Mergeback of rel_6_8

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/UrlPathTokenizer.java

@@ -19,18 +19,45 @@
  */
 package ca.uhn.fhir.util;
 
-import java.util.StringTokenizer;
+import ca.uhn.fhir.i18n.Msg;
+import org.apache.commons.lang3.ArrayUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.NoSuchElementException;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
 
 public class UrlPathTokenizer {
 
-	private final StringTokenizer myTok;
+	private String[] tokens;
+	private int curPos;
 
 	public UrlPathTokenizer(String theRequestPath) {
-		myTok = new StringTokenizer(theRequestPath, "/");
+		if (theRequestPath == null) {
+			theRequestPath = "";
+		}
+		tokens = removeBlanksAndSanitize(theRequestPath.split("/"));
+		curPos = 0;
 	}
 
 	public boolean hasMoreTokens() {
-		return myTok.hasMoreTokens();
+		return curPos < tokens.length;
+	}
+
+	public int countTokens() {
+		return tokens.length;
+	}
+
+	/**
+	 * Returns the next token without updating the current position.
+	 * Will throw NoSuchElementException if there are no more tokens.
+	 */
+	public String peek() {
+		if (!hasMoreTokens()) {
+			throw new NoSuchElementException(Msg.code(2420) + "Attempt to retrieve URL token out of bounds");
+		}
+		return tokens[curPos];
 	}
 
 	/**
@@ -43,6 +70,22 @@ public boolean hasMoreTokens() {
 	 * @see UrlUtil#unescape(String)
 	 */
 	public String nextTokenUnescapedAndSanitized() {
-		return UrlUtil.sanitizeUrlPart(UrlUtil.unescape(myTok.nextToken()));
+		String token = peek();
+		curPos++;
+		return token;
+	}
+
+	/**
+	 * Given an array of Strings, this method will return all the non-blank entries in that
+	 * array, after running sanitizeUrlPart() and unescape() on them.
+	 */
+	private static String[] removeBlanksAndSanitize(String[] theInput) {
+		List<String> output = new ArrayList<>();
+		for (String s : theInput) {
+			if (!isBlank(s)) {
+				output.add(UrlUtil.sanitizeUrlPart(UrlUtil.unescape(s)));
+			}
+		}
+		return output.toArray(ArrayUtils.EMPTY_STRING_ARRAY);
 	}
 }

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5117-fix-no-match-mdm-score-included-in-total-score.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5117
+title: "Previously, all MDM field scores, including `NO_MATCH`es, were included in the final total MDM score. This has 
+now been fixed so that only `MATCH`ed fields are included in the total MDM score."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5119-consent-removing-all-resources-suppresses-next-link-in-bundle.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5119
+jira: SMILE-7090
+title: "Previously, when the consent service would remove all resources to be returned, the response bundle would
+ not provide the previous/next link(s). This has been corrected."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_8_0/5126-hfj_res_ver_prov-might-cause-migration-error-on-db-that-automatically-indexes-the-primary-key.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 5126
+title: "Previously, updating from Hapi-fhir 6.6.0 to 6.8.0 would cause migration error, it is now fixed."

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -126,8 +126,13 @@ protected void init680() {
 				.withColumns("RES_VER_PID")
 				.failureAllowed();
 
+		// drop the index for any database that has RES_PID column already indexed from previous migrations
 		version.onTable("HFJ_RES_VER_PROV")
-				.addIndex("20230510.2", "IDX_RESVERPROV_RES_PID")
+				.dropIndex("20230510.2", "FK_RESVERPROV_RES_PID")
+				.failureAllowed();
+
+		version.onTable("HFJ_RES_VER_PROV")
+				.addIndex("20230510.3", "IDX_RESVERPROV_RES_PID")
 				.unique(false)
 				.withColumns("RES_PID");
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java

@@ -336,8 +336,13 @@ private NpmPackage addPackageToCacheInternal(NpmPackageData thePackageData) {
 
 			String dirName = "package";
 			NpmPackage.NpmPackageFolder packageFolder = npmPackage.getFolders().get(dirName);
-			for (Map.Entry<String, List<String>> nextTypeToFiles :
-					packageFolder.getTypes().entrySet()) {
+			Map<String, List<String>> packageFolderTypes = null;
+			try {
+				packageFolderTypes = packageFolder.getTypes();
+			} catch (IOException e) {
+				throw new InternalErrorException(Msg.code(2371) + e);
+			}
+			for (Map.Entry<String, List<String>> nextTypeToFiles : packageFolderTypes.entrySet()) {
 				String nextType = nextTypeToFiles.getKey();
 				for (String nextFile : nextTypeToFiles.getValue()) {
 

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/loader/PackageResourceParsingSvc.java

@@ -49,8 +49,13 @@ public List<IBaseResource> parseResourcesOfType(String theType, NpmPackage thePk
 			return Collections.emptyList();
 		}
 		ArrayList<IBaseResource> resources = new ArrayList<>();
-		List<String> filesForType =
-				thePkg.getFolders().get("package").getTypes().get(theType);
+		List<String> filesForType = null;
+		try {
+			filesForType = thePkg.getFolders().get("package").getTypes().get(theType);
+		} catch (IOException e) {
+			throw new InternalErrorException(
+					Msg.code(2370) + "Cannot install resource of type " + theType + ": Could not get types", e);
+		}
 		if (filesForType != null) {
 			for (String file : filesForType) {
 				try {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/interceptor/ForceOffsetSearchModeInterceptorTest.java

@@ -15,6 +15,7 @@
 import static org.hamcrest.Matchers.containsString;
 import static org.hamcrest.Matchers.empty;
 import static org.hamcrest.Matchers.emptyOrNullString;
+import static org.hamcrest.Matchers.hasSize;
 import static org.hamcrest.Matchers.is;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNull;
@@ -125,6 +126,36 @@ public void testSearch_NoExplicitCount() {
 
 	}
 
+	@Test
+	public void testPagingNextLink_whenAllResourcesHaveBeenReturned_willNotBePresent(){
+
+		myServer.setDefaultPageSize(5);
+
+		for (int i = 0; i < 10; i++) {
+			createPatient(withId("A" + i), withActiveTrue());
+		}
+
+		Bundle outcome = myClient
+			.search()
+			.forResource("Patient")
+			.where(Patient.ACTIVE.exactly().code("true"))
+			.returnBundle(Bundle.class)
+			.execute();
+
+		assertThat(outcome.getEntry(), hasSize(5));
+
+		Bundle secondPageBundle = myClient.loadPage().next(outcome).execute();
+
+		assertThat(secondPageBundle.getEntry(), hasSize(5));
+
+		Bundle thirdPageBundle = myClient.loadPage().next(secondPageBundle).execute();
+
+		assertThat(thirdPageBundle.getEntry(), hasSize(0));
+		assertNull(thirdPageBundle.getLink("next"), () -> thirdPageBundle.getLink("next").getUrl());
+
+	}
+
+
 
 	@Test
 	public void testSearch_WithExplicitCount() {
@@ -179,7 +210,6 @@ public void testSearch_WithExplicitCount() {
 		assertEquals(1, myCaptureQueriesListener.countCommits());
 		assertEquals(0, myCaptureQueriesListener.countRollbacks());
 
-		assertThat(outcome.getLink(Constants.LINK_NEXT).getUrl(), containsString("Patient?_count=7&_offset=14&active=true"));
 		assertThat(outcome.getLink(Constants.LINK_PREVIOUS).getUrl(), containsString("Patient?_count=7&_offset=0&active=true"));
 
 	}

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ConsentInterceptorResourceProviderR4Test.java

@@ -745,6 +745,42 @@ public void testGraphQL_MaskLinkedResource() throws IOException {
 
 	}
 
+	@Test
+	public void testPaging_whenResourceViewingIsRejected_responseBundleWillHaveNextLink(){
+		// given
+		create50Observations();
+
+		myConsentInterceptor = new ConsentInterceptor(new ConsentSvcRejectWillSeeResource());
+		myServer.getRestfulServer().getInterceptorService().registerInterceptor(myConsentInterceptor);
+
+		// when
+		Bundle results = myClient.search().forResource(Observation.class).count(10).returnBundle(Bundle.class).execute();
+		assertThat(results.getEntry(), hasSize(0));
+
+		// then
+		String nextUrl = BundleUtil.getLinkUrlOfType(myFhirContext, results, "next");
+		assertThat(nextUrl, containsString("_getpagesoffset=10"));
+
+	}
+
+	@Test
+	public void testPaging_whenResourceViewingIsRejected_secondPageWillHavePreviousLink(){
+		// given
+		create50Observations();
+
+		myConsentInterceptor = new ConsentInterceptor(new ConsentSvcRejectWillSeeResource());
+		myServer.getRestfulServer().getInterceptorService().registerInterceptor(myConsentInterceptor);
+
+		// when
+		Bundle results = myClient.search().forResource(Observation.class).count(10).returnBundle(Bundle.class).execute();
+		Bundle nextResults = myClient.loadPage().next(results).execute();
+
+		// then
+		String previous = BundleUtil.getLinkUrlOfType(myFhirContext, nextResults, "previous");
+		assertThat(previous, containsString("_getpagesoffset=0"));
+
+	}
+
 	private void createPatientAndOrg() {
 		myPatientIds = new ArrayList<>();
 
@@ -1062,5 +1098,15 @@ public void completeOperationFailure(RequestDetails theRequestDetails, BaseServe
 
 	}
 
+	private static class ConsentSvcRejectWillSeeResource implements IConsentService {
+		@Override
+		public ConsentOutcome willSeeResource(RequestDetails theRequestDetails, IBaseResource theResource, IConsentContextServices theContextServices) {
+			if("Bundle".equals(theResource.fhirType())){
+				return new ConsentOutcome(ConsentOperationStatusEnum.PROCEED);
+			}
+			return new ConsentOutcome(ConsentOperationStatusEnum.REJECT);
+		}
+
+	}
 
 }

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -2482,12 +2482,8 @@ public void testHistoryPaging() {
 			"Patient/A/_history/1"
 		));
 
-		history = myClient
-			.loadPage()
-			.next(history)
-			.execute();
-
-		assertEquals(0, history.getEntry().size());
+		// we got them all
+		assertNull(history.getLink("next"));
 
 		/*
 		 * Try with a date offset

hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsHooksContextBooterTest.java

@@ -28,7 +28,7 @@ void validateJsonReturnsNullWhenInputIsEmptyString() {
 	@Test
 	void validateJsonThrowsExceptionWhenInputIsInvalid() {
 		// setup
-		final String expected = "Invalid JSON: Unrecognized token 'abc': was expecting (JSON String, Number, Array, Object or token 'null', 'true' or 'false')\n" +
+		final String expected = "HAPI-2378: Invalid JSON: Unrecognized token 'abc': was expecting (JSON String, Number, Array, Object or token 'null', 'true' or 'false')\n" +
 			" at [Source: (String)\"abc\"; line: 1, column: 4]";
 		// execute
 		final UnprocessableEntityException actual = assertThrows(UnprocessableEntityException.class, () -> myFixture.validateJson("abc"));

hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/prefetch/CdsPrefetchFhirClientSvcTest.java

@@ -93,7 +93,7 @@ void testParseResourceWithNoResourceType() {
 			IBaseResource srq = myCdsPrefetchFhirClientSvc.resourceFromUrl(cdsServiceRequestJson, "1234");
 			fail("should throw, no resource present");
 		} catch (InvalidRequestException e) {
-			assertEquals("Unable to translate url 1234 into a resource or a bundle.", e.getMessage());
+			assertEquals("HAPI-2384: Unable to translate url 1234 into a resource or a bundle.", e.getMessage());
 		}
 	}
 
@@ -106,7 +106,7 @@ void testParseResourceWithNoResourceTypeAndSlash() {
 			IBaseResource srq = myCdsPrefetchFhirClientSvc.resourceFromUrl(cdsServiceRequestJson, "/1234");
 			fail("should throw, no resource present");
 		} catch (InvalidRequestException e) {
-			assertEquals("Failed to resolve /1234. Url does not start with a resource type.", e.getMessage());
+			assertEquals("HAPI-2383: Failed to resolve /1234. Url does not start with a resource type.", e.getMessage());
 		}
 	}
 }

hapi-fhir-server-cds-hooks/src/test/java/ca/uhn/hapi/fhir/cdshooks/svc/prefetch/PrefetchTemplateUtilTest.java

@@ -36,7 +36,7 @@ public void testShouldThrowForMissingPrefetchTokens() {
 			PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Either request context was empty or it did not provide a value for key <userId>.  Please make sure you are including a context with valid keys.", e.getMessage());
+			assertEquals("HAPI-2375: Either request context was empty or it did not provide a value for key <userId>.  Please make sure you are including a context with valid keys.", e.getMessage());
 		}
 	}
 
@@ -50,7 +50,7 @@ public void testShouldThrow400ForMissingContext() {
 			PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Either request context was empty or it did not provide a value for key <userId>.  Please make sure you are including a context with valid keys.", e.getMessage());
+			assertEquals("HAPI-2375: Either request context was empty or it did not provide a value for key <userId>.  Please make sure you are including a context with valid keys.", e.getMessage());
 		}
 	}
 
@@ -63,7 +63,7 @@ public void testShouldThrowForMissingNestedPrefetchTokens() {
 			PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Request context did not provide a value for key <draftOrders>.  Available keys in context are: [patientId]", e.getMessage());
+			assertEquals("HAPI-2372: Request context did not provide a value for key <draftOrders>.  Available keys in context are: [patientId]", e.getMessage());
 		}
 	}
 
@@ -119,7 +119,7 @@ public void testShouldThrowForDaVinciTemplateIfResourcesAreNotFoundInContextForR
 			PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
 			fail("substituteTemplate call was successful with a null context field.");
 		} catch (InvalidRequestException e) {
-			assertEquals("Request context did not provide for resource(s) matching template. ResourceType missing is: ServiceRequest", e.getMessage());
+			assertEquals("HAPI-2373: Request context did not provide for resource(s) matching template. ResourceType missing is: ServiceRequest", e.getMessage());
 		}
 	}
 
@@ -134,7 +134,7 @@ public void testShouldThrowForDaVinciTemplateIfResourceIsNotBundle() {
 			PrefetchTemplateUtil.substituteTemplate(template, context, FhirContext.forR4());
 			fail();
 		} catch (InvalidRequestException e) {
-			assertEquals("Request context did not provide valid " + fhirContextR4.getVersion().getVersion() + " Bundle resource for template key <draftOrders>" , e.getMessage());
+			assertEquals("HAPI-2374: Request context did not provide valid " + fhirContextR4.getVersion().getVersion() + " Bundle resource for template key <draftOrders>", e.getMessage());
 		}
 	}
 

hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvc.java

@@ -151,13 +151,13 @@ private MdmMatchOutcome getMatchOutcome(IBaseResource theLeftResource, IBaseReso
 						fieldComparator.getName(),
 						matchEvaluation.score,
 						vector);
+				score += matchEvaluation.score;
 			} else {
 				ourLog.trace(
 						"No match: Matcher {} did not match (score: {}).",
 						fieldComparator.getName(),
 						matchEvaluation.score);
 			}
-			score += matchEvaluation.score;
 			appliedRuleCount += 1;
 		}
 

hapi-fhir-server-mdm/src/test/java/ca/uhn/fhir/mdm/rules/svc/MdmResourceMatcherSvcR4Test.java

@@ -57,4 +57,19 @@ public void testMatchResult() {
 		patient3.addName().addGiven("Henry");
 		assertMatchResult(MdmMatchResultEnum.NO_MATCH, 0L, 0.0, false, false, myMdmResourceMatcherSvc.getMatchResult(myJohn, patient3));
 	}
+
+	@Test
+	public void testScoreOnlySummedWhenMatchFieldMatches() {
+		MdmMatchOutcome outcome = myMdmResourceMatcherSvc.getMatchResult(myJohn, myJohny);
+		assertMatchResult(MdmMatchResultEnum.POSSIBLE_MATCH, 1L, 0.816, false, false, outcome);
+
+		myJohn.addName().setFamily("Smith");
+		myJohny.addName().setFamily("htims");
+		outcome = myMdmResourceMatcherSvc.getMatchResult(myJohn, myJohny);
+		assertMatchResult(MdmMatchResultEnum.POSSIBLE_MATCH, 1L, 0.816, false, false, outcome);
+
+		myJohny.addName().setFamily("Smith");
+		outcome = myMdmResourceMatcherSvc.getMatchResult(myJohn, myJohny);
+		assertMatchResult(MdmMatchResultEnum.MATCH, 3L, 1.816, false, false, outcome);
+	}
 }