remove underlying modules

nfdi4plants · Oct 21, 2024 · 844ca8b · 844ca8b
1 parent fedc6d4
commit 844ca8b
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Showing 14 changed files with 239 additions and 287 deletions.
diff --git a/src/CWL/CWLTypes.fs b/src/CWL/CWLTypes.fs
@@ -2,57 +2,55 @@ namespace ARCtrl.CWL
 
 open DynamicObj
 
-module CWLTypes =
-
-    type FileInstance () =
-        inherit DynamicObj ()
-
-    type DirectoryInstance () =
-        inherit DynamicObj ()
-
-    type DirentInstance = {
-        // can be string or expression, but expression is string as well
-        Entry: string
-        Entryname: string option
-        Writable: bool option
-    }
-
-    /// Primitive types with the concept of a file and directory as a builtin type.
-    type CWLType =
-        /// Represents a file (or group of files when secondaryFiles is provided)
-        | File of FileInstance
-        /// Represents a directory to present to a command line tool.
-        /// Directories are represented as objects with class of Directory. Directory objects have a number of properties that provide metadata about the directory.
-        | Directory of DirectoryInstance
-        /// Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool.
-        /// May be the result of executing an expression, such as building a configuration file from a template.
-        | Dirent of DirentInstance
-        | String
-        | Int
-        | Long
-        | Float
-        | Double
-        | Boolean
-        | Stdout
-        | Null
-        | Array of CWLType
-
-    type InputRecordSchema () =
-        inherit DynamicObj ()
-
-    type InputEnumSchema () =
-        inherit DynamicObj ()
-
-    type InputArraySchema () =
-        inherit DynamicObj ()
-
-    type SchemaDefRequirementType (types, definitions) as this =
-        inherit DynamicObj ()
-        do
-            DynObj.setProperty (nameof types) definitions this
-
-    type SoftwarePackage = {
-        Package: string
-        Version: ResizeArray<string> option
-        Specs: ResizeArray<string> option
-    }
+type FileInstance () =
+    inherit DynamicObj ()
+
+type DirectoryInstance () =
+    inherit DynamicObj ()
+
+type DirentInstance = {
+    // can be string or expression, but expression is string as well
+    Entry: string
+    Entryname: string option
+    Writable: bool option
+}
+
+/// Primitive types with the concept of a file and directory as a builtin type.
+type CWLType =
+    /// Represents a file (or group of files when secondaryFiles is provided)
+    | File of FileInstance
+    /// Represents a directory to present to a command line tool.
+    /// Directories are represented as objects with class of Directory. Directory objects have a number of properties that provide metadata about the directory.
+    | Directory of DirectoryInstance
+    /// Define a file or subdirectory that must be placed in the designated output directory prior to executing the command line tool.
+    /// May be the result of executing an expression, such as building a configuration file from a template.
+    | Dirent of DirentInstance
+    | String
+    | Int
+    | Long
+    | Float
+    | Double
+    | Boolean
+    | Stdout
+    | Null
+    | Array of CWLType
+
+type InputRecordSchema () =
+    inherit DynamicObj ()
+
+type InputEnumSchema () =
+    inherit DynamicObj ()
+
+type InputArraySchema () =
+    inherit DynamicObj ()
+
+type SchemaDefRequirementType (types, definitions) as this =
+    inherit DynamicObj ()
+    do
+        DynObj.setProperty (nameof types) definitions this
+
+type SoftwarePackage = {
+    Package: string
+    Version: ResizeArray<string> option
+    Specs: ResizeArray<string> option
+}
diff --git a/src/CWL/Decode.fs b/src/CWL/Decode.fs
@@ -1,13 +1,7 @@
 namespace ARCtrl.CWL
 
-open ARCtrl
 open YAMLicious
 open YAMLicious.YAMLiciousTypes
-open CWLTypes
-open Requirements
-open Inputs
-open Outputs
-open WorkflowSteps
 open DynamicObj
 
 module ResizeArray =
@@ -141,7 +135,7 @@ module Decode =
         )
 
     /// Decode a YAMLElement into an Output Array
-    let outputArrayDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<Output>) =
+    let outputArrayDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<CWLOutput>) =
         Decode.object (fun get ->
             let dict = get.Overflow.FieldList []
             [|
@@ -154,7 +148,7 @@ module Decode =
                         | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value get |> fst
                         | _ -> cwlTypeDecoder value |> fst
                     let output =
-                        Output(
+                        CWLOutput(
                             key,
                             cwlType
                         )
@@ -168,7 +162,7 @@ module Decode =
         )
 
     /// Access the outputs field and decode a YAMLElement into an Output Array
-    let outputsDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<Output>) =
+    let outputsDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<CWLOutput>) =
         Decode.object (fun get ->
             let outputs = get.Required.Field "outputs" outputArrayDecoder
             outputs
@@ -321,7 +315,7 @@ module Decode =
         )
 
     /// Decode a YAMLElement into an Input array
-    let inputArrayDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<Input>) =
+    let inputArrayDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<CWLInput>) =
         Decode.object (fun get ->
             let dict = get.Overflow.FieldList []
             [|
@@ -333,7 +327,7 @@ module Decode =
                         | YAMLElement.Object [YAMLElement.Value v] -> cwlTypeStringMatcher v.Value get
                         | _ -> cwlTypeDecoder value
                     let input =
-                        Input(
+                        CWLInput(
                             key,
                             cwlType
                         )
@@ -347,7 +341,7 @@ module Decode =
         )
 
     /// Access the inputs field and decode the YAMLElements into an Input array
-    let inputsDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<Input> option) =
+    let inputsDecoder: (YAMLiciousTypes.YAMLElement -> ResizeArray<CWLInput> option) =
         Decode.object (fun get ->
             let outputs = get.Optional.Field "inputs" inputArrayDecoder
             outputs

diff --git a/src/CWL/Inputs.fs b/src/CWL/Inputs.fs
@@ -1,31 +1,28 @@
 namespace ARCtrl.CWL
 
-open CWLTypes
 open DynamicObj
 open Fable.Core
 
-module Inputs =
+type InputBinding = {
+    Prefix: string option
+    Position: int option
+    ItemSeparator: string option
+    Separate: bool option
+}
 
-    type InputBinding = {
-        Prefix: string option
-        Position: int option
-        ItemSeparator: string option
-        Separate: bool option
-    }
-
-    [<AttachMembers>]
-    type Input (
-        name: string,
-        ?type_: CWLType,
-        ?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
+[<AttachMembers>]
+type CWLInput (
+    name: string,
+    ?type_: CWLType,
+    ?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
diff --git a/src/CWL/Outputs.fs b/src/CWL/Outputs.fs
@@ -1,28 +1,25 @@
 namespace ARCtrl.CWL
 
-open CWLTypes
 open DynamicObj
 open Fable.Core
 
-module Outputs =
+type OutputBinding = {
+    Glob: string option
+}
 
-    type OutputBinding = {
-        Glob: string option
-    }
-
-    [<AttachMembers>]
-    type Output (
-        name: string,
-        ?type_: CWLType,
-        ?outputBinding: OutputBinding,
-        ?outputSource: string
-    ) as this =
-        inherit DynamicObj ()
-        do
-            DynObj.setOptionalProperty ("type") type_ this
-            DynObj.setOptionalProperty ("outputBinding") outputBinding this
-            DynObj.setOptionalProperty ("outputSource") outputSource this
-        member this.Name = name
-        member this.Type_ = DynObj.tryGetTypedPropertyValue<CWLType> ("type") this
-        member this.OutputBinding = DynObj.tryGetTypedPropertyValue<OutputBinding> ("outputBinding") this
-        member this.OutputSource = DynObj.tryGetTypedPropertyValue<string> ("outputSource") this
+[<AttachMembers>]
+type CWLOutput (
+    name: string,
+    ?type_: CWLType,
+    ?outputBinding: OutputBinding,
+    ?outputSource: string
+) as this =
+    inherit DynamicObj ()
+    do
+        DynObj.setOptionalProperty ("type") type_ this
+        DynObj.setOptionalProperty ("outputBinding") outputBinding this
+        DynObj.setOptionalProperty ("outputSource") outputSource this
+    member this.Name = name
+    member this.Type_ = DynObj.tryGetTypedPropertyValue<CWLType> ("type") this
+    member this.OutputBinding = DynObj.tryGetTypedPropertyValue<OutputBinding> ("outputBinding") this
+    member this.OutputSource = DynObj.tryGetTypedPropertyValue<string> ("outputSource") this