configure caregaps operation and properties

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -6,6 +6,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 
+import ca.uhn.fhir.cr.config.CrProperties;
 import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
@@ -28,58 +29,36 @@ import ca.uhn.fhir.rest.api.EncodingEnum;
 @Configuration
 @EnableConfigurationProperties
 public class AppProperties {
-
+	//cql settings
 	private CqlEngineOptions cqlEngineOptions = CqlEngineOptions.defaultOptions();
 	private Boolean cql_use_embedded_libraries = true;
 	private Boolean cql_runtime_debug_logging_enabled = false;
 	private Boolean cql_runtime_enable_validation = false;
 	private Boolean cql_runtime_enable_expression_caching = false;
 	private Boolean cql_compiler_validate_units = true;
-
 	private Boolean cql_compiler_verify_only = false;
-
 	private String cql_compiler_compatibility_level = "1.5";
-
 	private CqlCompilerException.ErrorSeverity cql_compiler_error_level = CqlCompilerException.ErrorSeverity.Info;
-
 	private LibraryBuilder.SignatureLevel cql_compiler_signature_level = LibraryBuilder.SignatureLevel.All;
-
 	private Boolean cql_compiler_analyze_data_requirements = false;
-
 	private Boolean cql_compiler_collapse_data_requirements = false;
-
 	private CqlTranslator.Format cql_compiler_translator_format = CqlTranslator.Format.JSON;
-
 	private Boolean cql_compiler_enable_date_range_optimization = false;
-
 	private Boolean cql_compiler_enable_annotations = false;
-
 	private Boolean cql_compiler_enable_locators = false;
-
 	private Boolean cql_compiler_enable_results_type = false;
-
 	private Boolean cql_compiler_enable_detailed_errors = false;
-
 	private Boolean cql_compiler_disable_list_traversal = false;
-
 	private Boolean cql_compiler_disable_list_demotion = false;
-
 	private Boolean cql_compiler_disable_list_promotion = false;
-
 	private Boolean cql_compiler_enable_interval_demotion = false;
-
 	private Boolean cql_compiler_enable_interval_promotion = false;
-
 	private Boolean cql_compiler_disable_method_invocation = false;
-
 	private Boolean cql_compiler_require_from_keyword = false;
-
 	private Boolean cql_compiler_disable_default_model_info_load = false;
-
+	// Care-gaps Settings
-	// private CqlEngineOptions cqlEngineOptions =
+	private String caregaps_reporter = "default";
-	// CqlEngineOptions.defaultOptions();
+	private String caregaps_section_author = "default";
-	// private CqlTranslatorOptions cqlTranslatorOptions =
-	// CqlTranslatorOptions.defaultOptions();
 	private Boolean cr_enabled = false;
 	private Boolean ips_enabled = false;
 	private Boolean openapi_enabled = false;
@@ -122,7 +101,6 @@ public class AppProperties {
 	private List<String> supported_resource_types = new ArrayList<>();
 	private List<Bundle.BundleType> allowed_bundle_types = null;
 	private Boolean narrative_enabled = true;
-
 	private Validation validation = new Validation();
 	private Map<String, Tester> tester = new HashMap<>();
 	private Logger logger = new Logger();
@@ -132,7 +110,6 @@ public class AppProperties {
 	private Boolean install_transitive_ig_dependencies = true;
 	private Boolean reload_existing_implementationguides = false;
 	private Map<String, ImplementationGuide> implementationGuides = null;
-
 	private String staticLocation = null;
 
 	private Boolean lastn_enabled = false;
@@ -460,7 +437,27 @@ public class AppProperties {
 	public void setCr_enabled(Boolean cr_enabled) {
 		this.cr_enabled = cr_enabled;
 	}
+	public String getCareGapsReporter() {
+		return caregaps_reporter;
+	}
+	public String getCareGapsSectionAuthor() {
+		return caregaps_section_author;
+	}
 
+	public void setCareGapsSectionAuthor(String theCareGapsSectionAuthor) {this.caregaps_section_author = theCareGapsSectionAuthor;}
+	public void setCareGapsReporter(String theCareGapsReporter) {
+		this.caregaps_reporter = theCareGapsReporter;
+	}
+	public CrProperties.MeasureProperties getMeasureProperties(){
+		var measureProperties = new CrProperties.MeasureProperties();
+		var measureReportConfiguration = new CrProperties.MeasureProperties.MeasureReportConfiguration();
+		measureReportConfiguration.setCareGapsReporter(this.getCareGapsReporter());
+		measureReportConfiguration.setCareGapsCompositionSectionAuthor(this.getCareGapsSectionAuthor());
+
+		measureProperties.setMeasureReportConfiguration(measureReportConfiguration);
+
+		return measureProperties;
+	}
 	public Boolean getIps_enabled() {
 		return ips_enabled;
 	}

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrDstu3Config.java

@@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.starter.cr;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.cr.config.CrDstu3Config;
+import ca.uhn.fhir.cr.config.CrProperties;
 import ca.uhn.fhir.cr.dstu3.IActivityDefinitionProcessorFactory;
 import ca.uhn.fhir.cr.dstu3.IPlanDefinitionProcessorFactory;
 import ca.uhn.fhir.cr.dstu3.IQuestionnaireProcessorFactory;
@@ -99,6 +100,11 @@ public class StarterCrDstu3Config {
 		return theAppProperties.getCqlOptions();
 	}
 
+	@Primary
+	@Bean
+	public CrProperties.MeasureProperties measureProperties(AppProperties theAppProperties) {
+		return theAppProperties.getMeasureProperties();
+	}
 	@Primary
 	@Bean
 	public CqlTranslatorOptions cqlTranslatorOptions(FhirContext theFhirContext, AppProperties theAppProperties) {

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java

@@ -4,19 +4,24 @@ import ca.uhn.fhir.IHapiBootOrder;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 
+import ca.uhn.fhir.cr.config.CrProperties;
 import ca.uhn.fhir.cr.config.CrR4Config;
 import ca.uhn.fhir.cr.r4.IActivityDefinitionProcessorFactory;
 import ca.uhn.fhir.cr.r4.IPlanDefinitionProcessorFactory;
 import ca.uhn.fhir.cr.r4.IQuestionnaireProcessorFactory;
 import ca.uhn.fhir.cr.r4.IQuestionnaireResponseProcessorFactory;
 import ca.uhn.fhir.cr.r4.activitydefinition.ActivityDefinitionOperationsProvider;
+import ca.uhn.fhir.cr.r4.measure.CareGapsOperationProvider;
+import ca.uhn.fhir.cr.r4.measure.CareGapsService;
 import ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionOperationsProvider;
 import ca.uhn.fhir.cr.r4.questionnaire.QuestionnaireOperationsProvider;
 import ca.uhn.fhir.cr.r4.questionnaireresponse.QuestionnaireResponseOperationsProvider;
 import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
+import org.apache.commons.lang3.StringUtils;
 import org.cqframework.cql.cql2elm.CqlTranslatorOptions;
 import org.opencds.cqf.cql.evaluator.CqlOptions;
 import org.opencds.cqf.cql.evaluator.activitydefinition.r4.ActivityDefinitionProcessor;
@@ -28,6 +33,8 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.context.annotation.*;
 
+import java.util.function.Function;
+
 @Configuration
 @Conditional({ OnR4Condition.class, CrConfigCondition.class })
 @Import({ CrR4Config.class })
@@ -102,6 +109,29 @@ public class StarterCrR4Config {
 		return theAppProperties.getCqlOptions();
 	}
 
+	@Primary
+	@Bean
+	public CrProperties.MeasureProperties measureProperties(AppProperties theAppProperties) {
+		return theAppProperties.getMeasureProperties();
+	}
+
+	@Primary
+	@Bean
+	CareGapsOperationProvider careGapsOperationProvider(Function<RequestDetails, CareGapsService> r4CareGapsServiceFactory, AppProperties theAppProperties) {
+		if(StringUtils.isBlank(theAppProperties.getCareGapsReporter()) || StringUtils.isBlank(theAppProperties.getCareGapsSectionAuthor())){
+			throw new RuntimeException("Configuration failed to register reporter or author properties for running care gaps functionality");
+		}
+		Function<RequestDetails, CareGapsService> careGapsServiceFunction = r4CareGapsServiceFactory.andThen(careGapsService -> {
+			var measureReportConfiguration = new CrProperties.MeasureProperties.MeasureReportConfiguration();
+			measureReportConfiguration.setCareGapsReporter(theAppProperties.getCareGapsReporter());
+			measureReportConfiguration.setCareGapsCompositionSectionAuthor(theAppProperties.getCareGapsSectionAuthor());
+			careGapsService.getCrProperties().getMeasureProperties().setMeasureReportConfiguration(measureReportConfiguration);
+			return careGapsService;
+		});
+		CareGapsOperationProvider careGapsOperationProvider = new CareGapsOperationProvider(careGapsServiceFunction);
+		return careGapsOperationProvider;
+	}
+
 	@Primary
 	@Bean
 	public CqlTranslatorOptions cqlTranslatorOptions(FhirContext theFhirContext, AppProperties theAppProperties) {

src/test/java/ca/uhn/fhir/jpa/starter/ExampleServerR4IT.java

@@ -10,21 +10,20 @@ import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import org.eclipse.jetty.websocket.api.Session;
 import org.eclipse.jetty.websocket.client.ClientUpgradeRequest;
 import org.eclipse.jetty.websocket.client.WebSocketClient;
-import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Parameters;
+import org.hl7.fhir.r4.model.*;
-import org.hl7.fhir.r4.model.StringType;
 import org.hl7.fhir.instance.model.api.IIdType;
-import org.hl7.fhir.r4.model.Bundle;
-import org.hl7.fhir.r4.model.Observation;
-import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Subscription;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.context.properties.EnableConfigurationProperties;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.web.server.LocalServerPort;
 import org.springframework.context.ApplicationContext;
-import org.springframework.context.annotation.AnnotationConfigApplicationContext;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
 
 import java.io.IOException;
 import java.net.URI;
@@ -39,15 +38,21 @@ import static org.awaitility.Awaitility.await;
 import static org.junit.jupiter.api.Assertions.*;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
+@ExtendWith(SpringExtension.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
+	classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class},
+	properties = {
 		"spring.datasource.url=jdbc:h2:mem:dbr4",
 		"hapi.fhir.enable_repository_validating_interceptor=true",
 		"hapi.fhir.fhir_version=r4",
 		"hapi.fhir.subscription.websocket_enabled=true",
 		"hapi.fhir.mdm_enabled=true",
 		"hapi.fhir.cr_enabled=true",
+		"hapi.fhir.caregaps_section_author=Organization/alphora-author",
+		"hapi.fhir.caregaps_reporter=Organization/alphora",
 		"hapi.fhir.implementationguides.dk-core.name=hl7.fhir.dk.core",
 		"hapi.fhir.implementationguides.dk-core.version=1.1.0",
+		"hapi.fhir.auto_create_placeholder_reference_targets=true",
 		// Override is currently required when using MDM as the construction of the MDM
 		// beans are ambiguous as they are constructed multiple places. This is evident
 		// when running in a spring boot environment
@@ -58,6 +63,8 @@ class ExampleServerR4IT implements IServerSupport{
 	private FhirContext ourCtx;
 	private ApplicationContext ctx;
 
+	@Autowired private AppProperties appProperties;
+
 	@LocalServerPort
 	private int port;
 
@@ -133,6 +140,16 @@ class ExampleServerR4IT implements IServerSupport{
 		org.hl7.fhir.r4.model.Bundle result = theClient.transaction().withBundle(bundle).execute();
 		return result;
 	}
+
+	private IBaseResource loadRec(String theLocation, FhirContext theCtx, IGenericClient theClient) throws IOException {
+		String json = stringFromResource(theLocation);
+		List<IBaseResource> resList = new ArrayList<>();
+		IBaseResource resource = (IBaseResource) theCtx.newJsonParser().parseResource(json);
+		resList.add(resource);
+		var result = theClient.transaction().withResources(resList).execute();
+			//.withResources(resource).execute();
+		return result.get(0);
+	}
 	@Test
 	public void testBatchPutWithIdenticalTags() {
 		String batchPuts = "{\n" +
@@ -241,6 +258,42 @@ class ExampleServerR4IT implements IServerSupport{
 		ourClient.delete().resourceById(mySubscriptionId).execute();
 	}
 
+	@Test
+	void testCareGaps() throws IOException {
+
+		var reporter = appProperties.getCareGapsReporter();
+		var author = appProperties.getCareGapsSectionAuthor();
+
+		assertTrue(reporter.equals("Organization/alphora"));
+		assertTrue(author.equals("Organization/alphora-author"));
+
+		 String periodStartValid = "2019-01-01";
+		 String periodEndValid = "2019-12-31";
+		 String subjectPatientValid = "Patient/numer-EXM125";
+		 String statusValid = "open-gap";
+		 String measureIdValid = "BreastCancerScreeningFHIR";
+
+		loadBundle("r4/CareGaps/authreporter-bundle.json", ourCtx, ourClient);
+		loadBundle("r4/CareGaps/BreastCancerScreeningFHIR-bundle.json", ourCtx, ourClient);
+
+		Parameters params = new Parameters();
+		params.addParameter().setName("periodStart").setValue(new DateType(periodStartValid));
+		params.addParameter().setName("subject").setValue(new DateType(periodEndValid));
+		params.addParameter().setName("status").setValue(new StringType(subjectPatientValid));
+		params.addParameter().setName("measureId").setValue(new StringType(statusValid));
+		params.addParameter().setName("").setValue(new StringType(measureIdValid));
+
+
+		assertDoesNotThrow(() -> {
+			ourClient.operation()
+				.onType(Measure.class)
+				.named("$care-gaps")
+				.withParameters(params)
+				.returnResourceType(Parameters.class)
+				.execute();
+		});
+	}
+
 	private int activeSubscriptionCount() {
 		return ourClient.search().forResource(Subscription.class).where(Subscription.STATUS.exactly().code("active"))
 			.cacheControl(new CacheControlDirective().setNoCache(true)).returnBundle(Bundle.class).execute().getEntry()

src/test/resources/r4/CareGaps/authreporter-bundle.json

@@ -0,0 +1,204 @@
+{
+    "resourceType": "Bundle",
+    "id": "AlphoraOrgAuth-bundle",
+    "type": "transaction",
+    "entry": [
+        {
+            "resource": {
+                "resourceType": "Organization",
+                "id": "alphora",
+                "meta": {
+                    "profile": [
+                        "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+                    ]
+                },
+                "identifier": [
+                    {
+                        "use": "official",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "TAX",
+                                    "display": "Tax ID number"
+                                }
+                            ]
+                        },
+                        "system": "urn:oid:2.16.840.1.113883.4.4",
+                        "value": "123456789",
+                        "assigner": {
+                            "display": "www.irs.gov"
+                        }
+                    }
+                ],
+                "active": true,
+                "type": [
+                    {
+                        "coding": [
+                            {
+                                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                                "code": "prov",
+                                "display": "Healthcare Provider"
+                            }
+                        ]
+                    }
+                ],
+                "name": "alphora",
+                "telecom": [
+                    {
+                        "system": "phone",
+                        "value": "(+1) 401-555-1212"
+                    }
+                ],
+                "address": [
+                    {
+                        "line": [
+                            "73 Lakewood Street"
+                        ],
+                        "city": "Warwick",
+                        "state": "RI",
+                        "postalCode": "02886",
+                        "country": "USA"
+                    }
+                ]
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Organization/alphora"
+            }
+        },
+        {
+            "resource": {
+                "resourceType": "Organization",
+                "id": "alphora-author",
+                "meta": {
+                    "profile": [
+                        "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/organization-deqm"
+                    ]
+                },
+                "identifier": [
+                    {
+                        "use": "official",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "TAX",
+                                    "display": "Tax ID number"
+                                }
+                            ]
+                        },
+                        "system": "urn:oid:2.16.840.1.113883.4.4",
+                        "value": "12345678910",
+                        "assigner": {
+                            "display": "www.irs.gov"
+                        }
+                    }
+                ],
+                "active": true,
+                "type": [
+                    {
+                        "coding": [
+                            {
+                                "system": "http://terminology.hl7.org/CodeSystem/organization-type",
+                                "code": "prov",
+                                "display": "Healthcare Provider"
+                            }
+                        ]
+                    }
+                ],
+                "name": "alphora-author",
+                "telecom": [
+                    {
+                        "system": "phone",
+                        "value": "(+1) 401-555-1313"
+                    }
+                ],
+                "address": [
+                    {
+                        "line": [
+                            "737 Lakewood Street"
+                        ],
+                        "city": "Warwick",
+                        "state": "RI",
+                        "postalCode": "02886",
+                        "country": "USA"
+                    }
+                ]
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Organization/alphora-author"
+            }
+        },
+        {
+            "resource": {
+                "resourceType": "Patient",
+                "id": "numer-EXM125",
+                "meta": {
+                    "profile": [
+                        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+                    ]
+                },
+                "extension": [
+                    {
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+                        "extension": [
+                            {
+                                "url": "ombCategory",
+                                "valueCoding": {
+                                    "system": "urn:oid:2.16.840.1.113883.6.238",
+                                    "code": "2028-9",
+                                    "display": "Asian"
+                                }
+                            }
+                        ]
+                    },
+                    {
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+                        "extension": [
+                            {
+                                "url": "ombCategory",
+                                "valueCoding": {
+                                    "system": "urn:oid:2.16.840.1.113883.6.238",
+                                    "code": "2135-2",
+                                    "display": "Hispanic or Latino"
+                                }
+                            }
+                        ]
+                    }
+                ],
+                "identifier": [
+                    {
+                        "use": "usual",
+                        "type": {
+                            "coding": [
+                                {
+                                    "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+                                    "code": "MR",
+                                    "display": "Medical Record Number"
+                                }
+                            ]
+                        },
+                        "system": "http://hospital.smarthealthit.org",
+                        "value": "999999995"
+                    }
+                ],
+                "name": [
+                    {
+                        "family": "McCarren",
+                        "given": [
+                            "Karen"
+                        ]
+                    }
+                ],
+                "gender": "female",
+                "birthDate": "1965-01-01"
+            },
+            "request": {
+                "method": "PUT",
+                "url": "Patient/numer-EXM125"
+            }
+        }
+    ]
+}

src/test/resources/r4/CareGaps/numer-EXM125-patient.json

@@ -0,0 +1,63 @@
+{
+	"resourceType": "Patient",
+	"id": "numer-EXM125",
+	"meta": {
+		"profile": [
+			"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient"
+		]
+	},
+	"extension": [
+		{
+			"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
+			"extension": [
+				{
+					"url": "ombCategory",
+					"valueCoding": {
+						"system": "urn:oid:2.16.840.1.113883.6.238",
+						"code": "2028-9",
+						"display": "Asian"
+					}
+				}
+			]
+		},
+		{
+			"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
+			"extension": [
+				{
+					"url": "ombCategory",
+					"valueCoding": {
+						"system": "urn:oid:2.16.840.1.113883.6.238",
+						"code": "2135-2",
+						"display": "Hispanic or Latino"
+					}
+				}
+			]
+		}
+	],
+	"identifier": [
+		{
+			"use": "usual",
+			"type": {
+				"coding": [
+					{
+						"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+						"code": "MR",
+						"display": "Medical Record Number"
+					}
+				]
+			},
+			"system": "http://hospital.smarthealthit.org",
+			"value": "999999995"
+		}
+	],
+	"name": [
+		{
+			"family": "McCarren",
+			"given": [
+				"Karen"
+			]
+		}
+	],
+	"gender": "female",
+	"birthDate": "1965-01-01"
+}