new IntegerType(123));
@ -248,7 +249,7 @@ public class PartitionManagementProviderTest {
}
@NotNull
@Nonnull
private static Answer<Object> createAnswer() {
return t -> t.getArgument(0, PartitionEntity.class);
}

10
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmControllerSvcImpl.java
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@ -20,23 +20,23 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.IGoldenResourceMergerSvc;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmLinkQuerySvc;
import ca.uhn.fhir.mdm.api.IMdmLinkUpdaterSvc;
import ca.uhn.fhir.mdm.api.IGoldenResourceMergerSvc;
import ca.uhn.fhir.mdm.api.MdmLinkJson;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
import ca.uhn.fhir.mdm.provider.MdmControllerUtil;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.jetbrains.annotations.Nullable;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nullable;
import java.util.stream.Stream;
/**

17
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmResourceDaoSvc.java
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@ -20,23 +20,23 @@ package ca.uhn.fhir.jpa.mdm.svc;
* #L%
*/
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import java.util.List;
import java.util.Optional;
@ -60,10 +60,11 @@ public class MdmResourceDaoSvc {
}
/**
* Given a resource, remove its Golden Resource tag.
* @param theGoldenResource the {@link IAnyResource} to remove the tag from.
* @param theResourcetype the type of that resource
*/
* Given a resource, remove its Golden Resource tag.
*
* @param theGoldenResource the {@link IAnyResource} to remove the tag from.
* @param theResourcetype the type of that resource
*/
public void removeGoldenResourceTag(IAnyResource theGoldenResource, String theResourcetype) {
IFhirResourceDao resourceDao = myDaoRegistry.getResourceDao(theResourcetype);
resourceDao.removeTag(theGoldenResource.getIdElement(), TagTypeEnum.TAG, MdmConstants.SYSTEM_GOLDEN_RECORD_STATUS, MdmConstants.CODE_GOLDEN_RECORD);
@ -99,7 +100,7 @@ public class MdmResourceDaoSvc {
}
}
@NotNull
@Nonnull
private SearchParameterMap buildEidSearchParameterMap(String theTheEid) {
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);

3
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java
View File

@ -48,7 +48,6 @@ import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.Reference;
import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.extension.ExtendWith;
@ -431,7 +430,7 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
return getPatientsByTag(MdmConstants.CODE_GOLDEN_RECORD_REDIRECTED);
}
@NotNull
@Nonnull
private List<IBaseResource> getPatientsByTag(String theCode) {
SearchParameterMap map = new SearchParameterMap();
map.setLoadSynchronous(true);

3
hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java
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@ -23,7 +23,8 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.jetbrains.annotations.Nullable;
import javax.annotation.Nullable;
public abstract class BaseTableColumnTypeTask extends BaseTableColumnTask {
private ColumnTypeEnum myColumnType;