From 081ca0452bad26245525872637662e18bdb16bef Mon Sep 17 00:00:00 2001
From: Caroline Ott <caroline.ott1994@gmail.com>
Date: Fri, 19 Jul 2024 10:42:20 +0200
Subject: [PATCH] Add cwl model

---
 src/CWL/CWL.fs          | 56 +++++++++++++++++++++++++++++++++++++++++
 src/CWL/CWLTypes.fs     | 37 +++++++++++++++++++++++++++
 src/CWL/Inputs.fs       | 18 +++++++++++++
 src/CWL/Outputs.fs      | 16 ++++++++++++
 src/CWL/Requirements.fs | 51 +++++++++++++++++++++++++++++++++++++
 5 files changed, 178 insertions(+)
 create mode 100644 src/CWL/CWL.fs
 create mode 100644 src/CWL/CWLTypes.fs
 create mode 100644 src/CWL/Inputs.fs
 create mode 100644 src/CWL/Outputs.fs
 create mode 100644 src/CWL/Requirements.fs

diff --git a/src/CWL/CWL.fs b/src/CWL/CWL.fs
new file mode 100644
index 00000000..1f12b369
--- /dev/null
+++ b/src/CWL/CWL.fs
@@ -0,0 +1,56 @@
+namespace ARCtrl.CWL
+
+open DynamicObj
+open CWLTypes
+open Requirements
+open Inputs
+open Outputs
+
+module CWL =
+
+    type CWL (
+            cwlVersion: string,
+            cls: Class,
+            outputs: Output [],
+            ?baseCommand: string [],
+            ?requirements: Requirement [],
+            ?hints: Requirement [],
+            ?inputs: Input []
+        ) =
+        inherit DynamicObj ()
+
+        let mutable _cwlVersion: string = cwlVersion
+        let mutable _class: Class = cls
+        let mutable _outputs: Output [] = outputs
+        let mutable _baseCommand: string [] option = baseCommand
+        let mutable _requirements: Requirement [] option = requirements
+        let mutable _hints: Requirement [] option = hints
+        let mutable _inputs: Input [] option = inputs
+
+        member this.CWLVersion
+            with get() = _cwlVersion
+            and set(version) = _cwlVersion <- version
+
+        member this.Class
+            with get() = _class
+            and set(cls) = _class <- cls
+
+        member this.Outputs
+            with get() = _outputs
+            and set(outputs) = _outputs <- outputs
+
+        member this.BaseCommand
+            with get() = _baseCommand
+            and set(baseCommand) = _baseCommand <- baseCommand
+
+        member this.Requirements
+            with get() = _requirements
+            and set(requirements) = _requirements <- requirements
+
+        member this.Hints
+            with get() = _hints
+            and set(hints) = _hints <- hints
+
+        member this.Inputs
+            with get() = _inputs
+            and set(inputs) = _inputs <- inputs
\ No newline at end of file
diff --git a/src/CWL/CWLTypes.fs b/src/CWL/CWLTypes.fs
new file mode 100644
index 00000000..fcfa5c74
--- /dev/null
+++ b/src/CWL/CWLTypes.fs
@@ -0,0 +1,37 @@
+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
+    }
+
+    type CWLType =
+        | File of FileInstance
+        | Directory of DirectoryInstance
+        | Dirent of DirentInstance
+        | String
+        | Int
+        | Long
+        | Float
+        | Double
+        | Boolean
+        | Stdout
+        | Null
+        | Array of CWLType
+
+    type Class = 
+    | Workflow
+    | CommandLineTool
+    | ExpressionTool
diff --git a/src/CWL/Inputs.fs b/src/CWL/Inputs.fs
new file mode 100644
index 00000000..9e03907d
--- /dev/null
+++ b/src/CWL/Inputs.fs
@@ -0,0 +1,18 @@
+namespace ARCtrl.CWL
+
+open CWLTypes
+
+module Inputs =
+
+    type InputBinding = {
+        Prefix: string option
+        Position: int option
+        ItemSeparator: string option
+        Separate: bool option
+    }
+    
+    type Input = {
+        Name: string
+        Type: CWLType
+        InputBinding: InputBinding option
+    }
diff --git a/src/CWL/Outputs.fs b/src/CWL/Outputs.fs
new file mode 100644
index 00000000..f6240ec3
--- /dev/null
+++ b/src/CWL/Outputs.fs
@@ -0,0 +1,16 @@
+namespace ARCtrl.CWL
+
+open CWLTypes
+
+module Outputs =
+
+    type OutputBinding = {
+        Glob: string option
+    }
+
+    type Output = {
+        Name: string
+        Type: CWLType
+        OutputBinding: OutputBinding option
+    }
+
diff --git a/src/CWL/Requirements.fs b/src/CWL/Requirements.fs
new file mode 100644
index 00000000..f00a0929
--- /dev/null
+++ b/src/CWL/Requirements.fs
@@ -0,0 +1,51 @@
+namespace ARCtrl.CWL
+
+open DynamicObj
+open CWLTypes
+
+module Requirements =
+    type DockerRequirement = {
+        DockerPull: string option
+        DockerFile: string option
+        DockerImageId: string option
+    }
+
+    type InputRecordSchema () =
+        inherit DynamicObj ()
+
+    type InputEnumSchema () =
+        inherit DynamicObj ()
+
+    type InputArraySchema () =
+        inherit DynamicObj ()
+
+    type SchemaDefRequirementType =
+        | InputRecordSchema of InputRecordSchema
+        | InputEnumSchema of InputEnumSchema
+        | InputArraySchema of InputArraySchema
+
+    type SoftwarePackage = {
+        Package: string
+        Version: string [] option
+        Specs: string [] option
+    }
+
+    type EnvironmentDef = {
+        EnvName: string
+        EnvValue: string
+    }
+
+    type ResourceRequirementInstance () =
+        inherit DynamicObj ()
+
+    type Requirement = 
+        | InlineJavascriptRequirement
+        | SchemaDefRequirement of SchemaDefRequirementType []
+        | DockerRequirement of DockerRequirement
+        | SoftwareRequirement of SoftwarePackage []
+        | InitialWorkDirRequirement of CWLType []
+        | EnvVarRequirement of EnvironmentDef
+        | ShellCommandRequirement
+        | ResourceRequirement of ResourceRequirementInstance
+        | NetworkAccessRequirement
+