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Library evaluation provider into CR (#394)
* library evaluate provider * testing for library evaluate and cql evaluate * removing file errors * more test coverage, update class names
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70 changes: 70 additions & 0 deletions
70
cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/cpg/r4/R4LibraryEvaluationService.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,70 @@ | ||
| package org.opencds.cqf.fhir.cr.cpg.r4; | ||
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| import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters; | ||
| import static org.opencds.cqf.fhir.utility.r4.Parameters.part; | ||
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| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.Endpoint; | ||
| import org.hl7.fhir.r4.model.IdType; | ||
| import org.hl7.fhir.r4.model.Library; | ||
| import org.hl7.fhir.r4.model.OperationOutcome; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
| import org.opencds.cqf.fhir.api.Repository; | ||
| import org.opencds.cqf.fhir.cql.Engines; | ||
| import org.opencds.cqf.fhir.cql.EvaluationSettings; | ||
| import org.opencds.cqf.fhir.cql.LibraryEngine; | ||
| import org.opencds.cqf.fhir.cr.cpg.BaseCqlExecutionProcessor; | ||
| import org.opencds.cqf.fhir.utility.repository.Repositories; | ||
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| public class R4LibraryEvaluationService { | ||
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| protected Repository repository; | ||
| protected EvaluationSettings evaluationSettings; | ||
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| public R4LibraryEvaluationService(Repository repository, EvaluationSettings evaluationSettings) { | ||
| this.repository = repository; | ||
| this.evaluationSettings = evaluationSettings; | ||
| } | ||
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| public Parameters evaluate( | ||
| IdType theId, | ||
| String subject, | ||
| List<String> expression, | ||
| Parameters parameters, | ||
| Bundle data, | ||
| List<Parameters> prefetchData, | ||
| Endpoint dataEndpoint, | ||
| Endpoint contentEndpoint, | ||
| Endpoint terminologyEndpoint) { | ||
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| var baseCqlExecutionProcessor = new BaseCqlExecutionProcessor(); | ||
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| if (prefetchData != null) { | ||
| return parameters(part("invalid parameters", (OperationOutcome) | ||
| baseCqlExecutionProcessor.createIssue("warning", "prefetchData is not yet supported", repository))); | ||
| } | ||
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| if (contentEndpoint != null) { | ||
| repository = Repositories.proxy(repository, dataEndpoint, contentEndpoint, terminologyEndpoint); | ||
| } | ||
| var libraryEngine = new LibraryEngine(repository, this.evaluationSettings); | ||
| var library = repository.read(Library.class, theId); | ||
| var engine = Engines.forRepositoryAndSettings(evaluationSettings, repository, data); | ||
| var libraryManager = engine.getEnvironment().getLibraryManager(); | ||
| var libraryIdentifier = baseCqlExecutionProcessor.resolveLibraryIdentifier(null, library, libraryManager); | ||
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| Set<String> expressionSet = null; | ||
| if (expression != null) { | ||
| expressionSet = new HashSet<>(expression); | ||
| } | ||
| try { | ||
| return (Parameters) libraryEngine.evaluate(libraryIdentifier, subject, parameters, data, expressionSet); | ||
| } catch (Exception e) { | ||
| return parameters(part("evaluation error", (OperationOutcome) | ||
| baseCqlExecutionProcessor.createIssue("error", e.getMessage(), repository))); | ||
| } | ||
| } | ||
| } |
128 changes: 128 additions & 0 deletions
128
cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/cpg/r4/CqlEvaluationServiceTest.java
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| @@ -0,0 +1,128 @@ | ||
| package org.opencds.cqf.fhir.cr.cpg.r4; | ||
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| import static org.junit.jupiter.api.Assertions.assertEquals; | ||
| import static org.junit.jupiter.api.Assertions.assertFalse; | ||
| import static org.junit.jupiter.api.Assertions.assertTrue; | ||
| import static org.opencds.cqf.fhir.utility.r4.Parameters.datePart; | ||
| import static org.opencds.cqf.fhir.utility.r4.Parameters.parameters; | ||
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| import org.hl7.fhir.r4.model.BooleanType; | ||
| import org.hl7.fhir.r4.model.IntegerType; | ||
| import org.hl7.fhir.r4.model.OperationOutcome; | ||
| import org.hl7.fhir.r4.model.Parameters; | ||
| import org.junit.jupiter.api.Test; | ||
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| public class CqlEvaluationServiceTest { | ||
| @Test | ||
| void libraryEvaluationService_inlineAsthma() { | ||
| var content = "library AsthmaTest version '1.0.0'\n" + "\n" | ||
| + "using FHIR version '4.0.1'\n" | ||
| + "\n" | ||
| + "include FHIRHelpers version '4.0.1'\n" | ||
| + "\n" | ||
| + "codesystem \"SNOMED\": 'http://snomed.info/sct'\n" | ||
| + "\n" | ||
| + "code \"Asthma\": '195967001' from \"SNOMED\"\n" | ||
| + "\n" | ||
| + "context Patient\n" | ||
| + "\n" | ||
| + "define \"Asthma Diagnosis\":\n" | ||
| + " [Condition: \"Asthma\"]\n" | ||
| + "\n" | ||
| + "define \"Has Asthma Diagnosis\":\n" | ||
| + " exists(\"Asthma Diagnosis\")\n"; | ||
| var when = Library.given() | ||
| .repositoryFor("libraryeval") | ||
| .when() | ||
| .subject("Patient/SimplePatient") | ||
| .content(content) | ||
| .evaluateCql(); | ||
| var results = when.then().parameters(); | ||
| assertTrue(results.hasParameter()); | ||
| assertEquals(3, results.getParameter().size()); | ||
| } | ||
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| @Test | ||
| void libraryEvaluationService_contentAndExpression() { | ||
| var content = "library SimpleR4Library\n" + "\n" | ||
| + "using FHIR version '4.0.1'\n" | ||
| + "\n" | ||
| + "include FHIRHelpers version '4.0.1' called FHIRHelpers\n" | ||
| + "\n" | ||
| + "context Patient\n" | ||
| + "\n" | ||
| + "define simpleBooleanExpression: true\n" | ||
| + "\n" | ||
| + "define observationRetrieve: [Observation]\n" | ||
| + "\n" | ||
| + "define observationHasCode: not IsNull(([Observation]).code)\n" | ||
| + "\n" | ||
| + "define \"Initial Population\": observationHasCode\n" | ||
| + "\n" | ||
| + "define \"Denominator\": \"Initial Population\"\n" | ||
| + "\n" | ||
| + "define \"Numerator\": \"Denominator\""; | ||
| var when = Library.given() | ||
| .repositoryFor("libraryeval") | ||
| .when() | ||
| .subject("Patient/SimplePatient") | ||
| .expression("Numerator") | ||
| .content(content) | ||
| .evaluateCql(); | ||
| var results = when.then().parameters(); | ||
| assertFalse(results.isEmpty()); | ||
| assertEquals(1, results.getParameter().size()); | ||
| assertTrue(results.getParameter("Numerator").getValue() instanceof BooleanType); | ||
| assertTrue(((BooleanType) results.getParameter("Numerator").getValue()).booleanValue()); | ||
| ; | ||
| } | ||
|
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| @Test | ||
| void libraryEvaluationService_arithmetic() { | ||
| var when = Library.given() | ||
| .repositoryFor("libraryeval") | ||
| .when() | ||
| .expression("5*5") | ||
| .evaluateCql(); | ||
| var results = when.then().parameters(); | ||
| assertTrue(results.getParameter("return").getValue() instanceof IntegerType); | ||
| assertEquals("25", ((IntegerType) results.getParameter("return").getValue()).asStringValue()); | ||
| } | ||
|
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| @Test | ||
| void libraryEvaluationService_paramsAndExpression() { | ||
| Parameters evaluationParams = parameters(datePart("%inputDate", "2019-11-01")); | ||
| var when = Library.given() | ||
| .repositoryFor("libraryeval") | ||
| .when() | ||
| .subject("Patient/SimplePatient") | ||
| .parameters(evaluationParams) | ||
| .expression("year from %inputDate before 2020") | ||
| .evaluateCql(); | ||
| var results = when.then().parameters(); | ||
| assertTrue(results.getParameter("return").getValue() instanceof BooleanType); | ||
| assertTrue(((BooleanType) results.getParameter("return").getValue()).booleanValue()); | ||
| } | ||
|
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| @Test | ||
| void libraryEvaluationService_ErrorLibrary() { | ||
| var expression = "Interval[1,5]"; | ||
| var when = Library.given() | ||
| .repositoryFor("libraryeval") | ||
| .when() | ||
| .expression(expression) | ||
| .evaluateCql(); | ||
| var report = when.then().parameters(); | ||
| assertTrue(report.hasParameter()); | ||
| assertTrue(report.getParameterFirstRep().hasName()); | ||
| assertEquals("evaluation error", report.getParameterFirstRep().getName()); | ||
| assertTrue(report.getParameterFirstRep().hasResource()); | ||
| assertTrue(report.getParameterFirstRep().getResource() instanceof OperationOutcome); | ||
| assertEquals( | ||
| "Unsupported interval point type for FHIR conversion java.lang.Integer", | ||
| ((OperationOutcome) report.getParameterFirstRep().getResource()) | ||
| .getIssueFirstRep() | ||
| .getDetails() | ||
| .getText()); | ||
| } | ||
| } |
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