Update document header tag parsing (WIP)

playground.fsx

@@ -1,3 +1,88 @@
+#I "src/OBO.NET/bin/Debug/netstandard2.0"
+#I "src/OBO.NET/bin/Release/netstandard2.0"
+#I "src/OBO.NET.CodeGeneration/bin/Debug/netstandard2.0"
+#I "src/OBO.NET.CodeGeneration/bin/Release/netstandard2.0"
+
+#r "OBO.NET.dll"
+#r "OBO.NET.CodeGeneration.dll"
+
+open OBO.NET
+open OBO.NET.DBXref
+open OBO.NET.CodeGeneration
+
+#r "nuget: FSharpAux"
+#r "nuget: ARCTokenization"
+
+open FSharpAux
+open ARCTokenization.Terms
+
+open type System.Environment
+
+
+
+
+type OboOntology =
+
+    {
+        Terms           : OboTerm list
+        TypeDefs        : OboTypeDef list
+        FormatVersion   : string
+        DataVersion     : string option
+        Ontology        : string option
+        Date            : System.DateTime option
+        SavedBy         : string option
+        AutoGeneratedBy : string option
+        Subsetdef       : string option
+        Import          : string option
+        Synonymtypedef  : TermSynonym option    // rethink type, maybe create a mother t
+    }
+
+    static member create terms typedefs formatVersion =
+        {
+            Terms = terms
+            TypeDefs = typedefs
+            FormatVersion = formatVersion
+        }
+
+    /// Reads an OBO Ontology containing term and type def stanzas from lines.
+    static member fromLines verbose (input : seq<string>) =
+
+        let en = input.GetEnumerator()
+        let rec loop (en:System.Collections.Generic.IEnumerator<string>) terms typedefs lineNumber =
+
+            match en.MoveNext() with
+            | true ->             
+                match (en.Current |> trimComment) with
+                | "[Term]"    -> 
+                    let lineNumber,parsedTerm = OboTerm.fromLines verbose en lineNumber "" "" false [] "" "" [] [] [] [] [] [] [] [] false [] [] [] false "" ""
+                    loop en (parsedTerm :: terms) typedefs lineNumber
+                | "[Typedef]" -> 
+                    let lineNumber,parsedTypeDef = OboTypeDef.fromLines verbose en lineNumber "" "" "" "" [] [] false false false false false false false
+                    loop en terms (parsedTypeDef :: typedefs) lineNumber
+                | _ -> loop en terms typedefs (lineNumber + 1)
+            | false -> OboOntology.create (List.rev terms) (List.rev typedefs)
+
+        loop en [] [] 1
+
+
+
+
+let expected = 
+    $"namespace ARCTokenization.StructuralOntology{NewLine}{NewLine}    open ControlledVocabulary{NewLine}{NewLine}    module Investigation ={NewLine}{NewLine}        let Investigation_Metadata = CvTerm.create(\"INVMSO:00000001\", \"Investigation Metadata\", \"INVMSO\"){NewLine}{NewLine}        let ONTOLOGY_SOURCE_REFERENCE = CvTerm.create(\"INVMSO:00000002\", \"ONTOLOGY SOURCE REFERENCE\", \"INVMSO\"){NewLine}{NewLine}        let Term_Source_Name = CvTerm.create(\"INVMSO:00000003\", \"Term Source Name\", \"INVMSO\")"
+    |> String.replace "\r" ""
+let actual = 
+    CodeGeneration.toSourceCode "Investigation" InvestigationMetadata.ontology 
+    |> String.splitS NewLine 
+    |> Array.take 11 
+    |> String.concat "\n"
+    |> String.replace "\r" ""
+
+OBO.NET.OboOntology.toFile @"C:\Repos\CSBiology\OBO.NET\tests\OBO.NET.CodeGeneration.Tests\References\ReferenceOboFile.obo" InvestigationMetadata.ontology
+
+
+// DEPRECATED
+
+
 #I "src/FsOboParser/bin/Debug/netstandard2.0"
 #I "src/FsOboParser/bin/Release/netstandard2.0"
 #r "FsOboParser.dll"