Get content search working correctly

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

@@ -800,8 +800,14 @@ public class JsonParser extends BaseParser implements IParser {
 
 		if (theResource instanceof IBaseBinary) {
 			IBaseBinary bin = (IBaseBinary) theResource;
-			theEventWriter.write("contentType", bin.getContentType());
+			String contentType = bin.getContentType();
-			theEventWriter.write("content", bin.getContentAsBase64());
+			if (isNotBlank(contentType)) {
+				theEventWriter.write("contentType", contentType);
+			}
+			String contentAsBase64 = bin.getContentAsBase64();
+			if (isNotBlank(contentAsBase64)) {
+				theEventWriter.write("content", contentAsBase64);
+			}
 		} else {
 			encodeCompositeElementToStreamWriter(theResDef, theResource, theResource, theEventWriter, resDef, theContainedResource, new CompositeChildElement(resDef));
 		}

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

@@ -52,8 +52,10 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.Validate;
 import org.apache.http.NameValuePair;
 import org.apache.http.client.utils.URLEncodedUtils;
+import org.hl7.fhir.instance.model.api.IBaseDatatype;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.TransactionStatus;
@@ -695,7 +697,11 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 		}
 
-		for (ResourceTag next : new ArrayList<ResourceTag>(theEntity.getTags())) {
+		ArrayList<ResourceTag> existingTags = new ArrayList<ResourceTag>();
+		if (theEntity.isHasTags()) {
+			existingTags.addAll(theEntity.getTags());
+		}
+		for (ResourceTag next : existingTags) {
 			TagDefinition nextDef = next.getTag();
 			if (!allDefs.contains(nextDef)) {
 				if (shouldDroppedTagBeRemovedOnUpdate(theEntity, next)) {
@@ -1224,23 +1230,38 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			theEntity.setVersion(theEntity.getVersion() + 1);
 		}
 
-		boolean paramsStringPopulated = theEntity.isParamsStringPopulated();
+		Collection<ResourceIndexedSearchParamString> paramsString = new ArrayList<ResourceIndexedSearchParamString>();
-		boolean paramsTokenPopulated = theEntity.isParamsTokenPopulated();
+		if (theEntity.isParamsStringPopulated()) {
-		boolean paramsNumberPopulated = theEntity.isParamsNumberPopulated();
+			paramsString.addAll(theEntity.getParamsString());
-		boolean paramsQuantityPopulated = theEntity.isParamsQuantityPopulated();
+		}
-		boolean paramsDatePopulated = theEntity.isParamsDatePopulated();
+		Collection<ResourceIndexedSearchParamToken> paramsToken = new ArrayList<ResourceIndexedSearchParamToken>();
-		boolean paramsCoordsPopulated = theEntity.isParamsCoordsPopulated();
+		if (theEntity.isParamsTokenPopulated()) {
-		boolean paramsUriPopulated = theEntity.isParamsUriPopulated();
+			paramsToken.addAll(theEntity.getParamsToken());
-		boolean hasLinks = theEntity.isHasLinks();
+		}
-
+		Collection<ResourceIndexedSearchParamNumber> paramsNumber = new ArrayList<ResourceIndexedSearchParamNumber>();
-		Collection<ResourceIndexedSearchParamString> paramsString = new ArrayList<ResourceIndexedSearchParamString>(theEntity.getParamsString()); // TODO: use the isPopulated method to decide whether to call this
+		if (theEntity.isParamsNumberPopulated()) {
-		Collection<ResourceIndexedSearchParamToken> paramsToken = new ArrayList<ResourceIndexedSearchParamToken>(theEntity.getParamsToken());
+			paramsNumber.addAll(theEntity.getParamsNumber());
-		Collection<ResourceIndexedSearchParamNumber> paramsNumber = new ArrayList<ResourceIndexedSearchParamNumber>(theEntity.getParamsNumber());
+		}
-		Collection<ResourceIndexedSearchParamQuantity> paramsQuantity = new ArrayList<ResourceIndexedSearchParamQuantity>(theEntity.getParamsQuantity());
+		Collection<ResourceIndexedSearchParamQuantity> paramsQuantity = new ArrayList<ResourceIndexedSearchParamQuantity>();
-		Collection<ResourceIndexedSearchParamDate> paramsDate = new ArrayList<ResourceIndexedSearchParamDate>(theEntity.getParamsDate());
+		if (theEntity.isParamsQuantityPopulated()) {
-		Collection<ResourceIndexedSearchParamUri> paramsUri = new ArrayList<ResourceIndexedSearchParamUri>(theEntity.getParamsUri());
+			paramsQuantity.addAll(theEntity.getParamsQuantity());
-		Collection<ResourceIndexedSearchParamCoords> paramsCoords = new ArrayList<ResourceIndexedSearchParamCoords>(theEntity.getParamsCoords());
+		}
-		Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>(theEntity.getResourceLinks());
+		Collection<ResourceIndexedSearchParamDate> paramsDate = new ArrayList<ResourceIndexedSearchParamDate>();
+		if (theEntity.isParamsDatePopulated()) {
+			paramsDate.addAll(theEntity.getParamsDate());
+		}
+		Collection<ResourceIndexedSearchParamUri> paramsUri = new ArrayList<ResourceIndexedSearchParamUri>();
+		if (theEntity.isParamsUriPopulated()) {
+			paramsUri.addAll(theEntity.getParamsUri());
+		}
+		Collection<ResourceIndexedSearchParamCoords> paramsCoords = new ArrayList<ResourceIndexedSearchParamCoords>();
+		if (theEntity.isParamsCoordsPopulated()) {
+			paramsCoords.addAll(theEntity.getParamsCoords());
+		}
+		Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>();
+		if (theEntity.isHasLinks()) {
+			resourceLinks.addAll(theEntity.getResourceLinks());
+		}
 
 		Set<ResourceIndexedSearchParamString> stringParams = null;
 		Set<ResourceIndexedSearchParamToken> tokenParams = null;
@@ -1264,6 +1285,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			theEntity.setDeleted(theDeletedTimestampOrNull);
 			theEntity.setUpdated(theDeletedTimestampOrNull);
 			theEntity.setNarrativeTextParsedIntoWords(null);
+			theEntity.setContentTextParsedIntoWords(null);
 
 		} else {
 
@@ -1313,6 +1335,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				theEntity.setHasLinks(links.isEmpty() == false);
 				theEntity.setIndexStatus(INDEX_STATUS_INDEXED);
 				theEntity.setNarrativeTextParsedIntoWords(parseNarrativeTextIntoWords(theResource));
+				theEntity.setContentTextParsedIntoWords(parseContentTextIntoWords(theResource));
 
 			} else {
 
@@ -1342,83 +1365,69 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 
 		if (thePerformIndexing) {
 
-			if (paramsStringPopulated) {
 			for (ResourceIndexedSearchParamString next : paramsString) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamString next : stringParams) {
 				myEntityManager.persist(next);
 			}
 
-			if (paramsTokenPopulated) {
 			for (ResourceIndexedSearchParamToken next : paramsToken) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamToken next : tokenParams) {
 				myEntityManager.persist(next);
 			}
 
-			if (paramsNumberPopulated) {
 			for (ResourceIndexedSearchParamNumber next : paramsNumber) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamNumber next : numberParams) {
 				myEntityManager.persist(next);
 			}
 
-			if (paramsQuantityPopulated) {
 			for (ResourceIndexedSearchParamQuantity next : paramsQuantity) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamQuantity next : quantityParams) {
 				myEntityManager.persist(next);
 			}
 
 			// Store date SP's
-			if (paramsDatePopulated) {
 			for (ResourceIndexedSearchParamDate next : paramsDate) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamDate next : dateParams) {
 				myEntityManager.persist(next);
 			}
 
 			// Store URI SP's
-			if (paramsUriPopulated) {
 			for (ResourceIndexedSearchParamUri next : paramsUri) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamUri next : uriParams) {
 				myEntityManager.persist(next);
 			}
 
 			// Store Coords SP's
-			if (paramsCoordsPopulated) {
 			for (ResourceIndexedSearchParamCoords next : paramsCoords) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceIndexedSearchParamCoords next : coordsParams) {
 				myEntityManager.persist(next);
 			}
 
-			if (hasLinks) {
 			for (ResourceLink next : resourceLinks) {
 				myEntityManager.remove(next);
 			}
-			}
 			for (ResourceLink next : links) {
 				myEntityManager.persist(next);
 			}
 
 		} // if thePerformIndexing
 
+		theEntity = myEntityManager.merge(theEntity);
+
 		myEntityManager.flush();
 
 		if (theResource != null) {
@@ -1502,4 +1511,20 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return b.toString();
 	}
 
+	private String parseContentTextIntoWords(IResource theResource) {
+		StringBuilder b = new StringBuilder();
+		@SuppressWarnings("rawtypes")
+		List<IPrimitiveType> childElements = getContext().newTerser().getAllPopulatedChildElementsOfType(theResource, IPrimitiveType.class);
+		for (@SuppressWarnings("rawtypes") IPrimitiveType nextType : childElements) {
+			String nextValue = nextType.getValueAsString();
+			if (isNotBlank(nextValue)) {
+				if (b.length() > 0 && b.charAt(b.length() - 1) != ' ') {
+					b.append(' ');
+				}
+				b.append(nextValue);
+			}
+		}
+		return b.toString();
+	}
+
 }

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

@@ -44,7 +44,7 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
 		BooleanJunction<?> bool = qb.bool();
 		
 		List<List<? extends IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
-		addTextSearch(qb, bool, contentAndTerms, "myParamsString.myValueComplete");
+		addTextSearch(qb, bool, contentAndTerms, "myContentText");
 		
 		List<List<? extends IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
 		addTextSearch(qb, bool, textAndTerms, "myNarrativeText");

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

@@ -30,6 +30,7 @@ import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.MappedSuperclass;
 
+import org.hibernate.search.annotations.ContainedIn;
 import org.hibernate.search.annotations.Field;
 
 @MappedSuperclass
@@ -50,6 +51,7 @@ public abstract class BaseResourceIndexedSearchParam implements Serializable {
 
 	@ManyToOne(optional = false)
 	@JoinColumn(name = "RES_ID", referencedColumnName="RES_ID")
+	@ContainedIn
 	private ResourceTable myResource;
 
 	@Field

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.entity;
 import java.io.Serializable;
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
@@ -31,6 +32,7 @@ import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
+@Embeddable
 @Entity
 @Table(name = "HFJ_HISTORY_TAG")
 public class ResourceHistoryTag extends BaseTag implements Serializable {

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.Table;
 
@@ -29,9 +30,9 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.search.annotations.Field;
-import org.hibernate.search.annotations.Indexed;
 
 //@formatter:off
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_COORDS" /* , indexes = { @Index(name = "IDX_SP_TOKEN", columnList = "SP_SYSTEM,SP_VALUE") } */)
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_COORDS", indexes = { 

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.entity;
 import java.util.Date;
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.Table;
 import javax.persistence.Temporal;
@@ -33,9 +34,9 @@ import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.search.annotations.Field;
-import org.hibernate.search.annotations.Indexed;
 
 //@formatter:off
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_DATE" /*, indexes= {@Index(name="IDX_SP_DATE", columnList= "SP_VALUE_LOW,SP_VALUE_HIGH")}*/)
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_DATE", indexes= {

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.entity;
 import java.math.BigDecimal;
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.Table;
 
@@ -38,6 +39,7 @@ import org.hibernate.search.annotations.NumericField;
 import ca.uhn.fhir.jpa.util.BigDecimalNumericFieldBridge;
 
 //@formatter:off
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_NUMBER" /*, indexes= {@Index(name="IDX_SP_NUMBER", columnList="SP_VALUE")}*/ )
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_NUMBER", indexes= {

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

@@ -23,6 +23,7 @@ package ca.uhn.fhir.jpa.entity;
 import java.math.BigDecimal;
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.Table;
 
@@ -38,6 +39,7 @@ import org.hibernate.search.annotations.NumericField;
 import ca.uhn.fhir.jpa.util.BigDecimalNumericFieldBridge;
 
 //@formatter:off
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_QUANTITY" /*, indexes= {@Index(name="IDX_SP_NUMBER", columnList="SP_VALUE")}*/ )
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_QUANTITY", indexes= {

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

@@ -21,7 +21,10 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.StringUtils;
@@ -29,9 +32,10 @@ import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.hibernate.search.annotations.ContainedIn;
 import org.hibernate.search.annotations.Field;
-import org.hibernate.search.annotations.Indexed;
 
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_STRING"/* , indexes= {@Index(name="IDX_SP_STRING", columnList="SP_VALUE_NORMALIZED")} */)
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_STRING", indexes = { 
@@ -49,9 +53,11 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 	@Column(name = "SP_VALUE_NORMALIZED", length = MAX_LENGTH, nullable = true)
 	private String myValueNormalized;
 
-	@Column(name="SP_VALUE_EXACT", insertable=false, updatable=false)
+	@ManyToOne(optional = false)
-	@Field
+	@JoinColumn(name = "RES_ID", referencedColumnName="RES_ID", insertable=false, updatable=false)
-	private String myValueComplete;
+	@ContainedIn
+	private ResourceTable myResourceTable;
+
 
 	public ResourceIndexedSearchParamString() {
 	}
@@ -103,7 +109,6 @@ public class ResourceIndexedSearchParamString extends BaseResourceIndexedSearchP
 			throw new IllegalArgumentException("Value is too long: " + theValueExact.length());
 		}
 		myValueExact = theValueExact;
-		myValueComplete = theValueExact;
 	}
 
 	public void setValueNormalized(String theValueNormalized) {

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.Table;
 
@@ -32,6 +33,7 @@ import org.apache.commons.lang3.builder.ToStringStyle;
 import org.hibernate.search.annotations.Field;
 import org.hibernate.search.annotations.Indexed;
 
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_TOKEN" /* , indexes = { @Index(name = "IDX_SP_TOKEN", columnList = "SP_SYSTEM,SP_VALUE") } */)
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_TOKEN", indexes = { @org.hibernate.annotations.Index(name = "IDX_SP_TOKEN", columnNames = { "RES_TYPE", "SP_NAME", "SP_SYSTEM", "SP_VALUE" }),

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

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.entity;
  */
 
 import javax.persistence.Column;
+import javax.persistence.Embeddable;
 import javax.persistence.Entity;
 import javax.persistence.Table;
 
@@ -33,6 +34,7 @@ import org.hibernate.search.annotations.Field;
 import org.hibernate.search.annotations.Indexed;
 
 //@formatter:off
+@Embeddable
 @Entity
 @Table(name = "HFJ_SPIDX_URI" /* , indexes = { @Index(name = "IDX_SP_TOKEN", columnList = "SP_SYSTEM,SP_VALUE") } */)
 @org.hibernate.annotations.Table(appliesTo = "HFJ_SPIDX_URI", indexes = { 

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

@@ -49,7 +49,7 @@ import ca.uhn.fhir.rest.server.Constants;
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 
 //@formatter:off
-@Indexed(interceptor=IndexNonDeletedInterceptor.class)	
+@Indexed(/*interceptor=IndexNonDeletedInterceptor.class*/)	
 @Entity
 @Table(name = "HFJ_RESOURCE", uniqueConstraints = {}, indexes= {
 	@Index(name = "IDX_RES_DATE", columnList="RES_UPDATED"), 
@@ -86,55 +86,56 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	/**
 	 * Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
 	 */
-	@Column(name = "SP_NARRATIVE_TEXT", length = Integer.MAX_VALUE - 1)
+	@Column(name = "SP_NARRATIVE_TEXT", length = Integer.MAX_VALUE - 1, nullable=true)
 	@Lob
 	@Field()
 	private String myNarrativeText;
 
+	/**
+	 * Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
+	 */
+	@Column(name = "SP_CONTENT_TEXT", length = Integer.MAX_VALUE - 1, nullable=true)
+	@Lob
+	@Field()
+	private String myContentText;
+
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamCoords> myParamsCoords;
 
 	@Column(name = "SP_COORDS_PRESENT")
 	private boolean myParamsCoordsPopulated;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamDate> myParamsDate;
 
 	@Column(name = "SP_DATE_PRESENT")
 	private boolean myParamsDatePopulated;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamNumber> myParamsNumber;
 
 	@Column(name = "SP_NUMBER_PRESENT")
 	private boolean myParamsNumberPopulated;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamQuantity> myParamsQuantity;
 
 	@Column(name = "SP_QUANTITY_PRESENT")
 	private boolean myParamsQuantityPopulated;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamString> myParamsString;
 
 	@Column(name = "SP_STRING_PRESENT")
 	private boolean myParamsStringPopulated;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamToken> myParamsToken;
 
 	@Column(name = "SP_TOKEN_PRESENT")
 	private boolean myParamsTokenPopulated;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)
-	@IndexedEmbedded
 	private Collection<ResourceIndexedSearchParamUri> myParamsUri;
 
 	@Column(name = "SP_URI_PRESENT")
@@ -324,6 +325,10 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		myNarrativeText = theNarrativeText;
 	}
 
+	public void setContentTextParsedIntoWords(String theContentText) {
+		myContentText = theContentText;
+	}
+
 	public void setParamsCoords(Collection<ResourceIndexedSearchParamCoords> theParamsCoords) {
 		if (!isParamsTokenPopulated() && theParamsCoords.isEmpty()) {
 			return;
@@ -447,9 +452,11 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 		retVal.setDeleted(getDeleted());
 		retVal.setForcedId(getForcedId());
 
+		if (isHasTags()) {
 			for (ResourceTag next : getTags()) {
 				retVal.addTag(next);
 			}
+		}
 		
 		return retVal;
 	}

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

@@ -33,6 +33,6 @@ public class IndexNonDeletedInterceptor implements EntityIndexingInterceptor<Res
 
 	@Override
 	public IndexingOverride onCollectionUpdate(ResourceTable entity) {
-		return onUpdate(entity);
+		return IndexingOverride.APPLY_DEFAULT;
 	}
 }

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoDstu2SearchFtTest.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.dao;
 
+import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.empty;
 import static org.junit.Assert.assertThat;
 
 import java.util.List;
@@ -32,6 +34,53 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		ftem.flushToIndexes();
 	}
 
+	@Test
+	public void testSearchAndReindex() {
+		Patient patient;
+		SearchParameterMap map;
+		
+		patient = new Patient();
+		patient.getText().setDiv("<div>DIVAAA</div>");
+		patient.addName().addGiven("NAMEAAA");
+		IIdType pId1 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+		
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), contains(pId1));
+
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_TEXT, new StringParam("DIVAAA"));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), contains(pId1));
+		
+		/*
+		 * Reindex
+		 */
+		
+		patient = new Patient();
+		patient.setId(pId1);
+		patient.getText().setDiv("<div>DIVBBB</div>");
+		patient.addName().addGiven("NAMEBBB");
+		myPatientDao.update(patient);
+
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEAAA"));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), empty());
+
+		map = new SearchParameterMap();
+		map.add(Patient.SP_NAME, new StringParam("NAMEBBB"));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), contains(pId1));
+
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_CONTENT, new StringParam("NAMEBBB"));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), contains(pId1));
+
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_TEXT, new StringParam("DIVBBB"));
+		assertThat(toUnqualifiedVersionlessIds(myPatientDao.search(map)), contains(pId1));
+		
+
+	}
+
 	@Test
 	public void testSearchWithChainedParams() {
 		String methodName = "testSearchWithChainedParams";

hapi-fhir-jpaserver-base/src/test/resources/META-INF/persistence.xml

@@ -37,7 +37,7 @@
 			<property name="hibernate.cache.use_structured_entries" value="false" />
 			<property name="hibernate.search.default.directory_provider" value="filesystem"/>
 			<property name="hibernate.search.default.indexBase" value="./target/lucene_indexes"/>
-			<entry key="hibernate.search.lucene_version" value="LUCENE_CURRENT" />
+			<property name="hibernate.search.lucene_version" value="LUCENE_CURRENT" />
 			<!-- 
 			<property name="hibernate.ejb.naming_strategy" value="ca.uhn.fhir.jpa.util.CustomNamingStrategy" />
 			 -->

hapi-fhir-jpaserver-uhnfhirtest/src/main/resources/hapi-fhir-server-database-config-dstu2.xml

@@ -55,7 +55,7 @@
 				<entry key="hibernate.cache.use_second_level_cache" value="false" />
 				<entry key="hibernate.cache.use_structured_entries" value="false" />
 				<entry key="hibernate.search.default.directory_provider" value="filesystem" />
-				<entry key="hibernate.search.default.indexBase" value="#{systemProperties['fhir.lucene.location.dstu2']};" />
+				<entry key="hibernate.search.default.indexBase" value="#{systemProperties['fhir.lucene.location.dstu2']}" />
 				<entry key="hibernate.search.lucene_version" value="LUCENE_CURRENT" />
 			</map>
 		</property>

hapi-fhir-jpaserver-uhnfhirtest/src/main/webapp/WEB-INF/web.xml

@@ -17,6 +17,7 @@
 			classpath:hapi-fhir-server-resourceproviders-dstu1.xml
 			classpath:hapi-fhir-server-resourceproviders-dstu2.xml
 			classpath:fhir-spring-subscription-config-dstu2.xml
+			classpath:fhir-spring-search-config-dstu2.xml
 		</param-value>
 	</context-param>
 

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java

@@ -66,6 +66,13 @@ public class JsonParserDstu2Test {
 		assertThat(encoded, containsString("\"div\":\"" + expected.replace("\"", "\\\"") + "\""));
 	}
 	
+	
+	@Test
+	public void testEncodeEmptyBinary() {
+		String output = ourCtx.newJsonParser().encodeResourceToString(new Binary());
+		assertEquals("{\"resourceType\":\"Binary\"}", output);
+	}
+
 	@Test
 	public void testNamespacePreservationParse() throws Exception {
 		String input = "{\"resourceType\":\"Patient\",\"text\":{\"div\":\"<xhtml:div xmlns:xhtml=\\\"http://www.w3.org/1999/xhtml\\\"><xhtml:img src=\\\"foo\\\"/>@fhirabend</xhtml:div>\"}}";

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/XmlParserDstu2Test.java

@@ -124,6 +124,13 @@ public class XmlParserDstu2Test {
 
 	}
 	
+	@Test
+	public void testEncodeEmptyBinary() {
+		String output = ourCtx.newXmlParser().encodeResourceToString(new Binary());
+		assertEquals("<Binary xmlns=\"http://hl7.org/fhir\"/>", output);
+	}
+
+
 	@Test
 	public void testContainedResourceInExtensionUndeclared() {
 		Patient p = new Patient();

src/changes/changes.xml

@@ -170,6 +170,10 @@
 				number of unneeded dependencies. Thanks to Thomas Andersen
 				for the pull request!
 			</action>
+			<action type="fix">
+				Fix a crash when encoding a Binary resource in JSON encoding
+				if the resource has no content-type
+			</action>
 		</release>
 		<release version="1.2" date="2015-09-18">
 			<action type="add">