diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
index 8a291853cf2..369ae007b9d 100644
--- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_operations.md
@@ -601,7 +601,7 @@ This operation takes two optional Parameters.
0..1 |
The number of links that should be deleted at a time. If ommitted, then the batch size will be determined by the value
-of [Expunge Batch Size](/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
+of [Expunge Batch Size](/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/api/config/DaoConfig.html#getExpungeBatchSize())
property.
|
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_partitioning/partitioning.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_partitioning/partitioning.md
index 5fda22365d2..4ab1a4c4e98 100644
--- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_partitioning/partitioning.md
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_partitioning/partitioning.md
@@ -57,7 +57,7 @@ This fact can have security implications:
in use in another partition.
* In a server using the default configuration of
- SEQUENTIAL_NUMERIC [Server ID Strategy](/hapi-fhir/apidocs/hapi-fhir-storage-api/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceServerIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum))
+ SEQUENTIAL_NUMERIC [Server ID Strategy](/hapi-fhir/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/api/config/DaoConfig.html#setResourceServerIdStrategy(ca.uhn.fhir.jpa.api.config.DaoConfig.IdStrategyEnum))
a client may be able to infer the IDs of resources in other partitions based on the ID they were assigned.
These considerations can be addressed by using UUID Server ID Strategy, and disallowing client-assigned IDs.
diff --git a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/repository_validating_interceptor.md b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/repository_validating_interceptor.md
index b73ca302aa4..2ff77b30efd 100644
--- a/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/repository_validating_interceptor.md
+++ b/hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/validation/repository_validating_interceptor.md
@@ -38,7 +38,12 @@ This means that:
# Using the Repository Validating Interceptor
-Using the repository validating interceptor is as simple as creating a new instance of [RepositoryValidatingInterceptor](/hapi-fhir/apidocs/hapi-fhir-jpaserver-base/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptor.html) and registering it with the interceptor registry. The only tricky part is initializing your rules, which must be done using a [RepositoryValidatingRuleBuilder](/hapi-fhir/apidocs/hapi-fhir-jpaserver-base/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingRuleBuilder.html).
+Using the repository validating interceptor is as simple as creating a new instance
+of [RepositoryValidatingInterceptor](/hapi-fhir/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptor.html)
+and registering it with the interceptor registry. The only tricky part is initializing your rules, which must be done
+using
+a [RepositoryValidatingRuleBuilder](/hapi-fhir/apidocs/hapi-fhir-storage/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingRuleBuilder.html)
+.
The rule builder must be obtained from the Spring context, as shown below:
diff --git a/hapi-fhir-jacoco/pom.xml b/hapi-fhir-jacoco/pom.xml
index b3b32b8b321..b87e058dc54 100644
--- a/hapi-fhir-jacoco/pom.xml
+++ b/hapi-fhir-jacoco/pom.xml
@@ -11,7 +11,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
@@ -118,7 +118,7 @@
ca.uhn.hapi.fhir
- hapi-fhir-storage-api
+ hapi-fhir-storage
${project.version}
diff --git a/hapi-fhir-jaxrsserver-base/pom.xml b/hapi-fhir-jaxrsserver-base/pom.xml
index 4e860ecd4b0..75151eb29a6 100644
--- a/hapi-fhir-jaxrsserver-base/pom.xml
+++ b/hapi-fhir-jaxrsserver-base/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-jpa/pom.xml b/hapi-fhir-jpa/pom.xml
index 149ee8cb261..9950baea97b 100644
--- a/hapi-fhir-jpa/pom.xml
+++ b/hapi-fhir-jpa/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
4.0.0
diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
index 807371d55f8..82d92844f39 100644
--- a/hapi-fhir-jpaserver-base/pom.xml
+++ b/hapi-fhir-jpaserver-base/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
index f2a6ccfe046..94894a90974 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
@@ -123,6 +123,7 @@ import ca.uhn.fhir.jpa.search.cache.DatabaseSearchResultCacheSvcImpl;
import ca.uhn.fhir.jpa.search.cache.ISearchCacheSvc;
import ca.uhn.fhir.jpa.search.cache.ISearchResultCacheSvc;
import ca.uhn.fhir.jpa.search.elastic.IndexNamePrefixLayoutStrategy;
+import ca.uhn.fhir.jpa.search.reindex.BlockPolicy;
import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexer;
import ca.uhn.fhir.jpa.search.reindex.ResourceReindexingSvcImpl;
@@ -217,7 +218,6 @@ public abstract class BaseConfig {
public static final String PERSISTED_JPA_SEARCH_FIRST_PAGE_BUNDLE_PROVIDER = "PersistedJpaSearchFirstPageBundleProvider";
public static final String SEARCH_BUILDER = "SearchBuilder";
public static final String HISTORY_BUILDER = "HistoryBuilder";
- public static final String REPOSITORY_VALIDATING_RULE_BUILDER = "repositoryValidatingRuleBuilder";
private static final String HAPI_DEFAULT_SCHEDULER_GROUP = "HAPI";
@Autowired
protected Environment myEnv;
@@ -404,7 +404,7 @@ public abstract class BaseConfig {
asyncTaskExecutor.setQueueCapacity(0);
asyncTaskExecutor.setAllowCoreThreadTimeOut(true);
asyncTaskExecutor.setThreadNamePrefix("JobLauncher-");
- asyncTaskExecutor.setRejectedExecutionHandler(new ResourceReindexingSvcImpl.BlockPolicy());
+ asyncTaskExecutor.setRejectedExecutionHandler(new BlockPolicy());
asyncTaskExecutor.initialize();
return asyncTaskExecutor;
}
@@ -639,7 +639,7 @@ public abstract class BaseConfig {
return new PersistedJpaSearchFirstPageBundleProvider(theSearch, theSearchTask, theSearchBuilder, theRequest);
}
- @Bean(name = REPOSITORY_VALIDATING_RULE_BUILDER)
+ @Bean(name = RepositoryValidatingRuleBuilder.REPOSITORY_VALIDATING_RULE_BUILDER)
@Scope("prototype")
public RepositoryValidatingRuleBuilder repositoryValidatingRuleBuilder() {
return new RepositoryValidatingRuleBuilder();
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
index aebba0133b4..82aaf6fef7b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseDstu2Config.java
@@ -6,10 +6,9 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
+import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.JpaPersistedResourceValidationSupport;
-import ca.uhn.fhir.jpa.dao.TransactionProcessor;
import ca.uhn.fhir.jpa.dao.TransactionProcessorVersionAdapterDstu2;
-import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
import ca.uhn.fhir.jpa.term.TermReadSvcDstu2;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.ResourceCountCache;
@@ -97,7 +96,7 @@ public class BaseDstu2Config extends BaseConfig {
}
@Bean
- public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
+ public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterDstu2();
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
index 92529b25f5b..8f490c06417 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
@@ -6,7 +6,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
-import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.dstu3.TransactionProcessorVersionAdapterDstu3;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
@@ -83,7 +83,7 @@ public class BaseDstu3Config extends BaseConfigDstu3Plus {
}
@Bean
- public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
+ public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterDstu3();
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
index 6879d7dfd1b..fedd7e1b886 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
@@ -6,7 +6,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
-import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.r4.TransactionProcessorVersionAdapterR4;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
@@ -78,7 +78,7 @@ public class BaseR4Config extends BaseConfigDstu3Plus {
}
@Bean
- public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
+ public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterR4();
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
index c217a864907..db9d36c38e2 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java
@@ -6,7 +6,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.config.BaseConfigDstu3Plus;
import ca.uhn.fhir.jpa.dao.FulltextSearchSvcImpl;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
-import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.jpa.dao.r5.TransactionProcessorVersionAdapterR5;
import ca.uhn.fhir.jpa.provider.GraphQLProvider;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
@@ -76,7 +76,7 @@ public class BaseR5Config extends BaseConfigDstu3Plus {
}
@Bean
- public TransactionProcessor.ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
+ public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
return new TransactionProcessorVersionAdapterR5();
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
index d612b88fe50..ee6ac476fc1 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
@@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
import ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.index.SearchParamWithInlineReferencesExtractor;
+import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictService;
import ca.uhn.fhir.jpa.entity.PartitionEntity;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
@@ -77,7 +78,6 @@ import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
@@ -181,14 +181,8 @@ public abstract class BaseHapiFhirDao
extends BaseStora
public static final long INDEX_STATUS_INDEXED = 1L;
public static final long INDEX_STATUS_INDEXING_FAILED = 2L;
public static final String NS_JPA_PROFILE = "https://github.com/hapifhir/hapi-fhir/ns/jpa/profile";
- public static final String OO_SEVERITY_ERROR = "error";
- public static final String OO_SEVERITY_INFO = "information";
- public static final String OO_SEVERITY_WARN = "warning";
- public static final String XACT_USERDATA_KEY_RESOLVED_TAG_DEFINITIONS = BaseHapiFhirDao.class.getName() + "_RESOLVED_TAG_DEFINITIONS";
- public static final String XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS = BaseHapiFhirDao.class.getName() + "_EXISTING_SEARCH_PARAMS";
private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiFhirDao.class);
private static final Map ourRetrievalContexts = new HashMap<>();
- private static final String PROCESSING_SUB_REQUEST = "BaseHapiFhirDao.processingSubRequest";
private static boolean ourValidationDisabledForUnitTest;
private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
@@ -429,7 +423,7 @@ public abstract class BaseHapiFhirDao extends BaseStora
if (retVal == null) {
- HashMap resolvedTagDefinitions = theTransactionDetails.getOrCreateUserData(XACT_USERDATA_KEY_RESOLVED_TAG_DEFINITIONS, () -> new HashMap<>());
+ HashMap resolvedTagDefinitions = theTransactionDetails.getOrCreateUserData(HapiTransactionService.XACT_USERDATA_KEY_RESOLVED_TAG_DEFINITIONS, () -> new HashMap<>());
retVal = resolvedTagDefinitions.get(key);
if (retVal == null) {
@@ -508,19 +502,6 @@ public abstract class BaseHapiFhirDao extends BaseStora
return LogicalReferenceHelper.isLogicalReference(myConfig.getModelConfig(), theId);
}
- public void notifyInterceptors(RestOperationTypeEnum theOperationType, ActionRequestDetails theRequestDetails) {
- if (theRequestDetails.getId() != null && theRequestDetails.getId().hasResourceType() && isNotBlank(theRequestDetails.getResourceType())) {
- if (theRequestDetails.getId().getResourceType().equals(theRequestDetails.getResourceType()) == false) {
- throw new InternalErrorException(
- "Inconsistent server state - Resource types don't match: " + theRequestDetails.getId().getResourceType() + " / " + theRequestDetails.getResourceType());
- }
- }
-
- if (theRequestDetails.getUserData().get(PROCESSING_SUB_REQUEST) == Boolean.TRUE) {
- theRequestDetails.notifyIncomingRequestPreHandled(theOperationType);
- }
- }
-
/**
* Returns true if the resource has changed (either the contents or the tags)
*/
@@ -1195,7 +1176,7 @@ public abstract class BaseHapiFhirDao extends BaseStora
// CREATE or UPDATE
- IdentityHashMap existingSearchParams = theTransactionDetails.getOrCreateUserData(XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS, () -> new IdentityHashMap<>());
+ IdentityHashMap existingSearchParams = theTransactionDetails.getOrCreateUserData(HapiTransactionService.XACT_USERDATA_KEY_EXISTING_SEARCH_PARAMS, () -> new IdentityHashMap<>());
existingParams = existingSearchParams.get(entity);
if (existingParams == null) {
existingParams = new ResourceIndexedSearchParams(entity);
@@ -1682,18 +1663,6 @@ public abstract class BaseHapiFhirDao extends BaseStora
return retVal.toString();
}
- public static void clearRequestAsProcessingSubRequest(RequestDetails theRequestDetails) {
- if (theRequestDetails != null) {
- theRequestDetails.getUserData().remove(PROCESSING_SUB_REQUEST);
- }
- }
-
- public static void markRequestAsProcessingSubRequest(RequestDetails theRequestDetails) {
- if (theRequestDetails != null) {
- theRequestDetails.getUserData().put(PROCESSING_SUB_REQUEST, Boolean.TRUE);
- }
- }
-
public static void populateFullTextFields(final FhirContext theContext, final IBaseResource theResource, ResourceTable theEntity) {
if (theEntity.getDeleted() != null) {
theEntity.setNarrativeText(null);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
index 2afd65245eb..cf808379a17 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
@@ -36,7 +36,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
-import ca.uhn.fhir.jpa.delete.DeleteConflictService;
+import ca.uhn.fhir.jpa.delete.DeleteConflictUtil;
import ca.uhn.fhir.jpa.model.entity.BaseHasResource;
import ca.uhn.fhir.jpa.model.entity.BaseTag;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
@@ -86,6 +86,7 @@ import ca.uhn.fhir.rest.server.IRestfulServerDefaults;
import ca.uhn.fhir.rest.server.RestfulServerUtils;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
+import ca.uhn.fhir.rest.server.exceptions.NotImplementedOperationException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
@@ -136,12 +137,9 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
-import java.util.LinkedList;
import java.util.List;
-import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.UUID;
@@ -171,7 +169,7 @@ public abstract class BaseHapiFhirResourceDao extends B
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
@Autowired
- private HapiTransactionService myTransactionService;
+ protected HapiTransactionService myTransactionService;
@Autowired
private MatchUrlService myMatchUrlService;
@Autowired
@@ -223,9 +221,9 @@ public abstract class BaseHapiFhirResourceDao extends B
/**
* Called for FHIR create (POST) operations
*/
- private DaoMethodOutcome doCreateForPost(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
+ protected DaoMethodOutcome doCreateForPost(T theResource, String theIfNoneExist, boolean thePerformIndexing, TransactionDetails theTransactionDetails, RequestDetails theRequestDetails) {
if (theResource == null) {
- String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "missingBody");
+ String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "missingBody");
throw new InvalidRequestException(msg);
}
@@ -385,7 +383,7 @@ public abstract class BaseHapiFhirResourceDao extends B
outcome.setId(theResource.getIdElement());
}
- String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart());
+ String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulCreate", outcome.getId(), w.getMillisAndRestart());
outcome.setOperationOutcome(createInfoOperationOutcome(msg));
String forcedId = null;
@@ -417,7 +415,7 @@ public abstract class BaseHapiFhirResourceDao extends B
}
protected String getMessageSanitized(String theKey, String theIdPart) {
- return getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, theKey, theIdPart);
+ return getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, theKey, theIdPart);
}
private boolean isSystemRequest(RequestDetails theRequest) {
@@ -450,7 +448,7 @@ public abstract class BaseHapiFhirResourceDao extends B
DaoMethodOutcome retVal = delete(theId, deleteConflicts, theRequestDetails, transactionDetails);
- DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
+ DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
ourLog.debug("Processed delete on {} in {}ms", theId.getValue(), w.getMillisAndRestart());
return retVal;
@@ -477,7 +475,7 @@ public abstract class BaseHapiFhirResourceDao extends B
outcome.setId(id);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
- String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, 0);
+ String message = getContext().getLocalizer().getMessage(BaseStorageDao.class, "successfulDeletes", 1, 0);
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
@@ -526,7 +524,7 @@ public abstract class BaseHapiFhirResourceDao extends B
DaoMethodOutcome outcome = toMethodOutcome(theRequestDetails, savedEntity, resourceToDelete).setCreated(true);
IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(getContext());
- String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", 1, w.getMillis());
+ String message = getContext().getLocalizer().getMessage(BaseStorageDao.class, "successfulDeletes", 1, w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
@@ -549,7 +547,7 @@ public abstract class BaseHapiFhirResourceDao extends B
return myTransactionService.execute(theRequest, transactionDetails, tx -> {
DeleteConflictList deleteConflicts = new DeleteConflictList();
DeleteMethodOutcome outcome = deleteByUrl(theUrl, deleteConflicts, theRequest);
- DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
+ DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
return outcome;
});
}
@@ -588,6 +586,10 @@ public abstract class BaseHapiFhirResourceDao extends B
throw new MethodNotAllowedException("_expunge is not enabled on this server: " + getConfig().cannotDeleteExpungeReason());
}
+ if (theUrl.contains(Constants.PARAMETER_CASCADE_DELETE) || (theRequest.getHeader(Constants.HEADER_CASCADE) != null && theRequest.getHeader(Constants.HEADER_CASCADE).equals(Constants.CASCADE_DELETE))) {
+ throw new InvalidRequestException("_expunge cannot be used with _cascade");
+ }
+
List urlsToDeleteExpunge = Collections.singletonList(theUrl);
try {
JobExecution jobExecution = myDeleteExpungeJobSubmitter.submitJob(getConfig().getExpungeBatchSize(), urlsToDeleteExpunge, theRequest);
@@ -655,7 +657,7 @@ public abstract class BaseHapiFhirResourceDao extends B
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
} else {
oo = OperationOutcomeUtil.newInstance(getContext());
- String message = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
+ String message = getContext().getLocalizer().getMessage(BaseStorageDao.class, "successfulDeletes", deletedResources.size(), w.getMillis());
String severity = "information";
String code = "informational";
OperationOutcomeUtil.addIssue(getContext(), oo, severity, message, null, code);
@@ -671,7 +673,7 @@ public abstract class BaseHapiFhirResourceDao extends B
private void validateDeleteEnabled() {
if (!getConfig().isDeleteEnabled()) {
- String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "deleteBlockedBecauseDisabled");
+ String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "deleteBlockedBecauseDisabled");
throw new PreconditionFailedException(msg);
}
}
@@ -1265,7 +1267,7 @@ public abstract class BaseHapiFhirResourceDao extends B
if (theId.hasVersionIdPart()) {
if (theId.isVersionIdPartValidLong() == false) {
- throw new ResourceNotFoundException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless()));
+ throw new ResourceNotFoundException(getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless()));
}
if (entity.getVersion() != theId.getVersionIdPartAsLong()) {
entity = null;
@@ -1281,7 +1283,7 @@ public abstract class BaseHapiFhirResourceDao extends B
try {
entity = q.getSingleResult();
} catch (NoResultException e) {
- throw new ResourceNotFoundException(getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless()));
+ throw new ResourceNotFoundException(getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidVersion", theId.getVersionIdPart(), theId.toUnqualifiedVersionless()));
}
}
}
@@ -1586,12 +1588,12 @@ public abstract class BaseHapiFhirResourceDao extends B
@Override
public DaoMethodOutcome update(T theResource, String theMatchUrl, boolean thePerformIndexing, boolean theForceUpdateVersion, RequestDetails theRequest, @Nonnull TransactionDetails theTransactionDetails) {
if (theResource == null) {
- String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "missingBody");
+ String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "missingBody");
throw new InvalidRequestException(msg);
}
if (!theResource.getIdElement().hasIdPart() && isBlank(theMatchUrl)) {
String type = myFhirContext.getResourceType(theResource);
- String msg = myFhirContext.getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "updateWithNoId", type);
+ String msg = myFhirContext.getLocalizer().getMessage(BaseStorageDao.class, "updateWithNoId", type);
throw new InvalidRequestException(msg);
}
@@ -1731,7 +1733,7 @@ public abstract class BaseHapiFhirResourceDao extends B
outcome.setId(id);
}
- String msg = getContext().getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "successfulUpdate", outcome.getId(), w.getMillisAndRestart());
+ String msg = getContext().getLocalizer().getMessageSanitized(BaseStorageDao.class, "successfulUpdate", outcome.getId(), w.getMillisAndRestart());
outcome.setOperationOutcome(createInfoOperationOutcome(msg));
ourLog.debug(msg);
@@ -1760,7 +1762,7 @@ public abstract class BaseHapiFhirResourceDao extends B
if (getConfig().isEnforceReferentialIntegrityOnDelete()) {
myDeleteConflictService.validateOkToDelete(deleteConflicts, entity, true, theRequest, new TransactionDetails());
}
- DeleteConflictService.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
+ DeleteConflictUtil.validateDeleteConflictsEmptyOrThrowException(getContext(), deleteConflicts);
IBaseOperationOutcome oo = createInfoOperationOutcome("Ok to delete");
return new MethodOutcome(new IdDt(theId.getValue()), oo);
@@ -1788,7 +1790,7 @@ public abstract class BaseHapiFhirResourceDao extends B
if (resourceToValidateById != null) {
result = validator.validateWithResult(resourceToValidateById, options);
} else {
- String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "cantValidateWithNoResource");
+ String msg = getContext().getLocalizer().getMessage(BaseStorageDao.class, "cantValidateWithNoResource");
throw new InvalidRequestException(msg);
}
} else if (isNotBlank(theRawResource)) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java
index f1819cbbbb7..bb27591070a 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupport.java
@@ -24,15 +24,21 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.TermReadSvcUtil;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import com.github.benmanes.caffeine.cache.Cache;
import com.github.benmanes.caffeine.cache.Caffeine;
+import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -41,6 +47,7 @@ import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.ImplementationGuide;
import org.hl7.fhir.r4.model.Questionnaire;
import org.hl7.fhir.r4.model.StructureDefinition;
+import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -51,10 +58,13 @@ import javax.annotation.PostConstruct;
import javax.transaction.Transactional;
import java.util.Arrays;
import java.util.List;
+import java.util.Optional;
import java.util.concurrent.TimeUnit;
import java.util.function.Supplier;
import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_GENERIC_VALUESET_URL_PLUS_SLASH;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
/**
* This class is a {@link IValidationSupport Validation support} module that loads
@@ -71,6 +81,10 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
@Autowired
private DaoRegistry myDaoRegistry;
+
+ @Autowired
+ private ITermReadSvc myTermReadSvc;
+
private Class myCodeSystemType;
private Class myStructureDefinitionType;
private Class myValueSetType;
@@ -92,14 +106,55 @@ public class JpaPersistedResourceValidationSupport implements IValidationSupport
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
+ if (TermReadSvcUtil.isLoincNotGenericUnversionedCodeSystem(theSystem)) {
+ Optional currentCSOpt = getCodeSystemCurrentVersion(new UriType(theSystem));
+ if (! currentCSOpt.isPresent()) {
+ ourLog.info("Couldn't find current version of CodeSystem: " + theSystem);
+ }
+ return currentCSOpt.orElse(null);
+ }
+
return fetchResource(myCodeSystemType, theSystem);
}
+ /**
+ * Obtains the current version of a CodeSystem using the fact that the current
+ * version is always pointed by the ForcedId for the no-versioned CS
+ */
+ private Optional getCodeSystemCurrentVersion(UriType theUrl) {
+ if (! theUrl.getValueAsString().contains(LOINC_LOW)) return Optional.empty();
+
+ return myTermReadSvc.readCodeSystemByForcedId(LOINC_LOW);
+ }
+
+
@Override
public IBaseResource fetchValueSet(String theSystem) {
+ if (TermReadSvcUtil.isLoincNotGenericUnversionedValueSet(theSystem)) {
+ Optional currentVSOpt = getValueSetCurrentVersion(new UriType(theSystem));
+ return currentVSOpt.orElseThrow(() -> new ResourceNotFoundException(
+ "Unable to find current version of ValueSet for url: " + theSystem));
+ }
+
return fetchResource(myValueSetType, theSystem);
}
+ /**
+ * Obtains the current version of a ValueSet using the fact that the current
+ * version is always pointed by the ForcedId for the no-versioned VS
+ */
+ private Optional getValueSetCurrentVersion(UriType theUrl) {
+ if (TermReadSvcUtil.mustReturnEmptyValueSet(theUrl.getValueAsString())) return Optional.empty();
+
+ String forcedId = theUrl.getValue().substring(LOINC_GENERIC_VALUESET_URL_PLUS_SLASH.length());
+ if (StringUtils.isBlank(forcedId)) return Optional.empty();
+
+ IFhirResourceDao valueSetResourceDao = myDaoRegistry.getResourceDao(myValueSetType);
+ IBaseResource valueSet = valueSetResourceDao.read(new IdDt("ValueSet", forcedId));
+ return Optional.ofNullable(valueSet);
+ }
+
+
@Override
public IBaseResource fetchStructureDefinition(String theUrl) {
return fetchResource(myStructureDefinitionType, theUrl);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessorVersionAdapterDstu2.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessorVersionAdapterDstu2.java
index b1b87a079e1..63b914e2200 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessorVersionAdapterDstu2.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessorVersionAdapterDstu2.java
@@ -38,7 +38,7 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.Date;
import java.util.List;
-public class TransactionProcessorVersionAdapterDstu2 implements TransactionProcessor.ITransactionProcessorVersionAdapter {
+public class TransactionProcessorVersionAdapterDstu2 implements ITransactionProcessorVersionAdapter {
@Override
public void setResponseStatus(Bundle.Entry theBundleEntry, String theStatus) {
theBundleEntry.getResponse().setStatus(theStatus);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
index 2bb11d4f22a..fd5a5bc95ce 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetDao.java
@@ -47,6 +47,13 @@ public interface ITermValueSetDao extends JpaRepository {
@Query(value="SELECT vs FROM TermValueSet vs INNER JOIN ResourceTable r ON r.myId = vs.myResourcePid WHERE vs.myUrl = :url ORDER BY r.myUpdated DESC")
List findTermValueSetByUrl(Pageable thePage, @Param("url") String theUrl);
+ /**
+ * The current TermValueSet is not necessarily the last uploaded anymore, but the current VS resource
+ * is pointed by a specific ForcedId, so we locate current ValueSet as the one pointing to current VS resource
+ */
+ @Query(value="SELECT vs FROM ForcedId f, TermValueSet vs where f.myForcedId = :forcedId and vs.myResource = f.myResource")
+ Optional findTermValueSetByForcedId(@Param("forcedId") String theForcedId);
+
@Query("SELECT vs FROM TermValueSet vs WHERE vs.myUrl = :url AND vs.myVersion IS NULL")
Optional findTermValueSetByUrlAndNullVersion(@Param("url") String theUrl);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
index 62ebba77afc..2f6d1bacaea 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/PredicateBuilderReference.java
@@ -34,7 +34,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
@@ -48,9 +48,7 @@ import ca.uhn.fhir.jpa.model.search.StorageProcessingMessage;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.ResourceMetaParams;
import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
-import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import ca.uhn.fhir.jpa.searchparam.util.SourceParam;
-import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
@@ -75,6 +73,8 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
+import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
import com.google.common.collect.Lists;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
@@ -96,7 +96,6 @@ import javax.persistence.criteria.Subquery;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
-import java.util.HashSet;
import java.util.List;
import java.util.ListIterator;
import java.util.Set;
@@ -347,7 +346,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
}
if (!foundChainMatch) {
- throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
+ throw new InvalidRequestException(myContext.getLocalizer().getMessage(BaseStorageDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
}
if (candidateTargetTypes.size() > 1) {
@@ -684,7 +683,7 @@ class PredicateBuilderReference extends BasePredicateBuilder {
} else {
Collection validNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName);
- String msg = myContext.getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", theParamName, theResourceName, validNames);
+ String msg = myContext.getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidSearchParameter", theParamName, theResourceName, validNames);
throw new InvalidRequestException(msg);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
index 37ec5745cf4..b639c026754 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
@@ -25,6 +25,7 @@ import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -46,13 +47,16 @@ import org.hl7.fhir.r4.model.Coding;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
+import java.security.InvalidParameterException;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Set;
import static ca.uhn.fhir.jpa.dao.FhirResourceDaoValueSetDstu2.toStringOrNull;
+import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao implements IFhirResourceDaoCodeSystem {
@@ -173,4 +177,17 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao doCreateForPost(theResource, theIfNoneExist, thePerformIndexing, theTransactionDetails, theRequestDetails));
+ }
+
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
index 43226b5f2ff..82d2a97ccd4 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
@@ -28,7 +28,6 @@ import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/TransactionProcessorVersionAdapterR5.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/TransactionProcessorVersionAdapterR5.java
index f51f8e6bba9..07e2696a9c7 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/TransactionProcessorVersionAdapterR5.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/TransactionProcessorVersionAdapterR5.java
@@ -21,7 +21,7 @@ package ca.uhn.fhir.jpa.dao.r5;
*/
import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.jpa.dao.TransactionProcessor;
+import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.hl7.fhir.exceptions.FHIRException;
@@ -34,7 +34,7 @@ import org.hl7.fhir.r5.model.Resource;
import java.util.Date;
import java.util.List;
-public class TransactionProcessorVersionAdapterR5 implements TransactionProcessor.ITransactionProcessorVersionAdapter {
+public class TransactionProcessorVersionAdapterR5 implements ITransactionProcessorVersionAdapter {
@Override
public void setResponseStatus(Bundle.BundleEntryComponent theBundleEntry, String theStatus) {
theBundleEntry.getResponse().setStatus(theStatus);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictService.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictService.java
index 6bcd1f488c0..4a586a3a6b2 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictService.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictService.java
@@ -27,16 +27,16 @@ import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.DeleteConflict;
import ca.uhn.fhir.jpa.api.model.DeleteConflictList;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.data.IResourceLinkDao;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
-import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
import ca.uhn.fhir.util.OperationOutcomeUtil;
import com.google.common.annotations.VisibleForTesting;
import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
@@ -64,35 +64,6 @@ public class DeleteConflictService {
@Autowired
private FhirContext myFhirContext;
- public int validateOkToDelete(DeleteConflictList theDeleteConflicts, ResourceTable theEntity, boolean theForValidate, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
-
- // We want the list of resources that are marked to be the same list even as we
- // drill into conflict resolution stacks.. this allows us to not get caught by
- // circular references
- DeleteConflictList newConflicts = new DeleteConflictList(theDeleteConflicts);
-
- // In most cases, there will be no hooks, and so we only need to check if there is at least FIRST_QUERY_RESULT_COUNT conflict and populate that.
- // Only in the case where there is a hook do we need to go back and collect larger batches of conflicts for processing.
-
- DeleteConflictOutcome outcome = findAndHandleConflicts(theRequest, newConflicts, theEntity, theForValidate, FIRST_QUERY_RESULT_COUNT, theTransactionDetails);
-
- int retryCount = 0;
- while (outcome != null) {
- int shouldRetryCount = Math.min(outcome.getShouldRetryCount(), MAX_RETRY_ATTEMPTS);
- if (!(retryCount < shouldRetryCount)) break;
- newConflicts = new DeleteConflictList(newConflicts);
- outcome = findAndHandleConflicts(theRequest, newConflicts, theEntity, theForValidate, myDaoConfig.getMaximumDeleteConflictQueryCount(), theTransactionDetails);
- ++retryCount;
- }
- theDeleteConflicts.addAll(newConflicts);
- if (retryCount >= MAX_RETRY_ATTEMPTS && !theDeleteConflicts.isEmpty()) {
- IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(myFhirContext);
- OperationOutcomeUtil.addIssue(myFhirContext, oo, BaseHapiFhirDao.OO_SEVERITY_ERROR, MAX_RETRY_ATTEMPTS_EXCEEDED_MSG, null, "processing");
- throw new ResourceVersionConflictException(MAX_RETRY_ATTEMPTS_EXCEEDED_MSG, oo);
- }
- return retryCount;
- }
-
private DeleteConflictOutcome findAndHandleConflicts(RequestDetails theRequest, DeleteConflictList theDeleteConflicts, ResourceTable theEntity, boolean theForValidate, int theMinQueryResultCount, TransactionDetails theTransactionDetails) {
List resultList = myDeleteConflictFinderService.findConflicts(theEntity, theMinQueryResultCount);
if (resultList.isEmpty()) {
@@ -139,35 +110,33 @@ public class DeleteConflictService {
}
}
- public static void validateDeleteConflictsEmptyOrThrowException(FhirContext theFhirContext, DeleteConflictList theDeleteConflicts) {
- IBaseOperationOutcome oo = null;
- String firstMsg = null;
+ public int validateOkToDelete(DeleteConflictList theDeleteConflicts, ResourceTable theEntity, boolean theForValidate, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
- for (DeleteConflict next : theDeleteConflicts) {
+ // We want the list of resources that are marked to be the same list even as we
+ // drill into conflict resolution stacks.. this allows us to not get caught by
+ // circular references
+ DeleteConflictList newConflicts = new DeleteConflictList(theDeleteConflicts);
- if (theDeleteConflicts.isResourceIdToIgnoreConflict(next.getTargetId())) {
- continue;
- }
+ // In most cases, there will be no hooks, and so we only need to check if there is at least FIRST_QUERY_RESULT_COUNT conflict and populate that.
+ // Only in the case where there is a hook do we need to go back and collect larger batches of conflicts for processing.
- String msg = "Unable to delete " +
- next.getTargetId().toUnqualifiedVersionless().getValue() +
- " because at least one resource has a reference to this resource. First reference found was resource " +
- next.getSourceId().toUnqualifiedVersionless().getValue() +
- " in path " +
- next.getSourcePath();
+ DeleteConflictOutcome outcome = findAndHandleConflicts(theRequest, newConflicts, theEntity, theForValidate, FIRST_QUERY_RESULT_COUNT, theTransactionDetails);
- if (firstMsg == null) {
- firstMsg = msg;
- oo = OperationOutcomeUtil.newInstance(theFhirContext);
- }
- OperationOutcomeUtil.addIssue(theFhirContext, oo, BaseHapiFhirDao.OO_SEVERITY_ERROR, msg, null, "processing");
+ int retryCount = 0;
+ while (outcome != null) {
+ int shouldRetryCount = Math.min(outcome.getShouldRetryCount(), MAX_RETRY_ATTEMPTS);
+ if (!(retryCount < shouldRetryCount)) break;
+ newConflicts = new DeleteConflictList(newConflicts);
+ outcome = findAndHandleConflicts(theRequest, newConflicts, theEntity, theForValidate, myDaoConfig.getMaximumDeleteConflictQueryCount(), theTransactionDetails);
+ ++retryCount;
}
-
- if (firstMsg == null) {
- return;
+ theDeleteConflicts.addAll(newConflicts);
+ if (retryCount >= MAX_RETRY_ATTEMPTS && !theDeleteConflicts.isEmpty()) {
+ IBaseOperationOutcome oo = OperationOutcomeUtil.newInstance(myFhirContext);
+ OperationOutcomeUtil.addIssue(myFhirContext, oo, BaseStorageDao.OO_SEVERITY_ERROR, MAX_RETRY_ATTEMPTS_EXCEEDED_MSG, null, "processing");
+ throw new ResourceVersionConflictException(MAX_RETRY_ATTEMPTS_EXCEEDED_MSG, oo);
}
-
- throw new ResourceVersionConflictException(firstMsg, oo);
+ return retryCount;
}
@VisibleForTesting
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
index f625387b47e..688a4284029 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r4/BaseJpaResourceProviderCodeSystemR4.java
@@ -1,9 +1,13 @@
package ca.uhn.fhir.jpa.provider.r4;
-import java.util.List;
-
-import javax.servlet.http.HttpServletRequest;
-
+import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
+import ca.uhn.fhir.jpa.model.util.JpaConstants;
+import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
+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.api.server.RequestDetails;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
@@ -14,6 +18,9 @@ import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
+import javax.servlet.http.HttpServletRequest;
+import java.util.List;
+
/*
* #%L
* HAPI FHIR JPA Server
@@ -34,15 +41,6 @@ import org.hl7.fhir.r4.model.UriType;
* #L%
*/
-import ca.uhn.fhir.context.support.IValidationSupport;
-import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.model.util.JpaConstants;
-import ca.uhn.fhir.jpa.provider.BaseJpaResourceProviderValueSetDstu2;
-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.api.server.RequestDetails;
-
public class BaseJpaResourceProviderCodeSystemR4 extends JpaResourceProviderR4 {
/**
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
index 82bf3d886fe..475cba4758b 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
@@ -24,7 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.LegacySearchBuilder;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderToken;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
@@ -109,11 +109,9 @@ import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
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 java.util.function.Supplier;
import java.util.stream.Collectors;
@@ -443,7 +441,7 @@ public class QueryStack {
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(theResourceName, paramName);
if (searchParam == null) {
Collection validNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName);
- String msg = myFhirContext.getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", paramName, theResourceName, validNames);
+ String msg = myFhirContext.getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidSearchParameter", paramName, theResourceName, validNames);
throw new InvalidRequestException(msg);
}
RestSearchParameterTypeEnum typeEnum = searchParam.getParamType();
@@ -1204,7 +1202,7 @@ public class QueryStack {
}
} else {
- String msg = myFhirContext.getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSearchParameter", theParamName, theResourceName, mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName));
+ String msg = myFhirContext.getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidSearchParameter", theParamName, theResourceName, mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName));
throw new InvalidRequestException(msg);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
index 5d117ed14bb..7c82ae84f09 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
@@ -35,7 +35,7 @@ import ca.uhn.fhir.jpa.api.dao.IDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
import ca.uhn.fhir.jpa.dao.IResultIterator;
import ca.uhn.fhir.jpa.dao.ISearchBuilder;
@@ -51,6 +51,7 @@ 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.search.SearchConstants;
import ca.uhn.fhir.jpa.search.builder.sql.GeneratedSql;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryExecutor;
@@ -138,7 +139,8 @@ public class SearchBuilder implements ISearchBuilder {
* for an explanation of why we use the constant 800
*/
// NB: keep public
- public static final int MAXIMUM_PAGE_SIZE = 800;
+ @Deprecated
+ public static final int MAXIMUM_PAGE_SIZE = SearchConstants.MAX_PAGE_SIZE;
public static final int MAXIMUM_PAGE_SIZE_FOR_TESTING = 50;
private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
private static final ResourcePersistentId NO_MORE = new ResourcePersistentId(-1L);
@@ -547,7 +549,7 @@ public class SearchBuilder implements ISearchBuilder {
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(myResourceName, theSort.getParamName());
if (param == null) {
- String msg = myContext.getLocalizer().getMessageSanitized(BaseHapiFhirResourceDao.class, "invalidSortParameter", theSort.getParamName(), getResourceName(), mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(getResourceName()));
+ String msg = myContext.getLocalizer().getMessageSanitized(BaseStorageDao.class, "invalidSortParameter", theSort.getParamName(), getResourceName(), mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(getResourceName()));
throw new InvalidRequestException(msg);
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
index d18f2a87f46..50e6de2a610 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
@@ -34,7 +34,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.predicate.PredicateBuilderReference;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
@@ -400,7 +400,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
}
if (!foundChainMatch) {
- throw new InvalidRequestException(getFhirContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
+ throw new InvalidRequestException(getFhirContext().getLocalizer().getMessage(BaseStorageDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
}
candidateTargetTypes.add(nextType);
@@ -414,7 +414,7 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder {
}
if (candidateTargetTypes.isEmpty()) {
- throw new InvalidRequestException(getFhirContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
+ throw new InvalidRequestException(getFhirContext().getLocalizer().getMessage(BaseStorageDao.class, "invalidParameterChain", theParamName + '.' + theReferenceParam.getChain()));
}
if (candidateTargetTypes.size() > 1) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
index 8f9c583ce23..ce362dd59df 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
@@ -42,7 +42,6 @@ import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.concurrent.BasicThreadFactory;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.r4.model.InstantType;
-import javax.annotation.Nullable;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -54,6 +53,7 @@ import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionTemplate;
+import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
@@ -142,29 +142,6 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
);
}
- /**
- * A handler for rejected tasks that will have the caller block until space is available.
- * This was stolen from old hibernate search(5.X.X), as it has been removed in HS6. We can probably come up with a better solution though.
- */
- public static class BlockPolicy implements RejectedExecutionHandler {
-
- /**
- * Puts the Runnable to the blocking queue, effectively blocking the delegating thread until space is available.
- *
- * @param r the runnable task requested to be executed
- * @param e the executor attempting to execute this task
- */
- @Override
- public void rejectedExecution(Runnable r, ThreadPoolExecutor e) {
- try {
- e.getQueue().put( r );
- } catch (InterruptedException e1) {
- ourLog.error("Interrupted Execption for task: {}",r, e1 );
- Thread.currentThread().interrupt();
- }
- }
- }
-
public void scheduleJob() {
ScheduledJobDefinition jobDetail = new ScheduledJobDefinition();
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
index a66bf88efe9..5b185c5726d 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseTermReadSvcImpl.java
@@ -28,6 +28,7 @@ import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IDao;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.dao.IFulltextSearchSvc;
@@ -54,6 +55,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
+import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
@@ -123,6 +125,7 @@ import org.quartz.JobExecutionContext;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
@@ -138,6 +141,7 @@ import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
+import javax.persistence.NonUniqueResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import javax.persistence.TypedQuery;
@@ -157,6 +161,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
@@ -176,6 +181,8 @@ import static org.apache.commons.lang3.StringUtils.isNoneBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.lowerCase;
import static org.apache.commons.lang3.StringUtils.startsWithIgnoreCase;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_GENERIC_VALUESET_URL_PLUS_SLASH;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
public static final int DEFAULT_FETCH_SIZE = 250;
@@ -196,7 +203,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
@Autowired
- protected ITermValueSetDao myValueSetDao;
+ protected ITermValueSetDao myTermValueSetDao;
@Autowired
protected ITermValueSetConceptDao myValueSetConceptDao;
@Autowired
@@ -339,7 +346,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
public void deleteValueSetForResource(ResourceTable theResourceTable) {
// Get existing entity so it can be deleted.
- Optional optionalExistingTermValueSetById = myValueSetDao.findByResourcePid(theResourceTable.getId());
+ Optional optionalExistingTermValueSetById = myTermValueSetDao.findByResourcePid(theResourceTable.getId());
if (optionalExistingTermValueSetById.isPresent()) {
TermValueSet existingTermValueSet = optionalExistingTermValueSetById.get();
@@ -347,7 +354,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
myValueSetConceptDesignationDao.deleteByTermValueSetId(existingTermValueSet.getId());
myValueSetConceptDao.deleteByTermValueSetId(existingTermValueSet.getId());
- myValueSetDao.deleteById(existingTermValueSet.getId());
+ myTermValueSetDao.deleteById(existingTermValueSet.getId());
ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
}
}
@@ -443,14 +450,9 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
Optional optionalTermValueSet;
if (theValueSetToExpand.hasUrl()) {
if (theValueSetToExpand.hasVersion()) {
- optionalTermValueSet = myValueSetDao.findTermValueSetByUrlAndVersion(theValueSetToExpand.getUrl(), theValueSetToExpand.getVersion());
+ optionalTermValueSet = myTermValueSetDao.findTermValueSetByUrlAndVersion(theValueSetToExpand.getUrl(), theValueSetToExpand.getVersion());
} else {
- List termValueSets = myValueSetDao.findTermValueSetByUrl(PageRequest.of(0, 1), theValueSetToExpand.getUrl());
- if (termValueSets.size() > 0) {
- optionalTermValueSet = Optional.of(termValueSets.get(0));
- } else {
- optionalTermValueSet = Optional.empty();
- }
+ optionalTermValueSet = findCurrentTermValueSet(theValueSetToExpand.getUrl());
}
} else {
optionalTermValueSet = Optional.empty();
@@ -1455,7 +1457,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
@Override
public boolean isValueSetPreExpandedForCodeValidation(ValueSet theValueSet) {
ResourcePersistentId valueSetResourcePid = myConceptStorageSvc.getValueSetResourcePid(theValueSet.getIdElement());
- Optional optionalTermValueSet = myValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
+ Optional optionalTermValueSet = myTermValueSetDao.findByResourcePid(valueSetResourcePid.getIdAsLong());
if (!optionalTermValueSet.isPresent()) {
ourLog.warn("ValueSet is not present in terminology tables. Will perform in-memory code validation. {}", getValueSetInfo(theValueSet));
@@ -1760,7 +1762,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
TermValueSet termValueSet = optionalTermValueSet.get();
termValueSet.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANSION_IN_PROGRESS);
- return myValueSetDao.saveAndFlush(termValueSet);
+ return myTermValueSetDao.saveAndFlush(termValueSet);
});
if (valueSetToExpand == null) {
return;
@@ -1769,18 +1771,18 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
// We have a ValueSet to pre-expand.
try {
ValueSet valueSet = txTemplate.execute(t -> {
- TermValueSet refreshedValueSetToExpand = myValueSetDao.findById(valueSetToExpand.getId()).orElseThrow(() -> new IllegalStateException("Unknown VS ID: " + valueSetToExpand.getId()));
+ TermValueSet refreshedValueSetToExpand = myTermValueSetDao.findById(valueSetToExpand.getId()).orElseThrow(() -> new IllegalStateException("Unknown VS ID: " + valueSetToExpand.getId()));
return getValueSetFromResourceTable(refreshedValueSetToExpand.getResource());
});
assert valueSet != null;
- ValueSetConceptAccumulator accumulator = new ValueSetConceptAccumulator(valueSetToExpand, myValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao);
+ ValueSetConceptAccumulator accumulator = new ValueSetConceptAccumulator(valueSetToExpand, myTermValueSetDao, myValueSetConceptDao, myValueSetConceptDesignationDao);
expandValueSet(null, valueSet, accumulator);
// We are done with this ValueSet.
txTemplate.execute(t -> {
valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANDED);
- myValueSetDao.saveAndFlush(valueSetToExpand);
+ myTermValueSetDao.saveAndFlush(valueSetToExpand);
return null;
});
@@ -1790,7 +1792,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
txTemplate.execute(t -> {
valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
- myValueSetDao.saveAndFlush(valueSetToExpand);
+ myTermValueSetDao.saveAndFlush(valueSetToExpand);
return null;
});
}
@@ -1873,7 +1875,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
private Optional getNextTermValueSetNotExpanded() {
Optional retVal = Optional.empty();
- Slice page = myValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
+ Slice page = myTermValueSetDao.findByExpansionStatus(PageRequest.of(0, 1), TermValueSetPreExpansionStatusEnum.NOT_EXPANDED);
if (!page.getContent().isEmpty()) {
retVal = Optional.of(page.getContent().get(0));
@@ -1914,13 +1916,13 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
String version = termValueSet.getVersion();
Optional optionalExistingTermValueSetByUrl;
if (version != null) {
- optionalExistingTermValueSetByUrl = myValueSetDao.findTermValueSetByUrlAndVersion(url, version);
+ optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndVersion(url, version);
} else {
- optionalExistingTermValueSetByUrl = myValueSetDao.findTermValueSetByUrlAndNullVersion(url);
+ optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
}
if (!optionalExistingTermValueSetByUrl.isPresent()) {
- myValueSetDao.save(termValueSet);
+ myTermValueSetDao.save(termValueSet);
} else {
TermValueSet existingTermValueSet = optionalExistingTermValueSetByUrl.get();
@@ -2037,7 +2039,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
});
}
-
+
@Nullable
private ConceptSubsumptionOutcome testForSubsumption(SearchSession theSearchSession, TermConcept theLeft, TermConcept theRight, ConceptSubsumptionOutcome theOutput) {
List fetch = theSearchSession.search(TermConcept.class)
@@ -2338,6 +2340,29 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
return codeSystemValidateCode(codeSystemUrl, theVersion, code, display);
}
+
+ /**
+ * When the search is for unversioned loinc system it uses the forcedId to obtain the current
+ * version, as it is not necessarily the last one anymore.
+ * For other cases it keeps on considering the last uploaded as the current
+ */
+ @Override
+ public Optional findCurrentTermValueSet(String theUrl) {
+ if (TermReadSvcUtil.isLoincNotGenericUnversionedValueSet(theUrl)) {
+ if (TermReadSvcUtil.mustReturnEmptyValueSet(theUrl)) return Optional.empty();
+
+ String forcedId = theUrl.substring(LOINC_GENERIC_VALUESET_URL_PLUS_SLASH.length());
+ if (StringUtils.isBlank(forcedId)) return Optional.empty();
+
+ return myTermValueSetDao.findTermValueSetByForcedId(forcedId);
+ }
+
+ List termValueSetList = myTermValueSetDao.findTermValueSetByUrl(Pageable.ofSize(1), theUrl);
+ if (termValueSetList.isEmpty()) return Optional.empty();
+ return Optional.of(termValueSetList.get(0));
+ }
+
+
@SuppressWarnings("unchecked")
private CodeValidationResult codeSystemValidateCode(String theCodeSystemUrl, String theCodeSystemVersion, String theCode, String theDisplay) {
@@ -2364,10 +2389,16 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
predicates.add(criteriaBuilder.equal(systemJoin.get("myCodeSystemUri"), theCodeSystemUrl));
}
+ // for loinc CodeSystem last version is not necessarily the current anymore, so if no version is present
+ // we need to query for the current, which is that which version is null
if (isNoneBlank(theCodeSystemVersion)) {
predicates.add(criteriaBuilder.equal(systemVersionJoin.get("myCodeSystemVersionId"), theCodeSystemVersion));
} else {
- query.orderBy(criteriaBuilder.desc(root.get("myUpdated")));
+ if (theCodeSystemUrl.toLowerCase(Locale.ROOT).contains(LOINC_LOW)) {
+ predicates.add(criteriaBuilder.isNull(systemVersionJoin.get("myCodeSystemVersionId")));
+ } else {
+ query.orderBy(criteriaBuilder.desc(root.get("myUpdated")));
+ }
}
Predicate outerPredicate = criteriaBuilder.and(predicates.toArray(new Predicate[0]));
@@ -2489,7 +2520,26 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
// NOTE: return the designation when one of then is not specified.
if (theReqLang == null || theStoredLang == null)
return true;
-
+
return theReqLang.equalsIgnoreCase(theStoredLang);
}
+
+
+ @Override
+ public Optional readCodeSystemByForcedId(String theForcedId) {
+ @SuppressWarnings("unchecked")
+ List resultList = (List) myEntityManager.createQuery(
+ "select f.myResource from ForcedId f " +
+ "where f.myResourceType = 'CodeSystem' and f.myForcedId = '" + theForcedId + "'").getResultList();
+ if (resultList.isEmpty()) return Optional.empty();
+
+ if (resultList.size() > 1) throw new NonUniqueResultException(
+ "More than one CodeSystem is pointed by forcedId: " + theForcedId + ". Was constraint "
+ + ForcedId.IDX_FORCEDID_TYPE_FID + " removed?");
+
+ IFhirResourceDao csDao = myDaoRegistry.getResourceDao("CodeSystem");
+ IBaseResource cs = csDao.toResource(resultList.get(0), false);
+ return Optional.of(cs );
+ }
+
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
index 01a4acb5bd4..10b50bccab5 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
@@ -86,7 +86,9 @@ import java.util.UUID;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
+import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
private static final Logger ourLog = LoggerFactory.getLogger(TermCodeSystemStorageSvcImpl.class);
@@ -139,6 +141,9 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
CodeSystem codeSystemResource = new CodeSystem();
codeSystemResource.setUrl(theSystem);
codeSystemResource.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+ if (isBlank(codeSystemResource.getIdElement().getIdPart()) && theSystem.contains(LOINC_LOW)) {
+ codeSystemResource.setId(LOINC_LOW);
+ }
myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(codeSystemResource);
cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
@@ -470,10 +475,7 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
codeSystemToStore = myCodeSystemVersionDao.saveAndFlush(codeSystemToStore);
}
- // defaults to true
- boolean isMakeVersionCurrent = theRequestDetails == null ||
- (boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
-
+ boolean isMakeVersionCurrent = ITermCodeSystemStorageSvc.isMakeVersionCurrent(theRequestDetails);
if (isMakeVersionCurrent) {
codeSystem.setCurrentVersion(codeSystemToStore);
if (codeSystem.getPid() == null) {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcUtil.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcUtil.java
new file mode 100644
index 00000000000..d45872a048e
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcUtil.java
@@ -0,0 +1,62 @@
+package ca.uhn.fhir.jpa.term;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import org.apache.commons.lang3.StringUtils;
+
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_GENERIC_VALUESET_URL;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_GENERIC_VALUESET_URL_PLUS_SLASH;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
+
+public class TermReadSvcUtil {
+
+ public static boolean mustReturnEmptyValueSet(String theUrl) {
+ if (! theUrl.startsWith(LOINC_GENERIC_VALUESET_URL)) return true;
+
+ if (! theUrl.startsWith(LOINC_GENERIC_VALUESET_URL_PLUS_SLASH)) {
+ throw new InternalErrorException("Don't know how to extract ValueSet's ForcedId from url: " + theUrl);
+ }
+
+ String forcedId = theUrl.substring(LOINC_GENERIC_VALUESET_URL_PLUS_SLASH.length());
+ return StringUtils.isBlank(forcedId);
+ }
+
+
+ public static boolean isLoincNotGenericUnversionedValueSet(String theUrl) {
+ boolean isLoincCodeSystem = StringUtils.containsIgnoreCase(theUrl, LOINC_LOW);
+ boolean isNoVersion = ! theUrl.contains("|");
+ boolean isNotLoincGenericValueSet = ! theUrl.equals(LOINC_GENERIC_VALUESET_URL);
+
+ return isLoincCodeSystem && isNoVersion && isNotLoincGenericValueSet;
+ }
+
+
+ public static boolean isLoincNotGenericUnversionedCodeSystem(String theUrl) {
+ boolean isLoincCodeSystem = StringUtils.containsIgnoreCase(theUrl, LOINC_LOW);
+ boolean isNoVersion = ! theUrl.contains("|");
+
+ return isLoincCodeSystem && isNoVersion;
+ }
+
+
+
+}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java
index be3cf92be7e..38fbbd7a6d4 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4.java
@@ -33,7 +33,10 @@ import org.springframework.context.ApplicationContext;
import org.springframework.context.event.ContextRefreshedEvent;
import org.springframework.context.event.EventListener;
+import java.security.InvalidParameterException;
+
import static org.apache.commons.lang3.StringUtils.isBlank;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
public class TermVersionAdapterSvcR4 extends BaseTermVersionAdapterSvcImpl implements ITermVersionAdapterSvc {
private IFhirResourceDao myConceptMapResourceDao;
@@ -63,6 +66,9 @@ public class TermVersionAdapterSvcR4 extends BaseTermVersionAdapterSvcImpl imple
public IIdType createOrUpdateCodeSystem(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, RequestDetails theRequestDetails) {
validateCodeSystemForStorage(theCodeSystemResource);
if (isBlank(theCodeSystemResource.getIdElement().getIdPart())) {
+ if (theCodeSystemResource.getUrl().contains(LOINC_LOW)) {
+ throw new InvalidParameterException("'loinc' CodeSystem must have an 'ID' element");
+ }
String matchUrl = "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl());
return myCodeSystemResourceDao.update(theCodeSystemResource, matchUrl, theRequestDetails).getId();
} else {
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java
index 2c62f3d05b9..1f85e823720 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java
@@ -40,7 +40,16 @@ import java.util.List;
*/
public interface ITermCodeSystemStorageSvc {
- static final String MAKE_LOADING_VERSION_CURRENT = "make.loading.version.current";
+ String MAKE_LOADING_VERSION_CURRENT = "make.loading.version.current";
+
+
+ /**
+ * Defaults to true when parameter is null or entry is not present in requestDetails.myUserData
+ */
+ static boolean isMakeVersionCurrent(RequestDetails theRequestDetails) {
+ return theRequestDetails == null ||
+ (boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
+ }
void deleteCodeSystem(TermCodeSystem theCodeSystem);
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java
index 0f04f62bd8e..b02ffa30740 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermReadSvc.java
@@ -4,10 +4,8 @@ import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem;
-import ca.uhn.fhir.jpa.api.model.TranslationRequest;
import ca.uhn.fhir.jpa.entity.TermConcept;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElement;
-import ca.uhn.fhir.jpa.entity.TermConceptMapGroupElementTarget;
+import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.IValueSetConceptAccumulator;
import ca.uhn.fhir.util.FhirVersionIndependentConcept;
@@ -17,7 +15,6 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.hl7.fhir.r4.model.CodeSystem;
-import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import javax.annotation.Nonnull;
@@ -119,4 +116,14 @@ public interface ITermReadSvc extends IValidationSupport {
*/
CodeValidationResult codeSystemValidateCode(IIdType theCodeSystemId, String theValueSetUrl, String theVersion, String theCode, String theDisplay, IBaseDatatype theCoding, IBaseDatatype theCodeableConcept);
+ /**
+ * Version independent
+ */
+ Optional findCurrentTermValueSet(String theUrl);
+
+ /**
+ * Version independent
+ */
+ Optional readCodeSystemByForcedId(String theForcedId);
+
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
index 8e2f26f5490..20ebb162a05 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincUploadPropertiesEnum.java
@@ -33,6 +33,7 @@ public enum LoincUploadPropertiesEnum {
*/
LOINC_UPLOAD_PROPERTIES_FILE("loincupload.properties"),
+ LOINC_XML_FILE("loinc.xml"),
/*
* MANDATORY
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupportTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupportTest.java
new file mode 100644
index 00000000000..8be940c8dae
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/JpaPersistedResourceValidationSupportTest.java
@@ -0,0 +1,124 @@
+package ca.uhn.fhir.jpa.dao;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
+import com.github.benmanes.caffeine.cache.Cache;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.InjectMocks;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.test.util.ReflectionTestUtils;
+
+import java.util.function.Function;
+
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.isA;
+import static org.mockito.Mockito.never;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+@ExtendWith(MockitoExtension.class)
+class JpaPersistedResourceValidationSupportTest {
+
+ private FhirContext theFhirContext = FhirContext.forR4();
+
+ @Mock private ITermReadSvc myTermReadSvc;
+ @Mock private DaoRegistry myDaoRegistry;
+ @Mock private Cache myLoadCache;
+ @Mock private IFhirResourceDao myValueSetResourceDao;
+
+ @InjectMocks
+ private IValidationSupport testedClass =
+ new JpaPersistedResourceValidationSupport(theFhirContext);
+
+ private Class myCodeSystemType = CodeSystem.class;
+ private Class myValueSetType = ValueSet.class;
+
+
+ @BeforeEach
+ public void setup() {
+ ReflectionTestUtils.setField(testedClass, "myValueSetType", myValueSetType);
+ }
+
+
+ @Nested
+ public class FetchCodeSystemTests {
+
+ @Test
+ void fetchCodeSystemMustUseForcedId() {
+ testedClass.fetchCodeSystem("string-containing-loinc");
+
+ verify(myTermReadSvc, times(1)).readCodeSystemByForcedId(LOINC_LOW);
+ verify(myLoadCache, never()).get(anyString(), isA(Function.class));
+ }
+
+
+ @Test
+ void fetchCodeSystemMustNotUseForcedId() {
+ testedClass.fetchCodeSystem("string-not-containing-l-o-i-n-c");
+
+ verify(myTermReadSvc, never()).readCodeSystemByForcedId(LOINC_LOW);
+ verify(myLoadCache, times(1)).get(anyString(), isA(Function.class));
+ }
+
+ }
+
+
+ @Nested
+ public class FetchValueSetTests {
+
+ @Test
+ void fetchValueSetMustUseForcedId() {
+ final String valueSetId = "string-containing-loinc";
+ ResourceNotFoundException thrown = assertThrows(
+ ResourceNotFoundException.class,
+ () -> testedClass.fetchValueSet(valueSetId));
+
+ assertTrue(thrown.getMessage().contains("Unable to find current version of ValueSet for url: " + valueSetId));
+ }
+
+
+ @Test
+ void fetchValueSetMustNotUseForcedId() {
+ testedClass.fetchValueSet("string-not-containing-l-o-i-n-c");
+
+ verify(myLoadCache, times(1)).get(anyString(), isA(Function.class));
+ }
+
+ }
+
+
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
index 02a797f60f6..83b38ad4a17 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/TransactionProcessorTest.java
@@ -144,7 +144,7 @@ public class TransactionProcessorTest {
}
@Bean
- public BaseTransactionProcessor.ITransactionProcessorVersionAdapter versionAdapter() {
+ public ITransactionProcessorVersionAdapter versionAdapter() {
return new TransactionProcessorVersionAdapterR4();
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
index 71c2af076fc..1cae885a51b 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java
@@ -3,7 +3,7 @@ package ca.uhn.fhir.jpa.dao.dstu2;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3Test;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
@@ -416,15 +416,15 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
* If any of this ever fails, it means that one of the OperationOutcome issue severity codes has changed code value across versions. We store the string as a constant, so something will need to
* be fixed.
*/
- assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
- assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
- assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.ERROR.getCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
- assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_INFO);
- assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_INFO);
- assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.INFORMATION.getCode(), BaseHapiFhirResourceDao.OO_SEVERITY_INFO);
- assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_WARN);
- assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_WARN);
- assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.WARNING.getCode(), BaseHapiFhirResourceDao.OO_SEVERITY_WARN);
+ assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseStorageDao.OO_SEVERITY_ERROR);
+ assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseStorageDao.OO_SEVERITY_ERROR);
+ assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.ERROR.getCode(), BaseStorageDao.OO_SEVERITY_ERROR);
+ assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseStorageDao.OO_SEVERITY_INFO);
+ assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseStorageDao.OO_SEVERITY_INFO);
+ assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.INFORMATION.getCode(), BaseStorageDao.OO_SEVERITY_INFO);
+ assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseStorageDao.OO_SEVERITY_WARN);
+ assertEquals(org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseStorageDao.OO_SEVERITY_WARN);
+ assertEquals(ca.uhn.fhir.model.dstu2.valueset.IssueSeverityEnum.WARNING.getCode(), BaseStorageDao.OO_SEVERITY_WARN);
}
@Test
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeDaoTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeDaoTest.java
index c4b430c4e57..ba7712066cb 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeDaoTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/expunge/DeleteExpungeDaoTest.java
@@ -7,6 +7,8 @@ import ca.uhn.fhir.jpa.batch.writer.SqlExecutorWriter;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import ca.uhn.fhir.util.BundleBuilder;
import org.hl7.fhir.instance.model.api.IIdType;
@@ -15,9 +17,11 @@ import org.hl7.fhir.r4.model.OperationOutcome;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
+import org.hl7.fhir.r5.model.StructureDefinition;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.mockito.stubbing.Answer;
import org.springframework.batch.core.BatchStatus;
import org.springframework.batch.core.JobExecution;
import org.springframework.beans.factory.annotation.Autowired;
@@ -27,6 +31,9 @@ import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
class DeleteExpungeDaoTest extends BaseJpaR4Test {
@Autowired
@@ -51,6 +58,41 @@ class DeleteExpungeDaoTest extends BaseJpaR4Test {
myDaoConfig.setExpungeBatchSize(defaultDaoConfig.getExpungeBatchSize());
}
+ @Test
+ public void testDeleteCascadeExpungeReturns400() {
+ // Create new organization
+ Organization organization = new Organization();
+ organization.setName("FOO");
+ IIdType organizationId = myOrganizationDao.create(organization).getId().toUnqualifiedVersionless();
+
+ Patient patient = new Patient();
+ patient.setManagingOrganization(new Reference(organizationId));
+ IIdType patientId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+ // Try to delete _cascade and _expunge on the organization
+ BaseServerResponseException e = assertThrows(BaseServerResponseException.class, () -> {
+ myOrganizationDao
+ .deleteByUrl("Organization?" + "_cascade=delete&" + JpaConstants.PARAM_DELETE_EXPUNGE + "=true", mySrd);
+ });
+
+ // Get not implemented HTTP 400 error
+ assertEquals(Constants.STATUS_HTTP_400_BAD_REQUEST, e.getStatusCode());
+ assertEquals("_expunge cannot be used with _cascade", e.getMessage());
+
+
+ // Try to delete with header 'X-Cascade' = delete
+ when(mySrd.getHeader(Constants.HEADER_CASCADE)).thenReturn(Constants.CASCADE_DELETE);
+ e = assertThrows(BaseServerResponseException.class, () -> {
+ myOrganizationDao
+ .deleteByUrl("Organization?" + JpaConstants.PARAM_DELETE_EXPUNGE + "=true", mySrd);
+ });
+
+ // Get not implemented HTTP 400 error
+ assertEquals(Constants.STATUS_HTTP_400_BAD_REQUEST, e.getStatusCode());
+ assertEquals("_expunge cannot be used with _cascade", e.getMessage());
+ }
+
+
@Test
public void testDeleteExpungeThrowExceptionIfForeignKeyLinksExists() {
// setup
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
index e6794b6caea..c16ee84372d 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
@@ -5,7 +5,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.HistoryCountModeEnum;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
-import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.BaseStorageDao;
import ca.uhn.fhir.jpa.dao.JpaResourceDao;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.model.entity.NormalizedQuantitySearchLevel;
@@ -1014,13 +1014,13 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
* be fixed.
*/
assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirDao.OO_SEVERITY_ERROR);
- assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_ERROR);
+ assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseStorageDao.OO_SEVERITY_ERROR);
assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.ERROR.toCode(), BaseHapiFhirDao.OO_SEVERITY_ERROR);
assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirDao.OO_SEVERITY_INFO);
- assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_INFO);
+ assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseStorageDao.OO_SEVERITY_INFO);
assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.INFORMATION.toCode(), BaseHapiFhirDao.OO_SEVERITY_INFO);
assertEquals(org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirDao.OO_SEVERITY_WARN);
- assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirResourceDao.OO_SEVERITY_WARN);
+ assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseStorageDao.OO_SEVERITY_WARN);
assertEquals(org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity.WARNING.toCode(), BaseHapiFhirDao.OO_SEVERITY_WARN);
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
index 9925ea61f49..ae1488533af 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java
@@ -81,6 +81,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.fail;
@@ -501,7 +502,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.setUrl("http://loinc.org");
cs.addConcept().setCode("123-4").setDisplay("Code 123 4");
- myCodeSystemDao.create(cs);
+ cs.setId(LOINC_LOW);
+ myCodeSystemDao.update(cs);
Group group = new Group();
group.setId("ABC");
@@ -568,7 +570,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.setUrl("http://loinc.org");
cs.addConcept().setCode("123-4").setDisplay("Code 123 4");
- myCodeSystemDao.create(cs);
+ cs.setId(LOINC_LOW);
+ myCodeSystemDao.update(cs);
Group group = new Group();
group.setId("ABC");
@@ -635,7 +638,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.setUrl("http://loinc.org");
cs.addConcept().setCode("123-4").setDisplay("Code 123 4");
- myCodeSystemDao.create(cs);
+ cs.setId(LOINC_LOW);
+ myCodeSystemDao.update(cs);
Group group = new Group();
group.setId("ABC");
@@ -1710,7 +1714,8 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
cs.setUrl(ITermLoaderSvc.LOINC_URI);
cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
cs.addConcept().setCode("10013-1");
- myCodeSystemDao.create(cs);
+ cs.setId(LOINC_LOW);
+ myCodeSystemDao.update(cs);
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(new UriType("http://fooVs"), null, new StringType("10013-1"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
index fa188add3af..0ab9e18c19c 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/BaseJpaR5Test.java
@@ -141,7 +141,6 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationContext;
-import org.springframework.data.domain.Pageable;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.test.util.AopTestUtils;
@@ -158,7 +157,7 @@ import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.Mockito.mock;
@@ -569,9 +568,9 @@ public abstract class BaseJpaR5Test extends BaseJpaTest implements ITestDataBuil
public List getExpandedConceptsByValueSetUrl(String theValuesetUrl) {
return runInTransaction(() -> {
- List valueSets = myTermValueSetDao.findTermValueSetByUrl(Pageable.unpaged(), theValuesetUrl);
- assertEquals(1, valueSets.size());
- TermValueSet valueSet = valueSets.get(0);
+ Optional valueSetOpt = myTermSvc.findCurrentTermValueSet(theValuesetUrl);
+ assertTrue(valueSetOpt.isPresent());
+ TermValueSet valueSet = valueSetOpt.get();
List concepts = valueSet.getConcepts();
return concepts.stream().map(concept -> concept.getCode()).collect(Collectors.toList());
});
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorHttpR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorHttpR4Test.java
index cc5c9bc8795..ef3c36dfa05 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorHttpR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorHttpR4Test.java
@@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.interceptor.validation;
import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.rp.r4.ObservationResourceProvider;
import ca.uhn.fhir.rest.api.MethodOutcome;
@@ -76,7 +75,7 @@ public class RepositoryValidatingInterceptorHttpR4Test extends BaseJpaR4Test {
}
private RepositoryValidatingRuleBuilder newRuleBuilder() {
- return myApplicationContext.getBean(BaseConfig.REPOSITORY_VALIDATING_RULE_BUILDER, RepositoryValidatingRuleBuilder.class);
+ return myApplicationContext.getBean(RepositoryValidatingRuleBuilder.REPOSITORY_VALIDATING_RULE_BUILDER, RepositoryValidatingRuleBuilder.class);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java
index ca49294dcda..f5187b4f36d 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/RepositoryValidatingInterceptorR4Test.java
@@ -1,6 +1,5 @@
package ca.uhn.fhir.jpa.interceptor.validation;
-import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@@ -388,7 +387,7 @@ public class RepositoryValidatingInterceptorR4Test extends BaseJpaR4Test {
private RepositoryValidatingRuleBuilder newRuleBuilder() {
- return myApplicationContext.getBean(BaseConfig.REPOSITORY_VALIDATING_RULE_BUILDER, RepositoryValidatingRuleBuilder.class);
+ return myApplicationContext.getBean(RepositoryValidatingRuleBuilder.REPOSITORY_VALIDATING_RULE_BUILDER, RepositoryValidatingRuleBuilder.class);
}
}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/ValidationMessageSuppressingInterceptorTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/ValidationMessageSuppressingInterceptorTest.java
index abe8b152ee4..693e1809f14 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/ValidationMessageSuppressingInterceptorTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/interceptor/validation/ValidationMessageSuppressingInterceptorTest.java
@@ -1,7 +1,6 @@
package ca.uhn.fhir.jpa.interceptor.validation;
import ca.uhn.fhir.context.support.IValidationSupport;
-import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.provider.r4.BaseResourceProviderR4Test;
import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
@@ -23,7 +22,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import java.io.IOException;
-import java.util.Collections;
import java.util.List;
import static org.hamcrest.MatcherAssert.assertThat;
@@ -118,7 +116,7 @@ public class ValidationMessageSuppressingInterceptorTest extends BaseResourcePro
public void testRepositoryValidation() {
createPatient(withActiveTrue(), withId("A"));
- List rules = myApplicationContext.getBean(BaseConfig.REPOSITORY_VALIDATING_RULE_BUILDER, RepositoryValidatingRuleBuilder.class)
+ List rules = myApplicationContext.getBean(RepositoryValidatingRuleBuilder.REPOSITORY_VALIDATING_RULE_BUILDER, RepositoryValidatingRuleBuilder.class)
.forResourcesOfType("Encounter")
.requireValidationToDeclaredProfiles().withBestPracticeWarningLevel(IResourceValidator.BestPracticeWarningLevel.Ignore)
.build();
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
index 760542e197f..d76b937e110 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/BaseResourceProviderR4Test.java
@@ -1,35 +1,5 @@
package ca.uhn.fhir.jpa.provider.r4;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.concurrent.TimeUnit;
-
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
-import org.eclipse.jetty.server.Server;
-import org.eclipse.jetty.servlet.ServletContextHandler;
-import org.eclipse.jetty.servlet.ServletHolder;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.r4.model.Parameters;
-import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
-import org.hl7.fhir.r4.model.Patient;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.web.context.ContextLoader;
-import org.springframework.web.context.WebApplicationContext;
-import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
-import org.springframework.web.context.support.GenericWebApplicationContext;
-import org.springframework.web.context.support.WebApplicationContextUtils;
-import org.springframework.web.cors.CorsConfiguration;
-import org.springframework.web.servlet.DispatcherServlet;
-
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.svc.ISearchCoordinatorSvc;
@@ -56,6 +26,35 @@ import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import ca.uhn.fhir.rest.server.provider.DeleteExpungeProvider;
import ca.uhn.fhir.rest.server.provider.ReindexProvider;
import ca.uhn.fhir.test.utilities.JettyUtil;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
+import org.eclipse.jetty.server.Server;
+import org.eclipse.jetty.servlet.ServletContextHandler;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
+import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.context.ContextLoader;
+import org.springframework.web.context.WebApplicationContext;
+import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
+import org.springframework.web.context.support.GenericWebApplicationContext;
+import org.springframework.web.context.support.WebApplicationContextUtils;
+import org.springframework.web.cors.CorsConfiguration;
+import org.springframework.web.servlet.DispatcherServlet;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.concurrent.TimeUnit;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseResourceProviderR4Test extends BaseJpaR4Test {
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4Test.java
new file mode 100644
index 00000000000..915ead7dcf1
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermVersionAdapterSvcR4Test.java
@@ -0,0 +1,78 @@
+package ca.uhn.fhir.jpa.term;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.test.util.ReflectionTestUtils;
+
+import java.security.InvalidParameterException;
+
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+
+@ExtendWith(MockitoExtension.class)
+class TermVersionAdapterSvcR4Test {
+
+ private final TermVersionAdapterSvcR4 testedClass = new TermVersionAdapterSvcR4();
+
+ @Mock private IFhirResourceDao myCodeSystemResourceDao;
+ @Mock ServletRequestDetails theRequestDetails;
+ @Mock DaoMethodOutcome theDaoMethodOutcome;
+
+ @Test
+ void createOrUpdateCodeSystemMustHaveId() {
+ CodeSystem codeSystem = new CodeSystem();
+ codeSystem.setUrl("a-loinc-system");
+
+ InvalidParameterException thrown = assertThrows(
+ InvalidParameterException.class,
+ () -> testedClass.createOrUpdateCodeSystem(codeSystem, new ServletRequestDetails()));
+
+ assertTrue(thrown.getMessage().contains("'loinc' CodeSystem must have an 'ID' element"));
+ }
+
+
+ @Test
+ void createOrUpdateCodeSystemWithIdNoException() {
+ ReflectionTestUtils.setField(testedClass, "myCodeSystemResourceDao", myCodeSystemResourceDao);
+
+ CodeSystem codeSystem = new CodeSystem();
+ codeSystem.setUrl("a-loinc-system").setId(LOINC_LOW);
+
+ when(myCodeSystemResourceDao.update(codeSystem, theRequestDetails)).thenReturn(theDaoMethodOutcome);
+
+ testedClass.createOrUpdateCodeSystem(codeSystem, theRequestDetails);
+
+ verify(myCodeSystemResourceDao, Mockito.times(1)).update(codeSystem, theRequestDetails);
+ }
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
index 23feac7194b..8d30f018d32 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java
@@ -25,7 +25,6 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
-import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
@@ -75,6 +74,7 @@ import static org.hamcrest.Matchers.containsString;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
@@ -930,7 +930,7 @@ public class TerminologyLoaderSvcLoincTest extends BaseLoaderTest {
testProps.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), "false");
doReturn(mockFileDescriptors).when(testedSvc).getLoadedFileDescriptors(mockFileDescriptorList);
- InvalidRequestException thrown = Assertions.assertThrows(InvalidRequestException.class,
+ InvalidRequestException thrown = assertThrows(InvalidRequestException.class,
() -> testedSvc.loadLoinc(mockFileDescriptorList, mySrd) );
assertEquals("'" + LOINC_CODESYSTEM_VERSION.getCode() + "' property is required when '" +
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
new file mode 100644
index 00000000000..b34d1e008de
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
@@ -0,0 +1,702 @@
+package ca.uhn.fhir.jpa.term;
+
+import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.context.support.ValidationSupportContext;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.config.BaseConfig;
+import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.entity.TermConcept;
+import ca.uhn.fhir.jpa.entity.TermValueSet;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.param.UriParam;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
+import org.apache.commons.lang3.StringUtils;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.CodeType;
+import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.StringType;
+import org.hl7.fhir.r4.model.UriType;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.mockito.Answers;
+import org.mockito.Mock;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.util.ResourceUtils;
+
+import javax.persistence.EntityManager;
+import javax.servlet.http.HttpServletResponse;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Optional;
+import java.util.Properties;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_MAKE_CURRENT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DUPLICATE_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_TERMS_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_HIERARCHY_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PARENT_GROUP_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_PRIMARY_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_RSNA_PLAYBOOK_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_PROPERTIES_FILE;
+import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
+import static org.mockito.Mockito.when;
+
+/**
+ * Tests load and validate CodeSystem and ValueSet so test names as uploadFirstCurrent... mean uploadCodeSystemAndValueSetCurrent...
+ */
+public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
+ private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcImplCurrentVersionR4Test.class);
+
+ public static final String BASE_LOINC_URL = "http://loinc.org";
+ public static final String BASE_LOINC_VS_URL = BASE_LOINC_URL + "/vs/";
+
+ // some ValueSets have a version specified independent of the CS version being uploaded. This one doesn't
+ public static final String VS_NO_VERSIONED_ON_UPLOAD_ID = "loinc-rsna-radiology-playbook";
+ public static final String VS_NO_VERSIONED_ON_UPLOAD = BASE_LOINC_VS_URL + VS_NO_VERSIONED_ON_UPLOAD_ID;
+ public static final String VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE = "17787-3";
+ public static final String VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY = "NM Thyroid gland Study report";
+
+ // some ValueSets have a version specified independent of the CS version being uploaded. This is one of them
+ public static final String VS_VERSIONED_ON_UPLOAD_ID = "LL1000-0";
+ public static final String VS_VERSIONED_ON_UPLOAD = BASE_LOINC_VS_URL + VS_VERSIONED_ON_UPLOAD_ID;
+ public static final String VS_VERSIONED_ON_UPLOAD_FIRST_CODE = "LA13825-7";
+ public static final String VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY = "1 slice or 1 dinner roll";
+
+ public static final String VS_ANSWER_LIST_VERSION = "Beta.1";
+ public static final Set possibleVersions = Sets.newHashSet("2.67", "2.68", "2.69");
+
+ @Mock
+ private HttpServletResponse mockServletResponse;
+
+ @Mock(answer = Answers.RETURNS_DEEP_STUBS)
+ private ServletRequestDetails mockRequestDetails;
+
+ @Autowired
+ private EntityManager myEntityManager;
+
+ @Autowired
+ private TermLoaderSvcImpl myTermLoaderSvc;
+
+ @Autowired
+ private ITermReadSvc myITermReadSvc;
+
+ @Autowired
+ @Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT)
+ private IValidationSupport myJpaPersistedResourceValidationSupport;
+
+ private ZipCollectionBuilder myFiles;
+ private ServletRequestDetails myRequestDetails = new ServletRequestDetails();
+
+ private Properties uploadProperties;
+ private IFhirResourceDao myValueSetIFhirResourceDao;
+
+
+ @BeforeEach
+ public void beforeEach() throws Exception {
+ File file = ResourceUtils.getFile("classpath:loinc-ver/" + LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+ uploadProperties = new Properties();
+ uploadProperties.load(new FileInputStream(file));
+
+ myValueSetIFhirResourceDao = myDaoRegistry.getResourceDao(ValueSet.class);
+
+ when(mockRequestDetails.getServer().getDefaultPageSize()).thenReturn(25);
+ }
+
+
+ /**
+ * For input version or for current (when input is null) validates search, expand, lookup and validateCode operations
+ */
+ private void validateOperations(String currentVersion, Collection theExpectedVersions) {
+ validateValueSetSearch(theExpectedVersions);
+
+ validateValueExpand(currentVersion, theExpectedVersions);
+
+ validateValueLookup(currentVersion, theExpectedVersions);
+
+ validateValidateCode(currentVersion, theExpectedVersions);
+
+ // nothing to test for subsumes operation as it works only for concepts which share CodeSystem and version
+ }
+
+
+ private void validateValidateCode(String theCurrentVersion, Collection allVersions) {
+ IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null,
+ new UriType(BASE_LOINC_URL), null, new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
+ null, null, null, null);
+ assertNotNull(resultNoVersioned);
+ assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultNoVersioned.getDisplay());
+
+ IValidationSupport.CodeValidationResult resultVersioned = myCodeSystemDao.validateCode(null,
+ new UriType(BASE_LOINC_URL), null, new CodeType(VS_VERSIONED_ON_UPLOAD_FIRST_CODE),
+ null, null, null, null);
+ assertNotNull(resultVersioned);
+ assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
+
+ allVersions.forEach(this::validateValidateCodeForVersion);
+ }
+
+
+ private void validateValidateCodeForVersion(String theVersion) {
+ IValidationSupport.CodeValidationResult resultNoVersioned = myCodeSystemDao.validateCode(null,
+ new UriType(BASE_LOINC_URL), new StringType(theVersion), new CodeType(VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE),
+ null, null, null, null);
+ assertNotNull(resultNoVersioned);
+ assertEquals(prefixWithVersion(theVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultNoVersioned.getDisplay());
+
+ IValidationSupport.CodeValidationResult resultVersioned = myCodeSystemDao.validateCode(null,
+ new UriType(BASE_LOINC_URL), new StringType(theVersion), new CodeType(VS_VERSIONED_ON_UPLOAD_FIRST_CODE),
+ null, null, null, null);
+ assertNotNull(resultVersioned);
+ assertEquals(prefixWithVersion(theVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), resultVersioned.getDisplay());
+ }
+
+
+ private void validateValueLookup(String theCurrentVersion, Collection allVersions) {
+ IValidationSupport.LookupCodeResult resultNoVer = myValidationSupport.lookupCode(
+ new ValidationSupportContext(myValidationSupport), BASE_LOINC_URL, VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE, null);
+ assertNotNull(resultNoVer);
+ String expectedNoVer = prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
+ assertEquals(expectedNoVer, resultNoVer.getCodeDisplay());
+
+ IValidationSupport.LookupCodeResult resultWithVer = myValidationSupport.lookupCode(
+ new ValidationSupportContext(myValidationSupport), BASE_LOINC_URL, VS_VERSIONED_ON_UPLOAD_FIRST_CODE, null);
+ assertNotNull(resultWithVer);
+ String expectedWithVer = prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
+ assertEquals(expectedWithVer, resultWithVer.getCodeDisplay());
+
+ allVersions.forEach(this::lookupForVersion);
+ }
+
+
+ private void lookupForVersion(String theVersion) {
+ IValidationSupport.LookupCodeResult resultNoVer = myValidationSupport.lookupCode(
+ new ValidationSupportContext(myValidationSupport), BASE_LOINC_URL + "|" + theVersion,
+ VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE, null);
+ assertNotNull(resultNoVer);
+ String expectedNoVer = prefixWithVersion(theVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
+ assertEquals(expectedNoVer, resultNoVer.getCodeDisplay());
+
+ IValidationSupport.LookupCodeResult resultWithVer = myValidationSupport.lookupCode(
+ new ValidationSupportContext(myValidationSupport), BASE_LOINC_URL + "|" + theVersion,
+ VS_VERSIONED_ON_UPLOAD_FIRST_CODE, null);
+ assertNotNull(resultWithVer);
+ String expectedWithVer = prefixWithVersion(theVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY);
+ assertEquals(expectedWithVer, resultWithVer.getCodeDisplay());
+ }
+
+
+ private String prefixWithVersion(String version, String suffix) {
+ return (version == null ? "" : "v" + version + " ") + suffix;
+
+ }
+
+ private void validateValueExpand(String currentVersion, Collection theAllVersions) {
+ // for CS ver = null, VS ver = null
+ ValueSet vs = myValueSetDao.expandByIdentifier(VS_NO_VERSIONED_ON_UPLOAD, null);
+ assertEquals(1, vs.getExpansion().getContains().size());
+
+ // version was added prefixing code display to validate
+ assertEquals(prefixWithVersion(currentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
+ vs.getExpansion().getContains().iterator().next().getDisplay());
+
+
+ // for CS ver = null, VS ver != null
+ ValueSet vs1 = myValueSetDao.expandByIdentifier(
+ VS_VERSIONED_ON_UPLOAD + "|" + VS_ANSWER_LIST_VERSION, null);
+ assertEquals(3, vs1.getExpansion().getContains().size());
+
+ assertEquals(prefixWithVersion(currentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
+ vs1.getExpansion().getContains().iterator().next().getDisplay());
+
+
+ validateExpandedTermConcepts(currentVersion, theAllVersions);
+
+ // now for each uploaded version
+ theAllVersions.forEach(this::validateValueExpandForVersion);
+ }
+
+
+ private void validateExpandedTermConcepts(String theCurrentVersion, Collection theAllVersions) {
+ TermConcept termConceptNoVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
+ "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
+ VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
+ assertNotNull(termConceptNoVerCsvNoVer);
+ // data should have version because it was loaded with a version
+ assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvNoVer.getDisplay());
+
+ TermConcept termConceptVerCsvNoVer = (TermConcept) myEntityManager.createQuery(
+ "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
+ VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId is null").getSingleResult();
+ assertNotNull(termConceptVerCsvNoVer);
+ // data should have version because it was loaded with a version
+ assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvNoVer.getDisplay());
+
+ if (theCurrentVersion != null) {
+ TermConcept termConceptNoVerCsvVer = (TermConcept) myEntityManager.createQuery(
+ "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
+ VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
+ assertNotNull(termConceptNoVerCsvVer);
+ // data should have version because it was loaded with a version
+ assertEquals(prefixWithVersion(theCurrentVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVerCsvVer.getDisplay());
+
+ TermConcept termConceptVerCsvVer = (TermConcept) myEntityManager.createQuery(
+ "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
+ VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theCurrentVersion + "'").getSingleResult();
+ assertNotNull(termConceptVerCsvVer);
+ // data should have version because it was loaded with a version
+ assertEquals(prefixWithVersion(theCurrentVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVerCsvVer.getDisplay());
+ }
+
+
+ theAllVersions.forEach(this::validateExpandedTermConceptsForVersion);
+ }
+
+
+ private void validateExpandedTermConceptsForVersion(String theVersion) {
+ TermConcept termConceptNoVer = (TermConcept) myEntityManager.createQuery(
+ "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
+ VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theVersion + "'").getSingleResult();
+ assertNotNull(termConceptNoVer);
+ assertEquals(prefixWithVersion(theVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptNoVer.getDisplay());
+
+ TermConcept termConceptVer = (TermConcept) myEntityManager.createQuery(
+ "select tc from TermConcept tc join fetch tc.myCodeSystem tcsv where tc.myCode = '" +
+ VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' and tcsv.myCodeSystemVersionId = '" + theVersion + "'").getSingleResult();
+ assertNotNull(termConceptVer);
+ assertEquals(prefixWithVersion(theVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY), termConceptVer.getDisplay());
+ }
+
+
+ private void validateValueExpandForVersion(String theVersion) {
+ // for CS ver != null, VS ver = null
+
+ ValueSet vs2 = myValueSetDao.expandByIdentifier(
+ VS_NO_VERSIONED_ON_UPLOAD + "|" + theVersion, null);
+ assertEquals(1, vs2.getExpansion().getContains().size());
+
+ // version was added before code display to validate
+ assertEquals(prefixWithVersion(theVersion, VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
+ vs2.getExpansion().getContains().iterator().next().getDisplay());
+
+
+ // for CS ver != null, VS ver != null
+
+ ValueSet vs3 = myValueSetDao.expandByIdentifier(
+ VS_VERSIONED_ON_UPLOAD + "|" + VS_ANSWER_LIST_VERSION + "-" + theVersion, null);
+ assertEquals(3, vs3.getExpansion().getContains().size());
+
+ // version was added before code display to validate
+ assertEquals(prefixWithVersion(theVersion, VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
+ vs3.getExpansion().getContains().iterator().next().getDisplay());
+ }
+
+
+ private void validateValueSetSearch(Collection theExpectedIdVersions) {
+ // first validate search for CS ver = null VS ver = null
+
+ SearchParameterMap paramsNoUploadVer = new SearchParameterMap("url", new UriParam(VS_NO_VERSIONED_ON_UPLOAD));
+ int expectedResultQty = theExpectedIdVersions.size() + 1; // + 1 because an extra null version (the current) is always present
+ IBundleProvider noUploadVerResult = myValueSetIFhirResourceDao.search(paramsNoUploadVer, mockRequestDetails, mockServletResponse);
+ List noUploadVerValueSets = noUploadVerResult.getAllResources();
+ assertEquals(expectedResultQty, noUploadVerValueSets.size());
+
+ matchUnqualifiedIds(noUploadVerValueSets, theExpectedIdVersions);
+
+ // now validate search for CS ver = null VS ver != null
+
+ SearchParameterMap paramsUploadVer = new SearchParameterMap("url", new UriParam(VS_VERSIONED_ON_UPLOAD));
+ paramsUploadVer.add("version", new TokenParam(VS_ANSWER_LIST_VERSION));
+ IBundleProvider uploadVerResult = myValueSetIFhirResourceDao.search(paramsUploadVer, mockRequestDetails, mockServletResponse);
+ List uploadVerValueSets = uploadVerResult.getAllResources();
+ assertEquals(1, uploadVerValueSets.size());
+
+ assertEquals(VS_VERSIONED_ON_UPLOAD_ID, uploadVerValueSets.get(0).getIdElement().getIdPart());
+ assertEquals(VS_ANSWER_LIST_VERSION, ((ValueSet) uploadVerValueSets.get(0)).getVersion());
+
+ // now validate each specific uploaded version
+ theExpectedIdVersions.forEach(this::validateValueSetSearchForVersion);
+ }
+
+
+ /**
+ * Some ValueSets (IE: AnswerLists), can have a specific version, different than the version of the
+ * CodeSystem with which they were uploaded. That version is what we distinguish in both sets of tests here,
+ * no the CodeSystem version.
+ */
+ private void validateValueSetSearchForVersion(String theVersion) {
+ // for no versioned VS (VS version, different than CS version)
+
+ SearchParameterMap paramsUploadNoVer = new SearchParameterMap("url", new UriParam(VS_NO_VERSIONED_ON_UPLOAD));
+ paramsUploadNoVer.add("version", new TokenParam(theVersion));
+
+ IBundleProvider uploadNoVerResult = myValueSetIFhirResourceDao.search(paramsUploadNoVer, mockRequestDetails, mockServletResponse);
+ List uploadNoVerValueSets = uploadNoVerResult.getAllResources();
+ assertEquals(1, uploadNoVerValueSets.size());
+
+ ValueSet loadNoVersionValueSet = (ValueSet) uploadNoVerValueSets.get(0);
+ String expectedLoadNoVersionUnqualifiedId = VS_NO_VERSIONED_ON_UPLOAD_ID + (theVersion == null ? "" : "-" + theVersion);
+ assertEquals(expectedLoadNoVersionUnqualifiedId, loadNoVersionValueSet.getIdElement().getIdPart());
+
+
+ // versioned VS (VS version, different than CS version)
+
+ SearchParameterMap paramsUploadVer = new SearchParameterMap("url", new UriParam(VS_VERSIONED_ON_UPLOAD));
+ paramsUploadVer.add("version", new TokenParam(VS_ANSWER_LIST_VERSION + "-" + theVersion));
+
+ IBundleProvider uploadVerResult = myValueSetIFhirResourceDao.search(paramsUploadVer, mockRequestDetails, mockServletResponse);
+ List uploadVerValueSets = uploadVerResult.getAllResources();
+ assertEquals(1, uploadVerValueSets.size());
+
+ ValueSet loadVersionValueSet = (ValueSet) uploadVerValueSets.get(0);
+ String expectedLoadVersionUnqualifiedId = VS_VERSIONED_ON_UPLOAD_ID + (theVersion == null ? "" : "-" + theVersion);
+ assertEquals(expectedLoadVersionUnqualifiedId, loadVersionValueSet.getIdElement().getIdPart());
+ }
+
+
+ /**
+ * Validates that the collection of unqualified IDs of each element of theValueSets matches the expected
+ * unqualifiedIds corresponding to the uploaded versions plus one with no version
+ *
+ * @param theValueSets the ValueSet collection
+ * @param theExpectedIdVersions the collection of expected versions
+ */
+ private void matchUnqualifiedIds(List theValueSets, Collection theExpectedIdVersions) {
+ // set should contain one entry per expectedVersion
+ List expectedNoVersionUnqualifiedIds = theExpectedIdVersions.stream()
+ .map(expVer -> VS_NO_VERSIONED_ON_UPLOAD_ID + "-" + expVer)
+ .collect(Collectors.toList());
+
+ // plus one entry for null version
+ expectedNoVersionUnqualifiedIds.add(VS_NO_VERSIONED_ON_UPLOAD_ID);
+
+ List resultUnqualifiedIds = theValueSets.stream()
+ .map(r -> r.getIdElement().getIdPart())
+ .collect(Collectors.toList());
+
+ assertThat(resultUnqualifiedIds, containsInAnyOrder(resultUnqualifiedIds.toArray()));
+
+ Set theExpectedIdVersionsPlusNull = Sets.newHashSet(theExpectedIdVersions);
+ theExpectedIdVersionsPlusNull.add(null);
+ assertThat(theExpectedIdVersionsPlusNull, containsInAnyOrder(
+ theValueSets.stream().map(r -> ((ValueSet) r).getVersion()).toArray()));
+
+ }
+
+
+ /**
+ * Validates that:
+ * for CodeSystem:
+ * _ current CS has no version
+ * _ current TCS has no version
+ * for ValueSet:
+ * _ current TVSs with upload version have upload-version with no version append
+ * _ current TVSs with no upload version have null version
+ */
+ private void runCommonValidations(List theAllVersions) {
+ // for CodeSystem:
+
+ // _ current CS is present and has no version
+ CodeSystem codeSystem = myCodeSystemDao.read(new IdType(LOINC_LOW));
+ String csString = myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(codeSystem);
+ ourLog.info("CodeSystem:\n" + csString);
+
+ HashSet shouldNotBePresentVersions = new HashSet<>(possibleVersions);
+ theAllVersions.forEach(shouldNotBePresentVersions::remove);
+ shouldNotBePresentVersions.forEach(vv -> assertFalse(csString.contains(vv),
+ "Found version string: '" + vv + "' in CodeSystem: " + csString));
+
+ // same reading it from term service
+ CodeSystem cs = myITermReadSvc.fetchCanonicalCodeSystemFromCompleteContext(BASE_LOINC_URL);
+ assertEquals(BASE_LOINC_URL, cs.getUrl());
+ assertNull(cs.getVersion());
+
+ // _ current TermCodeSystem has no version
+ TermCodeSystemVersion termCSVersion = fetchCurrentCodeSystemVersion();
+ assertNotNull(termCSVersion);
+ assertNull(termCSVersion.getCodeSystemVersionId());
+
+ // for ValueSet:
+
+ // for ValueSet resource
+ ValueSet vs = (ValueSet) myJpaPersistedResourceValidationSupport.fetchValueSet(VS_NO_VERSIONED_ON_UPLOAD);
+ assertNotNull(vs);
+ assertEquals(VS_NO_VERSIONED_ON_UPLOAD, vs.getUrl());
+ assertNull(vs.getVersion());
+
+ // current TermVSs with no upload version have null version
+ Optional noUploadCurrentVsOpt = myITermReadSvc.findCurrentTermValueSet(VS_NO_VERSIONED_ON_UPLOAD);
+ assertTrue(noUploadCurrentVsOpt.isPresent());
+ assertNull(noUploadCurrentVsOpt.get().getVersion());
+
+ // current VSs with upload version have upload-version with no version append
+ Optional uploadCurrentVsOpt = myITermReadSvc.findCurrentTermValueSet(VS_VERSIONED_ON_UPLOAD);
+ assertTrue(uploadCurrentVsOpt.isPresent());
+ assertEquals(VS_ANSWER_LIST_VERSION, uploadCurrentVsOpt.get().getVersion());
+
+ }
+
+
+ @Test()
+ public void uploadCurrentNoVersion() throws Exception {
+ IIdType csId = uploadLoincCodeSystem(null, true);
+
+ runCommonValidations(Collections.emptyList());
+
+ // validate operation for current (no version parameter)
+ validateOperations(null, Collections.emptySet());
+
+ // tests conditions which were failing after VS expansion (before fix for issue-2995)
+ validateTermConcepts(Lists.newArrayList((String) null));
+ }
+
+
+ @Test()
+ public void uploadWithVersion() throws Exception {
+ String ver = "2.67";
+ IIdType csId = uploadLoincCodeSystem(ver, true);
+
+ runCommonValidations(Collections.singletonList(ver));
+
+ // validate operation for specific version
+ validateOperations(ver, Collections.singleton(ver));
+
+ // tests conditions which were failing after VS expansion (before fix for issue-2995)
+ validateTermConcepts(Lists.newArrayList(ver, ver));
+ }
+
+
+
+ @Test
+ public void uploadNoVersionThenNoCurrent() throws Exception {
+ uploadLoincCodeSystem(null, true);
+
+ String ver = "2.67";
+ uploadLoincCodeSystem(ver, false);
+
+// myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
+ runCommonValidations(Collections.singletonList(ver));
+
+ // validate operation for specific version
+ validateOperations(null, Collections.singleton(ver));
+
+ // tests conditions which were failing after VS expansion (before fix for issue-2995)
+ validateTermConcepts(Lists.newArrayList(null, ver));
+ }
+
+
+ @Test
+ public void uploadWithVersionThenNoCurrent() throws Exception {
+ String currentVer = "2.67";
+ uploadLoincCodeSystem(currentVer, true);
+
+ String nonCurrentVer = "2.68";
+ uploadLoincCodeSystem(nonCurrentVer, false);
+
+ // myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
+
+ runCommonValidations(Lists.newArrayList(currentVer, nonCurrentVer));
+
+ // validate operation for specific version
+ validateOperations(currentVer, Lists.newArrayList(currentVer, nonCurrentVer));
+
+ // tests conditions which were failing after VS expansion (before fix for issue-2995)
+ validateTermConcepts(Lists.newArrayList(currentVer, currentVer, nonCurrentVer));
+ }
+
+ /**
+ * Validates TermConcepts were created in the sequence indicated by the parameters
+ * and their displays match the expected versions
+ */
+ private void validateTermConcepts(ArrayList theExpectedVersions) {
+ @SuppressWarnings("unchecked")
+ List termConceptNoVerList = (List) myEntityManager.createQuery(
+ "from TermConcept where myCode = '" + VS_NO_VERSIONED_ON_UPLOAD_FIRST_CODE + "' order by myId").getResultList();
+ assertEquals(theExpectedVersions.size(), termConceptNoVerList.size());
+ for (int i = 0; i < theExpectedVersions.size(); i++) {
+ assertEquals( prefixWithVersion(theExpectedVersions.get(i), VS_NO_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
+ termConceptNoVerList.get(i).getDisplay(), "TermCode with id: " + i + " display");
+ }
+
+ @SuppressWarnings("unchecked")
+ List termConceptWithVerList = (List) myEntityManager.createQuery(
+ "from TermConcept where myCode = '" + VS_VERSIONED_ON_UPLOAD_FIRST_CODE + "' order by myId").getResultList();
+ assertEquals(theExpectedVersions.size(), termConceptWithVerList.size());
+ for (int i = 0; i < theExpectedVersions.size(); i++) {
+ assertEquals( prefixWithVersion(theExpectedVersions.get(i), VS_VERSIONED_ON_UPLOAD_FIRST_DISPLAY),
+ termConceptWithVerList.get(i).getDisplay(), "TermCode with id: " + i + " display");
+ }
+ }
+
+
+ @Test
+ public void uploadNoVersionThenNoCurrentThenCurrent() throws Exception {
+ uploadLoincCodeSystem(null, true);
+
+ String nonCurrentVer = "2.67";
+ uploadLoincCodeSystem(nonCurrentVer, false);
+
+ String currentVer = "2.68";
+ uploadLoincCodeSystem(currentVer, true);
+
+ runCommonValidations(Lists.newArrayList(nonCurrentVer, currentVer));
+
+ // validate operation for specific version
+ validateOperations(currentVer, Lists.newArrayList(nonCurrentVer, currentVer));
+
+ // tests conditions which were failing after VS expansion (before fix for issue-2995)
+ validateTermConcepts(Lists.newArrayList(nonCurrentVer, currentVer, currentVer));
+ }
+
+
+ @Test
+ public void uploadWithVersionThenNoCurrentThenCurrent() throws Exception {
+ String firstCurrentVer = "2.67";
+ uploadLoincCodeSystem(firstCurrentVer, true);
+
+ String noCurrentVer = "2.68";
+ uploadLoincCodeSystem(noCurrentVer, false);
+
+ String lastCurrentVer = "2.69";
+ uploadLoincCodeSystem(lastCurrentVer, true);
+
+ runCommonValidations(Lists.newArrayList(firstCurrentVer, noCurrentVer, lastCurrentVer));
+
+ // validate operation for specific version
+ validateOperations(lastCurrentVer, Lists.newArrayList(firstCurrentVer, noCurrentVer, lastCurrentVer));
+
+ // tests conditions which were failing after VS expansion (before fix for issue-2995)
+ validateTermConcepts(Lists.newArrayList(firstCurrentVer, noCurrentVer, lastCurrentVer, lastCurrentVer));
+ }
+
+
+
+
+ private IIdType uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception {
+ myFiles = new ZipCollectionBuilder();
+
+ myRequestDetails.getUserData().put(LOINC_CODESYSTEM_MAKE_CURRENT, theMakeItCurrent);
+ uploadProperties.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), Boolean.toString(theMakeItCurrent));
+
+ assertTrue(
+ theVersion == null || theVersion.equals("2.67") || theVersion.equals("2.68") || theVersion.equals("2.69"),
+ "Version supported are: 2.67, 2.68, 2.69 and null" );
+
+ if (StringUtils.isBlank(theVersion)) {
+ uploadProperties.remove(LOINC_CODESYSTEM_VERSION.getCode());
+ } else {
+ uploadProperties.put(LOINC_CODESYSTEM_VERSION.getCode(), theVersion);
+ }
+
+ addLoincMandatoryFilesToZip(myFiles, theVersion);
+
+ UploadStatistics stats = myTermLoaderSvc.loadLoinc(myFiles.getFiles(), mySrd);
+ myTerminologyDeferredStorageSvc.saveAllDeferred();
+
+ return stats.getTarget();
+ }
+
+
+ public void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles, String theVersion) throws IOException {
+ String theClassPathPrefix = getClassPathPrefix(theVersion);
+ addBaseLoincMandatoryFilesToZip(theFiles, true, theClassPathPrefix);
+ theFiles.addPropertiesZip(uploadProperties, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
+ }
+
+
+ private String getClassPathPrefix(String theVersion) {
+ String theClassPathPrefix = "/loinc-ver/v-no-version/";
+
+ if (StringUtils.isBlank(theVersion)) return theClassPathPrefix;
+
+ switch(theVersion) {
+ case "2.67": return "/loinc-ver/v267/";
+ case "2.68": return "/loinc-ver/v268/";
+ case "2.69": return "/loinc-ver/v269/";
+ }
+
+ fail("Setup failed. Unexpected version: " + theVersion);
+ return null;
+ }
+
+
+ private static void addBaseLoincMandatoryFilesToZip(
+ ZipCollectionBuilder theFiles, Boolean theIncludeTop2000, String theClassPathPrefix) throws IOException {
+ theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_DUPLICATE_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_HIERARCHY_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_PART_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
+ if (theIncludeTop2000) {
+ theFiles.addFileZip(theClassPathPrefix, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
+ theFiles.addFileZip(theClassPathPrefix, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
+ }
+ }
+
+ private TermCodeSystemVersion fetchCurrentCodeSystemVersion() {
+ return (TermCodeSystemVersion) myEntityManager.createQuery(
+ "select tcsv from TermCodeSystemVersion tcsv join fetch tcsv.myCodeSystem tcs " +
+ "where tcs.myCurrentVersion = tcsv" ).getSingleResult();
+ }
+
+
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
index 5d29b99a1d4..34d94192a4c 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
@@ -42,6 +42,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
+import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertSame;
@@ -406,7 +407,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.addFilter()
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.EQUAL)
- .setValue("loinc");
+ .setValue(LOINC_LOW);
outcome = myTermSvc.expandValueSet(null, vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("47239-9"));
@@ -478,7 +479,7 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
.addFilter()
.setProperty("copyright")
.setOp(ValueSet.FilterOperator.EQUAL)
- .setValue("loinc");
+ .setValue(LOINC_LOW);
outcome = myTermSvc.expandValueSet(null, vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("50015-7", "43343-3", "43343-4"));
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ZipCollectionBuilder.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ZipCollectionBuilder.java
index 026bd396e7d..1b887b37234 100644
--- a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ZipCollectionBuilder.java
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ZipCollectionBuilder.java
@@ -13,11 +13,15 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
+import java.util.Properties;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
public class ZipCollectionBuilder {
+ public static final String ZIP_ENTRY_PREFIX = "SnomedCT_Release_INT_20160131_Full/Terminology/";
+
+
private static final Logger ourLog = LoggerFactory.getLogger(ZipCollectionBuilder.class);
private final ArrayList myFiles;
@@ -58,7 +62,7 @@ public class ZipCollectionBuilder {
bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
ourLog.info("Adding {} to test zip", theClasspathFileName);
- zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + theOutputFilename));
+ zos.putNextEntry(new ZipEntry(ZIP_ENTRY_PREFIX + theOutputFilename));
zos.write(readFile(theClasspathPrefix, theClasspathFileName));
zos.closeEntry();
zos.close();
@@ -76,6 +80,36 @@ public class ZipCollectionBuilder {
});
}
+ public void addPropertiesZip(Properties properties, String theOutputFilename) throws IOException {
+
+ ByteArrayOutputStream bos;
+ bos = new ByteArrayOutputStream();
+ ZipOutputStream zos = new ZipOutputStream(bos);
+ ourLog.info("Adding properties to test zip");
+ zos.putNextEntry(new ZipEntry(ZIP_ENTRY_PREFIX + theOutputFilename));
+ zos.write(getPropertiesBytes(properties));
+ zos.closeEntry();
+ zos.close();
+ ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
+ myFiles.add(new ITermLoaderSvc.FileDescriptor() {
+ @Override
+ public String getFilename() {
+ return "AAA.zip";
+ }
+
+ @Override
+ public InputStream getInputStream() {
+ return new ByteArrayInputStream(bos.toByteArray());
+ }
+ });
+ }
+
+ private byte[] getPropertiesBytes(Properties theProperties) throws IOException {
+ ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+ theProperties.store(byteArrayOutputStream, "");
+ return byteArrayOutputStream.toByteArray();
+ }
+
private byte[] readFile(String theClasspathPrefix, String theClasspathFileName) throws IOException {
String classpathName = theClasspathPrefix + theClasspathFileName;
InputStream stream = getClass().getResourceAsStream(classpathName);
diff --git a/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcTest.java b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcTest.java
new file mode 100644
index 00000000000..c695bf8c0aa
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/api/ITermReadSvcTest.java
@@ -0,0 +1,239 @@
+package ca.uhn.fhir.jpa.term.api;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
+import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
+import ca.uhn.fhir.jpa.model.entity.ResourceTable;
+import ca.uhn.fhir.jpa.term.TermReadSvcR4;
+import ca.uhn.fhir.jpa.term.TermReadSvcUtil;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import com.google.common.collect.Lists;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.CodeSystem;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Answers;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.data.domain.Pageable;
+import org.springframework.test.util.ReflectionTestUtils;
+
+import javax.persistence.EntityManager;
+import javax.persistence.NonUniqueResultException;
+import java.util.Collections;
+import java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.ArgumentMatchers.isA;
+import static org.mockito.Mockito.never;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+@ExtendWith(MockitoExtension.class)
+class ITermReadSvcTest {
+
+ private final ITermReadSvc testedClass = new TermReadSvcR4();
+
+ @Mock private ITermValueSetDao myTermValueSetDao;
+ @Mock private DaoRegistry myDaoRegistry;
+ @Mock private IFhirResourceDao myFhirResourceDao;
+
+
+ @Nested
+ public class FindCurrentTermValueSet {
+
+ @BeforeEach
+ public void setup() {
+ ReflectionTestUtils.setField(testedClass, "myTermValueSetDao", myTermValueSetDao);
+ }
+
+ @Test
+ void forLoinc() {
+ String valueSetId = "a-loinc-value-set";
+ testedClass.findCurrentTermValueSet("http://loinc.org/vs/" + valueSetId);
+
+ verify(myTermValueSetDao, times(1)).findTermValueSetByForcedId(valueSetId);
+ verify(myTermValueSetDao, never()).findTermValueSetByUrl(isA(Pageable.class), anyString());
+ }
+
+ @Test
+ void forNotLoinc() {
+ String valueSetId = "not-a-loin-c-value-set";
+ testedClass.findCurrentTermValueSet("http://not-loin-c.org/vs/" + valueSetId);
+
+ verify(myTermValueSetDao, never()).findTermValueSetByForcedId(valueSetId);
+ verify(myTermValueSetDao, times(1)).findTermValueSetByUrl(isA(Pageable.class), anyString());
+ }
+ }
+
+
+ @Nested
+ public class MustReturnEmptyValueSet {
+
+ @Test
+ void doesntStartWithGenericVSReturnsTrue() {
+ boolean ret = TermReadSvcUtil.mustReturnEmptyValueSet("http://boing.org");
+ assertTrue(ret);
+ }
+
+ @Test
+ void doesntStartWithGenericVSPlusSlashThrows() {
+ InternalErrorException thrown = assertThrows(
+ InternalErrorException.class,
+ () -> TermReadSvcUtil.mustReturnEmptyValueSet("http://loinc.org/vs-no-slash-after-vs"));
+
+ assertTrue(thrown.getMessage().contains("Don't know how to extract ValueSet's ForcedId from url:"));
+ }
+
+ @Test
+ void blankVsIdReturnsTrue() {
+ boolean ret = TermReadSvcUtil.mustReturnEmptyValueSet("http://loinc.org/vs/");
+ assertTrue(ret);
+ }
+
+ @Test
+ void startsWithGenericPlusSlashPlusIdReturnsFalse() {
+ boolean ret = TermReadSvcUtil.mustReturnEmptyValueSet("http://loinc.org/vs/some-vs-id");
+ assertFalse(ret);
+ }
+
+ }
+
+
+ @Nested
+ public class IsLoincNotGenericUnversionedCodeSystem {
+
+ @Test
+ void doesntContainLoincReturnsFalse() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedCodeSystem("http://boing.org");
+ assertFalse(ret);
+ }
+
+ @Test
+ void hasVersionReturnsFalse() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedCodeSystem("http://boing.org|v2.68");
+ assertFalse(ret);
+ }
+
+ @Test
+ void containsLoincAndNoVersionReturnsTrue() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedCodeSystem("http://anything-plus-loinc.org");
+ assertTrue(ret);
+ }
+ }
+
+ @Nested
+ public class IsLoincNotGenericUnversionedValueSet {
+
+ @Test
+ void notLoincReturnsFalse() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedValueSet("http://anything-but-loin-c.org");
+ assertFalse(ret);
+ }
+
+ @Test
+ void isLoincAndHasVersionReturnsFalse() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedValueSet("http://loinc.org|v2.67");
+ assertFalse(ret);
+ }
+
+ @Test
+ void isLoincNoVersionButEqualsGenericValueSetUrlReturnsFalse() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedValueSet("http://loinc.org/vs");
+ assertFalse(ret);
+ }
+
+ @Test
+ void isLoincNoVersionStartsWithGenericValueSetPlusSlashPlusIdReturnsTrue() {
+ boolean ret = TermReadSvcUtil.isLoincNotGenericUnversionedValueSet("http://loinc.org/vs/vs-id");
+ assertTrue(ret);
+ }
+
+ }
+
+
+ @Nested
+ public class ReadByForcedId {
+
+ @Mock(answer = Answers.RETURNS_DEEP_STUBS)
+ private EntityManager myEntityManager;
+
+ @Mock private ResourceTable resource1;
+ @Mock private ResourceTable resource2;
+ @Mock private IBaseResource myCodeSystemResource;
+
+
+ @BeforeEach
+ public void setup() {
+ ReflectionTestUtils.setField(testedClass, "myEntityManager", myEntityManager);
+ }
+
+
+ @Test
+ void getNoneReturnsOptionalEmpty() {
+ when(myEntityManager.createQuery(anyString()).getResultList())
+ .thenReturn(Collections.emptyList());
+
+ Optional result = testedClass.readCodeSystemByForcedId("a-cs-id");
+ assertFalse(result.isPresent());
+ }
+
+ @Test
+ void getMultipleThrows() {
+ when(myEntityManager.createQuery(anyString()).getResultList())
+ .thenReturn(Lists.newArrayList(resource1, resource2));
+
+ NonUniqueResultException thrown = assertThrows(
+ NonUniqueResultException.class,
+ () -> testedClass.readCodeSystemByForcedId("a-cs-id"));
+
+ assertTrue(thrown.getMessage().contains("More than one CodeSystem is pointed by forcedId:"));
+ }
+
+ @Test
+ void getOneConvertToResource() {
+ ReflectionTestUtils.setField(testedClass, "myDaoRegistry", myDaoRegistry);
+
+ when(myEntityManager.createQuery(anyString()).getResultList())
+ .thenReturn(Lists.newArrayList(resource1));
+ when(myDaoRegistry.getResourceDao("CodeSystem")).thenReturn(myFhirResourceDao);
+ when(myFhirResourceDao.toResource(resource1, false)).thenReturn(myCodeSystemResource);
+
+
+ testedClass.readCodeSystemByForcedId("a-cs-id");
+
+
+ verify(myFhirResourceDao, times(1)).toResource(any(), eq(false));
+ }
+
+ }
+
+}
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/loincupload.properties b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/loincupload.properties
new file mode 100644
index 00000000000..3d36353cec0
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/loincupload.properties
@@ -0,0 +1,93 @@
+#################
+### MANDATORY ###
+#################
+
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## File must be present
+loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## File must be present
+loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
+
+# Document ontology
+## File must be present
+loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
+
+# LOINC codes
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## File must be present
+loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## File must be present
+loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
+
+# Part
+## File must be present
+loinc.part.file=AccessoryFiles/PartFile/Part.csv
+
+# Part link
+## File must be present
+loinc.part.link.primary.file=AccessoryFiles/PartFile/LoincPartLink_Primary.csv
+loinc.part.link.supplementary.file=AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
+
+# Part related code mapping
+## File must be present
+loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## File must be present
+loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## File must be present
+loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## File must be present
+loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## File must be present
+loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
+
+# This is the version identifier for uploaded ConceptMap resources
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+
+# Group
+## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
+## File may be omitted
+loinc.group.file=AccessoryFiles/GroupFile/Group.csv
+# Group terms
+## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
+# Parent group
+## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
+
+# Consumer Names
+## Default value if key not provided: AccessoryFiles/ConsumerName/ConsumerName.csv
+## File may be omitted
+loinc.consumer.name.file=AccessoryFiles/ConsumerName/ConsumerName.csv
+
+# Linguistic Variants
+## Default value if key not provided: AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
+## File may be omitted
+loinc.linguistic.variants.file=AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
\ No newline at end of file
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/loincupload_singlepartlink.properties b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/loincupload_singlepartlink.properties
new file mode 100644
index 00000000000..3164f533888
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/loincupload_singlepartlink.properties
@@ -0,0 +1,82 @@
+#################
+### MANDATORY ###
+#################
+
+# Answer lists (ValueSets of potential answers/values for LOINC "questions")
+## File must be present
+loinc.answerlist.file=AccessoryFiles/AnswerFile/AnswerList.csv
+# Answer list links (connects LOINC observation codes to answer list codes)
+## File must be present
+loinc.answerlist.link.file=AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
+
+# Document ontology
+## File must be present
+loinc.document.ontology.file=AccessoryFiles/DocumentOntology/DocumentOntology.csv
+
+# LOINC codes
+## File must be present
+loinc.file=LoincTable/Loinc.csv
+
+# LOINC hierarchy
+## File must be present
+loinc.hierarchy.file=AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
+
+# IEEE medical device codes
+## File must be present
+loinc.ieee.medical.device.code.mapping.table.file=AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
+
+# Imaging document codes
+## File must be present
+loinc.imaging.document.codes.file=AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
+
+# Part
+## File must be present
+loinc.part.file=AccessoryFiles/PartFile/Part.csv
+
+# Part link
+## File must be present
+loinc.part.link.file=AccessoryFiles/PartFile/LoincPartLink.csv
+
+# Part related code mapping
+## File must be present
+loinc.part.related.code.mapping.file=AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
+
+# RSNA playbook
+## File must be present
+loinc.rsna.playbook.file=AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
+
+# Top 2000 codes - SI
+## File must be present
+loinc.top2000.common.lab.results.si.file=AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
+# Top 2000 codes - US
+## File must be present
+loinc.top2000.common.lab.results.us.file=AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
+
+# Universal lab order ValueSet
+## File must be present
+loinc.universal.lab.order.valueset.file=AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
+
+################
+### OPTIONAL ###
+################
+
+# This is the version identifier for the answer list file
+## Key may be omitted
+loinc.answerlist.version=Beta.1
+
+# This is the version identifier for uploaded ConceptMap resources
+## Key may be omitted
+loinc.conceptmap.version=Beta.1
+
+# Group
+## Default value if key not provided: AccessoryFiles/GroupFile/Group.csv
+## File may be omitted
+loinc.group.file=AccessoryFiles/GroupFile/Group.csv
+# Group terms
+## Default value if key not provided: AccessoryFiles/GroupFile/GroupLoincTerms.csv
+## File may be omitted
+loinc.group.terms.file=AccessoryFiles/GroupFile/GroupLoincTerms.csv
+# Parent group
+## Default value if key not provided: AccessoryFiles/GroupFile/ParentGroup.csv
+## File may be omitted
+loinc.parent.group.file=AccessoryFiles/GroupFile/ParentGroup.csv
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/AnswerFile/AnswerList.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/AnswerFile/AnswerList.csv
new file mode 100644
index 00000000000..a448cf80f2d
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/AnswerFile/AnswerList.csv
@@ -0,0 +1,12 @@
+"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink" ,"AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName" ,"ExtCodeSystem" ,"ExtCodeSystemVersion" ,"ExtCodeSystemCopyrightNotice" ,"SubsequentTextPrompt","Description","Score"
+"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13825-7" ,"1" , ,1 ,"1 slice or 1 dinner roll" , , , , , , , ,
+"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13838-0" ,"2" , ,2 ,"2 slices or 2 dinner rolls" , , , , , , , ,
+"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13892-7" ,"3" , ,3 ,"More than 2 slices or 2 dinner rolls", , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA6270-8" ,"00" , ,1 ,"Never" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13836-4" ,"01" , ,2 ,"1-3 times per month" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13834-9" ,"02" , ,3 ,"1-2 times per week" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13853-9" ,"03" , ,4 ,"3-4 times per week" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13860-4" ,"04" , ,5 ,"5-6 times per week" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13827-3" ,"05" , ,6 ,"1 time per day" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA4389-8" ,"97" , ,11 ,"Refused" ,"443390004","Refused (qualifier value)","http://snomed.info/sct","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College", , ,
+"LL1892-0" ,"ICD-9_ICD-10" ,"1.3.6.1.4.1.12009.10.1.1069","Y" , ,"http://www.cdc.gov/nchs/icd.htm", , , , , , , , , , , , ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/AnswerFile/LoincAnswerListLink.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
new file mode 100644
index 00000000000..820602c77ad
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/AnswerFile/LoincAnswerListLink.csv
@@ -0,0 +1,11 @@
+"LoincNumber","LongCommonName" ,"AnswerListId","AnswerListName" ,"AnswerListLinkType","ApplicableContext"
+"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]","LL1000-0" ,"PhenX05_13_30D bread amt","NORMATIVE" ,
+"10061-0" ,"S' wave amplitude in lead I" ,"LL1311-1" ,"PhenX12_44" ,"EXAMPLE" ,
+"10331-7" ,"Rh [Type] in Blood" ,"LL360-9" ,"Pos|Neg" ,"EXAMPLE" ,
+"10389-5" ,"Blood product.other [Type]" ,"LL2413-4" ,"Othr bld prod" ,"EXAMPLE" ,
+"10390-3" ,"Blood product special preparation [Type]" ,"LL2422-5" ,"Blood prod treatment" ,"EXAMPLE" ,
+"10393-7" ,"Factor IX given [Type]" ,"LL2420-9" ,"Human/Recomb" ,"EXAMPLE" ,
+"10395-2" ,"Factor VIII given [Type]" ,"LL2420-9" ,"Human/Recomb" ,"EXAMPLE" ,
+"10401-8" ,"Immune serum globulin given [Type]" ,"LL2421-7" ,"IM/IV" ,"EXAMPLE" ,
+"10410-9" ,"Plasma given [Type]" ,"LL2417-5" ,"Plasma type" ,"EXAMPLE" ,
+"10568-4" ,"Clarity of Semen" ,"LL2427-4" ,"Clear/Opales/Milky" ,"EXAMPLE" ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/ConsumerName/ConsumerName.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/ConsumerName/ConsumerName.csv
new file mode 100644
index 00000000000..b4ec2907985
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/ConsumerName/ConsumerName.csv
@@ -0,0 +1,6 @@
+"LoincNumber","ConsumerName"
+"61438-8","Consumer Name 61438-8"
+,"Consumer Name X"
+47239-9",""
+"17787-3","Consumer Name 17787-3"
+"38699-5","1,1-Dichloroethane, Air"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/DocumentOntology/DocumentOntology.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/DocumentOntology/DocumentOntology.csv
new file mode 100644
index 00000000000..f857d7f297b
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/DocumentOntology/DocumentOntology.csv
@@ -0,0 +1,10 @@
+"LoincNumber","PartNumber","PartTypeName","PartSequenceOrder","PartName"
+"11488-4","LP173418-7","Document.Kind","1","Note"
+"11488-4","LP173110-0","Document.TypeOfService","1","Consultation"
+"11488-4","LP173061-5","Document.Setting","1","{Setting}"
+"11488-4","LP187187-2","Document.Role","1","{Role}"
+"11490-0","LP173418-7","Document.Kind","1","Note"
+"11490-0","LP173221-5","Document.TypeOfService","1","Discharge summary"
+"11490-0","LP173061-5","Document.Setting","1","{Setting}"
+"11490-0","LP173084-7","Document.Role","1","Physician"
+"11492-6","LP173418-7","Document.Kind","1","Note"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/Group.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/Group.csv
new file mode 100644
index 00000000000..66f5561ea1c
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/Group.csv
@@ -0,0 +1,2 @@
+"ParentGroupId","GroupId","Group","Archetype","Status","VersionFirstReleased"
+"LG100-4","LG1695-8","1,4-Dichlorobenzene|MCnc|Pt|ANYBldSerPl","","Active",""
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/GroupLoincTerms.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/GroupLoincTerms.csv
new file mode 100644
index 00000000000..04c19759cfb
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/GroupLoincTerms.csv
@@ -0,0 +1,3 @@
+"Category","GroupId","Archetype","LoincNumber","LongCommonName"
+"Flowsheet","LG1695-8","","17424-3","1,4-Dichlorobenzene [Mass/volume] in Blood"
+"Flowsheet","LG1695-8","","13006-2","1,4-Dichlorobenzene [Mass/volume] in Serum or Plasma"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/ParentGroup.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/ParentGroup.csv
new file mode 100644
index 00000000000..734a86c43dd
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/GroupFile/ParentGroup.csv
@@ -0,0 +1,2 @@
+"ParentGroupId","ParentGroup","Status"
+"LG100-4","Chem_DrugTox_Chal_Sero_Allergy","ACTIVE"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
new file mode 100644
index 00000000000..a26397639ff
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/ImagingDocuments/ImagingDocumentCodes.csv
@@ -0,0 +1,10 @@
+"LOINC_NUM","LONG_COMMON_NAME"
+"11525-3","US Pelvis Fetus for pregnancy"
+"17787-3","NM Thyroid gland Study report"
+"18744-3","Bronchoscopy study"
+"18746-8","Colonoscopy study"
+"18748-4","Diagnostic imaging study"
+"18751-8","Endoscopy study"
+"18753-4","Flexible sigmoidoscopy study"
+"24531-6","US Retroperitoneum"
+"24532-4","US Abdomen RUQ"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/LinguisticVariants.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
new file mode 100644
index 00000000000..c79b3197490
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/LinguisticVariants.csv
@@ -0,0 +1,9 @@
+"ID","ISO_LANGUAGE","ISO_COUNTRY","LANGUAGE_NAME","PRODUCER"
+"5","zh","CN","Chinese (CHINA)","Lin Zhang, A LOINC volunteer from China"
+"7","es","AR","Spanish (ARGENTINA)","Conceptum Medical Terminology Center"
+"8","fr","CA","French (CANADA)","Canada Health Infoway Inc."
+,"de","AT","German (AUSTRIA)","ELGA, Austria"
+"88",,"AT","German (AUSTRIA)","ELGA, Austria"
+"89","de",,"German (AUSTRIA)","ELGA, Austria"
+"90","de","AT",,"ELGA, Austria"
+"24","de","AT","German (AUSTRIA)","ELGA, Austria"
\ No newline at end of file
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/deAT24LinguisticVariant.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/deAT24LinguisticVariant.csv
new file mode 100644
index 00000000000..c6882d47504
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/deAT24LinguisticVariant.csv
@@ -0,0 +1,4 @@
+"LOINC_NUM","COMPONENT","PROPERTY","TIME_ASPCT","SYSTEM","SCALE_TYP","METHOD_TYP","CLASS","SHORTNAME","LONG_COMMON_NAME","RELATEDNAMES2","LinguisticVariantDisplayName"
+"61438-8","Entlassungsbrief Ärztlich","Ergebnis","Zeitpunkt","{Setting}","Dokument","Dermatologie","DOC.ONTOLOGY","de shortname","de long common name","de related names 2","de linguistic variant display name"
+"43730-1","","","","","","","","","","EBV-DNA qn. PCR","EBV-DNA quantitativ PCR"
+"17787-3","","","","","","","","","","CoV OC43 RNA ql/SM P","Coronavirus OC43 RNA ql. /Sondermaterial PCR"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/frCA8LinguisticVariant.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/frCA8LinguisticVariant.csv
new file mode 100644
index 00000000000..fa09e0cb242
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/frCA8LinguisticVariant.csv
@@ -0,0 +1,6 @@
+"LOINC_NUM","COMPONENT","PROPERTY","TIME_ASPCT","SYSTEM","SCALE_TYP","METHOD_TYP","CLASS","SHORTNAME","LONG_COMMON_NAME","RELATEDNAMES2","LinguisticVariantDisplayName"
+"61438-8","Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif","Immunofluorescence","Sérologie","","","",""
+"11704-4","Gliale nucléaire de type 1 , IgG","Titre","Temps ponctuel","LCR","Quantitatif","Immunofluorescence","Sérologie","","","",""
+,"Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif",,,"","","",""
+"17787-3","Virus respiratoire syncytial bovin","Présence-Seuil","Temps ponctuel","XXX","Ordinal","Culture spécifique à un microorganisme","Microbiologie","","","",""
+"17788-1","Cellules de Purkinje cytoplasmique type 2 , IgG","Titre","Temps ponctuel","Sérum","Quantitatif",,,"","","",""
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/zhCN5LinguisticVariant.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/zhCN5LinguisticVariant.csv
new file mode 100644
index 00000000000..48d07d9fdc3
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LinguisticVariants/zhCN5LinguisticVariant.csv
@@ -0,0 +1,9 @@
+"LOINC_NUM","COMPONENT","PROPERTY","TIME_ASPCT","SYSTEM","SCALE_TYP","METHOD_TYP","CLASS","SHORTNAME","LONG_COMMON_NAME","RELATEDNAMES2","LinguisticVariantDisplayName"
+"61438-8","血流速度.收缩期.最大值","速度","时间点","大脑中动脉","定量型","超声.多普勒","产科学检查与测量指标.超声","","","Cereb 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 大脑（Cerebral） 时刻;随机;随意;瞬间 术语""cerebral""指的是主要由中枢半球（大脑皮质和基底神经节）组成的那部分脑结构 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"11704-4","血流速度.收缩期.最大值","速度","时间点","动脉导管","定量型","超声.多普勒","产科学检查与测量指标.超声","","","动态 动脉管 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 时刻;随机;随意;瞬间 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"17787-3","血流速度.收缩期.最大值","速度","时间点","二尖瓣^胎儿","定量型","超声.多普勒","产科学检查与测量指标.超声","","","僧帽瓣 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 时刻;随机;随意;瞬间 流 流量;流速;流体 胎;超系统 - 胎儿 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"61438-6",,"速度","时间点","二尖瓣^胎儿","定量型","超声.多普勒","产科学检查与测量指标.超声","","","僧帽瓣 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 时刻;随机;随意;瞬间 流 流量;流速;流体 胎;超系统 - 胎儿 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"10000-8","血流速度.收缩期.最大值",,"时间点","二尖瓣^胎儿","定量型","超声.多普勒","产科学检查与测量指标.超声","","","僧帽瓣 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 时刻;随机;随意;瞬间 流 流量;流速;流体 胎;超系统 - 胎儿 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"17788-1","血流速度.收缩期.最大值","速度",,"大脑中动脉","定量型","超声.多普勒","产科学检查与测量指标.超声","","","Cereb 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 大脑（Cerebral） 时刻;随机;随意;瞬间 术语""cerebral""指的是主要由中枢半球（大脑皮质和基底神经节）组成的那部分脑结构 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"11488-4","血流速度.收缩期.最大值","速度","时间点",,"定量型","超声.多普勒","产科学检查与测量指标.超声","","","Cereb 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 大脑（Cerebral） 时刻;随机;随意;瞬间 术语""cerebral""指的是主要由中枢半球（大脑皮质和基底神经节）组成的那部分脑结构 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
+"47239-9","血流速度.收缩期.最大值","速度","时间点","大脑中动脉",,"超声.多普勒","产科学检查与测量指标.超声","","","Cereb 动态 可用数量表示的;定量性;数值型;数量型;连续数值型标尺 大脑（Cerebral） 时刻;随机;随意;瞬间 术语""cerebral""指的是主要由中枢半球（大脑皮质和基底神经节）组成的那部分脑结构 流 流量;流速;流体 血;全血 血流量;血液流量 速度(距离/时间);速率;速率(距离/时间)",""
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
new file mode 100644
index 00000000000..d8cf83cd09e
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincIeeeMedicalDeviceCodeMappingTable/LoincIeeeMedicalDeviceCodeMappingTable.csv
@@ -0,0 +1,10 @@
+LOINC_NUM,LOINC_LONG_COMMON_NAME,IEEE_CF_CODE10,IEEE_REFID,IEEE_DESCRIPTION,IEEE_DIM,IEEE_UOM_UCUM
+11556-8,Oxygen [Partial pressure] in Blood,160116,MDC_CONC_PO2_GEN,,LMT-2L-2 LMT-2L-2,kPa mm[Hg]
+11557-6,Carbon dioxide [Partial pressure] in Blood,160064,MDC_CONC_PCO2_GEN,,LMT-2L-2 LMT-2L-2,kPa mm[Hg]
+11558-4,pH of Blood,160004,MDC_CONC_PH_GEN,,[pH],[pH]
+12961-9,Urea nitrogen [Mass/volume] in Arterial blood,160080,MDC_CONC_UREA_ART,,ML-3 NL-3,mg/dL mmol/L
+14749-6,Glucose [Moles/volume] in Serum or Plasma,160196,MDC_CONC_GLU_VENOUS_PLASMA,Plasma glucose concentration taken from venous,NL-3 ,mmol/L
+14749-6,Glucose [Moles/volume] in Serum or Plasma,160368,MDC_CONC_GLU_UNDETERMINED_PLASMA,Plasma glucose concentration taken from undetermined sample source,NL-3 ,mmol/L
+15074-8,Glucose [Moles/volume] in Blood,160020,MDC_CONC_GLU_GEN,,NL-3,mmol/L
+15074-8,Glucose [Moles/volume] in Blood,160364,MDC_CONC_GLU_UNDETERMINED_WHOLEBLOOD,Whole blood glucose concentration taken from undetermined sample source,NL-3 ,mmol/L
+17861-6,Calcium [Mass/volume] in Serum or Plasma,160024,MDC_CONC_CA_GEN,,ML-3,mg/dL
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
new file mode 100644
index 00000000000..1acba586623
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincRsnaRadiologyPlaybook/LoincRsnaRadiologyPlaybook.csv
@@ -0,0 +1,10 @@
+"LoincNumber","LongCommonName" ,"PartNumber","PartTypeName" ,"PartName" ,"PartSequenceOrder","RID" ,"PreferredName" ,"RPID" ,"LongName"
+"17787-3" ,"NM Thyroid gland Study report","LP199995-4","Rad.Anatomic Location.Region Imaged","Neck" ,"A" ,"RID7488" ,"neck" ,"" ,""
+"17787-3" ,"NM Thyroid gland Study report","LP206648-0","Rad.Anatomic Location.Imaging Focus","Thyroid gland" ,"A" ,"RID7578" ,"thyroid gland" ,"" ,""
+"17787-3" ,"NM Thyroid gland Study report","LP208891-4","Rad.Modality.Modality type" ,"NM" ,"A" ,"RID10330","nuclear medicine imaging","" ,""
+"24531-6" ,"US Retroperitoneum" ,"LP207608-3","Rad.Modality.Modality type" ,"US" ,"A" ,"RID10326","Ultrasound" ,"RPID2142","US Retroperitoneum"
+"24531-6" ,"US Retroperitoneum" ,"LP199943-4","Rad.Anatomic Location.Imaging Focus","Retroperitoneum" ,"A" ,"RID431" ,"RETROPERITONEUM" ,"RPID2142","US Retroperitoneum"
+"24531-6" ,"US Retroperitoneum" ,"LP199956-6","Rad.Anatomic Location.Region Imaged","Abdomen" ,"A" ,"RID56" ,"Abdomen" ,"RPID2142","US Retroperitoneum"
+"24532-4" ,"US Abdomen RUQ" ,"LP199956-6","Rad.Anatomic Location.Region Imaged","Abdomen" ,"A" ,"RID56" ,"Abdomen" ,"" ,""
+"24532-4" ,"US Abdomen RUQ" ,"LP207608-3","Rad.Modality.Modality type" ,"US" ,"A" ,"RID10326","Ultrasound" ,"" ,""
+"24532-4" ,"US Abdomen RUQ" ,"LP208105-9","Rad.Anatomic Location.Imaging Focus","Right upper quadrant","A" ,"RID29994","Right upper quadrant" ,"" ,""
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
new file mode 100644
index 00000000000..72d95485a58
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/LoincUniversalLabOrdersValueSet/LoincUniversalLabOrdersValueSet.csv
@@ -0,0 +1,10 @@
+"LOINC_NUM","LONG_COMMON_NAME","ORDER_OBS"
+"42176-8","1,3 beta glucan [Mass/volume] in Serum","Both"
+"53835-5","1,5-Anhydroglucitol [Mass/volume] in Serum or Plasma","Both"
+"31019-3","10-Hydroxycarbazepine [Mass/volume] in Serum or Plasma","Both"
+"6765-2","17-Hydroxypregnenolone [Mass/volume] in Serum or Plasma","Both"
+"1668-3","17-Hydroxyprogesterone [Mass/volume] in Serum or Plasma","Both"
+"32854-2","17-Hydroxyprogesterone [Presence] in DBS","Both"
+"49054-0","25-Hydroxycalciferol [Mass/volume] in Serum or Plasma","Both"
+"62292-8","25-Hydroxyvitamin D2+25-Hydroxyvitamin D3 [Mass/volume] in Serum or Plasma","Both"
+"44907-4","5-Hydroxyindoleacetate panel - 24 hour Urine","Order"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
new file mode 100644
index 00000000000..527b8fd5cae
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/MultiAxialHierarchy/MultiAxialHierarchy.csv
@@ -0,0 +1,10 @@
+PATH_TO_ROOT,SEQUENCE,IMMEDIATE_PARENT,CODE,CODE_TEXT
+,1,,LP31755-9,Microbiology
+LP31755-9,1,LP31755-9,LP14559-6,Microorganism
+LP31755-9.LP14559-6,1,LP14559-6,LP98185-9,Bacteria
+LP31755-9.LP14559-6.LP98185-9,1,LP98185-9,LP14082-9,Bacteria
+LP31755-9.LP14559-6.LP98185-9.LP14082-9,1,LP14082-9,LP52258-8,Bacteria | Body Fluid
+LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52258-8,1,LP52258-8,41599-2,Bacteria Fld Ql Micro
+LP31755-9.LP14559-6.LP98185-9.LP14082-9,2,LP14082-9,LP52260-4,Bacteria | Cerebral spinal fluid
+LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52260-4,1,LP52260-4,41602-4,Bacteria CSF Ql Micro
+LP31755-9.LP14559-6.LP98185-9.LP14082-9,3,LP14082-9,LP52960-9,Bacteria | Cervix
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/AnswerList.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/AnswerList.csv
new file mode 100644
index 00000000000..a448cf80f2d
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/AnswerList.csv
@@ -0,0 +1,12 @@
+"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink" ,"AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName" ,"ExtCodeSystem" ,"ExtCodeSystemVersion" ,"ExtCodeSystemCopyrightNotice" ,"SubsequentTextPrompt","Description","Score"
+"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13825-7" ,"1" , ,1 ,"1 slice or 1 dinner roll" , , , , , , , ,
+"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13838-0" ,"2" , ,2 ,"2 slices or 2 dinner rolls" , , , , , , , ,
+"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165" ,"N" , , ,"LA13892-7" ,"3" , ,3 ,"More than 2 slices or 2 dinner rolls", , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA6270-8" ,"00" , ,1 ,"Never" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13836-4" ,"01" , ,2 ,"1-3 times per month" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13834-9" ,"02" , ,3 ,"1-2 times per week" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13853-9" ,"03" , ,4 ,"3-4 times per week" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13860-4" ,"04" , ,5 ,"5-6 times per week" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA13827-3" ,"05" , ,6 ,"1 time per day" , , , , , , , ,
+"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166" ,"N" , , ,"LA4389-8" ,"97" , ,11 ,"Refused" ,"443390004","Refused (qualifier value)","http://snomed.info/sct","http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College", , ,
+"LL1892-0" ,"ICD-9_ICD-10" ,"1.3.6.1.4.1.12009.10.1.1069","Y" , ,"http://www.cdc.gov/nchs/icd.htm", , , , , , , , , , , , ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/Loinc.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/Loinc.csv
new file mode 100644
index 00000000000..20379cb7f1d
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/Loinc.csv
@@ -0,0 +1,16 @@
+"LOINC_NUM","COMPONENT" ,"PROPERTY","TIME_ASPCT","SYSTEM" ,"SCALE_TYP","METHOD_TYP" ,"CLASS" ,"VersionLastChanged","CHNG_TYPE","DefinitionDescription" ,"STATUS","CONSUMER_NAME","CLASSTYPE","FORMULA","SPECIES","EXMPL_ANSWERS","SURVEY_QUEST_TEXT" ,"SURVEY_QUEST_SRC" ,"UNITSREQUIRED","SUBMITTED_UNITS","RELATEDNAMES2" ,"SHORTNAME" ,"ORDER_OBS" ,"CDISC_COMMON_TESTS","HL7_FIELD_SUBFIELD_ID","EXTERNAL_COPYRIGHT_NOTICE" ,"EXAMPLE_UNITS","LONG_COMMON_NAME" ,"UnitsAndRange","DOCUMENT_SECTION","EXAMPLE_UCUM_UNITS","EXAMPLE_SI_UCUM_UNITS","STATUS_REASON","STATUS_TEXT","CHANGE_REASON_PUBLIC" ,"COMMON_TEST_RANK","COMMON_ORDER_RANK","COMMON_SI_TEST_RANK","HL7_ATTACHMENT_STRUCTURE","EXTERNAL_COPYRIGHT_LINK","PanelType","AskAtOrderEntry","AssociatedObservations" ,"VersionFirstReleased","ValidHL7AttachmentRequest"
+"10013-1" ,"R' wave amplitude.lead I" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-I; R wave Amp L-I; Random; Right; Voltage" ,"R' wave Amp L-I" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead I" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10014-9" ,"R' wave amplitude.lead II" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"2; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-II; R wave Amp L-II; Random; Right; Voltage" ,"R' wave Amp L-II" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead II" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10015-6" ,"R' wave amplitude.lead III" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"3; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-III; R wave Amp L-III; Random; Right; Voltage" ,"R' wave Amp L-III" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead III" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10016-4" ,"R' wave amplitude.lead V1" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V1; R wave Amp L-V1; Random; Right; Voltage" ,"R' wave Amp L-V1" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V1" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"1001-7" ,"DBG Ab" ,"Pr" ,"Pt" ,"Ser/Plas^donor" ,"Ord" , ,"BLDBK" ,"2.44" ,"MIN" , ,"ACTIVE", ,1 , , , , , , , ,"ABS; Aby; Antby; Anti; Antibodies; Antibody; Autoantibodies; Autoantibody; BLOOD BANK; Donna Bennett-Goodspeed; Donr; Ordinal; Pl; Plasma; Plsm; Point in time; QL; Qual; Qualitative; Random; Screen; SerP; SerPl; SerPl^donor; SerPlas; Serum; Serum or plasma; SR" ,"DBG Ab SerPl Donr Ql" ,"Observation", , , , ,"DBG Ab [Presence] in Serum or Plasma from donor" , , , , , , ,"The Property has been changed from ACnc to Pr (Presence) to reflect the new model for ordinal terms where results are based on presence or absence." ,0 ,0 ,0 , , , , , , ,
+"10017-2" ,"R' wave amplitude.lead V2" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V2; R wave Amp L-V2; Random; Right; Voltage" ,"R' wave Amp L-V2" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V2" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10018-0" ,"R' wave amplitude.lead V3" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V3; R wave Amp L-V3; Random; Right; Voltage" ,"R' wave Amp L-V3" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V3" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10019-8" ,"R' wave amplitude.lead V4" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V4; R wave Amp L-V4; Random; Right; Voltage" ,"R' wave Amp L-V4" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V4" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10020-6" ,"R' wave amplitude.lead V5" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V5; R wave Amp L-V5; Random; Right; Voltage" ,"R' wave Amp L-V5" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V5" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30D","Find" ,"Pt" ,"^Patient" ,"Ord" ,"PhenX" ,"PHENX" ,"2.44" ,"MIN" , ,"TRIAL" , ,2 , , , ,"Each time you eat bread, toast or dinner rolls, how much do you usually eat?","PhenX.050201100100","N" , ,"Finding; Findings; How much bread in 30D; Last; Ordinal; Point in time; QL; Qual; Qualitative; Random; Screen" ,"How much bread in 30D PhenX", , , , , ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]", , , , , , , ,0 ,0 ,0 , , , , , , ,
+"10000-8" ,"R wave duration.lead AVR" ,"Time" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; Durat; ECG; EKG.MEASUREMENTS; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave dur L-AVR; R wave dur L-AVR; Random; Right" ,"R wave dur L-AVR" ,"Observation", , , ,"s" ,"R wave duration in lead AVR" , , ,"s" , , , , ,0 ,0 ,0 , , , , , , ,
+"17787-3" ,"Study report" ,"Find" ,"Pt" ,"Neck>Thyroid gland","Doc" ,"NM" ,"RAD" ,"2.61" ,"MIN" , ,"ACTIVE", ,2 , , , , , , , ,"Document; Finding; Findings; Imaging; Point in time; Radiology; Random; Study report; Thy" ,"NM Thyroid Study report" ,"Both" , , , , ,"NM Thyroid gland Study report" , , , , , , ,"Changed System from ""Thyroid"" for conformance with the LOINC/RadLex unified model.; Method of ""Radnuc"" was changed to ""NM"". The LOINC/RadLex Committee agreed to use a subset of the two-letter DICOM modality codes as the primary modality identifier." ,0 ,0 ,0 ,"IG exists" , , , ,"81220-6;72230-6" ,"1.0l" ,
+"17788-1" ,"Large unstained cells/100 leukocytes" ,"NFr" ,"Pt" ,"Bld" ,"Qn" ,"Automated count","HEM/BC" ,"2.50" ,"MIN" ,"Part of auto diff output of Bayer H*3S; peroxidase negative cells too large to be classified as lymph or basophil" ,"ACTIVE", ,1 , , , , , ,"Y" ,"%" ,"100WBC; Auto; Automated detection; Blood; Cell; Cellularity; Elec; Elect; Electr; HEMATOLOGY/CELL COUNTS; Leuc; Leuk; Leukocyte; Lkcs; LUC; Number Fraction; Percent; Point in time; QNT; Quan; Quant; Quantitative; Random; WB; WBC; WBCs; White blood cell; White blood cells; Whole blood" ,"LUC/leuk NFr Bld Auto" ,"Observation", , , ,"%" ,"Large unstained cells/100 leukocytes in Blood by Automated count" , , ,"%" , , , , ,1894 ,0 ,1894 , , , , , ,"1.0l" ,
+"11488-4" ,"Consultation note" ,"Find" ,"Pt" ,"{Setting}" ,"Doc" ,"{Role}" ,"DOC.ONTOLOGY","2.63" ,"MIN" , ,"ACTIVE", ,2 , , , , , , , ,"Consult note; DOC.ONT; Document; Encounter; Evaluation and management; Evaluation and management note; Finding; Findings; notes; Point in time; Random; Visit note" ,"Consult note" ,"Both" , , , , ,"Consult note" , , , , , , ,"Edit made because this term is conformant to the Document Ontology axis values and therefore are being placed in this class.; Based on Clinical LOINC Committee decision during the September 2014 meeting, {Provider} was changed to {Author Type} to emphasize a greater breadth of potential document authors. At the September 2015 Clinical LOINC Committee meeting, the Committee decided to change {Author Type} to {Role} to align with the 'Role' axis name in the LOINC Document Ontology.; Because it is too difficult to maintain and because the distinction between documents and sections is not clear-cut nor necessary in most cases, the DOCUMENT_SECTION field has been deemed to have little value. The field has been set to null in the December 2017 release in preparation for removal in the December 2018 release. These changes were approved by the Clinical LOINC Committee.",0 ,0 ,0 ,"IG exists" , , , ,"81222-2;72231-4;81243-8","1.0j-a" ,"Y"
+"47239-9" ,"Reason for stopping HIV Rx" ,"Type" ,"Pt" ,"^Patient" ,"Nom" ,"Reported" ,"ART" ,"2.50" ,"MIN" ,"Reason for stopping antiretroviral therapy" ,"ACTIVE", ,2 , , , , , ,"N" , ,"AIDS; Anti-retroviral therapy; ART; Human immunodeficiency virus; Nominal; Point in time; Random; Treatment; Typ" ,"Reason for stopping HIV Rx" ,"Observation", , ,"Copyright © 2006 World Health Organization. Used with permission. Publications of the World Health Organization can be obtained from WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel: +41 22 791 2476; fax: +41 22 791 4857; email: bookorders@who.int). Requests for permission to reproduce or translate WHO publications – whether for sale or for noncommercial distribution – should be addressed to WHO Press, at the above address (fax: +41 22 791 4806; email: permissions@who.int). The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted lines on maps represent approximate border lines for which there may not yet be full agreement. The mention of specific companies or of certain manufacturers’ products does not imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. Errors and omissions excepted, the names of proprietary products are distinguished by initial capital letters. All reasonable precautions have been taken by WHO to verify the information contained in this publication. However, the published material is being distributed without warranty of any kind, either express or implied. The responsibility for the interpretation and use of the material lies with the reader. In no event shall the World Health Organization be liable for damages arising from its use.", ,"Reason for stopping HIV treatment" , , , , , , , ,0 ,0 ,0 , ,"WHO_HIV" , , , ,"2.22" ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/LoincAnswerListLink.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/LoincAnswerListLink.csv
new file mode 100644
index 00000000000..820602c77ad
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PanelsAndForms/LoincAnswerListLink.csv
@@ -0,0 +1,11 @@
+"LoincNumber","LongCommonName" ,"AnswerListId","AnswerListName" ,"AnswerListLinkType","ApplicableContext"
+"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]","LL1000-0" ,"PhenX05_13_30D bread amt","NORMATIVE" ,
+"10061-0" ,"S' wave amplitude in lead I" ,"LL1311-1" ,"PhenX12_44" ,"EXAMPLE" ,
+"10331-7" ,"Rh [Type] in Blood" ,"LL360-9" ,"Pos|Neg" ,"EXAMPLE" ,
+"10389-5" ,"Blood product.other [Type]" ,"LL2413-4" ,"Othr bld prod" ,"EXAMPLE" ,
+"10390-3" ,"Blood product special preparation [Type]" ,"LL2422-5" ,"Blood prod treatment" ,"EXAMPLE" ,
+"10393-7" ,"Factor IX given [Type]" ,"LL2420-9" ,"Human/Recomb" ,"EXAMPLE" ,
+"10395-2" ,"Factor VIII given [Type]" ,"LL2420-9" ,"Human/Recomb" ,"EXAMPLE" ,
+"10401-8" ,"Immune serum globulin given [Type]" ,"LL2421-7" ,"IM/IV" ,"EXAMPLE" ,
+"10410-9" ,"Plasma given [Type]" ,"LL2417-5" ,"Plasma type" ,"EXAMPLE" ,
+"10568-4" ,"Clarity of Semen" ,"LL2427-4" ,"Clear/Opales/Milky" ,"EXAMPLE" ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink.csv
new file mode 100644
index 00000000000..36c84f3fe95
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink.csv
@@ -0,0 +1,10 @@
+"LoincNumber","LongCommonName","PartNumber","PartName","PartCodeSystem","PartTypeName","LinkTypeName","Property"
+"10013-1","R' wave amplitude in lead I","LP31101-6","R' wave amplitude.lead I","http://loinc.org","COMPONENT","Primary","http://loinc.org/property/COMPONENT"
+"10013-1","R' wave amplitude in lead I","LP6802-5","Elpot","http://loinc.org","PROPERTY","Primary","http://loinc.org/property/PROPERTY"
+"10013-1","R' wave amplitude in lead I","LP6960-1","Pt","http://loinc.org","TIME","Primary","http://loinc.org/property/TIME_ASPCT"
+"10013-1","R' wave amplitude in lead I","LP7289-4","Heart","http://loinc.org","SYSTEM","Primary","http://loinc.org/property/SYSTEM"
+"10013-1","R' wave amplitude in lead I","LP7753-9","Qn","http://loinc.org","SCALE","Primary","http://loinc.org/property/SCALE_TYP"
+"10013-1","R' wave amplitude in lead I","LP6244-0","EKG","http://loinc.org","METHOD","Primary","http://loinc.org/property/METHOD_TYP"
+"10013-1","R' wave amplitude in lead I","LP31101-6","R' wave amplitude.lead I","http://loinc.org","COMPONENT","DetailedModel","http://loinc.org/property/analyte"
+"10013-1","R' wave amplitude in lead I","LP6802-5","Elpot","http://loinc.org","PROPERTY","DetailedModel","http://loinc.org/property/PROPERTY"
+"10013-1","R' wave amplitude in lead I","LP6960-1","Pt","http://loinc.org","TIME","DetailedModel","http://loinc.org/property/time-core"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink_Primary.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink_Primary.csv
new file mode 100644
index 00000000000..8dbe575ffd2
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink_Primary.csv
@@ -0,0 +1,7 @@
+"LoincNumber","LongCommonName" ,"PartNumber","PartName" ,"PartCodeSystem" ,"PartTypeName","LinkTypeName","Property"
+"10013-1" ,"R' wave amplitude in lead I","LP31101-6" ,"R' wave amplitude.lead I","http://loinc.org","COMPONENT" ,"Primary" ,"http://loinc.org/property/COMPONENT"
+"10013-1" ,"R' wave amplitude in lead I","LP6802-5" ,"Elpot" ,"http://loinc.org","PROPERTY" ,"Primary" ,"http://loinc.org/property/PROPERTY"
+"10013-1" ,"R' wave amplitude in lead I","LP6960-1" ,"Pt" ,"http://loinc.org","TIME" ,"Primary" ,"http://loinc.org/property/TIME_ASPCT"
+"10013-1" ,"R' wave amplitude in lead I","LP7289-4" ,"Heart" ,"http://loinc.org","SYSTEM" ,"Primary" ,"http://loinc.org/property/SYSTEM"
+"10013-1" ,"R' wave amplitude in lead I","LP7753-9" ,"Qn" ,"http://loinc.org","SCALE" ,"Primary" ,"http://loinc.org/property/SCALE_TYP"
+"10013-1" ,"R' wave amplitude in lead I","LP6244-0" ,"EKG" ,"http://loinc.org","METHOD" ,"Primary" ,"http://loinc.org/property/METHOD_TYP"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
new file mode 100644
index 00000000000..869c2c1651d
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/LoincPartLink_Supplementary.csv
@@ -0,0 +1,13 @@
+"LoincNumber","LongCommonName" ,"PartNumber","PartName" ,"PartCodeSystem" ,"PartTypeName","LinkTypeName" ,"Property"
+"10013-1" ,"R' wave amplitude in lead I","LP31101-6" ,"R' wave amplitude.lead I","http://loinc.org","COMPONENT" ,"DetailedModel" ,"http://loinc.org/property/analyte"
+"10013-1" ,"R' wave amplitude in lead I","LP6802-5" ,"Elpot" ,"http://loinc.org","PROPERTY" ,"DetailedModel" ,"http://loinc.org/property/PROPERTY"
+"10013-1" ,"R' wave amplitude in lead I","LP6960-1" ,"Pt" ,"http://loinc.org","TIME" ,"DetailedModel" ,"http://loinc.org/property/time-core"
+"10013-1" ,"R' wave amplitude in lead I","LP7289-4" ,"Heart" ,"http://loinc.org","SYSTEM" ,"DetailedModel" ,"http://loinc.org/property/system-core"
+"10013-1" ,"R' wave amplitude in lead I","LP7753-9" ,"Qn" ,"http://loinc.org","SCALE" ,"DetailedModel" ,"http://loinc.org/property/SCALE_TYP"
+"10013-1" ,"R' wave amplitude in lead I","LP6244-0" ,"EKG" ,"http://loinc.org","METHOD" ,"DetailedModel" ,"http://loinc.org/property/METHOD_TYP"
+"10013-1" ,"R' wave amplitude in lead I","LP31101-6" ,"R' wave amplitude.lead I","http://loinc.org","COMPONENT" ,"SyntaxEnhancement","http://loinc.org/property/analyte-core"
+"10013-1" ,"R' wave amplitude in lead I","LP190563-9","Cardiology" ,"http://loinc.org","CLASS" ,"Metadata" ,"http://loinc.org/property/category"
+"10013-1" ,"R' wave amplitude in lead I","LP29708-2" ,"Cardiology" ,"http://loinc.org","CLASS" ,"Metadata" ,"http://loinc.org/property/category"
+"10013-1" ,"R' wave amplitude in lead I","LP7787-7" ,"Clinical" ,"http://loinc.org","CLASS" ,"Metadata" ,"http://loinc.org/property/category"
+"10013-1" ,"R' wave amplitude in lead I","LP7795-0" ,"EKG measurements" ,"http://loinc.org","CLASS" ,"Metadata" ,"http://loinc.org/property/category"
+"10013-1" ,"R' wave amplitude in lead I","LP7795-0" ,"EKG.MEAS" ,"http://loinc.org","CLASS" ,"Metadata" ,"http://loinc.org/property/CLASS"
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/Part.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/Part.csv
new file mode 100644
index 00000000000..d5816ead286
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/Part.csv
@@ -0,0 +1,46 @@
+"PartNumber","PartTypeName","PartName","PartDisplayName","Status"
+"LP101394-7","ADJUSTMENT","adjusted for maternal weight","adjusted for maternal weight","ACTIVE"
+"LP101907-6","ADJUSTMENT","corrected for age","corrected for age","ACTIVE"
+"LP115711-6","ADJUSTMENT","corrected for background","corrected for background","ACTIVE"
+"LP147359-6","ADJUSTMENT","adjusted for body weight","adjusted for body weight","ACTIVE"
+"LP173482-3","ADJUSTMENT","1st specimen","1st specimen","DEPRECATED"
+"LP173483-1","ADJUSTMENT","post cyanocobalamin",,"ACTIVE"
+"LP173484-9","ADJUSTMENT","W hyperextension)",,"ACTIVE"
+"LP6244-0","METHOD","EKG","Electrocardiogram (EKG)","ACTIVE"
+"LP18172-4","COMPONENT","Interferon.beta","Interferon beta","ACTIVE"
+"LP7289-4","SYSTEM","Heart","Heart","ACTIVE"
+"LP6960-1","TIME","Pt","Point in time (spot)","ACTIVE"
+"LP6802-5","PROPERTY","Elpot","Electrical Potential (Voltage)","ACTIVE"
+"LP7753-9","SCALE","Qn","Qn","ACTIVE"
+"LP31101-6","COMPONENT","R' wave amplitude.lead I","R' wave amplitude.lead I","ACTIVE"
+"LP31102-4","COMPONENT","R' wave amplitude.lead II","R' wave amplitude.lead II","ACTIVE"
+"LP31103-2","COMPONENT","R' wave amplitude.lead III","R' wave amplitude.lead III","ACTIVE"
+"LP31104-0","COMPONENT","R' wave amplitude.lead V1","R' wave amplitude.lead V1","ACTIVE"
+"LP31105-7","COMPONENT","R' wave amplitude.lead V2","R' wave amplitude.lead V2","ACTIVE"
+"LP31106-5","COMPONENT","R' wave amplitude.lead V3","R' wave amplitude.lead V3","ACTIVE"
+"LP31107-3","COMPONENT","R' wave amplitude.lead V4","R' wave amplitude.lead V4","ACTIVE"
+"LP31108-1","COMPONENT","R' wave amplitude.lead V5","R' wave amplitude.lead V5","ACTIVE"
+"LP31109-9","COMPONENT","R' wave amplitude.lead V6","R' wave amplitude.lead V6","ACTIVE"
+"LP31110-7","COMPONENT","R' wave duration.lead AVF","R' wave duration.lead AVF","ACTIVE"
+"LP30269-2","SYSTEM","Ser/Plas^donor",,"ACTIVE"
+"LP149220-8","PROPERTY","Pr","Presence","ACTIVE"
+"LP7751-3","SCALE","Ord","Ord","ACTIVE"
+"LP37904-7","COMPONENT","DBG Ab","DBG Ab","ACTIVE"
+"LP6813-2","PROPERTY","Find","Finding","ACTIVE"
+"LP95333-8","METHOD","PhenX","PhenX","ACTIVE"
+"LP102627-9","COMPONENT","Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30D","Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days","ACTIVE"
+"LP6879-3","PROPERTY","Time","Time (e.g. seconds)","ACTIVE"
+"LP31088-5","COMPONENT","R wave duration.lead AVR","R wave duration.lead AVR","ACTIVE"
+"LP206647-2","SYSTEM","Neck>Thyroid gland","Thyroid gland","ACTIVE"
+"LP208655-3","METHOD","NM","NM","ACTIVE"
+"LP32888-7","SCALE","Doc","Doc","ACTIVE"
+"LP31534-8","COMPONENT","Study report","Study report","ACTIVE"
+"LP7057-5","SYSTEM","Bld","Blood","ACTIVE"
+"LP6838-9","PROPERTY","NFr","Number Fraction","ACTIVE"
+"LP6141-8","METHOD","Automated count","Automated count","ACTIVE"
+"LP15842-5","COMPONENT","Pyridoxine","Pyridoxine","ACTIVE"
+"LP19258-0","COMPONENT","Large unstained cells","Large unstained cells","ACTIVE"
+"LP32887-9","SYSTEM","{Setting}","{Setting}","ACTIVE"
+"LP187178-1","METHOD","{Role}","Role-unspecified","ACTIVE"
+"LP72311-1","COMPONENT","Consultation note","Consultation note","ACTIVE"
+
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/PartRelatedCodeMapping.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
new file mode 100644
index 00000000000..495416894ce
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/PartFile/PartRelatedCodeMapping.csv
@@ -0,0 +1,12 @@
+"PartNumber","PartName" ,"PartTypeName","ExtCodeId" ,"ExtCodeDisplayName" ,"ExtCodeSystem" ,"Equivalence","ContentOrigin","ExtCodeSystemVersion" ,"ExtCodeSystemCopyrightNotice"
+"LP18172-4" ,"Interferon.beta" ,"COMPONENT" ," 420710006","Interferon beta (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP31706-2" ,"Nornicotine" ,"COMPONENT" ,"1018001" ,"Nornicotine (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP15826-8" ,"Prostaglandin F2","COMPONENT" ,"10192006" ,"Prostaglandin PGF2 (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP7400-7" ,"Liver" ,"SYSTEM" ,"10200004" ,"Liver structure (body structure)","http://snomed.info/sct" ,"wider" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP29165-5" ,"Liver.FNA" ,"SYSTEM" ,"10200004" ,"Liver structure (body structure)","http://snomed.info/sct" ,"narrower" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP15666-8" ,"Inosine" ,"COMPONENT" ,"102640000" ,"Inosine (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP15943-1" ,"Uronate" ,"COMPONENT" ,"102641001" ,"Uronic acid (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP15791-4" ,"Phenylketones" ,"COMPONENT" ,"102642008" ,"Phenylketones (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP15721-1" ,"Malonate" ,"COMPONENT" ,"102648007" ,"Malonic acid (substance)" ,"http://snomed.info/sct" ,"equivalent" ,"Both" ,"http://snomed.info/sct/900000000000207008/version/20170731","This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO) under license. All rights reserved. SNOMED CT® was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.This material includes content from the US Edition to SNOMED CT, which is developed and maintained by the U.S. National Library of Medicine and is available to authorized UMLS Metathesaurus Licensees from the UTS Downloads site at https://uts.nlm.nih.gov.Use of SNOMED CT content is subject to the terms and conditions set forth in the SNOMED CT Affiliate License Agreement. It is the responsibility of those implementing this product to ensure they are appropriately licensed and for more information on the license, including how to register as an Affiliate Licensee, please refer to http://www.snomed.org/snomed-ct/get-snomed-ct or info@snomed.org. This may incur a fee in SNOMED International non-Member countries."
+"LP15842-5" ,"Pyridoxine" ,"COMPONENT" ,"1054" ,"Pyridoxine" ,"http://pubchem.ncbi.nlm.nih.gov","equivalent" , , ,
+"LP15842-5" ,"Pyridoxine" ,"COMPONENT" ,"1054" ,"Pyridoxine" ,"http://foo/bar" ,"equivalent" , , ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
new file mode 100644
index 00000000000..1e9b3872892
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/Top2000Results/SI/Top2000CommonLabResultsSi.csv
@@ -0,0 +1,10 @@
+LOINC #,Long Common Name,Short Name,CLASS,Rank
+14682-9,Creatinine [Moles/volume] in Serum or Plasma,Creat SerPl-mCnc,Chem,1
+718-7,Hemoglobin [Mass/volume] in Blood,Hgb Bld-mCnc,HEM/BC,2
+2823-3,Potassium [Moles/volume] in Serum or Plasma,Potassium SerPl-sCnc,Chem,3
+14749-6,Glucose [Moles/volume] in Serum or Plasma,Glucose SerPl-mCnc,Chem,4
+2951-2,Sodium [Moles/volume] in Serum or Plasma,Sodium SerPl-sCnc,Chem,5
+3094-0,Urea nitrogen [Mass/volume] in Serum or Plasma,BUN SerPl-mCnc,Chem,6
+2028-9,"Carbon dioxide, total [Moles/volume] in Serum or Plasma",CO2 SerPl-sCnc,Chem,7
+2075-0,Chloride [Moles/volume] in Serum or Plasma,Chloride SerPl-sCnc,Chem,8
+789-8,Erythrocytes [#/volume] in Blood by Automated count,RBC # Bld Auto,HEM/BC,9
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
new file mode 100644
index 00000000000..c80db052dd3
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/AccessoryFiles/Top2000Results/US/Top2000CommonLabResultsUs.csv
@@ -0,0 +1,10 @@
+LOINC #,Long Common Name,Short Name,CLASS,Rank
+2160-0,Creatinine [Mass/volume] in Serum or Plasma,Creat SerPl-mCnc,Chem,1
+718-7,Hemoglobin [Mass/volume] in Blood,Hgb Bld-mCnc,HEM/BC,2
+2823-3,Potassium [Moles/volume] in Serum or Plasma,Potassium SerPl-sCnc,Chem,3
+2345-7,Glucose [Mass/volume] in Serum or Plasma,Glucose SerPl-mCnc,Chem,4
+2951-2,Sodium [Moles/volume] in Serum or Plasma,Sodium SerPl-sCnc,Chem,5
+3094-0,Urea nitrogen [Mass/volume] in Serum or Plasma,BUN SerPl-mCnc,Chem,6
+2028-9,"Carbon dioxide, total [Moles/volume] in Serum or Plasma",CO2 SerPl-sCnc,Chem,7
+2075-0,Chloride [Moles/volume] in Serum or Plasma,Chloride SerPl-sCnc,Chem,8
+789-8,Erythrocytes [#/volume] in Blood by Automated count,RBC # Bld Auto,HEM/BC,9
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/LoincTable/Loinc.csv b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/LoincTable/Loinc.csv
new file mode 100644
index 00000000000..20379cb7f1d
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/LoincTable/Loinc.csv
@@ -0,0 +1,16 @@
+"LOINC_NUM","COMPONENT" ,"PROPERTY","TIME_ASPCT","SYSTEM" ,"SCALE_TYP","METHOD_TYP" ,"CLASS" ,"VersionLastChanged","CHNG_TYPE","DefinitionDescription" ,"STATUS","CONSUMER_NAME","CLASSTYPE","FORMULA","SPECIES","EXMPL_ANSWERS","SURVEY_QUEST_TEXT" ,"SURVEY_QUEST_SRC" ,"UNITSREQUIRED","SUBMITTED_UNITS","RELATEDNAMES2" ,"SHORTNAME" ,"ORDER_OBS" ,"CDISC_COMMON_TESTS","HL7_FIELD_SUBFIELD_ID","EXTERNAL_COPYRIGHT_NOTICE" ,"EXAMPLE_UNITS","LONG_COMMON_NAME" ,"UnitsAndRange","DOCUMENT_SECTION","EXAMPLE_UCUM_UNITS","EXAMPLE_SI_UCUM_UNITS","STATUS_REASON","STATUS_TEXT","CHANGE_REASON_PUBLIC" ,"COMMON_TEST_RANK","COMMON_ORDER_RANK","COMMON_SI_TEST_RANK","HL7_ATTACHMENT_STRUCTURE","EXTERNAL_COPYRIGHT_LINK","PanelType","AskAtOrderEntry","AssociatedObservations" ,"VersionFirstReleased","ValidHL7AttachmentRequest"
+"10013-1" ,"R' wave amplitude.lead I" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-I; R wave Amp L-I; Random; Right; Voltage" ,"R' wave Amp L-I" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead I" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10014-9" ,"R' wave amplitude.lead II" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"2; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-II; R wave Amp L-II; Random; Right; Voltage" ,"R' wave Amp L-II" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead II" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10015-6" ,"R' wave amplitude.lead III" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"3; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-III; R wave Amp L-III; Random; Right; Voltage" ,"R' wave Amp L-III" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead III" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10016-4" ,"R' wave amplitude.lead V1" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V1; R wave Amp L-V1; Random; Right; Voltage" ,"R' wave Amp L-V1" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V1" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"1001-7" ,"DBG Ab" ,"Pr" ,"Pt" ,"Ser/Plas^donor" ,"Ord" , ,"BLDBK" ,"2.44" ,"MIN" , ,"ACTIVE", ,1 , , , , , , , ,"ABS; Aby; Antby; Anti; Antibodies; Antibody; Autoantibodies; Autoantibody; BLOOD BANK; Donna Bennett-Goodspeed; Donr; Ordinal; Pl; Plasma; Plsm; Point in time; QL; Qual; Qualitative; Random; Screen; SerP; SerPl; SerPl^donor; SerPlas; Serum; Serum or plasma; SR" ,"DBG Ab SerPl Donr Ql" ,"Observation", , , , ,"DBG Ab [Presence] in Serum or Plasma from donor" , , , , , , ,"The Property has been changed from ACnc to Pr (Presence) to reflect the new model for ordinal terms where results are based on presence or absence." ,0 ,0 ,0 , , , , , , ,
+"10017-2" ,"R' wave amplitude.lead V2" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V2; R wave Amp L-V2; Random; Right; Voltage" ,"R' wave Amp L-V2" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V2" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10018-0" ,"R' wave amplitude.lead V3" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V3; R wave Amp L-V3; Random; Right; Voltage" ,"R' wave Amp L-V3" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V3" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10019-8" ,"R' wave amplitude.lead V4" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V4; R wave Amp L-V4; Random; Right; Voltage" ,"R' wave Amp L-V4" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V4" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"10020-6" ,"R' wave amplitude.lead V5" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V5; R wave Amp L-V5; Random; Right; Voltage" ,"R' wave Amp L-V5" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V5" , , ,"mV" , , , , ,0 ,0 ,0 , , , , , , ,
+"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30D","Find" ,"Pt" ,"^Patient" ,"Ord" ,"PhenX" ,"PHENX" ,"2.44" ,"MIN" , ,"TRIAL" , ,2 , , , ,"Each time you eat bread, toast or dinner rolls, how much do you usually eat?","PhenX.050201100100","N" , ,"Finding; Findings; How much bread in 30D; Last; Ordinal; Point in time; QL; Qual; Qualitative; Random; Screen" ,"How much bread in 30D PhenX", , , , , ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]", , , , , , , ,0 ,0 ,0 , , , , , , ,
+"10000-8" ,"R wave duration.lead AVR" ,"Time" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; Durat; ECG; EKG.MEASUREMENTS; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave dur L-AVR; R wave dur L-AVR; Random; Right" ,"R wave dur L-AVR" ,"Observation", , , ,"s" ,"R wave duration in lead AVR" , , ,"s" , , , , ,0 ,0 ,0 , , , , , , ,
+"17787-3" ,"Study report" ,"Find" ,"Pt" ,"Neck>Thyroid gland","Doc" ,"NM" ,"RAD" ,"2.61" ,"MIN" , ,"ACTIVE", ,2 , , , , , , , ,"Document; Finding; Findings; Imaging; Point in time; Radiology; Random; Study report; Thy" ,"NM Thyroid Study report" ,"Both" , , , , ,"NM Thyroid gland Study report" , , , , , , ,"Changed System from ""Thyroid"" for conformance with the LOINC/RadLex unified model.; Method of ""Radnuc"" was changed to ""NM"". The LOINC/RadLex Committee agreed to use a subset of the two-letter DICOM modality codes as the primary modality identifier." ,0 ,0 ,0 ,"IG exists" , , , ,"81220-6;72230-6" ,"1.0l" ,
+"17788-1" ,"Large unstained cells/100 leukocytes" ,"NFr" ,"Pt" ,"Bld" ,"Qn" ,"Automated count","HEM/BC" ,"2.50" ,"MIN" ,"Part of auto diff output of Bayer H*3S; peroxidase negative cells too large to be classified as lymph or basophil" ,"ACTIVE", ,1 , , , , , ,"Y" ,"%" ,"100WBC; Auto; Automated detection; Blood; Cell; Cellularity; Elec; Elect; Electr; HEMATOLOGY/CELL COUNTS; Leuc; Leuk; Leukocyte; Lkcs; LUC; Number Fraction; Percent; Point in time; QNT; Quan; Quant; Quantitative; Random; WB; WBC; WBCs; White blood cell; White blood cells; Whole blood" ,"LUC/leuk NFr Bld Auto" ,"Observation", , , ,"%" ,"Large unstained cells/100 leukocytes in Blood by Automated count" , , ,"%" , , , , ,1894 ,0 ,1894 , , , , , ,"1.0l" ,
+"11488-4" ,"Consultation note" ,"Find" ,"Pt" ,"{Setting}" ,"Doc" ,"{Role}" ,"DOC.ONTOLOGY","2.63" ,"MIN" , ,"ACTIVE", ,2 , , , , , , , ,"Consult note; DOC.ONT; Document; Encounter; Evaluation and management; Evaluation and management note; Finding; Findings; notes; Point in time; Random; Visit note" ,"Consult note" ,"Both" , , , , ,"Consult note" , , , , , , ,"Edit made because this term is conformant to the Document Ontology axis values and therefore are being placed in this class.; Based on Clinical LOINC Committee decision during the September 2014 meeting, {Provider} was changed to {Author Type} to emphasize a greater breadth of potential document authors. At the September 2015 Clinical LOINC Committee meeting, the Committee decided to change {Author Type} to {Role} to align with the 'Role' axis name in the LOINC Document Ontology.; Because it is too difficult to maintain and because the distinction between documents and sections is not clear-cut nor necessary in most cases, the DOCUMENT_SECTION field has been deemed to have little value. The field has been set to null in the December 2017 release in preparation for removal in the December 2018 release. These changes were approved by the Clinical LOINC Committee.",0 ,0 ,0 ,"IG exists" , , , ,"81222-2;72231-4;81243-8","1.0j-a" ,"Y"
+"47239-9" ,"Reason for stopping HIV Rx" ,"Type" ,"Pt" ,"^Patient" ,"Nom" ,"Reported" ,"ART" ,"2.50" ,"MIN" ,"Reason for stopping antiretroviral therapy" ,"ACTIVE", ,2 , , , , , ,"N" , ,"AIDS; Anti-retroviral therapy; ART; Human immunodeficiency virus; Nominal; Point in time; Random; Treatment; Typ" ,"Reason for stopping HIV Rx" ,"Observation", , ,"Copyright © 2006 World Health Organization. Used with permission. Publications of the World Health Organization can be obtained from WHO Press, World Health Organization, 20 Avenue Appia, 1211 Geneva 27, Switzerland (tel: +41 22 791 2476; fax: +41 22 791 4857; email: bookorders@who.int). Requests for permission to reproduce or translate WHO publications – whether for sale or for noncommercial distribution – should be addressed to WHO Press, at the above address (fax: +41 22 791 4806; email: permissions@who.int). The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted lines on maps represent approximate border lines for which there may not yet be full agreement. The mention of specific companies or of certain manufacturers’ products does not imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. Errors and omissions excepted, the names of proprietary products are distinguished by initial capital letters. All reasonable precautions have been taken by WHO to verify the information contained in this publication. However, the published material is being distributed without warranty of any kind, either express or implied. The responsibility for the interpretation and use of the material lies with the reader. In no event shall the World Health Organization be liable for damages arising from its use.", ,"Reason for stopping HIV treatment" , , , , , , , ,0 ,0 ,0 , ,"WHO_HIV" , , , ,"2.22" ,
diff --git a/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/loinc.xml b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/loinc.xml
new file mode 100644
index 00000000000..ed461aab3e5
--- /dev/null
+++ b/hapi-fhir-jpaserver-base/src/test/resources/loinc-ver/v-no-version/loinc.xml
@@ -0,0 +1,543 @@
+
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* This method will put the value into the cache using {@link #putAfterCommit(CacheEnum, Object, Object)}.
*/
public T getThenPutAfterCommit(CacheEnum theCache, K theKey, Function theSupplier) {
@@ -140,7 +140,7 @@ public class MemoryCacheService {
* if and when the current database transaction successfully commits. If the
* transaction is rolled back, the key+value passed into this method will
* not be added to the cache.
- *
+ *
* This is useful for situations where you want to store something that has been
* resolved in the DB during the current transaction, but it's not yet guaranteed
* that this item will successfully save to the DB. Use this method in that case
@@ -247,6 +247,20 @@ public class MemoryCacheService {
myHashCode = new HashCodeBuilder().append(myTypeName).append(myInstanceId).toHashCode();
}
+ public static HistoryCountKey forSystem() {
+ return new HistoryCountKey(null, null);
+ }
+
+ public static HistoryCountKey forType(@Nonnull String theType) {
+ assert isNotBlank(theType);
+ return new HistoryCountKey(theType, null);
+ }
+
+ public static HistoryCountKey forInstance(@Nonnull Long theInstanceId) {
+ assert theInstanceId != null;
+ return new HistoryCountKey(null, theInstanceId);
+ }
+
@Override
public boolean equals(Object theO) {
boolean retVal = false;
@@ -262,20 +276,6 @@ public class MemoryCacheService {
return myHashCode;
}
- public static HistoryCountKey forSystem() {
- return new HistoryCountKey(null, null);
- }
-
- public static HistoryCountKey forType(@Nonnull String theType) {
- assert isNotBlank(theType);
- return new HistoryCountKey(theType, null);
- }
-
- public static HistoryCountKey forInstance(@Nonnull Long theInstanceId) {
- assert theInstanceId != null;
- return new HistoryCountKey(null, theInstanceId);
- }
-
}
}
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidationSettings.java b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidationSettings.java
similarity index 99%
rename from hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidationSettings.java
rename to hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidationSettings.java
index df3300dbed7..56707443461 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidationSettings.java
+++ b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidationSettings.java
@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.validation;
/*-
* #%L
- * HAPI FHIR JPA Server
+ * HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
similarity index 99%
rename from hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
rename to hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
index 290adfab468..8256aae493e 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
+++ b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/validation/ValidatorResourceFetcher.java
@@ -2,7 +2,7 @@ package ca.uhn.fhir.jpa.validation;
/*-
* #%L
- * HAPI FHIR JPA Server
+ * HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
diff --git a/hapi-fhir-storage-api/src/main/java/ca/uhn/fhir/mdm/log/Logs.java b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/mdm/log/Logs.java
similarity index 97%
rename from hapi-fhir-storage-api/src/main/java/ca/uhn/fhir/mdm/log/Logs.java
rename to hapi-fhir-storage/src/main/java/ca/uhn/fhir/mdm/log/Logs.java
index 1abc94d5593..573ad48ce9a 100644
--- a/hapi-fhir-storage-api/src/main/java/ca/uhn/fhir/mdm/log/Logs.java
+++ b/hapi-fhir-storage/src/main/java/ca/uhn/fhir/mdm/log/Logs.java
@@ -2,7 +2,7 @@ package ca.uhn.fhir.mdm.log;
/*-
* #%L
- * HAPI FHIR JPA API
+ * HAPI FHIR Storage api
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
diff --git a/hapi-fhir-storage-api/src/main/resources/.keep-jpaserver-api b/hapi-fhir-storage/src/main/resources/.keep-jpaserver-api
similarity index 100%
rename from hapi-fhir-storage-api/src/main/resources/.keep-jpaserver-api
rename to hapi-fhir-storage/src/main/resources/.keep-jpaserver-api
diff --git a/hapi-fhir-storage-api/src/test/java/.keep b/hapi-fhir-storage/src/test/java/.keep
similarity index 100%
rename from hapi-fhir-storage-api/src/test/java/.keep
rename to hapi-fhir-storage/src/test/java/.keep
diff --git a/hapi-fhir-storage-api/src/test/resources/.keep b/hapi-fhir-storage/src/test/resources/.keep
similarity index 100%
rename from hapi-fhir-storage-api/src/test/resources/.keep
rename to hapi-fhir-storage/src/test/resources/.keep
diff --git a/hapi-fhir-structures-dstu2.1/pom.xml b/hapi-fhir-structures-dstu2.1/pom.xml
index ef2bbef3f7e..bf94bc5a065 100644
--- a/hapi-fhir-structures-dstu2.1/pom.xml
+++ b/hapi-fhir-structures-dstu2.1/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-structures-dstu2/pom.xml b/hapi-fhir-structures-dstu2/pom.xml
index 2c81d57e6a9..e5e3e7e3567 100644
--- a/hapi-fhir-structures-dstu2/pom.xml
+++ b/hapi-fhir-structures-dstu2/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-structures-dstu3/pom.xml b/hapi-fhir-structures-dstu3/pom.xml
index b5a91f0ea57..8f86004e960 100644
--- a/hapi-fhir-structures-dstu3/pom.xml
+++ b/hapi-fhir-structures-dstu3/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-structures-hl7org-dstu2/pom.xml b/hapi-fhir-structures-hl7org-dstu2/pom.xml
index f62d30af447..85364d85658 100644
--- a/hapi-fhir-structures-hl7org-dstu2/pom.xml
+++ b/hapi-fhir-structures-hl7org-dstu2/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-structures-r4/pom.xml b/hapi-fhir-structures-r4/pom.xml
index a5b1177c900..cfc56be95f2 100644
--- a/hapi-fhir-structures-r4/pom.xml
+++ b/hapi-fhir-structures-r4/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-structures-r5/pom.xml b/hapi-fhir-structures-r5/pom.xml
index 63da59f558d..4bf070eca08 100644
--- a/hapi-fhir-structures-r5/pom.xml
+++ b/hapi-fhir-structures-r5/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-test-utilities/pom.xml b/hapi-fhir-test-utilities/pom.xml
index 17157ff1753..1e49272ee88 100644
--- a/hapi-fhir-test-utilities/pom.xml
+++ b/hapi-fhir-test-utilities/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-testpage-overlay/pom.xml b/hapi-fhir-testpage-overlay/pom.xml
index 5ab492a17c8..c1a4cb75a5d 100644
--- a/hapi-fhir-testpage-overlay/pom.xml
+++ b/hapi-fhir-testpage-overlay/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-fhir
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../pom.xml
diff --git a/hapi-fhir-validation-resources-dstu2.1/pom.xml b/hapi-fhir-validation-resources-dstu2.1/pom.xml
index 1635076b1e0..8895cb77810 100644
--- a/hapi-fhir-validation-resources-dstu2.1/pom.xml
+++ b/hapi-fhir-validation-resources-dstu2.1/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-validation-resources-dstu2/pom.xml b/hapi-fhir-validation-resources-dstu2/pom.xml
index cbace5aa862..685fe3c5f0f 100644
--- a/hapi-fhir-validation-resources-dstu2/pom.xml
+++ b/hapi-fhir-validation-resources-dstu2/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-validation-resources-dstu3/pom.xml b/hapi-fhir-validation-resources-dstu3/pom.xml
index e0ebab22cb0..8e350d1f617 100644
--- a/hapi-fhir-validation-resources-dstu3/pom.xml
+++ b/hapi-fhir-validation-resources-dstu3/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-validation-resources-r4/pom.xml b/hapi-fhir-validation-resources-r4/pom.xml
index 0b6dc70c454..97406693424 100644
--- a/hapi-fhir-validation-resources-r4/pom.xml
+++ b/hapi-fhir-validation-resources-r4/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-validation-resources-r5/pom.xml b/hapi-fhir-validation-resources-r5/pom.xml
index 18fee1725e9..f384daa3316 100644
--- a/hapi-fhir-validation-resources-r5/pom.xml
+++ b/hapi-fhir-validation-resources-r5/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-validation/pom.xml b/hapi-fhir-validation/pom.xml
index 2765d4804a5..7324dd9affd 100644
--- a/hapi-fhir-validation/pom.xml
+++ b/hapi-fhir-validation/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-deployable-pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../hapi-deployable-pom/pom.xml
diff --git a/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationConstants.java b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationConstants.java
new file mode 100644
index 00000000000..27a3b266f44
--- /dev/null
+++ b/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/ValidationConstants.java
@@ -0,0 +1,32 @@
+package org.hl7.fhir.common.hapi.validation.support;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2021 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
+public class ValidationConstants {
+
+ public static final String LOINC_LOW = "loinc";
+ public static final String LOINC_GENERIC_CODE_SYSTEM_URL = "http://loinc.org";
+ public static final String LOINC_GENERIC_VALUESET_URL = LOINC_GENERIC_CODE_SYSTEM_URL + "/vs";
+ public static final String LOINC_GENERIC_VALUESET_URL_PLUS_SLASH = LOINC_GENERIC_VALUESET_URL + "/";
+
+ // not to be instantiated
+ private ValidationConstants() { }
+}
diff --git a/hapi-tinder-plugin/pom.xml b/hapi-tinder-plugin/pom.xml
index ce03bcdfc4b..8926337ddbd 100644
--- a/hapi-tinder-plugin/pom.xml
+++ b/hapi-tinder-plugin/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-fhir
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../pom.xml
@@ -58,37 +58,37 @@
ca.uhn.hapi.fhir
hapi-fhir-structures-dstu3
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
ca.uhn.hapi.fhir
hapi-fhir-structures-hl7org-dstu2
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
ca.uhn.hapi.fhir
hapi-fhir-structures-r4
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
ca.uhn.hapi.fhir
hapi-fhir-structures-r5
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
ca.uhn.hapi.fhir
hapi-fhir-validation-resources-dstu2
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
ca.uhn.hapi.fhir
hapi-fhir-validation-resources-dstu3
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
ca.uhn.hapi.fhir
hapi-fhir-validation-resources-r4
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
org.apache.velocity
diff --git a/hapi-tinder-test/pom.xml b/hapi-tinder-test/pom.xml
index f4c47e7ea09..defeb81e95b 100644
--- a/hapi-tinder-test/pom.xml
+++ b/hapi-tinder-test/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-fhir
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../pom.xml
diff --git a/pom.xml b/pom.xml
index 1aca1b4d3a7..fb8d1b3c045 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
ca.uhn.hapi.fhir
hapi-fhir
pom
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
hapi-fhir-jpa
@@ -2775,7 +2775,7 @@
hapi-fhir-validation-resources-r4
hapi-fhir-structures-r5
hapi-fhir-validation-resources-r5
- hapi-fhir-storage-api
+ hapi-fhir-storage
hapi-fhir-jpaserver-cql
hapi-fhir-jpaserver-model
hapi-fhir-jpaserver-searchparam
diff --git a/tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml b/tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
index 365ce8e7c26..69067d0d06e 100644
--- a/tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
+++ b/tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
@@ -6,7 +6,7 @@
ca.uhn.hapi.fhir
hapi-fhir
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../../pom.xml
diff --git a/tests/hapi-fhir-base-test-mindeps-client/pom.xml b/tests/hapi-fhir-base-test-mindeps-client/pom.xml
index a8df44b7045..de95a77b6d1 100644
--- a/tests/hapi-fhir-base-test-mindeps-client/pom.xml
+++ b/tests/hapi-fhir-base-test-mindeps-client/pom.xml
@@ -4,7 +4,7 @@
ca.uhn.hapi.fhir
hapi-fhir
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../../pom.xml
diff --git a/tests/hapi-fhir-base-test-mindeps-server/pom.xml b/tests/hapi-fhir-base-test-mindeps-server/pom.xml
index 545ebba468a..84008fce624 100644
--- a/tests/hapi-fhir-base-test-mindeps-server/pom.xml
+++ b/tests/hapi-fhir-base-test-mindeps-server/pom.xml
@@ -5,7 +5,7 @@
ca.uhn.hapi.fhir
hapi-fhir
- 5.6.0-PRE6-SNAPSHOT
+ 5.6.0-PRE7-SNAPSHOT
../../pom.xml