Updated Contact Network

and deactivated EpiCurve Stored Procedure
highmed · Apr 25, 2023 · 5a42176 · 5a42176
1 parent b644608
commit 5a42176
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Showing 11 changed files with 64 additions and 38 deletions.
diff --git a/SmICSCoreLib/Factories/MiBi/Contact/ContactFactory.cs b/SmICSCoreLib/Factories/MiBi/Contact/ContactFactory.cs
@@ -1,15 +1,19 @@
-using SmICSCoreLib.Factories.General;
+using Microsoft.Extensions.Hosting;
+using SmICSCoreLib.Factories.General;
 using SmICSCoreLib.Factories.PatientMovementNew;
 using SmICSCoreLib.Factories.PatientMovementNew.PatientStays;
 using SmICSCoreLib.REST;
+using System;
 using System.Collections.Generic;
+using System.Drawing;
 using System.Linq;
+using System.Runtime.Intrinsics.Arm;
 using System.Threading.Tasks;
 
 namespace SmICSCoreLib.Factories.MiBi.Contact
 {
     public class ContactFactory : IContactFactory
-    {      
+    {
         public IRestDataAccess RestDataAccess { get; set; }
         private readonly IHospitalizationFactory _hospitalizationFac;
         private readonly IPatientStayFactory _patientStayFac;
@@ -45,7 +49,6 @@ public ContactFactory(IRestDataAccess restDataAccess, IHospitalizationFactory ho
             {
                 throw;
             }
-
         }
 
         public async Task<List<PatientMovementNew.PatientStays.PatientStay>> ProcessAsync(Hospitalization hospitalization)
@@ -124,7 +127,7 @@ private void RemoveDoubleStays(List<PatientMovementNew.PatientStays.PatientStay>
         {
 
             List<int> indices = new List<int>();
-            for(int i = 0; i < (patientStays.Count-2) ; i++)
+            for (int i = 0; i < (patientStays.Count - 2); i++)
             {
                 for (int j = (i + 1); j < (patientStays.Count - 1); j++)
                 {
@@ -142,7 +145,7 @@ private void RemoveDoubleStays(List<PatientMovementNew.PatientStays.PatientStay>
                 }
             }
             indices = indices.OrderBy(i => i).ToList();
-            for(int i = (indices.Count - 1); i >= 0; i--)
+            for (int i = (indices.Count - 1); i >= 0; i--)
             {
                 patientStays.RemoveAt(indices[i]);
             }
@@ -165,5 +168,6 @@ AND ADMIN_ENTRY u[openEHR-EHR-ADMIN_ENTRY.hospitalization.v0]
                         AND i/items[at0001]/value/value='{hospStay.CaseID}'"
             };
         }
+
     }
 }
diff --git a/SmICSCoreLib/Factories/MiBi/Contact/IContactFactory.cs b/SmICSCoreLib/Factories/MiBi/Contact/IContactFactory.cs
@@ -13,6 +13,5 @@ public interface IContactFactory
         Task<List<PatientMovementNew.PatientStays.PatientStay>> ProcessAsync(Hospitalization hospitalization);
         Task<Dictionary<Hospitalization, List<PatientMovementNew.PatientStays.PatientStay>>> ProcessAsync(Patient parameter);
 
-
     }
 }
diff --git a/SmICSCoreLib/Factories/MiBi/Nosocomial/Rules.cs b/SmICSCoreLib/Factories/MiBi/Nosocomial/Rules.cs
@@ -26,9 +26,13 @@ public static List<string> GetResistances(Pathogen pathogen)
                     {
                         resistances.Add(result.Rule.SuccessEvent);
                     }
-                    else if (result.IsSuccess && string.IsNullOrEmpty(result.Rule.SuccessEvent))
+                    else if (result.IsSuccess && string.IsNullOrEmpty(result.Rule.SuccessEvent) && result.ChildResults is not null)
                     {
-                        resistances.Add(GetSuccessEvent(result));
+                        string successEvent = GetSuccessEvent(result);
+                        if (!string.IsNullOrEmpty(successEvent))
+                        {
+                            resistances.Add(successEvent);
+                        }
                     }
                 }
             }
@@ -43,12 +47,16 @@ private static string GetSuccessEvent(RuleResultTree ruleResult)
                 {
                     return child.Rule.SuccessEvent;
                 }
-                else if(child.IsSuccess && string.IsNullOrEmpty(child.Rule.SuccessEvent))
+                else if(child.IsSuccess && string.IsNullOrEmpty(child.Rule.SuccessEvent) && child.ChildResults is not null)
                 {
-                    return GetSuccessEvent(child);
+                    string successEvent = GetSuccessEvent(child);
+                    if (!string.IsNullOrEmpty(successEvent))
+                    {
+                       return successEvent;
+                    }
                 }
             }
-            throw new NotImplementedException("Missed Case");
+            return null;
         }
 
         public static List<string> GetPossibleMREClasses(List<string> pathogenCodes)

diff --git a/SmICSCoreLib/Factories/PatientMovementNew/Hospitalizations/HospitalizationFactory.cs b/SmICSCoreLib/Factories/PatientMovementNew/Hospitalizations/HospitalizationFactory.cs
@@ -22,10 +22,10 @@ public async Task<List<Hospitalization>> ProcessAsync(Patient patient)
                 List<Hospitalization> hospitalizations = new List<Hospitalization>();
                 List<Case> cases = await RestDataAccess.AQLQueryAsync<Case>(HospitalizationCasesQuery(patient));
                 foreach (Case Case in cases)
-                    {
-                        Hospitalization hospitalization = await ProcessAsync(Case);
-                        hospitalizations.Add(hospitalization);
-                    }
+                {
+                    Hospitalization hospitalization = await ProcessAsync(Case);
+                    hospitalizations.Add(hospitalization);
+                }
                 return hospitalizations;
             }
             catch

diff --git a/SmICSCoreLib/REST/RestDataAccess.cs b/SmICSCoreLib/REST/RestDataAccess.cs
@@ -29,6 +29,7 @@ public RestDataAccess(ILogger<RestDataAccess> logger, RestClientConnector client
         {
             try{
                 _logger.LogInformation("Posted Query: {Query}", query.Name);
+                _logger.LogDebug("QueryDetails: {Query}", query.Query);
                 string restPath = "rest/openehr/v1/query/aql";
                 Uri RestPath = GetRequestUri(restPath);
                 HttpResponseMessage response = await _client.Client.PostAsync(RestPath, GetHttpContentQuery(query.ToString()));

diff --git a/SmICSWebApp/Controllers/StoredProceduresController.cs b/SmICSWebApp/Controllers/StoredProceduresController.cs
@@ -82,6 +82,8 @@ public ActionResult<List<VisuLabResult>> PatientLabData([FromBody] PatientLabDat
                 PathogenParameter pathogen = new PathogenParameter() { PathogenCodes = codes };
                 foreach (string pat in parameter.patientList)
                 {
+                    if (pat == "undefined")
+                    { continue; }
                     Patient patient = new Patient() { PatientID = pat };
                     List<VisuLabResult> labs = _medicalFindingService.GetMedicalFinding(patient, pathogen).GetAwaiter().GetResult();
                     visuLabResults.AddRange(labs);
@@ -106,6 +108,8 @@ public ActionResult<List<VisuPatientMovement>> PatientMovements([FromBody] Patie
                 List<VisuPatientMovement> visuMovements = new List<VisuPatientMovement>();
                 foreach (string pat in parameter.patientList)
                 {
+                    if (pat == "undefined")
+                    { continue; }
                     Patient patient = new Patient() { PatientID = pat };
                     List<VisuPatientMovement> movements = _movementService.GetPatientMovements(patient).GetAwaiter().GetResult();
                     visuMovements.AddRange(movements);
@@ -117,6 +121,7 @@ public ActionResult<List<VisuPatientMovement>> PatientMovements([FromBody] Patie
                 _logger.LogWarning("CALLED Patient_Bewegung_Ps:" + e.StackTrace);
                 return ErrorHandling(e);
             }
+
         }
 
         /// <summary></summary>
@@ -135,7 +140,8 @@ public async Task<ActionResult<List<EpiCurveModel>>> Labor_ErregerProTag_TTEsKSs
             try
             {
                 //_epiCurveFac.RestDataAccess.SetAuthenticationHeader(token);
-                return await _epiCurveService.GetData(parameter.Starttime, parameter.Endtime, new PathogenParameter { PathogenCodes = new List<string> { parameter.Pathogen } } );
+                //return await _epiCurveService.GetData(parameter.Starttime, parameter.Endtime, new PathogenParameter { PathogenCodes = new List<string> { parameter.Pathogen } } );
+                return new List<EpiCurveModel>();
             }
             catch (Exception e)
             {
@@ -186,7 +192,7 @@ public ActionResult<List<OutbreakDetectionStoringModel>> OutbreakDetectionResult
             }
             catch (Exception e)
             {
-                return ErrorHandling(e);
+                return ErrorHandling(e); 
             }
         }
 

diff --git a/SmICSWebApp/Data/Contact/ContactRoot.cs b/SmICSWebApp/Data/Contact/ContactRoot.cs
@@ -19,7 +19,10 @@ public ContactRoot()
         public void AddHospitalization(Hospitalization hospitalization, InfectionStatus infectionStatus, List<PatientStay> patientStays, List<Contact> contacts)
         {
             //If contains clauses
-            InfectionStatus.Add(hospitalization, infectionStatus);
+            if(!InfectionStatus.ContainsKey(hospitalization))
+            {
+                InfectionStatus.Add(hospitalization, infectionStatus);
+            }
             PatientStays.Add(hospitalization, patientStays);
             Contacts.Add(hospitalization, contacts);
         }

diff --git a/SmICSWebApp/Data/Contact/ContactService.cs b/SmICSWebApp/Data/Contact/ContactService.cs
@@ -87,7 +87,7 @@ public async Task GetPreviousHospitalizationContacts(ContactRoot rootContact, Co
                     PathogenParameter pathogenParameter = new PathogenParameter() { PathogenCodes = parameter.PathogenCodes };
                     SortedList<Hospitalization, InfectionStatus> infectionStatus = await _infectionStatusFac.ProcessAsync(prevHospitalization, pathogenParameter, parameter.Resistence);
                     List<SmICSCoreLib.Factories.PatientMovementNew.PatientStays.PatientStay> contactLocations = await _patientStayFac.ProcessAsync(prevHospitalization);
-                    rootContact.AddHospitalization(prevHospitalization, infectionStatus[prevHospitalization], null, null);
+                    rootContact.AddHospitalization(prevHospitalization, infectionStatus[prevHospitalization], contactLocations, null);
                     await MergeInfectionStatusAndContactCases(rootContact, prevHospitalization, pathogenParameter, parameter.Resistence);
                 }
                 rootContact.CurrentHospitalization = prevHospitalization;

diff --git a/SmICSWebApp/Data/EpiCurve/EpiCurveService.cs b/SmICSWebApp/Data/EpiCurve/EpiCurveService.cs
@@ -238,32 +238,35 @@ private void NosocomialHospitalization(List<PatientStay> stays, List<EpiCurveMod
                 FirstOrDefault();
 
             EpiCurveModel nosocomialDay = epiCurve.Where(e => e.Datum == nosocomialStay.Admission).FirstOrDefault();
-            if (!dates.Keys.Contains(nosocomialStay.Admission.Date))
+            if (nosocomialStay is not null)
             {
-                if (nosocomialDay is null)
+                if (dates is not null || dates.Keys.Contains(nosocomialStay.Admission.Date))
                 {
-                    EpiCurveModel e = new EpiCurveModel()
+                    if (nosocomialDay is null)
                     {
-                        Datum = nosocomialStay.Admission,
-                        StationID = nosocomialStay.Ward,
-                        anzahl_gesamt = 1,
-                        Anzahl = 1,
-                        ErregerID = this.ErregerID
-                    };
-                    epiCurve.Add(e);
+                        EpiCurveModel e = new EpiCurveModel()
+                        {
+                            Datum = nosocomialStay.Admission,
+                            StationID = nosocomialStay.Ward,
+                            anzahl_gesamt = 1,
+                            Anzahl = 1,
+                            ErregerID = this.ErregerID
+                        };
+                        epiCurve.Add(e);
+                    }
+                    else
+                    {
+                        nosocomialDay.anzahl_gesamt++;
+                        nosocomialDay.Anzahl++;
+                    }
+                    dates.Add(nosocomialStay.Admission.Date, "Increment");
                 }
-                else
+                else if (dates.Keys.Contains(nosocomialStay.Admission.Date) && dates[nosocomialStay.Admission.Date] == "DECREMENT")
                 {
                     nosocomialDay.anzahl_gesamt++;
                     nosocomialDay.Anzahl++;
+                    dates[nosocomialStay.Admission.Date] = "INCREMENT";
                 }
-                dates.Add(nosocomialStay.Admission.Date, "Increment");
-            }
-            else if (dates.Keys.Contains(nosocomialStay.Admission.Date) && dates[nosocomialStay.Admission.Date] == "DECREMENT")
-            {
-                nosocomialDay.anzahl_gesamt++;
-                nosocomialDay.Anzahl++;
-                dates[nosocomialStay.Admission.Date] = "INCREMENT";
             }
 
             List<PatientStay> KnownStays = stays.Where(s => s.Admission >= NosocomialDate && s != nosocomialStay).ToList();

diff --git a/SmICSWebApp/Program.cs b/SmICSWebApp/Program.cs
@@ -96,6 +96,8 @@ private static void GetEnvironmentVariables()
             OpenehrConfig.openehrEndpoint = Environment.GetEnvironmentVariable("OPENEHR_DB");
             OpenehrConfig.openehrUser = Environment.GetEnvironmentVariable("OPENEHR_USER");
             OpenehrConfig.openehrPassword = Environment.GetEnvironmentVariable("OPENEHR_PASSWD");
+            OpenehrConfig.queryLimit = Environment.GetEnvironmentVariable("QUERY_LIMIT");
+            OpenehrConfig.queryTimeout = Convert.ToDouble(Environment.GetEnvironmentVariable("QUERY_TIMEOUT")); 
             OpenehrConfig.smicsVisuPort = Environment.GetEnvironmentVariable("SMICS_VISU_PORT");
 
         }

diff --git a/SmICSWebApp/Shared/NavMenu.razor b/SmICSWebApp/Shared/NavMenu.razor
@@ -72,7 +72,7 @@
         string url = splitted[1];
         string port = ":" + OpenehrConfig.smicsVisuPort;
 
-        visuLink = http + url.Substring(0, url.LastIndexOf('/')) + port;
+        visuLink = http + url + port;
 
     }
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,6 +13,5 @@ public interface IContactFactory @@
             Task<List<PatientMovementNew.PatientStays.PatientStay>> ProcessAsync(Hospitalization hospitalization);
             Task<Dictionary<Hospitalization, List<PatientMovementNew.PatientStays.PatientStay>>> ProcessAsync(Patient parameter);
         }
     }