Fulltext searching works

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/OperationParameter.java

@@ -110,7 +110,7 @@ public class OperationParameter implements IParameter {
 			myMax = 1;
 		}
 		
-		myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType);
+		myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType) || String.class.equals(myParameterType);
 		
 		/*
 		 * The parameter can be of type string for validation methods - This is a bit
@@ -173,6 +173,12 @@ public class OperationParameter implements IParameter {
 						DateRangeParam dateRangeParam = new DateRangeParam();
 						dateRangeParam.setValuesAsQueryTokens(parameters);
 						matchingParamValues.add(dateRangeParam);
+					} else if (String.class.isAssignableFrom(myParameterType)) {
+						
+						for (String next : paramValues) {
+							matchingParamValues.add(next);
+						}
+						
 					} else {
 						for (String nextValue : paramValues) {
 							FhirContext ctx = theRequest.getServer().getFhirContext();

hapi-fhir-jpaserver-base/pom.xml

@@ -78,7 +78,6 @@
 		<dependency>
 			<groupId>org.javassist</groupId>
 			<artifactId>javassist</artifactId>
-			<version>3.20.0-GA</version>
 		</dependency>
 
 		<dependency>
@@ -239,6 +238,14 @@
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-search-orm</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-highlighter</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-analyzers-phonetic</artifactId>
+		</dependency>
 
 		<!-- Misc -->
 		<dependency>

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

@@ -31,6 +31,7 @@ import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -1189,6 +1190,12 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		return translateForcedIdToPid(theId, myEntityManager);
 	}
 
+	public static void validateResourceType(BaseHasResource theEntity, String theResourceName) {
+		if (!theResourceName.equals(theEntity.getResourceType())) {
+			throw new ResourceNotFoundException("Resource with ID " + theEntity.getIdDt().getIdPart() + " exists but it is not of type " + theResourceName + ", found resource of type " + theEntity.getResourceType());
+		}
+	}
+
 	static Long translateForcedIdToPid(IIdType theId, EntityManager entityManager) {
 		if (isValidPid(theId)) {
 			return theId.getIdPartAsLong();
@@ -1271,9 +1278,9 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		if (theEntity.isParamsCoordsPopulated()) {
 			paramsCoords.addAll(theEntity.getParamsCoords());
 		}
-		Collection<ResourceLink> resourceLinks = new ArrayList<ResourceLink>();
+		Collection<ResourceLink> existingResourceLinks = new ArrayList<ResourceLink>();
 		if (theEntity.isHasLinks()) {
-			resourceLinks.addAll(theEntity.getResourceLinks());
+			existingResourceLinks.addAll(theEntity.getResourceLinks());
 		}
 
 		Set<ResourceIndexedSearchParamString> stringParams = null;
@@ -1326,6 +1333,19 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 				}
 
 				links = extractResourceLinks(theEntity, theResource);
+
+				/* 
+				 * If the existing resource already has links and those match links we still want,
+				 * use them instead of removing them and re adding them 
+				 */
+				for (Iterator<ResourceLink> existingLinkIter = existingResourceLinks.iterator(); existingLinkIter.hasNext(); ) {
+					ResourceLink nextExisting = existingLinkIter.next();
+					if (links.remove(nextExisting)) {
+						existingLinkIter.remove();
+						links.add(nextExisting);
+					}
+				}
+				
 				populateResourceIntoEntity(theResource, theEntity);
 
 				theEntity.setUpdated(theUpdateTime);
@@ -1431,7 +1451,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 			}
 
 			// Store resource links
-			for (ResourceLink next : resourceLinks) {
+			for (ResourceLink next : existingResourceLinks) {
 				myEntityManager.remove(next);
 			}
 			for (ResourceLink next : links) {

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

@@ -1045,9 +1045,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
 	}
 
 	private void validateResourceType(BaseHasResource entity) {
-		if (!myResourceName.equals(entity.getResourceType())) {
+		validateResourceType(entity, myResourceName);
-			throw new ResourceNotFoundException("Resource with ID " + entity.getIdDt().getIdPart() + " exists but it is not of type " + myResourceName + ", found resource of type " + entity.getResourceType());
-		}
 	}
 
 	private void validateResourceTypeAndThrowIllegalArgumentException(IIdType theId) {

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

@@ -23,7 +23,9 @@ package ca.uhn.fhir.jpa.dao;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
@@ -32,23 +34,37 @@ import javax.persistence.PersistenceContext;
 import javax.persistence.PersistenceContextType;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Validate;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+import org.apache.lucene.analysis.Analyzer;
+import org.apache.lucene.analysis.TokenStream;
+import org.apache.lucene.analysis.core.KeywordAnalyzer;
 import org.apache.lucene.search.Query;
+import org.apache.lucene.search.highlight.Formatter;
+import org.apache.lucene.search.highlight.Highlighter;
+import org.apache.lucene.search.highlight.QueryScorer;
+import org.apache.lucene.search.highlight.Scorer;
+import org.apache.lucene.search.highlight.SimpleHTMLFormatter;
+import org.apache.lucene.search.highlight.TokenGroup;
 import org.hibernate.search.jpa.FullTextEntityManager;
 import org.hibernate.search.jpa.FullTextQuery;
 import org.hibernate.search.query.dsl.BooleanJunction;
 import org.hibernate.search.query.dsl.QueryBuilder;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.transaction.annotation.Transactional;
 
-import ca.uhn.fhir.context.FhirContext;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
+
+import ca.uhn.fhir.jpa.dao.FhirSearchDao.MySuggestionFormatter;
 import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.model.api.IQueryParameterType;
 import ca.uhn.fhir.model.dstu.resource.BaseResource;
 import ca.uhn.fhir.model.primitive.IdDt;
 import ca.uhn.fhir.rest.param.StringParam;
 import ca.uhn.fhir.rest.server.Constants;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISearchDao {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirSearchDao.class);
@@ -56,61 +72,6 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	private EntityManager myEntityManager;
 
-	@Transactional()
-	@Override
-	public List<Long> search(String theResourceName, SearchParameterMap theParams) {
-		return doSearch(theResourceName, theParams, null);
-	}
-
-	private List<Long> doSearch(String theResourceName, SearchParameterMap theParams, Long theReferencingPid) {
-		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
-		
-		QueryBuilder qb = em
-				.getSearchFactory()
-				.buildQueryBuilder()
-				.forEntity(ResourceTable.class).get();
-		
-		BooleanJunction<?> bool = qb.bool();
-		
-		List<List<? extends IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
-		addTextSearch(qb, bool, contentAndTerms, "myContentText");
-		
-		List<List<? extends IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
-		addTextSearch(qb, bool, textAndTerms, "myNarrativeText");
-
-		if (theReferencingPid != null) {
-			bool.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(theReferencingPid).createQuery());
-		}
-		
-		if (bool.isEmpty()) {
-			return null;
-		}
-		
-		if (isNotBlank(theResourceName)) {
-			bool.must(qb.keyword().onField("myResourceType").matching(theResourceName).createQuery());
-		}
-		
-		Query luceneQuery = bool.createQuery();
-
-		// wrap Lucene query in a javax.persistence.Query
-		FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, ResourceTable.class);
-		jpaQuery.setProjection("myId");
-		
-		// execute search
-		List<?> result = jpaQuery.getResultList();
-		
-		ArrayList<Long> retVal = new ArrayList<Long>();
-		for (Object object : result) {
-			Object[] nextArray = (Object[]) object;
-			Long next = (Long)nextArray[0];
-			if (next != null) {
-				retVal.add(next);
-			}
-		}
-
-		return retVal;
-	}
-
 	private void addTextSearch(QueryBuilder qb, BooleanJunction<?> bool, List<List<? extends IQueryParameterType>> contentAndTerms, String field) {
 		if (contentAndTerms == null) {
 			return;
@@ -131,9 +92,55 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
 		}
 	}
 
+	private List<Long> doSearch(String theResourceName, SearchParameterMap theParams, Long theReferencingPid) {
+		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
+
+		QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
+
+		BooleanJunction<?> bool = qb.bool();
+
+		List<List<? extends IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
+		addTextSearch(qb, bool, contentAndTerms, "myContentText");
+
+		List<List<? extends IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
+		addTextSearch(qb, bool, textAndTerms, "myNarrativeText");
+
+		if (theReferencingPid != null) {
+			bool.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(theReferencingPid).createQuery());
+		}
+
+		if (bool.isEmpty()) {
+			return null;
+		}
+
+		if (isNotBlank(theResourceName)) {
+			bool.must(qb.keyword().onField("myResourceType").matching(theResourceName).createQuery());
+		}
+
+		Query luceneQuery = bool.createQuery();
+
+		// wrap Lucene query in a javax.persistence.Query
+		FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, ResourceTable.class);
+		jpaQuery.setProjection("myId");
+
+		// execute search
+		List<?> result = jpaQuery.getResultList();
+
+		ArrayList<Long> retVal = new ArrayList<Long>();
+		for (Object object : result) {
+			Object[] nextArray = (Object[]) object;
+			Long next = (Long) nextArray[0];
+			if (next != null) {
+				retVal.add(next);
+			}
+		}
+
+		return retVal;
+	}
+
 	@Override
 	public List<Long> everything(String theResourceName, SearchParameterMap theParams) {
-		
+
 		Long pid = null;
 		if (theParams.get(BaseResource.SP_RES_ID) != null) {
 			StringParam idParm = (StringParam) theParams.get(BaseResource.SP_RES_ID).get(0).get(0);
@@ -148,6 +155,133 @@ public class FhirSearchDao extends BaseHapiFhirDao<IBaseResource> implements ISe
 		return retVal;
 	}
 
+	@Transactional()
+	@Override
+	public List<Long> search(String theResourceName, SearchParameterMap theParams) {
+		return doSearch(theResourceName, theParams, null);
+	}
 
+	@Override
+	public List<Suggestion> suggestKeywords(String theContext, String theSearchParam, String theText) {
+		Validate.notBlank(theContext, "theContext must be provided");
+		Validate.notBlank(theSearchParam, "theSearchParam must be provided");
+		Validate.notBlank(theText, "theSearchParam must be provided");
+		
+		long start = System.currentTimeMillis();
+		
+		String[] contextParts = StringUtils.split(theContext, '/');
+		if (contextParts.length != 3 || "Patient".equals(contextParts[0]) == false || "$everything".equals(contextParts[2]) == false) {
+			throw new InvalidRequestException("Invalid context: " + theContext);
+		}
+		IdDt contextId = new IdDt(contextParts[0], contextParts[1]);
+		Long pid = BaseHapiFhirDao.translateForcedIdToPid(contextId, myEntityManager);
+		
+		FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
+
+		QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(ResourceTable.class).get();
+
+		//@formatter:off
+		Query textQuery = qb
+				.phrase()
+				.withSlop(2)
+				.onField("myContentText").boostedTo(4.0f)
+				.andField("myContentTextEdgeNGram").boostedTo(2.0f)
+				.andField("myContentTextNGram").boostedTo(1.0f)
+				.andField("myContentTextPhonetic").boostedTo(0.5f)
+				.sentence(theText.toLowerCase()).createQuery();
+		
+		Query query = qb.bool()
+				.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(pid).createQuery())
+				.must(textQuery)
+				.createQuery();
+		//@formatter:on
+
+		FullTextQuery ftq = em.createFullTextQuery(query, ResourceTable.class);
+		ftq.setProjection("myContentText");
+		ftq.setMaxResults(20);
+
+		List<?> resultList = ftq.getResultList();
+		List<Suggestion> suggestions = Lists.newArrayList();
+		for (Object next : resultList) {
+			Object[] nextAsArray = (Object[]) next;
+			String nextValue = (String) nextAsArray[0];
+
+			try {
+				MySuggestionFormatter formatter = new MySuggestionFormatter(suggestions);
+
+				Scorer scorer = new QueryScorer(textQuery);
+				Highlighter highlighter = new Highlighter(formatter, scorer);
+
+				Analyzer analyzer = em.getSearchFactory().getAnalyzer(ResourceTable.class);
+				highlighter.getBestFragment(analyzer.tokenStream("myContentText", nextValue), nextValue);
+				highlighter.getBestFragment(analyzer.tokenStream("myContentTextNGram", nextValue), nextValue);
+				highlighter.getBestFragment(analyzer.tokenStream("myContentTextEdgeNGram", nextValue), nextValue);
+				highlighter.getBestFragment(analyzer.tokenStream("myContentTextPhonetic", nextValue), nextValue);
+			} catch (Exception e) {
+				throw new InternalErrorException(e);
+			}
+
+		}
+
+		Collections.sort(suggestions);
+		
+		Set<String> terms = Sets.newHashSet();
+		for (Iterator<Suggestion> iter = suggestions.iterator(); iter.hasNext(); ) {
+			if (!terms.add(iter.next().getTerm())) {
+				iter.remove();
+			}
+		}
+		
+		long delay = System.currentTimeMillis()- start;
+		ourLog.info("Provided {} suggestions for term {} in {} ms", new Object[] {terms.size(), theText, delay});
+		
+		return suggestions;
+	}
+
+	public static class Suggestion implements Comparable<Suggestion> {
+		public Suggestion(String theTerm, float theScore) {
+			myTerm = theTerm;
+			myScore = theScore;
+		}
+
+		public String getTerm() {
+			return myTerm;
+		}
+
+		public float getScore() {
+			return myScore;
+		}
+
+		private String myTerm;
+		private float myScore;
+
+		@Override
+		public int compareTo(Suggestion theO) {
+			return Float.compare(theO.myScore, myScore);
+		}
+
+		@Override
+		public String toString() {
+			return "Suggestion[myTerm=" + myTerm + ", myScore=" + myScore + "]";
+		}
+	}
+
+	public class MySuggestionFormatter implements Formatter {
+
+		private List<Suggestion> mySuggestions;
+
+		public MySuggestionFormatter(List<Suggestion> theSuggestions) {
+			mySuggestions = theSuggestions;
+		}
+
+		@Override
+		public String highlightTerm(String theOriginalText, TokenGroup theTokenGroup) {
+			if (theTokenGroup.getTotalScore() > 0) {
+				mySuggestions.add(new Suggestion(theOriginalText, theTokenGroup.getTotalScore()));
+			}
+			return null;
+		}
+
+	}
 
 }

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

@@ -22,8 +22,12 @@ package ca.uhn.fhir.jpa.dao;
 
 import java.util.List;
 
+import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
+
 public interface ISearchDao {
 
+	List<Suggestion> suggestKeywords(String theContext, String theSearchParam, String theText);
+	
 	List<Long> search(String theResourceName, SearchParameterMap theParams);
 
 	List<Long> everything(String theResourceName, SearchParameterMap theParams);

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

@@ -36,7 +36,6 @@ import javax.persistence.Table;
 import org.apache.commons.lang3.Validate;
 import org.apache.commons.lang3.builder.EqualsBuilder;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.hibernate.search.annotations.ContainedIn;
 import org.hibernate.search.annotations.Field;
 
 @Entity
@@ -72,9 +71,9 @@ public class ResourceLink implements Serializable {
 	@Column(name = "TARGET_RESOURCE_ID", insertable = false, updatable = false, nullable = false)
 	@Field()
 	private Long myTargetResourcePid;
-
+	
 	public ResourceLink() {
-		// nothing
+		super();
 	}
 
 	public ResourceLink(String theSourcePath, ResourceTable theSourceResource, ResourceTable theTargetResource) {
@@ -101,7 +100,7 @@ public class ResourceLink implements Serializable {
 		EqualsBuilder b = new EqualsBuilder();
 		b.append(mySourcePath, obj.mySourcePath);
 		b.append(mySourceResource, obj.mySourceResource);
-		b.append(myTargetResource, obj.myTargetResource);
+		b.append(myTargetResourcePid, obj.myTargetResourcePid);
 		return b.isEquals();
 	}
 
@@ -130,7 +129,7 @@ public class ResourceLink implements Serializable {
 		HashCodeBuilder b = new HashCodeBuilder();
 		b.append(mySourcePath);
 		b.append(mySourceResource);
-		b.append(myTargetResource);
+		b.append(myTargetResourcePid);
 		return b.toHashCode();
 	}
 

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

@@ -29,7 +29,6 @@ import java.util.Set;
 
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
-import javax.persistence.Embedded;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
@@ -42,9 +41,29 @@ import javax.persistence.Transient;
 
 import org.apache.commons.lang3.builder.ToStringBuilder;
 import org.apache.commons.lang3.builder.ToStringStyle;
+import org.apache.lucene.analysis.core.KeywordTokenizerFactory;
+import org.apache.lucene.analysis.core.LowerCaseFilterFactory;
+import org.apache.lucene.analysis.core.StopFilterFactory;
+import org.apache.lucene.analysis.miscellaneous.WordDelimiterFilterFactory;
+import org.apache.lucene.analysis.ngram.EdgeNGramFilterFactory;
+import org.apache.lucene.analysis.ngram.NGramFilterFactory;
+import org.apache.lucene.analysis.pattern.PatternReplaceFilterFactory;
+import org.apache.lucene.analysis.phonetic.PhoneticFilterFactory;
+import org.apache.lucene.analysis.snowball.SnowballPorterFilterFactory;
+import org.apache.lucene.analysis.standard.StandardFilterFactory;
+import org.apache.lucene.analysis.standard.StandardTokenizerFactory;
+import org.hibernate.search.annotations.Analyze;
+import org.hibernate.search.annotations.Analyzer;
+import org.hibernate.search.annotations.AnalyzerDef;
+import org.hibernate.search.annotations.AnalyzerDefs;
 import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.Fields;
 import org.hibernate.search.annotations.Indexed;
 import org.hibernate.search.annotations.IndexedEmbedded;
+import org.hibernate.search.annotations.Parameter;
+import org.hibernate.search.annotations.Store;
+import org.hibernate.search.annotations.TokenFilterDef;
+import org.hibernate.search.annotations.TokenizerDef;
 
 import ca.uhn.fhir.jpa.search.IndexNonDeletedInterceptor;
 import ca.uhn.fhir.model.primitive.IdDt;
@@ -60,6 +79,62 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 	@Index(name = "IDX_RES_PROFILE", columnList="RES_PROFILE"),
 	@Index(name = "IDX_INDEXSTATUS", columnList="SP_INDEX_STATUS") 
 })
+@AnalyzerDefs({
+	@AnalyzerDef(name = "autocompleteEdgeAnalyzer",
+		tokenizer = @TokenizerDef(factory = KeywordTokenizerFactory.class),
+		filters = {
+			@TokenFilterDef(factory = PatternReplaceFilterFactory.class, params = {
+				@Parameter(name = "pattern",value = "([^a-zA-Z0-9\\.])"),
+				@Parameter(name = "replacement", value = " "),
+				@Parameter(name = "replace", value = "all") 
+			}),
+			@TokenFilterDef(factory = LowerCaseFilterFactory.class),
+			@TokenFilterDef(factory = StopFilterFactory.class),
+			@TokenFilterDef(factory = EdgeNGramFilterFactory.class, params = {
+				@Parameter(name = "minGramSize", value = "3"),
+				@Parameter(name = "maxGramSize", value = "50") 
+			}) 
+		}),
+	@AnalyzerDef(name = "autocompletePhoneticAnalyzer",
+		tokenizer = @TokenizerDef(factory=StandardTokenizerFactory.class),
+		filters = {
+			@TokenFilterDef(factory=StandardFilterFactory.class),
+			@TokenFilterDef(factory=StopFilterFactory.class),
+			@TokenFilterDef(factory=PhoneticFilterFactory.class, params = {
+	        	@Parameter(name="encoder", value="DoubleMetaphone")
+			}),
+			@TokenFilterDef(factory=SnowballPorterFilterFactory.class, params = {
+				@Parameter(name="language", value="English") 
+			})
+		}),
+	@AnalyzerDef(name = "autocompleteNGramAnalyzer",
+		tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
+		filters = {
+			@TokenFilterDef(factory = WordDelimiterFilterFactory.class),
+			@TokenFilterDef(factory = LowerCaseFilterFactory.class),
+			@TokenFilterDef(factory = NGramFilterFactory.class, params = {
+				@Parameter(name = "minGramSize", value = "3"),
+				@Parameter(name = "maxGramSize", value = "20") 
+			}),
+//			@TokenFilterDef(factory = PatternReplaceFilterFactory.class, params = {
+//				@Parameter(name = "pattern",value = "([^a-zA-Z0-9\\.])"),
+//				@Parameter(name = "replacement", value = " "),
+//				@Parameter(name = "replace", value = "all") 
+//			})
+		}),
+	@AnalyzerDef(name = "standardAnalyzer",
+		tokenizer = @TokenizerDef(factory = StandardTokenizerFactory.class),
+		filters = {
+//			@TokenFilterDef(factory = WordDelimiterFilterFactory.class),
+			@TokenFilterDef(factory = LowerCaseFilterFactory.class),
+//			@TokenFilterDef(factory = PatternReplaceFilterFactory.class, params = {
+//				@Parameter(name = "pattern", value = "([^a-zA-Z0-9\\.])"),
+//				@Parameter(name = "replacement", value = " "),
+//				@Parameter(name = "replace", value = "all")
+//			})
+		}) // Def
+	}
+)
 //@formatter:on
 public class ResourceTable extends BaseHasResource implements Serializable {
 	private static final int MAX_LANGUAGE_LENGTH = 20;
@@ -72,8 +147,15 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	/**
 	 * Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
 	 */
+	//@formatter:off
 	@Transient()
-	@Field()
+	@Fields({
+		@Field(name = "myContentText", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
+		@Field(name = "myContentTextEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
+		@Field(name = "myContentTextNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteNGramAnalyzer")),
+		@Field(name = "myContentTextPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
+	})
+	//@formatter:on
 	private String myContentText;
 
 	@Column(name = "SP_HAS_LINKS")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/JpaSystemProviderDstu2.java

@@ -1,5 +1,9 @@
 package ca.uhn.fhir.jpa.provider;
 
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
+import java.util.List;
+
 /*
  * #%L
  * HAPI FHIR JPA Server
@@ -29,11 +33,15 @@ import javax.servlet.http.HttpServletRequest;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 
+import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
 import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.dao.ISearchDao;
 import ca.uhn.fhir.model.api.annotation.Description;
 import ca.uhn.fhir.model.dstu2.composite.MetaDt;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
 import ca.uhn.fhir.model.dstu2.resource.Parameters;
+import ca.uhn.fhir.model.dstu2.resource.Parameters.Parameter;
+import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IntegerDt;
 import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.annotation.Operation;
@@ -41,12 +49,16 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
 import ca.uhn.fhir.rest.annotation.Transaction;
 import ca.uhn.fhir.rest.annotation.TransactionParam;
 import ca.uhn.fhir.rest.method.RequestDetails;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 
 public class JpaSystemProviderDstu2 extends BaseJpaSystemProvider<Bundle> {
 
 	@Autowired()
 	@Qualifier("mySystemDaoDstu2")
 	private IFhirSystemDao<Bundle> mySystemDao;
+
+	@Autowired
+	private ISearchDao mySearchDao;
 	
 	//@formatter:off
 	// This is generated by hand:
@@ -176,12 +188,43 @@ public class JpaSystemProviderDstu2 extends BaseJpaSystemProvider<Bundle> {
 		@OperationParam(name="return", type=MetaDt.class)
 	})
 	//@formatter:on
-	public Parameters operation() {
+	public Parameters meta() {
 		Parameters parameters = new Parameters();
 		parameters.addParameter().setName("return").setValue(getDao().metaGetOperation());
 		return parameters;
 	}
 	
+	@Operation(name="$suggest-keywords", idempotent=true)
+	public Parameters suggestKeywords(
+			@OperationParam(name="context", min=1, max=1) String theContext,
+			@OperationParam(name="searchParam", min=1, max=1) String theSearchParam,
+			@OperationParam(name="text", min=1, max=1) String theText
+		) {
+		
+		if (isBlank(theContext)) {
+			throw new InvalidRequestException("Parameter 'context' must be provided");
+		}
+		if (isBlank(theSearchParam)) {
+			throw new InvalidRequestException("Parameter 'searchParam' must be provided");
+		}
+		if (isBlank(theText)) {
+			throw new InvalidRequestException("Parameter 'text' must be provided");
+		}
+		
+		List<Suggestion> keywords = mySearchDao.suggestKeywords(theContext, theSearchParam, theText);
+		
+		Parameters retVal = new Parameters();
+		for (Suggestion next : keywords) {
+			//@formatter:off
+			retVal.addParameter()
+					.addPart(new Parameter().setName("keyword").setValue(new StringDt(next.getTerm())))
+					.addPart(new Parameter().setName("score").setValue(new DecimalDt(next.getScore())));
+			//@formatter:on
+		}
+
+		return retVal;
+	}
+	
 	@Transaction
 	public Bundle transaction(RequestDetails theRequestDetails, @TransactionParam Bundle theResources) {
 		startRequest(theRequestDetails);

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaDstu2Test.java

@@ -7,7 +7,6 @@ import java.io.IOException;
 import java.io.InputStream;
 
 import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
 
 import org.apache.commons.io.IOUtils;
 import org.hibernate.search.jpa.FullTextEntityManager;
@@ -77,7 +76,8 @@ public abstract class BaseJpaDstu2Test extends BaseJpaTest {
 
 	@Autowired
 	protected ApplicationContext myAppCtx;
-
+	@Autowired
+	protected ISearchDao mySearchDao;
 	@Autowired
 	@Qualifier("myConceptMapDaoDstu2")
 	protected IFhirResourceDao<ConceptMap> myConceptMapDao;

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

@@ -4,8 +4,7 @@ import static org.hamcrest.Matchers.contains;
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.not;
-import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertThat;
 import static org.mockito.Mockito.mock;
 
 import java.util.List;
@@ -15,6 +14,7 @@ import javax.servlet.http.HttpServletRequest;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.Test;
 
+import ca.uhn.fhir.jpa.dao.FhirSearchDao.Suggestion;
 import ca.uhn.fhir.model.dstu2.resource.Device;
 import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
@@ -27,6 +27,72 @@ import ca.uhn.fhir.rest.server.Constants;
 public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 	
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoDstu2SearchFtTest.class);
+
+	@Test
+	public void testSuggest() {
+		Patient patient = new Patient();
+		patient.addName().addFamily("testSuggest");
+		IIdType ptId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		Observation obs = new Observation();
+		obs.getSubject().setReference(ptId);
+		obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
+		myObservationDao.create(obs);
+
+		obs = new Observation();
+		obs.getSubject().setReference(ptId);
+		obs.getCode().setText("MNBVCXZ");
+		myObservationDao.create(obs);
+
+		obs = new Observation();
+		obs.getSubject().setReference(ptId);
+		obs.getCode().setText("ZXC HELLO");
+		myObservationDao.create(obs);
+
+		/*
+		 * These shouldn't match since they're for another patient
+		 */
+		patient = new Patient();
+		patient.addName().addFamily("testSuggest2");
+		IIdType ptId2 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		Observation obs2 = new Observation();
+		obs2.getSubject().setReference(ptId2);
+		obs2.getCode().setText("ZXCVBNMZZ");
+		myObservationDao.create(obs2);
+
+		List<Suggestion> output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZXCVBNM");
+		ourLog.info("Found: " + output);
+		assertEquals(4, output.size());
+		assertEquals("ZXCVBNM", output.get(0).getTerm());
+		assertEquals("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL", output.get(1).getTerm());
+		assertEquals("ZXC", output.get(2).getTerm());
+		assertEquals("ZXC HELLO", output.get(3).getTerm());
+
+		output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZXC");
+		ourLog.info("Found: " + output);
+		assertEquals(4, output.size());
+		assertEquals("ZXC", output.get(0).getTerm());
+		assertEquals("ZXC HELLO", output.get(1).getTerm());
+		assertEquals("ZXCVBNM", output.get(2).getTerm());
+		assertEquals("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL", output.get(3).getTerm());
+
+		output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "HELO");
+		ourLog.info("Found: " + output);
+		assertEquals(1, output.size());
+		assertEquals("HELLO", output.get(0).getTerm());
+		
+		output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "Z");
+		ourLog.info("Found: " + output);
+		assertEquals(0, output.size());
+
+		output = mySearchDao.suggestKeywords("Patient/" + ptId.getIdPart() + "/$everything", "_content", "ZX");
+		ourLog.info("Found: " + output);
+		assertEquals(1, output.size());
+		assertEquals("ZXC", output.get(0).getTerm());
+
+	}
+	
 	
 	@Test
 	public void testSearchAndReindex() {
@@ -320,7 +386,7 @@ public class FhirResourceDaoDstu2SearchFtTest extends BaseJpaDstu2Test {
 		IIdType pId1;
 		{
 			Patient patient = new Patient();
-			patient.addName().addGiven("methodName");
+			patient.addName().addGiven(methodName);
 			patient.addAddress().addLine("My fulltext address");
 			pId1 = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
 		}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/FhirSearchDaoDstu2Test.java

@@ -6,15 +6,9 @@ import static org.junit.Assert.assertThat;
 
 import java.util.List;
 
-import org.hibernate.search.jpa.FullTextEntityManager;
-import org.hibernate.search.jpa.Search;
-import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.transaction.annotation.Transactional;
 
-import ca.uhn.fhir.jpa.entity.ResourceTable;
 import ca.uhn.fhir.model.dstu2.resource.Organization;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.rest.param.StringAndListParam;
@@ -27,14 +21,6 @@ public class FhirSearchDaoDstu2Test extends BaseJpaDstu2Test {
 	@Autowired
 	private ISearchDao mySearchDao;
 	
-	@Before
-	@Transactional
-	public void beforeFlushFT() {
-		  FullTextEntityManager ftem = Search.getFullTextEntityManager(myEntityManager);
-		  ftem.purgeAll(ResourceTable.class);
-		  ftem.flushToIndexes();
-	}
-	
 	@Test
 	public void testContentSearch() {
 		Long id1;

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -21,9 +21,12 @@ import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
 import org.eclipse.jetty.server.Server;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.dao.BaseJpaDstu2Test;
@@ -32,12 +35,16 @@ import ca.uhn.fhir.jpa.rp.dstu2.OrganizationResourceProvider;
 import ca.uhn.fhir.jpa.rp.dstu2.PatientResourceProvider;
 import ca.uhn.fhir.jpa.testutil.RandomServerPortProvider;
 import ca.uhn.fhir.model.dstu2.resource.Bundle;
+import ca.uhn.fhir.model.dstu2.resource.Observation;
 import ca.uhn.fhir.model.dstu2.resource.OperationDefinition;
 import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
+import ca.uhn.fhir.model.dstu2.resource.Parameters;
 import ca.uhn.fhir.model.dstu2.resource.Patient;
 import ca.uhn.fhir.model.dstu2.valueset.BundleTypeEnum;
 import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
+import ca.uhn.fhir.model.primitive.DecimalDt;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.model.primitive.StringDt;
 import ca.uhn.fhir.rest.client.IGenericClient;
 import ca.uhn.fhir.rest.server.EncodingEnum;
 import ca.uhn.fhir.rest.server.FifoMemoryPagingProvider;
@@ -177,6 +184,90 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 		}
 	}
 
+	@Transactional(propagation=Propagation.NEVER)
+	@Test
+	public void testSuggestKeywords() throws Exception {
+		
+		Patient patient = new Patient();
+		patient.addName().addFamily("testSuggest");
+		IIdType ptId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		Observation obs = new Observation();
+		obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
+		obs.getSubject().setReference(ptId);
+		IIdType obsId = myObservationDao.create(obs).getId().toUnqualifiedVersionless();
+
+		obs = new Observation();
+		obs.setId(obsId);
+		obs.getSubject().setReference(ptId);
+		obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
+		myObservationDao.update(obs);
+		
+		HttpGet get = new HttpGet(ourServerBase + "/$suggest-keywords?context=Patient/" + ptId.getIdPart() + "/$everything&searchParam=_content&text=zxc&_pretty=true&_format=xml");
+		CloseableHttpResponse http = ourHttpClient.execute(get);
+		try {
+			assertEquals(200, http.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(http.getEntity().getContent());
+			ourLog.info(output);
+			
+			Parameters parameters = ourCtx.newXmlParser().parseResource(Parameters.class, output);
+			assertEquals(2, parameters.getParameter().size());
+			assertEquals("keyword", parameters.getParameter().get(0).getPart().get(0).getName());
+			assertEquals(new StringDt("ZXCVBNM"), parameters.getParameter().get(0).getPart().get(0).getValue());
+			assertEquals("score", parameters.getParameter().get(0).getPart().get(1).getName());
+			assertEquals(new DecimalDt("1.0"), parameters.getParameter().get(0).getPart().get(1).getValue());
+			
+		} finally {
+			http.close();
+		}
+	}
+
+	@Test
+	public void testSuggestKeywordsInvalid() throws Exception {
+		Patient patient = new Patient();
+		patient.addName().addFamily("testSuggest");
+		IIdType ptId = myPatientDao.create(patient).getId().toUnqualifiedVersionless();
+
+		Observation obs = new Observation();
+		obs.getSubject().setReference(ptId);
+		obs.getCode().setText("ZXCVBNM ASDFGHJKL QWERTYUIOPASDFGHJKL");
+		myObservationDao.create(obs);
+		
+		HttpGet get = new HttpGet(ourServerBase + "/$suggest-keywords");
+		CloseableHttpResponse http = ourHttpClient.execute(get);
+		try {
+			assertEquals(400, http.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(http.getEntity().getContent());
+			ourLog.info(output);
+			assertThat(output, containsString("Parameter 'context' must be provided"));
+		} finally {
+			http.close();
+		}
+		
+		get = new HttpGet(ourServerBase + "/$suggest-keywords?context=Patient/" + ptId.getIdPart() + "/$everything");
+		http = ourHttpClient.execute(get);
+		try {
+			assertEquals(400, http.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(http.getEntity().getContent());
+			ourLog.info(output);
+			assertThat(output, containsString("Parameter 'searchParam' must be provided"));
+		} finally {
+			http.close();
+		}
+
+		get = new HttpGet(ourServerBase + "/$suggest-keywords?context=Patient/" + ptId.getIdPart() + "/$everything&searchParam=aa");
+		http = ourHttpClient.execute(get);
+		try {
+			assertEquals(400, http.getStatusLine().getStatusCode());
+			String output = IOUtils.toString(http.getEntity().getContent());
+			ourLog.info(output);
+			assertThat(output, containsString("Parameter 'text' must be provided"));
+		} finally {
+			http.close();
+		}
+
+	}
+
 	@Test
 	public void testGetOperationDefinition() {
 		OperationDefinition op = ourClient.read(OperationDefinition.class, "get-resource-counts");

pom.xml

@@ -367,6 +367,16 @@
 				<artifactId>httpcore</artifactId>
 				<version>4.4</version>
 			</dependency>
+			<dependency>
+				<groupId>org.apache.lucene</groupId>
+				<artifactId>lucene-highlighter</artifactId>
+				<version>5.3.0</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.lucene</groupId>
+				<artifactId>lucene-analyzers-phonetic</artifactId>
+				<version>5.3.0</version>
+			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.doxia</groupId>
 				<artifactId>doxia-module-markdown</artifactId>