Aphl 300 valueset interceptor

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/CrConfig.java

@@ -110,6 +110,12 @@ public RepositoryService repositoryService() {
 		return new RepositoryService();
 	}
 
+	@Bean
+	@Conditional(OnR4Condition.class)
+	public ValueSetSynonymUpdateInterceptor valueSetInterceptor() {
+		return new ValueSetSynonymUpdateInterceptor(this.crRulerProperties().getRckmsSynonymsUrl());
+	}
+
 	@Bean
 	@Conditional(OnR4Condition.class)
 	public KnowledgeArtifactProcessor knowledgeArtifactProcessor() {

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/CrRulerProperties.java

@@ -20,6 +20,12 @@ public void setEnabled(boolean enabled) {
 		this.enabled = enabled;
 	}
 
+	private final String rckmsSynonymsUrl = "http://ersd.aimsplatform.org/fhir/ValueSet/rckms-condition-codes";
+
+	public String getRckmsSynonymsUrl() {
+		return this.rckmsSynonymsUrl;
+	}
+
 	private String vsacUsername;
 
 	public String getVsacUsername() { return vsacUsername; }
@@ -32,4 +38,5 @@ public void setEnabled(boolean enabled) {
 
 	public void setVsacApiKey(String vsacApiKey) { this.vsacApiKey = vsacApiKey; }
 
+
 }

plugin/cr/src/main/java/org/opencds/cqf/ruler/cr/ValueSetSynonymUpdateInterceptor.java

@@ -0,0 +1,94 @@
+package org.opencds.cqf.ruler.cr;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.cqframework.fhir.api.FhirDal;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Library;
+import org.hl7.fhir.r4.model.RelatedArtifact;
+import org.hl7.fhir.r4.model.ResourceType;
+import org.hl7.fhir.r4.model.ValueSet;
+import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent;
+import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent;
+import org.opencds.cqf.ruler.behavior.DaoRegistryUser;
+import org.opencds.cqf.ruler.utility.TypedBundleProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ca.uhn.fhir.interceptor.api.Hook;
+import ca.uhn.fhir.interceptor.api.Pointcut;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.param.TokenParam;
+import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
+
+public class ValueSetSynonymUpdateInterceptor implements org.opencds.cqf.ruler.api.Interceptor, DaoRegistryUser {
+  	@Autowired
+	  private DaoRegistry myDaoRegistry;
+
+    private String synonymUrl;
+
+    ValueSetSynonymUpdateInterceptor(String synonymUrl) {
+      this.synonymUrl = synonymUrl;
+    }
+
+    public DaoRegistry getDaoRegistry() {
+      return myDaoRegistry;
+    }
+
+    /** Handle updates */
+   @Hook(Pointcut.STORAGE_PRESTORAGE_RESOURCE_UPDATED)
+   public void update(
+    IBaseResource theOldResource,
+    IBaseResource theResource,
+    RequestDetails theRequestDetails) throws UnprocessableEntityException {
+      if (theResource.fhirType().equals(ResourceType.ValueSet.toString())) {
+        ValueSet vs = (ValueSet) theResource;
+        if (vs.getUrl().equals(this.synonymUrl)) {
+          FhirDal fhirDal = new JpaFhirDal(myDaoRegistry,theRequestDetails);
+          List<ConceptSetComponent> sets = vs.getCompose().getInclude();
+          List<Library> librariesToUpdate = new ArrayList<Library>();
+          for (ConceptSetComponent set: sets) {
+            // for each system in the value set
+            String system = set.getSystem();
+            List<ConceptReferenceComponent> concepts = set.getConcept();
+            for (ConceptReferenceComponent concept:concepts) {
+              // for each concept.code need to update the extension.valueCodeableConcept.coding.display to concept.designation(where code = synonym).value
+              TokenParam token = new TokenParam(system,concept.getCode());
+              SearchParameterMap map = new SearchParameterMap("manifest-contains-code",token);
+              TypedBundleProvider<Library> result = search(Library.class, map);
+              result.getAllResourcesTyped().stream().forEach(lib -> {
+                Library getCachedLibraryOrAdd = librariesToUpdate
+                  .stream().filter(existing -> existing.getId().equals(lib.getId())).findFirst()
+                  .orElseGet(() -> {
+                    librariesToUpdate.add(lib);
+                    return lib;
+                  });
+                String newText = concept.getDesignation()
+                  .stream().filter(designation -> designation.getUse().getCode().equals("synonym"))
+                  .findFirst().orElseThrow(()-> new UnprocessableEntityException("No synonym found for code: " + system + "|" + concept.getCode()))
+                  .getValue();
+                updateConditionWithNewSynonym(getCachedLibraryOrAdd,system, concept.getCode(),newText );
+              });
+            }
+          }
+          for (Library library:librariesToUpdate) {
+            fhirDal.update(library);
+          }
+        }
+      }
+   }
+   private void updateConditionWithNewSynonym(Library library, String system, String code, String newText) {
+    List<RelatedArtifact> relatedArtifacts = library.getRelatedArtifact();
+    relatedArtifacts.stream()
+      .map(ra -> ra.getExtensionByUrl(KnowledgeArtifactProcessor.valueSetConditionUrl))
+      .filter(ext -> ext != null)
+      .map(ext -> (CodeableConcept)ext.getValue())
+      .filter(concept -> concept.getCoding().stream().anyMatch(coding -> coding.getSystem().equals(system) && coding.getCode().equals(code)))
+      .forEach(concept -> {
+        concept.setText(newText);
+      });
+   }
+}

plugin/cr/src/test/java/org/opencds/cqf/ruler/cr/r4/RepositoryServiceTest.java

@@ -34,6 +34,7 @@
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.Enumerations;
 import org.hl7.fhir.r4.model.Extension;
+import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.IntegerType;
 import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.Measure;
@@ -1446,6 +1447,48 @@ void validatePackageOutput() {
 	}
 
 	@Test
+	void update_rckms_valueset_updates_Libraries() {
+		// setup
+		ValueSet conditions = (ValueSet) loadResource("rckms-condition-codes.json");
+		IdType id = new IdType(conditions.getId());
+		// just remove the history part or it causes problems later
+		conditions.setId(id.getResourceType()+"/"+id.getIdPart());
+		loadResource("manifest-code-search-parameter.json");
+		loadTransaction("libraries-with-conditions-bundle.json");
+
+		// if we update 2 synonyms
+		updateSynonym(conditions, "767146004", "testUpdate1");
+		updateSynonym(conditions, "49649001", "testUpdate2");
+		getClient().update().resource(conditions).execute();
+		String valueSetUrl = "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1146.1506|1.0.0";
+		Library lib1 = (Library)getClient().read().resource("Library").withId("lib1").execute();
+		Library lib2 = (Library)getClient().read().resource("Library").withId("lib2").execute();
+		List<Extension> condition1 = getConditionExtensionForValueSet(valueSetUrl,lib1);
+		assertTrue(condition1.size() > 0);
+		// see a change in both libraries
+		assertTrue(((CodeableConcept)condition1.get(0).getValue()).getText().equals("testUpdate1"));
+		List<Extension> condition2 = getConditionExtensionForValueSet(valueSetUrl,lib2);
+		assertTrue(condition2.size() > 0);
+		// see a change in both libraries
+		assertTrue(((CodeableConcept)condition2.get(0).getValue()).getText().equals("testUpdate2"));
+
+	}
+	private void updateSynonym(ValueSet vs, String code, String newText) {
+		vs.getCompose()
+			.getInclude().get(0)
+			.getConcept()
+			.stream().filter(c -> c.getCode().equals(code)).findFirst().get()
+			.getDesignation().get(0)
+			.setValue(newText);
+	}
+	private List<Extension> getConditionExtensionForValueSet(String valueSetUrl, Library library) {
+		return library.getRelatedArtifact().stream()
+			.filter(ra -> ra.hasResource() && ra.getResource().equals(valueSetUrl))
+			.map(ra -> ra.getExtensionByUrl(KnowledgeArtifactProcessor.valueSetConditionUrl))
+			.filter(ext -> ext != null)
+			.collect(Collectors.toList());
+	}
+
 	void basic_artifact_diff() {
 		loadTransaction("ersd-small-active-bundle.json");
 		Bundle bundle = (Bundle) loadTransaction("small-drafted-ersd-bundle.json");

plugin/cr/src/test/resources/libraries-with-conditions-bundle.json

@@ -0,0 +1,69 @@
+{
+	"resourceType": "Bundle",
+	"id": "bundle-ersd-specification-example",
+	"type": "transaction",
+	"entry": [
+		{
+			"fullUrl": "http://hl7.org/fhir/us/ecr/Library/SpecificationLibrary",
+			"resource": {
+				"resourceType": "Library",
+				"id": "lib1",
+				"relatedArtifact": [
+					{
+						"extension": [
+							{
+								"url": "http://aphl.org/fhir/vsm/StructureDefinition/vsm-valueset-condition",
+								"valueCodeableConcept": {
+									"coding": [
+										{
+											"system": "http://snomed.info/sct",
+											"code": "767146004"
+										}
+									],
+									"text": "Infection caused by Acanthamoeba (disorder)"
+								}
+							}
+						],
+						"type": "depends-on",
+						"resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1146.1506|1.0.0"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Library/lib1"
+			}
+		},
+		{
+			"fullUrl": "http://hl7.org/fhir/us/ecr/Library/SpecificationLibrary",
+			"resource": {
+				"resourceType": "Library",
+				"id": "lib2",
+				"relatedArtifact": [
+					{
+						"extension": [
+							{
+								"url": "http://aphl.org/fhir/vsm/StructureDefinition/vsm-valueset-condition",
+								"valueCodeableConcept": {
+									"coding": [
+										{
+											"system": "http://snomed.info/sct",
+											"code": "49649001"
+										}
+									],
+									"text": "Infection caused by Acanthamoeba (disorder)"
+								}
+							}
+						],
+						"type": "depends-on",
+						"resource": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1146.1506|1.0.0"
+					}
+				]
+			},
+			"request": {
+				"method": "PUT",
+				"url": "Library/lib2"
+			}
+		}
+	]
+}

plugin/cr/src/test/resources/manifest-code-search-parameter.json

@@ -0,0 +1,10 @@
+{
+	"resourceType": "SearchParameter",
+	"id": "manifest-contains-code",
+	"status": "active",
+	"code": "manifest-contains-code",
+	"base": ["Library"],
+	"type": "token",
+	"description": "Return all Libraries which reference a particular code",
+	"expression": "Library.relatedArtifact.extension.where(url.contains('vsm-valueset-condition')).value as CodeableConcept"
+}