Merge branch 'master' of github.com:jamesagnew/hapi-fhir

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

@@ -2071,6 +2071,7 @@ public class SearchBuilder implements ISearchBuilder {
 				outerQuery.multiselect(myBuilder.countDistinct(myResourceTableRoot));
 			} else {
 				outerQuery.multiselect(myResourceTableRoot.get("myId").as(Long.class));
+				outerQuery.distinct(true);
 			}
 
 		}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BinaryAccessProvider.java

@@ -1,31 +0,0 @@
-package ca.uhn.fhir.jpa.provider;
-
-/*-
- * #%L
- * HAPI FHIR JPA Server
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * 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%
- */
-
-/**
- * @deprecated Use ca.uhn.fhir.jpa.binstore.BinaryAccessProvider instead
- */
-@Deprecated
-public class BinaryAccessProvider extends ca.uhn.fhir.jpa.binstore.BinaryAccessProvider {
-
-	// FIXME: JA delete before 4.0.0
-
-}

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

@@ -233,6 +233,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 				ourLog.trace("Going to try to start next search");
 				Optional<Search> newSearch = mySearchCacheSvc.tryToMarkSearchAsInProgress(search);
 				if (newSearch.isPresent()) {
+					ourLog.trace("Launching new search");
 					search = newSearch.get();
 					String resourceType = search.getResourceType();
 					SearchParameterMap params = search.getSearchParameterMap().orElseThrow(() -> new IllegalStateException("No map in PASSCOMPLET search"));
@@ -1113,7 +1114,7 @@ public class SearchCoordinatorSvcImpl implements ISearchCoordinatorSvc {
 						throw newResourceGoneException(getSearch().getUuid());
 					}
 
-					ourLog.debug("Have {} previously added IDs in search: {}", previouslyAddedResourcePids.size(), getSearch().getUuid());
+					ourLog.trace("Have {} previously added IDs in search: {}", previouslyAddedResourcePids.size(), getSearch().getUuid());
 					setPreviouslyAddedResourcePids(previouslyAddedResourcePids);
 					return null;
 				});

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderCustomSearchParamR4Test.java

@@ -1,21 +1,19 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
-import ca.uhn.fhir.interceptor.api.Hook;
-import ca.uhn.fhir.interceptor.api.Pointcut;
 import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
+import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
+import ca.uhn.fhir.jpa.entity.Search;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
 import ca.uhn.fhir.jpa.model.search.SearchStatusEnum;
-import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
-import ca.uhn.fhir.jpa.search.SearchCoordinatorSvcImpl;
 import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
-import ca.uhn.fhir.jpa.util.SpringObjectCaster;
 import ca.uhn.fhir.rest.api.Constants;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.gclient.ReferenceClientParam;
 import ca.uhn.fhir.rest.gclient.TokenClientParam;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+import ca.uhn.fhir.util.BundleUtil;
 import ca.uhn.fhir.util.TestUtil;
 import org.apache.commons.io.IOUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
@@ -33,9 +31,6 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
-import org.springframework.aop.support.AopUtils;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.util.ProxyUtils;
 import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
@@ -48,7 +43,11 @@ import java.util.Map;
 
 import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsString;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.fail;
 
 public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProviderR4Test {
 
@@ -80,7 +79,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	}
 
 	private Map<String, CapabilityStatementRestResourceSearchParamComponent> extractSearchParams(CapabilityStatement conformance, String resType) {
-		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = new HashMap<String, CapabilityStatement.CapabilityStatementRestResourceSearchParamComponent>();
+		Map<String, CapabilityStatementRestResourceSearchParamComponent> map = new HashMap<>();
 		for (CapabilityStatementRestComponent nextRest : conformance.getRest()) {
 			for (CapabilityStatementRestResourceComponent nextResource : nextRest.getResource()) {
 				if (!resType.equals(nextResource.getType())) {
@@ -95,7 +94,7 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
 	}
 
 	@Test
-	public void saveCreateSearchParamInvalidWithMissingStatus() throws IOException {
+	public void saveCreateSearchParamInvalidWithMissingStatus() {
 		SearchParameter sp = new SearchParameter();
 		sp.setCode("foo");
 		sp.setExpression("Patient.gender");

hapi-fhir-jpaserver-base/src/test/resources/r4/impact-sp.json

@@ -0,0 +1,29 @@
+{
+	"resourceType": "SearchParameter",
+	"id": "54805",
+	"meta": {
+		"versionId": "1",
+		"lastUpdated": "2019-11-04T18:33:47.918+00:00",
+		"source": "#pt4ERkOO6LGm5ZoA"
+	},
+	"text": {
+		"status": "generated",
+		"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">Search for a questionnaire by item.text nested field - up to 3 levels.</div>"
+	},
+	"url": "https://impact-fhir.mitre.org/r4/SearchParameter/QuestionnaireItemText",
+	"version": "0.0.1",
+	"name": "QuestionnaireItemText",
+	"status": "active",
+	"date": "2019-10-25T15:38:45-04:00",
+	"description": "Search for a questionnaire by item.text nested field - up to 3 levels.",
+	"code": "item-text",
+	"base": [
+		"Questionnaire"
+	],
+	"type": "string",
+	"expression": "Questionnaire.item.text | Questionnaire.item.item.text | Questionnaire.item.item.item.text",
+	"xpathUsage": "normal",
+	"modifier": [
+		"contains"
+	]
+}

src/changes/changes.xml

@@ -506,6 +506,13 @@
 				filter could bring in search results of the wrong type. Thanks to Anthony Sute for the Pull
 				Request and Jens Villadsen for reporting!
 			</action>
+			<action type="fix" issue="1300">
+				In some cases where where a single search parameter matches the same resource many times with 
+				different distinct values (e.g. a search by Patient:name where there are hundreds of patients having
+				hundreds of distinct names each) the Search Coordinator would end up in an infinite loop and never
+				return all of the possible results. Thanks to @imranmoezkhan for reporting, and to 
+				Tim Shaffer for providing a reproducible test case!
+			</action>
 		</release>
 		<release version="4.0.3" date="2019-09-03" description="Igloo (Point Release)">
 			<action type="fix">