Refactor JPA SearchBuilder

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/IQueryParameterType.java

@@ -70,7 +70,9 @@ public interface IQueryParameterType {
 	/**
 	 * If set to non-null value, indicates that this parameter has been populated with a "[name]:missing=true" or "[name]:missing=false" vale 
 	 * instead of a normal value
+	 *  
+	 * @return Returns a reference to <code>this</code> for easier method chaining
 	 */
-	void setMissing(Boolean theMissing);
+	IQueryParameterType setMissing(Boolean theMissing);
 
 }

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/base/composite/BaseCodingDt.java

@@ -194,7 +194,7 @@ public abstract class BaseCodingDt extends BaseIdentifiableElement implements IC
 	 */
 	@Deprecated
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public IQueryParameterType setMissing(Boolean theMissing) {
 		throw new UnsupportedOperationException("get/setMissing is not supported in StringDt. Use {@link StringParam} instead if you need this functionality");
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/base/composite/BaseIdentifierDt.java

@@ -135,7 +135,7 @@ public abstract class BaseIdentifierDt extends BaseIdentifiableElement implement
 	 */
 	@Deprecated
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public IQueryParameterType setMissing(Boolean theMissing) {
 		throw new UnsupportedOperationException("get/setMissing is not supported in StringDt. Use {@link StringParam} instead if you need this functionality");
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/base/composite/BaseQuantityDt.java

@@ -231,7 +231,7 @@ public abstract class BaseQuantityDt extends BaseIdentifiableElement implements
 	 */
 	@Deprecated
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public IQueryParameterType setMissing(Boolean theMissing) {
 		throw new UnsupportedOperationException("get/setMissing is not supported in StringDt. Use {@link StringParam} instead if you need this functionality");
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/StringDt.java

@@ -144,7 +144,7 @@ public class StringDt extends BasePrimitive<String> implements IQueryParameterTy
 	 */
 	@Deprecated
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public IQueryParameterType setMissing(Boolean theMissing) {
 		throw new UnsupportedOperationException("get/setMissing is not supported in StringDt. Use {@link StringParam} instead if you need this functionality");
 	}
 

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/BaseParam.java

@@ -61,11 +61,16 @@ abstract class BaseParam implements IQueryParameterType {
 	}
 
 	/**
-	 * If set to non-null value, indicates that this parameter has been populated with a "[name]:missing=true" or "[name]:missing=false" vale instead of a normal value
+	 * If set to non-null value, indicates that this parameter has been populated 
+	 * with a "[name]:missing=true" or "[name]:missing=false" vale instead of a 
+	 * normal value
+	 * 
+	 * @return Returns a reference to <code>this</code> for easier method chaining
 	 */
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public BaseParam setMissing(Boolean theMissing) {
 		myMissing = theMissing;
+		return this;
 	}
 
 	@Override

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/InternalCodingDt.java

@@ -24,6 +24,7 @@ import java.util.List;
 
 import ca.uhn.fhir.model.api.ICompositeDatatype;
 import ca.uhn.fhir.model.api.IElement;
+import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.api.annotation.Child;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.base.composite.BaseCodingDt;
@@ -297,7 +298,7 @@ public class InternalCodingDt extends BaseCodingDt implements ICompositeDatatype
 	}
 
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public IQueryParameterType setMissing(Boolean theMissing) {
 		throw new UnsupportedOperationException();
 	}
 

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

@@ -936,7 +936,6 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	 * @param theTag
 	 *           The tag
 	 * @return Returns <code>true</code> if the tag should be removed
-	 * @see <a href="http://hl7.org/fhir/2015Sep/resource.html#1.11.3.7">Updates to Tags, Profiles, and Security Labels</a> for a description of the logic that the default behaviour folows.
 	 */
 	@SuppressWarnings("unused")
 	protected void postPersist(ResourceTable theEntity, T theResource) {
@@ -966,7 +965,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 
 		IFhirResourceDao<R> dao = getDao(theResourceType);
-		Set<Long> ids = dao.searchForIdsWithAndOr(paramMap, new HashSet<Long>(), paramMap.getLastUpdated());
+		Set<Long> ids = dao.searchForIdsWithAndOr(paramMap, paramMap.getLastUpdated());
 
 		return ids;
 	}
@@ -1168,14 +1167,16 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	 * The default implementation removes any profile declarations, but leaves tags and security labels in place.
 	 * Subclasses may choose to override and change this behaviour.
 	 * </p>
+	 * <p>
+	 * See <a href="http://hl7.org/fhir/2015Sep/resource.html#1.11.3.7">Updates to Tags, Profiles, and Security
+	 *      Labels</a> for a description of the logic that the default behaviour folows.
+	 * </p>
 	 * 
 	 * @param theEntity
 	 *           The entity being updated (Do not modify the entity! Undefined behaviour will occur!)
 	 * @param theTag
 	 *           The tag
 	 * @return Retturns <code>true</code> if the tag should be removed
-	 * @see <a href="http://hl7.org/fhir/2015Sep/resource.html#1.11.3.7">Updates to Tags, Profiles, and Security
-	 *      Labels</a> for a description of the logic that the default behaviour folows.
 	 */
 	protected boolean shouldDroppedTagBeRemovedOnUpdate(ResourceTable theEntity, ResourceTag theTag) {
 		if (theTag.getTag().getTagType() == TagTypeEnum.PROFILE) {

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

@@ -932,7 +932,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 		for (Entry<String, IQueryParameterType> nextEntry : theParams.entrySet()) {
 			map.add(nextEntry.getKey(), (nextEntry.getValue()));
 		}
-		return searchForIdsWithAndOr(map, null, null);
+		return searchForIdsWithAndOr(map, null);
 	}
 
 	@Override
@@ -941,10 +941,11 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	}
 
 	@Override
-	public Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams, Collection<Long> theInitialPids, DateRangeParam theLastUpdated) {
+	public Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams, DateRangeParam theLastUpdated) {
 		SearchBuilder builder = new SearchBuilder(getContext(), myEntityManager, myPlatformTransactionManager, mySearchDao, mySearchResultDao, this, myResourceIndexedSearchParamUriDao);
 		builder.setType(getResourceType(), getResourceName());
-		return builder.searchForIdsWithAndOr(theParams, theInitialPids, theLastUpdated);
+		builder.searchForIdsWithAndOr(theParams, theLastUpdated);
+		return builder.doGetPids();
 	}
 
 	@SuppressWarnings("unchecked")

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

@@ -1,7 +1,5 @@
 package ca.uhn.fhir.jpa.dao;
 
-import java.util.Collection;
-
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -164,7 +162,7 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
 
 	Set<Long> searchForIds(String theParameterName, IQueryParameterType theValue);
 
-	Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams, Collection<Long> theInitialPids, DateRangeParam theLastUpdated);
+	Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams, DateRangeParam theLastUpdated);
 
 	DaoMethodOutcome update(T theResource, RequestDetails theRequestDetails);
 

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

@@ -53,13 +53,13 @@ public class Search implements Serializable {
 
 	@GeneratedValue(strategy = GenerationType.AUTO, generator="SEQ_SEARCH")
 	@SequenceGenerator(name="SEQ_SEARCH", sequenceName="SEQ_SEARCH")
-	@Id
 	@Column(name = "PID")
 	private Long myId;
 
 	@Column(name="TOTAL_COUNT")
 	private int myTotalCount;
 	
+	@Id
 	@Column(name="SEARCH_UUID", length=40, nullable=false)
 	private String myUuid;
 

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

@@ -4,10 +4,9 @@ import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.Set;
 
-import javax.transaction.Transactional;
-import javax.transaction.Transactional.TxType;
-
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.validation.ValidationUtils;
 
 import ca.uhn.fhir.context.FhirContext;
@@ -44,7 +43,7 @@ public class TerminologySvcImpl implements ITerminologySvc {
 	
 	
 	@Override
-	@Transactional(value=TxType.REQUIRED)
+	@Transactional(propagation=Propagation.REQUIRED)
 	public void storeNewCodeSystemVersion(String theSystemUri, TermCodeSystemVersion theCodeSystem) {
 		ourLog.info("Storing code system");
 		
@@ -108,7 +107,7 @@ public class TerminologySvcImpl implements ITerminologySvc {
 		theConceptsStack.remove(theConcept);
 	}
 
-	@Transactional(value=TxType.REQUIRED)
+	@Transactional(propagation=Propagation.REQUIRED)
 	@Override
 	public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
 		TermCodeSystemVersion codeSystem = myCodeSystemVersionDao.findByCodeSystemResourceAndVersion(theCodeSystemResourcePid, theCodeSystemVersionPid);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2SearchNoFtTest.java

@@ -395,6 +395,60 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 
 	}
 
+	@SuppressWarnings("unused")
+	@Test
+	public void testSearchResourceReferenceMissing() {
+		IIdType oid1;
+		{
+			Organization org = new Organization();
+			org.setName("ORG1");
+			oid1 = myOrganizationDao.create(org, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		}
+
+		IIdType pid1;
+		{
+			Patient patient = new Patient();
+			patient.addName().addFamily("FAMILY1");
+			pid1 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		}
+		IIdType pid2;
+		{
+			Patient patient = new Patient();
+			patient.addName().addFamily("FAMILY1");
+			patient.getManagingOrganization().setReference(oid1);
+			pid2 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		}
+		IIdType pid3;
+		{
+			Patient patient = new Patient();
+			patient.addName().addFamily("FAMILY2");
+			pid3 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		}
+		IIdType pid4;
+		{
+			Patient patient = new Patient();
+			patient.addName().addFamily("FAMILY2");
+			patient.getManagingOrganization().setReference(oid1);
+			pid4 = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
+		}
+
+		SearchParameterMap params;
+		
+		params = new SearchParameterMap();
+		params.add(Patient.SP_NAME, new StringParam("FAMILY1"));
+		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(pid1));
+
+		params = new SearchParameterMap();
+		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), containsInAnyOrder(pid1, pid3));
+
+		params = new SearchParameterMap();
+		params.add(Patient.SP_NAME, new StringParam("FAMILY9999"));
+		params.add(Patient.SP_ORGANIZATION, new ReferenceParam().setMissing(true));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(params)), empty());
+	}
+	
 	@Test
 	public void testSearchByIdParamOr() {
 		IIdType id1;
@@ -1290,6 +1344,23 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 		patient.addName().addFamily("Tester").addGiven("testSearchTokenParam2");
 		myPatientDao.create(patient, new ServletRequestDetails());
 
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.add(Patient.SP_LANGUAGE, new TokenParam(null, "testSearchTokenParamCode", true));
+			assertEquals(0, myPatientDao.search(map).size());
+		}
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.add(Patient.SP_LANGUAGE, new TokenParam(null, "testSearchTokenParamCode", true));
+			map.add(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testSearchTokenParam001"));
+			assertEquals(0, myPatientDao.search(map).size());
+		}
+		{
+			SearchParameterMap map = new SearchParameterMap();
+			map.add(Patient.SP_LANGUAGE, new TokenParam(null, "testSearchTokenParamComText", true));
+			map.add(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testSearchTokenParam001"));
+			assertEquals(1, myPatientDao.search(map).size());
+		}
 		{
 			SearchParameterMap map = new SearchParameterMap();
 			map.add(Patient.SP_IDENTIFIER, new IdentifierDt("urn:system", "testSearchTokenParam001"));
@@ -1307,11 +1378,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			map.add(Patient.SP_LANGUAGE, new IdentifierDt("testSearchTokenParamSystem", "testSearchTokenParamCode"));
 			assertEquals(1, myPatientDao.search(map).size());
 		}
-		{
-			SearchParameterMap map = new SearchParameterMap();
-			map.add(Patient.SP_LANGUAGE, new TokenParam(null, "testSearchTokenParamCode", true));
-			assertEquals(0, myPatientDao.search(map).size());
-		}
 		{
 			// Complete match
 			SearchParameterMap map = new SearchParameterMap();
@@ -1896,15 +1962,6 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			notMissing = myPatientDao.create(patient, new ServletRequestDetails()).getId().toUnqualifiedVersionless();
 		}
 		// String Param
-		{
-			HashMap<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
-			StringParam param = new StringParam();
-			param.setMissing(false);
-			params.put(Patient.SP_FAMILY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
-			assertThat(patients, containsInRelativeOrder(notMissing));
-		}
 		{
 			Map<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
 			StringParam param = new StringParam();
@@ -1914,8 +1971,47 @@ public class FhirResourceDaoDstu2SearchNoFtTest extends BaseJpaDstu2Test {
 			assertThat(patients, containsInRelativeOrder(missing));
 			assertThat(patients, not(containsInRelativeOrder(notMissing)));
 		}
+		{
+			HashMap<String, IQueryParameterType> params = new HashMap<String, IQueryParameterType>();
+			StringParam param = new StringParam();
+			param.setMissing(false);
+			params.put(Patient.SP_FAMILY, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
+			assertThat(patients, containsInRelativeOrder(notMissing));
+		}
 	}
 
+	/**
+	 * See #310
+	 */
+	@Test
+	@Ignore
+	public void testSearchMultiMatches() {
+		
+		for (int i = 0; i < 100; i++) {
+			Practitioner p = new Practitioner();
+			p.addAddress().addLine("FOO");
+			IIdType pid = myPractitionerDao.create(p, mySrd).getId().toUnqualifiedVersionless();
+			
+			Patient pt = new Patient();
+			pt.addCareProvider().setReference(pid);
+			IIdType ptid = myPatientDao.create(pt, mySrd).getId().toUnqualifiedVersionless();
+			
+			Observation obs = new Observation();
+			obs.setSubject(new ResourceReferenceDt(ptid));
+			myObservationDao.create(obs, mySrd);
+		}
+		
+		SearchParameterMap map = new SearchParameterMap();
+		map.addInclude(new Include("Patient:careprovider"));
+		map.addRevInclude(new Include("Observation:patient"));
+
+		myPatientDao.search(map);
+		
+	}
+	
+	
 	@Test
 	public void testSearchWithNoResults() {
 		Device dev = new Device();

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoDstu2Test.java

@@ -2186,7 +2186,7 @@ public class FhirResourceDaoDstu2Test extends BaseJpaDstu2Test {
 		map.add(Organization.SP_NAME, new StringParam("X" + methodName + "X"));
 		map.setRevIncludes(Collections.singleton(Patient.INCLUDE_ORGANIZATION));
 		IBundleProvider resultsP = myOrganizationDao.search(map);
-		assertEquals(2, resultsP.size());
+		assertEquals(1, resultsP.size());
 
 		List<IBaseResource> results = resultsP.getResources(0, resultsP.size());
 		assertEquals(2, results.size());

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java

@@ -2250,7 +2250,7 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
 		map.add(Organization.SP_NAME, new StringParam("X" + methodName + "X"));
 		map.setRevIncludes(Collections.singleton(Patient.INCLUDE_ORGANIZATION));
 		IBundleProvider resultsP = myOrganizationDao.search(map);
-		assertEquals(2, resultsP.size());
+		assertEquals(1, resultsP.size());
 
 		List<IBaseResource> results = resultsP.getResources(0, resultsP.size());
 		assertEquals(2, results.size());

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/testmodel/IdentifierDt.java

@@ -424,7 +424,7 @@ public class IdentifierDt
 	 */
 	@Deprecated
 	@Override
-	public void setMissing(Boolean theMissing) {
+	public IQueryParameterType setMissing(Boolean theMissing) {
 		throw new UnsupportedOperationException("get/setMissing is not supported in StringDt. Use {@link StringParam} instead if you need this functionality");
 	}
 

pom.xml

@@ -846,6 +846,10 @@
 							<groupId>org.apache.maven.scm</groupId>
 							<artifactId>maven-scm-api</artifactId>
 						</dependency>
+						<dependency>
+						    <groupId>org.apache.maven.doxia</groupId>
+						    <artifactId>doxia-core</artifactId>
+						</dependency>						
 						<dependency>
 							<groupId>org.apache.maven.doxia</groupId>
 							<artifactId>doxia-module-markdown</artifactId>
@@ -1263,6 +1267,11 @@
 						<artifactId>maven-scm-api</artifactId>
 						<version>1.9.4</version>
 					</dependency>
+					<dependency>
+						<groupId>org.apache.maven.doxia</groupId>
+						<artifactId>doxia-core</artifactId>
+						<version>1.7</version>
+					</dependency>						
 					<dependency>
 						<groupId>org.apache.maven.doxia</groupId>
 						<artifactId>doxia-module-markdown</artifactId>

src/site/site.xml

@@ -32,14 +32,13 @@
 	<body>
 	
 		<head>
+			<![CDATA[
 			<!-- Syntax Highlighter -->
-			<!--
+			<script type="text/javascript" src="syntaxhighlighter/shCore.js" />
-			-->
+			<script type="text/javascript" src="syntaxhighlighter/shBrushJScript.js" />
-			<script type="text/javascript" src="syntaxhighlighter/shCore.js"></script>
+			<script type="text/javascript" src="syntaxhighlighter/shBrushJava.js" />
-			<script type="text/javascript" src="syntaxhighlighter/shBrushJScript.js"></script>
+			<script type="text/javascript" src="syntaxhighlighter/shBrushBash.js" />
-			<script type="text/javascript" src="syntaxhighlighter/shBrushJava.js"></script>
+			<script type="text/javascript" src="syntaxhighlighter/shBrushXml.js" />
-			<script type="text/javascript" src="syntaxhighlighter/shBrushBash.js"></script>
-			<script type="text/javascript" src="syntaxhighlighter/shBrushXml.js"></script>
 			<link href="syntaxhighlighter/shCore.css" rel="stylesheet" type="text/css" />
 			<link href="syntaxhighlighter/shThemeDefault.css" rel="stylesheet" type="text/css" />
 			
@@ -47,12 +46,11 @@
 			   HAPI stylesheet comes after because it overwrites the Syntax Highlighter
 			   font size
 			 -->
-			<!--
-			-->
 			<link rel="shortcut icon" href="http://jamesagnew.github.io/hapi-fhir/images/favicon.png" />
 			<link rel="stylesheet" type="text/css" href="hapi.css" />
 			
 			<link rel="stylesheet" href="http://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css" />
+			]]>
 		</head>
 		
 		<breadcrumbs>