Merge pull request #176 from nfdi4plants/hotfix_protocolHandling

Hotfix protocol handling
nfdi4plants · Aug 17, 2023 · 21f56b2 · 21f56b2
2 parents 3d666dc + a3f2ed5
commit 21f56b2
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Showing 3 changed files with 11 additions and 5 deletions.
diff --git a/src/ISA/ISA/ArcTypes/ArcTable.fs b/src/ISA/ISA/ArcTypes/ArcTable.fs
@@ -465,7 +465,7 @@ type ArcTable =
     /// The table will have at most one row, with the protocol information and the component values
     static member fromProtocol (p : Protocol) : ArcTable = 
 
-        let t = ArcTable.init (p.Name |> Option.defaultValue "")
+        let t = ArcTable.init (p.Name |> Option.defaultValue (Identifier.createMissingIdentifier()))
 
         for pp in p.Parameters |> Option.defaultValue [] do
 
@@ -506,13 +506,13 @@ type ArcTable =
                     let c = Component.create(ComponentType = oa)
                     Protocol.addComponent c p
                 | _ -> p
-            ) Protocol.empty
+            ) (Protocol.create(Name = this.Name))
             |> List.singleton
         else
             List.init this.RowCount (fun i ->
                 this.GetRow(i) 
                 |> Seq.zip this.Headers
-                |> CompositeRow.toProtocol                    
+                |> CompositeRow.toProtocol this.Name                   
             )
             |> List.distinct
 

diff --git a/src/ISA/ISA/ArcTypes/CompositeRow.fs b/src/ISA/ISA/ArcTypes/CompositeRow.fs
@@ -1,6 +1,6 @@
 module ARCtrl.ISA.CompositeRow
 
-let toProtocol (row : (CompositeHeader*CompositeCell) seq) =
+let toProtocol (tableName : string) (row : (CompositeHeader*CompositeCell) seq) =
     row
     |> Seq.fold (fun p hc ->
         match hc with
@@ -20,4 +20,4 @@ let toProtocol (row : (CompositeHeader*CompositeCell) seq) =
             let c = Component.create(ComponentType = oa, Value = Value.Ontology t)
             Protocol.addComponent c p     
         | _ -> p
-    ) Protocol.empty
+    ) (Protocol.create(Name = tableName))
diff --git a/tests/ISA/ISA.Tests/ArcJsonConversionTests.fs b/tests/ISA/ISA.Tests/ArcJsonConversionTests.fs
@@ -527,6 +527,7 @@ let private tests_protocolTransformation =
             let t = p |> ArcTable.fromProtocol
 
             Expect.equal t.ColumnCount 0 "ColumnCount should be 0"
+            Expect.isTrue (Identifier.isMissingIdentifier t.Name) $"Name should be missing identifier, not \"{t.Name}\""
         )
         testCase "FromProtocol SingleParameter" (fun () ->
             let p = Protocol.create(Parameters = [pParam1])
@@ -580,7 +581,12 @@ let private tests_protocolTransformation =
             let c = c.Value
             Expect.equal c expected "Cell value does not match"
         )
+        testCase "GetProtocols NoName" (fun () ->           
+            let t = ArcTable.init "TestTable"
+            let expected = [Protocol.create(Name = "TestTable")]
 
+            TestingUtils.mySequenceEqual (t.GetProtocols()) expected "Protocol Name should be ArcTable name."
+        )
         testCase "GetProtocols SingleName" (fun () ->           
             let t = ArcTable.init "TestTable"
             let name = "Name"