Merge remote-tracking branch 'origin/LNK-3102' into LNK-3102

Azure_Pipelines/azure-pipelines.measureeval.cd.yaml

@@ -73,7 +73,7 @@ steps:
         Write-Host "Set MyTag to: $myTag1"
 
   - task: Docker@2
-    displayName: "Build & Push Audit Docker Image"
+    displayName: "Build & Push MeasureEval Docker Image"
     condition: always()
     inputs:
       containerRegistry: $(containerRegistry)
@@ -89,3 +89,16 @@ steps:
     inputs:
       targetPath: '$(Build.ArtifactStagingDirectory)'
       artifact: 'manifest'
+
+  - task: Maven@2
+    displayName: Package CLI
+    inputs:
+      mavenPomFile: 'Java/pom.xml'
+      goals: 'clean package'
+      options: '-P cli -pl measureeval -am'
+
+  - task: PublishPipelineArtifact@1
+    displayName: 'Publish MeasureEval CLI Jar'
+    inputs:
+      targetPath: 'Java/measureeval/target/measureeval-cli.jar'
+      artifact: 'measureeval-cli-jar'

Java/measureeval/pom.xml

@@ -190,7 +190,6 @@
             <id>cli</id>
             <properties>
                 <mainClass>com.lantanagroup.link.measureeval.FileSystemInvocation</mainClass>
-                <logback.configurationFile>src/main/resources/logback-cli.xml</logback.configurationFile>
             </properties>
             <build>
                 <finalName>measureeval-cli</finalName>

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/FileSystemInvocation.java

@@ -1,7 +1,12 @@
 package com.lantanagroup.link.measureeval;
 
 import ca.uhn.fhir.context.FhirContext;
+import ch.qos.logback.classic.LoggerContext;
+import ch.qos.logback.classic.joran.JoranConfigurator;
+import ch.qos.logback.core.joran.spi.JoranException;
 import com.lantanagroup.link.measureeval.services.MeasureEvaluator;
+import com.lantanagroup.link.measureeval.utils.CqlLogAppender;
+import com.lantanagroup.link.measureeval.utils.CqlUtils;
 import com.lantanagroup.link.measureeval.utils.StreamUtils;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
@@ -28,6 +33,15 @@ public class FileSystemInvocation {
     private static final FhirContext fhirContext = FhirContext.forR4Cached();
     private static final Logger logger = LoggerFactory.getLogger(FileSystemInvocation.class);
 
+    private static void configureLogging(Bundle bundle) throws JoranException {
+        LoggerContext context = (LoggerContext) LoggerFactory.getILoggerFactory();
+        context.reset();
+        JoranConfigurator configurator = new JoranConfigurator();
+        configurator.setContext(context);
+        configurator.doConfigure(ClassLoader.getSystemResource("logback-cli.xml"));
+        CqlLogAppender.start(context, libraryId -> CqlUtils.getLibrary(bundle, libraryId));
+    }
+
     private static Bundle getBundle(String measureBundlePath) throws IOException {
         logger.info("Loading measure bundle from: {}", measureBundlePath);
 
@@ -138,7 +152,7 @@ private static Patient findPatient(Bundle bundle) {
                 .orElseThrow(() -> new IllegalArgumentException("Patient resource not found in bundle"));
     }
 
-    private static void evaluatePatientBundle(String patientBundlePath, Bundle patientBundle, String start, String end, MeasureEvaluator evaluator) {
+    private static void evaluatePatientBundle(Bundle patientBundle, String start, String end, MeasureEvaluator evaluator, boolean isDebug) {
         Patient patient = findPatient(patientBundle);
         var report = evaluator.evaluate(
                 new DateTimeType(start),
@@ -162,6 +176,7 @@ public static void main(String[] args) {
 
         try {
             Bundle measureBundle = getBundle(measureBundlePath);
+            configureLogging(measureBundle);
             MeasureEvaluator evaluator = MeasureEvaluator.compile(fhirContext, measureBundle, true);
 
             File patientBundleFile = new File(patientBundlePath);
@@ -171,11 +186,11 @@ public static void main(String[] args) {
 
                 for (Bundle patientBundle : patientBundles) {
                     logger.info("\n===================================================");
-                    evaluatePatientBundle(patientBundlePath, patientBundle, start, end, evaluator);
+                    evaluatePatientBundle(patientBundle, start, end, evaluator, true);
                 }
             } else {
                 Bundle patientBundle = getBundle(patientBundlePath);
-                evaluatePatientBundle(patientBundlePath, patientBundle, start, end, evaluator);
+                evaluatePatientBundle(patientBundle, start, end, evaluator, true);
             }
         } catch (Exception e) {
             System.err.println("Error occurred while evaluating measure: " + e.getMessage());

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/MeasureEvalApplication.java

@@ -1,9 +1,14 @@
 package com.lantanagroup.link.measureeval;
 
+import ch.qos.logback.classic.LoggerContext;
+import com.lantanagroup.link.measureeval.services.MeasureEvaluatorCache;
+import com.lantanagroup.link.measureeval.utils.CqlLogAppender;
+import org.slf4j.LoggerFactory;
 import org.springframework.boot.Banner;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.context.properties.ConfigurationPropertiesScan;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;
 import org.springframework.data.mongodb.config.EnableMongoAuditing;
 
@@ -20,4 +25,10 @@ public static void main(String[] args) {
         application.setBannerMode(Banner.Mode.OFF);
         application.run(args);
     }
+
+    @Bean
+    public CqlLogAppender cqlLogAppender(MeasureEvaluatorCache measureEvaluatorCache) {
+        LoggerContext loggerContext = (LoggerContext) LoggerFactory.getILoggerFactory();
+        return CqlLogAppender.start(loggerContext, measureEvaluatorCache);
+    }
 }

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/configs/LinkConfig.java

@@ -16,6 +16,8 @@
 public class LinkConfig {
     private String reportabilityPredicate;
 
+    private boolean cqlDebug = false;
+
     @Bean
     @SuppressWarnings("unchecked")
     public Predicate<MeasureReport> reportabilityPredicate() throws Exception {

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/controllers/MeasureDefinitionController.java

@@ -1,15 +1,19 @@
 package com.lantanagroup.link.measureeval.controllers;
 
+import ca.uhn.fhir.context.FhirContext;
 import com.fasterxml.jackson.annotation.JsonView;
 import com.lantanagroup.link.measureeval.entities.MeasureDefinition;
 import com.lantanagroup.link.measureeval.repositories.MeasureDefinitionRepository;
 import com.lantanagroup.link.measureeval.serdes.Views;
 import com.lantanagroup.link.measureeval.services.MeasureDefinitionBundleValidator;
 import com.lantanagroup.link.measureeval.services.MeasureEvaluator;
 import com.lantanagroup.link.measureeval.services.MeasureEvaluatorCache;
+import com.lantanagroup.link.measureeval.utils.CqlUtils;
 import com.lantanagroup.link.shared.auth.PrincipalUser;
 import io.opentelemetry.api.trace.Span;
 import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.Parameter;
+import javassist.NotFoundException;
 import org.apache.commons.text.StringEscapeUtils;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.MeasureReport;
@@ -98,21 +102,50 @@ public MeasureDefinition put(@AuthenticationPrincipal PrincipalUser user, @PathV
         return entity;
     }
 
+    @GetMapping("/{id}/{library-id}/$cql")
+    @PreAuthorize("hasAuthority('IsLinkAdmin')")
+    @Operation(summary = "Get the CQL for a measure definition's library", tags = {"Measure Definitions"})
+    @Parameter(name = "id", description = "The ID of the measure definition", required = true)
+    @Parameter(name = "library-id", description = "The ID of the library in the measure definition", required = true)
+    @Parameter(name = "range", description = "The range of the CQL to return (e.g. 37:1-38:22)", required = false)
+    public String getMeasureLibraryCQL(
+            @PathVariable("id") String measureId,
+            @PathVariable("library-id") String libraryId,
+            @RequestParam(value = "range", required = false) String range) {
+
+        // Test that the range format is correct (i.e. "37:1-38:22")
+        if (range != null && !range.matches("\\d+:\\d+-\\d+:\\d+")) {
+            throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Invalid range format");
+        }
+
+        // Get the measure definition from the repo by ID
+        MeasureDefinition measureDefinition = repository.findById(measureId).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND));
+
+        try {
+            return CqlUtils.getCql(measureDefinition.getBundle(), libraryId, range);
+        } catch (NotFoundException e) {
+            throw new ResponseStatusException(HttpStatus.NOT_FOUND, e.getMessage(), e);
+        }
+    }
+
     @PostMapping("/{id}/$evaluate")
     @PreAuthorize("hasAuthority('IsLinkAdmin')")
     @Operation(summary = "Evaluate a measure against data in request body", tags = {"Measure Definitions"})
-    public MeasureReport evaluate(@AuthenticationPrincipal PrincipalUser user, @PathVariable String id, @RequestBody Parameters parameters) {
+    @Parameter(name = "id", description = "The ID of the measure definition", required = true)
+    @Parameter(name = "parameters", description = "The parameters to use in the evaluation", required = true)
+    @Parameter(name = "debug", description = "Whether to log CQL debugging information during evaluation", required = false)
+    public MeasureReport evaluate(@AuthenticationPrincipal PrincipalUser user, @PathVariable String id, @RequestBody Parameters parameters, @RequestParam(required = false, defaultValue = "false") boolean debug) {
 
         if (user != null){
             Span currentSpan = Span.current();
             currentSpan.setAttribute("user", user.getEmailAddress());
         }
-        MeasureEvaluator evaluator = evaluatorCache.get(id);
-        if (evaluator == null) {
-            throw new ResponseStatusException(HttpStatus.NOT_FOUND);
-        }
+
         try {
-            return evaluator.evaluate(parameters);
+            // Ensure that a measure evaluator is cached (so that CQL logging can use it)
+            MeasureEvaluator evaluator = evaluatorCache.get(id);
+            // But recompile the bundle every time because the debug flag may not match what's in the cache
+            return MeasureEvaluator.compileAndEvaluate(FhirContext.forR4(), evaluator.getBundle(), parameters, debug);
         } catch (Exception e) {
             throw new ResponseStatusException(HttpStatus.BAD_REQUEST, e.getMessage(), e);
         }

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/repositories/LinkInMemoryFhirRepository.java

@@ -0,0 +1,57 @@
+package com.lantanagroup.link.measureeval.repositories;
+
+import ca.uhn.fhir.context.FhirContext;
+import org.hl7.fhir.instance.model.api.IBaseBundle;
+import org.hl7.fhir.r4.model.Bundle;
+import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+/**
+ * This class extends the InMemoryFhirRepository to provide a transaction method that will update the resources in the repository.
+ * This implementation is primarily used to avoid the exception stack trace that is thrown when the InMemoryFhirRepository.transaction method is called by measure eval, but is not implemented
+ * in the default InMemoryFhirRepository.
+ */
+public class LinkInMemoryFhirRepository extends InMemoryFhirRepository {
+    private static final Logger logger = LoggerFactory.getLogger(LinkInMemoryFhirRepository.class);
+
+    public LinkInMemoryFhirRepository(FhirContext context) {
+        super(context);
+    }
+
+    public LinkInMemoryFhirRepository(FhirContext context, IBaseBundle bundle) {
+        super(context, bundle);
+    }
+
+    @Override
+    public <B extends IBaseBundle> B transaction(B transaction, Map<String, String> headers) {
+        if (!(transaction instanceof Bundle)) {
+            return transaction;
+        }
+
+        Bundle bundle = (Bundle) transaction;
+
+        if (bundle.getEntry() == null || bundle.getEntry().size() == 0) {
+            return transaction;
+        }
+
+        for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
+            if (entry != null && entry.hasResource()) {
+                try {
+                    // Ensure each resource has an ID, or create a GUID for them
+                    if (!entry.getResource().hasId()) {
+                        entry.getResource().setId(java.util.UUID.randomUUID().toString());
+                    }
+
+                    this.update(entry.getResource());
+                } catch (Exception ex) {
+                    logger.warn("Failed to process resource in transaction", ex);
+                }
+            }
+        }
+
+        return transaction;
+    }
+}

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/services/LibraryResolver.java

@@ -0,0 +1,7 @@
+package com.lantanagroup.link.measureeval.services;
+
+import org.hl7.fhir.r4.model.Library;
+
+public interface LibraryResolver {
+    Library resolve(String libraryId);
+}