LNK-4635: Submission bundle getting not reportable patients as submitted with zero count (#1346)

* Skip submission of non-reportable patients

* Deduplicate `OperationOutcome` in submission

Use a single `OperationOutcome` (i.e., one with the same ID) across all
measures of a multi-measure report.  This prevents duplicates in the
submission.

* Prefer `error` severity over `fatal`

Use `error` to indicate invalid content, rather than `fatal`, which
could indicate "hard failure" of the validation process itself.

Author: smailliwcs

DotNet/Report/Domain/Queries/SubmissionEntryQueries.cs

@@ -246,9 +246,11 @@ public async Task<bool> PatientAllReadyForValidation(
         string patientId,
         CancellationToken cancellationToken = default)
     {
-        return await (from entry in _context.PatientSubmissionEntries
-                      where entry.ReportScheduleId == reportScheduleId && entry.FacilityId == facilityId && entry.PatientId == patientId 
-                      select entry.Status).AllAsync(s => s == PatientSubmissionStatus.ReadyForValidation || s == PatientSubmissionStatus.NotReportable);
+        List<PatientSubmissionStatus> statuses = await (from entry in _context.PatientSubmissionEntries
+                                                        where entry.ReportScheduleId == reportScheduleId && entry.FacilityId == facilityId && entry.PatientId == patientId
+                                                        select entry.Status).ToListAsync(cancellationToken);
+        return statuses.All(s => s == PatientSubmissionStatus.ReadyForValidation || s == PatientSubmissionStatus.NotReportable) &&
+            statuses.Any(s => s == PatientSubmissionStatus.ReadyForValidation);
     }
 
     public async Task<PagedConfigModel<ResourceSummary>> GetResourceSummary(string facilityId, string reportScheduleId, ResourceType? resourceType, int pageSize, int pageNumber,

DotNet/Report/KafkaProducers/ReportManifestProducer.cs

@@ -235,7 +235,7 @@ private OperationOutcome CreateOperationOutcome(List<PatientSubmissionEntry> fai
                 // Assuming PatientSubmissionEntry has a ValidationMessage property; adjust as per actual model
                 operationOutcome.Issue.Add(new OperationOutcome.IssueComponent
                 {
-                    Severity = OperationOutcome.IssueSeverity.Fatal,
+                    Severity = OperationOutcome.IssueSeverity.Error,
                     Code = OperationOutcome.IssueType.Invalid,
                     Diagnostics = $"Validation failed for patient {entry.PatientId}"
                 });

DotNet/Report/Listeners/ValidationCompleteListener.cs

@@ -19,6 +19,7 @@
 using System.Text;
 using LantanaGroup.Link.Shared.Application.Services.Security;
 using Task = System.Threading.Tasks.Task;
+using Hl7.Fhir.Support;
 
 namespace LantanaGroup.Link.Report.Listeners
 {
@@ -190,18 +191,12 @@ public async Task ProcessMessageAsync(ConsumeResult<string, ValidationCompleteVa
                 throw new DeadLetterException($"No Patient Submission Entries were found for schedule ID {schedule.Id}, patient ID {value.PatientId}, in status {PatientSubmissionStatus.ValidationRequested}");
             }
 
+            var operationOutcome = GetOperationOutcome();
+
             foreach (var entry in submissionEntries)
             {
                 if (!value.IsValid)
                 {
-                    var operationOutcome = new OperationOutcome();
-                    var issue = new OperationOutcome.IssueComponent
-                    {
-                        Severity = OperationOutcome.IssueSeverity.Fatal,
-                        Code = OperationOutcome.IssueType.Invalid,
-                        Diagnostics = "Patient has failed Validation"
-                    };
-                    operationOutcome.Issue = new List<OperationOutcome.IssueComponent> { issue };
                     await submissionEntryManager.AddResourceAsync(entry, operationOutcome, ResourceCategoryType.Patient, cancellationToken);
                 }
 
@@ -269,6 +264,21 @@ await submissionEntryManager.UpdateAsync(new PatientSubmissionEntryUpdateModel
             await _reportManifestProducer.Produce(schedule, correlationIdStr);
         }
 
+        private static OperationOutcome GetOperationOutcome()
+        {
+            OperationOutcome operationOutcome = new()
+            {
+                Id = Guid.NewGuid().ToString()
+            };
+            operationOutcome.AddIssue(new OperationOutcome.IssueComponent
+            {
+                Severity = OperationOutcome.IssueSeverity.Error,
+                Code = OperationOutcome.IssueType.Invalid,
+                Diagnostics = "Patient has failed Validation"
+            });
+            return operationOutcome;
+        }
+
         private static string GetFacilityIdFromHeader(Headers headers)
         {
             string facilityId = string.Empty;