Merge branch 'rel_5_7'

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3371-fix-error-indexing-contained-lucene.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 3371
+title: "Enhanced Lucene Indexing failed when indexing contained resources.
+   Contained resources are not indexed in Lucene/Elasticsearch, but this no longer causes an exception."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/search/ExtendedLuceneSearchBuilder.java

@@ -60,7 +60,7 @@ public class ExtendedLuceneSearchBuilder {
 				// each and clause may have a different modifier, so split down to the ORs
 				.flatMap(andList -> andList.getValue().stream())
 				.flatMap(Collection::stream)
-				.anyMatch(this::isParamSupported);
+				.anyMatch(this::isParamTypeSupported);
 	}
 
 	/**
@@ -68,7 +68,7 @@ public class ExtendedLuceneSearchBuilder {
 	 * <p>
 	 * NOTE - keep this in sync with addAndConsumeAdvancedQueryClauses() below.
 	 */
-	private boolean isParamSupported(IQueryParameterType param) {
+	private boolean isParamTypeSupported(IQueryParameterType param) {
 		String modifier = StringUtils.defaultString(param.getQueryParameterQualifier(), EMPTY_MODIFIER);
 		if (param instanceof TokenParam) {
 			switch (modifier) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchWithElasticSearchIT.java

@@ -19,6 +19,7 @@ import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
+import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
 import ca.uhn.fhir.jpa.search.reindex.IResourceReindexingSvc;
@@ -135,7 +136,6 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 	@BeforeEach
 	public void beforePurgeDatabase() {
 		purgeDatabase(myDaoConfig, mySystemDao, myResourceReindexingSvc, mySearchCoordinatorSvc, mySearchParamRegistry, myBulkDataExportSvc);
-		myDaoConfig.setAdvancedLuceneIndexing(true);
 	}
 
 	@Override
@@ -149,14 +149,16 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 	}
 
 	@BeforeEach
-	public void enableContains() {
+	public void enableContainsAndLucene() {
-		myContainsSettings = myDaoConfig.isAllowContainsSearches();
 		myDaoConfig.setAllowContainsSearches(true);
+		myDaoConfig.setAdvancedLuceneIndexing(true);
 	}
 
 	@AfterEach
 	public void restoreContains() {
-		myDaoConfig.setAllowContainsSearches(myContainsSettings);
+		DaoConfig defaultConfig = new DaoConfig();
+		myDaoConfig.setAllowContainsSearches(defaultConfig.isAllowContainsSearches());
+		myDaoConfig.setAdvancedLuceneIndexing(defaultConfig.isAdvancedLuceneIndexing());
 	}
 
 	@Test
@@ -513,6 +515,48 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 		assertThat(message, toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(iIdTypes)));
 	}
 
+	@Nested
+	public class WithContainedIndexing {
+		@BeforeEach
+		public void enableContains() {
+			// we don't support chained or contained yet, but turn it on to test we don't blow up.
+			myDaoConfig.getModelConfig().setIndexOnContainedResources(true);
+			myDaoConfig.getModelConfig().setIndexOnContainedResourcesRecursively(true);
+		}
+
+		@AfterEach
+		public void restoreContains() {
+			ModelConfig defaultModelConfig = new ModelConfig();
+			myDaoConfig.getModelConfig().setIndexOnContainedResources(defaultModelConfig.isIndexOnContainedResources());
+			myDaoConfig.getModelConfig().setIndexOnContainedResourcesRecursively(defaultModelConfig.isIndexOnContainedResourcesRecursively());
+		}
+		/**
+		 * We were throwing when indexing contained.
+		 * https://github.com/hapifhir/hapi-fhir/issues/3371
+		 */
+		@Test
+		public void ignoreContainedResources_noError() {
+			// given
+			String json =
+				"{" +
+					"\"resourceType\": \"Observation\"," +
+					"\"contained\": [{" +
+					"\"resourceType\": \"Patient\"," +
+					"\"id\": \"contained-patient\"," +
+					"\"name\": [{ \"family\": \"Smith\"}]" +
+					"}]," +
+					"\"subject\": { \"reference\": \"#contained-patient\" }" +
+					"}";
+			Observation o = myFhirCtx.newJsonParser().parseResource(Observation.class, json);
+
+			myObservationDao.create(o, mySrd).getId().toUnqualifiedVersionless();
+
+			// no error.
+		}
+	}
+
+
+
 	@Test
 	public void testExpandWithIsAInExternalValueSet() {
 		createExternalCsAndLocalVs();
@@ -529,7 +573,6 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
 		assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
 	}
 
-
 	@Test
 	public void testExpandWithFilter() {
 		createExternalCsAndLocalVs();

hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/search/ExtendedLuceneIndexData.java

@@ -28,6 +28,8 @@ import org.hibernate.search.engine.backend.document.DocumentElement;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.function.BiConsumer;
+
 import java.util.Date;
 
 /**
@@ -47,14 +49,24 @@ public class ExtendedLuceneIndexData {
 		this.myFhirContext = theFhirContext;
 	}
 
+	private <V> BiConsumer<String, V> ifNotContained(BiConsumer<String, V> theIndexWriter) {
+		return (s,v) -> {
+			// Ignore contained resources for now.
+			if (!s.contains(".")) {
+				theIndexWriter.accept(s,v);
+			}
+		};
+	}
 	public void writeIndexElements(DocumentElement theDocument) {
 		HibernateSearchIndexWriter indexWriter = HibernateSearchIndexWriter.forRoot(myFhirContext, theDocument);
 
+		ourLog.debug("Writing JPA index to Hibernate Search");
+
+		mySearchParamStrings.forEach(ifNotContained(indexWriter::writeStringIndex));
+		mySearchParamTokens.forEach(ifNotContained(indexWriter::writeTokenIndex));
+		mySearchParamLinks.forEach(ifNotContained(indexWriter::writeReferenceIndex));
 		// TODO MB Use RestSearchParameterTypeEnum to define templates.
-		mySearchParamStrings.forEach(indexWriter::writeStringIndex);
+		mySearchParamDates.forEach(ifNotContained(indexWriter::writeDateIndex));
-		mySearchParamTokens.forEach(indexWriter::writeTokenIndex);
-		mySearchParamLinks.forEach(indexWriter::writeReferenceIndex);
-		mySearchParamDates.forEach(indexWriter::writeDateIndex);
 	}
 
 	public void addStringIndexData(String theSpName, String theText) {