TECH_DEBT: Measure debuggability

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

@@ -138,7 +138,7 @@ 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),
@@ -171,11 +171,11 @@ 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/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 +1,18 @@
 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 org.apache.commons.text.StringEscapeUtils;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.MeasureReport;
@@ -98,21 +101,44 @@ public MeasureDefinition put(@AuthenticationPrincipal PrincipalUser user, @PathV
         return entity;
     }
 
+    @GetMapping("/{id}/{library-id}/$cql")
+    @PreAuthorize("hasAuthority('IsLinkAdmin')")
+    @Operation(summary = "Get the CQL for a measure definition's library", tags = {"Measure Definitions"})
+    @Parameter(name = "id", description = "The ID of the measure definition", required = true)
+    @Parameter(name = "library-id", description = "The ID of the library in the measure definition", required = true)
+    @Parameter(name = "range", description = "The range of the CQL to return (e.g. 37:1-38:22)", required = false)
+    public String getMeasureLibraryCQL(
+            @PathVariable("id") String measureId,
+            @PathVariable("library-id") String libraryId,
+            @RequestParam(value = "range", required = false) String range) {
+
+        // Test that the range format is correct (i.e. "37:1-38:22")
+        if (range != null && !range.matches("\\d+:\\d+-\\d+:\\d+")) {
+            throw new ResponseStatusException(HttpStatus.BAD_REQUEST, "Invalid range format");
+        }
+
+        // Get the measure definition from the repo by ID
+        MeasureDefinition measureDefinition = repository.findById(measureId).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND));
+        return CqlUtils.getCql(measureDefinition.getBundle(), libraryId, range);
+    }
+
     @PostMapping("/{id}/$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);
+            // Compile the measure every time because the debug flag may have changed from what's in the cache
+            MeasureDefinition measureDefinition = repository.findById(id).orElseThrow(() -> new ResponseStatusException(HttpStatus.NOT_FOUND));
+            return MeasureEvaluator.compileAndEvaluate(FhirContext.forR4(), measureDefinition.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 +1,52 @@
+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;
+
+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/MeasureEvaluator.java

@@ -3,8 +3,10 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
+import com.lantanagroup.link.measureeval.repositories.LinkInMemoryFhirRepository;
 import com.lantanagroup.link.measureeval.utils.ParametersUtils;
 import com.lantanagroup.link.measureeval.utils.StreamUtils;
+import lombok.Getter;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
 import org.hl7.fhir.r4.model.*;
 import org.opencds.cqf.fhir.api.Repository;
@@ -14,7 +16,6 @@
 import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
 import org.opencds.cqf.fhir.cr.measure.r4.R4MeasureService;
 import org.opencds.cqf.fhir.utility.monad.Eithers;
-import org.opencds.cqf.fhir.utility.repository.InMemoryFhirRepository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -28,6 +29,7 @@ public class MeasureEvaluator {
 
     private final FhirContext fhirContext;
     private final MeasureEvaluationOptions options;
+    @Getter
     private final Bundle bundle;
     private final Measure measure;
 
@@ -74,10 +76,6 @@ private MeasureEvaluator(FhirContext fhirContext, Bundle bundle, boolean isDebug
         }
     }
 
-    public static MeasureEvaluator compile(FhirContext fhirContext, Bundle bundle) {
-        return compile(fhirContext, bundle, false);
-    }
-
     public static MeasureEvaluator compile(FhirContext fhirContext, Bundle bundle, boolean isDebug) {
         MeasureEvaluator instance = new MeasureEvaluator(fhirContext, bundle, isDebug);
         instance.compile();
@@ -94,12 +92,21 @@ private void compile() {
         doEvaluate(null, null, new StringType(subject), additionalData);
     }
 
+    public static MeasureReport compileAndEvaluate(FhirContext fhirContext, Bundle bundle, Parameters parameters, boolean isDebug) {
+        MeasureEvaluator evaluator = new MeasureEvaluator(fhirContext, bundle, isDebug);
+        DateTimeType periodStart = ParametersUtils.getValue(parameters, "periodStart", DateTimeType.class);
+        DateTimeType periodEnd = ParametersUtils.getValue(parameters, "periodEnd", DateTimeType.class);
+        StringType subject = ParametersUtils.getValue(parameters, "subject", StringType.class);
+        Bundle additionalData = ParametersUtils.getResource(parameters, "additionalData", Bundle.class);
+        return evaluator.doEvaluate(periodStart, periodEnd, subject, additionalData);
+    }
+
     private MeasureReport doEvaluate(
             DateTimeType periodStart,
             DateTimeType periodEnd,
             StringType subject,
             Bundle additionalData) {
-        Repository repository = new InMemoryFhirRepository(fhirContext, bundle);
+        Repository repository = new LinkInMemoryFhirRepository(fhirContext, bundle);
         R4MeasureService measureService = new R4MeasureService(repository, options);
         return measureService.evaluate(
                 Eithers.forRight3(measure),
@@ -117,38 +124,50 @@ private MeasureReport doEvaluate(
                 null);
     }
 
+    public MeasureReport evaluate(Date periodStart, Date periodEnd, String patientId, Bundle additionalData) {
+        TimeZone utc = TimeZone.getTimeZone(ZoneOffset.UTC);
+        return evaluate(
+                new DateTimeType(periodStart, TemporalPrecisionEnum.MILLI, utc),
+                new DateTimeType(periodEnd, TemporalPrecisionEnum.MILLI, utc),
+                new StringType(new IdType(ResourceType.Patient.name(), patientId).getValue()),
+                additionalData);
+    }
+
+    public MeasureReport evaluate(Parameters parameters) {
+        DateTimeType periodStart = ParametersUtils.getValue(parameters, "periodStart", DateTimeType.class);
+        DateTimeType periodEnd = ParametersUtils.getValue(parameters, "periodEnd", DateTimeType.class);
+        StringType subject = ParametersUtils.getValue(parameters, "subject", StringType.class);
+        Bundle additionalData = ParametersUtils.getResource(parameters, "additionalData", Bundle.class);
+        return evaluate(periodStart, periodEnd, subject, additionalData);
+    }
+
     public MeasureReport evaluate(
             DateTimeType periodStart,
             DateTimeType periodEnd,
             StringType subject,
             Bundle additionalData) {
         List<Bundle.BundleEntryComponent> entries = additionalData.getEntry();
+
         logger.debug(
                 "Evaluating measure: MEASURE=[{}] START=[{}] END=[{}] SUBJECT=[{}] RESOURCES=[{}]",
                 measure.getUrl(), periodStart.asStringValue(), periodEnd.asStringValue(), subject, entries.size());
+
+        // Output debug/trace information about the results of the evaluation
         if (logger.isTraceEnabled()) {
+            // Output the group/population counts
+            for (MeasureReport.MeasureReportGroupComponent group : doEvaluate(periodStart, periodEnd, subject, additionalData).getGroup()) {
+                logger.trace("Group {}: {}", group.getId(), group.getPopulation().size());
+                for (MeasureReport.MeasureReportGroupPopulationComponent population : group.getPopulation()) {
+                    logger.trace("Population {}: {} - {}", population.getCode().getCodingFirstRep().getDisplay(), population.getCount());
+                }
+            }
+
+            // Output each resource in the bundle
             for (int entryIndex = 0; entryIndex < entries.size(); entryIndex++) {
                 Resource resource = entries.get(entryIndex).getResource();
                 logger.trace("Resource {}: {}/{}", entryIndex, resource.getResourceType(), resource.getIdPart());
             }
         }
         return doEvaluate(periodStart, periodEnd, subject, additionalData);
     }
-
-    public MeasureReport evaluate(Date periodStart, Date periodEnd, String patientId, Bundle additionalData) {
-        TimeZone utc = TimeZone.getTimeZone(ZoneOffset.UTC);
-        return evaluate(
-                new DateTimeType(periodStart, TemporalPrecisionEnum.MILLI, utc),
-                new DateTimeType(periodEnd, TemporalPrecisionEnum.MILLI, utc),
-                new StringType(new IdType(ResourceType.Patient.name(), patientId).getValue()),
-                additionalData);
-    }
-
-    public MeasureReport evaluate(Parameters parameters) {
-        DateTimeType periodStart = ParametersUtils.getValue(parameters, "periodStart", DateTimeType.class);
-        DateTimeType periodEnd = ParametersUtils.getValue(parameters, "periodEnd", DateTimeType.class);
-        StringType subject = ParametersUtils.getValue(parameters, "subject", StringType.class);
-        Bundle additionalData = ParametersUtils.getResource(parameters, "additionalData", Bundle.class);
-        return evaluate(periodStart, periodEnd, subject, additionalData);
-    }
 }

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

@@ -1,6 +1,7 @@
 package com.lantanagroup.link.measureeval.services;
 
 import ca.uhn.fhir.context.FhirContext;
+import com.lantanagroup.link.measureeval.configs.LinkConfig;
 import com.lantanagroup.link.measureeval.entities.MeasureDefinition;
 import com.lantanagroup.link.measureeval.repositories.MeasureDefinitionRepository;
 import org.springframework.stereotype.Service;
@@ -13,10 +14,12 @@ public class MeasureEvaluatorCache {
     private final FhirContext fhirContext;
     private final MeasureDefinitionRepository definitionRepository;
     private final Map<String, MeasureEvaluator> instancesById = new ConcurrentHashMap<>();
+    private final LinkConfig linkConfig;
 
-    public MeasureEvaluatorCache(FhirContext fhirContext, MeasureDefinitionRepository definitionRepository) {
+    public MeasureEvaluatorCache(FhirContext fhirContext, MeasureDefinitionRepository definitionRepository, LinkConfig linkConfig) {
         this.fhirContext = fhirContext;
         this.definitionRepository = definitionRepository;
+        this.linkConfig = linkConfig;
     }
 
     public MeasureEvaluator get(String id) {
@@ -25,7 +28,7 @@ public MeasureEvaluator get(String id) {
             if (measureDefinition == null) {
                 return null;
             }
-            return MeasureEvaluator.compile(fhirContext, measureDefinition.getBundle());
+            return MeasureEvaluator.compile(fhirContext, measureDefinition.getBundle(), this.linkConfig.isCqlDebug());
         });
     }
 

Java/measureeval/src/main/java/com/lantanagroup/link/measureeval/utils/ApplicationContextProvider.java

@@ -0,0 +1,19 @@
+package com.lantanagroup.link.measureeval.utils;
+
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.ApplicationContextAware;
+import org.springframework.stereotype.Component;
+
+@Component
+public class ApplicationContextProvider implements ApplicationContextAware {
+    private static ApplicationContext context;
+
+    public static ApplicationContext getApplicationContext() {
+        return context;
+    }
+
+    @Override
+    public void setApplicationContext(ApplicationContext applicationContext) {
+        context = applicationContext;
+    }
+}