add optional field to inputs

nfdi4plants · Oct 18, 2024 · 7c60965 · 7c60965
1 parent 741d07e
commit 7c60965
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Showing 5 changed files with 99 additions and 40 deletions.
diff --git a/src/CWL/Decode.fs b/src/CWL/Decode.fs
@@ -90,9 +90,14 @@ module Decode =
             | _ -> failwith "Invalid CWL type"
         )
 
-    /// Match the input string to the possible CWL types
-    let cwlTypeStringMatcher t (get: Decode.IGetters) =
-        match t with
+    /// Match the input string to the possible CWL types and checks if it is optional
+    let cwlTypeStringMatcher (t: string) (get: Decode.IGetters) =
+        let optional, newT =
+            if t.EndsWith("?") then
+                true, t.Replace("?", "")
+            else
+                false, t
+        match newT with
         | "File" -> File (FileInstance ())
         | "Directory" -> Directory (DirectoryInstance ())
         | "Dirent" -> (get.Required.Field "listing" direntDecoder)
@@ -114,9 +119,10 @@ module Decode =
         | "stdout" -> Stdout
         | "null" -> Null
         | _ -> failwith "Invalid CWL type"
+        , optional
 
     /// Access the type field and decode a YAMLElement into a CWLType
-    let cwlTypeDecoder: (YAMLiciousTypes.YAMLElement -> CWLType) =
+    let cwlTypeDecoder: (YAMLiciousTypes.YAMLElement -> CWLType*bool) =
         Decode.object (fun get ->
             let cwlType = 
                 get.Required.Field 
@@ -133,7 +139,7 @@ module Decode =
                 cwlTypeStringMatcher t get
             | None -> 
                 let cwlTypeArray = get.Required.Field "type" cwlArrayTypeDecoder
-                cwlTypeArray
+                cwlTypeArray, false
         )
 
     /// Decode a YAMLElement into an Output Array
@@ -147,8 +153,8 @@ module Decode =
                     let outputSource = get.Optional.Field "outputSource" Decode.string
                     let cwlType = 
                         match value with
-                        | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value get
-                        | _ -> cwlTypeDecoder value
+                        | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value get |> fst
+                        | _ -> cwlTypeDecoder value |> fst
                     let output =
                         Output(
                             key,
@@ -324,7 +330,7 @@ module Decode =
                 for key in dict.Keys do
                     let value = dict.[key]
                     let inputBinding = inputBindingDecoder value
-                    let cwlType = 
+                    let cwlType,optional = 
                         match value with
                         | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value get
                         | _ -> cwlTypeDecoder value
@@ -335,6 +341,8 @@ module Decode =
                         )
                     if inputBinding.IsSome then
                         DynObj.setOptionalProperty "inputBinding" inputBinding input
+                    if optional then
+                        DynObj.setOptionalProperty "optional" (Some true) input
                     input
             |]
             |> ResizeArray

diff --git a/src/CWL/Inputs.fs b/src/CWL/Inputs.fs
@@ -18,15 +18,18 @@ module Inputs =
     type Input (
         name: string,
         ?type_: CWLType,
-        ?inputBinding: InputBinding
+        ?inputBinding: InputBinding,
+        ?optional: bool
     ) as this =
         inherit DynamicObj ()
         do
             DynObj.setOptionalProperty ("type") type_ this
             DynObj.setOptionalProperty ("inputBinding") inputBinding this
+            DynObj.setOptionalProperty ("optional") optional this
         member this.Name = name
         member this.Type_ = DynObj.tryGetTypedPropertyValue<CWLType> ("type") this
         member this.InputBinding = DynObj.tryGetTypedPropertyValue<InputBinding> ("inputBinding") this
+        member this.Optional = DynObj.tryGetTypedPropertyValue<bool> ("optional") this
 
     module Workflow =
 

diff --git a/tests/CWL/Inputs.Tests.fs b/tests/CWL/Inputs.Tests.fs
@@ -14,7 +14,7 @@ let decodeInput =
 
 let testInput =
     testList "Decode" [
-        testCase "Length" <| fun _ -> Expect.equal 3 decodeInput.Count ""
+        testCase "Length" <| fun _ -> Expect.equal 5 decodeInput.Count ""
         testList "Directory" [
             let directoryItem = decodeInput.[0]
             testCase "Name" <| fun _ -> Expect.equal "arcDirectory"  directoryItem.Name ""
@@ -26,8 +26,20 @@ let testInput =
             testCase "Type" <| fun _ -> Expect.equal (File (FileInstance()))  fileItem.Type_.Value ""
             testCase "InputBinding" <| fun _ -> Expect.equal (Some {Position = Some 1; Prefix = Some "--example"; ItemSeparator = None; Separate = None}) fileItem.InputBinding ""
         ]
+        testList "File optional" [
+            let fileItem = decodeInput.[2]
+            testCase "Name" <| fun _ -> Expect.equal "argOptional"  fileItem.Name ""
+            testCase "Type" <| fun _ -> Expect.equal (File (FileInstance()))  fileItem.Type_.Value ""
+            testCase "Optional" <| fun _ -> Expect.equal (Some true) fileItem.Optional ""
+        ]
+        testList "File array optional" [
+            let fileItem = decodeInput.[3]
+            testCase "Name" <| fun _ -> Expect.equal "argOptionalMap"  fileItem.Name ""
+            testCase "Type" <| fun _ -> Expect.equal (Array (File (FileInstance())))  fileItem.Type_.Value ""
+            testCase "Optional" <| fun _ -> Expect.equal (Some true) fileItem.Optional ""
+        ]
         testList "String" [
-            let stringItem = decodeInput.[2]
+            let stringItem = decodeInput.[4]
             testCase "Name" <| fun _ -> Expect.equal "secondArg"  stringItem.Name ""
             testCase "Type" <| fun _ ->
                 let expected = String

diff --git a/tests/TestingUtils/TestObjects.CWL/Inputs.fs b/tests/TestingUtils/TestObjects.CWL/Inputs.fs
@@ -7,6 +7,9 @@ let inputsFileContent ="""inputs:
     inputBinding:
       position: 1
       prefix: --example
+  argOptional:
+    type: File?
+  argOptionalMap: File[]?
   secondArg:
     type: string
     inputBinding:

diff --git a/tests/TestingUtils/packages.lock.json b/tests/TestingUtils/packages.lock.json
@@ -25,10 +25,10 @@
       },
       "Fable.Browser.Blob": {
         "type": "Transitive",
-        "resolved": "1.1.0",
-        "contentHash": "xMX7hPFwBUGuj75xLlH6VsVThZjRlGW4zOqXb1X+byRPLSBE91vtn9EueNUB+YpGhE9LfrtakIPNGy+dkoMkjg==",
+        "resolved": "1.2.0",
+        "contentHash": "bM4zbtIeycTFFCH7o4WuN28W70dTxNTMZiMvR70XUTYrBnbz7GpS5XxzUy5caDB4l7s2l7wiuVDhh52t7NXxDg==",
         "dependencies": {
-          "FSharp.Core": "4.6.2",
+          "FSharp.Core": "4.7.2",
           "Fable.Core": "3.0.0"
         }
       },
@@ -46,10 +46,20 @@
       },
       "Fable.Browser.Event": {
         "type": "Transitive",
-        "resolved": "1.0.0",
-        "contentHash": "T1bGrlRJ4A2fxOfAVPzJpxanR6lkzPgJroPdSN1IU5CLdKtvRakWmYq6QKqu4dz6ZV9Z3fIPTWLZkoGKEOEo3w==",
+        "resolved": "1.5.0",
+        "contentHash": "Bx2AOOASIG1Eq1Pe8869H8baMePte6STmKGccGuOYMT2p6nWVS8G6ZBZb5encQ0tAL2/0vhA4KJOl4bYwUaQqg==",
         "dependencies": {
-          "FSharp.Core": "4.5.2",
+          "FSharp.Core": "4.7.2",
+          "Fable.Browser.Gamepad": "1.1.0",
+          "Fable.Core": "3.0.0"
+        }
+      },
+      "Fable.Browser.Gamepad": {
+        "type": "Transitive",
+        "resolved": "1.1.0",
+        "contentHash": "8m/Ae/mrH2Hb2ue435rTPEeVb2FhfWsRJJLpCxMvk+5EUOO2+IIjIkLq4thUfRL98uQVt9V5cQd14h2aBf2XJA==",
+        "dependencies": {
+          "FSharp.Core": "4.7.2",
           "Fable.Core": "3.0.0"
         }
       },
@@ -74,6 +84,15 @@
           "Fable.Core": "3.0.0"
         }
       },
+      "Fable.Promise": {
+        "type": "Transitive",
+        "resolved": "2.2.2",
+        "contentHash": "yHFSo7GCY0l/Wjskh/HESuFoGzXIoRM22UlrARA5ewnX736Y1wM27kcqCWeGcIzaEsgJnZcDkp093M0gQyMcWA==",
+        "dependencies": {
+          "FSharp.Core": "4.7.2",
+          "Fable.Core": "3.1.5"
+        }
+      },
       "Fable.Python": {
         "type": "Transitive",
         "resolved": "4.3.0",
@@ -130,15 +149,7 @@
           "Fable.Core": "[4.3.0, )"
         }
       },
-      "arctrl.json": {
-        "type": "Project",
-        "dependencies": {
-          "ARCtrl.Core": "[1.0.0, )",
-          "ARCtrl.ROCrate": "[1.0.0, )",
-          "Thoth.Json.Core": "[0.4.0, )"
-        }
-      },
-      "arctrl.python": {
+      "arctrl.javascript": {
         "type": "Project",
         "dependencies": {
           "ARCtrl.CWL": "[1.0.0, )",
@@ -147,7 +158,17 @@
           "ARCtrl.Json": "[1.0.0, )",
           "ARCtrl.ROCrate": "[1.0.0, )",
           "ARCtrl.Spreadsheet": "[1.0.0, )",
-          "Thoth.Json.Python": "[0.4.0, )"
+          "Fable.Fetch": "[2.6.0, )",
+          "Fable.SimpleHttp": "[3.5.0, )",
+          "Thoth.Json.Javascript": "[0.3.0, )"
+        }
+      },
+      "arctrl.json": {
+        "type": "Project",
+        "dependencies": {
+          "ARCtrl.Core": "[1.0.0, )",
+          "ARCtrl.ROCrate": "[1.0.0, )",
+          "Thoth.Json.Core": "[0.4.0, )"
         }
       },
       "arctrl.rocrate": {
@@ -195,6 +216,19 @@
         "resolved": "4.3.0",
         "contentHash": "sbK+hYs7H7I3b3sbgttI4GlvQfNPcIqSz1qPSagF3QbVA46KJ/pWSXC/Dwv0s9M6AeRGmoqcIeD7GUaLn41zkA=="
       },
+      "Fable.Fetch": {
+        "type": "CentralTransitive",
+        "requested": "[2.6.0, )",
+        "resolved": "2.6.0",
+        "contentHash": "zhCl95EYeuKcc7bk2jGHLSuLhkPqvRcrlwC91GqgX51BlQ7WJF2IQ7mUxW2n1mg74M1D2VOwEKqQpTAZDCVa8Q==",
+        "dependencies": {
+          "FSharp.Core": "4.7.2",
+          "Fable.Browser.Blob": "1.2.0",
+          "Fable.Browser.Event": "1.5.0",
+          "Fable.Core": "3.7.1",
+          "Fable.Promise": "2.2.2"
+        }
+      },
       "Fable.SimpleHttp": {
         "type": "CentralTransitive",
         "requested": "[3.5.0, )",
@@ -235,6 +269,18 @@
           "Fable.Package.SDK": "1.0.0"
         }
       },
+      "Thoth.Json.JavaScript": {
+        "type": "CentralTransitive",
+        "requested": "[0.3.0, )",
+        "resolved": "0.3.0",
+        "contentHash": "A4Cwv+RigC52/OdcrU2woEvjd6rsiDlQGDNTqwXYe3Yh6cdzcLWTfmmwTuCOXgV8SMbcSkviqiS2AG5BS42ayg==",
+        "dependencies": {
+          "FSharp.Core": "5.0.0",
+          "Fable.Core": "4.1.0",
+          "Fable.Package.SDK": "1.0.0",
+          "Thoth.Json.Core": "0.4.0"
+        }
+      },
       "Thoth.Json.Newtonsoft": {
         "type": "CentralTransitive",
         "requested": "[0.2.0, )",
@@ -248,19 +294,6 @@
           "Thoth.Json.Core": "0.3.0"
         }
       },
-      "Thoth.Json.Python": {
-        "type": "CentralTransitive",
-        "requested": "[0.4.0, )",
-        "resolved": "0.4.0",
-        "contentHash": "O86Oisv/91NpbHENz11poZh9zrTRJdAjDXHVC1JqvDDsscelI7HxOmWgks8ZFvYxbBzNJCG+FKQHC10KzyMf8g==",
-        "dependencies": {
-          "FSharp.Core": "5.0.0",
-          "Fable.Core": "4.1.0",
-          "Fable.Package.SDK": "1.0.0",
-          "Fable.Python": "4.3.0",
-          "Thoth.Json.Core": "0.4.0"
-        }
-      },
       "YAMLicious": {
         "type": "CentralTransitive",
         "requested": "[0.0.3, )",