Release v1.10.0 - See CHANGELOG.md

CHANGELOG.md

@@ -1,5 +1,14 @@
 ### Change Log/Revision History
 
+NOTE:  WHEN UPDATING THIS LIBRARY
+If you update the config.xml file, this file needs to be copied to the MedsView mapper project
+AND the mhrSimulator (cdaExtractorConfig.xml)
+
+1.10.0
+-------------
+Added "Australian Immunisation Register" Data
+Added "Pharmacist Shared Medicines List" Data
+
 1.9.0
 -------------
 Added "Pathology Report" Data

src/CdaExtractor.Sample/Properties/AssemblyInfo.cs

@@ -31,5 +31,5 @@
 // You can specify all the values or you can default the Build and Revision Numbers 
 // by using the '*' as shown below:
 // [assembly: AssemblyVersion("1.0.*")]
-[assembly: AssemblyVersion("1.9.0.0")]
-[assembly: AssemblyFileVersion("1.9.0.0")]
+[assembly: AssemblyVersion("1.0.0.0")]
+[assembly: AssemblyFileVersion("1.0.0.0")]

src/CdaExtractor/CdaDataExtractor.cs

@@ -61,6 +61,10 @@ public CdaDocument Extract(XmlDocument cdaDocument)
             var immunisationsEx = new ImmunisationsExtractor(documentXPaths);
             var immunisations = immunisationsEx.Extract(cdaXmlDocument);
 
+            var immunisationRegisterEx = new ImmunisationRegisterExtractor(documentXPaths);
+            var immunisationRegister = immunisationRegisterEx.Extract(cdaXmlDocument);
+
+
             var consumerNoteEx = new ConsumerNoteExtractor(documentXPaths);
             var consumerNote = consumerNoteEx.Extract(cdaXmlDocument);
 
@@ -76,6 +80,9 @@ public CdaDocument Extract(XmlDocument cdaDocument)
             var pathologyExtractor = new PathologyExtractor(documentXPaths);
             var pathology = pathologyExtractor.Extract(cdaXmlDocument);
 
+            var psmlExtractor = new PsmlExtractor(documentXPaths);
+            var psml = psmlExtractor.Extract(cdaXmlDocument);
+
             var document = new CdaDocument
             {
                 Author = author,
@@ -85,11 +92,13 @@ public CdaDocument Extract(XmlDocument cdaDocument)
                 DocumentMetadata = documentMetadata,
                 SubjectOfCare = subjectOfCare,
                 ImmunisationItems = immunisations,
+                ImmunisationRegisterItems = immunisationRegister,
                 ConsumerNote = consumerNote,
                 AdvanceCareInformation = advanceCareInformation,
                 PharmaceuticalBenefitItems = pbs,
                 Pathology = pathology,
-                DiagnosticImaging = diagnosticImaging
+                DiagnosticImaging = diagnosticImaging,
+                Psml = psml
             };
 
             return document;

src/CdaExtractor/CdaExtractor.csproj

@@ -50,11 +50,13 @@
     <Compile Include="Extractor\AdvanceCareInformationExtractor.cs" />
     <Compile Include="Extractor\AuthorExtractor.cs" />
     <Compile Include="Extractor\ConsumerNoteExtractor.cs" />
+    <Compile Include="Extractor\ImmunisationRegisterExtractor.cs" />
     <Compile Include="Extractor\ImmunisationsExtractor.cs" />
     <Compile Include="Extractor\DocumentMetadataExtractor.cs" />
     <Compile Include="Extractor\ICdaExtractor.cs" />
     <Compile Include="Extractor\MedicalHistoryExtractor.cs" />
     <Compile Include="Extractor\DiagnosticImagingExtractor.cs" />
+    <Compile Include="Extractor\PsmlExtractor.cs" />
     <Compile Include="Extractor\PharmaceuticalBenefitItemExtractor.cs" />
     <Compile Include="Extractor\PathologyExtractor.cs" />
     <Compile Include="Extractor\SubjectOfCareExtractor.cs" />
@@ -64,6 +66,8 @@
     <Compile Include="IDocumentXPathProvider.cs" />
     <Compile Include="Model\DiagnosticImaging.cs" />
     <Compile Include="Model\ImagingExaminationResult.cs" />
+    <Compile Include="Model\ImmunisationRegister.cs" />
+    <Compile Include="Model\Psml.cs" />
     <Compile Include="Model\PathologyTestResult.cs" />
     <Compile Include="Model\Pathology.cs" />
     <Compile Include="Model\AdverseReaction.cs" />

src/CdaExtractor/CdaXmlDocument.cs

@@ -224,6 +224,11 @@ public Id GetId(XmlNode node, string xpath)
 
         #region DateTime / Interval Functions
 
+        public DateTime? GetDateTime(string value)
+        {
+            return string.IsNullOrWhiteSpace(value) ? null : DateTimeHelper.ConvertISO8601DateTimeStringToDateTime(value);
+        }
+
         public DateTime? GetDateTimeValue(string xpath)
         {
             return string.IsNullOrWhiteSpace(xpath) ? null : DateTimeHelper.ConvertISO8601DateTimeStringToDateTime(GetString(xpath));
@@ -377,6 +382,10 @@ private static XmlNode GetPreferredName(XmlNodeList nameNodes)
         }
 
         #endregion
+
+
+
+
     }
 
     public static class Extensions

src/CdaExtractor/Extractor/DocumentMetadataExtractor.cs

@@ -1,4 +1,7 @@
-using System.Collections.Generic;
+using System;
+using System.Collections.Generic;
+using System.Runtime.InteropServices;
+using System.Xml;
 using Nehta.VendorLibrary.CdaExtractor.Model;
 
 namespace Nehta.VendorLibrary.CdaExtractor.Extractor
@@ -7,6 +10,10 @@ public class DocumentMetadataExtractor : ICdaExtractor<DocumentMetadata>
     {
         private readonly IDictionary<string, string> _documentXPaths;
 
+        private DateTime _effectiveDateTime;
+        private DateTime _eventStartDateTime;
+        private DateTime _eventEndDateTime;
+
         public DocumentMetadataExtractor(IDictionary<string, string>  documentXPaths)
         {
             _documentXPaths = documentXPaths;
@@ -17,8 +24,12 @@ public DocumentMetadata Extract(CdaXmlDocument cdaDocument)
             // Document code
             var documentCode = cdaDocument.GetCodableText(_documentXPaths.Get("DocumentCode"));
 
-            // Effective time
-            var effectiveDateTime = cdaDocument.GetDateTimeValue(_documentXPaths.Get("EffectiveTime"));
+            // Effective time - if this fails, there is a problem!
+            var effectiveTime = cdaDocument.GetDateTimeValue(_documentXPaths.Get("EffectiveTime"));
+            _effectiveDateTime = effectiveTime.HasValue ? effectiveTime.Value : DateTime.Now;
+
+            // For Certain Documents get a different DateTime
+            SetDateTimes(cdaDocument, documentCode.Code);
 
             // Document ID
             var documentId = cdaDocument.GetId(_documentXPaths.Get("DocumentId"));
@@ -37,13 +48,146 @@ public DocumentMetadata Extract(CdaXmlDocument cdaDocument)
             {
                 TemplateId = cdaDocument.TemplateId,
                 DocumentCode = documentCode,
-                EffectiveTime = effectiveDateTime,
+                EffectiveTime = _effectiveDateTime,
+                EventStartDateTime = _eventStartDateTime,
+                EventEndDateTime = _eventEndDateTime,
                 DocumentId = documentId,
                 Title = title,
                 LinkId = linkId
             };
 
             return documentMetadata;
         }
+
+        void SetDateTimes(CdaXmlDocument cdaDocument, string documentTypeCode)
+        {
+            // Set service start and stop time
+            if (documentTypeCode == "51852-2")
+            {
+                // If document is Specialist Letter
+                _eventStartDateTime = _effectiveDateTime;
+                _eventEndDateTime = _effectiveDateTime;
+            }
+            else if (documentTypeCode == "100.16764")
+            {
+                // If document is Prescription Record
+                var authorTime = cdaDocument.GetDateTimeValue("/cda:ClinicalDocument/cda:author/cda:time/@value");
+
+                _eventStartDateTime = authorTime.HasValue?  authorTime.Value : _effectiveDateTime;
+                _eventEndDateTime = _eventStartDateTime;
+            }
+            else if (documentTypeCode == "100.16765")
+            {
+                // If document is PCEHR Dispense Record
+                var supplyTime = cdaDocument.GetDateTimeValue("/cda:ClinicalDocument/cda:component/cda:structuredBody/" +
+                    "cda:component/cda:section[cda:code/@code='102.16210' and cda:code/@codeSystem='1.2.36.1.2001.1001.101']/cda:entry/" +
+                    "cda:substanceAdministration/cda:entryRelationship/cda:supply/cda:_effectiveDateTime/@value");
+
+                _eventStartDateTime = supplyTime.HasValue ? supplyTime.Value : _effectiveDateTime;
+                _eventEndDateTime = _eventStartDateTime;
+            }
+            else if (documentTypeCode == "100.32001")
+            {
+                // R5: If document is Pathology Report - Could contain multiple records
+                // Need to get LATEST Date - if multiple returned
+
+                XmlNodeList nList = cdaDocument.SelectNodes("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component" +
+                                                                                     "/cda:section[cda:code/@code='101.20018']/cda:component" +
+                                                                                     "/cda:section[cda:code/@code='102.16144']/cda:entry/cda:observation" +
+                                                                                     "/cda:entryRelationship/cda:observation[cda:code/@code='102.16156']" +
+                                                                                     "/cda:effectiveTime/@value");
+
+                var firstCollectionDateTime = "";
+                var lastCollectionDateTime = "";
+                if (nList.Count == 1)
+                {
+                    firstCollectionDateTime = nList[0].Value;
+                    lastCollectionDateTime = nList[0].Value;
+                }
+                else if (nList.Count > 1)
+                {
+                    string[] sDates = new string[nList.Count];
+                    for (int i = 0; i < nList.Count; i++)
+                    {
+                        sDates[i] = nList[i].Value;
+                    }
+                    Array.Sort(sDates);
+                    //Get last entry
+                    firstCollectionDateTime = sDates[0];
+                    lastCollectionDateTime = sDates[nList.Count - 1];
+                }
+
+                _eventStartDateTime = !string.IsNullOrWhiteSpace(firstCollectionDateTime)
+                    ? cdaDocument.GetDateTime(firstCollectionDateTime).Value
+                    : _effectiveDateTime;
+                _eventEndDateTime = !string.IsNullOrWhiteSpace(lastCollectionDateTime)
+                    ? cdaDocument.GetDateTime(lastCollectionDateTime).Value
+                    : _effectiveDateTime;
+            }
+            else if (documentTypeCode == "100.16957")
+            {
+                // R5: If document is Diagnostic Imaging - Could contain multiple records
+                // Need to get LATEST Date - if multiple returned
+
+                XmlNodeList nList = cdaDocument.SelectNodes("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component" +
+                                                                                  "/cda:section/cda:component/cda:section/cda:entry/cda:observation" +
+                                                                                  "/cda:entryRelationship/cda:act[cda:code/@code='102.16511']/cda:entryRelationship" +
+                                                                                  "/cda:observation/cda:effectiveTime/@value");
+                var firstImagingDateTime = "";
+                var lastImagingDateTime = "";
+                if (nList.Count == 1)
+                {
+                    firstImagingDateTime = nList[0].Value;
+                    lastImagingDateTime = nList[0].Value;
+                }
+                else if (nList.Count > 1)
+                {
+                    string[] sDates = new string[nList.Count];
+                    for (int i = 0; i < nList.Count; i++)
+                    {
+                        sDates[i] = nList[i].Value;
+                    }
+                    Array.Sort(sDates);
+                    //Get last entry
+                    firstImagingDateTime = sDates[0];
+                    lastImagingDateTime = sDates[nList.Count - 1];
+                }
+
+                _eventStartDateTime = !string.IsNullOrWhiteSpace(firstImagingDateTime)
+                    ? cdaDocument.GetDateTime(firstImagingDateTime).Value
+                    : _effectiveDateTime;
+                _eventEndDateTime = !string.IsNullOrWhiteSpace(lastImagingDateTime)
+                    ? cdaDocument.GetDateTime(lastImagingDateTime).Value
+                    : _effectiveDateTime;
+            }
+            else if (documentTypeCode == "100.16975")
+            {
+                // Advance Care Planning Document
+                var authorTime = cdaDocument.GetDateTimeValue("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:code/@code='101.16973']/cda:entry/cda:act/cda:author/cda:time/@value");
+                _eventStartDateTime = authorTime.Value;
+                _eventEndDateTime = _eventStartDateTime;
+            }
+            else
+            {
+                // For other document types set service start and stop time to encompassingEncounter/_effectiveDateTime if available
+                var startTime1 = cdaDocument.GetDateTimeValue("/cda:ClinicalDocument/cda:componentOf/cda:encompassingEncounter/cda:_effectiveDateTime/@value");
+                var startTime2 = cdaDocument.GetDateTimeValue("/cda:ClinicalDocument/cda:componentOf/cda:encompassingEncounter/cda:_effectiveDateTime/cda:low/@value");
+                var stopTime = cdaDocument.GetDateTimeValue("/cda:ClinicalDocument/cda:componentOf/cda:encompassingEncounter/cda:_effectiveDateTime/cda:high/@value");
+
+                _eventStartDateTime = startTime1.HasValue
+                                       ? startTime1.Value
+                                       : startTime2.HasValue
+                                             ? startTime2.Value
+                                             : _effectiveDateTime;
+
+                _eventEndDateTime = stopTime.HasValue
+                                      ? stopTime.Value
+                                      : startTime1.HasValue
+                                            ? startTime1.Value
+                                            : _effectiveDateTime;
+
+            }
+        }
+
     }
 }

src/CdaExtractor/Extractor/ImmunisationRegisterExtractor.cs

@@ -0,0 +1,33 @@
+using System.Collections.Generic;
+using System.Linq;
+using System.Xml;
+using Nehta.VendorLibrary.CdaExtractor.Model;
+
+namespace Nehta.VendorLibrary.CdaExtractor.Extractor
+{
+    public class ImmunisationRegisterExtractor : ICdaExtractor<List<ImmunisationRegister>>
+    {
+        private readonly IDictionary<string, string> _documentXPaths;
+
+        public ImmunisationRegisterExtractor(IDictionary<string, string> documentXPaths)
+        {
+            _documentXPaths = documentXPaths;
+        }
+
+        public List<ImmunisationRegister> Extract(CdaXmlDocument document)
+        {
+            var nodes = document.SelectNodes(_documentXPaths.Get("ImmunisationRegister"));
+            if(nodes == null || nodes.Count == 0) return null;
+
+            return
+                (from XmlNode node in nodes
+                 select new ImmunisationRegister
+                 {
+                        DateTime = document.GetDateTimeValue(node, _documentXPaths.Get("ImmunisationDateTime")),
+                        Immunisation = document.GetRelativeCode(node, _documentXPaths.Get("Immunisation")),
+                        BrandName = document.GetRelativeCode(node, _documentXPaths.Get("BrandName"))
+                    }
+                ).ToList();
+        }
+    }
+}

src/CdaExtractor/Extractor/PsmlExtractor.cs

@@ -0,0 +1,38 @@
+using System.Collections.Generic;
+using System.Linq;
+using System.Xml;
+using Nehta.VendorLibrary.CdaExtractor.Model;
+
+namespace Nehta.VendorLibrary.CdaExtractor.Extractor
+{
+    public class PsmlExtractor : ICdaExtractor<Psml>
+    {
+        private readonly IDictionary<string, string> _documentXPaths;
+
+        public PsmlExtractor(IDictionary<string, string> documentXPaths)
+        {
+            _documentXPaths = documentXPaths;
+        }
+
+        public Psml Extract(CdaXmlDocument cdaDocument)
+        {
+            var psml = new Psml();
+
+            var attachmentNode = cdaDocument.SelectSingleNode(_documentXPaths.Get("Attachment"));
+
+            if (attachmentNode != null)
+            {
+                var attachmentIntegrityCheck = cdaDocument.SelectSingleNode(attachmentNode, _documentXPaths.Get("AttachmentIntegrityCheck"));
+                if (attachmentIntegrityCheck != null) psml.ReportIntegrityCheck = attachmentIntegrityCheck.Value;
+
+                var attachmentMediaType = cdaDocument.SelectSingleNode(attachmentNode, _documentXPaths.Get("AttachmentMediaType"));
+                if (attachmentMediaType != null) psml.ReportMediaType = attachmentMediaType.Value;
+
+                var attachmentName = cdaDocument.SelectSingleNode(attachmentNode, _documentXPaths.Get("AttachmentName"));
+                if (attachmentName != null) psml.ReportDocName = attachmentName.Value;
+            }
+
+            return psml;
+        }
+    }
+}

src/CdaExtractor/Model/CdaDocument.cs

@@ -12,9 +12,13 @@ public class CdaDocument
         public List<PharmaceuticalBenefitItem> PharmaceuticalBenefitItems { get; set; }
         public List<MedicalHistory> MedicalHistoryItems { get; set; }
         public List<Immunisation> ImmunisationItems { get; set; }
+        public List<ImmunisationRegister> ImmunisationRegisterItems { get; set; }
         public ConsumerNote ConsumerNote { get; set; }
         public AdvanceCareInformation AdvanceCareInformation { get; set; }
         public Pathology Pathology { get; set; }
         public DiagnosticImaging DiagnosticImaging { get; set; }
+        public Psml Psml { get; set; }
+
+
     }
 }

src/CdaExtractor/Model/DocumentMetadata.cs

@@ -10,5 +10,7 @@ public class DocumentMetadata
         public string Title { get; set; }
         public DateTime? EffectiveTime { get; set; }
         public Id LinkId { get; set; }
+        public DateTime? EventStartDateTime { get; set; }
+        public DateTime? EventEndDateTime { get; set; }
     }
 }

src/CdaExtractor/Model/ImmunisationRegister.cs

@@ -0,0 +1,11 @@
+using System;
+
+namespace Nehta.VendorLibrary.CdaExtractor.Model
+{
+    public class ImmunisationRegister
+    {
+        public DateTime? DateTime { get; set; }
+        public CodableText Immunisation { get; set; }
+        public CodableText BrandName { get; set; }
+    }
+}