Adding cleaning up of the resources owned by the terminology service.

terminology/src/main/java/au/csiro/pathling/fhir/DefaultTerminologyClient.java

@@ -17,6 +17,7 @@
 
 package au.csiro.pathling.fhir;
 
+import au.csiro.pathling.utilities.ResourceCloser;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.gclient.IOperationUntypedWithInput;
 import javax.annotation.Nonnull;
@@ -29,16 +30,19 @@
 import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.r4.model.UriType;
 import org.hl7.fhir.r4.model.ValueSet;
+import java.io.Closeable;
 
 /**
  * An implementation of {@link TerminologyClient} that uses cacheable GET requests.
  */
-class DefaultTerminologyClient implements TerminologyClient {
+class DefaultTerminologyClient extends ResourceCloser implements TerminologyClient {
 
   @Nonnull
   final IGenericClient fhirClient;
 
-  DefaultTerminologyClient(@Nonnull final IGenericClient fhirClient) {
+  DefaultTerminologyClient(@Nonnull final IGenericClient fhirClient, @Nonnull final Closeable...
+      resourcesToAdopt) {
+    super(resourcesToAdopt);
     this.fhirClient = fhirClient;
   }
 

terminology/src/main/java/au/csiro/pathling/fhir/TerminologyClient.java

@@ -39,14 +39,15 @@
 import org.hl7.fhir.r4.model.ValueSet;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import java.io.Closeable;
 
 /**
  * The client interface to FHIR terminology operations.
  *
  * @author John Grimes
  * @author Piotr Szul
  */
-public interface TerminologyClient {
+public interface TerminologyClient extends Closeable {
 
   Logger log = LoggerFactory.getLogger(TerminologyClient.class);
 
@@ -56,8 +57,7 @@ public interface TerminologyClient {
    * @param version the version of the code system to validate against
    * @param code the code to validate
    * @return a {@link Parameters} resource
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/valueset-operation-validate-code.html">ValueSet/$validate-code</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/valueset-operation-validate-code.html">ValueSet/$validate-code</a>
    */
   @Operation(name = "$validate-code", type = ValueSet.class, idempotent = true)
   @Nonnull
@@ -76,8 +76,7 @@ Parameters validateCode(
    * @param version the version of the code system to validate against
    * @param code the code to validate
    * @return an {@link IOperationUntypedWithInput} that can be customized and executed later
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/valueset-operation-validate-code.html">ValueSet/$validate-code</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/valueset-operation-validate-code.html">ValueSet/$validate-code</a>
    */
   IOperationUntypedWithInput<Parameters> buildValidateCode(@Nonnull UriType url,
       @Nonnull UriType system,
@@ -91,8 +90,7 @@ IOperationUntypedWithInput<Parameters> buildValidateCode(@Nonnull UriType url,
    * @param reverse if true, the translation will be reversed
    * @param target the URL of the value set within which the translation is sought
    * @return a {@link Parameters} resource
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/operation-conceptmap-translate.html">ConceptMap/$translate</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/operation-conceptmap-translate.html">ConceptMap/$translate</a>
    */
   @Operation(name = "$translate", type = CodeSystem.class, idempotent = true)
   @Nonnull
@@ -115,8 +113,7 @@ Parameters translate(
    * @param reverse if true, the translation will be reversed
    * @param target the URL of the value set within which the translation is sought
    * @return an {@link IOperationUntypedWithInput} that can be customized and executed later
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/operation-conceptmap-translate.html">ConceptMap/$translate</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/operation-conceptmap-translate.html">ConceptMap/$translate</a>
    */
   @Nonnull
   IOperationUntypedWithInput<Parameters> buildTranslate(@Nonnull UriType url,
@@ -130,8 +127,7 @@ IOperationUntypedWithInput<Parameters> buildTranslate(@Nonnull UriType url,
    * @param system the system of the codes being tested
    * @param version the version of the code system that the codes are from
    * @return a {@link Parameters} resource
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/codesystem-operation-subsumes.html">CodeSystem/$subsumes</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/codesystem-operation-subsumes.html">CodeSystem/$subsumes</a>
    */
   @Operation(name = "$subsumes", type = CodeSystem.class, idempotent = true)
   @Nonnull
@@ -150,8 +146,7 @@ Parameters subsumes(
    * @param system the system of the codes being tested
    * @param version the version of the code system that the codes are from
    * @return an {@link IOperationUntypedWithInput} that can be customized and executed later
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/codesystem-operation-subsumes.html">CodeSystem/$subsumes</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/codesystem-operation-subsumes.html">CodeSystem/$subsumes</a>
    */
   @Nonnull
   IOperationUntypedWithInput<Parameters> buildSubsumes(@Nonnull CodeType codeA,
@@ -163,8 +158,7 @@ IOperationUntypedWithInput<Parameters> buildSubsumes(@Nonnull CodeType codeA,
    * @param code the code to lookup
    * @param property the property or properties to be returned in the response
    * @return a {@link Parameters} resource
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/codesystem-operation-lookup.html">CodeSystem/$lookup</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/codesystem-operation-lookup.html">CodeSystem/$lookup</a>
    */
   @Operation(name = "$lookup", type = CodeSystem.class, idempotent = true)
   @Nonnull
@@ -183,8 +177,7 @@ Parameters lookup(
    * @param code the code to lookup
    * @param property the property or properties to be returned in the response
    * @return an {@link IOperationUntypedWithInput} that can be customized and executed later
-   * @see <a
-   * href="https://www.hl7.org/fhir/R4/codesystem-operation-lookup.html">CodeSystem/$lookup</a>
+   * @see <a href="https://www.hl7.org/fhir/R4/codesystem-operation-lookup.html">CodeSystem/$lookup</a>
    */
   @Nonnull
   IOperationUntypedWithInput<Parameters> buildLookup(@Nonnull UriType system,
@@ -223,9 +216,13 @@ static TerminologyClient build(@Nonnull final FhirContext fhirContext,
     // sending them.
     final TerminologyAuthConfiguration authConfig = terminologyConfiguration.getAuthentication();
     if (authConfig.isEnabled()) {
-      genericClient.registerInterceptor(new ClientAuthInterceptor(authConfig));
+      final ClientAuthInterceptor clientAuthInterceptor = new ClientAuthInterceptor(authConfig);
+      genericClient.registerInterceptor(clientAuthInterceptor);
+      // pass the client auth interceptor as a resource to close when the client is closed
+      return new DefaultTerminologyClient(genericClient, clientAuthInterceptor);
+    } else {
+      return new DefaultTerminologyClient(genericClient);
     }
-    return new DefaultTerminologyClient(genericClient);
   }
 
   @Nonnull

terminology/src/main/java/au/csiro/pathling/terminology/BaseTerminologyService.java

@@ -17,12 +17,10 @@
 
 package au.csiro.pathling.terminology;
 
-import static java.util.Objects.nonNull;
-
 import au.csiro.pathling.fhir.TerminologyClient;
+import au.csiro.pathling.utilities.ResourceCloser;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import java.io.Closeable;
-import java.io.IOException;
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 
@@ -31,18 +29,15 @@
  *
  * @author John Grimes
  */
-public abstract class BaseTerminologyService implements TerminologyService, Closeable {
+public abstract class BaseTerminologyService extends ResourceCloser implements TerminologyService {
 
   @Nonnull
   protected final TerminologyClient terminologyClient;
 
-  @Nullable
-  protected final Closeable toClose;
-
   public BaseTerminologyService(@Nonnull final TerminologyClient terminologyClient,
-      @Nullable final Closeable toClose) {
+      @Nonnull final Closeable... resourcesToClose) {
+    super(resourcesToClose);
     this.terminologyClient = terminologyClient;
-    this.toClose = toClose;
   }
 
   /**
@@ -64,12 +59,4 @@ public static <ResultType> ResultType handleError(@Nonnull final BaseServerRespo
       throw e;
     }
   }
-
-  @Override
-  public void close() throws IOException {
-    if (nonNull(toClose)) {
-      toClose.close();
-    }
-  }
-
 }

terminology/src/main/java/au/csiro/pathling/terminology/DefaultTerminologyService.java

@@ -49,10 +49,10 @@
 public class DefaultTerminologyService extends BaseTerminologyService {
 
   public DefaultTerminologyService(@Nonnull final TerminologyClient terminologyClient,
-      @Nullable final Closeable toClose) {
-    super(terminologyClient, toClose);
+      @Nonnull final Closeable... resourcesToClose) {
+    super(terminologyClient, resourcesToClose);
   }
-
+  
   @Override
   public boolean validateCode(@Nonnull final String valueSetUrl, @Nonnull final Coding coding) {
     final ValidateCodeParameters parameters = new ValidateCodeParameters(valueSetUrl,

terminology/src/main/java/au/csiro/pathling/terminology/DefaultTerminologyServiceFactory.java

@@ -97,19 +97,21 @@ private TerminologyService createService() {
       // If caching is enabled and storage type is disk, use a persistent caching terminology 
       // service implementation.
       log.debug("Creating PersistentCachingTerminologyService with cache config: {}", cacheConfig);
-      return new PersistentCachingTerminologyService(terminologyClient, httpClient, cacheConfig);
+      return new PersistentCachingTerminologyService(terminologyClient, cacheConfig, httpClient,
+          terminologyClient);
 
     } else if (cacheConfig.isEnabled() && cacheConfig.getStorageType().equals(
         HttpClientCachingStorageType.MEMORY)) {
       // If caching is enabled and storage type is memory, use an in-memory caching terminology
       // service implementation.
       log.debug("Creating InMemoryCachingTerminologyService with cache config: {}", cacheConfig);
-      return new InMemoryCachingTerminologyService(terminologyClient, httpClient, cacheConfig);
+      return new InMemoryCachingTerminologyService(terminologyClient, cacheConfig, httpClient,
+          terminologyClient);
 
     } else {
       // If caching is disabled, use a terminology service implementation that does not cache.
       log.debug("Creating DefaultTerminologyService with no caching");
-      return new DefaultTerminologyService(terminologyClient, httpClient);
+      return new DefaultTerminologyService(terminologyClient, httpClient, terminologyClient);
     }
   }
 

terminology/src/main/java/au/csiro/pathling/terminology/caching/CachingTerminologyService.java

@@ -91,11 +91,12 @@ public abstract class CachingTerminologyService extends BaseTerminologyService {
 
   @SuppressWarnings("unchecked")
   public CachingTerminologyService(@Nonnull final TerminologyClient terminologyClient,
-      @Nullable final Closeable toClose,
-      @Nonnull final HttpClientCachingConfiguration configuration) {
-    super(terminologyClient, toClose);
+      @Nonnull final HttpClientCachingConfiguration configuration,
+      @Nonnull final Closeable... resourcesToClose) {
+    super(terminologyClient, resourcesToClose);
     this.configuration = configuration;
-    cacheManager = buildCacheManager();
+    // register manager as a closeable resource
+    cacheManager = registerResource(buildCacheManager());
     validateCodeCache = (Cache<Integer, TerminologyResult<Boolean>>) buildCache(cacheManager,
         VALIDATE_CODE_CACHE_NAME);
     subsumesCache = (Cache<Integer, TerminologyResult<ConceptSubsumptionOutcome>>) buildCache(

terminology/src/main/java/au/csiro/pathling/terminology/caching/InMemoryCachingTerminologyService.java

@@ -21,7 +21,6 @@
 import au.csiro.pathling.fhir.TerminologyClient;
 import java.io.Closeable;
 import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
 import org.infinispan.Cache;
 import org.infinispan.configuration.cache.Configuration;
 import org.infinispan.configuration.cache.ConfigurationBuilder;
@@ -37,9 +36,9 @@
 public class InMemoryCachingTerminologyService extends CachingTerminologyService {
 
   public InMemoryCachingTerminologyService(@Nonnull final TerminologyClient terminologyClient,
-      @Nullable final Closeable toClose,
-      @Nonnull final HttpClientCachingConfiguration configuration) {
-    super(terminologyClient, toClose, configuration);
+      @Nonnull final HttpClientCachingConfiguration configuration,
+      @Nonnull final Closeable... resourcesToClose) {
+    super(terminologyClient, configuration, resourcesToClose);
   }
 
   @Override

terminology/src/main/java/au/csiro/pathling/terminology/caching/PersistentCachingTerminologyService.java

@@ -24,7 +24,7 @@
 import java.io.Closeable;
 import java.nio.file.Path;
 import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
+import lombok.extern.slf4j.Slf4j;
 import org.infinispan.Cache;
 import org.infinispan.commons.marshall.JavaSerializationMarshaller;
 import org.infinispan.configuration.cache.Configuration;
@@ -42,15 +42,16 @@
  *
  * @author John Grimes
  */
+@Slf4j
 public class PersistentCachingTerminologyService extends CachingTerminologyService {
 
   private static final String DATA_DIRECTORY = "data";
   private static final String INDEX_DIRECTORY = "index";
 
   public PersistentCachingTerminologyService(@Nonnull final TerminologyClient terminologyClient,
-      @Nullable final Closeable toClose,
-      @Nonnull final HttpClientCachingConfiguration configuration) {
-    super(terminologyClient, toClose, configuration);
+      @Nonnull final HttpClientCachingConfiguration configuration,
+      @Nonnull final Closeable... resourcesToClose) {
+    super(terminologyClient, configuration, resourcesToClose);
   }
 
   @Override

terminology/src/test/java/au/csiro/pathling/terminology/DefaultTerminologyServiceTest.java

@@ -99,7 +99,7 @@ private static Parameters translation(@Nonnull final Translation... entries) {
   void setUp() {
     terminologyClient = mock(TerminologyClient.class);
     terminologyService = new DefaultTerminologyService(
-        terminologyClient, null);
+        terminologyClient);
   }
 
   @Test

utilities/pom.xml

@@ -67,6 +67,10 @@
       <artifactId>scala-library</artifactId>
       <scope>provided</scope>
     </dependency>
+    <dependency>
+      <groupId>commons-io</groupId>
+      <artifactId>commons-io</artifactId>
+    </dependency>
 
     <dependency>
       <groupId>org.junit.jupiter</groupId>
@@ -84,13 +88,13 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>commons-io</groupId>
-      <artifactId>commons-io</artifactId>
+      <groupId>com.google.code.gson</groupId>
+      <artifactId>gson</artifactId>
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>com.google.code.gson</groupId>
-      <artifactId>gson</artifactId>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-core</artifactId>
       <scope>test</scope>
     </dependency>
   </dependencies>