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Merge branch 'master' into 6469-reduce-memory-overhead-of-searches

This commit is contained in:
leif stawnyczy 2024-11-22 16:12:50 -05:00
parent 2d9db1ce74 d4f1766ca5
commit dcf0c7158b
349 changed files with 5681 additions and 2816 deletions
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2
hapi-deployable-pom/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

33
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/RuntimeSearchParam.java
View File

@ -60,6 +60,7 @@ public class RuntimeSearchParam {
private final List<Component> myComponents;
private final IIdType myIdUnqualifiedVersionless;
private IPhoneticEncoder myPhoneticEncoder;
private boolean myEnabledForSearching = true;
/**
* Constructor
@ -166,6 +167,24 @@ public class RuntimeSearchParam {
}
}
/**
* Is this search parameter actually enabled for being used in searches (as opposed to only being used for
* generating indexes, which might be desired while the search parameter is still being indexed). This
* setting defaults to {@literal true} if it isn't set otherwise.
*/
public boolean isEnabledForSearching() {
return myEnabledForSearching;
}
/**
* Is this search parameter actually enabled for being used in searches (as opposed to only being used for
* generating indexes, which might be desired while the search parameter is still being indexed). This
* setting defaults to {@literal true} if it isn't set otherwise.
*/
public void setEnabledForSearching(boolean theEnabledForSearching) {
myEnabledForSearching = theEnabledForSearching;
}
public List<Component> getComponents() {
return myComponents;
}
@ -361,13 +380,6 @@ public class RuntimeSearchParam {
return !myUpliftRefchains.isEmpty();
}
public enum RuntimeSearchParamStatusEnum {
ACTIVE,
DRAFT,
RETIRED,
UNKNOWN
}
/**
* This method tests whether a given FHIRPath expression <i>could</i>
* possibly apply to the given resource type.
@ -413,6 +425,13 @@ public class RuntimeSearchParam {
return false;
}
public enum RuntimeSearchParamStatusEnum {
ACTIVE,
DRAFT,
RETIRED,
UNKNOWN
}
public static class Component {
private final String myExpression;
private final String myReference;

11
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IFhirVersion.java
View File

@ -63,6 +63,17 @@ public interface IFhirVersion {
IIdType newIdType();
/**
* Creates a new {@link IIdType} instance for the given version with the given value
*
* @since 8.0.0
*/
default IIdType newIdType(String theValue) {
IIdType retVal = newIdType();
retVal.setValue(theValue);
return retVal;
}
/**
* Returns an instance of <code>IFhirVersionServer<code> for this version.
* Note that this method may only be called if the <code>hapi-fhir-server</code>

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
View File

@ -110,6 +110,12 @@ public class HapiExtensions {
public static final String EXT_SP_UNIQUE = "http://hapifhir.io/fhir/StructureDefinition/sp-unique";
/**
* URL for extension on a Search Parameter which determines whether it should be enabled for searching for resources
*/
public static final String EXT_SEARCHPARAM_ENABLED_FOR_SEARCHING =
"http://hapifhir.io/fhir/StructureDefinition/searchparameter-enabled-for-searching";
/**
* URL for extension on a Phonetic String SearchParameter indicating that text values should be phonetically indexed with the named encoder
*/

16
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TaskChunker.java
View File

@ -40,13 +40,22 @@ import java.util.stream.Stream;
*/
public class TaskChunker<T> {
public void chunk(Collection<T> theInput, int theChunkSize, Consumer<List<T>> theBatchConsumer) {
public static <T> void chunk(List<T> theInput, int theChunkSize, Consumer<List<T>> theBatchConsumer) {
if (theInput.size() <= theChunkSize) {
theBatchConsumer.accept(theInput);
return;
}
chunk((Collection<T>) theInput, theChunkSize, theBatchConsumer);
}
public static <T> void chunk(Collection<T> theInput, int theChunkSize, Consumer<List<T>> theBatchConsumer) {
List<T> input;
if (theInput instanceof List) {
input = (List<T>) theInput;
} else {
input = new ArrayList<>(theInput);
}
for (int i = 0; i < input.size(); i += theChunkSize) {
int to = i + theChunkSize;
to = Math.min(to, input.size());
@ -56,12 +65,11 @@ public class TaskChunker<T> {
}
@Nonnull
public <T> Stream<List<T>> chunk(Stream<T> theStream, int theChunkSize) {
public static <T> Stream<List<T>> chunk(Stream<T> theStream, int theChunkSize) {
return StreamUtil.partition(theStream, theChunkSize);
}
@Nonnull
public void chunk(Iterator<T> theIterator, int theChunkSize, Consumer<List<T>> theListConsumer) {
public static <T> void chunk(Iterator<T> theIterator, int theChunkSize, Consumer<List<T>> theListConsumer) {
chunk(Streams.stream(theIterator), theChunkSize).forEach(theListConsumer);
}
}

1
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

@ -166,6 +166,7 @@ public enum VersionEnum {
V7_4_2,
V7_4_3,
V7_4_4,
V7_4_5,
V7_5_0,
V7_6_0,

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -87,6 +87,7 @@ ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFail
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The operation has failed with a client-assigned ID constraint failure. This typically means that multiple client threads are trying to create a new resource with the same client-assigned ID at the same time, and this thread was chosen to be rejected. It can also happen when a request disables the Upsert Existence Check.
ca.uhn.fhir.jpa.binary.interceptor.BinaryStorageInterceptor.externalizedBinaryStorageExtensionFoundInRequestBody=Illegal extension found in request payload - URL "{0}" and value "{1}"
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.cantUndeleteWithDeletesDisabled=Unable to restore previously deleted resource as deletes are disabled on this server.
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.incomingNoopInTransaction=Transaction contains resource with operation NOOP. This is only valid as a response operation, not in a request
ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.invalidMatchUrlInvalidResourceType=Invalid match URL "{0}" - Unknown resource type: "{1}"
ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidMatchUrlNoMatches=Invalid match URL "{0}" - No resources match this search
@ -133,6 +134,7 @@ ca.uhn.fhir.jpa.dao.BaseStorageDao.successfulTimingSuffix=Took {0}ms.
ca.uhn.fhir.jpa.dao.BaseStorageDao.deleteResourceNotExisting=Not deleted, resource {0} does not exist.
ca.uhn.fhir.jpa.dao.BaseStorageDao.deleteResourceAlreadyDeleted=Not deleted, resource {0} was already deleted.
ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSearchParameter=Unknown search parameter "{0}" for resource type "{1}". Valid search parameters for this search are: {2}
ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSearchParameterNotEnabledForSearch=Search parameter "{0}" for resource type "{1}" is not active for searching. Valid search parameters for this search are: {2}
ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSortParameter=Unknown _sort parameter value "{0}" for resource type "{1}" (Note: sort parameters values must use a valid Search Parameter). Valid values for this search are: {2}
ca.uhn.fhir.jpa.dao.BaseStorageDao.invalidSortParameterTooManyChains=Invalid _sort expression, can not chain more than once in a sort expression: {0}
@ -199,6 +201,7 @@ ca.uhn.fhir.jpa.search.builder.predicate.ResourceLinkPredicateBuilder.invalidTar
ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl.invalidResourceType=Invalid/unsupported resource type: "{0}"
ca.uhn.fhir.jpa.dao.index.IdHelperService.nonUniqueForcedId=Non-unique ID specified, can not process request
ca.uhn.fhir.jpa.dao.index.IdHelperService.deletedId=Resource {0} has been deleted
ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.noIdSupplied=No Partition ID supplied
ca.uhn.fhir.jpa.partition.PartitionLookupSvcImpl.missingPartitionIdOrName=Partition must have an ID and a Name

2
hapi-fhir-base/src/test/java/ca/uhn/fhir/util/TaskChunkerTest.java
View File

@ -37,7 +37,7 @@ public class TaskChunkerTest {
List<Integer> input = newIntRangeList(0, 35);
// Execute
new TaskChunker<Integer>().chunk(input, 10, myConsumer);
TaskChunker.chunk(input, 10, myConsumer);
// Verify
verify(myConsumer, times(4)).accept(myConsumerCaptor.capture());

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

@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
@ -12,7 +12,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

9
hapi-fhir-client-okhttp/src/test/java/ca/uhn/fhir/okhttp/GenericOkHttpClientDstu2Test.java
View File

@ -1357,7 +1357,9 @@ public class GenericOkHttpClientDstu2Test {
.returnBundle(Bundle.class)
.execute();
assertEquals(ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname", MY_SERVLET.ourRequestUri);
assertThat(MY_SERVLET.ourRequestUri).isIn(
ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname",
ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=name%2Cidentifier");
// assertThat(MY_SERVLET.ourRequestUri,
// either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() +
@ -1391,7 +1393,10 @@ public class GenericOkHttpClientDstu2Test {
.execute();
assertThat(MY_SERVLET.ourRequestUri).contains(ourServer.getBaseUrl() + "/fhir/Patient/_search?");
assertThat(MY_SERVLET.ourRequestUri).contains("_elements=identifier%2Cname");
assertThat(MY_SERVLET.ourRequestUri).satisfiesAnyOf(
s -> assertThat(s).contains("_elements=identifier%2Cname"),
s -> assertThat(s).contains("_elements=name%2Cidentifier")
);
assertThat(MY_SERVLET.ourRequestUri).doesNotContain("_format=json");
// assertThat(MY_SERVLET.ourRequestUri,

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/AuthorizationInterceptors.java
View File

@ -330,7 +330,7 @@ public class AuthorizationInterceptors {
SearchNarrowingConsentService consentService =
new SearchNarrowingConsentService(validationSupport, searchParamRegistry);
// Create a ConsentIntereptor to apply the ConsentService and register it with the server
// Create a ConsentInterceptor to apply the ConsentService and register it with the server
ConsentInterceptor consentInterceptor = new ConsentInterceptor();
consentInterceptor.registerConsentService(consentService);
restfulServer.registerInterceptor(consentInterceptor);

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/1_4/changes.yaml
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@ -7,7 +7,7 @@
title: "Remove a dependency on a Java 1.7 class (ReflectiveOperationException) in several spots in the codebase. This dependency was accidentally introduced in 1.3, and animal-sniffer-plugin failed to detect it (sigh)."
- item:
type: "add"
title: "Add two new server interceptors: RequestValidatingInterceptor and ResponseValidatingInterceptor which can be used to validate incoming requests or outgoing responses using the standard FHIR validation tools. See the Server Validation Page for examples of how to use these interceptors. These intereptors have both been enabled on the <a href=\"http://fhirtest.uhn.ca\">public test page</a>."
title: "Add two new server interceptors: RequestValidatingInterceptor and ResponseValidatingInterceptor which can be used to validate incoming requests or outgoing responses using the standard FHIR validation tools. See the Server Validation Page for examples of how to use these interceptors. These interceptors have both been enabled on the <a href=\"http://fhirtest.uhn.ca\">public test page</a>."
- item:
issue: "259"
type: "fix"

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/4_0_0/changes.yaml
View File

@ -32,7 +32,7 @@
title: "<b>New Feature</b>: The JPA server now supports the <code>_filter</code> search parameter when configured to do so. The <a href=\"http://hl7.org/fhir/search_filter.html\">filter search parameter</a> is an extremely flexible and powerful feature, allowing for advanced grouping and order of operations on searches. It can be dangerous however, as it potentially allows users to create queries for which no database indexes exist in the default configuration so it is disabled by default. Thanks to Anthony Sute for the pull request and all of his support in what turned out to be a lengthy merge!"
- item:
type: "add"
title: "<b>New Feature</b>: A new interceptor called CascadingDeleteInterceptor has been added to the JPA project. This interceptor allows deletes to cascade when a specific URL parameter or header is added to the request. Cascading deletes can also be controlled by a new flag in the AuthorizationIntereptor RuleBuilder, in order to ensure that cascading deletes are only available to users with sufficient permission."
title: "<b>New Feature</b>: A new interceptor called CascadingDeleteInterceptor has been added to the JPA project. This interceptor allows deletes to cascade when a specific URL parameter or header is added to the request. Cascading deletes can also be controlled by a new flag in the AuthorizationInterceptor RuleBuilder, in order to ensure that cascading deletes are only available to users with sufficient permission."
- item:
type: "add"
title: "Several enhancements have been made to the <code>AuthorizationInterceptor</code> : <ul> <li>The interceptor now registers against the <code>STORAGE_PRESHOW_RESOURCES</code> interceptor hook, which allows it to successfully authorize JPA operations that don't actually return resource content, such as GraphQL responses, and resources that have been filtered using the <code>_elements</code> parameter.</li> <li> </li>The rule list is now cached on a per-request basis, which should improve performance</ul>"

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/version.yaml
View File

@ -1,3 +1,3 @@
---
release-date: "2023-02-18"
release-date: "2024-02-18"
codename: "Apollo"

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_2_0/version.yaml
View File

@ -1,3 +1,3 @@
---
release-date: "2023-05-18"
release-date: "2024-05-18"
codename: "Borealis"

0
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/QueryParameterUtilsTest.java → hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_5/upgrade.md
View File

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_4_5/version.yaml Normal file
View File

@ -0,0 +1,3 @@
---
release-date: "2024-10-21"
codename: "Copernicus"

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_6_0/6372-lucene-and-jpa-search-combine-issues.yaml
View File

@ -1,6 +1,8 @@
---
type: fix
issue: 6372
jira: SMILE-9073
backport: 7.4.5
title: "Searches that combined full-text searching (i.e. `_text` or `_content`)
with other search parameters could fail to return all results if we encountered
1600 matches against the full-text index where none of them match the rest of the query.

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6107-allow-sp-disabling.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: add
issue: 6107
title: "A new extension has been created for use on SearchParameter resources in the JPA server. This extension causes
a SearchParameter to be indexed, but to not be available for use in searches. This can be set when a new SP is created
in order to prevent it from being used before an index has been completed. See
[Introducing Search Parameters on Existing Data](https://smilecdr.com/docs/fhir_standard/fhir_search_custom_search_parameters.html) for more information."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6224-resolve-tag-definition-in-same-thread.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 6224
title: "The JPA server will no longer use a separate thread and database connection
to resolve tag definitions. This should improve performance in some cases, and
resolves compatibility issues for some environments. Thanks to Ibrahim (Trifork A/S)
for the pull request!"

10
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6258-improve-auth-interceptor-operation-handling.yaml Normal file
View File

@ -0,0 +1,10 @@
---
type: fix
issue: 6258
title: "The AuthorizationInterceptor handling for operations has been improved
so that operation rules now directly test the contents of response Bundle
or Parameters objects returned by the operation when configure to require
explicit response authorization. This fixes a regression in 7.4.0 where
operation responses could sometimes be denied even if appropriate
permissions were granted to view resources in a response bundle. Thanks to
Gijsbert van den Brink for reporting the issue with a sample test!"

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6395-allow-submit-subscription-synchronously.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 6395
title: "A new configuration option has been added to `SubsciptionSubmitterConfig` which
causes Subscription resources to be submitted to the processing queue synchronously
instead of asynchronously as all other resources are. This is useful for cases where
subscriptions need to be activated quickly. Thanks to Michal Sevcik for the contribution!"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6398-add-author-search-to-npm-search.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 6398
title: "The NPM package search module has been enhanced to support searching by
the package author and the package version attributes."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6407-missing-conformity-to-ihe-balp.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 6407
title: "Corrected IHE BALP AuditEvent generation, so that it records one Audit Event per resource owner. Thanks to Jens Villadsen (@jkiddo) for the contribution!"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-dont-store-reslink-target-partition-date.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: change
issue: 6460
title: "The HFJ_RES_LINK table with no longer store the `PARTITION_DATE` value for the indexed link target
resource, as this was an unused feature which has been removed as a part of a larger performance optimization."

9
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-improve-transaction-performance-for-external-refs.yaml Normal file
View File

@ -0,0 +1,9 @@
---
type: perf
issue: 6460
title: "The JPA server FHIR transaction processor will now pre-fetch the target
resource state for references to resources that don't also appear in the
transaction bundle. This means that if you process a large FHIR transaction containing
many references to other resources in the repository that are not also being
updated in the same transaction, you should see a very significant improvement
in performance."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-improve-transaction-performance-for-ids.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 6460
title: "The JPA server FHIR transaction processor will now more aggressively cache
resource IDs for previously seen resources, reducing the number of database reads
required when processing transactions. This should provide a noticeable improvement
in performance when processing transactions which update pre-existing resources."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-prevent-undeleting-if-deletes-disabled.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: change
issue: 6460
title: "If deletes are disabled in the JPA server, it is no longer possible to un-delete
a resource (i.e. update a previously deleted resource to make it non-deleted)."

9
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6460-version-delete-and-update-in-same-transaction-separately.yaml Normal file
View File

@ -0,0 +1,9 @@
---
type: change
issue: 6460
title: "When performing a FHIR Transaction which deletes and then updates (or otherwise
un-deletes) the same resource within a single transaction, the delete was previously
not stored as a distinct version (meaning that the resource version was only
incremented once, and no delete was actually stored in the resource history. This
has been changed so that deletes will always appear as a distinct entry in the
resource history."

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6464-mdm-virtualization-interceptor.yaml Normal file
View File

@ -0,0 +1,8 @@
---
type: add
issue: 6464
title: "A new experimental interceptor called the MdmReadVirtualizationInterceptor
has been added. This interceptor rewrites results when querying an MDM-enabled
JPA server in order to always include linked resources and rerwrites query results
to link to the MDM golden resource. This interceptor is still being developed
and should be used with caution."

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/6475-fix-excessive-hibernate-warnings.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: fix
issue: 6475
jira: SMILE-8490
title: "Previously, submitting a transaction bundle containing a conditional delete, a conditional create, and a
resource which relied on this conditional create as a reference would lead to excessive Hibernate warnings in the logs.
This has been fixed."

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_8_0/changes.yaml Normal file
View File

@ -0,0 +1,8 @@
---
- item:
type: "add"
title: "The version of a few dependencies have been bumped to more recent versions
(dependent HAPI modules listed in brackets):
<ul>
<li>org.hl7.fhir.core (Base): 6.3.25 -&gt; 6.4.0</li>
</ul>"

8
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/contributing/hacking_guide.md
View File

@ -51,6 +51,14 @@ HAPI is built primary using [Apache Maven](http://maven.apache.org/). Even if yo
[INFO] Finished at: 2016-02-27T15:05:35+00:00
```
# Rebuilding the Database Schema
Database schema is built as part of your maven build, but in case you need to rebuild it later, you can use the command:
```bash
mvn hapi-tinder:generate-ddl
```
# Troubleshooting
If the build fails to execute successfully, try the following:

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa/search.md
View File

@ -238,3 +238,7 @@ In order to improve sorting performance when chained sorts are needed, an [Uplif
# _include and _revinclude order
By default, all _revincludes will be performed first and then all _includes are performed afterwards. However, if any _revinclude parameters are modified with :iterate (or :recurse for earlier versions of FHIR) then all _include parameters will be evaluated first.
# Custom Search Parameters
HAPI FHIR has the ability to index and use custom search parameters, including parameters which enforce uniqueness, parametrs which index combinations of parameters, and parameters which are indexed but not used for searches until they are ready. See [Custom Search Parameters](https://smilecdr.com/docs/fhir_standard/fhir_search_custom_search_parameters.html) for more information.

2
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md
View File

@ -287,7 +287,7 @@ Dates are a special case, since it is a fairly common scenario to want to match
# Resource Includes (_include)
FHIR allows clients to request that specific linked resources be included as contained resources, which means that they will be "embedded" in a special container called "contained" within the parent resource.
Using the `_include` FHIR parameter, clients can request that specific linked resources be embedded directly within search results. These included resources will have a search.mode of "include".
HAPI allows you to add a parameter for accepting includes if you wish to support them for specific search methods.

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

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

9
hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu2Test.java
View File

@ -1474,7 +1474,9 @@ public class GenericJaxRsClientDstu2Test {
.execute();
assertEquals(ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname", CAPTURE_SERVLET.ourRequestUri);
assertThat(CAPTURE_SERVLET.ourRequestUri).isIn(
ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname",
ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=name%2Cidentifier");
// assertThat(MY_SERVLET.ourRequestUri,
// either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));
@ -1511,7 +1513,10 @@ public class GenericJaxRsClientDstu2Test {
assertThat(CAPTURE_SERVLET.ourRequestUri).contains(ourServer.getBaseUrl() + "/fhir/Patient/_search?");
assertThat(CAPTURE_SERVLET.ourRequestUri).contains("_elements=identifier%2Cname");
assertThat(CAPTURE_SERVLET.ourRequestUri).satisfiesAnyOf(
s -> assertThat(s).contains("_elements=identifier%2Cname"),
s -> assertThat(s).contains("_elements=name%2Cidentifier")
);
// assertThat(MY_SERVLET.ourRequestUri,
// either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));

9
hapi-fhir-jaxrsserver-base/src/test/java/ca/uhn/fhir/jaxrs/client/GenericJaxRsClientDstu3Test.java
View File

@ -1546,7 +1546,9 @@ public class GenericJaxRsClientDstu3Test {
.execute();
//@formatter:on
assertEquals(ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname", MY_SERVLET.ourRequestUri);
assertThat(MY_SERVLET.ourRequestUri).isIn(
ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=identifier%2Cname",
ourServer.getBaseUrl() + "/fhir/Patient/_search?_elements=name%2Cidentifier");
// assertThat(MY_SERVLET.ourRequestUri,
// either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));
@ -1583,7 +1585,10 @@ public class GenericJaxRsClientDstu3Test {
//@formatter:on
assertThat(MY_SERVLET.ourRequestUri).contains(ourServer.getBaseUrl() + "/fhir/Patient/_search?");
assertThat(MY_SERVLET.ourRequestUri).contains("_elements=identifier%2Cname");
assertThat(MY_SERVLET.ourRequestUri).satisfiesAnyOf(
s -> assertThat(s).contains("_elements=identifier%2Cname"),
s -> assertThat(s).contains("_elements=name%2Cidentifier")
);
// assertThat(MY_SERVLET.ourRequestUri,
// either(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=name%2Cidentifier")).or(equalTo(ourServer.getBaseUrl() + "/fhir/Patient?name=james&_elements=identifier%2Cname")));

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

38
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/config/HapiFhirLocalContainerEntityManagerFactoryBean.java
View File

@ -20,7 +20,11 @@
package ca.uhn.fhir.jpa.config;
import com.google.common.base.Strings;
import org.hibernate.cfg.AvailableSettings;
import jakarta.annotation.Nonnull;
import org.hibernate.cfg.BatchSettings;
import org.hibernate.cfg.JdbcSettings;
import org.hibernate.cfg.ManagedBeanSettings;
import org.hibernate.cfg.QuerySettings;
import org.hibernate.query.criteria.ValueHandlingMode;
import org.hibernate.resource.jdbc.spi.PhysicalConnectionHandlingMode;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
@ -46,18 +50,19 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
myConfigurableListableBeanFactory = theConfigurableListableBeanFactory;
}
@Nonnull
@Override
public Map<String, Object> getJpaPropertyMap() {
Map<String, Object> retVal = super.getJpaPropertyMap();
// SOMEDAY these defaults can be set in the constructor. setJpaProperties does a merge.
if (!retVal.containsKey(AvailableSettings.CRITERIA_VALUE_HANDLING_MODE)) {
retVal.put(AvailableSettings.CRITERIA_VALUE_HANDLING_MODE, ValueHandlingMode.BIND);
if (!retVal.containsKey(QuerySettings.CRITERIA_VALUE_HANDLING_MODE)) {
retVal.put(QuerySettings.CRITERIA_VALUE_HANDLING_MODE, ValueHandlingMode.BIND);
}
if (!retVal.containsKey(AvailableSettings.CONNECTION_HANDLING)) {
if (!retVal.containsKey(JdbcSettings.CONNECTION_HANDLING)) {
retVal.put(
AvailableSettings.CONNECTION_HANDLING,
JdbcSettings.CONNECTION_HANDLING,
PhysicalConnectionHandlingMode.DELAYED_ACQUISITION_AND_RELEASE_AFTER_TRANSACTION);
}
@ -65,26 +70,25 @@ public class HapiFhirLocalContainerEntityManagerFactoryBean extends LocalContain
* Set some performance options
*/
if (!retVal.containsKey(AvailableSettings.STATEMENT_BATCH_SIZE)) {
retVal.put(AvailableSettings.STATEMENT_BATCH_SIZE, "30");
if (!retVal.containsKey(BatchSettings.STATEMENT_BATCH_SIZE)) {
retVal.put(BatchSettings.STATEMENT_BATCH_SIZE, "30");
}
if (!retVal.containsKey(AvailableSettings.ORDER_INSERTS)) {
retVal.put(AvailableSettings.ORDER_INSERTS, "true");
if (!retVal.containsKey(BatchSettings.ORDER_INSERTS)) {
retVal.put(BatchSettings.ORDER_INSERTS, "true");
}
if (!retVal.containsKey(AvailableSettings.ORDER_UPDATES)) {
retVal.put(AvailableSettings.ORDER_UPDATES, "true");
if (!retVal.containsKey(BatchSettings.ORDER_UPDATES)) {
retVal.put(BatchSettings.ORDER_UPDATES, "true");
}
if (!retVal.containsKey(AvailableSettings.BATCH_VERSIONED_DATA)) {
retVal.put(AvailableSettings.BATCH_VERSIONED_DATA, "true");
if (!retVal.containsKey(BatchSettings.BATCH_VERSIONED_DATA)) {
retVal.put(BatchSettings.BATCH_VERSIONED_DATA, "true");
}
// Why is this here, you ask? LocalContainerEntityManagerFactoryBean actually clobbers the setting hibernate
// needs
// in order to be able to resolve beans, so we add it back in manually here
if (!retVal.containsKey(AvailableSettings.BEAN_CONTAINER)) {
retVal.put(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(myConfigurableListableBeanFactory));
// needs in order to be able to resolve beans, so we add it back in manually here
if (!retVal.containsKey(ManagedBeanSettings.BEAN_CONTAINER)) {
retVal.put(ManagedBeanSettings.BEAN_CONTAINER, new SpringBeanContainer(myConfigurableListableBeanFactory));
}
return retVal;

5
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -414,7 +414,6 @@
<plugin>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-plugin</artifactId>
<version>${project.version}</version>
<executions>
<execution>
<id>build_dstu2</id>
@ -525,7 +524,6 @@
<plugin>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-tinder-plugin</artifactId>
<version>${project.version}</version>
<executions>
<execution>
<goals>
@ -534,6 +532,7 @@
</execution>
</executions>
<configuration>
<skip>false</skip>
<packageNames>
<packageName>ca.uhn.fhir.jpa.entity</packageName>
<packageName>ca.uhn.fhir.jpa.model.entity</packageName>

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessor.java
View File

@ -42,7 +42,6 @@ import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.search.SearchBuilderLoadIncludesParameters;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.model.MdmPidTuple;
@ -59,6 +58,7 @@ import ca.uhn.fhir.util.ExtensionUtil;
import ca.uhn.fhir.util.HapiExtensions;
import ca.uhn.fhir.util.Logs;
import ca.uhn.fhir.util.SearchParameterUtil;
import ca.uhn.fhir.util.TaskChunker;
import jakarta.annotation.Nonnull;
import jakarta.persistence.EntityManager;
import org.apache.commons.lang3.StringUtils;
@ -315,8 +315,7 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
// for each patient pid ->
// search for the target resources, with their correct patient references, chunked.
// The results will be jammed into myReadPids
QueryChunker<JpaPid> queryChunker = new QueryChunker<>();
queryChunker.chunk(expandedMemberResourceIds, QUERY_CHUNK_SIZE, (idChunk) -> {
TaskChunker.chunk(expandedMemberResourceIds, QUERY_CHUNK_SIZE, (idChunk) -> {
try {
queryResourceTypeWithReferencesToPatients(pids, idChunk, theParams, theDef);
} catch (IOException ex) {
@ -625,7 +624,8 @@ public class JpaBulkExportProcessor implements IBulkExportProcessor<JpaPid> {
resourceToCheck = "Patient";
activeSearchParamName = "organization";
}
return mySearchParamRegistry.getActiveSearchParam(resourceToCheck, activeSearchParamName);
return mySearchParamRegistry.getActiveSearchParam(
resourceToCheck, activeSearchParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
}
/**

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/JpaConfig.java
View File

@ -43,6 +43,7 @@ import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.svc.BulkDataImportSvcImpl;
import ca.uhn.fhir.jpa.cache.IResourceVersionSvc;
import ca.uhn.fhir.jpa.cache.ResourceVersionSvcDaoImpl;
import ca.uhn.fhir.jpa.dao.CacheTagDefinitionDao;
import ca.uhn.fhir.jpa.dao.DaoSearchParamProvider;
import ca.uhn.fhir.jpa.dao.HistoryBuilder;
import ca.uhn.fhir.jpa.dao.HistoryBuilderFactory;
@ -56,6 +57,7 @@ import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.TransactionProcessor;
import ca.uhn.fhir.jpa.dao.data.IResourceModifiedDao;
import ca.uhn.fhir.jpa.dao.data.IResourceSearchUrlDao;
import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeEverythingService;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeOperation;
import ca.uhn.fhir.jpa.dao.expunge.ExpungeService;
@ -377,17 +379,17 @@ public class JpaConfig {
@Bean
public TaskScheduler taskScheduler() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
retVal.setConcurrentExecutor(scheduledExecutorService().getObject());
retVal.setScheduledExecutor(scheduledExecutorService().getObject());
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler(
scheduledExecutorService().getObject(),
scheduledExecutorService().getObject());
return retVal;
}
@Bean(name = TASK_EXECUTOR_NAME)
public AsyncTaskExecutor taskExecutor() {
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler();
retVal.setConcurrentExecutor(scheduledExecutorService().getObject());
retVal.setScheduledExecutor(scheduledExecutorService().getObject());
ConcurrentTaskScheduler retVal = new ConcurrentTaskScheduler(
scheduledExecutorService().getObject(),
scheduledExecutorService().getObject());
return retVal;
}
@ -893,4 +895,10 @@ public class JpaConfig {
FhirContext theFhirContext, HibernatePropertiesProvider theHibernatePropertiesProvider) {
return new ResourceHistoryCalculator(theFhirContext, theHibernatePropertiesProvider.isOracleDialect());
}
@Bean
public CacheTagDefinitionDao tagDefinitionDao(
ITagDefinitionDao tagDefinitionDao, MemoryCacheService memoryCacheService) {
return new CacheTagDefinitionDao(tagDefinitionDao, memoryCacheService);
}
}

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

@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.mdm.dao.IMdmLinkDao;
import ca.uhn.fhir.mdm.dao.IMdmLinkImplFactory;
import ca.uhn.fhir.mdm.svc.MdmLinkExpandSvc;
import ca.uhn.fhir.mdm.svc.MdmSearchExpansionSvc;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
@ -40,6 +41,11 @@ public class MdmJpaConfig {
return new MdmLinkExpandSvc();
}
@Bean
public MdmSearchExpansionSvc mdmSearchExpansionSvc() {
return new MdmSearchExpansionSvc();
}
@Bean
public IMdmLinkDao<JpaPid, MdmLink> mdmLinkDao() {
return new MdmLinkDaoJpaImpl();

241
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -75,7 +75,6 @@ import ca.uhn.fhir.jpa.searchparam.matcher.InMemoryResourceMatcher;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.api.ITermReadSvc;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
@ -89,7 +88,6 @@ import ca.uhn.fhir.rest.api.InterceptorInvocationTimingEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
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.UnprocessableEntityException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
@ -107,14 +105,8 @@ import jakarta.annotation.Nonnull;
import jakarta.annotation.Nullable;
import jakarta.annotation.PostConstruct;
import jakarta.persistence.EntityManager;
import jakarta.persistence.NoResultException;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.PersistenceContextType;
import jakarta.persistence.TypedQuery;
import jakarta.persistence.criteria.CriteriaBuilder;
import jakarta.persistence.criteria.CriteriaQuery;
import jakarta.persistence.criteria.Predicate;
import jakarta.persistence.criteria.Root;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@ -136,19 +128,11 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.stereotype.Repository;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallback;
import org.springframework.transaction.support.TransactionSynchronization;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import org.springframework.transaction.support.TransactionTemplate;
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.IdentityHashMap;
import java.util.List;
@ -158,7 +142,6 @@ import java.util.stream.Collectors;
import javax.xml.stream.events.Characters;
import javax.xml.stream.events.XMLEvent;
import static java.util.Objects.isNull;
import static java.util.Objects.nonNull;
import static org.apache.commons.collections4.CollectionUtils.isEqualCollection;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -182,8 +165,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> 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";
// total attempts to do a tag transaction
private static final int TOTAL_TAG_READ_ATTEMPTS = 10;
private static final Logger ourLog = LoggerFactory.getLogger(BaseHapiFhirDao.class);
private static boolean ourValidationDisabledForUnitTest;
private static boolean ourDisableIncrementOnUpdateForUnitTest = false;
@ -248,17 +229,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
@Autowired
private IPartitionLookupSvc myPartitionLookupSvc;
@Autowired
private MemoryCacheService myMemoryCacheService;
@Autowired(required = false)
private IFulltextSearchSvc myFulltextSearchSvc;
@Autowired
private PlatformTransactionManager myTransactionManager;
protected ResourceHistoryCalculator myResourceHistoryCalculator;
@Autowired
protected ResourceHistoryCalculator myResourceHistoryCalculator;
protected CacheTagDefinitionDao cacheTagDefinitionDao;
protected final CodingSpy myCodingSpy = new CodingSpy();
@ -307,7 +285,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
TagList tagList = ResourceMetadataKeyEnum.TAG_LIST.get(theResource);
if (tagList != null) {
for (Tag next : tagList) {
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails,
TagTypeEnum.TAG,
next.getScheme(),
@ -326,7 +304,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
List<BaseCodingDt> securityLabels = ResourceMetadataKeyEnum.SECURITY_LABELS.get(theResource);
if (securityLabels != null) {
for (BaseCodingDt next : securityLabels) {
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails,
TagTypeEnum.SECURITY_LABEL,
next.getSystemElement().getValue(),
@ -345,7 +323,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
List<IdDt> profiles = ResourceMetadataKeyEnum.PROFILES.get(theResource);
if (profiles != null) {
for (IIdType next : profiles) {
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null, null, null);
if (def != null) {
ResourceTag tag = theEntity.addTag(def);
@ -364,7 +342,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
List<? extends IBaseCoding> tagList = theResource.getMeta().getTag();
if (tagList != null) {
for (IBaseCoding next : tagList) {
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails,
TagTypeEnum.TAG,
next.getSystem(),
@ -383,7 +361,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
List<? extends IBaseCoding> securityLabels = theResource.getMeta().getSecurity();
if (securityLabels != null) {
for (IBaseCoding next : securityLabels) {
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails,
TagTypeEnum.SECURITY_LABEL,
next.getSystem(),
@ -402,7 +380,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
List<? extends IPrimitiveType<String>> profiles = theResource.getMeta().getProfile();
if (profiles != null) {
for (IPrimitiveType<String> next : profiles) {
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, next.getValue(), null, null, null);
if (def != null) {
ResourceTag tag = theEntity.addTag(def);
@ -422,7 +400,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
if (!def.isStandardType()) {
String profile = def.getResourceProfile("");
if (isNotBlank(profile)) {
TagDefinition profileDef = getTagOrNull(
TagDefinition profileDef = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails, TagTypeEnum.PROFILE, NS_JPA_PROFILE, profile, null, null, null);
ResourceTag tag = theEntity.addTag(profileDef);
@ -456,164 +434,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
myContext = theContext;
}
/**
* <code>null</code> will only be returned if the scheme and tag are both blank
*/
protected TagDefinition getTagOrNull(
TransactionDetails theTransactionDetails,
TagTypeEnum theTagType,
String theScheme,
String theTerm,
String theLabel,
String theVersion,
Boolean theUserSelected) {
if (isBlank(theScheme) && isBlank(theTerm) && isBlank(theLabel)) {
return null;
}
MemoryCacheService.TagDefinitionCacheKey key =
toTagDefinitionMemoryCacheKey(theTagType, theScheme, theTerm, theVersion, theUserSelected);
TagDefinition retVal = myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.TAG_DEFINITION, key);
if (retVal == null) {
HashMap<MemoryCacheService.TagDefinitionCacheKey, TagDefinition> resolvedTagDefinitions =
theTransactionDetails.getOrCreateUserData(
HapiTransactionService.XACT_USERDATA_KEY_RESOLVED_TAG_DEFINITIONS, HashMap::new);
retVal = resolvedTagDefinitions.get(key);
if (retVal == null) {
// actual DB hit(s) happen here
retVal = getOrCreateTag(theTagType, theScheme, theTerm, theLabel, theVersion, theUserSelected);
TransactionSynchronization sync = new AddTagDefinitionToCacheAfterCommitSynchronization(key, retVal);
TransactionSynchronizationManager.registerSynchronization(sync);
resolvedTagDefinitions.put(key, retVal);
}
}
return retVal;
}
/**
* Gets the tag defined by the fed in values, or saves it if it does not
* exist.
* <p>
* Can also throw an InternalErrorException if something bad happens.
*/
private TagDefinition getOrCreateTag(
TagTypeEnum theTagType,
String theScheme,
String theTerm,
String theLabel,
String theVersion,
Boolean theUserSelected) {
TypedQuery<TagDefinition> q = buildTagQuery(theTagType, theScheme, theTerm, theVersion, theUserSelected);
q.setMaxResults(1);
TransactionTemplate template = new TransactionTemplate(myTransactionManager);
template.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
// this transaction will attempt to get or create the tag,
// repeating (on any failure) 10 times.
// if it fails more than this, we will throw exceptions
TagDefinition retVal;
int count = 0;
HashSet<Throwable> throwables = new HashSet<>();
do {
try {
retVal = template.execute(new TransactionCallback<TagDefinition>() {
// do the actual DB call(s) to read and/or write the values
private TagDefinition readOrCreate() {
TagDefinition val;
try {
val = q.getSingleResult();
} catch (NoResultException e) {
val = new TagDefinition(theTagType, theScheme, theTerm, theLabel);
val.setVersion(theVersion);
val.setUserSelected(theUserSelected);
myEntityManager.persist(val);
}
return val;
}
@Override
public TagDefinition doInTransaction(TransactionStatus status) {
TagDefinition tag = null;
try {
tag = readOrCreate();
} catch (Exception ex) {
// log any exceptions - just in case
// they may be signs of things to come...
ourLog.warn(
"Tag read/write failed: "
+ ex.getMessage() + ". "
+ "This is not a failure on its own, "
+ "but could be useful information in the result of an actual failure.",
ex);
throwables.add(ex);
}
return tag;
}
});
} catch (Exception ex) {
// transaction template can fail if connections to db are exhausted and/or timeout
ourLog.warn(
"Transaction failed with: {}. Transaction will rollback and be reattempted.", ex.getMessage());
retVal = null;
}
count++;
} while (retVal == null && count < TOTAL_TAG_READ_ATTEMPTS);
if (retVal == null) {
// if tag is still null,
// something bad must be happening
// - throw
String msg = throwables.stream().map(Throwable::getMessage).collect(Collectors.joining(", "));
throw new InternalErrorException(Msg.code(2023)
+ "Tag get/create failed after "
+ TOTAL_TAG_READ_ATTEMPTS
+ " attempts with error(s): "
+ msg);
}
return retVal;
}
private TypedQuery<TagDefinition> buildTagQuery(
TagTypeEnum theTagType, String theScheme, String theTerm, String theVersion, Boolean theUserSelected) {
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<TagDefinition> cq = builder.createQuery(TagDefinition.class);
Root<TagDefinition> from = cq.from(TagDefinition.class);
List<Predicate> predicates = new ArrayList<>();
predicates.add(builder.and(
builder.equal(from.get("myTagType"), theTagType), builder.equal(from.get("myCode"), theTerm)));
predicates.add(
isBlank(theScheme)
? builder.isNull(from.get("mySystem"))
: builder.equal(from.get("mySystem"), theScheme));
predicates.add(
isBlank(theVersion)
? builder.isNull(from.get("myVersion"))
: builder.equal(from.get("myVersion"), theVersion));
predicates.add(
isNull(theUserSelected)
? builder.isNull(from.get("myUserSelected"))
: builder.equal(from.get("myUserSelected"), theUserSelected));
cq.where(predicates.toArray(new Predicate[0]));
return myEntityManager.createQuery(cq);
}
void incrementId(T theResource, ResourceTable theSavedEntity, IIdType theResourceId) {
if (theResourceId == null || theResourceId.getVersionIdPart() == null) {
theSavedEntity.initializeVersion();
@ -933,7 +753,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
@Override
@CoverageIgnore
public BaseHasResource readEntity(IIdType theValueId, RequestDetails theRequest) {
throw new NotImplementedException(Msg.code(927) + "");
throw new NotImplementedException(Msg.code(927));
}
/**
@ -1200,6 +1020,10 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
if (entity.getId() == null) {
myEntityManager.persist(entity);
if (entity.getFhirId() == null) {
entity.setFhirId(Long.toString(entity.getResourceId()));
}
postPersist(entity, (T) theResource, theRequest);
} else if (entity.getDeleted() != null) {
@ -1499,7 +1323,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
* the previous version entity.
*/
if (historyEntry == null) {
historyEntry = theEntity.toHistory(versionedTags);
historyEntry = theEntity.toHistory(versionedTags && theEntity.getDeleted() == null);
}
historyEntry.setEncoding(theChanged.getEncoding());
@ -1507,7 +1331,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
historyEntry.setResourceTextVc(theChanged.getResourceText());
ourLog.debug("Saving history entry ID[{}] for RES_ID[{}]", historyEntry.getId(), historyEntry.getResourceId());
myResourceHistoryTableDao.save(historyEntry);
myEntityManager.persist(historyEntry);
theEntity.setCurrentVersionEntity(historyEntry);
// Save resource source
@ -1665,6 +1489,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
wasDeleted = theOldResource.isDeleted();
}
if (wasDeleted && !myStorageSettings.isDeleteEnabled()) {
String msg = myContext.getLocalizer().getMessage(BaseHapiFhirDao.class, "cantUndeleteWithDeletesDisabled");
throw new InvalidRequestException(Msg.code(2573) + msg);
}
DaoMethodOutcome outcome = toMethodOutcome(
theRequestDetails, savedEntity, theResource, theMatchUrl, theOperationType)
.setCreated(wasDeleted);
@ -1839,9 +1668,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
}
@PostConstruct
public void start() {
// nothing yet
}
public void start() {}
@VisibleForTesting
public void setStorageSettingsForUnitTest(JpaStorageSettings theStorageSettings) {
@ -1880,30 +1707,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> extends BaseStora
myJpaStorageResourceParser = theJpaStorageResourceParser;
}
private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
private final TagDefinition myTagDefinition;
private final MemoryCacheService.TagDefinitionCacheKey myKey;
public AddTagDefinitionToCacheAfterCommitSynchronization(
MemoryCacheService.TagDefinitionCacheKey theKey, TagDefinition theTagDefinition) {
myTagDefinition = theTagDefinition;
myKey = theKey;
}
@Override
public void afterCommit() {
myMemoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, myKey, myTagDefinition);
}
}
@Nonnull
public static MemoryCacheService.TagDefinitionCacheKey toTagDefinitionMemoryCacheKey(
TagTypeEnum theTagType, String theScheme, String theTerm, String theVersion, Boolean theUserSelected) {
return new MemoryCacheService.TagDefinitionCacheKey(
theTagType, theScheme, theTerm, theVersion, theUserSelected);
}
@SuppressWarnings("unchecked")
public static String parseContentTextIntoWords(FhirContext theContext, IBaseResource theResource) {

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -43,6 +43,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
import ca.uhn.fhir.jpa.api.model.LazyDaoMethodOutcome;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.delete.DeleteConflictUtil;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
@ -567,8 +568,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
// Pre-cache the resource ID
jpaPid.setAssociatedResourceId(entity.getIdType(myFhirContext));
myIdHelperService.addResolvedPidToForcedId(
jpaPid, theRequestPartitionId, getResourceName(), entity.getFhirId(), null);
String fhirId = entity.getFhirId();
if (fhirId == null) {
fhirId = Long.toString(entity.getId());
}
myIdHelperService.addResolvedPidToFhirId(jpaPid, theRequestPartitionId, getResourceName(), fhirId, null);
theTransactionDetails.addResolvedResourceId(jpaPid.getAssociatedResourceId(), jpaPid);
theTransactionDetails.addResolvedResource(jpaPid.getAssociatedResourceId(), theResource);
@ -1043,7 +1047,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
if (!entityHasTag) {
theEntity.setHasTags(true);
TagDefinition def = getTagOrNull(
TagDefinition def = cacheTagDefinitionDao.getTagOrNull(
theTransactionDetails,
nextDef.getTagType(),
nextDef.getSystem(),
@ -1736,8 +1740,13 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
validateResourceTypeAndThrowInvalidRequestException(theId);
BaseHasResource entity;
JpaPid pid = myIdHelperService.resolveResourcePersistentIds(
requestPartitionId, getResourceName(), theId.getIdPart());
JpaPid pid = myIdHelperService
.resolveResourceIdentity(
requestPartitionId,
getResourceName(),
theId.getIdPart(),
ResolveIdentityMode.includeDeleted().cacheOk())
.getPersistentId();
Set<Integer> readPartitions = null;
if (requestPartitionId.isAllPartitions()) {
entity = myEntityManager.find(ResourceTable.class, pid.getId());
@ -1779,10 +1788,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
if (entity == null) {
throw new ResourceNotFoundException(Msg.code(1996) + "Resource " + theId + " is not known");
}
if (theId.hasVersionIdPart()) {
if (!theId.isVersionIdPartValidLong()) {
throw new ResourceNotFoundException(Msg.code(978)
@ -1822,7 +1827,10 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
Validate.notNull(entity);
if (entity == null) {
throw new ResourceNotFoundException(Msg.code(1996) + "Resource " + theId + " is not known");
}
validateResourceType(entity);
if (theCheckForForcedId) {
@ -1871,8 +1879,27 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
if (persistentId == null) {
persistentId = myIdHelperService.resolveResourcePersistentIds(
theRequestPartitionId, getResourceName(), theId.getIdPart());
String resourceName = getResourceName();
if (myStorageSettings.getResourceClientIdStrategy()
== JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC) {
if (theId.isIdPartValidLong()) {
/*
* If it's a pure numeric ID and we are in ALPHANUMERIC mode, then the number
* corresponds to a DB PID. In this case we want to resolve it regardless of
* which type the client has supplied. This is because DB PIDs are unique across
* all resource types (unlike FHIR_IDs which are namespaced to the resource type).
* We want to load the resource with that PID regardless of type because if
* the user is trying to update it we want to fail if the type is wrong, as
* opposed to trying to create a new instance.
*/
resourceName = null;
}
}
persistentId = myIdHelperService.resolveResourceIdentityPid(
theRequestPartitionId,
resourceName,
theId.getIdPart(),
ResolveIdentityMode.includeDeleted().cacheOk());
}
ResourceTable entity = myEntityManager.find(ResourceTable.class, persistentId.getId());

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

@ -192,7 +192,7 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
HapiTransactionService.requireTransaction();
List<Long> pids = theResolvedIds.stream().map(t -> ((JpaPid) t).getId()).collect(Collectors.toList());
new QueryChunker<Long>().chunk(pids, idChunk -> {
QueryChunker.chunk(pids, idChunk -> {
/*
* Pre-fetch the resources we're touching in this transaction in mass - this reduced the

132
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/CacheTagDefinitionDao.java Normal file
View File

@ -0,0 +1,132 @@
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2024 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%
*/
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.jpa.dao.data.ITagDefinitionDao;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import jakarta.annotation.Nonnull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.data.domain.Pageable;
import org.springframework.stereotype.Repository;
import org.springframework.transaction.support.TransactionSynchronization;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import java.util.HashMap;
import java.util.List;
import static org.apache.commons.lang3.StringUtils.isBlank;
@Repository
public class CacheTagDefinitionDao {
private static final Logger ourLog = LoggerFactory.getLogger(CacheTagDefinitionDao.class);
private final ITagDefinitionDao tagDefinitionDao;
private final MemoryCacheService memoryCacheService;
public CacheTagDefinitionDao(ITagDefinitionDao tagDefinitionDao, MemoryCacheService memoryCacheService) {
this.tagDefinitionDao = tagDefinitionDao;
this.memoryCacheService = memoryCacheService;
}
/**
* Returns a TagDefinition or null if the scheme, term, and label are all blank.
*/
protected TagDefinition getTagOrNull(
TransactionDetails transactionDetails,
TagTypeEnum tagType,
String scheme,
String term,
String label,
String version,
Boolean userSelected) {
if (isBlank(scheme) && isBlank(term) && isBlank(label)) {
return null;
}
MemoryCacheService.TagDefinitionCacheKey key =
toTagDefinitionMemoryCacheKey(tagType, scheme, term, version, userSelected);
TagDefinition tagDefinition = memoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.TAG_DEFINITION, key);
if (tagDefinition == null) {
HashMap<MemoryCacheService.TagDefinitionCacheKey, TagDefinition> resolvedTagDefinitions =
transactionDetails.getOrCreateUserData("resolvedTagDefinitions", HashMap::new);
tagDefinition = resolvedTagDefinitions.get(key);
if (tagDefinition == null) {
tagDefinition = getOrCreateTag(tagType, scheme, term, label, version, userSelected);
TransactionSynchronization sync =
new AddTagDefinitionToCacheAfterCommitSynchronization(key, tagDefinition);
TransactionSynchronizationManager.registerSynchronization(sync);
resolvedTagDefinitions.put(key, tagDefinition);
}
}
return tagDefinition;
}
/**
* Gets or creates a TagDefinition entity.
*/
private TagDefinition getOrCreateTag(
TagTypeEnum tagType, String scheme, String term, String label, String version, Boolean userSelected) {
List<TagDefinition> result = tagDefinitionDao.findByTagTypeAndSchemeAndTermAndVersionAndUserSelected(
tagType, scheme, term, version, userSelected, Pageable.ofSize(1));
if (!result.isEmpty()) {
return result.get(0);
} else {
// Create a new TagDefinition if no result is found
TagDefinition newTag = new TagDefinition(tagType, scheme, term, label);
newTag.setVersion(version);
newTag.setUserSelected(userSelected);
return tagDefinitionDao.save(newTag);
}
}
@Nonnull
private static MemoryCacheService.TagDefinitionCacheKey toTagDefinitionMemoryCacheKey(
TagTypeEnum tagType, String scheme, String term, String version, Boolean userSelected) {
return new MemoryCacheService.TagDefinitionCacheKey(tagType, scheme, term, version, userSelected);
}
private class AddTagDefinitionToCacheAfterCommitSynchronization implements TransactionSynchronization {
private final TagDefinition tagDefinition;
private final MemoryCacheService.TagDefinitionCacheKey key;
public AddTagDefinitionToCacheAfterCommitSynchronization(
MemoryCacheService.TagDefinitionCacheKey key, TagDefinition tagDefinition) {
this.tagDefinition = tagDefinition;
this.key = key;
}
@Override
public void afterCommit() {
memoryCacheService.put(MemoryCacheService.CacheEnum.TAG_DEFINITION, key, tagDefinition);
}
}
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FulltextSearchSvcImpl.java
View File

@ -137,7 +137,8 @@ public class FulltextSearchSvcImpl implements IFulltextSearchSvc {
public ExtendedHSearchIndexData extractLuceneIndexData(
IBaseResource theResource, ResourceIndexedSearchParams theNewParams) {
String resourceType = myFhirContext.getResourceType(theResource);
ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(resourceType);
ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(
resourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
ExtendedHSearchIndexExtractor extractor = new ExtendedHSearchIndexExtractor(
myStorageSettings, myFhirContext, activeSearchParams, mySearchParamExtractor);
return extractor.extract(theResource, theNewParams);

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

@ -81,7 +81,7 @@ public class HistoryBuilder {
private FhirContext myCtx;
@Autowired
private IIdHelperService myIdHelperService;
private IIdHelperService<JpaPid> myIdHelperService;
/**
* Constructor
@ -150,13 +150,13 @@ public class HistoryBuilder {
query.setMaxResults(theToIndex - theFromIndex);
List<ResourceHistoryTable> tables = query.getResultList();
if (tables.size() > 0) {
if (!tables.isEmpty()) {
ImmutableListMultimap<Long, ResourceHistoryTable> resourceIdToHistoryEntries =
Multimaps.index(tables, ResourceHistoryTable::getResourceId);
Set<JpaPid> pids = resourceIdToHistoryEntries.keySet().stream()
.map(JpaPid::fromId)
.collect(Collectors.toSet());
PersistentIdToForcedIdMap pidToForcedId = myIdHelperService.translatePidsToForcedIds(pids);
PersistentIdToForcedIdMap<JpaPid> pidToForcedId = myIdHelperService.translatePidsToForcedIds(pids);
ourLog.trace("Translated IDs: {}", pidToForcedId.getResourcePersistentIdOptionalMap());
for (Long nextResourceId : resourceIdToHistoryEntries.keySet()) {
@ -172,8 +172,9 @@ public class HistoryBuilder {
// For that reason, strip the prefix before setting the transientForcedId below.
// If not stripped this messes up the id of the resource as the resourceType would be repeated
// twice like Patient/Patient/1234 in the resource constructed
if (resourceId.startsWith(myResourceType + "/")) {
resourceId = resourceId.substring(myResourceType.length() + 1);
int slashIdx = resourceId.indexOf('/');
if (slashIdx != -1) {
resourceId = resourceId.substring(slashIdx + 1);
}
} else {
resourceId = nextResourceId.toString();

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaResourceDaoCodeSystem.java
View File

@ -242,13 +242,15 @@ public class JpaResourceDaoCodeSystem<T extends IBaseResource> extends BaseHapiF
theTransactionDetails,
theForceUpdate,
theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (thePerformIndexing) {
if (!retVal.isUnchangedInCurrentOperation()) {
org.hl7.fhir.r4.model.CodeSystem cs = myVersionCanonicalizer.codeSystemToCanonical(theResource);
addPidToResource(theEntity, cs);
org.hl7.fhir.r4.model.CodeSystem cs = myVersionCanonicalizer.codeSystemToCanonical(theResource);
addPidToResource(theEntity, cs);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(
cs, (ResourceTable) theEntity, theRequest);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(
cs, (ResourceTable) theEntity, theRequest);
}
}
return retVal;

21
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaResourceDaoObservation.java
View File

@ -22,6 +22,8 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -39,12 +41,15 @@ import jakarta.persistence.PersistenceContext;
import jakarta.persistence.PersistenceContextType;
import jakarta.servlet.http.HttpServletResponse;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Observation;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.support.TransactionTemplate;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapiFhirResourceDao<T>
@ -138,13 +143,14 @@ public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapi
patientParams.addAll(theSearchParameterMap.get(getSubjectParamName()));
}
Map<IIdType, ReferenceParam> ids = new HashMap<>();
for (List<? extends IQueryParameterType> nextPatientList : patientParams) {
for (IQueryParameterType nextOr : nextPatientList) {
if (nextOr instanceof ReferenceParam) {
ReferenceParam ref = (ReferenceParam) nextOr;
JpaPid pid = myIdHelperService.resolveResourcePersistentIds(
requestPartitionId, ref.getResourceType(), ref.getIdPart());
orderedSubjectReferenceMap.put(pid.getId(), nextOr);
IIdType id = myFhirContext.getVersion().newIdType();
id.setParts(null, ref.getResourceType(), ref.getIdPart(), null);
ids.put(id, ref);
} else {
throw new IllegalArgumentException(
Msg.code(942) + "Invalid token type (expecting ReferenceParam): " + nextOr.getClass());
@ -152,6 +158,15 @@ public class JpaResourceDaoObservation<T extends IBaseResource> extends BaseHapi
}
}
Map<IIdType, IResourceLookup<JpaPid>> resolvedIds = myIdHelperService.resolveResourceIdentities(
requestPartitionId,
ids.keySet(),
ResolveIdentityMode.includeDeleted().cacheOk());
for (Map.Entry<IIdType, ReferenceParam> entry : ids.entrySet()) {
IResourceLookup<JpaPid> lookup = resolvedIds.get(entry.getKey());
orderedSubjectReferenceMap.put(lookup.getPersistentId().getId(), entry.getValue());
}
theSearchParameterMap.remove(getSubjectParamName());
theSearchParameterMap.remove(getPatientParamName());

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

@ -303,12 +303,14 @@ public class JpaResourceDaoValueSet<T extends IBaseResource> extends BaseHapiFhi
theForceUpdate,
theCreateNewHistoryEntry);
if (getStorageSettings().isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = myVersionCanonicalizer.valueSetToCanonical(theResource);
myTerminologySvc.storeTermValueSet(retVal, valueSet);
} else {
myTerminologySvc.deleteValueSetAndChildren(retVal);
if (thePerformIndexing) {
if (getStorageSettings().isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = myVersionCanonicalizer.valueSetToCanonical(theResource);
myTerminologySvc.storeTermValueSet(retVal, valueSet);
} else {
myTerminologySvc.deleteValueSetAndChildren(retVal);
}
}
}

168
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java
View File

@ -26,25 +26,29 @@ import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.StorageSettings;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.TaskChunker;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import jakarta.annotation.Nullable;
import jakarta.persistence.EntityManager;
import jakarta.persistence.FlushModeType;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.PersistenceContextType;
import jakarta.persistence.PersistenceException;
@ -67,6 +71,7 @@ import org.springframework.context.ApplicationContext;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
@ -83,6 +88,7 @@ public class TransactionProcessor extends BaseTransactionProcessor {
public static final Pattern SINGLE_PARAMETER_MATCH_URL_PATTERN = Pattern.compile("^[^?]+[?][a-z0-9-]+=[^&,]+$");
private static final Logger ourLog = LoggerFactory.getLogger(TransactionProcessor.class);
public static final int CONDITIONAL_URL_FETCH_CHUNK_SIZE = 100;
@Autowired
private ApplicationContext myApplicationContext;
@ -146,25 +152,51 @@ public class TransactionProcessor extends BaseTransactionProcessor {
List<IBase> theEntries,
StopWatch theTransactionStopWatch) {
ITransactionProcessorVersionAdapter<?, ?> versionAdapter = getVersionAdapter();
RequestPartitionId requestPartitionId =
super.determineRequestPartitionIdForWriteEntries(theRequest, theEntries);
/*
* We temporarily set the flush mode for the duration of the DB transaction
* from the default of AUTO to the temporary value of COMMIT here. We do this
* because in AUTO mode, if any SQL SELECTs are required during the
* processing of an individual transaction entry, the server will flush the
* pending INSERTs/UPDATEs to the database before executing the SELECT.
* This hurts performance since we don't get the benefit of batching those
* write operations as much as possible. The tradeoff here is that we
* could theoretically have transaction operations which try to read
* data previously written in the same transaction, and they won't see it.
* This shouldn't actually be an issue anyhow - we pre-fetch conditional
* URLs and reference targets at the start of the transaction. But this
* tradeoff still feels worth it, since the most common use of transactions
* is for fast writing of data.
*
* Note that it's probably not necessary to reset it back, it should
* automatically go back to the default value after the transaction but
* we reset it just to be safe.
*/
FlushModeType initialFlushMode = myEntityManager.getFlushMode();
try {
myEntityManager.setFlushMode(FlushModeType.COMMIT);
if (requestPartitionId != null) {
preFetch(theTransactionDetails, theEntries, versionAdapter, requestPartitionId);
ITransactionProcessorVersionAdapter<?, ?> versionAdapter = getVersionAdapter();
RequestPartitionId requestPartitionId =
super.determineRequestPartitionIdForWriteEntries(theRequest, theEntries);
if (requestPartitionId != null) {
preFetch(theTransactionDetails, theEntries, versionAdapter, requestPartitionId);
}
return super.doTransactionWriteOperations(
theRequest,
theActionName,
theTransactionDetails,
theAllIds,
theIdSubstitutions,
theIdToPersistedOutcome,
theResponse,
theOriginalRequestOrder,
theEntries,
theTransactionStopWatch);
} finally {
myEntityManager.setFlushMode(initialFlushMode);
}
return super.doTransactionWriteOperations(
theRequest,
theActionName,
theTransactionDetails,
theAllIds,
theIdSubstitutions,
theIdToPersistedOutcome,
theResponse,
theOriginalRequestOrder,
theEntries,
theTransactionStopWatch);
}
private void preFetch(
@ -199,40 +231,100 @@ public class TransactionProcessor extends BaseTransactionProcessor {
RequestPartitionId theRequestPartitionId,
Set<String> foundIds,
List<Long> idsToPreFetch) {
List<IIdType> idsToPreResolve = new ArrayList<>();
FhirTerser terser = myFhirContext.newTerser();
// Key: The ID of the resource
// Value: TRUE if we should prefetch the existing resource details and all stored indexes,
// FALSE if we should prefetch only the identity (resource ID and deleted status)
Map<IIdType, Boolean> idsToPreResolve = new HashMap<>(theEntries.size() * 3);
for (IBase nextEntry : theEntries) {
IBaseResource resource = theVersionAdapter.getResource(nextEntry);
if (resource != null) {
String verb = theVersionAdapter.getEntryRequestVerb(myFhirContext, nextEntry);
/*
* Pre-fetch any resources that are potentially being directly updated by ID
*/
if ("PUT".equals(verb) || "PATCH".equals(verb)) {
String requestUrl = theVersionAdapter.getEntryRequestUrl(nextEntry);
if (countMatches(requestUrl, '/') == 1 && countMatches(requestUrl, '?') == 0) {
if (countMatches(requestUrl, '?') == 0) {
IIdType id = myFhirContext.getVersion().newIdType();
id.setValue(requestUrl);
idsToPreResolve.add(id);
IIdType unqualifiedVersionless = id.toUnqualifiedVersionless();
idsToPreResolve.put(unqualifiedVersionless, Boolean.TRUE);
}
}
/*
* Pre-fetch any resources that are referred to directly by ID (don't replace
* the TRUE flag with FALSE in case we're updating a resource but also
* pointing to that resource elsewhere in the bundle)
*/
if ("PUT".equals(verb) || "POST".equals(verb)) {
for (ResourceReferenceInfo referenceInfo : terser.getAllResourceReferences(resource)) {
IIdType reference = referenceInfo.getResourceReference().getReferenceElement();
if (reference != null
&& !reference.isLocal()
&& !reference.isUuid()
&& reference.hasResourceType()
&& reference.hasIdPart()
&& !reference.getValue().contains("?")) {
idsToPreResolve.putIfAbsent(reference.toUnqualifiedVersionless(), Boolean.FALSE);
}
}
}
}
}
List<JpaPid> outcome =
myIdHelperService.resolveResourcePersistentIdsWithCache(theRequestPartitionId, idsToPreResolve).stream()
.collect(Collectors.toList());
for (JpaPid next : outcome) {
foundIds.add(
next.getAssociatedResourceId().toUnqualifiedVersionless().getValue());
theTransactionDetails.addResolvedResourceId(next.getAssociatedResourceId(), next);
if (myStorageSettings.getResourceClientIdStrategy() != JpaStorageSettings.ClientIdStrategyEnum.ANY
|| !next.getAssociatedResourceId().isIdPartValidLong()) {
idsToPreFetch.add(next.getId());
/*
* If all the entries in the pre-fetch ID map have a value of TRUE, this
* means we only have IDs associated with resources we're going to directly
* update/patch within the transaction. In that case, it's fine to include
* deleted resources, since updating them will bring them back to life.
*
* If we have any FALSE entries, we're also pre-fetching reference targets
* which means we don't want deleted resources, because those are not OK
* to reference.
*/
boolean preFetchIncludesReferences = idsToPreResolve.values().stream().anyMatch(t -> !t);
ResolveIdentityMode resolveMode = preFetchIncludesReferences
? ResolveIdentityMode.excludeDeleted().noCacheUnlessDeletesDisabled()
: ResolveIdentityMode.includeDeleted().cacheOk();
Map<IIdType, IResourceLookup<JpaPid>> outcomes = myIdHelperService.resolveResourceIdentities(
theRequestPartitionId, idsToPreResolve.keySet(), resolveMode);
for (Map.Entry<IIdType, IResourceLookup<JpaPid>> entry : outcomes.entrySet()) {
JpaPid next = (JpaPid) entry.getValue().getPersistentId();
IIdType unqualifiedVersionlessId = entry.getKey();
foundIds.add(unqualifiedVersionlessId.getValue());
theTransactionDetails.addResolvedResourceId(unqualifiedVersionlessId, next);
if (idsToPreResolve.get(unqualifiedVersionlessId) == Boolean.TRUE) {
if (myStorageSettings.getResourceClientIdStrategy() != JpaStorageSettings.ClientIdStrategyEnum.ANY
|| (next.getAssociatedResourceId() != null
&& !next.getAssociatedResourceId().isIdPartValidLong())) {
idsToPreFetch.add(next.getId());
}
}
}
for (IIdType next : idsToPreResolve) {
if (!foundIds.contains(next.toUnqualifiedVersionless().getValue())) {
// Any IDs that could not be resolved are presumably not there, so
// cache that fact so we don't look again later
for (IIdType next : idsToPreResolve.keySet()) {
if (!foundIds.contains(next.getValue())) {
theTransactionDetails.addResolvedResourceId(next.toUnqualifiedVersionless(), null);
}
}
}
@Override
protected void handleVerbChangeInTransactionWriteOperations() {
super.handleVerbChangeInTransactionWriteOperations();
myEntityManager.flush();
}
private void preFetchConditionalUrls(
TransactionDetails theTransactionDetails,
List<IBase> theEntries,
@ -274,12 +366,10 @@ public class TransactionProcessor extends BaseTransactionProcessor {
}
}
new QueryChunker<MatchUrlToResolve>()
.chunk(
searchParameterMapsToResolve,
100,
map -> preFetchSearchParameterMaps(
theTransactionDetails, theRequestPartitionId, map, idsToPreFetch));
TaskChunker.chunk(
searchParameterMapsToResolve,
CONDITIONAL_URL_FETCH_CHUNK_SIZE,
map -> preFetchSearchParameterMaps(theTransactionDetails, theRequestPartitionId, map, idsToPreFetch));
}
/**

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IMdmLinkJpaRepository.java
View File

@ -29,6 +29,7 @@ import org.springframework.data.repository.history.RevisionRepository;
import org.springframework.data.repository.query.Param;
import org.springframework.stereotype.Repository;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Optional;
@ -122,6 +123,20 @@ public interface IMdmLinkJpaRepository
List<MdmPidTuple> expandPidsByGoldenResourcePidAndMatchResult(
@Param("goldenPid") Long theSourcePid, @Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
@Query(
"SELECT lookup_link.myGoldenResourcePid as goldenPid, gld_rt.myPartitionIdValue as goldenPartitionId, lookup_link.mySourcePid as sourcePid, lookup_link.myPartitionIdValue as sourcePartitionId "
+ "FROM MdmLink lookup_link "
+ "INNER JOIN ResourceTable gld_rt "
+ "on lookup_link.myGoldenResourcePid=gld_rt.myId "
+ "WHERE "
+ " (lookup_link.myGoldenResourcePid IN (:pids) "
+ " OR"
+ " lookup_link.mySourcePid IN (:pids))"
+ "AND lookup_link.myMatchResult = :matchResult")
List<MdmPidTuple> expandPidsByGoldenResourcePidsOrSourcePidsAndMatchResult(
@Param("pids") Collection<Long> theSourcePid,
@Param("matchResult") MdmMatchResultEnum theMdmMatchResultEnum);
@Query(
"SELECT ml.myId FROM MdmLink ml WHERE ml.myMdmSourceType = :resourceName AND ml.myCreated <= :highThreshold ORDER BY ml.myCreated DESC")
List<Long> findPidByResourceNameAndThreshold(

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITagDefinitionDao.java
View File

@ -20,8 +20,25 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.List;
public interface ITagDefinitionDao extends JpaRepository<TagDefinition, Long>, IHapiFhirJpaRepository {
// nothing
@Query("SELECT t FROM TagDefinition t WHERE " + "t.myTagType = :tagType AND "
+ "( :scheme IS NULL OR :scheme = '' OR t.mySystem = :scheme ) AND "
+ "t.myCode = :term AND "
+ "( :version IS NULL OR :version = '' OR t.myVersion = :version ) AND "
+ "( :userSelected IS NULL OR t.myUserSelected = :userSelected )")
List<TagDefinition> findByTagTypeAndSchemeAndTermAndVersionAndUserSelected(
@Param("tagType") TagTypeEnum tagType,
@Param("scheme") String scheme,
@Param("term") String term,
@Param("version") String version,
@Param("userSelected") Boolean userSelected,
Pageable pageable);
}

581
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.model.PersistentIdToForcedIdMap;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
@ -35,11 +36,12 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.search.builder.SearchBuilder;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.BaseResourcePersistentId;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TaskChunker;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.collect.ListMultimap;
import com.google.common.collect.MultimapBuilder;
@ -60,11 +62,12 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.IdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.support.TransactionSynchronizationManager;
import java.time.LocalDate;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@ -79,6 +82,7 @@ import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.search.builder.predicate.BaseJoiningPredicateBuilder.replaceDefaultPartitionIdIfNonNull;
import static ca.uhn.fhir.model.primitive.IdDt.isValidLong;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
@ -102,6 +106,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
public class IdHelperService implements IIdHelperService<JpaPid> {
public static final Predicate[] EMPTY_PREDICATE_ARRAY = new Predicate[0];
public static final String RESOURCE_PID = "RESOURCE_PID";
private static final Logger ourLog = LoggerFactory.getLogger(IdHelperService.class);
@Autowired
protected IResourceTableDao myResourceTableDao;
@ -128,20 +133,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
myDontCheckActiveTransactionForUnitTest = theDontCheckActiveTransactionForUnitTest;
}
/**
* Given a forced ID, convert it to its Long value. Since you are allowed to use string IDs for resources, we need to
* convert those to the underlying Long values that are stored, for lookup and comparison purposes.
*
* @throws ResourceNotFoundException If the ID can not be found
*/
@Override
@Nonnull
public IResourceLookup<JpaPid> resolveResourceIdentity(
@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theResourceId)
throws ResourceNotFoundException {
return resolveResourceIdentity(theRequestPartitionId, theResourceType, theResourceId, false);
}
/**
* Given a forced ID, convert it to its Long value. Since you are allowed to use string IDs for resources, we need to
* convert those to the underlying Long values that are stored, for lookup and comparison purposes.
@ -153,48 +144,236 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
@Nonnull
public IResourceLookup<JpaPid> resolveResourceIdentity(
@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
final String theResourceId,
boolean theExcludeDeleted)
@Nullable String theResourceType,
@Nonnull final String theResourceId,
@Nonnull ResolveIdentityMode theMode)
throws ResourceNotFoundException {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive()
: "no transaction active";
String resourceIdToUse = theResourceId;
if (resourceIdToUse.contains("/")) {
resourceIdToUse = theResourceId.substring(resourceIdToUse.indexOf("/") + 1);
IIdType id;
if (theResourceType != null) {
id = newIdType(theResourceType + "/" + theResourceId);
} else {
id = newIdType(theResourceId);
}
IdDt id = new IdDt(theResourceType, resourceIdToUse);
Map<String, List<IResourceLookup<JpaPid>>> matches =
translateForcedIdToPids(theRequestPartitionId, Collections.singletonList(id), theExcludeDeleted);
List<IIdType> ids = List.of(id);
Map<IIdType, IResourceLookup<JpaPid>> outcome = resolveResourceIdentities(theRequestPartitionId, ids, theMode);
// We only pass 1 input in so only 0..1 will come back
if (matches.isEmpty() || !matches.containsKey(resourceIdToUse)) {
if (!outcome.containsKey(id)) {
throw new ResourceNotFoundException(Msg.code(2001) + "Resource " + id + " is not known");
}
if (matches.size() > 1 || matches.get(resourceIdToUse).size() > 1) {
/*
* This means that:
* 1. There are two resources with the exact same resource type and forced id
* 2. The unique constraint on this column-pair has been dropped
*/
String msg = myFhirCtx.getLocalizer().getMessage(IdHelperService.class, "nonUniqueForcedId");
throw new PreconditionFailedException(Msg.code(1099) + msg);
return outcome.get(id);
}
@Nonnull
@Override
public Map<IIdType, IResourceLookup<JpaPid>> resolveResourceIdentities(
@Nonnull RequestPartitionId theRequestPartitionId,
Collection<IIdType> theIds,
ResolveIdentityMode theMode) {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive()
: "no transaction active";
if (theIds.isEmpty()) {
return new HashMap<>();
}
return matches.get(resourceIdToUse).get(0);
Collection<IIdType> ids = new ArrayList<>(theIds);
ids.forEach(id -> Validate.isTrue(id.hasIdPart()));
RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId);
ListMultimap<IIdType, IResourceLookup<JpaPid>> idToLookup =
MultimapBuilder.hashKeys(theIds.size()).arrayListValues(1).build();
// Do we have any FHIR ID lookups cached for any of the IDs
if (theMode.isUseCache(myStorageSettings.isDeleteEnabled()) && !ids.isEmpty()) {
resolveResourceIdentitiesForFhirIdsUsingCache(requestPartitionId, theMode, ids, idToLookup);
}
// We still haven't found IDs, let's look them up in the DB
if (!ids.isEmpty()) {
resolveResourceIdentitiesForFhirIdsUsingDatabase(requestPartitionId, ids, idToLookup);
}
// Convert the multimap into a simple map
Map<IIdType, IResourceLookup<JpaPid>> retVal = new HashMap<>();
for (Map.Entry<IIdType, IResourceLookup<JpaPid>> next : idToLookup.entries()) {
if (next.getValue().getDeleted() != null) {
if (theMode.isFailOnDeleted()) {
String msg = myFhirCtx
.getLocalizer()
.getMessageSanitized(
IdHelperService.class,
"deletedId",
next.getKey().getValue());
throw new ResourceGoneException(Msg.code(2572) + msg);
}
if (!theMode.isIncludeDeleted()) {
continue;
}
}
IResourceLookup previousValue = retVal.put(next.getKey(), next.getValue());
if (previousValue != null) {
/*
* This means that either:
* 1. There are two resources with the exact same resource type and forced
* id. The most likely reason for that is that someone is performing a
* multi-partition search and there are resources on each partition
* with the same ID.
* 2. The unique constraint on the FHIR_ID column has been dropped
*/
ourLog.warn(
"Resource ID[{}] corresponds to lookups: {} and {}",
next.getKey(),
previousValue,
next.getValue());
String msg = myFhirCtx.getLocalizer().getMessage(IdHelperService.class, "nonUniqueForcedId");
throw new PreconditionFailedException(Msg.code(1099) + msg);
}
}
return retVal;
}
/**
* Returns a mapping of Id -> IResourcePersistentId.
* If any resource is not found, it will throw ResourceNotFound exception (and no map will be returned)
* Fetch the resource identity ({@link IResourceLookup}) for a collection of
* resource IDs from the internal memory cache if possible. Note that we only
* use cached results if deletes are disabled on the server (since it is
* therefore not possible that we have an entry in the cache that has since
* been deleted but the cache doesn't know about the deletion), or if we
* aren't excluding deleted results anyhow.
*
* @param theRequestPartitionId The partition(s) to search
* @param theIdsToResolve The IDs we should look up. Any IDs that are resolved
* will be removed from this list. Any IDs remaining in
* the list after calling this method still haven't
* been attempted to be resolved.
* @param theMapToPopulate The results will be populated into this map
*/
@Override
@Nonnull
public Map<String, JpaPid> resolveResourcePersistentIds(
@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, List<String> theIds) {
return resolveResourcePersistentIds(theRequestPartitionId, theResourceType, theIds, false);
private void resolveResourceIdentitiesForFhirIdsUsingCache(
@Nonnull RequestPartitionId theRequestPartitionId,
ResolveIdentityMode theMode,
Collection<IIdType> theIdsToResolve,
ListMultimap<IIdType, IResourceLookup<JpaPid>> theMapToPopulate) {
for (Iterator<IIdType> idIterator = theIdsToResolve.iterator(); idIterator.hasNext(); ) {
IIdType nextForcedId = idIterator.next();
MemoryCacheService.ForcedIdCacheKey nextKey = new MemoryCacheService.ForcedIdCacheKey(
nextForcedId.getResourceType(), nextForcedId.getIdPart(), theRequestPartitionId);
if (theMode.isUseCache(myStorageSettings.isDeleteEnabled())) {
List<IResourceLookup<JpaPid>> cachedLookups = myMemoryCacheService.getIfPresent(
MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, nextKey);
if (cachedLookups != null && !cachedLookups.isEmpty()) {
idIterator.remove();
for (IResourceLookup<JpaPid> cachedLookup : cachedLookups) {
if (theMode.isIncludeDeleted() || cachedLookup.getDeleted() == null) {
theMapToPopulate.put(nextKey.toIdType(myFhirCtx), cachedLookup);
}
}
}
}
}
}
/**
* Fetch the resource identity ({@link IResourceLookup}) for a collection of
* resource IDs from the database
*
* @param theRequestPartitionId The partition(s) to search
* @param theIdsToResolve The IDs we should look up
* @param theMapToPopulate The results will be populated into this map
*/
private void resolveResourceIdentitiesForFhirIdsUsingDatabase(
RequestPartitionId theRequestPartitionId,
Collection<IIdType> theIdsToResolve,
ListMultimap<IIdType, IResourceLookup<JpaPid>> theMapToPopulate) {
/*
* If we have more than a threshold of IDs, we need to chunk the execution to
* avoid having too many parameters in one SQL statement
*/
int maxPageSize = (SearchBuilder.getMaximumPageSize() / 2) - 10;
if (theIdsToResolve.size() > maxPageSize) {
TaskChunker.chunk(
theIdsToResolve,
maxPageSize,
chunk -> resolveResourceIdentitiesForFhirIdsUsingDatabase(
theRequestPartitionId, chunk, theMapToPopulate));
return;
}
CriteriaBuilder cb = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> criteriaQuery = cb.createTupleQuery();
Root<ResourceTable> from = criteriaQuery.from(ResourceTable.class);
criteriaQuery.multiselect(
from.get("myId"),
from.get("myResourceType"),
from.get("myFhirId"),
from.get("myDeleted"),
from.get("myPartitionIdValue"));
List<Predicate> outerAndPredicates = new ArrayList<>(2);
if (!theRequestPartitionId.isAllPartitions()) {
getOptionalPartitionPredicate(theRequestPartitionId, cb, from).ifPresent(outerAndPredicates::add);
}
// one create one clause per id.
List<Predicate> innerIdPredicates = new ArrayList<>(theIdsToResolve.size());
boolean haveUntypedIds = false;
for (IIdType next : theIdsToResolve) {
if (!next.hasResourceType()) {
haveUntypedIds = true;
}
List<Predicate> idPredicates = new ArrayList<>(2);
if (myStorageSettings.getResourceClientIdStrategy() == JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC
&& next.isIdPartValidLong()) {
Predicate typeCriteria = cb.equal(from.get("myId"), next.getIdPartAsLong());
idPredicates.add(typeCriteria);
} else {
if (isNotBlank(next.getResourceType())) {
Predicate typeCriteria = cb.equal(from.get("myResourceType"), next.getResourceType());
idPredicates.add(typeCriteria);
}
Predicate idCriteria = cb.equal(from.get("myFhirId"), next.getIdPart());
idPredicates.add(idCriteria);
}
innerIdPredicates.add(cb.and(idPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
}
outerAndPredicates.add(cb.or(innerIdPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
criteriaQuery.where(cb.and(outerAndPredicates.toArray(EMPTY_PREDICATE_ARRAY)));
TypedQuery<Tuple> query = myEntityManager.createQuery(criteriaQuery);
List<Tuple> results = query.getResultList();
for (Tuple nextId : results) {
// Check if the nextId has a resource ID. It may have a null resource ID if a commit is still pending.
Long resourcePid = nextId.get(0, Long.class);
String resourceType = nextId.get(1, String.class);
String fhirId = nextId.get(2, String.class);
Date deletedAd = nextId.get(3, Date.class);
Integer partitionId = nextId.get(4, Integer.class);
if (resourcePid != null) {
JpaResourceLookup lookup = new JpaResourceLookup(
resourceType, resourcePid, deletedAd, PartitionablePartitionId.with(partitionId, null));
MemoryCacheService.ForcedIdCacheKey nextKey =
new MemoryCacheService.ForcedIdCacheKey(resourceType, fhirId, theRequestPartitionId);
IIdType id = nextKey.toIdType(myFhirCtx);
theMapToPopulate.put(id, lookup);
if (haveUntypedIds) {
id = nextKey.toIdTypeWithoutResourceType(myFhirCtx);
theMapToPopulate.put(id, lookup);
}
List<IResourceLookup<JpaPid>> valueToCache = theMapToPopulate.get(id);
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, nextKey, valueToCache);
}
}
}
/**
@ -208,7 +387,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
List<String> theIds,
boolean theExcludeDeleted) {
ResolveIdentityMode theMode) {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
Validate.notNull(theIds, "theIds cannot be null");
Validate.isTrue(!theIds.isEmpty(), "theIds must not be empty");
@ -224,7 +403,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
// is a forced id
// we must resolve!
if (myStorageSettings.isDeleteEnabled()) {
retVal = resolveResourceIdentity(theRequestPartitionId, theResourceType, id, theExcludeDeleted)
retVal = resolveResourceIdentity(theRequestPartitionId, theResourceType, id, theMode)
.getPersistentId();
retVals.put(id, retVal);
} else {
@ -249,18 +428,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
return retVals;
}
/**
* Given a resource type and ID, determines the internal persistent ID for the resource.
*
* @throws ResourceNotFoundException If the ID can not be found
*/
@Override
@Nonnull
public JpaPid resolveResourcePersistentIds(
@Nonnull RequestPartitionId theRequestPartitionId, String theResourceType, String theId) {
return resolveResourcePersistentIds(theRequestPartitionId, theResourceType, theId, false);
}
/**
* Given a resource type and ID, determines the internal persistent ID for the resource.
* Optionally filters out deleted resources.
@ -273,11 +440,11 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
String theId,
boolean theExcludeDeleted) {
ResolveIdentityMode theMode) {
Validate.notNull(theId, "theId must not be null");
Map<String, JpaPid> retVal = resolveResourcePersistentIds(
theRequestPartitionId, theResourceType, Collections.singletonList(theId), theExcludeDeleted);
theRequestPartitionId, theResourceType, Collections.singletonList(theId), theMode);
return retVal.get(theId); // should be only one
}
@ -359,11 +526,11 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
idsToCheck.add(nextId);
}
new QueryChunker<IIdType>()
.chunk(
idsToCheck,
SearchBuilder.getMaximumPageSize() / 2,
ids -> doResolvePersistentIds(theRequestPartitionId, ids, retVal));
new QueryChunker<IIdType>();
TaskChunker.chunk(
idsToCheck,
SearchBuilder.getMaximumPageSize() / 2,
ids -> doResolvePersistentIds(theRequestPartitionId, ids, retVal));
}
return retVal;
@ -430,18 +597,30 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
RequestPartitionId theRequestPartitionId, CriteriaBuilder cb, Root<ResourceTable> from) {
if (myPartitionSettings.isAllowUnqualifiedCrossPartitionReference()) {
return Optional.empty();
} else if (theRequestPartitionId.isDefaultPartition() && myPartitionSettings.getDefaultPartitionId() == null) {
Predicate partitionIdCriteria = cb.isNull(from.get("myPartitionIdValue"));
return Optional.of(partitionIdCriteria);
} else if (!theRequestPartitionId.isAllPartitions()) {
} else if (theRequestPartitionId.isAllPartitions()) {
return Optional.empty();
} else {
List<Integer> partitionIds = theRequestPartitionId.getPartitionIds();
partitionIds = replaceDefaultPartitionIdIfNonNull(myPartitionSettings, partitionIds);
if (partitionIds.size() > 1) {
Predicate partitionIdCriteria = from.get("myPartitionIdValue").in(partitionIds);
return Optional.of(partitionIdCriteria);
} else if (partitionIds.size() == 1) {
Predicate partitionIdCriteria = cb.equal(from.get("myPartitionIdValue"), partitionIds.get(0));
return Optional.of(partitionIdCriteria);
if (partitionIds.contains(null)) {
Predicate partitionIdNullCriteria =
from.get("myPartitionIdValue").isNull();
if (partitionIds.size() == 1) {
return Optional.of(partitionIdNullCriteria);
} else {
Predicate partitionIdCriteria = from.get("myPartitionIdValue")
.in(partitionIds.stream().filter(t -> t != null).collect(Collectors.toList()));
return Optional.of(cb.or(partitionIdCriteria, partitionIdNullCriteria));
}
} else {
if (partitionIds.size() > 1) {
Predicate partitionIdCriteria =
from.get("myPartitionIdValue").in(partitionIds);
return Optional.of(partitionIdCriteria);
} else if (partitionIds.size() == 1) {
Predicate partitionIdCriteria = cb.equal(from.get("myPartitionIdValue"), partitionIds.get(0));
return Optional.of(partitionIdCriteria);
}
}
}
return Optional.empty();
@ -475,6 +654,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
return retVal;
}
@SuppressWarnings("OptionalAssignedToNull")
@Override
public Optional<String> translatePidIdToForcedIdWithCache(JpaPid theId) {
// do getIfPresent and then put to avoid doing I/O inside the cache.
@ -492,112 +672,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
return forcedId;
}
private ListMultimap<String, String> organizeIdsByResourceType(Collection<IIdType> theIds) {
ListMultimap<String, String> typeToIds =
MultimapBuilder.hashKeys().arrayListValues().build();
for (IIdType nextId : theIds) {
if (myStorageSettings.getResourceClientIdStrategy() == JpaStorageSettings.ClientIdStrategyEnum.ANY
|| !isValidPid(nextId)) {
if (nextId.hasResourceType()) {
typeToIds.put(nextId.getResourceType(), nextId.getIdPart());
} else {
typeToIds.put("", nextId.getIdPart());
}
}
}
return typeToIds;
}
private Map<String, List<IResourceLookup<JpaPid>>> translateForcedIdToPids(
@Nonnull RequestPartitionId theRequestPartitionId, Collection<IIdType> theId, boolean theExcludeDeleted) {
theId.forEach(id -> Validate.isTrue(id.hasIdPart()));
if (theId.isEmpty()) {
return new HashMap<>();
}
Map<String, List<IResourceLookup<JpaPid>>> retVal = new HashMap<>();
RequestPartitionId requestPartitionId = replaceDefault(theRequestPartitionId);
if (myStorageSettings.getResourceClientIdStrategy() != JpaStorageSettings.ClientIdStrategyEnum.ANY) {
List<Long> pids = theId.stream()
.filter(t -> isValidPid(t))
.map(IIdType::getIdPartAsLong)
.collect(Collectors.toList());
if (!pids.isEmpty()) {
resolvePids(requestPartitionId, pids, retVal);
}
}
// returns a map of resourcetype->id
ListMultimap<String, String> typeToIds = organizeIdsByResourceType(theId);
for (Map.Entry<String, Collection<String>> nextEntry : typeToIds.asMap().entrySet()) {
String nextResourceType = nextEntry.getKey();
Collection<String> nextIds = nextEntry.getValue();
if (!myStorageSettings.isDeleteEnabled()) {
for (Iterator<String> forcedIdIterator = nextIds.iterator(); forcedIdIterator.hasNext(); ) {
String nextForcedId = forcedIdIterator.next();
String nextKey = nextResourceType + "/" + nextForcedId;
IResourceLookup<JpaPid> cachedLookup =
myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
if (cachedLookup != null) {
forcedIdIterator.remove();
retVal.computeIfAbsent(nextForcedId, id -> new ArrayList<>())
.add(cachedLookup);
}
}
}
if (!nextIds.isEmpty()) {
Collection<Object[]> views;
assert isNotBlank(nextResourceType);
if (requestPartitionId.isAllPartitions()) {
views = myResourceTableDao.findAndResolveByForcedIdWithNoType(
nextResourceType, nextIds, theExcludeDeleted);
} else {
if (requestPartitionId.isDefaultPartition()) {
views = myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartitionNull(
nextResourceType, nextIds, theExcludeDeleted);
} else if (requestPartitionId.hasDefaultPartitionId()) {
views = myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartitionIdOrNullPartitionId(
nextResourceType,
nextIds,
requestPartitionId.getPartitionIdsWithoutDefault(),
theExcludeDeleted);
} else {
views = myResourceTableDao.findAndResolveByForcedIdWithNoTypeInPartition(
nextResourceType, nextIds, requestPartitionId.getPartitionIds(), theExcludeDeleted);
}
}
for (Object[] next : views) {
String resourceType = (String) next[0];
Long resourcePid = (Long) next[1];
String forcedId = (String) next[2];
Date deletedAt = (Date) next[3];
Integer partitionId = (Integer) next[4];
LocalDate partitionDate = (LocalDate) next[5];
JpaResourceLookup lookup = new JpaResourceLookup(
resourceType,
resourcePid,
deletedAt,
PartitionablePartitionId.with(partitionId, partitionDate));
retVal.computeIfAbsent(forcedId, id -> new ArrayList<>()).add(lookup);
if (!myStorageSettings.isDeleteEnabled()) {
String key = resourceType + "/" + forcedId;
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, key, lookup);
}
}
}
}
return retVal;
}
public RequestPartitionId replaceDefault(RequestPartitionId theRequestPartitionId) {
if (myPartitionSettings.getDefaultPartitionId() != null) {
if (!theRequestPartitionId.isAllPartitions() && theRequestPartitionId.hasDefaultPartitionId()) {
@ -610,59 +684,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
return theRequestPartitionId;
}
private void resolvePids(
@Nonnull RequestPartitionId theRequestPartitionId,
List<Long> thePidsToResolve,
Map<String, List<IResourceLookup<JpaPid>>> theTargets) {
if (!myStorageSettings.isDeleteEnabled()) {
for (Iterator<Long> forcedIdIterator = thePidsToResolve.iterator(); forcedIdIterator.hasNext(); ) {
Long nextPid = forcedIdIterator.next();
String nextKey = Long.toString(nextPid);
IResourceLookup<JpaPid> cachedLookup =
myMemoryCacheService.getIfPresent(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey);
if (cachedLookup != null) {
forcedIdIterator.remove();
theTargets.computeIfAbsent(nextKey, id -> new ArrayList<>()).add(cachedLookup);
}
}
}
if (!thePidsToResolve.isEmpty()) {
Collection<Object[]> lookup;
if (theRequestPartitionId.isAllPartitions()) {
lookup = myResourceTableDao.findLookupFieldsByResourcePid(thePidsToResolve);
} else {
if (theRequestPartitionId.isDefaultPartition()) {
lookup = myResourceTableDao.findLookupFieldsByResourcePidInPartitionNull(thePidsToResolve);
} else if (theRequestPartitionId.hasDefaultPartitionId()) {
lookup = myResourceTableDao.findLookupFieldsByResourcePidInPartitionIdsOrNullPartition(
thePidsToResolve, theRequestPartitionId.getPartitionIdsWithoutDefault());
} else {
lookup = myResourceTableDao.findLookupFieldsByResourcePidInPartitionIds(
thePidsToResolve, theRequestPartitionId.getPartitionIds());
}
}
lookup.stream()
.map(t -> new JpaResourceLookup(
(String) t[0],
(Long) t[1],
(Date) t[2],
PartitionablePartitionId.with((Integer) t[3], (LocalDate) t[4])))
.forEach(t -> {
String id = t.getPersistentId().toString();
if (!theTargets.containsKey(id)) {
theTargets.put(id, new ArrayList<>());
}
theTargets.get(id).add(t);
if (!myStorageSettings.isDeleteEnabled()) {
String nextKey = t.getPersistentId().toString();
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, t);
}
});
}
}
@Override
public PersistentIdToForcedIdMap<JpaPid> translatePidsToForcedIds(Set<JpaPid> theResourceIds) {
assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
@ -673,7 +694,7 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
List<Long> remainingPids =
thePids.stream().filter(t -> !retVal.containsKey(t)).collect(Collectors.toList());
new QueryChunker<Long>().chunk(remainingPids, t -> {
QueryChunker.chunk(remainingPids, t -> {
List<ResourceTable> resourceEntities = myResourceTableDao.findAllById(t);
for (ResourceTable nextResourceEntity : resourceEntities) {
@ -701,33 +722,39 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
* Pre-cache a PID-to-Resource-ID mapping for later retrieval by {@link #translatePidsToForcedIds(Set)} and related methods
*/
@Override
public void addResolvedPidToForcedId(
JpaPid theJpaPid,
public void addResolvedPidToFhirId(
@Nonnull JpaPid theJpaPid,
@Nonnull RequestPartitionId theRequestPartitionId,
String theResourceType,
@Nullable String theForcedId,
@Nonnull String theResourceType,
@Nonnull String theFhirId,
@Nullable Date theDeletedAt) {
if (theForcedId != null) {
if (theJpaPid.getAssociatedResourceId() == null) {
populateAssociatedResourceId(theResourceType, theForcedId, theJpaPid);
}
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.PID_TO_FORCED_ID,
theJpaPid.getId(),
Optional.of(theResourceType + "/" + theForcedId));
String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theForcedId);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theJpaPid);
} else {
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.PID_TO_FORCED_ID, theJpaPid.getId(), Optional.empty());
if (theJpaPid.getAssociatedResourceId() == null) {
populateAssociatedResourceId(theResourceType, theFhirId, theJpaPid);
}
if (!myStorageSettings.isDeleteEnabled()) {
JpaResourceLookup lookup = new JpaResourceLookup(
theResourceType, theJpaPid.getId(), theDeletedAt, theJpaPid.getPartitionablePartitionId());
String nextKey = theJpaPid.toString();
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.RESOURCE_LOOKUP, nextKey, lookup);
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.PID_TO_FORCED_ID,
theJpaPid.getId(),
Optional.of(theResourceType + "/" + theFhirId));
String key = toForcedIdToPidKey(theRequestPartitionId, theResourceType, theFhirId);
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, theJpaPid);
JpaResourceLookup lookup = new JpaResourceLookup(
theResourceType, theJpaPid.getId(), theDeletedAt, theJpaPid.getPartitionablePartitionId());
MemoryCacheService.ForcedIdCacheKey fhirIdKey =
new MemoryCacheService.ForcedIdCacheKey(theResourceType, theFhirId, theRequestPartitionId);
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, fhirIdKey, List.of(lookup));
// If it's a pure-numeric ID, store it in the cache without a type as well
// so that we can resolve it this way when loading entities for update
if (myStorageSettings.getResourceClientIdStrategy() == JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC
&& isValidLong(theFhirId)) {
MemoryCacheService.ForcedIdCacheKey fhirIdKeyWithoutType =
new MemoryCacheService.ForcedIdCacheKey(null, theFhirId, theRequestPartitionId);
myMemoryCacheService.putAfterCommit(
MemoryCacheService.CacheEnum.RESOURCE_LOOKUP_BY_FORCED_ID, fhirIdKeyWithoutType, List.of(lookup));
}
}
@ -736,19 +763,6 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
myPartitionSettings = thePartitionSettings;
}
public static boolean isValidPid(IIdType theId) {
if (theId == null) {
return false;
}
String idPart = theId.getIdPart();
return isValidPid(idPart);
}
public static boolean isValidPid(String theIdPart) {
return StringUtils.isNumeric(theIdPart);
}
@Override
@Nonnull
public List<JpaPid> getPidsOrThrowException(
@ -764,7 +778,11 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
if (resourceId == null) {
IIdType id = theResource.getIdElement();
try {
retVal = resolveResourcePersistentIds(theRequestPartitionId, id.getResourceType(), id.getIdPart());
retVal = resolveResourceIdentityPid(
theRequestPartitionId,
id.getResourceType(),
id.getIdPart(),
ResolveIdentityMode.includeDeleted().cacheOk());
} catch (ResourceNotFoundException e) {
retVal = null;
}
@ -836,4 +854,23 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
public JpaPid newPidFromStringIdAndResourceName(String thePid, String theResourceName) {
return JpaPid.fromIdAndResourceType(Long.parseLong(thePid), theResourceName);
}
private IIdType newIdType(String theValue) {
IIdType retVal = myFhirCtx.getVersion().newIdType();
retVal.setValue(theValue);
return retVal;
}
public static boolean isValidPid(IIdType theId) {
if (theId == null) {
return false;
}
String idPart = theId.getIdPart();
return isValidPid(idPart);
}
public static boolean isValidPid(String theIdPart) {
return StringUtils.isNumeric(theIdPart);
}
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/mdm/MdmLinkDaoJpaImpl.java
View File

@ -69,6 +69,7 @@ import org.springframework.data.domain.Pageable;
import org.springframework.data.history.Revisions;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.List;
@ -150,6 +151,17 @@ public class MdmLinkDaoJpaImpl implements IMdmLinkDao<JpaPid, MdmLink> {
.collect(Collectors.toList());
}
@Override
public Collection<MdmPidTuple<JpaPid>> resolveGoldenResources(List<JpaPid> theSourcePids) {
return myMdmLinkDao
.expandPidsByGoldenResourcePidsOrSourcePidsAndMatchResult(
JpaPid.toLongList(theSourcePids), MdmMatchResultEnum.MATCH)
.stream()
.map(this::daoTupleToMdmTuple)
.distinct()
.collect(Collectors.toList());
}
@Override
public List<JpaPid> findPidByResourceNameAndThreshold(
String theResourceName, Date theHighThreshold, Pageable thePageable) {

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

@ -92,7 +92,8 @@ public class ExtendedHSearchSearchBuilder {
String theResourceType, SearchParameterMap myParams, ISearchParamRegistry theSearchParamRegistry) {
boolean canUseHibernate = false;
ResourceSearchParams resourceActiveSearchParams = theSearchParamRegistry.getActiveSearchParams(theResourceType);
ResourceSearchParams resourceActiveSearchParams = theSearchParamRegistry.getActiveSearchParams(
theResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
for (String paramName : myParams.keySet()) {
// is this parameter supported?
if (illegalForHibernateSearch(paramName, resourceActiveSearchParams)) {
@ -218,7 +219,8 @@ public class ExtendedHSearchSearchBuilder {
// copy the keys to avoid concurrent modification error
ArrayList<String> paramNames = compileParamNames(searchParameterMap);
ResourceSearchParams activeSearchParams = searchParamRegistry.getActiveSearchParams(resourceType);
ResourceSearchParams activeSearchParams = searchParamRegistry.getActiveSearchParams(
resourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
for (String nextParam : paramNames) {
if (illegalForHibernateSearch(nextParam, activeSearchParams)) {
// ignore magic params handled in JPA

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/HSearchSortHelperImpl.java
View File

@ -151,7 +151,8 @@ public class HSearchSortHelperImpl implements IHSearchSortHelper {
*/
@VisibleForTesting
Optional<RestSearchParameterTypeEnum> getParamType(String theResourceTypeName, String theParamName) {
ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theResourceTypeName);
ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(
theResourceTypeName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
RuntimeSearchParam searchParam = activeSearchParams.get(theParamName);
if (searchParam == null) {
return Optional.empty();

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

@ -267,13 +267,14 @@ public class TermValueSet implements Serializable {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("id", myId)
.append("url", myUrl)
.append(myResource != null ? ("resource=" + myResource.toString()) : ("resource=(null)"))
.append("version", myVersion)
.append("resourcePid", myResourcePid)
.append("name", myName)
.append(myConcepts != null ? ("concepts - size=" + myConcepts.size()) : ("concepts=(null)"))
.append(myConcepts != null ? ("conceptCount=" + myConcepts.size()) : ("concepts=(null)"))
.append("totalConcepts", myTotalConcepts)
.append("totalConceptDesignations", myTotalConceptDesignations)
.append("expansionStatus", myExpansionStatus)
.append(myResource != null ? ("resId=" + myResource) : ("resource=(null)"))
.toString();
}
}

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

@ -181,7 +181,8 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider {
for (String nextResourceType : theResourceTypes) {
StructureDefinition sd = fetchStructureDefinition(nextResourceType);
List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry
.getActiveSearchParams(nextResourceType)
.getActiveSearchParams(
nextResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
.values());
myGenerator.generateResource(writer, sd, parameters, theOperations);
}
@ -198,7 +199,8 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider {
}
if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.SEARCH)) {
List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry
.getActiveSearchParams(nextResourceType)
.getActiveSearchParams(
nextResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
.values());
myGenerator.generateListAccessQuery(writer, parameters, nextResourceType);
myGenerator.generateConnectionAccessQuery(writer, parameters, nextResourceType);

27
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -125,6 +125,33 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
init700();
init720();
init740();
init780();
}
protected void init780() {
final Builder version = forVersion(VersionEnum.V7_8_0);
version.onTable("NPM_PACKAGE_VER")
.addColumn("20241023.10", "PKG_AUTHOR")
.nullable()
.type(ColumnTypeEnum.STRING, 512);
version.onTable("NPM_PACKAGE_VER")
.addColumn("20241023.20", "AUTHOR_UPPER")
.nullable()
.type(ColumnTypeEnum.STRING, 512);
version.onTable("NPM_PACKAGE_VER")
.modifyColumn("20241023.30", "PKG_DESC")
.nullable()
.withType(ColumnTypeEnum.STRING, 512);
version.onTable("NPM_PACKAGE_VER")
.modifyColumn("20241023.40", "DESC_UPPER")
.nullable()
.withType(ColumnTypeEnum.STRING, 512);
version.onTable("NPM_PACKAGE")
.modifyColumn("20241023.50", "PACKAGE_DESC")
.nullable()
.withType(ColumnTypeEnum.STRING, 512);
}
protected void init740() {

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/model/cross/JpaResourceLookup.java
View File

@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.model.cross;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.PartitionablePartitionId;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import java.util.Date;
@ -59,4 +61,14 @@ public class JpaResourceLookup implements IResourceLookup<JpaPid> {
return jpaPid;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("resType", myResourceType)
.append("resPid", myResourcePid)
.append("deletedAt", myDeletedAt)
.append("partId", myPartitionablePartitionId)
.toString();
}
}

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
View File

@ -301,15 +301,10 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
boolean currentVersion =
updateCurrentVersionFlagForAllPackagesBasedOnNewIncomingVersion(packageId, packageVersionId);
String packageDesc = null;
if (npmPackage.description() != null) {
if (npmPackage.description().length() > NpmPackageVersionEntity.PACKAGE_DESC_LENGTH) {
packageDesc = npmPackage.description().substring(0, NpmPackageVersionEntity.PACKAGE_DESC_LENGTH - 4)
+ "...";
} else {
packageDesc = npmPackage.description();
}
}
String packageDesc = truncateStorageString(npmPackage.description());
String packageAuthor = truncateStorageString(npmPackage.getNpm().asString("author"));
if (currentVersion) {
getProcessingMessages(npmPackage)
.add("Marking package " + packageId + "#" + initialPackageVersionId + " as current version");
@ -327,6 +322,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
packageVersion.setPackage(pkg);
packageVersion.setPackageBinary(persistedPackage);
packageVersion.setSavedTime(new Date());
packageVersion.setAuthor(packageAuthor);
packageVersion.setDescription(packageDesc);
packageVersion.setFhirVersionId(npmPackage.fhirVersion());
packageVersion.setFhirVersion(fhirVersion);
@ -625,6 +621,7 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
NpmPackageMetadataJson.Version version = new NpmPackageMetadataJson.Version();
version.setFhirVersion(next.getFhirVersionId());
version.setAuthor(next.getAuthor());
version.setDescription(next.getDescription());
version.setName(next.getPackageId());
version.setVersion(next.getVersionId());
@ -682,7 +679,8 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
retVal.addObject()
.getPackage()
.setName(next.getPackageId())
.setDescription(next.getPackage().getDescription())
.setAuthor(next.getAuthor())
.setDescription(next.getDescription())
.setVersion(next.getVersionId())
.addFhirVersion(next.getFhirVersionId())
.setBytes(next.getPackageSizeBytes());
@ -791,10 +789,21 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
predicates.add(theCb.equal(resources.get("myCanonicalUrl"), thePackageSearchSpec.getResourceUrl()));
}
if (isNotBlank(thePackageSearchSpec.getVersion())) {
String searchTerm = thePackageSearchSpec.getVersion() + "%";
predicates.add(theCb.like(theRoot.get("myVersionId"), searchTerm));
}
if (isNotBlank(thePackageSearchSpec.getDescription())) {
String searchTerm = "%" + thePackageSearchSpec.getDescription() + "%";
searchTerm = StringUtil.normalizeStringForSearchIndexing(searchTerm);
predicates.add(theCb.like(theRoot.get("myDescriptionUpper"), searchTerm));
predicates.add(theCb.like(theCb.upper(theRoot.get("myDescriptionUpper")), searchTerm));
}
if (isNotBlank(thePackageSearchSpec.getAuthor())) {
String searchTerm = "%" + thePackageSearchSpec.getAuthor() + "%";
searchTerm = StringUtil.normalizeStringForSearchIndexing(searchTerm);
predicates.add(theCb.like(theRoot.get("myAuthorUpper"), searchTerm));
}
if (isNotBlank(thePackageSearchSpec.getFhirVersion())) {
@ -816,4 +825,21 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
return (List<String>)
thePackage.getUserData().computeIfAbsent("JpPackageCache_ProcessingMessages", t -> new ArrayList<>());
}
/**
* Truncates a string to {@link NpmPackageVersionEntity#PACKAGE_DESC_LENGTH} which is
* the maximum length used on several columns in {@link NpmPackageVersionEntity}. If the
* string is longer than the maximum allowed, the last 3 characters are replaced with "..."
*/
private static String truncateStorageString(String theInput) {
String retVal = null;
if (theInput != null) {
if (theInput.length() > NpmPackageVersionEntity.PACKAGE_DESC_LENGTH) {
retVal = theInput.substring(0, NpmPackageVersionEntity.PACKAGE_DESC_LENGTH - 4) + "...";
} else {
retVal = theInput;
}
}
return retVal;
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/NpmPackageMetadataJson.java
View File

@ -115,6 +115,9 @@ public class NpmPackageMetadataJson {
@JsonProperty("version")
private String myVersion;
@JsonProperty("author")
private String myAuthor;
@JsonProperty("description")
private String myDescription;
@ -125,6 +128,14 @@ public class NpmPackageMetadataJson {
@JsonProperty("_bytes")
private long myBytes;
public String getAuthor() {
return myAuthor;
}
public void setAuthor(String theAuthor) {
myAuthor = theAuthor;
}
public String getName() {
return myName;
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/NpmPackageSearchResultJson.java
View File

@ -111,6 +111,9 @@ public class NpmPackageSearchResultJson {
@JsonProperty("version")
private String myVersion;
@JsonProperty("author")
private String myAuthor;
@JsonProperty("description")
private String myDescription;
@ -171,5 +174,14 @@ public class NpmPackageSearchResultJson {
}
return this;
}
public String getAuthor() {
return myAuthor;
}
public Package setAuthor(String theAuthor) {
myAuthor = theAuthor;
return this;
}
}
}

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/PackageSearchSpec.java
View File

@ -27,6 +27,8 @@ public class PackageSearchSpec {
private String myResourceUrl;
private CharSequence myDescription;
private String myFhirVersion;
private String myVersion;
private String myAuthor;
public String getFhirVersion() {
return myFhirVersion;
@ -69,4 +71,20 @@ public class PackageSearchSpec {
public void setDescription(CharSequence theDescription) {
myDescription = theDescription;
}
public String getVersion() {
return myVersion;
}
public void setVersion(String theVersion) {
myVersion = theVersion;
}
public void setAuthor(String theAuthor) {
myAuthor = theAuthor;
}
public String getAuthor() {
return myAuthor;
}
}

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/JpaConformanceProviderDstu3.java
View File

@ -190,11 +190,12 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
* global params like _lastUpdated
*/
ResourceSearchParams searchParams;
ResourceSearchParams serverConfigurationActiveSearchParams =
myServerConfiguration.getActiveSearchParams(theResourceName);
ResourceSearchParams serverConfigurationActiveSearchParams = myServerConfiguration.getActiveSearchParams(
theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (mySearchParamRegistry != null) {
searchParams =
mySearchParamRegistry.getActiveSearchParams(theResourceName).makeCopy();
searchParams = mySearchParamRegistry
.getActiveSearchParams(theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
.makeCopy();
if (searchParams == null) {
return ResourceSearchParams.empty(theResourceName);
}
@ -229,8 +230,8 @@ public class JpaConformanceProviderDstu3 extends org.hl7.fhir.dstu3.hapi.rest.se
if (isBlank(otherResourceType)) {
continue;
}
ResourceSearchParams activeSearchParams =
mySearchParamRegistry.getActiveSearchParams(otherResourceType);
ResourceSearchParams activeSearchParams = mySearchParamRegistry.getActiveSearchParams(
otherResourceType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
activeSearchParams.values().stream()
.filter(t -> isNotBlank(t.getName()))
.filter(t -> t.getTargets().contains(resourcename))

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

@ -489,8 +489,13 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc<JpaPid> {
}
if (!Constants.INCLUDE_STAR.equals(paramName)
&& mySearchParamRegistry.getActiveSearchParam(paramType, paramName) == null) {
List<String> validNames = mySearchParamRegistry.getActiveSearchParams(paramType).values().stream()
&& mySearchParamRegistry.getActiveSearchParam(
paramType, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
== null) {
List<String> validNames = mySearchParamRegistry
.getActiveSearchParams(paramType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
.values()
.stream()
.filter(t -> t.getParamType() == RestSearchParameterTypeEnum.REFERENCE)
.map(t -> UrlUtil.sanitizeUrlPart(t.getName()))
.sorted()

98
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/QueryStack.java
View File

@ -318,7 +318,8 @@ public class QueryStack {
}
String targetType = null;
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (theReferenceTargetType != null) {
targetType = theReferenceTargetType;
} else if (param.getTargets().size() > 1) {
@ -334,17 +335,20 @@ public class QueryStack {
+ "' as this parameter as this parameter does not define a target type. Please specify the target type.");
}
RuntimeSearchParam targetSearchParameter = mySearchParamRegistry.getActiveSearchParam(targetType, theChain);
RuntimeSearchParam targetSearchParameter = mySearchParamRegistry.getActiveSearchParam(
targetType, theChain, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (targetSearchParameter == null) {
Collection<String> validSearchParameterNames =
mySearchParamRegistry.getActiveSearchParams(targetType).values().stream()
.filter(t -> t.getParamType() == RestSearchParameterTypeEnum.STRING
|| t.getParamType() == RestSearchParameterTypeEnum.TOKEN
|| t.getParamType() == RestSearchParameterTypeEnum.DATE)
.map(RuntimeSearchParam::getName)
.sorted()
.distinct()
.collect(Collectors.toList());
Collection<String> validSearchParameterNames = mySearchParamRegistry
.getActiveSearchParams(targetType, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
.values()
.stream()
.filter(t -> t.getParamType() == RestSearchParameterTypeEnum.STRING
|| t.getParamType() == RestSearchParameterTypeEnum.TOKEN
|| t.getParamType() == RestSearchParameterTypeEnum.DATE)
.map(RuntimeSearchParam::getName)
.sorted()
.distinct()
.collect(Collectors.toList());
String msg = myFhirContext
.getLocalizer()
.getMessageSanitized(
@ -1007,10 +1011,11 @@ public class QueryStack {
return createPredicateSource(null, Collections.singletonList(param));
}
default:
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(theResourceName, paramName);
RuntimeSearchParam searchParam = mySearchParamRegistry.getActiveSearchParam(
theResourceName, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (searchParam == null) {
Collection<String> validNames =
mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName);
Collection<String> validNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
String msg = myFhirContext
.getLocalizer()
.getMessageSanitized(
@ -1168,13 +1173,14 @@ public class QueryStack {
// Ensure that the name of the search param
// (e.g. the `code` in Patient?_has:Observation:subject:code=sys|val)
// exists on the target resource type.
RuntimeSearchParam owningParameterDef =
mySearchParamRegistry.getRuntimeSearchParam(targetResourceType, paramName);
RuntimeSearchParam owningParameterDef = mySearchParamRegistry.getRuntimeSearchParam(
targetResourceType, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
// Ensure that the name of the back-referenced search param on the target (e.g. the `subject` in
// Patient?_has:Observation:subject:code=sys|val)
// exists on the target resource, or in the top-level Resource resource.
mySearchParamRegistry.getRuntimeSearchParam(targetResourceType, paramReference);
mySearchParamRegistry.getRuntimeSearchParam(
targetResourceType, paramReference, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
IQueryParameterAnd<?> parsedParam = JpaParamUtil.parseQueryParams(
mySearchParamRegistry, myFhirContext, owningParameterDef, paramName, parameters);
@ -1364,7 +1370,7 @@ public class QueryStack {
theRequestPartitionId));
} else {
List<QuantityParam> quantityParams =
theList.stream().map(t -> QuantityParam.toQuantityParam(t)).collect(Collectors.toList());
theList.stream().map(QuantityParam::toQuantityParam).collect(Collectors.toList());
BaseQuantityPredicateBuilder join = null;
boolean normalizedSearchEnabled = myStorageSettings
@ -1372,8 +1378,8 @@ public class QueryStack {
.equals(NormalizedQuantitySearchLevel.NORMALIZED_QUANTITY_SEARCH_SUPPORTED);
if (normalizedSearchEnabled) {
List<QuantityParam> normalizedQuantityParams = quantityParams.stream()
.map(t -> UcumServiceUtil.toCanonicalQuantityOrNull(t))
.filter(t -> t != null)
.map(UcumServiceUtil::toCanonicalQuantityOrNull)
.filter(Objects::nonNull)
.collect(Collectors.toList());
if (normalizedQuantityParams.size() == quantityParams.size()) {
@ -2494,7 +2500,8 @@ public class QueryStack {
RequestDetails theRequest,
RequestPartitionId theRequestPartitionId) {
List<Condition> andPredicates = new ArrayList<>();
RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (nextParamDef != null) {
if (myPartitionSettings.isPartitioningEnabled() && myPartitionSettings.isIncludePartitionInSearchHashes()) {
@ -2701,15 +2708,33 @@ public class QueryStack {
}
} else {
String msg = myFhirContext
.getLocalizer()
.getMessageSanitized(
BaseStorageDao.class,
"invalidSearchParameter",
theParamName,
theResourceName,
mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName));
throw new InvalidRequestException(Msg.code(1223) + msg);
RuntimeSearchParam notEnabledForSearchParam = mySearchParamRegistry.getActiveSearchParam(
theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.ALL);
if (notEnabledForSearchParam == null) {
String msg = myFhirContext
.getLocalizer()
.getMessageSanitized(
BaseStorageDao.class,
"invalidSearchParameter",
theParamName,
theResourceName,
mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
theResourceName,
ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH));
throw new InvalidRequestException(Msg.code(1223) + msg);
} else {
String msg = myFhirContext
.getLocalizer()
.getMessageSanitized(
BaseStorageDao.class,
"invalidSearchParameterNotEnabledForSearch",
theParamName,
theResourceName,
mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
theResourceName,
ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH));
throw new InvalidRequestException(Msg.code(2540) + msg);
}
}
}
}
@ -2740,8 +2765,8 @@ public class QueryStack {
ReferenceParam param = (ReferenceParam) nextAnd.get(0);
if (isNotBlank(param.getChain())) {
String fullName = theParamName + "." + param.getChain();
RuntimeSearchParam fullChainParam =
mySearchParamRegistry.getActiveSearchParam(theResourceName, fullName);
RuntimeSearchParam fullChainParam = mySearchParamRegistry.getActiveSearchParam(
theResourceName, fullName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (fullChainParam != null) {
List<IQueryParameterType> swappedParamTypes = nextAnd.stream()
.map(t -> newParameterInstance(fullChainParam, null, t.getValueAsQueryToken(myFhirContext)))
@ -2808,8 +2833,10 @@ public class QueryStack {
if (indexOnContainedResources) {
return true;
}
RuntimeSearchParam param =
mySearchParamRegistry.getActiveSearchParam(theResourceType, theParameterName);
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
theResourceType,
theParameterName,
ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
return param != null && param.hasUpliftRefchain(t);
});
@ -3049,7 +3076,8 @@ public class QueryStack {
for (String nextTarget : thePreviousSearchParam.getTargets()) {
RuntimeSearchParam nextSearchParam = null;
if (isBlank(theResourceType) || theResourceType.equals(nextTarget)) {
nextSearchParam = mySearchParamRegistry.getActiveSearchParam(nextTarget, nextParamName);
nextSearchParam = mySearchParamRegistry.getActiveSearchParam(
nextTarget, nextParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
}
if (nextSearchParam != null) {
searchParamFound = true;

93
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/SearchBuilder.java
View File

@ -36,6 +36,7 @@ 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.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.config.HapiFhirLocalContainerEntityManagerFactoryBean;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.dao.BaseStorageDao;
@ -49,6 +50,7 @@ import ca.uhn.fhir.jpa.dao.search.ResourceNotFoundInIndexException;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.interceptor.JpaPreResourceAccessDetails;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.IBaseResourceEntity;
@ -84,6 +86,7 @@ import ca.uhn.fhir.rest.api.SortOrderEnum;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.api.server.IPreResourceAccessDetails;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
import ca.uhn.fhir.rest.param.BaseParamWithPrefix;
import ca.uhn.fhir.rest.param.DateParam;
import ca.uhn.fhir.rest.param.DateRangeParam;
@ -117,6 +120,7 @@ import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -554,10 +558,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
throw new InvalidRequestException(Msg.code(2027)
+ "LastN operation is not enabled on this service, can not process this request");
}
return myFulltextSearchSvc.lastN(myParams, theMaximumResults).stream()
.map(lastNResourceId -> myIdHelperService.resolveResourcePersistentIds(
myRequestPartitionId, myResourceName, String.valueOf(lastNResourceId)))
.collect(Collectors.toList());
List<IResourcePersistentId> persistentIds = myFulltextSearchSvc.lastN(myParams, theMaximumResults);
return persistentIds.stream().map(t -> (JpaPid) t).collect(Collectors.toList());
} else {
throw new InvalidRequestException(
Msg.code(2033) + "LastN operation is not enabled on this service, can not process this request");
@ -578,7 +580,13 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
idParamValue = idParm.getValue();
}
pid = myIdHelperService.resolveResourcePersistentIds(myRequestPartitionId, myResourceName, idParamValue);
pid = myIdHelperService
.resolveResourceIdentity(
myRequestPartitionId,
myResourceName,
idParamValue,
ResolveIdentityMode.includeDeleted().cacheOk())
.getPersistentId();
}
return myFulltextSearchSvc.everything(myResourceName, myParams, pid, theRequestDetails);
}
@ -600,37 +608,46 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
/**
* Combs through the params for any _id parameters and extracts the PIDs for them
*
* @param theTargetPids
*/
private void extractTargetPidsFromIdParams(Set<Long> theTargetPids) {
// get all the IQueryParameterType objects
// for _id -> these should all be StringParam values
HashSet<String> ids = new HashSet<>();
HashSet<IIdType> ids = new HashSet<>();
List<List<IQueryParameterType>> params = myParams.get(IAnyResource.SP_RES_ID);
for (List<IQueryParameterType> paramList : params) {
for (IQueryParameterType param : paramList) {
String id;
if (param instanceof StringParam) {
// we expect all _id values to be StringParams
ids.add(((StringParam) param).getValue());
id = ((StringParam) param).getValue();
} else if (param instanceof TokenParam) {
ids.add(((TokenParam) param).getValue());
id = ((TokenParam) param).getValue();
} else {
// we do not expect the _id parameter to be a non-string value
throw new IllegalArgumentException(
Msg.code(1193) + "_id parameter must be a StringParam or TokenParam");
}
IIdType idType = myContext.getVersion().newIdType();
if (id.contains("/")) {
idType.setValue(id);
} else {
idType.setValue(myResourceName + "/" + id);
}
ids.add(idType);
}
}
// fetch our target Pids
// this will throw if an id is not found
Map<String, JpaPid> idToPid = myIdHelperService.resolveResourcePersistentIds(
myRequestPartitionId, myResourceName, new ArrayList<>(ids));
Map<IIdType, IResourceLookup<JpaPid>> idToIdentity = myIdHelperService.resolveResourceIdentities(
myRequestPartitionId,
new ArrayList<>(ids),
ResolveIdentityMode.failOnDeleted().noCacheUnlessDeletesDisabled());
// add the pids to targetPids
for (JpaPid pid : idToPid.values()) {
theTargetPids.add(pid.getId());
for (IResourceLookup pid : idToIdentity.values()) {
theTargetPids.add((Long) pid.getPersistentId().getId());
}
}
@ -676,8 +693,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
|| theParams.getSort() != null
|| theParams.keySet().contains(Constants.PARAM_HAS)
|| isPotentiallyContainedReferenceParameterExistsAtRoot(theParams)) {
List<RuntimeSearchParam> activeComboParams =
mySearchParamRegistry.getActiveComboSearchParams(myResourceName, theParams.keySet());
List<RuntimeSearchParam> activeComboParams = mySearchParamRegistry.getActiveComboSearchParams(
myResourceName, theParams.keySet(), ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (activeComboParams.isEmpty()) {
sqlBuilder.setNeedResourceTableRoot(true);
}
@ -952,8 +969,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
theQueryStack.addSortOnLastUpdated(ascending);
} else {
RuntimeSearchParam param =
mySearchParamRegistry.getActiveSearchParam(myResourceName, theSort.getParamName());
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
myResourceName, theSort.getParamName(), ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
/*
* If we have a sort like _sort=subject.name and we have an
@ -977,8 +994,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
referenceParamTargetType = referenceParam.substring(0, colonIdx);
referenceParam = referenceParam.substring(colonIdx + 1);
}
RuntimeSearchParam outerParam =
mySearchParamRegistry.getActiveSearchParam(myResourceName, referenceParam);
RuntimeSearchParam outerParam = mySearchParamRegistry.getActiveSearchParam(
myResourceName, referenceParam, ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
if (outerParam == null) {
throwInvalidRequestExceptionForUnknownSortParameter(myResourceName, referenceParam);
} else if (outerParam.hasUpliftRefchain(targetParam)) {
@ -986,8 +1003,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
if (referenceParamTargetType != null && !referenceParamTargetType.equals(nextTargetType)) {
continue;
}
RuntimeSearchParam innerParam =
mySearchParamRegistry.getActiveSearchParam(nextTargetType, targetParam);
RuntimeSearchParam innerParam = mySearchParamRegistry.getActiveSearchParam(
nextTargetType,
targetParam,
ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
if (innerParam != null) {
param = innerParam;
break;
@ -1021,7 +1040,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
}
if (param == null) {
param = mySearchParamRegistry.getActiveSearchParam(myResourceName, paramName);
param = mySearchParamRegistry.getActiveSearchParam(
myResourceName, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
}
if (param == null) {
@ -1100,8 +1120,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
}
private void throwInvalidRequestExceptionForUnknownSortParameter(String theResourceName, String theParamName) {
Collection<String> validSearchParameterNames =
mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(theResourceName);
Collection<String> validSearchParameterNames = mySearchParamRegistry.getValidSearchParameterNamesIncludingMeta(
theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SORT);
String msg = myContext
.getLocalizer()
.getMessageSanitized(
@ -1564,7 +1584,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
String paramName = nextInclude.getParamName();
if (isNotBlank(paramName)) {
param = mySearchParamRegistry.getActiveSearchParam(resType, paramName);
param = mySearchParamRegistry.getActiveSearchParam(
resType, paramName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
} else {
param = null;
}
@ -1903,7 +1924,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
// in this context, so let's just assume it could be anything.
targetResourceTypes = possibleTypes;
} else {
for (var next : mySearchParamRegistry.getActiveSearchParams(myResourceName).values().stream()
for (var next : mySearchParamRegistry
.getActiveSearchParams(myResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH)
.values()
.stream()
.filter(t -> t.getParamType().equals(RestSearchParameterTypeEnum.REFERENCE))
.collect(Collectors.toList())) {
@ -1986,16 +2010,16 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
QueryStack theQueryStack, @Nonnull SearchParameterMap theParams, RequestDetails theRequest) {
RuntimeSearchParam comboParam = null;
List<String> comboParamNames = null;
List<RuntimeSearchParam> exactMatchParams =
mySearchParamRegistry.getActiveComboSearchParams(myResourceName, theParams.keySet());
List<RuntimeSearchParam> exactMatchParams = mySearchParamRegistry.getActiveComboSearchParams(
myResourceName, theParams.keySet(), ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (!exactMatchParams.isEmpty()) {
comboParam = exactMatchParams.get(0);
comboParamNames = new ArrayList<>(theParams.keySet());
}
if (comboParam == null) {
List<RuntimeSearchParam> candidateComboParams =
mySearchParamRegistry.getActiveComboSearchParams(myResourceName);
List<RuntimeSearchParam> candidateComboParams = mySearchParamRegistry.getActiveComboSearchParams(
myResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
for (RuntimeSearchParam nextCandidate : candidateComboParams) {
List<String> nextCandidateParamNames =
JpaParamUtil.resolveComponentParameters(mySearchParamRegistry, nextCandidate).stream()
@ -2064,8 +2088,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
IQueryParameterType nextOr = nextPermutation.get(paramIndex);
String nextOrValue = nextOr.getValueAsQueryToken(myContext);
RuntimeSearchParam nextParamDef =
mySearchParamRegistry.getActiveSearchParam(myResourceName, nextParamName);
RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
myResourceName, nextParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (theComboParam.getComboSearchParamType() == ComboSearchParamType.NON_UNIQUE) {
if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.STRING) {
nextOrValue = StringUtil.normalizeStringForSearchIndexing(nextOrValue);
@ -2180,7 +2204,8 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
// Reference params are only eligible for using a composite index if they
// are qualified
RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(myResourceName, nextParamName);
RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
myResourceName, nextParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.REFERENCE) {
ReferenceParam param = (ReferenceParam) nextValues.get(0).get(0);
if (isBlank(param.getResourceType())) {

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ComboUniqueSearchParameterPredicateBuilder.java
View File

@ -20,6 +20,7 @@
package ca.uhn.fhir.jpa.search.builder.predicate;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedComboStringUnique;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import com.healthmarketscience.sqlbuilder.Condition;
@ -35,7 +36,9 @@ public class ComboUniqueSearchParameterPredicateBuilder extends BaseSearchParamP
* Constructor
*/
public ComboUniqueSearchParameterPredicateBuilder(SearchQueryBuilder theSearchSqlBuilder) {
super(theSearchSqlBuilder, theSearchSqlBuilder.addTable("HFJ_IDX_CMP_STRING_UNIQ"));
super(
theSearchSqlBuilder,
theSearchSqlBuilder.addTable(ResourceIndexedComboStringUnique.HFJ_IDX_CMP_STRING_UNIQ));
myColumnString = getTable().addColumn("IDX_STRING");
}

49
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceIdPredicateBuilder.java
View File

@ -21,24 +21,27 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.dao.predicate.SearchFilterParser;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import ca.uhn.fhir.jpa.util.QueryParameterUtils;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.TokenParamModifier;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import com.healthmarketscience.sqlbuilder.Condition;
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
import jakarta.annotation.Nullable;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.instance.model.api.IIdType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
@ -68,9 +71,8 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
Set<JpaPid> allOrPids = null;
SearchFilterParser.CompareOperation defaultOperation = SearchFilterParser.CompareOperation.eq;
boolean allIdsAreForcedIds = true;
for (List<? extends IQueryParameterType> nextValue : theValues) {
Set<JpaPid> orPids = new HashSet<>();
Set<IIdType> ids = new LinkedHashSet<>();
boolean haveValue = false;
for (IQueryParameterType next : nextValue) {
String value = next.getValueAsQueryToken(getFhirContext());
@ -78,21 +80,14 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
value = value.substring(1);
}
IdType valueAsId = new IdType(value);
if (isNotBlank(value)) {
if (!myIdHelperService.idRequiresForcedId(valueAsId.getIdPart()) && allIdsAreForcedIds) {
allIdsAreForcedIds = false;
}
haveValue = true;
try {
boolean excludeDeleted = true;
JpaPid pid = myIdHelperService.resolveResourcePersistentIds(
theRequestPartitionId, theResourceName, valueAsId.getIdPart(), excludeDeleted);
orPids.add(pid);
} catch (ResourceNotFoundException e) {
// This is not an error in a search, it just results in no matches
ourLog.debug("Resource ID {} was requested but does not exist", valueAsId.getIdPart());
if (!value.contains("/")) {
value = theResourceName + "/" + value;
}
IIdType id = getFhirContext().getVersion().newIdType();
id.setValue(value);
ids.add(id);
}
if (next instanceof TokenParam) {
@ -101,6 +96,20 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
}
}
}
Set<JpaPid> orPids = new HashSet<>();
// We're joining this to a query that will explicitly ask for non-deleted,
// so we really only want the PID and can safely cache (even if a previously
// deleted status was cached, since it might now be undeleted)
Map<IIdType, IResourceLookup<JpaPid>> resolvedPids = myIdHelperService.resolveResourceIdentities(
theRequestPartitionId,
ids,
ResolveIdentityMode.includeDeleted().cacheOk());
for (IResourceLookup<JpaPid> lookup : resolvedPids.values()) {
orPids.add(lookup.getPersistentId());
}
if (haveValue) {
if (allOrPids == null) {
allOrPids = orPids;
@ -122,17 +131,19 @@ public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
List<Long> resourceIds = JpaPid.toLongList(allOrPids);
if (theSourceJoinColumn == null) {
BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable(!allIdsAreForcedIds);
BaseJoiningPredicateBuilder queryRootTable = super.getOrCreateQueryRootTable(true);
Condition predicate;
switch (operation) {
default:
case eq:
predicate = queryRootTable.createPredicateResourceIds(false, resourceIds);
return queryRootTable.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
break;
case ne:
predicate = queryRootTable.createPredicateResourceIds(true, resourceIds);
return queryRootTable.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
break;
}
predicate = queryRootTable.combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
return predicate;
} else {
DbColumn resIdColumn = getResourceIdColumn(theSourceJoinColumn);
return QueryParameterUtils.toEqualToOrInPredicate(

23
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/ResourceLinkPredicateBuilder.java
View File

@ -497,7 +497,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
RuntimeSearchParam param = null;
if (!isMeta) {
param = mySearchParamRegistry.getActiveSearchParam(nextType, chain);
param = mySearchParamRegistry.getActiveSearchParam(
nextType, chain, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (param == null) {
ourLog.debug("Type {} doesn't have search param {}", nextType, param);
continue;
@ -586,8 +587,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
resourceTypes = determineResourceTypes(Collections.singleton(theResourceName), theParamName);
if (resourceTypes.isEmpty()) {
RuntimeSearchParam searchParamByName =
mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
RuntimeSearchParam searchParamByName = mySearchParamRegistry.getActiveSearchParam(
theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (searchParamByName == null) {
throw new InternalErrorException(Msg.code(1244) + "Could not find parameter " + theParamName);
}
@ -659,7 +660,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
if (linkIndex == -1) {
Set<Class<? extends IBaseResource>> resourceTypes = new HashSet<>();
for (String resourceName : theResourceNames) {
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(resourceName, theParamNameChain);
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
resourceName, theParamNameChain, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (param != null && param.hasTargets()) {
Set<String> targetTypes = param.getTargets();
@ -675,7 +677,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
String paramNameTail = theParamNameChain.substring(linkIndex + 1);
Set<String> targetResourceTypeNames = new HashSet<>();
for (String resourceName : theResourceNames) {
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(resourceName, paramNameHead);
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
resourceName, paramNameHead, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (param != null && param.hasTargets()) {
targetResourceTypeNames.addAll(param.getTargets());
@ -687,7 +690,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
public List<String> createResourceLinkPaths(
String theResourceName, String theParamName, List<String> theParamQualifiers) {
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(theResourceName, theParamName);
RuntimeSearchParam param = mySearchParamRegistry.getActiveSearchParam(
theResourceName, theParamName, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (param != null) {
List<String> path = param.getPathsSplit();
@ -718,7 +722,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
? theParamQualifiers.subList(1, theParamQualifiers.size())
: List.of();
param = mySearchParamRegistry.getActiveSearchParam(theResourceName, paramNameHead);
param = mySearchParamRegistry.getActiveSearchParam(
theResourceName, paramNameHead, ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
if (param != null) {
Set<String> tailPaths = param.getTargets().stream()
.filter(t -> isBlank(qualifier) || qualifier.equals(t))
@ -832,8 +837,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
subquery.addFromTable(getTable());
String resourceType = theParams.getResourceTablePredicateBuilder().getResourceType();
RuntimeSearchParam paramDefinition =
mySearchParamRegistry.getRuntimeSearchParam(resourceType, theParams.getParamName());
RuntimeSearchParam paramDefinition = mySearchParamRegistry.getRuntimeSearchParam(
resourceType, theParams.getParamName(), ISearchParamRegistry.SearchParamLookupContextEnum.SEARCH);
List<String> pathList = paramDefinition.getPathsSplitForResourceType(resourceType);
Condition subQueryCondition = ComboCondition.and(

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/sql/ColumnTupleObject.java
View File

@ -1,3 +1,22 @@
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2024 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%
*/
package ca.uhn.fhir.jpa.search.builder.sql;
import com.healthmarketscience.common.util.AppendableExt;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/InstanceReindexServiceImpl.java
View File

@ -158,7 +158,7 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
return myVersionCanonicalizer.parametersFromCanonical(retValCanonical);
}
@SuppressWarnings({"unchecked", "rawtypes"})
@SuppressWarnings({"rawtypes"})
@Nonnull
private Parameters reindexInTransaction(RequestDetails theRequestDetails, IIdType theResourceId) {
StopWatch sw = new StopWatch();
@ -441,7 +441,8 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
private void fillInParamNames(
ResourceTable theEntity, Collection<SearchParamPresentEntity> theTarget, String theResourceName) {
Map<Long, String> hashes = new HashMap<>();
ResourceSearchParams searchParams = mySearchParamRegistry.getActiveSearchParams(theResourceName);
ResourceSearchParams searchParams = mySearchParamRegistry.getActiveSearchParams(
theResourceName, ISearchParamRegistry.SearchParamLookupContextEnum.ALL);
for (RuntimeSearchParam next : searchParams.values()) {
hashes.put(
SearchParamPresentEntity.calculateHashPresence(

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
@ -382,8 +383,11 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
// Note that this creates the TermCodeSystem and TermCodeSystemVersion entities if needed
IIdType csId = myTerminologyVersionAdapterSvc.createOrUpdateCodeSystem(theCodeSystemResource, theRequest);
JpaPid codeSystemResourcePid = myIdHelperService.resolveResourcePersistentIds(
RequestPartitionId.allPartitions(), csId.getResourceType(), csId.getIdPart());
JpaPid codeSystemResourcePid = myIdHelperService.resolveResourceIdentityPid(
RequestPartitionId.allPartitions(),
csId.getResourceType(),
csId.getIdPart(),
ResolveIdentityMode.includeDeleted().cacheOk());
ResourceTable resource = myResourceTableDao.getOne(codeSystemResourcePid.getId());
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());

50
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermReadSvcImpl.java
View File

@ -34,6 +34,7 @@ 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.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.config.HibernatePropertiesProvider;
import ca.uhn.fhir.jpa.config.util.ConnectionPoolInfoProvider;
import ca.uhn.fhir.jpa.config.util.IConnectionPoolInfoProvider;
@ -470,7 +471,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
myCodeSystemCurrentVersionCache.invalidateAll();
}
public void deleteValueSetForResource(ResourceTable theResourceTable) {
public Optional<TermValueSet> deleteValueSetForResource(ResourceTable theResourceTable) {
// Get existing entity so it can be deleted.
Optional<TermValueSet> optionalExistingTermValueSetById =
myTermValueSetDao.findByResourcePid(theResourceTable.getId());
@ -481,8 +482,19 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
ourLog.info("Deleting existing TermValueSet[{}] and its children...", existingTermValueSet.getId());
deletePreCalculatedValueSetContents(existingTermValueSet);
myTermValueSetDao.deleteById(existingTermValueSet.getId());
/*
* If we're updating an existing ValueSet within a transaction, we need to make
* sure to manually flush now since otherwise we'll try to create a new
* TermValueSet entity and fail with a constraint error on the URL, since
* this one won't be deleted yet
*/
myTermValueSetDao.flush();
ourLog.info("Done deleting existing TermValueSet[{}] and its children.", existingTermValueSet.getId());
}
return optionalExistingTermValueSetById;
}
private void deletePreCalculatedValueSetContents(TermValueSet theValueSet) {
@ -2081,10 +2093,11 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
}
private JpaPid getValueSetResourcePersistentId(ValueSet theValueSet) {
return myIdHelperService.resolveResourcePersistentIds(
return myIdHelperService.resolveResourceIdentityPid(
RequestPartitionId.allPartitions(),
theValueSet.getIdElement().getResourceType(),
theValueSet.getIdElement().getIdPart());
theValueSet.getIdElement().getIdPart(),
ResolveIdentityMode.includeDeleted().cacheOk());
}
protected IValidationSupport.CodeValidationResult validateCodeIsInPreExpandedValueSet(
@ -2527,6 +2540,13 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
@Override
@Transactional
public void storeTermValueSet(ResourceTable theResourceTable, ValueSet theValueSet) {
// If we're in a transaction, we need to flush now so that we can correctly detect
// duplicates if there are multiple ValueSets in the same TX with the same URL
// (which is an error, but we need to catch it). It'd be better to catch this by
// inspecting the URLs in the bundle or something, since flushing hurts performance
// but it's not expected that loading valuesets is going to be a huge high frequency
// thing so it probably doesn't matter
myEntityManager.flush();
ValidateUtil.isTrueOrThrowInvalidRequest(theResourceTable != null, "No resource supplied");
if (isPlaceholder(theValueSet)) {
@ -2552,7 +2572,7 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
termValueSet.setName(theValueSet.hasName() ? theValueSet.getName() : null);
// Delete version being replaced
deleteValueSetForResource(theResourceTable);
Optional<TermValueSet> deletedTrmValueSet = deleteValueSetForResource(theResourceTable);
/*
* Do the upload.
@ -2560,11 +2580,17 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
String url = termValueSet.getUrl();
String version = termValueSet.getVersion();
Optional<TermValueSet> optionalExistingTermValueSetByUrl;
if (version != null) {
optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndVersion(url, version);
if (deletedTrmValueSet.isPresent()
&& Objects.equals(deletedTrmValueSet.get().getUrl(), url)
&& Objects.equals(deletedTrmValueSet.get().getVersion(), version)) {
// If we just deleted the valueset marker, we don't need to check if it exists
// in the database
optionalExistingTermValueSetByUrl = Optional.empty();
} else {
optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
optionalExistingTermValueSetByUrl = getTermValueSet(version, url);
}
if (optionalExistingTermValueSetByUrl.isEmpty()) {
myTermValueSetDao.save(termValueSet);
@ -2602,6 +2628,16 @@ public class TermReadSvcImpl implements ITermReadSvc, IHasScheduledJobs {
}
}
private Optional<TermValueSet> getTermValueSet(String version, String url) {
Optional<TermValueSet> optionalExistingTermValueSetByUrl;
if (version != null) {
optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndVersion(url, version);
} else {
optionalExistingTermValueSetByUrl = myTermValueSetDao.findTermValueSetByUrlAndNullVersion(url);
}
return optionalExistingTermValueSetByUrl;
}
@Override
@Transactional
public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(

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

@ -35,11 +35,11 @@ import java.util.stream.Stream;
*/
public class QueryChunker<T> extends TaskChunker<T> {
public void chunk(Collection<T> theInput, Consumer<List<T>> theBatchConsumer) {
public static <T> void chunk(Collection<T> theInput, Consumer<List<T>> theBatchConsumer) {
chunk(theInput, SearchBuilder.getMaximumPageSize(), theBatchConsumer);
}
public Stream<List<T>> chunk(Stream<T> theStream) {
public static <T> Stream<List<T>> chunk(Stream<T> theStream) {
return chunk(theStream, SearchBuilder.getMaximumPageSize());
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/export/svc/JpaBulkExportProcessorTest.java
View File

@ -423,7 +423,7 @@ public class JpaBulkExportProcessorTest {
// when
RuntimeSearchParam searchParam = new RuntimeSearchParam(new IdType("1"), "", "", "", "", RestSearchParameterTypeEnum.STRING, Collections.singleton(""), Collections.singleton(""), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE, Collections.singleton(""));
when(mySearchParamRegistry.getActiveSearchParam(any(), any())).thenReturn(searchParam);
when(mySearchParamRegistry.getActiveSearchParam(any(), any(), any())).thenReturn(searchParam);
// expandAllPatientPidsFromGroup
when(myDaoRegistry.getResourceDao(eq("Group")))
.thenReturn(groupDao);

81
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/index/IdHelperServiceTest.java
View File

@ -3,36 +3,39 @@ package ca.uhn.fhir.jpa.dao.index;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
import ca.uhn.fhir.jpa.api.svc.ResolveIdentityMode;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.dao.JpaPid;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import jakarta.persistence.EntityManager;
import jakarta.persistence.Tuple;
import jakarta.persistence.criteria.Path;
import jakarta.persistence.criteria.Root;
import jakarta.persistence.TypedQuery;
import jakarta.persistence.criteria.CriteriaQuery;
import org.hibernate.sql.results.internal.TupleImpl;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.ArgumentMatchers;
import org.mockito.Answers;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.Spy;
import org.mockito.junit.jupiter.MockitoExtension;
import java.util.Date;
import java.util.List;
import java.util.Map;
import static org.assertj.core.api.Assertions.assertThat;
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.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.lenient;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@ -40,7 +43,6 @@ import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.mockito.Mockito.eq;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class IdHelperServiceTest {
@ -60,29 +62,33 @@ public class IdHelperServiceTest {
@Mock
private MemoryCacheService myMemoryCacheService;
@Mock
@Mock(answer = Answers.RETURNS_DEEP_STUBS)
private EntityManager myEntityManager;
@Mock
private PartitionSettings myPartitionSettings;
@BeforeEach
@Mock
private TypedQuery myTypedQuery;
@BeforeEach
void setUp() {
myHelperSvc.setDontCheckActiveTransactionForUnitTest(true);
// lenient because some tests require this setup, and others do not
lenient().doReturn(true).when(myStorageSettings).isDeleteEnabled();
lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY).when(myStorageSettings).getResourceClientIdStrategy();
}
@Test
public void testResolveResourcePersistentIds() {
lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY).when(myStorageSettings).getResourceClientIdStrategy();
//prepare params
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionIdAndName(1, "Partition-A");
String resourceType = "Patient";
Long id = 123L;
List<String> ids = List.of(String.valueOf(id));
boolean theExcludeDeleted = false;
ResolveIdentityMode mode = ResolveIdentityMode.includeDeleted().noCacheUnlessDeletesDisabled();
//prepare results
Patient expectedPatient = new Patient();
@ -91,19 +97,21 @@ public class IdHelperServiceTest {
// configure mock behaviour
when(myStorageSettings.isDeleteEnabled()).thenReturn(true);
final ResourceNotFoundException resourceNotFoundException = assertThrows(ResourceNotFoundException.class, () -> myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, theExcludeDeleted));
final ResourceNotFoundException resourceNotFoundException = assertThrows(ResourceNotFoundException.class, () -> myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, mode));
assertEquals("HAPI-2001: Resource Patient/123 is not known", resourceNotFoundException.getMessage());
}
@Test
public void testResolveResourcePersistentIdsDeleteFalse() {
lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ANY).when(myStorageSettings).getResourceClientIdStrategy();
//prepare Params
RequestPartitionId requestPartitionId = RequestPartitionId.fromPartitionIdAndName(1, "Partition-A");
Long id = 123L;
String resourceType = "Patient";
List<String> ids = List.of(String.valueOf(id));
String forcedId = "(all)/" + resourceType + "/" + id;
boolean theExcludeDeleted = false;
ResolveIdentityMode mode = ResolveIdentityMode.includeDeleted().noCacheUnlessDeletesDisabled();
//prepare results
Patient expectedPatient = new Patient();
@ -112,7 +120,7 @@ public class IdHelperServiceTest {
// configure mock behaviour
when(myStorageSettings.isDeleteEnabled()).thenReturn(false);
Map<String, JpaPid> actualIds = myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, theExcludeDeleted);
Map<String, JpaPid> actualIds = myHelperSvc.resolveResourcePersistentIds(requestPartitionId, resourceType, ids, mode);
//verifyResult
assertFalse(actualIds.isEmpty());
@ -120,20 +128,35 @@ public class IdHelperServiceTest {
}
private Root<ResourceTable> getMockedFrom() {
@SuppressWarnings("unchecked")
Path<Object> path = mock(Path.class);
@SuppressWarnings("unchecked")
Root<ResourceTable> from = mock(Root.class);
when(from.get(ArgumentMatchers.<String>any())).thenReturn(path);
return from;
}
private List<Tuple> getMockedTupleList(Long idNumber, String resourceType, String id) {
Tuple tuple = mock(Tuple.class);
when(tuple.get(eq(0), eq(Long.class))).thenReturn(idNumber);
when(tuple.get(eq(1), eq(String.class))).thenReturn(resourceType);
when(tuple.get(eq(2), eq(String.class))).thenReturn(id);
return List.of(tuple);
}
@Test
public void testResolveResourceIdentity_defaultFunctionality(){
lenient().doReturn(JpaStorageSettings.ClientIdStrategyEnum.ALPHANUMERIC).when(myStorageSettings).getResourceClientIdStrategy();
RequestPartitionId partitionId = RequestPartitionId.fromPartitionIdAndName(1, "partition");
String resourceType = "Patient";
String resourceForcedId = "AAA";
Object[] tuple = new Object[] {
1L,
"Patient",
"AAA",
new Date(),
null
};
when(myEntityManager.createQuery(any(CriteriaQuery.class))).thenReturn(myTypedQuery);
when(myTypedQuery.getResultList()).thenReturn(List.of(
new TupleImpl(null, tuple)
));
IResourceLookup<JpaPid> result = myHelperSvc.resolveResourceIdentity(partitionId, resourceType, resourceForcedId, ResolveIdentityMode.includeDeleted().noCacheUnlessDeletesDisabled());
assertEquals(tuple[0], result.getPersistentId().getId());
assertEquals(tuple[1], result.getResourceType());
assertEquals(tuple[3], result.getDeleted());
}
}

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

@ -23,6 +23,8 @@ import java.util.Optional;
import static org.assertj.core.api.Assertions.assertThat;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@ -68,13 +70,13 @@ class HSearchSortHelperImplTest {
void testGetParamType() {
SortSpec sortSpec = new SortSpec();
sortSpec.setParamName("_tag");
when(mockSearchParamRegistry.getActiveSearchParams("Observation")).thenReturn(mockResourceSearchParams);
when(mockSearchParamRegistry.getActiveSearchParams(eq("Observation"), any())).thenReturn(mockResourceSearchParams);
when(mockResourceSearchParams.get("the-param-name")).thenReturn(mockRuntimeSearchParam);
when(mockRuntimeSearchParam.getParamType()).thenReturn(RestSearchParameterTypeEnum.TOKEN);
Optional<RestSearchParameterTypeEnum> paramType = tested.getParamType("Observation", "the-param-name");
verify(mockSearchParamRegistry, times(1)).getActiveSearchParams("Observation");
verify(mockSearchParamRegistry, times(1)).getActiveSearchParams(eq("Observation"), any());
verify(mockResourceSearchParams, times(1)).get("the-param-name");
assertFalse(paramType.isEmpty());
}

2
hapi-fhir-jpaserver-elastic-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>7.7.0-SNAPSHOT</version>
<version>7.7.7-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

5
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseR4SearchLastN.java
View File

@ -72,7 +72,7 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
protected static IIdType patient2Id = null;
// Using static variables including the flag below so that we can initalize the database and indexes once
// (all of the tests only read from the DB and indexes and so no need to re-initialze them for each test).
private static Calendar observationDate = new GregorianCalendar();
private static final Calendar observationDate = new GregorianCalendar();
protected final String observationCd0 = "code0";
protected final String observationCd1 = "code1";
protected final String observationCd2 = "code2";
@ -120,9 +120,10 @@ abstract public class BaseR4SearchLastN extends BaseJpaTest {
// enabled to also create extended lucene index during creation of test data
boolean hsearchSaved = myStorageSettings.isAdvancedHSearchIndexing();
myStorageSettings.setAdvancedHSearchIndexing(true);
myStorageSettings.setDeleteEnabled(false);
// Using a static flag to ensure that test data and elasticsearch index is only created once.
// Creating this data and the index is time consuming and as such want to avoid having to repeat for each test.
// Creating this data and the index is time-consuming and as such want to avoid having to repeat for each test.
// Normally would use a static @BeforeClass method for this purpose, but Autowired objects cannot be accessed in static methods.
Patient pt = new Patient();

7
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java
View File

@ -120,9 +120,10 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
ourLog.info("Queries:\n * " + String.join("\n * ", queries));
// 1 query to resolve the subject PIDs
// 3 queries to actually perform the search
// 1 query to lookup up Search from cache, and 2 chunked queries to retrieve resources by PID.
assertThat(queries).hasSize(6);
assertThat(queries).hasSize(7);
// The first chunked query should have a full complement of PIDs
StringBuilder firstQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
@ -130,7 +131,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
firstQueryPattern.append(",'[0-9]+'");
}
firstQueryPattern.append("\\).*");
assertThat(queries.get(4)).matches(firstQueryPattern.toString());
assertThat(queries.get(5)).matches(firstQueryPattern.toString());
// the second chunked query should be padded with "-1".
StringBuilder secondQueryPattern = new StringBuilder(".*RES_ID in \\('[0-9]+'");
@ -141,7 +142,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
secondQueryPattern.append(",'-1'");
}
secondQueryPattern.append("\\).*");
assertThat(queries.get(5)).matches(secondQueryPattern.toString());
assertThat(queries.get(6)).matches(secondQueryPattern.toString());
}

4
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
View File

@ -79,6 +79,10 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
// Set chunk size to 50
SearchBuilder.setMaxPageSizeForTest(50);
// Run once to fill caches
toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(), null));
// Actually test
myCaptureQueriesListener.clear();
List<String> results = toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(), null));
assertThat(results).hasSize(75);

3
hapi-fhir-jpaserver-elastic-test-utilities/src/test/java/ca/uhn/fhir/jpa/term/ValueSetExpansionR4ElasticsearchIT.java
View File

@ -277,8 +277,7 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest implements I
myTermCodeSystemStorageSvc.storeNewCodeSystemVersion(codeSystem, codeSystemVersion,
new SystemRequestDetails(), Collections.singletonList(valueSet), Collections.emptyList());
// myTerminologyDeferredStorageSvc.saveAllDeferred();
await().atMost(10, SECONDS).until(() -> {
await().atMost(20, SECONDS).until(() -> {
myTerminologyDeferredStorageSvc.saveDeferred();
return myTerminologyDeferredStorageSvc.isStorageQueueEmpty(true);
});

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