Merge pull request #136 from palladiumkenya/dev

NUPI and HTS
palladiumkenya · Aug 18, 2022 · a63dbe9 · a63dbe9
2 parents 71d7e9b + 60583c7
commit a63dbe9
Show file tree

Hide file tree

Showing 141 changed files with 244,032 additions and 235 deletions.
diff --git a/src/Dwapi.Contracts/Ct/IPatient.cs b/src/Dwapi.Contracts/Ct/IPatient.cs
@@ -4,5 +4,6 @@ public interface IPatient
     {
         string Pkv { get; set; }
         string Occupation { get; set; }
+        string NUPI { get; set; }
     }
 }
diff --git a/src/Dwapi.Contracts/Ct/IVisit.cs b/src/Dwapi.Contracts/Ct/IVisit.cs
@@ -1,3 +1,5 @@
+using System;
+
 namespace Dwapi.Contracts.Ct
 {
     public interface IVisit
@@ -31,5 +33,6 @@ public interface IVisit
         string Abdomen {get;set;}
         string CNS {get;set;}
         string Genitourinary {get;set;}
+        DateTime? RefillDate { get; set; }
     }
 }
diff --git a/src/Dwapi.Contracts/Mnch/IPatientMnch.cs b/src/Dwapi.Contracts/Mnch/IPatientMnch.cs
@@ -20,5 +20,6 @@ public interface IPatientMnch
         string InSchool { get; set; }
         DateTime? Date_Created { get; set; }
         DateTime? Date_Last_Modified { get; set; }
+        string NUPI { get; set; }
     }
 }
diff --git a/src/Dwapi.Contracts/Prep/IPatientPrep.cs b/src/Dwapi.Contracts/Prep/IPatientPrep.cs
@@ -33,5 +33,6 @@ public interface IPatientPrep
     DateTime? DateLastUsedPrev { get; set; }
     DateTime? Date_Created { get; set; }
     DateTime? Date_Last_Modified { get; set; }
+    string NUPI { get; set; }
   }
 }
diff --git a/src/Dwapi.ExtractsManagement.Core/Cleaner/Hts/ClearHtsExtracts.cs b/src/Dwapi.ExtractsManagement.Core/Cleaner/Hts/ClearHtsExtracts.cs
@@ -39,6 +39,7 @@ public async Task Clear(List<Guid> extractIds)
             DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsPartnerTracing) + "Extracts", "clearing...")));
             DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsClientLinkage) + "Extracts", "clearing...")));
             DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsClients) + "Extracts", "clearing...")));
+            DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsEligibilityExtract) + "Extracts", "clearing...")));
 
 
             foreach (var extractId in extractIds)

diff --git a/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHTSClientHandler.cs b/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHTSClientHandler.cs
@@ -1,4 +1,5 @@
-using System.Threading;
+using System;
+using System.Threading;
 using System.Threading.Tasks;
 using Dwapi.ExtractsManagement.Core.Commands.Hts;
 using Dwapi.ExtractsManagement.Core.Interfaces.Extratcors.Hts;
@@ -15,6 +16,7 @@
 
 namespace Dwapi.ExtractsManagement.Core.ComandHandlers.Hts
 {
+    [Obsolete("No longer Used")]
     public class ExtractHTSClientHandler :IRequestHandler<ExtractHTSClient,bool>
     {
         private readonly IHTSClientSourceExtractor _patientSourceExtractor;

diff --git a/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHTSClientLinkageHandler.cs b/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHTSClientLinkageHandler.cs
@@ -1,4 +1,5 @@
-using System.Threading;
+using System;
+using System.Threading;
 using System.Threading.Tasks;
 using Dwapi.ExtractsManagement.Core.Commands.Hts;
 using Dwapi.ExtractsManagement.Core.Interfaces.Extratcors.Hts;
@@ -14,6 +15,7 @@
 
 namespace Dwapi.ExtractsManagement.Core.ComandHandlers.Hts
 {
+    [Obsolete("No longer Used")]
     public class ExtractHTSClientLinkageHandler : IRequestHandler<ExtractHTSClientLinkage, bool>
     {
         private readonly IHTSClientLinkageSourceExtractor _patientAdverseEventSourceExtractor;

diff --git a/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHTSClientPartnerHandler.cs b/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHTSClientPartnerHandler.cs
@@ -1,4 +1,5 @@
-using System.Threading;
+using System;
+using System.Threading;
 using System.Threading.Tasks;
 using Dwapi.ExtractsManagement.Core.Commands.Hts;
 using Dwapi.ExtractsManagement.Core.Interfaces.Extratcors.Hts;
@@ -14,6 +15,7 @@
 
 namespace Dwapi.ExtractsManagement.Core.ComandHandlers.Hts
 {
+    [Obsolete("No longer Used")]
     public class ExtractHTSClientPartnerHandler :IRequestHandler<ExtractHTSClientPartner,bool>
     {
         private readonly IHTSClientPartnerSourceExtractor _patientLaboratorySourceExtractor;

diff --git a/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHtsEligibilityHandler.cs b/src/Dwapi.ExtractsManagement.Core/ComandHandlers/Hts/ExtractHtsEligibilityHandler.cs
@@ -0,0 +1,67 @@
+using System.Threading;
+using System.Threading.Tasks;
+using Dwapi.ExtractsManagement.Core.Commands.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Cleaner.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Extratcors.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Loaders.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Repository;
+using Dwapi.ExtractsManagement.Core.Interfaces.Repository.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Validators.Hts;
+using Dwapi.ExtractsManagement.Core.Model.Destination.Hts.NewHts;
+using Dwapi.ExtractsManagement.Core.Notifications;
+using Dwapi.SharedKernel.Enum;
+using Dwapi.SharedKernel.Events;
+using Dwapi.SharedKernel.Model;
+using MediatR;
+
+namespace Dwapi.ExtractsManagement.Core.ComandHandlers.Hts
+{ 
+    public class ExtractHtsEligibilityHandler : IRequestHandler<ExtractHtsEligibilityExtract, bool>
+    {
+        private readonly IHtsEligibilityExtractSourceExtractor _patientSourceExtractor;
+        private readonly IHtsExtractValidator _extractValidator;
+        private readonly IHtsEligibilityExtractLoader _patientLoader;
+        private readonly IClearHtsExtracts _clearDwhExtracts;
+        private readonly ITempHtsEligibilityExtractRepository _tempPatientExtractRepository;
+        private readonly IExtractHistoryRepository _extractHistoryRepository;
+
+        public ExtractHtsEligibilityHandler(IHtsEligibilityExtractSourceExtractor patientSourceExtractor, IHtsExtractValidator extractValidator, IHtsEligibilityExtractLoader patientLoader, IClearHtsExtracts clearDwhExtracts, ITempHtsEligibilityExtractRepository tempPatientExtractRepository, IExtractHistoryRepository extractHistoryRepository)
+        {
+            _patientSourceExtractor = patientSourceExtractor;
+            _extractValidator = extractValidator;
+            _patientLoader = patientLoader;
+            _clearDwhExtracts = clearDwhExtracts;
+            _tempPatientExtractRepository = tempPatientExtractRepository;
+            _extractHistoryRepository = extractHistoryRepository;
+        }
+
+        public async Task<bool> Handle(ExtractHtsEligibilityExtract request, CancellationToken cancellationToken)
+        {
+
+            //Extract
+            int found = await _patientSourceExtractor.Extract(request.Extract, request.DatabaseProtocol);
+
+
+            //Validate
+            await _extractValidator.Validate(request.Extract.Id, found, "HtsEligibilityExtracts", "TempHtsEligibilityExtracts");
+
+            //Load
+            int loaded = await _patientLoader.Load(request.Extract.Id, found, false);
+
+            int rejected =
+                _extractHistoryRepository.ProcessRejected(request.Extract.Id, found - loaded, request.Extract);
+
+
+            _extractHistoryRepository.ProcessExcluded(request.Extract.Id, rejected, request.Extract);
+
+            //notify loaded
+            DomainEvents.Dispatch(
+                new HtsExtractActivityNotification(request.Extract.Id, new ExtractProgress(
+                    nameof(HtsEligibilityExtract),
+                    nameof(ExtractStatus.Loaded),
+                    found, loaded, rejected, loaded, 0)));
+
+            return true;
+        }
+    }
+}
diff --git a/src/Dwapi.ExtractsManagement.Core/ComandHandlers/LoadHtsFromEmrCommandHandler.cs b/src/Dwapi.ExtractsManagement.Core/ComandHandlers/LoadHtsFromEmrCommandHandler.cs
@@ -48,7 +48,8 @@ public async Task<bool> Handle(LoadHtsFromEmrCommand request, CancellationToken
 
         private async Task<bool> ExtractAll(LoadHtsFromEmrCommand request, CancellationToken cancellationToken)
         {
-            Task<bool>  ClientTestTask = null, TestKitTask = null, ClientTracingTask = null, PartnerTracingTask = null, PNSTask = null, ClientLinkageTask = null;
+            Task<bool>  ClientTestTask = null, TestKitTask = null, ClientTracingTask = null, PartnerTracingTask = null, 
+                PNSTask = null, ClientLinkageTask = null, HtsEligibilityExtractTask = null;
 
             // HtsClientTestExtract
             var HtsClientTestExtractProfile = request.Extracts.FirstOrDefault(x => x.Extract.Name == "HtsClientTests");
@@ -121,9 +122,23 @@ private async Task<bool> ExtractAll(LoadHtsFromEmrCommand request, CancellationT
                 };
                 ClientLinkageTask = _mediator.Send(command, cancellationToken);
             }
+
+            // HtsEligibilityExtract
+            var HtsEligibilityExtractProfile = request.Extracts.FirstOrDefault(x => x.Extract.Name == "HtsEligibilityExtract");
+            if (null != HtsEligibilityExtractProfile)
+            {
+                var command = new ExtractHtsEligibilityExtract()
+                {
+                    Extract = HtsEligibilityExtractProfile?.Extract,
+                    DatabaseProtocol = HtsEligibilityExtractProfile?.DatabaseProtocol
+                };
+                HtsEligibilityExtractTask = _mediator.Send(command, cancellationToken);
+            }
 
+
+
             // await all tasks
-            var ts = new List<Task<bool>> { ClientTestTask, TestKitTask, ClientTracingTask, PartnerTracingTask, PNSTask, ClientLinkageTask };
+            var ts = new List<Task<bool>> { ClientTestTask, TestKitTask, ClientTracingTask, PartnerTracingTask, PNSTask, ClientLinkageTask, HtsEligibilityExtractTask };
             var result = await Task.WhenAll(ts);
 
             return result.All(x=>x);

diff --git a/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHTSClient.cs b/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHTSClient.cs
@@ -1,8 +1,10 @@
-using Dwapi.SharedKernel.Model;
+using System;
+using Dwapi.SharedKernel.Model;
 using MediatR;
 
 namespace Dwapi.ExtractsManagement.Core.Commands.Hts
 {
+    [Obsolete("No longer Used")]
     public class ExtractHTSClient : IRequest<bool>
     {
         public DbExtract Extract { get; set; }

diff --git a/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHTSClientLinkage.cs b/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHTSClientLinkage.cs
@@ -1,8 +1,10 @@
+using System;
 using Dwapi.SharedKernel.Model;
 using MediatR;
 
 namespace Dwapi.ExtractsManagement.Core.Commands.Hts
 {
+    [Obsolete("No longer Used")]
     public class ExtractHTSClientLinkage : IRequest<bool>
     {
         public DbExtract Extract { get; set; }

diff --git a/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHTSClientPartner.cs b/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHTSClientPartner.cs
@@ -1,8 +1,10 @@
+using System;
 using Dwapi.SharedKernel.Model;
 using MediatR;
 
 namespace Dwapi.ExtractsManagement.Core.Commands.Hts
 {
+    [Obsolete("No longer Used")]
     public class ExtractHTSClientPartner : IRequest<bool>
     {
         public DbExtract Extract { get; set; }

diff --git a/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHtsEligibilityScreening.cs b/src/Dwapi.ExtractsManagement.Core/Commands/Hts/ExtractHtsEligibilityScreening.cs
@@ -0,0 +1,11 @@
+using Dwapi.SharedKernel.Model;
+using MediatR;
+
+namespace Dwapi.ExtractsManagement.Core.Commands.Hts
+{
+    public class ExtractHtsEligibilityExtract: IRequest<bool>
+    {
+        public DbExtract Extract { get; set; }
+        public DbProtocol DatabaseProtocol { get; set; }
+    }
+}
diff --git a/src/Dwapi.ExtractsManagement.Core/Extractors/Hts/HTSClientSourceExtractor.cs b/src/Dwapi.ExtractsManagement.Core/Extractors/Hts/HTSClientSourceExtractor.cs
@@ -19,7 +19,7 @@
 
 namespace Dwapi.ExtractsManagement.Core.Extractors.Hts
 {
-    [Obsolete]
+    [Obsolete("No longer Used")]
     public class HTSClientSourceExtractor : IHTSClientSourceExtractor
     {
         private readonly IHTSExtractSourceReader _reader;

diff --git a/src/Dwapi.ExtractsManagement.Core/Extractors/Hts/HtsEligibilityExtractSourceExtractor.cs b/src/Dwapi.ExtractsManagement.Core/Extractors/Hts/HtsEligibilityExtractSourceExtractor.cs
@@ -0,0 +1,110 @@
+using System;
+using System.Collections.Generic;
+using System.Data;
+using System.Threading.Tasks;
+using AutoMapper;
+using Dwapi.ExtractsManagement.Core.Interfaces.Extratcors.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Reader.Hts;
+using Dwapi.ExtractsManagement.Core.Interfaces.Repository.Hts;
+using Dwapi.ExtractsManagement.Core.Model.Destination.Hts.NewHts;
+using Dwapi.ExtractsManagement.Core.Model.Source.Hts.NewHts;
+using Dwapi.ExtractsManagement.Core.Notifications;
+using Dwapi.ExtractsManagement.Core.Profiles;
+using Dwapi.SharedKernel.Enum;
+using Dwapi.SharedKernel.Events;
+using Dwapi.SharedKernel.Model;
+using Dwapi.SharedKernel.Utility;
+using MediatR;
+using Serilog;
+
+namespace Dwapi.ExtractsManagement.Core.Extractors.Hts
+{
+    public class HtsEligibilityExtractSourceExtractor : IHtsEligibilityExtractSourceExtractor
+    {
+        private readonly IHTSExtractSourceReader _reader;
+        private readonly IMediator _mediator;
+        private readonly ITempHtsEligibilityExtractRepository _extractRepository;
+
+        public HtsEligibilityExtractSourceExtractor(IHTSExtractSourceReader reader, IMediator mediator, ITempHtsEligibilityExtractRepository extractRepository)
+        {
+            _reader = reader;
+            _mediator = mediator;
+            _extractRepository = extractRepository;
+        }
+
+        public async Task<int> Extract(DbExtract extract, DbProtocol dbProtocol)
+        {
+            var mapper = dbProtocol.SupportsDifferential ? ExtractDiffMapper.Instance : ExtractMapper.Instance;
+            int batch = 500;
+
+            DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsEligibilityExtract), "extracting...")));
+            //DomainEvents.Dispatch(new CbsStatusNotification(extract.Id,ExtractStatus.Loading));
+
+            var list = new List<TempHtsEligibilityExtract>();
+
+            int count = 0;
+            int totalCount = 0;
+
+            using (var rdr = await _reader.ExecuteReader(dbProtocol, extract))
+            {
+                while (rdr.Read())
+                {
+                    totalCount++;
+                    count++;
+                    // AutoMapper profiles
+                    var extractRecord = mapper.Map<IDataRecord, TempHtsEligibilityExtract>(rdr);
+                    extractRecord.Id = LiveGuid.NewGuid();
+                    list.Add(extractRecord);
+
+                    if (count == batch)
+                    {
+                        // TODO: batch and save
+                        _extractRepository.BatchInsert(list);
+
+                        try
+                        {
+                            DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsEligibilityExtract), "extracting...", totalCount, count, 0, 0, 0)));
+                        }
+                        catch (Exception e)
+                        {
+                            Log.Error(e, "Notification error");
+
+                        }
+                        count = 0;
+                        list = new List<TempHtsEligibilityExtract>();
+                    }
+
+                    // TODO: Notify progress...
+
+
+                }
+
+                if (count > 0)
+                {
+                    _extractRepository.BatchInsert(list);
+                }
+                _extractRepository.CloseConnection();
+            }
+
+            try
+            {
+
+                DomainEvents.Dispatch(new HtsNotification(new ExtractProgress(nameof(HtsEligibilityExtract), "extracted", totalCount, 0, 0, 0, 0)));
+                DomainEvents.Dispatch(new HtsStatusNotification(extract.Id, ExtractStatus.Found, totalCount));
+                DomainEvents.Dispatch(new HtsStatusNotification(extract.Id, ExtractStatus.Loaded, totalCount));
+            }
+            catch (Exception e)
+            {
+                Log.Error(e, "Notification error");
+
+            }
+
+            return totalCount;
+        }
+
+        public Task<int> ReadExtract(DbExtract extract, DbProtocol dbProtocol)
+        {
+            throw new NotImplementedException();
+        }
+    }
+}
diff --git a/...xtractsManagement.Core/Interfaces/Extratcors/Hts/IHtsEligibilityExtractSourceExtractor.cs b/...xtractsManagement.Core/Interfaces/Extratcors/Hts/IHtsEligibilityExtractSourceExtractor.cs
@@ -0,0 +1,10 @@
+using Dwapi.ExtractsManagement.Core.Model.Source.Hts.NewHts;
+using Dwapi.SharedKernel.Interfaces;
+
+namespace Dwapi.ExtractsManagement.Core.Interfaces.Extratcors.Hts
+{
+    public interface IHtsEligibilityExtractSourceExtractor: ISourceExtractor<TempHtsEligibilityExtract>
+    {
+
+    }
+}
diff --git a/src/Dwapi.ExtractsManagement.Core/Interfaces/Loaders/Hts/IHtsEligibilityLoader.cs b/src/Dwapi.ExtractsManagement.Core/Interfaces/Loaders/Hts/IHtsEligibilityLoader.cs
@@ -0,0 +1,9 @@
+using Dwapi.ExtractsManagement.Core.Model.Source.Hts.NewHts;
+
+namespace Dwapi.ExtractsManagement.Core.Interfaces.Loaders.Hts
+{
+    public interface IHtsEligibilityExtractLoader: ILoader<TempHtsEligibilityExtract>
+    {
+
+    }
+}
diff --git a/...api.ExtractsManagement.Core/Interfaces/Repository/Hts/IHtsEligibilityExtractRepository.cs b/...api.ExtractsManagement.Core/Interfaces/Repository/Hts/IHtsEligibilityExtractRepository.cs
@@ -0,0 +1,15 @@
+using System;
+using System.Collections.Generic;
+using Dwapi.ExtractsManagement.Core.Model.Destination.Hts.NewHts;
+using Dwapi.SharedKernel.Interfaces;
+using Dwapi.SharedKernel.Model;
+
+namespace Dwapi.ExtractsManagement.Core.Interfaces.Repository.Hts
+{
+    public interface IHtsEligibilityExtractRepository : IRepository<HtsEligibilityExtract, Guid>
+    {
+        bool BatchInsert(IEnumerable<HtsEligibilityExtract> extracts);
+        IEnumerable<HtsEligibilityExtract> GetView();
+        void UpdateSendStatus(List<SentItem> sentItems);
+    }
+}