support direct type mappings for inputs and outputs

nfdi4plants · Oct 21, 2024 · 95dab47 · 95dab47
1 parent 3db45c6
commit 95dab47
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Showing 4 changed files with 71 additions and 38 deletions.
diff --git a/src/CWL/Decode.fs b/src/CWL/Decode.fs
@@ -19,9 +19,9 @@ module Decode =
             { Glob = glob }
         )
 
-    let outputBindingDecoder: (YAMLiciousTypes.YAMLElement -> OutputBinding) =
+    let outputBindingDecoder: (YAMLiciousTypes.YAMLElement -> OutputBinding option) =
         Decode.object(fun get ->
-            let outputBinding = get.Required.Field "outputBinding" outputBindingGlobDecoder
+            let outputBinding = get.Optional.Field "outputBinding" outputBindingGlobDecoder
             outputBinding
         )
 
@@ -41,6 +41,30 @@ module Decode =
             | _ -> failwith "Invalid CWL type"
         )
 
+    let cwlTypeStringMatcher t =
+        match t with
+        | "File" -> File (FileInstance ())
+        | "Directory" -> Directory (DirectoryInstance ())
+        | "Dirent" -> Dirent { Entry = ""; Entryname = None; Writable = None }
+        | "string" -> String
+        | "int" -> Int
+        | "long" -> Long
+        | "float" -> Float
+        | "double" -> Double
+        | "boolean" -> Boolean
+        | "File[]" -> Array (File (FileInstance ()))
+        | "Directory[]" -> Array (Directory (DirectoryInstance ()))
+        | "Dirent[]" -> Array (Dirent { Entry = ""; Entryname = None; Writable = None })
+        | "string[]" -> Array String
+        | "int[]" -> Array Int
+        | "long[]" -> Array Long
+        | "float[]" -> Array Float
+        | "double[]" -> Array Double
+        | "boolean[]" -> Array Boolean
+        | "stdout" -> Stdout
+        | "null" -> Null
+        | _ -> failwith "Invalid CWL type"
+
     let cwlTypeDecoder: (YAMLiciousTypes.YAMLElement -> CWLType) =
         Decode.object (fun get ->
             let cwlType = 
@@ -55,28 +79,7 @@ module Decode =
                     )
             match cwlType with
             | Some t ->
-                match t with
-                | "File" -> File (FileInstance ())
-                | "Directory" -> Directory (DirectoryInstance ())
-                | "Dirent" -> Dirent { Entry = ""; Entryname = None; Writable = None }
-                | "string" -> String
-                | "int" -> Int
-                | "long" -> Long
-                | "float" -> Float
-                | "double" -> Double
-                | "boolean" -> Boolean
-                | "File[]" -> Array (File (FileInstance ()))
-                | "Directory[]" -> Array (Directory (DirectoryInstance ()))
-                | "Dirent[]" -> Array (Dirent { Entry = ""; Entryname = None; Writable = None })
-                | "string[]" -> Array String
-                | "int[]" -> Array Int
-                | "long[]" -> Array Long
-                | "float[]" -> Array Float
-                | "double[]" -> Array Double
-                | "boolean[]" -> Array Boolean
-                | "stdout" -> Stdout
-                | "null" -> Null
-                | _ -> failwith "Invalid CWL type"
+                cwlTypeStringMatcher t
             | None -> 
                 let cwlTypeArray = get.Required.Field "type" cwlArrayTypeDecoder
                 cwlTypeArray
@@ -89,12 +92,18 @@ module Decode =
                 for key in dict.Keys do
                     let value = dict.[key]
                     let outputBinding = outputBindingDecoder value
-                    let cwlType = cwlTypeDecoder value
-                    Output(
-                        key,
-                        cwlType,
-                        outputBinding
-                    )
+                    let cwlType = 
+                        match value with
+                        | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value
+                        | _ -> cwlTypeDecoder value
+                    let output =
+                        Output(
+                            key,
+                            cwlType
+                        )
+                    if outputBinding.IsSome then
+                        DynObj.setValueOpt output "outputBinding" outputBinding
+                    output
             |]     
         )
 
@@ -258,7 +267,10 @@ module Decode =
                 for key in dict.Keys do
                     let value = dict.[key]
                     let inputBinding = inputBindingDecoder value
-                    let cwlType = cwlTypeDecoder value
+                    let cwlType = 
+                        match value with
+                        | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value
+                        | _ -> cwlTypeDecoder value
                     let input =
                         Input(
                             key,

diff --git a/tests/CWL/Outputs.Tests.fs b/tests/CWL/Outputs.Tests.fs
@@ -14,7 +14,7 @@ let decodeOutput =
 let testOutput =
     testList "outputs with basetypes and array" [
         testCase "Length" <| fun _ ->
-            let expected = 4
+            let expected = 5
             let actual = decodeOutput.Length
             Expect.isTrue
                 (expected = actual)
@@ -43,7 +43,7 @@ let testOutput =
         testList "Directory" [
             let directoryItem = decodeOutput.[1]
             testCase "Name" <| fun _ ->
-                let expected = "example"
+                let expected = "example1"
                 let actual = directoryItem.Name
                 Expect.isTrue
                     (expected = actual)
@@ -61,8 +61,29 @@ let testOutput =
                     (expected = actual)
                     $"Expected: {expected}\nActual: {actual}"
         ]
+        testList "Directory 2" [
+            let directoryItem = decodeOutput.[2]
+            testCase "Name" <| fun _ ->
+                let expected = "example2"
+                let actual = directoryItem.Name
+                Expect.isTrue
+                    (expected = actual)
+                    $"Expected: {expected}\nActual: {actual}"
+            testCase "Type" <| fun _ ->
+                let expected = Directory (DirectoryInstance())
+                let actual = directoryItem.Type.Value
+                Expect.isTrue
+                    (expected = actual)
+                    $"Expected: {expected}\nActual: {actual}"
+            testCase "OutputBinding" <| fun _ ->
+                let expected = None
+                let actual = directoryItem.OutputBinding
+                Expect.isTrue
+                    (expected = actual)
+                    $"Expected: {expected}\nActual: {actual}"
+        ]
         testList "File Array" [
-            let fileArrayItem = decodeOutput.[2]
+            let fileArrayItem = decodeOutput.[3]
             testCase "Name" <| fun _ ->
                 let expected = "exampleArray1"
                 let actual = fileArrayItem.Name
@@ -83,7 +104,7 @@ let testOutput =
                     $"Expected: {expected}\nActual: {actual}"
         ]
         testList "File Array 2" [
-            let fileArrayItem = decodeOutput.[3]
+            let fileArrayItem = decodeOutput.[4]
             testCase "Name" <| fun _ ->
                 let expected = "exampleArray2"
                 let actual = fileArrayItem.Name

diff --git a/tests/TestingUtils/TestObjects.CWL/Inputs.fs b/tests/TestingUtils/TestObjects.CWL/Inputs.fs
@@ -1,8 +1,7 @@
 module TestObjects.CWL.Inputs
 
 let inputs ="""inputs:
-  arcDirectory:
-    type: Directory
+  arcDirectory: Directory
   firstArg:
     type: File
     inputBinding:

diff --git a/tests/TestingUtils/TestObjects.CWL/Outputs.fs b/tests/TestingUtils/TestObjects.CWL/Outputs.fs
@@ -5,10 +5,11 @@ let outputs ="""outputs:
     type: File
     outputBinding:
       glob: ./arc/runs/fsResult1/result.csv
-  example:
+  example1:
     type: Directory
     outputBinding:
       glob: ./arc/runs/fsResult1/example.csv
+  example2: Directory
   exampleArray1:
     type: File[]
     outputBinding: