Fix synonym obo writing #27 Add tests ✅

src/OBO.NET/OboTerm.fs

@@ -496,7 +496,7 @@ type OboTerm =
             if term.Definition = "" |> not then yield $"def: {term.Definition}"
             if term.Comment = "" |> not then yield $"comment: {term.Comment}"
             for subset in term.Subsets do yield $"subset: {subset}"
-            for synonym in term.Synonyms do yield $"synonym: {synonym}"
+            for synonym in term.Synonyms do yield $"synonym: {synonym.ToLine()}"
             for xref in term.Xrefs do yield $"xref: {xref.Name}"
             if term.BuiltIn then yield "builtin"
             for property_value in term.PropertyValues do yield $"property_value: {property_value}"

src/OBO.NET/TermSynonym.fs

@@ -4,14 +4,14 @@
 open DBXref
 
 
-//The value consists of a quote enclosed synonym text, a scope identifier, an optional synonym type name, and an optional dbxref list, like this:
-//synonym: "The other white meat" EXACT MARKETING_SLOGAN [MEAT:00324, BACONBASE:03021]
-
-//The synonym scope may be one of four values: EXACT, BROAD, NARROW, RELATED. If the first form is used to specify a synonym, the scope is assumed to be RELATED.
-
-//The synonym type must be the id of a synonym type defined by a synonymtypedef line in the header. If the synonym type has a default scope, that scope is used regardless of any scope declaration given by a synonym tag.
-
-//The dbxref list is formatted as specified in dbxref formatting. A term may have any number of synonyms.
+///The value consists of a quote enclosed synonym text, a scope identifier, an optional synonym type name, and an optional dbxref list, like this:
+///synonym: "The other white meat" EXACT MARKETING_SLOGAN [MEAT:00324, BACONBASE:03021]
+///
+///The synonym scope may be one of four values: EXACT, BROAD, NARROW, RELATED. If the first form is used to specify a synonym, the scope is assumed to be RELATED.
+///
+///The synonym type must be the id of a synonym type defined by a synonymtypedef line in the header. If the synonym type has a default scope, that scope is used regardless of any scope declaration given by a synonym tag.
+///
+///The dbxref list is formatted as specified in dbxref formatting. A term may have any number of synonyms.
 type TermSynonymScope =
     | Exact   
     | Broad   
@@ -27,13 +27,28 @@ type TermSynonymScope =
         | _         ->  printfn "[WARNING@L %i]unable to recognize %s as synonym scope" line s
                         Related
 
+    member this.ToOboString() =
+        match this with
+        | Exact     -> "EXACT"
+        | Broad     -> "BROAD"
+        | Narrow    -> "NARROW"
+        | Related   -> "RELATED"
+
 
 type TermSynonym = {
     Text        : string
     Scope       : TermSynonymScope
     TypeName    : string
     DBXrefs     : DBXref list
-}
+} with
+    static member create(text: string, scope: TermSynonymScope, typeName: string, dbxrefs: DBXref list) = {
+        Text        = text
+        Scope       = scope
+        TypeName    = typeName
+        DBXrefs     = dbxrefs
+    }
+
+    member this.ToLine() = $"{this.Text} {this.Scope.ToOboString()} {this.TypeName} {this.DBXrefs}"
 
 
 module TermSynonym =

tests/OBO.NET.Tests/OBO.NET.Tests.fsproj

@@ -9,6 +9,7 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <Compile Include="TermSynonym.Tests.fs" />
     <Compile Include="OboTerm.Tests.fs" />
     <Compile Include="OboOntology.Tests.fs" />
     <Compile Include="Main.fs" />
@@ -24,4 +25,8 @@
     <PackageReference Include="YoloDev.Expecto.TestSdk" Version="0.14.1" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Update="FSharp.Core" Version="7.0.401" />
+  </ItemGroup>
+
 </Project>

tests/OBO.NET.Tests/OboTerm.Tests.fs

@@ -22,4 +22,17 @@ module OboTermTests =
                     let expected = ["id:1", "related_to", "id:2"; "id:1", "unrelated_to", "id:3"]
                     Expect.sequenceEqual actual expected "is not equal"
             ]
+            testList "ToLines" [
+                testCase "synonym" <| fun _ ->
+                    let actual = 
+                        OboTerm.Create("NCBITaxon:562", Name="Escherichia coli", Synonyms=[TermSynonym.create("\"Bacillus coli\"", Related, "synonym", [])]) 
+                        |> OboTerm.toLines
+                        |> List.ofSeq
+                    let expected = [
+                        "id: NCBITaxon:562"
+                        "name: Escherichia coli"
+                        "synonym: \"Bacillus coli\" RELATED synonym []"
+                    ]
+                    Expect.sequenceEqual actual expected ""
+            ]
         ]

tests/OBO.NET.Tests/TermSynonym.Tests.fs

@@ -0,0 +1,21 @@
+namespace OBO.NET.Tests
+
+open Expecto
+open OBO.NET
+
+module TermSynonymTests =
+
+    [<Tests>]
+    let main =
+        testList "TermSynonym" [
+            testCase "create" <| fun _ ->
+                let actual = TermSynonym.create("\"Bacillus coli\"", Related, "synonym", [])
+                Expect.equal actual.Text "\"Bacillus coli\"" "text"
+                Expect.equal actual.Scope Related "scope"
+                Expect.equal actual.TypeName "synonym" "typeName"
+                Expect.equal actual.DBXrefs [] "dbxrefs"
+            testCase "ToOboString" <| fun _ ->
+                let actual = TermSynonym.create("\"Bacillus coli\"", Related, "synonym", []).ToLine()
+                let expected = "\"Bacillus coli\" RELATED synonym []"
+                Expect.equal actual expected "is not equal"
+        ]