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

hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplConditional.java

@@ -27,7 +27,7 @@ public class RuleImplConditional extends BaseRule implements IAuthRule {
 			return null;
 		}
 		
-		if (theOperation == RestOperationTypeEnum.UPDATE) {
+		if (theOperation == myOperationType) {
 			switch (myAppliesTo) {
 			case ALL_RESOURCES:
 				break;

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

@@ -1077,7 +1077,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 	@SuppressWarnings("unchecked")
 	protected ResourceTable updateEntity(final IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
 			boolean theUpdateVersion, Date theUpdateTime) {
-		ourLog.info("Starting entity update");
+		ourLog.debug("Starting entity update");
 
 		/*
 		 * This should be the very first thing..
@@ -1094,7 +1094,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
 		}
 
 		if (theEntity.getPublished() == null) {
-			ourLog.info("Entity has published time: {}", new InstantDt(theUpdateTime));
+			ourLog.debug("Entity has published time: {}", new InstantDt(theUpdateTime));
 
 			theEntity.setPublished(theUpdateTime);
 		}

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

@@ -27,7 +27,6 @@ import java.util.Collections;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 
 import javax.persistence.EntityManager;
@@ -67,7 +66,7 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 	@PersistenceContext(type = PersistenceContextType.TRANSACTION)
 	private EntityManager myEntityManager;
 
-	private void addTextSearch(QueryBuilder theQueryBuilder, BooleanJunction<?> theBoolean, List<List<? extends IQueryParameterType>> theTerms, String theFieldName) {
+	private void addTextSearch(QueryBuilder theQueryBuilder, BooleanJunction<?> theBoolean, List<List<? extends IQueryParameterType>> theTerms, String theFieldName, String theFieldNameEdgeNGram, String theFieldNameNGram) {
 		if (theTerms == null) {
 			return;
 		}
@@ -81,8 +80,21 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 				}
 			}
 			if (terms.isEmpty() == false) {
-				String joinedTerms = StringUtils.join(terms, ' ');
+				if (terms.size() == 1) {
-				theBoolean.must(theQueryBuilder.keyword().onField(theFieldName).matching(joinedTerms).createQuery());
+					//@formatter:off
+					Query textQuery = theQueryBuilder
+						.phrase()
+						.withSlop(2)
+						.onField(theFieldName).boostedTo(4.0f)
+//						.andField(theFieldNameEdgeNGram).boostedTo(2.0f)
+//						.andField(theFieldNameNGram).boostedTo(1.0f)
+						.sentence(terms.iterator().next().toLowerCase()).createQuery();
+					//@formatter:on
+					
+					theBoolean.must(textQuery);
+				} else {
+					String joinedTerms = StringUtils.join(terms, ' ');
+					theBoolean.must(theQueryBuilder.keyword().onField(theFieldName).matching(joinedTerms).createQuery());				}
 			}
 		}
 	}
@@ -144,13 +156,13 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 		 * Handle _content parameter (resource body content)
 		 */
 		List<List<? extends IQueryParameterType>> contentAndTerms = theParams.remove(Constants.PARAM_CONTENT);
-		addTextSearch(qb, bool, contentAndTerms, "myContentText");
+		addTextSearch(qb, bool, contentAndTerms, "myContentText", "myContentTextEdgeNGram", "myContentTextNGram");
 
 		/*
 		 * Handle _text parameter (resource narrative content)
 		 */
 		List<List<? extends IQueryParameterType>> textAndTerms = theParams.remove(Constants.PARAM_TEXT);
-		addTextSearch(qb, bool, textAndTerms, "myNarrativeText");
+		addTextSearch(qb, bool, textAndTerms, "myNarrativeText", "myNarrativeTextEdgeNGram", "myNarrativeTextNGram");
 
 		if (theReferencingPid != null) {
 			bool.must(qb.keyword().onField("myResourceLinks.myTargetResourcePid").matching(theReferencingPid).createQuery());
@@ -354,7 +366,7 @@ public class FulltextSearchSvcImpl extends BaseHapiFhirDao<IBaseResource> implem
 			myPartialMatchScores.add(1.0f);
 		}
 
-		public void setAnalyzer(String theString) {
+		public void setAnalyzer(String theString) { 
 			myAnalyzer = theString;
 		}
 

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

@@ -174,7 +174,12 @@ public class ResourceTable extends BaseHasResource implements Serializable {
 	 * Holds the narrative text only - Used for Fulltext searching but not directly stored in the DB
 	 */
 	@Transient()
-	@Field()
+	@Fields({
+		@Field(name = "myNarrativeText", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
+		@Field(name = "myNarrativeTextEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
+		@Field(name = "myNarrativeTextNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteNGramAnalyzer")),
+		@Field(name = "myNarrativeTextPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
+	})
 	private String myNarrativeText;
 
 	@OneToMany(mappedBy = "myResource", cascade = {}, fetch = FetchType.LAZY, orphanRemoval = false)

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchFtTest.java

@@ -48,7 +48,6 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 
 
 	@Test
-	@Ignore
 	public void testCodeTextSearch() {
 		Observation obs1 = new Observation();
 		obs1.getCode().setText("Systolic Blood Pressure");
@@ -66,15 +65,51 @@ public class FhirResourceDaoDstu3SearchFtTest extends BaseJpaDstu3Test {
 		SearchParameterMap map;
 		
 		map = new SearchParameterMap();
-		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
+		map.add(Observation.SP_CODE, new TokenParam(null, "systolic").setModifier(TokenParamModifier.TEXT));
+		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
+
+//		map = new SearchParameterMap();
+//		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
+//		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
+//
+//		map = new SearchParameterMap();
+//		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
+//		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(map)), empty());
+//
+//		map = new SearchParameterMap();
+//		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
+//		map.add(Constants.PARAM_CONTENT, new StringParam("obs1"));
+//		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
+
+	}
+
+
+	@Test
+	public void testResourceTextSearch() {
+		Observation obs1 = new Observation();
+		obs1.getCode().setText("Systolic Blood Pressure");
+		obs1.setStatus(ObservationStatus.FINAL);
+		obs1.setValue(new Quantity(123));
+		obs1.setComment("obs1");
+		IIdType id1 = myObservationDao.create(obs1, mySrd).getId().toUnqualifiedVersionless();
+		
+		Observation obs2 = new Observation();
+		obs2.getCode().setText("Diastolic Blood Pressure");
+		obs2.setStatus(ObservationStatus.FINAL);
+		obs2.setValue(new Quantity(81));
+		IIdType id2 = myObservationDao.create(obs2, mySrd).getId().toUnqualifiedVersionless();
+		
+		SearchParameterMap map;
+		
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_CONTENT, new StringParam("systolic"));
+		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
+
+		map = new SearchParameterMap();
+		map.add(Constants.PARAM_CONTENT, new StringParam("blood"));
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1, id2)));
 
 		map = new SearchParameterMap();
-		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
-		assertThat(toUnqualifiedVersionlessIdValues(myPatientDao.search(map)), empty());
-
-		map = new SearchParameterMap();
-		map.add(Observation.SP_CODE, new TokenParam(null, "blood").setModifier(TokenParamModifier.TEXT));
 		map.add(Constants.PARAM_CONTENT, new StringParam("obs1"));
 		assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(map)), containsInAnyOrder(toValues(id1)));
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirSearchDaoDstu3Test.java

@@ -126,6 +126,11 @@ public class FhirSearchDaoDstu3Test extends BaseJpaDstu3Test {
 			patient.getText().setDivAsString("<div>AAAB<p>FOO</p> CCC    </div>");
 			id2 = myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
 		}
+		{
+			Patient patient = new Patient();
+			patient.getText().setDivAsString("<div>ZZYZXY</div>");
+			myPatientDao.create(patient, mySrd).getId().toUnqualifiedVersionless().getIdPartAsLong();
+		}
 
 		SearchParameterMap map = new SearchParameterMap();
 		String resourceName = "Patient";

hapi-fhir-jpaserver-base/src/test/resources/mihin-resource-dstu3.json

@@ -0,0 +1,129 @@
+{
+	"resourceType": "Patient",
+	"id": "Patient-66468",
+	"meta": {
+		"versionId": "5",
+		"lastUpdated": "2016-08-14T19:18:18.000-04:00"
+	},
+	"text": {
+		"status": "generated",
+		"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"> <div class=\"hapiHeaderText\"> Shawn Freeman <b>MACK </b> </div> <table class=\"hapiPropertyTable\"> <tbody> <tr> <td>Identifier</td> <td>000066468</td> </tr> <tr> <td>Address</td> <td> <span>170 NE Cherry Circle </span> <br/> <span>Detroit </span> <span>MI </span> </td> </tr> <tr> <td>Date of birth</td> <td> <span>12 April 2036</span> </td> </tr> </tbody> </table> </div>"
+	},
+	"extension": [
+		{
+			"url": "http://hl7.org/fhir/StructureDefinition/us-core-race",
+			"valueCodeableConcept": {
+				"coding": [
+					{
+						"system": "http://hl7.org/fhir/v3/Race",
+						"code": "2056-0",
+						"display": "Black"
+					}
+				]
+			}
+		},
+		{
+			"url": "http://hl7.org/fhir/StructureDefinition/us-core-ethnicity",
+			"valueCodeableConcept": {
+				"coding": [
+					{
+						"system": "http://hl7.org/fhir/v3/Ethnicity",
+						"code": "2186-5",
+						"display": "Not Hispanic or Latino"
+					}
+				]
+			}
+		},
+		{
+			"url": "http://hl7.org/fhir/StructureDefinition/us-core-religion",
+			"valueCodeableConcept": {
+				"coding": [
+					{
+						"system": "http://hl7.org/fhir/v3/ReligiousAffiliation",
+						"code": "1013",
+						"display": "Christian (non-Catholic, non-specific) "
+					}
+				]
+			}
+		}
+	],
+	"identifier": [
+		{
+			"use": "official",
+			"type": {
+				"coding": [
+					{
+						"system": "http://hl7.org/fhir/identifier-type",
+						"code": "SB",
+						"display": "Social Beneficiary Identifier"
+					}
+				],
+				"text": "US Social Security Number"
+			},
+			"system": "http://hl7.org/fhir/sid/us-ssn",
+			"value": "000066468"
+		},
+		{
+			"use": "official",
+			"type": {
+				"coding": [
+					{
+						"system": "http://hl7.org/fhir/identifier-type",
+						"code": "SB",
+						"display": "Social Beneficiary Identifier"
+					}
+				],
+				"text": "Michigan Common Key Service Identifier"
+			},
+			"system": "http://mihin.org/fhir/cks",
+			"value": "31d50ab72d5a4239b36594f8f67eb3ab"
+		}
+	],
+	"active": false,
+	"name": [
+		{
+			"family": [
+				"Mack"
+			],
+			"given": [
+				"Shawn",
+				"Freeman"
+			]
+		}
+	],
+	"telecom": [
+		{
+			"system": "phone",
+			"value": "313.555.0956",
+			"use": "home"
+		},
+		{
+			"system": "phone",
+			"value": "313.555.8028",
+			"use": "work"
+		},
+		{
+			"extension": [
+				{
+					"url": "http://hl7.org/fhir/StructureDefinition/us-core-direct",
+					"valueBoolean": true
+				}
+			],
+			"system": "email",
+			"value": "Shawn.F.Mack@direct.mihintest.org",
+			"use": "home"
+		}
+	],
+	"gender": "male",
+	"birthDate": "2036-04-12",
+	"address": [
+		{
+			"line": [
+				"170 NE Cherry Circle"
+			],
+			"city": "Detroit",
+			"state": "MI",
+			"postalCode": "48227"
+		}
+	]
+}

hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/rest/server/interceptor/auth/AuthorizationInterceptorDstu2Test.java

@@ -1053,7 +1053,7 @@ public class AuthorizationInterceptorDstu2Test {
 		httpPost.setEntity(createFhirResourceEntity(createPatient(null)));
 		status = ourClient.execute(httpPost);
 		response = extractResponseAndClose(status);
-		assertEquals(200, status.getStatusLine().getStatusCode());
+		assertEquals(201, status.getStatusLine().getStatusCode());
 		assertTrue(ourHitMethod);
 
 	}
@@ -1078,11 +1078,13 @@ public class AuthorizationInterceptorDstu2Test {
 		HttpResponse status;
 		String response;
 
+		ourReturn = Arrays.asList(createPatient(1));
+
 		ourHitMethod = false;
 		httpDelete = new HttpDelete("http://localhost:" + ourPort + "/Patient?foo=bar");
 		status = ourClient.execute(httpDelete);
 		response = extractResponseAndClose(status);
-		assertEquals(200, status.getStatusLine().getStatusCode());
+		assertEquals(204, status.getStatusLine().getStatusCode());
 		assertTrue(ourHitMethod);
 
 	}

src/changes/changes.xml

@@ -161,6 +161,10 @@
 				if it contained custom fields that also used custom
 				types. Thanks to GitHub user @sjanic for reporting!
 			</action>
+			<action type="add">
+				Inprove handling of _text and _content searches in JPA server to do better
+				matching on partial strings
+			</action>
 			<action type="add">
 				Servers in STU3 mode will now ignore any ID or VersionID found in the
 				resource body provided by the client when processing FHIR