Rel 7 0 mb 2

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

@@ -136,7 +136,6 @@ public enum VersionEnum {
 
 	V7_0_0,
 	V7_0_1,
-
 	V7_1_0,
 	V7_2_0;
 

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5654-measurescorer-bug.yaml

@@ -0,0 +1,5 @@
+type: fix
+issue: 5654
+title: "Fixed a MeasureReport measureScoring bug impacting any measures currently using denominator-exception population will 
+incorrectly calculate the score without following specification. This bug adds an extension to MeasureReport Groups to capture calculated denominator and
+numerator to bring transparency to the measureScore calculation and act as a dataSource of measureScore instead of behind the scenes calculations."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5680-npe-on-poll-export-status-system-export-with-patientid-partitioning.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 5680
+title: "Previously, after registering built-in interceptor `PatientIdPartitionInterceptor`, while performing 
+an async system bulk export, the `$poll-export-status` operation would fail with a `NullPointerException`. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5700-remote-terminology-service-throws-exception-unsupported-property-types.yaml

@@ -0,0 +1,6 @@
+---
+type: fix
+issue: 5700
+title: "Previously (this release cycle), when you call `RemoteTerminologyServiceValidationSupport` method `lookupCode` 
+with a `CodeSystem` that has properties that are not `string` or `Coding`, the method would throw an exception. 
+It should instead accept any type and convert any unsupported type to `string`. This has been fixed."

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

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.interceptor;
 
 import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.interceptor.model.ReadPartitionIdRequestDetails;
+import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ResourceTable;
@@ -10,19 +12,28 @@
 import ca.uhn.fhir.jpa.util.SqlQuery;
 import ca.uhn.fhir.model.api.Include;
 import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
 import ca.uhn.fhir.rest.api.server.IBundleProvider;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.bulk.BulkExportJobParameters;
 import ca.uhn.fhir.rest.param.ReferenceParam;
 import ca.uhn.fhir.rest.param.TokenOrListParam;
 import ca.uhn.fhir.rest.param.TokenParam;
 import ca.uhn.fhir.rest.server.exceptions.MethodNotAllowedException;
+import ca.uhn.fhir.rest.server.provider.BulkDataExportProvider;
 import ca.uhn.fhir.rest.server.provider.ProviderConstants;
 import ca.uhn.fhir.util.BundleBuilder;
 import ca.uhn.fhir.util.MultimapCollector;
+import com.google.common.base.Charsets;
 import com.google.common.collect.ListMultimap;
 import com.google.common.collect.Multimap;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpPost;
+import org.apache.commons.io.IOUtils;
+import org.apache.http.Header;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Encounter;
 import org.hl7.fhir.r4.model.Enumerations;
@@ -36,6 +47,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.mock.mockito.SpyBean;
 
 import java.io.IOException;
 import java.util.List;
@@ -49,8 +61,11 @@
 import static org.hamcrest.Matchers.either;
 import static org.hamcrest.Matchers.matchesPattern;
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.verify;
 
 public class PatientIdPartitionInterceptorTest extends BaseResourceProviderR4Test {
 	public static final int ALTERNATE_DEFAULT_ID = -1;
@@ -542,6 +557,70 @@ private Patient createPatientA() {
 		return (Patient)update.getResource();
 	}
 
+	@Test
+	public void testIdentifyForRead_serverOperation_returnsAllPartitions() {
+		ReadPartitionIdRequestDetails readRequestDetails = ReadPartitionIdRequestDetails.forServerOperation(ProviderConstants.OPERATION_EXPORT);
+		RequestPartitionId requestPartitionId = mySvc.identifyForRead(readRequestDetails, mySrd);
+		assertEquals(requestPartitionId, RequestPartitionId.allPartitions());
+		assertEquals(RestOperationTypeEnum.EXTENDED_OPERATION_SERVER, readRequestDetails.getRestOperationType());
+	}
+
+	@Test
+	public void testSystemBulkExport_withPatientIdPartitioningWithNoResourceType_usesNonPatientSpecificPartition() throws IOException {
+		HttpPost post = new HttpPost(myServer.getBaseUrl() + "/" + ProviderConstants.OPERATION_EXPORT);
+		post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+
+		try (CloseableHttpResponse postResponse = myServer.getHttpClient().execute(post)){
+			ourLog.info("Response: {}",postResponse);
+			assertEquals(202, postResponse.getStatusLine().getStatusCode());
+			assertEquals("Accepted", postResponse.getStatusLine().getReasonPhrase());
+		}
+	}
+
+	@Test
+	public void testSystemBulkExport_withPatientIdPartitioningWithResourceType_exportUsesNonPatientSpecificPartition() throws IOException {
+		HttpPost post = new HttpPost(myServer.getBaseUrl() + "/" + ProviderConstants.OPERATION_EXPORT);
+		post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		post.addHeader(BulkDataExportProvider.PARAM_EXPORT_TYPE, "Patient");
+		post.addHeader(BulkDataExportProvider.PARAM_EXPORT_TYPE_FILTER, "Patient?");
+
+		try (CloseableHttpResponse postResponse = myServer.getHttpClient().execute(post)){
+			ourLog.info("Response: {}",postResponse);
+			assertEquals(202, postResponse.getStatusLine().getStatusCode());
+			assertEquals("Accepted", postResponse.getStatusLine().getReasonPhrase());
+		}
+	}
+
+	@Test
+	public void testSystemBulkExport_withPatientIdPartitioningWithResourceType_pollSuccessful() throws IOException {
+		final BulkExportJobParameters options = new BulkExportJobParameters();
+		options.setExportStyle(BulkExportJobParameters.ExportStyle.SYSTEM);
+		options.setOutputFormat(Constants.CT_FHIR_NDJSON);
+
+		HttpPost post = new HttpPost(myServer.getBaseUrl() + "/" + ProviderConstants.OPERATION_EXPORT);
+		post.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RESPOND_ASYNC);
+		post.addHeader(BulkDataExportProvider.PARAM_EXPORT_TYPE, "Patient"); // ignored when computing partition
+		post.addHeader(BulkDataExportProvider.PARAM_EXPORT_TYPE_FILTER, "Patient?");
+
+		String locationUrl;
+
+		try (CloseableHttpResponse postResponse = myServer.getHttpClient().execute(post)){
+			ourLog.info("Response: {}",postResponse);
+			assertEquals(202, postResponse.getStatusLine().getStatusCode());
+			assertEquals("Accepted", postResponse.getStatusLine().getReasonPhrase());
+
+			Header locationHeader = postResponse.getFirstHeader(Constants.HEADER_CONTENT_LOCATION);
+			assertNotNull(locationHeader);
+			locationUrl = locationHeader.getValue();
+		}
+
+		HttpGet get = new HttpGet(locationUrl);
+		try (CloseableHttpResponse postResponse = myServer.getHttpClient().execute(get)) {
+			String responseContent = IOUtils.toString(postResponse.getEntity().getContent(), Charsets.UTF_8);
+			ourLog.info("Response: {}", responseContent);
+			assertEquals(202, postResponse.getStatusLine().getStatusCode());
+		}
+	}
 	@Test
 	public void testSystemOperation_withNoResourceType_success() throws IOException {
 		HttpPost post = new HttpPost(myServer.getBaseUrl() + "/" + ProviderConstants.OPERATION_EXPORT);

hapi-fhir-storage-cr/src/test/resources/BCSEHEDISMY2022-bundle.json

@@ -1843,6 +1843,7 @@
       "guidance": "* For Medicare plans, I-SNP and LTI exclusions are not included in the measure calculation logic and need to be programmed manually. Administrative data must be used for these exclusions.\n*Non-administrative data may be used for the frailty and advanced illness exclusion.\n<p>**Allocation:**<br/>The member was enrolled with a medical benefit throughout the Participation Period.</p><p>No more than one gap in enrollment of up to 45 days for each full calendar year of the Participation Period (i.e., the Measurement Period and the year prior to the Measurement Period).</p><p>No gaps in enrollment are allowed from October 1 two years prior to the Measurement Period through December 31 two years prior to the Measurement Period.</p><p>**Reporting:**<br/>For Medicare plans, the SES stratifications are mutually exclusive. NCQA calculates a total rate for Medicare plans by adding all six Medicare stratifications.</p><p>SES and product line stratifications are not included in the measure calculation logic and need to be programmed manually.</p><p>**Stratification:**<br/>1. Commercial.\n2. Medicaid.\n3. Medicare: Non-LIS/DE, Nondisability.\n4. Medicare: LIS/DE.\n5. Medicare: Disability\n6. Medicare: LIS/DE and Disability.\n7. Medicare: Other.\n8. Medicare: Unknown.</p>",
       "group": [ {
         "population": [ {
+			  "id": "initial-population",
           "code": {
             "coding": [ {
               "system": "http://terminology.hl7.org/CodeSystem/measure-population",
@@ -1856,6 +1857,7 @@
             "expression": "Initial Population"
           }
         }, {
+			  "id": "denominator",
           "code": {
             "coding": [ {
               "system": "http://terminology.hl7.org/CodeSystem/measure-population",
@@ -1869,6 +1871,7 @@
             "expression": "Denominator"
           }
         }, {
+			  "id": "denominator-exclusion",
           "code": {
             "coding": [ {
               "system": "http://terminology.hl7.org/CodeSystem/measure-population",
@@ -1882,6 +1885,7 @@
             "expression": "Exclusions"
           }
         }, {
+			  "id": "numerator",
           "code": {
             "coding": [ {
               "system": "http://terminology.hl7.org/CodeSystem/measure-population",
@@ -1897,6 +1901,7 @@
         } ]
       } ],
       "supplementalData": [ {
+			"id": "Enrolled-During-Participation-Period",
         "code": {
           "text": "Enrolled During Participation Period"
         },
@@ -1911,6 +1916,7 @@
           "expression": "Enrolled During Participation Period"
         }
       }, {
+			"id": "participation-period",
         "code": {
           "text": "Participation Period"
         },

hapi-fhir-storage-cr/src/test/resources/ColorectalCancerScreeningsFHIR-bundle.json

@@ -147712,7 +147712,7 @@
 					}
 				],
 				"library": [
-					"http://ecqi.healthit.gov/ecqms/Library/ColorectalCancerScreeningsFHIR|0.0.001"
+					"http://ecqi.healthit.gov/ecqms/Library/ColorectalCancerScreeningsFHIR"
 				],
 				"disclaimer": "The performance Measure is not a clinical guideline and does not establish a standard of medical care, and has not been tested for all potential applications. THE MEASURE AND SPECIFICATIONS ARE PROVIDED \"AS IS\" WITHOUT WARRANTY OF ANY KIND.\n \nDue to technical limitations, registered trademarks are indicated by (R) or [R] and unregistered trademarks are indicated by (TM) or [TM].",
 				"scoring": {

hapi-fhir-storage-cr/src/test/resources/Exm104FhirR4MeasureBundle.json

@@ -140,7 +140,7 @@
 					}
 				],
 				"library": [
-					"http://localhost:8080/fhir/Library/library-EXM104|8.2.000"
+					"http://localhost:8080/fhir/Library/EXM104|8.2.000"
 				],
 				"disclaimer": "These performance measures are not clinical guidelines and do not establish a standard of medical care, and have not been tested for all potential applications. The measures and specifications are provided without warranty.",
 				"scoring": {
@@ -177,6 +177,7 @@
 						"id": "group-1",
 						"population": [
 							{
+								"id": "initial-population",
 								"code": {
 									"coding": [
 										{
@@ -192,6 +193,7 @@
 								}
 							},
 							{
+								"id": "numerator",
 								"code": {
 									"coding": [
 										{
@@ -207,6 +209,7 @@
 								}
 							},
 							{
+								"id": "denominator",
 								"code": {
 									"coding": [
 										{
@@ -222,6 +225,7 @@
 								}
 							},
 							{
+								"id": "denominator-exclusion",
 								"code": {
 									"coding": [
 										{
@@ -237,6 +241,7 @@
 								}
 							},
 							{
+								"id": "denominator-exception",
 								"code": {
 									"coding": [
 										{
@@ -341,7 +346,7 @@
 		{
 			"resource": {
 				"resourceType": "Library",
-				"id": "library-EXM104",
+				"id": "EXM104",
 				"extension": [
 					{
 						"url": "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-softwaresystem",
@@ -350,7 +355,7 @@
 						}
 					}
 				],
-				"url": "http://localhost:8080/fhir/Library/library-EXM104",
+				"url": "http://localhost:8080/fhir/Library/EXM104",
 				"version": "8.2.000",
 				"name": "library-EXM104",
 				"status": "active",
@@ -600,7 +605,7 @@
 			},
 			"request": {
 				"method": "PUT",
-				"url": "Library/library-EXM104"
+				"url": "Library/EXM104"
 			}
 		},
 		{

hapi-fhir-storage-cr/src/test/resources/largeValueSetMeasureTest-Bundle.json

@@ -1377,6 +1377,7 @@
             "id": "group-1",
             "population": [
               {
+					  "id": "initial-population",
                 "code": {
                   "coding": [
                     {
@@ -1392,6 +1393,7 @@
                 }
               },
               {
+					  "id": "denominator",
                 "code": {
                   "coding": [
                     {
@@ -1407,6 +1409,7 @@
                 }
               },
               {
+					  "id": "numerator",
                 "code": {
                   "coding": [
                     {

hapi-fhir-storage-cr/src/test/resources/multiversion/EXM124-7.0.000-bundle.json

@@ -1372,6 +1372,7 @@
 						"id": "group-1",
 						"population": [
 							{
+								"id": "initial-population",
 								"code": {
 									"coding": [
 										{
@@ -1387,6 +1388,7 @@
 								}
 							},
 							{
+								"id": "numerator",
 								"code": {
 									"coding": [
 										{
@@ -1402,6 +1404,7 @@
 								}
 							},
 							{
+								"id": "denominator",
 								"code": {
 									"coding": [
 										{
@@ -1417,6 +1420,7 @@
 								}
 							},
 							{
+								"id": "denominator-exclusion",
 								"code": {
 									"coding": [
 										{
@@ -1436,6 +1440,7 @@
 				],
 				"supplementalData": [
 					{
+						"id": "sde-ethnicity",
 						"code": {
 							"text": "sde-ethnicity"
 						},
@@ -1455,6 +1460,7 @@
 						}
 					},
 					{
+						"id": "sde-payer",
 						"code": {
 							"text": "sde-payer"
 						},
@@ -1474,6 +1480,7 @@
 						}
 					},
 					{
+						"id": "sde-race",
 						"code": {
 							"text": "sde-race"
 						},
@@ -1493,6 +1500,7 @@
 						}
 					},
 					{
+						"id": "sde-sex",
 						"code": {
 							"text": "sde-sex"
 						},