Merge pull request #692 from lantanagroup/LNK-1828

Lnk 1828

api/src/main/java/com/lantanagroup/link/api/MeasureEvaluator.java

@@ -2,6 +2,7 @@
 
 import com.lantanagroup.link.Constants;
 import com.lantanagroup.link.FhirDataProvider;
+import com.lantanagroup.link.Helper;
 import com.lantanagroup.link.ReportIdHelper;
 import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.TenantService;
@@ -62,6 +63,12 @@ private MeasureReport generateMeasureReport() {
       patientBundle = PatientData.asBundle(tenantService.findPatientData(reportContext.getMasterIdentifierValue(), patientId));
     }
 
+    // if patient is in the debugPatients list or debugPatients = "*" then write the patient data bundle to the file system
+    if (reportContext.getDebugPatients().contains("Patient/" + patientId) || reportContext.getDebugPatients().contains("*")) {
+      String fileName = ReportIdHelper.getPatientBundleFileName(reportContext.getMasterIdentifierValue(), patientId) + ".json";
+      Helper.dumpToFile(patientBundle, config.getDebugPath(), fileName);
+    }
+
     logger.info("Executing $evaluate-measure for measure: {}, start: {}, end: {}, patient: {}, resources: {}", measureId, start, end, patientId, patientBundle.getEntry().size());
 
     Parameters parameters = new Parameters();

api/src/main/java/com/lantanagroup/link/api/controller/ReportController.java

@@ -166,7 +166,7 @@ public Report generateReport(
     }
 
     TenantService tenantService = TenantService.create(this.sharedService, tenantId);
-    return generateResponse(tenantService, user, request, input.getPackageId(), input.getBundleIds(), input.getPeriodStart(), input.getPeriodEnd(), input.isRegenerate(), input.isValidate(), input.isSkipQuery());
+    return generateResponse(tenantService, user, request, input.getPackageId(), input.getBundleIds(), input.getPeriodStart(), input.getPeriodEnd(), input.isRegenerate(), input.isValidate(), input.isSkipQuery(), input.getDebugPatients());
   }
 
   /**
@@ -185,7 +185,8 @@ public Report generateReport(
           @PathVariable String tenantId,
           @RequestParam boolean regenerate,
           @RequestParam(defaultValue = "true") boolean validate,
-          @RequestParam(defaultValue = "false") boolean skipQuery)
+          @RequestParam(defaultValue = "false") boolean skipQuery,
+          @RequestParam(required = false, defaultValue = "") List<String> debugPatients)
           throws Exception {
     List<String> singleMeasureBundleIds;
 
@@ -198,6 +199,8 @@ public Report generateReport(
       }
     }
 
+    Optional<List<String>> debugPatientList = Optional.of(debugPatients);
+
     // get the associated bundle-ids
     if (!apiMeasurePackage.isPresent()) {
       throw new IllegalStateException(String.format("Multimeasure %s is not set-up.", multiMeasureBundleId));
@@ -206,7 +209,7 @@ public Report generateReport(
     TenantService tenantService = TenantService.create(this.sharedService, tenantId);
 
     singleMeasureBundleIds = apiMeasurePackage.get().getMeasureIds();
-    return generateResponse(tenantService, user, request, multiMeasureBundleId, singleMeasureBundleIds, periodStart, periodEnd, regenerate, validate, skipQuery);
+    return generateResponse(tenantService, user, request, multiMeasureBundleId, singleMeasureBundleIds, periodStart, periodEnd, regenerate, validate, skipQuery, debugPatients);
   }
 
   private void checkReportingPlan(TenantService tenantService, String periodStart, List<String> measureIds) throws ParseException, URISyntaxException, IOException {
@@ -244,7 +247,7 @@ private void checkReportingPlan(TenantService tenantService, String periodStart,
   /**
    * generates a response with one or multiple reports
    */
-  private Report generateResponse(TenantService tenantService, LinkCredentials user, HttpServletRequest request, String packageId, List<String> measureIds, String periodStart, String periodEnd, boolean regenerate, boolean validate, boolean skipQuery) throws Exception {
+  private Report generateResponse(TenantService tenantService, LinkCredentials user, HttpServletRequest request, String packageId, List<String> measureIds, String periodStart, String periodEnd, boolean regenerate, boolean validate, boolean skipQuery, List<String>  debugPatients) throws Exception {
     Report report = null;
     try(var stopwatch = stopwatchManager.start(Constants.REPORT_GENERATION_TASK, Constants.CATEGORY_REPORT)) {
       this.checkReportingPlan(tenantService, periodStart, measureIds);
@@ -299,6 +302,17 @@ private Report generateResponse(TenantService tenantService, LinkCredentials use
       }
       reportContext.setQueryPlan(queryPlan);
 
+      // Validate the debug patients against the patient of interest list
+      if(!debugPatients.isEmpty() && !debugPatients.contains("*")) {
+        List<String> invalidDebugPatientsList = debugPatients.stream().filter(dp -> !reportContext.getPatientsOfInterest().stream().map(PatientOfInterestModel::getReference).collect(Collectors.toList()).contains(dp)).collect(Collectors.toList());
+        if (!invalidDebugPatientsList.isEmpty()) {
+          String msg = String.format("Debugging patients: %s do not exist", invalidDebugPatientsList);
+          logger.error(msg);
+          throw new ResponseStatusException(HttpStatus.BAD_REQUEST, msg);
+        }
+      }
+      reportContext.setDebugPatients(debugPatients);
+
       report = new Report();
       report.setId(masterIdentifierValue);
       report.setPeriodStart(criteria.getPeriodStart());

api/src/main/resources/application.yml

@@ -14,6 +14,7 @@ api:
   sender: com.lantanagroup.link.sender.FileSystemSender
   patient-id-resolver: com.lantanagroup.link.nhsn.StoredListProvider
   report-aggregator: com.lantanagroup.link.nhsn.ReportAggregator
+  debugPath: '%TEMP%'
   data-processor:
     csv: com.lantanagroup.link.thsa.GenericCSVProcessor
     xlsx: com.lantanagroup.link.thsa.GenericXLSXProcessor
@@ -92,4 +93,4 @@ data-governance:
   report-retention:
 sender:
   file:
-    path: '%TEMP%'
+    path: '%TEMP%'

core/src/main/java/com/lantanagroup/link/Helper.java

@@ -1,9 +1,9 @@
 package com.lantanagroup.link;
 
+import ca.uhn.fhir.parser.IParser;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
-import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.TenantService;
 import com.lantanagroup.link.db.model.Aggregate;
 import com.lantanagroup.link.db.model.Report;
@@ -13,14 +13,14 @@
 import org.apache.commons.text.StringEscapeUtils;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CapabilityStatement;
+import org.hl7.fhir.r4.model.Resource;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
+import java.io.*;
 import java.net.URL;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Paths;
 import java.sql.Driver;
 import java.sql.DriverPropertyInfo;
 import java.sql.SQLException;
@@ -192,6 +192,22 @@ public static String expandEnvVars(String text) {
     return text;
   }
 
+  public static void dumpToFile(Resource resource, String path, String fileName) {
+
+    IParser parser = FhirContextProvider.getFhirContext().newJsonParser();
+    String folderPath = Helper.expandEnvVars(path);
+    String filePath = Paths.get(folderPath, fileName).toString();
+    try (Writer writer = new FileWriter(filePath, StandardCharsets.UTF_8)) {
+      parser.encodeResourceToWriter(resource, writer);
+    }
+    catch (Exception e) {
+      logger.error("Error writing resource {} to file system", resource.getId(), e);
+    }
+    finally {
+      logger.info("Done writing resource {} to file system {}", resource.getId(), filePath);
+    }
+  }
+
   public static Bundle generateBundle(TenantService tenantService, Report report, EventService eventService) {
     FhirBundler bundler = new FhirBundler(eventService, tenantService);
     logger.info("Building Bundle for MeasureReport to send...");

core/src/main/java/com/lantanagroup/link/ReportIdHelper.java

@@ -41,4 +41,8 @@ public static String getPatientMeasureReportId(String masterMeasureReportId, Str
   public static String getPatientDataBundleId(String masterIdentifierValue, String patientId) {
     return combine(masterIdentifierValue, hash(patientId));
   }
+
+  public static String getPatientBundleFileName(String masterIdentifierValue, String patientId) {
+    return combine("patient-bundle-for-cqf-", masterIdentifierValue, "-" + patientId);
+  }
 }

core/src/main/java/com/lantanagroup/link/config/api/ApiConfig.java

@@ -151,6 +151,10 @@ public class ApiConfig {
   @Getter
   private String socketTimeout;
 
+  @Getter
+  @NotNull
+  private String debugPath;
+
   /**
    * <strong>api.measure-evaluation-threads</strong><br>The number of threads to use for patient measure report generation.
    */
@@ -177,4 +181,5 @@ public class ApiConfig {
   private boolean allowQaEndpoints = false;
 
   private List<ApiInfoGroup> infoGroups = new ArrayList<>();
+
 }

core/src/main/java/com/lantanagroup/link/model/GenerateRequest.java

@@ -16,4 +16,5 @@ public class GenerateRequest {
   private String periodEnd;
   boolean validate = true;
   boolean skipQuery = false;
+  private List<String> debugPatients = new ArrayList<>();
 }

core/src/main/java/com/lantanagroup/link/model/ReportContext.java

@@ -25,6 +25,7 @@ public class ReportContext {
   private List<PatientOfInterestModel> patientsOfInterest = new ArrayList<>();
   private List<MeasureContext> measureContexts = new ArrayList<>();
   private QueryPlan queryPlan;
+  private List<String> debugPatients = new ArrayList<>();
 
   public ReportContext() {
   }