Misc improvements to Device generation (#708)

* Removing unnecessary arguments from Validator constructor
Keeping track of ImplementationGuide resources found in NpmPackages within the `Validator` separately from the `PrePopulatedValidationSupport` since `PrePopulatedValidationSupport` doesn't do anything with ImplementationGuide
Loading Device.notes with list of implementation guides that are loaded at the time of validation
Update Device.notes in the report when a report is re-validated
Changing interface for IPatientIdProvider to not return the patient list, since it just loads it into the report context anyways and the return value isn't used.
Change `Device` generated to use `note` for events and concept maps. Much more readable. Conferred with Karen and Dave, who agreed.

* Removing unused constant and unnecessary valueset-timing-abbreviation.json
Not logging parse errors in LenientErrorHandler. We only care if there's an exception, and we're catching and logging those anyways.
Bringing the IG status forward from the original IG.
Parsing resources from packages using a stream instead of loading a string up first.
Handling exception during parsing a little nicer for logging

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

@@ -6,7 +6,6 @@
 import com.lantanagroup.link.FhirContextProvider;
 import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.config.api.ApiConfig;
-import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.validation.Validator;
 import org.springframework.beans.factory.InitializingBean;
 import org.springframework.boot.SpringApplication;
@@ -74,8 +73,8 @@ public ApiInit apiInit() {
   }
 
   @Bean
-  public Validator validator(SharedService sharedService, ApiConfig apiConfig) {
-    return new Validator(sharedService, apiConfig);
+  public Validator validator(ApiConfig apiConfig) {
+    return new Validator(apiConfig);
   }
 
   /**

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

@@ -23,6 +23,7 @@
 import com.lantanagroup.link.time.StopwatchManager;
 import com.lantanagroup.link.validation.ValidationService;
 import com.lantanagroup.link.validation.Validator;
+import jakarta.servlet.http.HttpServletRequest;
 import lombok.Setter;
 import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.io.IOUtils;
@@ -41,7 +42,6 @@
 import org.springframework.web.bind.annotation.*;
 import org.springframework.web.server.ResponseStatusException;
 
-import jakarta.servlet.http.HttpServletRequest;
 import java.io.IOException;
 import java.lang.reflect.InvocationTargetException;
 import java.net.URISyntaxException;
@@ -143,14 +143,76 @@ private void queryFhir(TenantService tenantService, ReportCriteria criteria, Rep
     }
   }
 
-  private List<PatientOfInterestModel> getPatientIdentifiers(TenantService tenantService, ReportCriteria criteria, ReportContext context) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
-    List<PatientOfInterestModel> patientOfInterestModelList;
-
+  private void loadPatientIdentifiers(TenantService tenantService, ReportCriteria criteria, ReportContext context) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, InstantiationException, IllegalAccessException {
     Class<?> patientIdResolverClass = Class.forName(this.config.getPatientIdResolver());
     IPatientIdProvider provider = (IPatientIdProvider) this.context.getBean(patientIdResolverClass);
-    patientOfInterestModelList = provider.getPatientsOfInterest(tenantService, criteria, context);
+    provider.loadPatientsOfInterest(tenantService, criteria, context);
+  }
+
+  @PostMapping("/{reportId}/$regenerate")
+  public Report regenerateReport(
+          @AuthenticationPrincipal LinkCredentials user,
+          HttpServletRequest request,
+          @PathVariable String tenantId,
+          @PathVariable String reportId,
+          @RequestBody GenerateRequest input)
+          throws Exception {
+    TenantService tenantService = TenantService.create(this.sharedService, tenantId);
+
+    if (tenantService == null) {
+      throw new ResponseStatusException(HttpStatus.NOT_FOUND, "Tenant not found");
+    }
+
+    Report report = tenantService.getReport(reportId);
+
+    if (report == null) {
+      throw new ResponseStatusException(HttpStatus.NOT_FOUND, "Report not found");
+    }
+
+    GenerateRequest generateRequest = new GenerateRequest();
+    generateRequest.setBundleIds(report.getMeasureIds());
+    generateRequest.setPeriodStart(report.getPeriodStart());
+    generateRequest.setPeriodEnd(report.getPeriodEnd());
+    generateRequest.setRegenerate(true);
+    generateRequest.setValidate(input.isValidate());
+    generateRequest.setSkipQuery(input.isSkipQuery());
+    generateRequest.setDebugPatients(input.getDebugPatients());
+
+    return generateReport(user, request, tenantId, generateRequest);
+  }
+
+  @GetMapping("/{reportId}/$regenerate")
+  public Report regenerateReport(
+          @AuthenticationPrincipal LinkCredentials user,
+          HttpServletRequest request,
+          @PathVariable String tenantId,
+          @PathVariable String reportId,
+          @RequestParam(defaultValue = "true") boolean validate,
+          @RequestParam(defaultValue = "false") boolean skipQuery,
+          @RequestParam(required = false, defaultValue = "") List<String> debugPatients)
+          throws Exception {
+    TenantService tenantService = TenantService.create(this.sharedService, tenantId);
+
+    if (tenantService == null) {
+      throw new ResponseStatusException(HttpStatus.NOT_FOUND, "Tenant not found");
+    }
+
+    Report report = tenantService.getReport(reportId);
+
+    if (report == null) {
+      throw new ResponseStatusException(HttpStatus.NOT_FOUND, "Report not found");
+    }
+
+    GenerateRequest generateRequest = new GenerateRequest();
+    generateRequest.setBundleIds(report.getMeasureIds());
+    generateRequest.setPeriodStart(report.getPeriodStart());
+    generateRequest.setPeriodEnd(report.getPeriodEnd());
+    generateRequest.setRegenerate(true);
+    generateRequest.setValidate(validate);
+    generateRequest.setSkipQuery(skipQuery);
+    generateRequest.setDebugPatients(debugPatients);
 
-    return patientOfInterestModelList;
+    return generateReport(user, request, tenantId, generateRequest);
   }
 
   @PostMapping("/$generate")
@@ -286,9 +348,9 @@ private Report generateResponse(TenantService tenantService, LinkCredentials use
       this.eventService.triggerEvent(tenantService, EventTypes.BeforePatientOfInterestLookup, criteria, reportContext);
 
       // Get the patient identifiers for the given date
-      this.getPatientIdentifiers(tenantService, criteria, reportContext);
+      this.loadPatientIdentifiers(tenantService, criteria, reportContext);
 
-      if (reportContext.getPatientLists() == null || reportContext.getPatientLists().size() < 1) {
+      if (reportContext.getPatientLists() == null || reportContext.getPatientLists().isEmpty()) {
         String msg = "A census for the specified criteria was not found.";
         logger.error(msg);
         throw new ResponseStatusException(HttpStatus.NOT_FOUND, msg);
@@ -318,7 +380,7 @@ private Report generateResponse(TenantService tenantService, LinkCredentials use
       report.setPeriodStart(criteria.getPeriodStart());
       report.setPeriodEnd(criteria.getPeriodEnd());
       report.setMeasureIds(measureIds);
-      report.setDeviceInfo(FhirHelper.getDevice(this.config, tenantService));
+      report.setDeviceInfo(FhirHelper.getDevice(this.config, tenantService, validator));
       report.setQueryPlan(new YAMLMapper().writeValueAsString(queryPlan));
 
       // Preserve the version of the already-existing report

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

@@ -1,7 +1,9 @@
 package com.lantanagroup.link.api.controller;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.lantanagroup.link.FhirHelper;
 import com.lantanagroup.link.ValidationCategorizer;
+import com.lantanagroup.link.config.api.ApiConfig;
 import com.lantanagroup.link.db.SharedService;
 import com.lantanagroup.link.db.TenantService;
 import com.lantanagroup.link.db.mappers.ValidationResultMapper;
@@ -41,6 +43,8 @@ public class ValidationController extends BaseController {
   private SharedService sharedService;
   @Autowired
   private ValidationService validationService;
+  @Autowired
+  private ApiConfig apiConfig;
 
   /**
    * Validates a Bundle provided in the request body
@@ -324,6 +328,14 @@ public OperationOutcome validate(@PathVariable String tenantId, @PathVariable St
       outcome.addContained(report.getDeviceInfo());
     }
 
+    // Update the report's device with the current list of implementation guides
+    Device device = report.getDeviceInfo();
+    if (device == null) {
+      device = FhirHelper.getDevice(this.apiConfig);
+    }
+    FhirHelper.setImplementationGuideNotes(device, this.validator);
+    tenantService.saveReport(report);
+
     return outcome;
   }
 

api/src/main/resources/swagger.yml

@@ -670,6 +670,91 @@ paths:
           $ref: '#/components/responses/Unauthorized'
         '404':
           $ref: '#/components/responses/NotFound'
+  /api/{tenantId}/report/{reportId}/$regenerate:
+    get:
+      tags:
+        - Reports
+      summary: Regenerate a report
+      operationId: regenerateReport
+      parameters:
+        - name: tenantId
+          in: path
+          description: The id of the tenant
+          required: true
+          schema:
+            type: string
+        - name: reportId
+          in: path
+          description: The id of the report to regenerate
+          required: true
+          schema:
+            type: string
+        - name: validate
+          in: query
+          description: Whether to validate the report at the end of generation
+          schema:
+            type: boolean
+            default: true
+        - name: skipQuery
+          in: query
+          description: Whether to skip querying the EHR for data
+          schema:
+            type: boolean
+            default: false
+        - name: debugPatients
+          in: query
+          description: A comma separated list of patient ids to include in the report
+          schema:
+            type: string
+      responses:
+        '200':
+          description: successful response
+          content:
+            'application/json':
+              schema:
+                $ref: '#/components/schemas/Report'
+        '401':
+          $ref: '#/components/responses/Unauthorized'
+        '403':
+          $ref: '#/components/responses/Unauthorized'
+        '404':
+          $ref: '#/components/responses/NotFound'
+    post:
+      tags:
+        - Reports
+      summary: Regenerate a report
+      operationId: regenerateReportPost
+      parameters:
+        - name: tenantId
+          in: path
+          description: The id of the tenant
+          required: true
+          schema:
+            type: string
+        - name: reportId
+          in: path
+          description: The id of the report to regenerate
+          required: true
+          schema:
+            type: string
+      requestBody:
+        content:
+          application/json:
+            schema:
+              $ref: '#/components/schemas/GenerateReport'
+      responses:
+        '200':
+          description: successful response
+          content:
+            'application/json':
+              schema:
+                $ref: '#/components/schemas/Report'
+        '401':
+          $ref: '#/components/responses/Unauthorized'
+        '403':
+          $ref: '#/components/responses/Unauthorized'
+        '404':
+          $ref: '#/components/responses/NotFound'
   /api/{tenantId}/report/$generate:
     post:
       tags:

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

@@ -18,7 +18,6 @@ public class Constants {
   public static final String MeasureScoringCodeSystem = "http://terminology.hl7.org/CodeSystem/measure-scoring";
   public static final String MeasureImprovementNotationCodeSystem = "http://terminology.hl7.org/CodeSystem/measure-improvement-notation";
   public static final String LinkDeviceVersionCodeSystem = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/CodeSystem/codesystem-link-device-version";
-  public static final String LinkDevicePropertiesCodeSystem = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/CodeSystem/codesystem-link-device-properties";
   public static final String ReportBundleProfileUrl = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/StructureDefinition/nhsn-measurereport-bundle";
   public static final String IndividualMeasureReportProfileUrl = "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/indv-measurereport-deqm";
   public static final String CensusProfileUrl = "http://www.cdc.gov/nhsn/fhirportal/dqm/ig/StructureDefinition/poi-list";

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

@@ -61,18 +61,6 @@ private Organization getOrg() {
     return this.org;
   }
 
-  private Device createDevice(Report report) {
-    if (report.getDeviceInfo() == null) {
-      return null;
-    }
-
-    Device device = report.getDeviceInfo().copy();
-    device.setId(UUID.randomUUID().toString());
-    device.getMeta().addProfile(Constants.SubmittingDeviceProfile);
-
-    return device;
-  }
-
   /**
    * Creates a Library resource that contains the query plan used for the report
    *
@@ -102,7 +90,7 @@ private Library createQueryPlanLibrary(Report report) {
   public Bundle generateBundle(Collection<Aggregate> aggregates, Report report) {
     Bundle bundle = this.createBundle();
     bundle.addEntry().setResource(this.getOrg());
-    Device device = this.createDevice(report);
+    Device device = report.getDeviceInfo();
     if (device != null) {
       bundle.addEntry().setResource(device);
     }