fix EnvVarRequirement

nfdi4plants · Oct 21, 2024 · 86913f6 · 86913f6
1 parent 3c5e2f8
commit 86913f6
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Showing 5 changed files with 24 additions and 4 deletions.
diff --git a/src/CWL/Decode.fs b/src/CWL/Decode.fs
@@ -104,6 +104,24 @@ module Decode =
         }
         dockerReq
 
+    let envVarRequirementDecoder (get: Decode.IGetters): EnvironmentDef[] =
+        let envDef = 
+            get.Required.Field
+                "envDef"
+                (
+                    Decode.seq 
+                        (
+                            Decode.object (fun get2 ->
+                                {
+                                    EnvName = get2.Required.Field "envName" Decode.string
+                                    EnvValue = get2.Required.Field "envValue" Decode.string
+                                }
+                            )
+                        )
+                )
+        envDef
+        |> Seq.toArray
+
     let requirementArrayDecoder: (YAMLiciousTypes.YAMLElement -> Requirement[]) =
         Decode.array 
             (
@@ -115,7 +133,7 @@ module Decode =
                     | "DockerRequirement" -> DockerRequirement (dockerRequirementDecoder get)
                     | "SoftwareRequirement" -> SoftwareRequirement [||]
                     | "InitialWorkDirRequirement" -> InitialWorkDirRequirement [||]
-                    | "EnvVarRequirement" -> EnvVarRequirement {EnvName = ""; EnvValue = ""}
+                    | "EnvVarRequirement" -> EnvVarRequirement (envVarRequirementDecoder get)
                     | "ShellCommandRequirement" -> ShellCommandRequirement
                     | "ResourceRequirement" -> ResourceRequirement (ResourceRequirementInstance())
                     | "NetworkAccess" -> NetworkAccessRequirement

diff --git a/src/CWL/Requirements.fs b/src/CWL/Requirements.fs
@@ -44,7 +44,7 @@ module Requirements =
         | DockerRequirement of DockerRequirement
         | SoftwareRequirement of SoftwarePackage []
         | InitialWorkDirRequirement of CWLType []
-        | EnvVarRequirement of EnvironmentDef
+        | EnvVarRequirement of EnvironmentDef []
         | ShellCommandRequirement
         | ResourceRequirement of ResourceRequirementInstance
         | NetworkAccessRequirement

diff --git a/tests/CWL/CWLObject.Tests.fs b/tests/CWL/CWLObject.Tests.fs
@@ -50,7 +50,7 @@ let testCWLToolDescription =
                     (expected = actual)
                     $"Expected: {expected}\nActual: {actual}"
             testCase "EnvVarRequirement" <| fun _ ->
-                let expected = EnvVarRequirement {EnvName = ""; EnvValue = ""}
+                let expected = EnvVarRequirement [|{EnvName = "DOTNET_NOLOGO"; EnvValue = "true"}|]
                 let actual = requirementsItem.Value.[1]
                 Expect.isTrue
                     (expected = actual)

diff --git a/tests/CWL/Requirements.Tests.fs b/tests/CWL/Requirements.Tests.fs
@@ -38,7 +38,7 @@ let testRequirement =
         testList "EnvVarRequirement" [
             let envVarItem = decodeRequirement.[2]
             testCase "Class" <| fun _ ->
-                let expected = EnvVarRequirement {EnvName = ""; EnvValue = ""}
+                let expected = EnvVarRequirement [|{EnvName = "DOTNET_NOLOGO"; EnvValue = "true"}; {EnvName = "TEST"; EnvValue = "false"}|]
                 let actual = envVarItem
                 Expect.isTrue
                     (expected = actual)

diff --git a/tests/TestingUtils/TestObjects.CWL/Requirements.fs b/tests/TestingUtils/TestObjects.CWL/Requirements.fs
@@ -13,5 +13,7 @@ let requirements ="""requirements:
     envDef:
       - envName: DOTNET_NOLOGO
         envValue: "true"
+      - envName: TEST
+        envValue: "false"
   - class: NetworkAccess
     networkAccess: true"""