Merging master into working branch to resolve conflicts.

# Conflicts:
#	src/changes/changes.xml

README.md

@@ -17,5 +17,3 @@ http://hapi.fhir.org/
 This project is Open Source, licensed under the Apache Software License 2.0.
 
 Please see [this wiki page](https://github.com/jamesagnew/hapi-fhir/wiki/Getting-Help) for information on where to get help with HAPI FHIR. Please see [Smile CDR](https://smilecdr.com) for information on commercial support.
-
----

azure-pipelines.yml

@@ -1,7 +1,4 @@
-# Starter pipeline
+# HAPI FHIR Build Pipeline
-# Start with a minimal pipeline that you can customize to build and deploy your code.
-# Add steps that build, run tests, deploy, and more:
-# https://aka.ms/yaml
 
 variables:
   MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
@@ -13,7 +10,6 @@ trigger:
 pool:
   vmImage: 'ubuntu-latest'
 
-
 jobs:
   - job: Build
     timeoutInMinutes: 360
@@ -23,37 +19,37 @@ jobs:
           key: maven
           path: $(MAVEN_CACHE_FOLDER)
           displayName: Cache Maven local repo
-
       - task: Maven@3
         inputs:
-          #mavenPomFile: 'pom.xml' 
+          goals: 'clean install'
-          goals: 'clean install' # Optional
+          # These are Maven CLI options (and show up in the build logs) - "-nsu"=Don't update snapshots. We can remove this when Maven OSS is more healthy
-          options: '-P ALLMODULES,JACOCO'
+          options: '-P ALLMODULES,JACOCO -nsu'
-          #publishJUnitResults: true 
+          # These are JVM options (and don't show up in the build logs)
-          #testResultsFiles: '**/surefire-reports/TEST-*.xml' # Required when publishJUnitResults == True
+          mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS -Duser.timezone=America/Toronto'
-          #testRunTitle: # Optional
-          #codeCoverageToolOption: 'None' # Optional. Options: none, cobertura, jaCoCo. Enabling code coverage inserts the `clean` goal into the Maven goals list when Maven runs.
-          #codeCoverageClassFilter: # Optional. Comma-separated list of filters to include or exclude classes from collecting code coverage. For example: +:com.*,+:org.*,-:my.app*.*
-          #codeCoverageClassFilesDirectories: # Optional
-          #codeCoverageSourceDirectories: # Optional
-          #codeCoverageFailIfEmpty: false # Optional
-          #javaHomeOption: 'JDKVersion' # Options: jDKVersion, path
-          #jdkVersionOption: 'default' # Optional. Options: default, 1.11, 1.10, 1.9, 1.8, 1.7, 1.6
-          #jdkDirectory: # Required when javaHomeOption == Path
-          #jdkArchitectureOption: 'x64' # Optional. Options: x86, x64
-          #mavenVersionOption: 'Default' # Options: default, path
-          #mavenDirectory: # Required when mavenVersionOption == Path
-          #mavenSetM2Home: false # Required when mavenVersionOption == Path
-          mavenOptions: '-Xmx2048m $(MAVEN_OPTS) -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat=HH:mm:ss,SSS' # Optional
-          #mavenAuthenticateFeed: false 
-          #effectivePomSkip: false 
-          #sonarQubeRunAnalysis: false 
-          #sqMavenPluginVersionChoice: 'latest' # Required when sonarQubeRunAnalysis == True# Options: latest, pom
-          #checkStyleRunAnalysis: false # Optional
-          #pmdRunAnalysis: false # Optional
-          #findBugsRunAnalysis: false # Optional
-
       - script: bash <(curl https://codecov.io/bash) -t $(CODECOV_TOKEN)
         displayName: 'codecov'
 
 
+# Potential Additional Maven3 Options:
+#publishJUnitResults: true
+#testResultsFiles: '**/surefire-reports/TEST-*.xml' # Required when publishJUnitResults == True
+#testRunTitle: # Optional
+#codeCoverageToolOption: 'None' # Optional. Options: none, cobertura, jaCoCo. Enabling code coverage inserts the `clean` goal into the Maven goals list when Maven runs.
+#codeCoverageClassFilter: # Optional. Comma-separated list of filters to include or exclude classes from collecting code coverage. For example: +:com.*,+:org.*,-:my.app*.*
+#codeCoverageClassFilesDirectories: # Optional
+#codeCoverageSourceDirectories: # Optional
+#codeCoverageFailIfEmpty: false # Optional
+#javaHomeOption: 'JDKVersion' # Options: jDKVersion, path
+#jdkVersionOption: 'default' # Optional. Options: default, 1.11, 1.10, 1.9, 1.8, 1.7, 1.6
+#jdkDirectory: # Required when javaHomeOption == Path
+#jdkArchitectureOption: 'x64' # Optional. Options: x86, x64
+#mavenVersionOption: 'Default' # Options: default, path
+#mavenDirectory: # Required when mavenVersionOption == Path
+#mavenSetM2Home: false # Required when mavenVersionOption == Path
+#mavenAuthenticateFeed: false
+#effectivePomSkip: false
+#sonarQubeRunAnalysis: false
+#sqMavenPluginVersionChoice: 'latest' # Required when sonarQubeRunAnalysis == True# Options: latest, pom
+#checkStyleRunAnalysis: false # Optional
+#pmdRunAnalysis: false # Optional
+#findBugsRunAnalysis: false # Optional

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/json/GsonStructure.java

@@ -52,15 +52,6 @@ public class GsonStructure implements JsonLikeStructure {
 		super();
 	}
 	
-	public GsonStructure (JsonObject json) {
-		super();
-		setNativeObject(json);
-	}
-	public GsonStructure (JsonArray json) {
-		super();
-		setNativeArray(json);
-	}
-	
 	public void setNativeObject (JsonObject json) {
 		this.rootType = ROOT_TYPE.OBJECT;
 		this.nativeRoot = json;
@@ -111,8 +102,7 @@ public class GsonStructure implements JsonLikeStructure {
 			if (nextInt == '{') {
 				JsonObject root = gson.fromJson(pbr, JsonObject.class);
 				setNativeObject(root);
-			} else
+			} else if (nextInt == '[') {
-			if (nextInt == '[') {
 				JsonArray root = gson.fromJson(pbr, JsonArray.class);
 				setNativeArray(root);
 			}

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/OperationOutcomeUtil.java

@@ -108,9 +108,13 @@ public class OperationOutcomeUtil {
 		if (theOutcome == null) {
 			return false;
 		}
+		return getIssueCount(theCtx, theOutcome) > 0;
+	}
+
+	public static int getIssueCount(FhirContext theCtx, IBaseOperationOutcome theOutcome) {
 		RuntimeResourceDefinition ooDef = theCtx.getResourceDefinition(theOutcome);
 		BaseRuntimeChildDefinition issueChild = ooDef.getChildByName("issue");
-		return issueChild.getAccessor().getValues(theOutcome).size() > 0;
+		return issueChild.getAccessor().getValues(theOutcome).size();
 	}
 
 	public static IBaseOperationOutcome newInstance(FhirContext theCtx) {
@@ -152,5 +156,4 @@ public class OperationOutcomeUtil {
 			locationChild.getMutator().addValue(theIssue, locationElem);
 		}
 	}
-
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/Search.java

@@ -53,21 +53,6 @@ public class Search implements ICachedSearchDetails, Serializable {
 	private static final int FAILURE_MESSAGE_LENGTH = 500;
 	private static final long serialVersionUID = 1L;
 	private static final Logger ourLog = LoggerFactory.getLogger(Search.class);
-
-	@Override
-	public String toString() {
-		return new ToStringBuilder(this)
-			.append("myLastUpdatedHigh", myLastUpdatedHigh)
-			.append("myLastUpdatedLow", myLastUpdatedLow)
-			.append("myNumFound", myNumFound)
-			.append("myNumBlocked", myNumBlocked)
-			.append("myStatus", myStatus)
-			.append("myTotalCount", myTotalCount)
-			.append("myUuid", myUuid)
-			.append("myVersion", myVersion)
-			.toString();
-	}
-
 	@Temporal(TemporalType.TIMESTAMP)
 	@Column(name = "CREATED", nullable = false, updatable = false)
 	private Date myCreated;
@@ -139,6 +124,20 @@ public class Search implements ICachedSearchDetails, Serializable {
 		super();
 	}
 
+	@Override
+	public String toString() {
+		return new ToStringBuilder(this)
+			.append("myLastUpdatedHigh", myLastUpdatedHigh)
+			.append("myLastUpdatedLow", myLastUpdatedLow)
+			.append("myNumFound", myNumFound)
+			.append("myNumBlocked", myNumBlocked)
+			.append("myStatus", myStatus)
+			.append("myTotalCount", myTotalCount)
+			.append("myUuid", myUuid)
+			.append("myVersion", myVersion)
+			.toString();
+	}
+
 	public int getNumBlocked() {
 		return myNumBlocked != null ? myNumBlocked : 0;
 	}
@@ -351,8 +350,8 @@ public class Search implements ICachedSearchDetails, Serializable {
 		return myVersion;
 	}
 
-	public SearchParameterMap getSearchParameterMap() {
+	public Optional<SearchParameterMap> getSearchParameterMap() {
-		return SerializationUtils.deserialize(mySearchParameterMap);
+		return Optional.ofNullable(mySearchParameterMap).map(t -> SerializationUtils.deserialize(mySearchParameterMap));
 	}
 
 	public void setSearchParameterMap(SearchParameterMap theSearchParameterMap) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java

@@ -173,4 +173,11 @@ public class TermCodeSystemVersion implements Serializable {
 			"Version ID exceeds maximum length (" + MAX_VERSION_LENGTH + "): " + length(theCodeSystemDisplayName));
 		myCodeSystemDisplayName = theCodeSystemDisplayName;
 	}
+
+	public TermConcept addConcept() {
+		TermConcept concept = new TermConcept();
+		concept.setCodeSystemVersion(this);
+		getConcepts().add(concept);
+		return concept;
+	}
 }

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

@@ -28,6 +28,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 
 import javax.annotation.Nullable;
 import java.util.List;
+import java.util.Optional;
 
 public interface ISearchCoordinatorSvc {
 
@@ -37,4 +38,10 @@ public interface ISearchCoordinatorSvc {
 
 	IBundleProvider registerSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, CacheControlDirective theCacheControlDirective, @Nullable RequestDetails theRequestDetails);
 
+	/**
+	 * Fetch the total number of search results for the given currently executing search, if one is currently executing and
+	 * the total is known. Will return empty otherwise
+	 */
+	Optional<Integer> getSearchTotal(String theUuid);
+
 }

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

@@ -191,12 +191,12 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		if (mySearchEntity == null) {
 			ensureDependenciesInjected();
 
-			Optional<Search> search = mySearchCacheSvc.fetchByUuid(myUuid);
+			Optional<Search> searchOpt = mySearchCacheSvc.fetchByUuid(myUuid);
-			if (!search.isPresent()) {
+			if (!searchOpt.isPresent()) {
 				return false;
 			}
 
-			setSearchEntity(search.get());
+			setSearchEntity(searchOpt.get());
 
 			ourLog.trace("Retrieved search with version {} and total {}", mySearchEntity.getVersion(), mySearchEntity.getTotalCount());
 
@@ -292,12 +292,18 @@ public class PersistedJpaBundleProvider implements IBundleProvider {
 		SearchCoordinatorSvcImpl.verifySearchHasntFailedOrThrowInternalErrorException(mySearchEntity);
 
 		Integer size = mySearchEntity.getTotalCount();
-		if (size == null) {
+		if (size != null) {
-			return null;
-		}
 			return Math.max(0, size);
 		}
 
+		if (mySearchEntity.getSearchType() == SearchTypeEnum.HISTORY) {
+			return null;
+		} else {
+			return mySearchCoordinatorSvc.getSearchTotal(myUuid).orElse(null);
+		}
+
+	}
+
 	// Note: Leave as protected, HSPC depends on this
 	@SuppressWarnings("WeakerAccess")
 	protected List<IBaseResource> toResourceList(ISearchBuilder theSearchBuilder, List<Long> thePids) {

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

@@ -62,6 +62,8 @@ public class PersistedJpaSearchFirstPageBundleProvider extends PersistedJpaBundl
 	public List<IBaseResource> getResources(int theFromIndex, int theToIndex) {
 		SearchCoordinatorSvcImpl.verifySearchHasntFailedOrThrowInternalErrorException(mySearch);
 
+		mySearchTask.awaitInitialSync();
+
 		ourLog.trace("Fetching search resource PIDs from task: {}", mySearchTask.getClass());
 		final List<Long> pids = mySearchTask.getResourcePids(theFromIndex, theToIndex);
 		ourLog.trace("Done fetching search resource PIDs");

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

@@ -92,7 +92,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	public static final int DEFAULT_SYNC_SIZE = 250;
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SearchCoordinatorSvcImpl.class);
-	private final ConcurrentHashMap<String, BaseTask> myIdToSearchTask = new ConcurrentHashMap<>();
+	private final ConcurrentHashMap<String, SearchTask> myIdToSearchTask = new ConcurrentHashMap<>();
 	@Autowired
 	private FhirContext myContext;
 	@Autowired
@@ -151,7 +151,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 	@Override
 	public void cancelAllActiveSearches() {
-		for (BaseTask next : myIdToSearchTask.values()) {
+		for (SearchTask next : myIdToSearchTask.values()) {
 			next.requestImmediateAbort();
 			try {
 				next.getCompletionLatch().await(30, TimeUnit.SECONDS);
@@ -171,36 +171,54 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
 
+		// If we're actively searching right now, don't try to do anything until at least one batch has been
+		// persisted in the DB
+		SearchTask searchTask = myIdToSearchTask.get(theUuid);
+		if (searchTask != null) {
+			searchTask.awaitInitialSync();
+		}
+
+		ourLog.trace("About to start looking for resources {}-{}", theFrom, theTo);
+
 		Search search;
 		StopWatch sw = new StopWatch();
 		while (true) {
 
 			if (myNeverUseLocalSearchForUnitTests == false) {
-				BaseTask task = myIdToSearchTask.get(theUuid);
+				if (searchTask != null) {
-				if (task != null) {
 					ourLog.trace("Local search found");
-					List<Long> resourcePids = task.getResourcePids(theFrom, theTo);
+					List<Long> resourcePids = searchTask.getResourcePids(theFrom, theTo);
 					if (resourcePids != null) {
+						ourLog.trace("Local search returned {} pids, wanted {}-{} - Search: {}", resourcePids.size(), theFrom, theTo, searchTask.getSearch());
+
+						/*
+						 * Generally, if a search task is open, the fastest possible thing is to just return its results. This
+						 * will work most of the time, but can fail if the task hit a search threshold and the client is requesting
+						 * results beyond that threashold. In that case, we'll keep going below, since that will trigger another
+						 * task.
+						 */
+						if ((searchTask.getSearch().getNumFound() - searchTask.getSearch().getNumBlocked()) >= theTo || resourcePids.size() == (theTo - theFrom)) {
 							return resourcePids;
 						}
 					}
 				}
+			}
 
 			search = mySearchCacheSvc
 				.fetchByUuid(theUuid)
 				.orElseThrow(() -> {
-					ourLog.debug("Client requested unknown paging ID[{}]", theUuid);
+					ourLog.trace("Client requested unknown paging ID[{}]", theUuid);
 					String msg = myContext.getLocalizer().getMessage(PageMethodBinding.class, "unknownSearchId", theUuid);
 					return new ResourceGoneException(msg);
 				});
 
 			verifySearchHasntFailedOrThrowInternalErrorException(search);
 			if (search.getStatus() == SearchStatusEnum.FINISHED) {
-				ourLog.debug("Search entity marked as finished with {} results", search.getNumFound());
+				ourLog.trace("Search entity marked as finished with {} results", search.getNumFound());
 				break;
 			}
 			if (search.getNumFound() >= theTo) {
-				ourLog.debug("Search entity has {} results so far", search.getNumFound());
+				ourLog.trace("Search entity has {} results so far", search.getNumFound());
 				break;
 			}
 
@@ -212,11 +230,12 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			// If the search was saved in "pass complete mode" it's probably time to
 			// start a new pass
 			if (search.getStatus() == SearchStatusEnum.PASSCMPLET) {
+				ourLog.trace("Going to try to start next search");
 				Optional<Search> newSearch = mySearchCacheSvc.tryToMarkSearchAsInProgress(search);
 				if (newSearch.isPresent()) {
 					search = newSearch.get();
 					String resourceType = search.getResourceType();
-					SearchParameterMap params = search.getSearchParameterMap();
+					SearchParameterMap params = search.getSearchParameterMap().orElseThrow(() -> new IllegalStateException("No map in PASSCOMPLET search"));
 					IFhirResourceDao<?> resourceDao = myDaoRegistry.getResourceDao(resourceType);
 					SearchContinuationTask task = new SearchContinuationTask(search, resourceDao, params, resourceType, theRequestDetails);
 					myIdToSearchTask.put(search.getUuid(), task);
@@ -231,10 +250,11 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			}
 		}
 
+		ourLog.trace("Finished looping");
 
 		List<Long> pids = mySearchResultCacheSvc.fetchResultPids(search, theFrom, theTo);
 
-
+		ourLog.trace("Fetched {} results", pids.size());
 
 		return pids;
 	}
@@ -290,6 +310,38 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 	}
 
+	@Override
+	public Optional<Integer> getSearchTotal(String theUuid) {
+		SearchTask task = myIdToSearchTask.get(theUuid);
+		if (task != null) {
+			return Optional.ofNullable(task.awaitInitialSync());
+		}
+
+		/*
+		 * In case there is no running search, if the total is listed as accurate we know one is coming
+		 * so let's wait a bit for it to show up
+		 */
+		TransactionTemplate txTemplate = new TransactionTemplate(myManagedTxManager);
+		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
+		Optional<Search> search = mySearchCacheSvc.fetchByUuid(theUuid);
+		if (search.isPresent()) {
+			Optional<SearchParameterMap> searchParameterMap = search.get().getSearchParameterMap();
+			if (searchParameterMap.isPresent() && searchParameterMap.get().getSearchTotalMode() == SearchTotalModeEnum.ACCURATE) {
+				for (int i = 0; i < 10; i++) {
+					if (search.isPresent()) {
+						verifySearchHasntFailedOrThrowInternalErrorException(search.get());
+						if (search.get().getTotalCount() != null) {
+							return Optional.of(search.get().getTotalCount());
+						}
+					}
+					search = mySearchCacheSvc.fetchByUuid(theUuid);
+				}
+			}
+		}
+
+		return Optional.empty();
+	}
+
 	@NotNull
 	private IBundleProvider submitSearch(IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails, String theSearchUuid, ISearchBuilder theSb, String theQueryString) {
 		StopWatch w = new StopWatch();
@@ -516,7 +568,20 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		myInterceptorBroadcaster = theInterceptorBroadcaster;
 	}
 
-	public abstract class BaseTask implements Callable<Void> {
+	/**
+	 * A search task is a Callable task that runs in
+	 * a thread pool to handle an individual search. One instance
+	 * is created for any requested search and runs from the
+	 * beginning to the end of the search.
+	 * <p>
+	 * Understand:
+	 * This class executes in its own thread separate from the
+	 * web server client thread that made the request. We do that
+	 * so that we can return to the client as soon as possible,
+	 * but keep the search going in the background (and have
+	 * the next page of results ready to go when the client asks).
+	 */
+	public class SearchTask implements Callable<Void> {
 		private final SearchParameterMap myParams;
 		private final IDao myCallingDao;
 		private final String myResourceType;
@@ -538,7 +603,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 		/**
 		 * Constructor
 		 */
-		protected BaseTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequest) {
+		protected SearchTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequest) {
 			mySearch = theSearch;
 			myCallingDao = theCallingDao;
 			myParams = theParams;
@@ -549,6 +614,29 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 			myRequest = theRequest;
 		}
 
+		/**
+		 * This method is called by the server HTTP thread, and
+		 * will block until at least one page of results have been
+		 * fetched from the DB, and will never block after that.
+		 */
+		Integer awaitInitialSync() {
+			ourLog.trace("Awaiting initial sync");
+			do {
+				try {
+					if (getInitialCollectionLatch().await(250, TimeUnit.MILLISECONDS)) {
+						break;
+					}
+				} catch (InterruptedException e) {
+					// Shouldn't happen
+					Thread.currentThread().interrupt();
+					throw new InternalErrorException(e);
+				}
+			} while (getSearch().getStatus() == SearchStatusEnum.LOADING);
+			ourLog.trace("Initial sync completed");
+
+			return getSearch().getTotalCount();
+		}
+
 		protected Search getSearch() {
 			return mySearch;
 		}
@@ -1010,7 +1098,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 	}
 
 
-	public class SearchContinuationTask extends BaseTask {
+	public class SearchContinuationTask extends SearchTask {
 
 		public SearchContinuationTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequest) {
 			super(theSearch, theCallingDao, theParams, theResourceType, theRequest);
@@ -1041,51 +1129,6 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 
 	}
 
-	/**
-	 * A search task is a Callable task that runs in
-	 * a thread pool to handle an individual search. One instance
-	 * is created for any requested search and runs from the
-	 * beginning to the end of the search.
-	 * <p>
-	 * Understand:
-	 * This class executes in its own thread separate from the
-	 * web server client thread that made the request. We do that
-	 * so that we can return to the client as soon as possible,
-	 * but keep the search going in the background (and have
-	 * the next page of results ready to go when the client asks).
-	 */
-	class SearchTask extends BaseTask {
-
-		/**
-		 * Constructor
-		 */
-		SearchTask(Search theSearch, IDao theCallingDao, SearchParameterMap theParams, String theResourceType, RequestDetails theRequestDetails) {
-			super(theSearch, theCallingDao, theParams, theResourceType, theRequestDetails);
-		}
-
-		/**
-		 * This method is called by the server HTTP thread, and
-		 * will block until at least one page of results have been
-		 * fetched from the DB, and will never block after that.
-		 */
-		Integer awaitInitialSync() {
-			ourLog.trace("Awaiting initial sync");
-			do {
-				try {
-					if (getInitialCollectionLatch().await(250, TimeUnit.MILLISECONDS)) {
-						break;
-					}
-				} catch (InterruptedException e) {
-					// Shouldn't happen
-					throw new InternalErrorException(e);
-				}
-			} while (getSearch().getStatus() == SearchStatusEnum.LOADING);
-			ourLog.trace("Initial sync completed");
-
-			return getSearch().getTotalCount();
-		}
-
-	}
 
 	public static void populateSearchEntity(SearchParameterMap theParams, String theResourceType, String theSearchUuid, String theQueryString, Search theSearch) {
 		theSearch.setDeleted(false);

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/cache/DatabaseSearchResultCacheSvcImpl.java

@@ -58,9 +58,6 @@ public class DatabaseSearchResultCacheSvcImpl implements ISearchResultCacheSvc {
 
 		ourLog.debug("fetchResultPids for range {}-{} returned {} pids", theFrom, theTo, retVal.size());
 
-		// FIXME: should we remove the blocked number from this message?
-		Validate.isTrue((theSearch.getNumFound() - theSearch.getNumBlocked()) < theTo || retVal.size() == (theTo - theFrom), "Failed to find results in cache, requested %d - %d and got %d with total found=%d and blocked %s", theFrom, theTo, retVal.size(), theSearch.getNumFound(), theSearch.getNumBlocked());
-
 		return new ArrayList<>(retVal);
 	}
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR5.java

@@ -270,7 +270,7 @@ public class HapiTerminologySvcR5 extends BaseHapiTerminologySvcImpl implements
 	public IValidationSupport.CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
 		TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
 		txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-		return txTemplate.execute(t-> {
+		return txTemplate.execute(t -> {
 			Optional<TermConcept> codeOpt = findCode(theCodeSystem, theCode);
 			if (codeOpt.isPresent()) {
 				TermConcept code = codeOpt.get();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/BaseJpaR4Test.java

@@ -367,6 +367,11 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 		myInterceptorRegistry.registerInterceptor(myPerformanceTracingLoggingInterceptor);
 	}
 
+	@Before
+	public void beforeUnregisterAllSubscriptions() {
+		mySubscriptionRegistry.unregisterAllSubscriptions();
+	}
+
 	@Before
 	public void beforeFlushFT() {
 		runInTransaction(() -> {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchOptimizedTest.java

@@ -120,20 +120,24 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		myPatientDao.update(p);
 
 		myDaoConfig.setSearchPreFetchThresholds(Arrays.asList(20, 50, 190));
+		SearchParameterMap params;
+		IBundleProvider results;
+		String uuid;
+		List<String> ids;
 
 		// Search with count only
-		SearchParameterMap params = new SearchParameterMap();
+		params = new SearchParameterMap();
 		params.add(Patient.SP_NAME, new StringParam("FAM"));
 		params.setSummaryMode((SummaryEnum.COUNT));
-		IBundleProvider results = myPatientDao.search(params);
+		results = myPatientDao.search(params);
-		String uuid = results.getUuid();
+		uuid = results.getUuid();
 		ourLog.info("** Search returned UUID: {}", uuid);
 		assertEquals(201, results.size().intValue());
-		List<String> ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
+		ids = toUnqualifiedVersionlessIdValues(results, 0, 10, true);
 		assertThat(ids, empty());
 		assertEquals(201, myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size().intValue());
 
-		// Seach with total explicitly requested
+		// Search with total explicitly requested
 		params = new SearchParameterMap();
 		params.add(Patient.SP_NAME, new StringParam("FAM"));
 		params.setSearchTotalMode(SearchTotalModeEnum.ACCURATE);
@@ -213,7 +217,6 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals("Patient/PT00009", ids.get(9));
 
-		await().until(() -> myDatabaseBackedPagingProvider.retrieveResultList(null, uuid).size() != null);
 		results = myDatabaseBackedPagingProvider.retrieveResultList(null, uuid);
 		Integer resultsSize = results.size();
 		assertEquals(200, resultsSize.intValue());
@@ -354,6 +357,15 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		 * 20 should be prefetched since that's the initial page size
 		 */
 
+		await().until(()->{
+			return runInTransaction(()->{
+				return mySearchEntityDao
+					.findByUuidAndFetchIncludes(uuid)
+					.orElseThrow(() -> new InternalErrorException(""))
+					.getStatus() == SearchStatusEnum.PASSCMPLET;
+			});
+		});
+
 		runInTransaction(() -> {
 			Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
 			assertEquals(20, search.getNumFound());
@@ -636,6 +648,10 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		assertEquals("Patient/PT00000", ids.get(0));
 		assertEquals(1, ids.size());
 
+		await().until(()-> runInTransaction(()-> mySearchEntityDao
+			.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""))
+			.getStatus() == SearchStatusEnum.FINISHED));
+
 		runInTransaction(() -> {
 			Search search = mySearchEntityDao.findByUuidAndFetchIncludes(uuid).orElseThrow(() -> new InternalErrorException(""));
 			assertEquals(SearchStatusEnum.FINISHED, search.getStatus());
@@ -778,6 +794,7 @@ public class FhirResourceDaoR4SearchOptimizedTest extends BaseJpaR4Test {
 		search.getResources(0, 20);
 		ourLog.info("** Done retrieving resources");
 
+		await().until(()->myCaptureQueriesListener.countSelectQueries() == 4);
 
 		myCaptureQueriesListener.logSelectQueriesForCurrentThread();
 		assertEquals(4, myCaptureQueriesListener.countSelectQueries());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4ValidateTest.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.dao.r4;
 
 import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
+import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
 import ca.uhn.fhir.rest.api.EncodingEnum;
 import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.ValidationModeEnum;
@@ -8,10 +10,12 @@ import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.OperationOutcomeUtil;
 import ca.uhn.fhir.util.StopWatch;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.validation.IValidatorModule;
 import org.apache.commons.io.IOUtils;
+import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.hapi.validation.FhirInstanceValidator;
@@ -28,16 +32,18 @@ import org.springframework.test.util.AopTestUtils;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.util.Collections;
 
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.assertThat;
+import static org.junit.Assert.*;
-import static org.junit.Assert.fail;
 
 public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4ValidateTest.class);
 	@Autowired
 	private IValidatorModule myValidatorModule;
+	@Autowired
+	private IHapiTerminologySvc myTerminologySvc;
 
 	@Test
 	public void testValidateStructureDefinition() throws Exception {
@@ -106,6 +112,43 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
 		assertThat(ooString, containsString("Element '/f:Observation.device': minimum required = 1, but only found 0"));
 	}
 
+	@Test
+	public void testValidateUsingExternallyDefinedCode() {
+		CodeSystem codeSystem = new CodeSystem();
+		codeSystem.setUrl("http://foo");
+		codeSystem.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
+		IIdType csId = myCodeSystemDao.create(codeSystem).getId();
+
+		TermCodeSystemVersion csv = new TermCodeSystemVersion();
+		csv.addConcept().setCode("bar").setDisplay("Bar Code");
+		myTerminologySvc.storeNewCodeSystemVersion(codeSystem, csv, mySrd, Collections.emptyList(), Collections.emptyList());
+
+		// Validate a resource containing this codesystem in a field with an extendable binding
+		Patient patient = new Patient();
+		patient.getText().setStatus(Narrative.NarrativeStatus.GENERATED).setDivAsString("<div>hello</div>");
+		patient
+			.addIdentifier()
+			.setSystem("http://example.com")
+			.setValue("12345")
+			.getType()
+			.addCoding()
+			.setSystem("http://foo")
+			.setCode("bar");
+		MethodOutcome outcome = myPatientDao.validate(patient, null, encode(patient), EncodingEnum.JSON, ValidationModeEnum.CREATE, null, mySrd);
+		IBaseOperationOutcome oo = outcome.getOperationOutcome();
+		ourLog.info(myFhirCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(oo));
+
+		// It would be ok for this to produce 0 issues, or just an information message too
+		assertEquals(1, OperationOutcomeUtil.getIssueCount(myFhirCtx, oo));
+		assertEquals("None of the codes provided are in the value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type, and a code should come from this value set unless it has no suitable code) (codes = http://foo#bar)", OperationOutcomeUtil.getFirstIssueDetails(myFhirCtx, oo));
+
+	}
+
+	private String encode(Patient thePatient) {
+		return myFhirCtx.newJsonParser().encodeResourceToString(thePatient);
+	}
+
+
 	private OperationOutcome doTestValidateResourceContainingProfileDeclaration(String methodName, EncodingEnum enc) throws IOException {
 		Bundle vss = loadResourceFromClasspath(Bundle.class, "/org/hl7/fhir/r4/model/valueset/valuesets.xml");
 		myValueSetDao.update((ValueSet) findResourceByIdInBundle(vss, "observation-status"), mySrd);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/SearchCoordinatorSvcImplTest.java

@@ -293,6 +293,7 @@ public class SearchCoordinatorSvcImplTest {
 		myExpectedNumberOfSearchBuildersCreated = 4;
 	}
 
+
 	@Test
 	public void testAsyncSearchSmallResultSetSameCoordinator() {
 		SearchParameterMap params = new SearchParameterMap();

hapi-fhir-validation/src/main/java/org/hl7/fhir/dstu3/hapi/validation/ValidationSupportChain.java

@@ -98,13 +98,11 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theSystem)) {
 			CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
 			if (retVal != null) {
 				return retVal;
 			}
 		}
-		}
 		return null;
 	}
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/r4/hapi/validation/ValidationSupportChain.java

@@ -77,13 +77,11 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theSystem)) {
 			CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
 			if (retVal != null) {
 				return retVal;
 			}
 		}
-		}
 		return null;
 	}
 

hapi-fhir-validation/src/main/java/org/hl7/fhir/r5/hapi/validation/ValidationSupportChain.java

@@ -75,13 +75,11 @@ public class ValidationSupportChain implements IValidationSupport {
 	@Override
 	public CodeSystem fetchCodeSystem(FhirContext theCtx, String theSystem) {
 		for (IValidationSupport next : myChain) {
-			if (next.isCodeSystemSupported(theCtx, theSystem)) {
 			CodeSystem retVal = next.fetchCodeSystem(theCtx, theSystem);
 			if (retVal != null) {
 				return retVal;
 			}
 		}
-		}
 		return null;
 	}
 

src/changes/changes.xml

@@ -248,6 +248,10 @@
 				<![CDATA[<code>=</code>]]> or <![CDATA[<code>in</code>]]> operators. At present, the
 				<![CDATA[<code>ancestor</code>]]> filter can only be used with the <![CDATA[<code>=</code>]]> operator.
 			</action>
+			<action type="fix">
+				The JPA server failed to find codes defined in not-present codesystems in some cases, and reported
+				that the CodeSystem did not exist. This has been corrected.
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">