Added notion of table level documentation. Added support for callouts…

… in documentation for VisitDetail and VisitOccurrence

OmopTransformer/Annotations/CalloutType.cs

@@ -0,0 +1,10 @@
+namespace OmopTransformer.Annotations;
+
+internal enum CalloutType
+{
+    none = 0,
+    highlight, 
+    important, 
+    note,
+    warning
+}

OmopTransformer/Annotations/NotesAttribute.cs

@@ -0,0 +1,13 @@
+namespace OmopTransformer.Annotations;
+
+internal class NotesAttribute : Attribute
+{
+    public NotesAttribute(string value, CalloutType calloutType = CalloutType.none)
+    {
+        Value = value;
+        CalloutType = calloutType;
+    }
+
+    public string Value { get; }
+    public CalloutType CalloutType { get; }
+}

OmopTransformer/CDS/CdsMappingNotes.cs

@@ -0,0 +1,11 @@
+namespace OmopTransformer.CDS;
+
+internal class CdsMappingNotes
+{
+    public const string VisitOccurrenceVisitDetailsNotes = 
+           "### Assumptions\r\n" +
+           "* `Emergency` covers a visit to A&E within the given Hospital Provider, and hence covers Admission Code 21 and 24 only\r\n" +
+           "* `Location Class` ID 24 is a Consultant Clinic within the Health Care Provider.\r\n" +
+           "* `Patient Classification` ID 1 is the only entry that covers 24 hours or more with the use of a bed, and whilst others may be a day/night only, they will be discounted because they are less than 24 hours. Also, maternity is also not taken as an \"\"Inpatient\"\" visit.\r\n" +
+           "* No calculations to be made between Start and end visit date to try to calculate 24 hours, but instead the \"Patient Classification\" will be sufficient\r\n";
+}

OmopTransformer/CDS/VisitDetails/CdsVisitDetail.cs

@@ -4,6 +4,7 @@
 
 namespace OmopTransformer.CDS.VisitDetails;
 
+[Notes(CdsMappingNotes.VisitOccurrenceVisitDetailsNotes, CalloutType.note)]
 internal class CdsVisitDetail : OmopVisitDetail<CdsVisitDetailsRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

OmopTransformer/CDS/VisitOccurrenceWithSpell/CdsVisitOccurrenceWithSpell.cs

@@ -4,6 +4,7 @@
 
 namespace OmopTransformer.CDS.VisitOccurrenceWithSpell;
 
+[Notes(CdsMappingNotes.VisitOccurrenceVisitDetailsNotes, CalloutType.note)]
 internal class CdsVisitOccurrenceWithSpell : OmopVisitOccurrence<CdsVisitOccurrenceWithSpellRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

OmopTransformer/CDS/VisitOccurrenceWithoutSpell/CdsVisitOccurrenceWithoutSpell.cs

@@ -4,6 +4,7 @@
 
 namespace OmopTransformer.CDS.VisitOccurrenceWithoutSpell;
 
+[Notes(CdsMappingNotes.VisitOccurrenceVisitDetailsNotes, CalloutType.note)]
 internal class CdsVisitOccurrenceWithoutSpell : OmopVisitOccurrence<CdsVisitOccurrenceWithoutSpellRecord>
 {
     [CopyValue(nameof(Source.NHSNumber))]

OmopTransformer/Documentation/DocumentationRenderer.cs

@@ -150,6 +150,15 @@ public IEnumerable<Document> Render()
                 omopTable.AppendLine($"## {target.MapperType.Name}");
                 omopTable.AppendLine($"<a href=\"{target.MapperType.Name}.svg\" target=\"_blank\"><img src=\"{target.MapperType.Name}.svg\" /></a>");
                 omopTable.AppendLine();
+
+                var notes = target.MapperType.GetCustomAttributes(typeof(NotesAttribute)).Cast<NotesAttribute>();
+
+                foreach (var note in notes)
+                {
+                    omopTable.AppendLine($"{{: .{(note.CalloutType == CalloutType.none ? "highlight" : note.CalloutType.ToString())} }}");
+                    omopTable.AppendLine(note.Value);
+                }
+
                 omopTable.AppendLine($"[Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title={target.MapperType.Name}%20mapping){{: .btn }}");
             }
 

docs/transformation-documentation/ConditionOccurrence_condition_start_date.md

@@ -188,6 +188,8 @@ where NonPrimaryRecurrenceOriginalDiagnosis is not null;
 Source column  `NonPrimaryDiagnosisDate`.
 Converts text to dates.
 
+* `NonPrimaryDiagnosisDate` DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) is the date where the Non Primary Cancer PATIENT DIAGNOSIS was confirmed or agreed. [DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)](https://www.datadictionary.nhs.uk/data_elements/date_of_non_primary_cancer_diagnosis__clinically_agreed_.html)
+
 ```sql
 ;with 
     XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),

docs/transformation-documentation/CosdV9ConditionOccurrenceProgression.json

@@ -23,7 +23,18 @@
     {
       "name": "condition_start_date",
       "operation_description": "Converts text to dates.",
-      "dataSource": [],
+      "dataSource": [
+        {
+          "name": "NonPrimaryDiagnosisDate",
+          "description": "DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED) is the date where the Non Primary Cancer PATIENT DIAGNOSIS was confirmed or agreed.",
+          "origins": [
+            {
+              "origin": "DATE OF NON PRIMARY CANCER DIAGNOSIS (CLINICALLY AGREED)",
+              "url": "https://www.datadictionary.nhs.uk/data_elements/date_of_non_primary_cancer_diagnosis__clinically_agreed_.html"
+            }
+          ]
+        }
+      ],
       "query": "\n;with \n    XMLNAMESPACES('http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1' AS COSD901),\n    CosdRecords as ( \n\n    select\n            T.staging.value('(Id/@root)[1]', 'uniqueidentifier') as Id,\n            T.staging.query('.') as Node\n    from omop_staging.cosd_staging\n    cross apply content.nodes('COSD901:COSD/*') as T(staging)\n    where T.staging.exist('Id/@root') = 1\n            and Content.value('namespace-uri((/*:COSD)[1])','nvarchar(max)') = 'http://www.datadictionary.nhs.uk/messages/COSD-v9-0-1'\n            and substring (FileName, 15, 2) = 'CO'\n), CO as (\n\tselect\n\t\tId,\n\t\tNode,\n\t\tNode.value('(ColorectalRecord/LinkagePatientId/NhsNumber/@extension)[1]', 'varchar(max)') as NhsNumber,\n\t\tNode.value('(ColorectalRecord/NonPrimaryPathway/DateOfNonPrimaryCancerDiagnosisClinicallyAgreed)[1]', 'varchar(max)') as NonPrimaryDiagnosisDate,\n\t\tNode.value('(ColorectalRecord/NonPrimaryPathway/Progression/ProgressionIcd/@code)[1]', 'varchar(max)') as NonPrimaryProgressionOriginalDiagnosis\n\tfrom CosdRecords\n)\nselect \n\tdistinct \n        NhsNumber,\n        NonPrimaryDiagnosisDate,\n\t\tNonPrimaryProgressionOriginalDiagnosis\nfrom CO\nwhere NonPrimaryProgressionOriginalDiagnosis is not null;\n\t",
       "lookup_table_markdown": null
     },

docs/transformation-documentation/VisitDetail.md

@@ -24,4 +24,11 @@ has_toc: false
 ## CdsVisitDetail
 <a href="CdsVisitDetail.svg" target="_blank"><img src="CdsVisitDetail.svg" /></a>
 
+{: .note }
+### Assumptions
+* `Emergency` covers a visit to A&E within the given Hospital Provider, and hence covers Admission Code 21 and 24 only
+* `Location Class` ID 24 is a Consultant Clinic within the Health Care Provider.
+* `Patient Classification` ID 1 is the only entry that covers 24 hours or more with the use of a bed, and whilst others may be a day/night only, they will be discounted because they are less than 24 hours. Also, maternity is also not taken as an ""Inpatient"" visit.
+* No calculations to be made between Start and end visit date to try to calculate 24 hours, but instead the "Patient Classification" will be sufficient
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsVisitDetail%20mapping){: .btn }

docs/transformation-documentation/VisitOccurrence.md

@@ -24,8 +24,22 @@ has_toc: false
 ## CdsVisitOccurrenceWithSpell
 <a href="CdsVisitOccurrenceWithSpell.svg" target="_blank"><img src="CdsVisitOccurrenceWithSpell.svg" /></a>
 
+{: .note }
+### Assumptions
+* `Emergency` covers a visit to A&E within the given Hospital Provider, and hence covers Admission Code 21 and 24 only
+* `Location Class` ID 24 is a Consultant Clinic within the Health Care Provider.
+* `Patient Classification` ID 1 is the only entry that covers 24 hours or more with the use of a bed, and whilst others may be a day/night only, they will be discounted because they are less than 24 hours. Also, maternity is also not taken as an ""Inpatient"" visit.
+* No calculations to be made between Start and end visit date to try to calculate 24 hours, but instead the "Patient Classification" will be sufficient
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsVisitOccurrenceWithSpell%20mapping){: .btn }
 ## CdsVisitOccurrenceWithoutSpell
 <a href="CdsVisitOccurrenceWithoutSpell.svg" target="_blank"><img src="CdsVisitOccurrenceWithoutSpell.svg" /></a>
 
+{: .note }
+### Assumptions
+* `Emergency` covers a visit to A&E within the given Hospital Provider, and hence covers Admission Code 21 and 24 only
+* `Location Class` ID 24 is a Consultant Clinic within the Health Care Provider.
+* `Patient Classification` ID 1 is the only entry that covers 24 hours or more with the use of a bed, and whilst others may be a day/night only, they will be discounted because they are less than 24 hours. Also, maternity is also not taken as an ""Inpatient"" visit.
+* No calculations to be made between Start and end visit date to try to calculate 24 hours, but instead the "Patient Classification" will be sufficient
+
 [Comment or raise an issue for this mapping.](https://github.com/answerdigital/oxford-omop-data-mapper/issues/new?title=CdsVisitOccurrenceWithoutSpell%20mapping){: .btn }