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

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

@@ -1464,12 +1464,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				}
 
 				Set<Entry<String, RuntimeSearchParam>> activeSearchParams = mySearchParamRegistry.getActiveSearchParams(theEntity.getResourceType()).entrySet();
-				findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.STRING, stringParams);
+				if (myConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
-				findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.NUMBER, numberParams);
+					findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.STRING, stringParams);
-				findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.QUANTITY, quantityParams);
+					findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.NUMBER, numberParams);
-				findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.DATE, dateParams);
+					findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.QUANTITY, quantityParams);
-				findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.URI, uriParams);
+					findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.DATE, dateParams);
-				findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.TOKEN, tokenParams);
+					findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.URI, uriParams);
+					findMissingSearchParams(theEntity, activeSearchParams, RestSearchParameterTypeEnum.TOKEN, tokenParams);
+				}
 
 				setUpdatedTime(stringParams, theUpdateTime);
 				setUpdatedTime(numberParams, theUpdateTime);

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

@@ -34,10 +34,7 @@ import ca.uhn.fhir.jpa.util.DeleteConflict;
 import ca.uhn.fhir.jpa.util.StopWatch;
 import ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils;
 import ca.uhn.fhir.jpa.util.xmlpatch.XmlPatchUtils;
-import ca.uhn.fhir.model.api.IQueryParameterAnd;
+import ca.uhn.fhir.model.api.*;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
-import ca.uhn.fhir.model.api.TagList;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.api.PatchTypeEnum;
 import ca.uhn.fhir.rest.api.QualifiedParamList;
@@ -900,6 +897,19 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 	@Transactional(propagation = Propagation.SUPPORTS)
 	@Override
 	public IBundleProvider search(final SearchParameterMap theParams, RequestDetails theRequestDetails) {
+
+		if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
+			for (List<List<? extends IQueryParameterType>> nextAnds : theParams.values()) {
+				for (List<? extends IQueryParameterType> nextOrs : nextAnds) {
+					for (IQueryParameterType next : nextOrs) {
+						if (next.getMissing() != null) {
+							throw new MethodNotAllowedException(":missing modifier is disabled on this server");
+						}
+					}
+				}
+			}
+		}
+
 		// Notify interceptors
 		if (theRequestDetails != null) {
 			ActionRequestDetails requestDetails = new ActionRequestDetails(theRequestDetails, getContext(), getResourceName(), null);

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

@@ -30,15 +30,6 @@ import java.util.*;
 
 public class DaoConfig {
 
-	/**
-	 * Constructor
-	 */
-	public DaoConfig() {
-		setSubscriptionEnabled(true);
-		setSubscriptionPollDelay(0);
-		setSubscriptionPurgeInactiveAfterMillis(Long.MAX_VALUE);
-	}
-
 	/**
 	 * Default {@link #getTreatReferencesAsLogical() logical URL bases}. Includes the following
 	 * values:
@@ -64,25 +55,22 @@ public class DaoConfig {
 	 * @see #setMaximumSearchResultCountInTransaction(Integer)
 	 */
 	private static final Integer DEFAULT_MAXIMUM_SEARCH_RESULT_COUNT_IN_TRANSACTION = null;
+	private IndexEnabledEnum myIndexMissingFieldsEnabled = IndexEnabledEnum.ENABLED;
 	/**
 	 * update setter javadoc if default changes
 	 */
 	private boolean myAllowExternalReferences = false;
-
 	/**
 	 * update setter javadoc if default changes
 	 */
 	private boolean myAllowInlineMatchUrlReferences = true;
 	private boolean myAllowMultipleDelete;
 	private boolean myDefaultSearchParamsCanBeOverridden = false;
-
 	/**
 	 * update setter javadoc if default changes
 	 */
 	private int myDeferIndexingForCodesystemsOfSize = 2000;
-
 	private boolean myDeleteStaleSearches = true;
-
 	private boolean myEnforceReferentialIntegrityOnDelete = true;
 	private boolean myUniqueIndexesEnabled = true;
 	private boolean myUniqueIndexesCheckedBeforeSave = true;
@@ -119,6 +107,14 @@ public class DaoConfig {
 	private Set<String> myTreatBaseUrlsAsLocal = new HashSet<String>();
 	private Set<String> myTreatReferencesAsLogical = new HashSet<String>(DEFAULT_LOGICAL_BASE_URLS);
 	private boolean myAutoCreatePlaceholderReferenceTargets;
+	/**
+	 * Constructor
+	 */
+	public DaoConfig() {
+		setSubscriptionEnabled(true);
+		setSubscriptionPollDelay(0);
+		setSubscriptionPurgeInactiveAfterMillis(Long.MAX_VALUE);
+	}
 
 	/**
 	 * Add a value to the {@link #setTreatReferencesAsLogical(Set) logical references list}.
@@ -287,6 +283,35 @@ public class DaoConfig {
 		myIncludeLimit = theIncludeLimit;
 	}
 
+	/**
+	 * If set to {@link IndexEnabledEnum#DISABLED} (default is {@link IndexEnabledEnum#ENABLED})
+	 * the server will not create search indexes for search parameters with no values in resources.
+	 * <p>
+	 * Disabling this feature means that the <code>:missing</code> search modifier will not be
+	 * supported on the server, but also means that storage and indexing (i.e. writes to the
+	 * database) may be much faster on servers which have lots of search parameters and need
+	 * to write quickly.
+	 * </p>
+	 */
+	public IndexEnabledEnum getIndexMissingFields() {
+		return myIndexMissingFieldsEnabled;
+	}
+
+	/**
+	 * If set to {@link IndexEnabledEnum#DISABLED} (default is {@link IndexEnabledEnum#ENABLED})
+	 * the server will not create search indexes for search parameters with no values in resources.
+	 * <p>
+	 * Disabling this feature means that the <code>:missing</code> search modifier will not be
+	 * supported on the server, but also means that storage and indexing (i.e. writes to the
+	 * database) may be much faster on servers which have lots of search parameters and need
+	 * to write quickly.
+	 * </p>
+	 */
+	public void setIndexMissingFields(IndexEnabledEnum theIndexMissingFields) {
+		Validate.notNull(theIndexMissingFields, "theIndexMissingFields must not be null");
+		myIndexMissingFieldsEnabled = theIndexMissingFields;
+	}
+
 	/**
 	 * Returns the interceptors which will be notified of operations.
 	 *
@@ -420,24 +445,6 @@ public class DaoConfig {
 		myReuseCachedSearchResultsForMillis = theReuseCachedSearchResultsForMillis;
 	}
 
-	/**
-	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
-	 * detecting changes, so this setting has no effect
-	 */
-	@Deprecated
-	public void setSubscriptionPollDelay(long theSubscriptionPollDelay) {
-		// ignore
-	}
-
-	/**
-	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
-	 * detecting changes, so this setting has no effect
-	 */
-	@Deprecated
-	public void setSubscriptionPurgeInactiveAfterMillis(Long theMillis) {
-		// ignore
-	}
-
 	/**
 	 * This setting may be used to advise the server that any references found in
 	 * resources that have any of the base URLs given here will be replaced with
@@ -814,16 +821,6 @@ public class DaoConfig {
 		mySchedulingDisabled = theSchedulingDisabled;
 	}
 
-
-	/**
-	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
-	 * detecting changes, so this setting has no effect
-	 */
-	@Deprecated
-	public void setSubscriptionEnabled(boolean theSubscriptionEnabled) {
-		// nothing
-	}
-
 	/**
 	 * If set to {@literal true} (default is true), if a client performs an update which does not actually
 	 * result in any chance to a given resource (e.g. an update where the resource body matches the
@@ -926,6 +923,33 @@ public class DaoConfig {
 		}
 	}
 
+	/**
+	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
+	 * detecting changes, so this setting has no effect
+	 */
+	@Deprecated
+	public void setSubscriptionEnabled(boolean theSubscriptionEnabled) {
+		// nothing
+	}
+
+	/**
+	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
+	 * detecting changes, so this setting has no effect
+	 */
+	@Deprecated
+	public void setSubscriptionPollDelay(long theSubscriptionPollDelay) {
+		// ignore
+	}
+
+	/**
+	 * @deprecated As of HAPI FHIR 3.0.0, subscriptions no longer use polling for
+	 * detecting changes, so this setting has no effect
+	 */
+	@Deprecated
+	public void setSubscriptionPurgeInactiveAfterMillis(Long theMillis) {
+		// ignore
+	}
+
 	public void setSubscriptionPurgeInactiveAfterSeconds(int theSeconds) {
 		setSubscriptionPurgeInactiveAfterMillis(theSeconds * DateUtils.MILLIS_PER_SECOND);
 	}
@@ -942,4 +966,9 @@ public class DaoConfig {
 
 	}
 
+	public enum IndexEnabledEnum {
+		ENABLED,
+		DISABLED
+	}
+
 }

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

@@ -136,7 +136,7 @@ public class ResourceIndexedSearchParamCoords extends BaseResourceIndexedSearchP
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		b.append("paramName", getParamName());
-		b.append("resourceId", getResource().getId()); // TODO: add a field so we don't need to resolve this
+		b.append("resourceId", getResourcePid());
 		b.append("lat", getLatitude());
 		b.append("lon", getLongitude());
 		return b.build();

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

@@ -146,7 +146,7 @@ public class ResourceIndexedSearchParamQuantity extends BaseResourceIndexedSearc
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		b.append("paramName", getParamName());
-		b.append("resourceId", getResource().getId()); // TODO: add a field so we don't need to resolve this
+		b.append("resourceId", getResourcePid());
 		b.append("system", getSystem());
 		b.append("units", getUnits());
 		b.append("value", getValue());

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

@@ -118,6 +118,7 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 	private String myValueNormalized;
 
 	public ResourceIndexedSearchParamString() {
+		super();
 	}
 
 
@@ -191,7 +192,7 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		b.append("paramName", getParamName());
-		b.append("resourceId", getResource().getId()); // TODO: add a field so we don't need to resolve this
+		b.append("resourceId", getResourcePid());
 		b.append("value", getValueNormalized());
 		return b.build();
 	}

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

@@ -127,7 +127,7 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
 	public String toString() {
 		ToStringBuilder b = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
 		b.append("paramName", getParamName());
-		b.append("resourceId", getResource().getId()); // TODO: add a field so we don't need to resolve this
+		b.append("resourceId", getResourcePid());
 		b.append("system", getSystem());
 		b.append("value", getValue());
 		return b.build();

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

@@ -113,11 +113,12 @@ public class ResourceIndexedSearchParamUri extends BaseResourceIndexedSearchPara
 
 	@Override
 	public String toString() {
-		ToStringBuilder builder = new ToStringBuilder(this);
+		ToStringBuilder b = new ToStringBuilder(this);
-		builder.append("id", getId());
+		b.append("id", getId());
-		builder.append("paramName", getParamName());
+		b.append("resourceId", getResourcePid());
-		builder.append("uri", myUri);
+		b.append("paramName", getParamName());
-		return builder.toString();
+		b.append("uri", myUri);
+		return b.toString();
 	}
 
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java

@@ -24,6 +24,7 @@ import java.util.*;
 import java.util.Map.Entry;
 import java.util.concurrent.ConcurrentHashMap;
 
+import ca.uhn.fhir.jpa.dao.DaoConfig;
 import org.apache.commons.lang3.tuple.Pair;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -45,8 +46,14 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
 	@Autowired
 	private ISearchParamPresentDao mySearchParamPresentDao;
 
+	@Autowired
+	private DaoConfig myDaoConfig;
+
 	@Override
 	public void updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
+		if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
+			return;
+		}
 
 		Map<String, Boolean> presenceMap = new HashMap<String, Boolean>(theParamNameToPresence);
 		List<SearchParamPresent> entitiesToSave = new ArrayList<SearchParamPresent>();

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

@@ -56,9 +56,19 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
 	private static JpaValidationSupportChainR4 ourJpaValidationSupportChainR4;
 	private static IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> ourValueSetDao;
 
+	@Autowired
+	protected ISearchParamDao mySearchParamDao;
+	@Autowired
+	protected ISearchParamPresentDao mySearchParamPresentDao;
 	@Autowired
 	protected IResourceIndexedSearchParamStringDao myResourceIndexedSearchParamStringDao;
 	@Autowired
+	protected IResourceIndexedSearchParamTokenDao myResourceIndexedSearchParamTokenDao;
+	@Autowired
+	protected IResourceIndexedSearchParamQuantityDao myResourceIndexedSearchParamQuantityDao;
+	@Autowired
+	protected IResourceIndexedSearchParamDateDao myResourceIndexedSearchParamDateDao;
+	@Autowired
 	protected IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
 	@Autowired
 	@Qualifier("myAllergyIntoleranceDaoR4")

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchMissingTest.java

@@ -0,0 +1,340 @@
+package ca.uhn.fhir.jpa.dao.r4;
+
+import ca.uhn.fhir.jpa.dao.DaoConfig;
+import ca.uhn.fhir.jpa.dao.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.*;
+import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
+import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.*;
+import org.junit.Before;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+
+import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.*;
+
+public class FhirResourceDaoR4SearchMissingTest extends BaseJpaR4Test {
+	private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4SearchMissingTest.class);
+
+	@Before
+	public void beforeResetMissing() {
+		myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
+	}
+
+	@Test
+	public void testIndexMissingFieldsDisabledDontAllowInSearch() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
+
+		SearchParameterMap params = new SearchParameterMap();
+		params.add("foo", new StringParam().setMissing(true));
+		try {
+			myPatientDao.search(params);
+		} catch (MethodNotAllowedException e) {
+			assertEquals(":missing modifier is disabled on this server", e.getMessage());
+		}
+	}
+
+	@Test
+	public void testIndexMissingFieldsDisabledDontCreateIndexes() {
+		myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.DISABLED);
+		Organization org = new Organization();
+		org.setActive(true);
+		myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
+
+		assertThat(mySearchParamDao.findAll(), empty());
+		assertThat(mySearchParamPresentDao.findAll(), empty());
+		assertThat(myResourceIndexedSearchParamStringDao.findAll(), empty());
+		assertThat(myResourceIndexedSearchParamDateDao.findAll(), empty());
+		assertThat(myResourceIndexedSearchParamTokenDao.findAll(), hasSize(1));
+		assertThat(myResourceIndexedSearchParamQuantityDao.findAll(), empty());
+
+	}
+
+	@SuppressWarnings("unused")
+	@Test
+	public void testSearchResourceReferenceMissingChain() {
+		IIdType oid1;
+		{
+			Organization org = new Organization();
+			org.setActive(true);
+			oid1 = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
+		}
+		IIdType tid1;
+		{
+			Task task = new Task();
+			task.getRequester().setOnBehalfOf(new Reference(oid1));
+			tid1 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
+		}
+		IIdType tid2;
+		{
+			Task task = new Task();
+			task.setOwner(new Reference(oid1));
+			tid2 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		IIdType oid2;
+		{
+			Organization org = new Organization();
+			org.setActive(true);
+			org.setName("NAME");
+			oid2 = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
+		}
+		IIdType tid3;
+		{
+			Task task = new Task();
+			task.getRequester().setOnBehalfOf(new Reference(oid2));
+			tid3 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
+		}
+
+		SearchParameterMap map;
+		List<IIdType> ids;
+
+		map = new SearchParameterMap();
+		map.add(Organization.SP_NAME, new StringParam().setMissing(true));
+		ids = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
+		assertThat(ids, contains(oid1));
+
+		ourLog.info("Starting Search 2");
+
+		map = new SearchParameterMap();
+		map.add(Task.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "true"));
+		ids = toUnqualifiedVersionlessIds(myTaskDao.search(map));
+		assertThat(ids, contains(tid1)); // NOT tid2
+
+		map = new SearchParameterMap();
+		map.add(Task.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "false"));
+		ids = toUnqualifiedVersionlessIds(myTaskDao.search(map));
+		assertThat(ids, contains(tid3));
+
+		map = new SearchParameterMap();
+		map.add(Task.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "true"));
+		ids = toUnqualifiedVersionlessIds(myPatientDao.search(map));
+		assertThat(ids, empty());
+
+	}
+
+	@Test
+	public void testSearchWithMissingDate() {
+		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId();
+		IIdType notMissing;
+		IIdType missing;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
+			missing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
+			patient.addName().setFamily("Tester_testSearchStringParam").addGiven("John");
+			patient.setBirthDateElement(new DateType("2011-01-01"));
+			patient.getManagingOrganization().setReferenceElement(orgId);
+			notMissing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		// Date Param
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			DateParam param = new DateParam();
+			param.setMissing(false);
+			params.add(Patient.SP_BIRTHDATE, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, containsInRelativeOrder(notMissing));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
+		}
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			DateParam param = new DateParam();
+			param.setMissing(true);
+			params.add(Patient.SP_BIRTHDATE, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, containsInRelativeOrder(missing));
+			assertThat(patients, not(containsInRelativeOrder(notMissing)));
+		}
+	}
+
+	@Test
+	public void testSearchWithMissingDate2() {
+		MedicationRequest mr1 = new MedicationRequest();
+		mr1.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
+		mr1.addDosageInstruction().getTiming().addEventElement().setValueAsString("2017-01-01");
+		IIdType id1 = myMedicationRequestDao.create(mr1).getId().toUnqualifiedVersionless();
+
+		MedicationRequest mr2 = new MedicationRequest();
+		mr2.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
+		IIdType id2 = myMedicationRequestDao.create(mr2).getId().toUnqualifiedVersionless();
+
+		SearchParameterMap map = new SearchParameterMap();
+		map.add(MedicationRequest.SP_DATE, new DateParam().setMissing(true));
+		IBundleProvider results = myMedicationRequestDao.search(map);
+		List<String> ids = toUnqualifiedVersionlessIdValues(results);
+
+		assertThat(ids, contains(id2.getValue()));
+
+	}
+
+	@Test
+	public void testSearchWithMissingQuantity() {
+		IIdType notMissing;
+		IIdType missing;
+		{
+			Observation obs = new Observation();
+			obs.addIdentifier().setSystem("urn:system").setValue("001");
+			missing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+		{
+			Observation obs = new Observation();
+			obs.addIdentifier().setSystem("urn:system").setValue("002");
+			obs.setValue(new Quantity(123));
+			notMissing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+		// Quantity Param
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			QuantityParam param = new QuantityParam();
+			param.setMissing(false);
+			params.add(Observation.SP_VALUE_QUANTITY, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
+			assertThat(patients, containsInRelativeOrder(notMissing));
+		}
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			QuantityParam param = new QuantityParam();
+			param.setMissing(true);
+			params.add(Observation.SP_VALUE_QUANTITY, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients, containsInRelativeOrder(missing));
+			assertThat(patients, not(containsInRelativeOrder(notMissing)));
+		}
+	}
+
+	@Test
+	public void testSearchWithMissingReference() {
+		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId().toUnqualifiedVersionless();
+		IIdType notMissing;
+		IIdType missing;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
+			missing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
+			patient.addName().setFamily("Tester_testSearchStringParam").addGiven("John");
+			patient.setBirthDateElement(new DateType("2011-01-01"));
+			patient.getManagingOrganization().setReferenceElement(orgId);
+			notMissing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		// Reference Param
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			ReferenceParam param = new ReferenceParam();
+			param.setMissing(false);
+			params.add(Patient.SP_ORGANIZATION, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
+			assertThat(patients, containsInRelativeOrder(notMissing));
+		}
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			ReferenceParam param = new ReferenceParam();
+			param.setMissing(true);
+			params.add(Patient.SP_ORGANIZATION, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, containsInRelativeOrder(missing));
+			assertThat(patients, not(containsInRelativeOrder(notMissing)));
+			assertThat(patients, not(containsInRelativeOrder(orgId)));
+		}
+	}
+
+	@Test
+	public void testSearchWithMissingString() {
+		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId();
+		IIdType notMissing;
+		IIdType missing;
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("001");
+			missing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		{
+			Patient patient = new Patient();
+			patient.addIdentifier().setSystem("urn:system").setValue("002");
+			patient.addName().setFamily("Tester_testSearchStringParam").addGiven("John");
+			patient.setBirthDateElement(new DateType("2011-01-01"));
+			patient.getManagingOrganization().setReferenceElement(orgId);
+			notMissing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
+		}
+		// String Param
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			StringParam param = new StringParam();
+			param.setMissing(false);
+			params.add(Patient.SP_FAMILY, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
+			assertThat(patients, containsInRelativeOrder(notMissing));
+		}
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			StringParam param = new StringParam();
+			param.setMissing(true);
+			params.add(Patient.SP_FAMILY, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
+			assertThat(patients, containsInRelativeOrder(missing));
+			assertThat(patients, not(containsInRelativeOrder(notMissing)));
+		}
+	}
+
+	@Test
+	public void testSearchWithToken() {
+		IIdType notMissing;
+		IIdType missing;
+		{
+			Observation obs = new Observation();
+			obs.addIdentifier().setSystem("urn:system").setValue("001");
+			missing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+		{
+			Observation obs = new Observation();
+			obs.addIdentifier().setSystem("urn:system").setValue("002");
+			obs.getCode().addCoding().setSystem("urn:system").setCode("002");
+			notMissing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
+		}
+		// Token Param
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			TokenParam param = new TokenParam();
+			param.setMissing(false);
+			params.add(Observation.SP_CODE, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients, not(containsInRelativeOrder(missing)));
+			assertThat(patients, containsInRelativeOrder(notMissing));
+		}
+		{
+			SearchParameterMap params = new SearchParameterMap();
+			params.setLoadSynchronous(true);
+			TokenParam param = new TokenParam();
+			param.setMissing(true);
+			params.add(Observation.SP_CODE, param);
+			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
+			assertThat(patients, containsInRelativeOrder(missing));
+			assertThat(patients, not(containsInRelativeOrder(notMissing)));
+		}
+	}
+
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchNoFtTest.java

@@ -1782,68 +1782,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
-	@SuppressWarnings("unused")
-	@Test
-	public void testSearchResourceReferenceMissingChain() {
-		IIdType oid1;
-		{
-			Organization org = new Organization();
-			org.setActive(true);
-			oid1 = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
-		}
-		IIdType tid1;
-		{
-			Task task = new Task();
-			task.getRequester().setOnBehalfOf(new Reference(oid1));
-			tid1 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
-		}
-		IIdType tid2;
-		{
-			Task task = new Task();
-			task.setOwner(new Reference(oid1));
-			tid2 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
-		}
-
-		IIdType oid2;
-		{
-			Organization org = new Organization();
-			org.setActive(true);
-			org.setName("NAME");
-			oid2 = myOrganizationDao.create(org, mySrd).getId().toUnqualifiedVersionless();
-		}
-		IIdType tid3;
-		{
-			Task task = new Task();
-			task.getRequester().setOnBehalfOf(new Reference(oid2));
-			tid3 = myTaskDao.create(task, mySrd).getId().toUnqualifiedVersionless();
-		}
-
-		SearchParameterMap map;
-		List<IIdType> ids;
-
-		map = new SearchParameterMap();
-		map.add(Organization.SP_NAME, new StringParam().setMissing(true));
-		ids = toUnqualifiedVersionlessIds(myOrganizationDao.search(map));
-		assertThat(ids, contains(oid1));
-
-		ourLog.info("Starting Search 2");
-
-		map = new SearchParameterMap();
-		map.add(Task.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "true"));
-		ids = toUnqualifiedVersionlessIds(myTaskDao.search(map));
-		assertThat(ids, contains(tid1)); // NOT tid2
-
-		map = new SearchParameterMap();
-		map.add(Task.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "false"));
-		ids = toUnqualifiedVersionlessIds(myTaskDao.search(map));
-		assertThat(ids, contains(tid3));
-
-		map = new SearchParameterMap();
-		map.add(Task.SP_ORGANIZATION, new ReferenceParam("Organization", "name:missing", "true"));
-		ids = toUnqualifiedVersionlessIds(myPatientDao.search(map));
-		assertThat(ids, empty());
-
-	}
 
 	@SuppressWarnings("unused")
 	@Test
@@ -2665,187 +2603,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 
 	}
 
-	@Test
-	public void testSearchWithMissingDate() {
-		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId();
-		IIdType notMissing;
-		IIdType missing;
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("001");
-			missing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("002");
-			patient.addName().setFamily("Tester_testSearchStringParam").addGiven("John");
-			patient.setBirthDateElement(new DateType("2011-01-01"));
-			patient.getManagingOrganization().setReferenceElement(orgId);
-			notMissing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		// Date Param
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			DateParam param = new DateParam();
-			param.setMissing(false);
-			params.add(Patient.SP_BIRTHDATE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, containsInRelativeOrder(notMissing));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
-		}
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			DateParam param = new DateParam();
-			param.setMissing(true);
-			params.add(Patient.SP_BIRTHDATE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, containsInRelativeOrder(missing));
-			assertThat(patients, not(containsInRelativeOrder(notMissing)));
-		}
-	}
-
-	@Test
-	public void testSearchWithMissingDate2() {
-		MedicationRequest mr1 = new MedicationRequest();
-		mr1.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
-		mr1.addDosageInstruction().getTiming().addEventElement().setValueAsString("2017-01-01");
-		IIdType id1 = myMedicationRequestDao.create(mr1).getId().toUnqualifiedVersionless();
-		
-		MedicationRequest mr2 = new MedicationRequest();
-		mr2.getCategory().addCoding().setSystem("urn:medicationroute").setCode("oral");
-		IIdType id2 = myMedicationRequestDao.create(mr2).getId().toUnqualifiedVersionless();
-
-		SearchParameterMap map = new SearchParameterMap();
-		map.add(MedicationRequest.SP_DATE, new DateParam().setMissing(true));
-		IBundleProvider results = myMedicationRequestDao.search(map);
-		List<String> ids = toUnqualifiedVersionlessIdValues(results);
-
-		assertThat(ids, contains(id2.getValue()));
-		
-	}
-
-	@Test
-	public void testSearchWithMissingQuantity() {
-		IIdType notMissing;
-		IIdType missing;
-		{
-			Observation obs = new Observation();
-			obs.addIdentifier().setSystem("urn:system").setValue("001");
-			missing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
-		}
-		{
-			Observation obs = new Observation();
-			obs.addIdentifier().setSystem("urn:system").setValue("002");
-			obs.setValue(new Quantity(123));
-			notMissing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
-		}
-		// Quantity Param
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			QuantityParam param = new QuantityParam();
-			param.setMissing(false);
-			params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
-			assertThat(patients, containsInRelativeOrder(notMissing));
-		}
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			QuantityParam param = new QuantityParam();
-			param.setMissing(true);
-			params.add(Observation.SP_VALUE_QUANTITY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
-			assertThat(patients, containsInRelativeOrder(missing));
-			assertThat(patients, not(containsInRelativeOrder(notMissing)));
-		}
-	}
-
-	@Test
-	public void testSearchWithMissingReference() {
-		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId().toUnqualifiedVersionless();
-		IIdType notMissing;
-		IIdType missing;
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("001");
-			missing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("002");
-			patient.addName().setFamily("Tester_testSearchStringParam").addGiven("John");
-			patient.setBirthDateElement(new DateType("2011-01-01"));
-			patient.getManagingOrganization().setReferenceElement(orgId);
-			notMissing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		// Reference Param
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			ReferenceParam param = new ReferenceParam();
-			param.setMissing(false);
-			params.add(Patient.SP_ORGANIZATION, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
-			assertThat(patients, containsInRelativeOrder(notMissing));
-		}
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			ReferenceParam param = new ReferenceParam();
-			param.setMissing(true);
-			params.add(Patient.SP_ORGANIZATION, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, containsInRelativeOrder(missing));
-			assertThat(patients, not(containsInRelativeOrder(notMissing)));
-			assertThat(patients, not(containsInRelativeOrder(orgId)));
-		}
-	}
-
-	@Test
-	public void testSearchWithMissingString() {
-		IIdType orgId = myOrganizationDao.create(new Organization(), mySrd).getId();
-		IIdType notMissing;
-		IIdType missing;
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("001");
-			missing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		{
-			Patient patient = new Patient();
-			patient.addIdentifier().setSystem("urn:system").setValue("002");
-			patient.addName().setFamily("Tester_testSearchStringParam").addGiven("John");
-			patient.setBirthDateElement(new DateType("2011-01-01"));
-			patient.getManagingOrganization().setReferenceElement(orgId);
-			notMissing = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless();
-		}
-		// String Param
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			StringParam param = new StringParam();
-			param.setMissing(false);
-			params.add(Patient.SP_FAMILY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
-			assertThat(patients, containsInRelativeOrder(notMissing));
-		}
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			StringParam param = new StringParam();
-			param.setMissing(true);
-			params.add(Patient.SP_FAMILY, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myPatientDao.search(params));
-			assertThat(patients, containsInRelativeOrder(missing));
-			assertThat(patients, not(containsInRelativeOrder(notMissing)));
-		}
-	}
 
 	@Test
 	public void testSearchWithNoResults() {
@@ -3063,43 +2820,6 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
 		}
 	}
 
-	@Test
-	public void testSearchWithToken() {
-		IIdType notMissing;
-		IIdType missing;
-		{
-			Observation obs = new Observation();
-			obs.addIdentifier().setSystem("urn:system").setValue("001");
-			missing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
-		}
-		{
-			Observation obs = new Observation();
-			obs.addIdentifier().setSystem("urn:system").setValue("002");
-			obs.getCode().addCoding().setSystem("urn:system").setCode("002");
-			notMissing = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
-		}
-		// Token Param
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			TokenParam param = new TokenParam();
-			param.setMissing(false);
-			params.add(Observation.SP_CODE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
-			assertThat(patients, not(containsInRelativeOrder(missing)));
-			assertThat(patients, containsInRelativeOrder(notMissing));
-		}
-		{
-			SearchParameterMap params = new SearchParameterMap();
-			params.setLoadSynchronous(true);
-			TokenParam param = new TokenParam();
-			param.setMissing(true);
-			params.add(Observation.SP_CODE, param);
-			List<IIdType> patients = toUnqualifiedVersionlessIds(myObservationDao.search(params));
-			assertThat(patients, containsInRelativeOrder(missing));
-			assertThat(patients, not(containsInRelativeOrder(notMissing)));
-		}
-	}
 
 	/**
 	 * https://chat.fhir.org/#narrow/stream/implementers/topic/Understanding.20_include

src/changes/changes.xml

@@ -379,6 +379,11 @@
 				Subscriptions in JPA server now support "email" delivery type through the 
 				use of a new interceptor which handles that type
 			</action>
+			<action type="add">
+				JPA server can now be configured to not support
+				<![CDATA[<code>:missing</code>]]> modifiers, which
+				increases write performance since fewer indexes are written
+			</action>
 		</release>
 		<release version="2.5" date="2017-06-08">
 			<action type="fix">