From 0f7ee5a04bbc83adf4b2aa8f6d1bdade74a2bbb6 Mon Sep 17 00:00:00 2001
From: Caroline Ott <caroline.ott1994@gmail.com>
Date: Fri, 2 Feb 2024 18:59:29 +0100
Subject: [PATCH] add different cwl use cases
---
workflows/ARCMount/FSharpArcCapsule.cwl | 26 +++++++++++++++
workflows/ARCMount/script.fsx | 20 +++++++++++
workflows/Devcontainer/.gitkeep | 0
workflows/Devcontainer/FSharpArcCapsule.cwl | 27 +++++++++++++++
.../.config/dotnet-tools.json | 5 +++
.../.devcontainer/devcontainer.json | 15 +++++++++
.../.devcontainer/settings.vscode.json | 3 ++
.../Devcontainer/FSharpArcCapsule/Dockerfile | 10 ++++++
.../Devcontainer/FSharpArcCapsule/script.fsx | 20 +++++++++++
workflows/FixedScript/FSharpArcCapsule.cwl | 33 +++++++++++++++++++
workflows/FixedScript/script.fsx | 22 +++++++++++++
11 files changed, 181 insertions(+)
create mode 100644 workflows/ARCMount/FSharpArcCapsule.cwl
create mode 100644 workflows/ARCMount/script.fsx
create mode 100644 workflows/Devcontainer/.gitkeep
create mode 100644 workflows/Devcontainer/FSharpArcCapsule.cwl
create mode 100644 workflows/Devcontainer/FSharpArcCapsule/.config/dotnet-tools.json
create mode 100644 workflows/Devcontainer/FSharpArcCapsule/.devcontainer/devcontainer.json
create mode 100644 workflows/Devcontainer/FSharpArcCapsule/.devcontainer/settings.vscode.json
create mode 100644 workflows/Devcontainer/FSharpArcCapsule/Dockerfile
create mode 100644 workflows/Devcontainer/FSharpArcCapsule/script.fsx
create mode 100644 workflows/FixedScript/FSharpArcCapsule.cwl
create mode 100644 workflows/FixedScript/script.fsx
diff --git a/workflows/ARCMount/FSharpArcCapsule.cwl b/workflows/ARCMount/FSharpArcCapsule.cwl
new file mode 100644
index 0000000..2602936
--- /dev/null
+++ b/workflows/ARCMount/FSharpArcCapsule.cwl
@@ -0,0 +1,26 @@
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: arc
+ entry: $(inputs.arcDirectory)
+ writable: true
+ - class: EnvVarRequirement
+ envDef:
+ - envName: DOTNET_NOLOGO
+ envValue: "true"
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [dotnet, fsi, "./arc/workflows/FSharpArcCapsule/script.fsx"]
+inputs:
+ arcDirectory:
+ type: Directory
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "./arc/runs/fsResult1/result.csv"
\ No newline at end of file
diff --git a/workflows/ARCMount/script.fsx b/workflows/ARCMount/script.fsx
new file mode 100644
index 0000000..155693f
--- /dev/null
+++ b/workflows/ARCMount/script.fsx
@@ -0,0 +1,20 @@
+#r "nuget: FSharp.Data, 5.0.2"
+
+open FSharp.Data
+open System.IO
+
+printfn "%A" (System.IO.Directory.GetCurrentDirectory())
+
+let data =
+ CsvFile
+ .Load(Path.Combine(System.IO.Directory.GetCurrentDirectory(),"./arc/assays/measurement1/dataset/table.csv"))
+ .Cache()
+
+let r =
+ [
+ yield "Sum_1-2"
+ for row in data.Rows do
+ yield sprintf "%f" ((row.["value_1"].AsFloat()) + (row.["value_2"].AsFloat()))
+ ]
+
+System.IO.File.WriteAllLines("./arc/runs/fsResult1/result.csv",r)
\ No newline at end of file
diff --git a/workflows/Devcontainer/.gitkeep b/workflows/Devcontainer/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/workflows/Devcontainer/FSharpArcCapsule.cwl b/workflows/Devcontainer/FSharpArcCapsule.cwl
new file mode 100644
index 0000000..c8c166c
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule.cwl
@@ -0,0 +1,27 @@
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerImageId: "devcontainer"
+ dockerFile: {$include: "FSharpArcCapsule/Dockerfile"}
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: arc
+ entry: $(inputs.arcDirectory)
+ writable: true
+ - class: EnvVarRequirement
+ envDef:
+ - envName: DOTNET_NOLOGO
+ envValue: "true"
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [dotnet, fsi, "./arc/workflows/Devcontainer/FSharpArcCapsule/script.fsx"]
+inputs:
+ arcDirectory:
+ type: Directory
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "./arc/runs/fsResult1/result.csv"
\ No newline at end of file
diff --git a/workflows/Devcontainer/FSharpArcCapsule/.config/dotnet-tools.json b/workflows/Devcontainer/FSharpArcCapsule/.config/dotnet-tools.json
new file mode 100644
index 0000000..b0e38ab
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule/.config/dotnet-tools.json
@@ -0,0 +1,5 @@
+{
+ "version": 1,
+ "isRoot": true,
+ "tools": {}
+}
\ No newline at end of file
diff --git a/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/devcontainer.json b/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..71ac9e7
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/devcontainer.json
@@ -0,0 +1,15 @@
+{
+ "name": "F#ARC-Capsule",
+ "dockerFile": "../Dockerfile",
+ "appPort": [8080],
+ "extensions": [
+ "ionide.ionide-fsharp",
+ "ms-vscode.csharp",
+ "editorconfig.editorconfig",
+ "ionide.ionide-paket",
+ "ionide.ionide-fake"
+ ],
+ "mounts": [
+ "source=${localWorkspaceFolder}/../../,target=/arc,type=bind,consistency=cached"
+ ]
+}
\ No newline at end of file
diff --git a/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/settings.vscode.json b/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/settings.vscode.json
new file mode 100644
index 0000000..5b238fa
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule/.devcontainer/settings.vscode.json
@@ -0,0 +1,3 @@
+{
+ "FSharp.fsacRuntime":"netcore"
+}
\ No newline at end of file
diff --git a/workflows/Devcontainer/FSharpArcCapsule/Dockerfile b/workflows/Devcontainer/FSharpArcCapsule/Dockerfile
new file mode 100644
index 0000000..982b4cd
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule/Dockerfile
@@ -0,0 +1,10 @@
+#FROM rocker/r-ver:3.4.4
+FROM mcr.microsoft.com/dotnet/sdk:6.0
+#FROM r-base
+# Copy endpoint specific user settings into container to specify
+# .NET Core should be used as the runtime.
+COPY *.devcontainer/settings.vscode.json /root/.vscode-remote/data/Machine/settings.json
+
+# Install git, process tools
+RUN apt-get update && apt-get -y install git procps
+
diff --git a/workflows/Devcontainer/FSharpArcCapsule/script.fsx b/workflows/Devcontainer/FSharpArcCapsule/script.fsx
new file mode 100644
index 0000000..155693f
--- /dev/null
+++ b/workflows/Devcontainer/FSharpArcCapsule/script.fsx
@@ -0,0 +1,20 @@
+#r "nuget: FSharp.Data, 5.0.2"
+
+open FSharp.Data
+open System.IO
+
+printfn "%A" (System.IO.Directory.GetCurrentDirectory())
+
+let data =
+ CsvFile
+ .Load(Path.Combine(System.IO.Directory.GetCurrentDirectory(),"./arc/assays/measurement1/dataset/table.csv"))
+ .Cache()
+
+let r =
+ [
+ yield "Sum_1-2"
+ for row in data.Rows do
+ yield sprintf "%f" ((row.["value_1"].AsFloat()) + (row.["value_2"].AsFloat()))
+ ]
+
+System.IO.File.WriteAllLines("./arc/runs/fsResult1/result.csv",r)
\ No newline at end of file
diff --git a/workflows/FixedScript/FSharpArcCapsule.cwl b/workflows/FixedScript/FSharpArcCapsule.cwl
new file mode 100644
index 0000000..e70401e
--- /dev/null
+++ b/workflows/FixedScript/FSharpArcCapsule.cwl
@@ -0,0 +1,33 @@
+cwlVersion: v1.2
+class: CommandLineTool
+hints:
+ DockerRequirement:
+ dockerPull: mcr.microsoft.com/dotnet/sdk:6.0
+requirements:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entryname: script.fsx
+ entry:
+ $include: script.fsx
+ - class: EnvVarRequirement
+ envDef:
+ - envName: DOTNET_NOLOGO
+ envValue: "true"
+ - class: NetworkAccess
+ networkAccess: true
+baseCommand: [dotnet, fsi, script.fsx]
+inputs:
+ firstArg:
+ type: File
+ inputBinding:
+ position: 1
+ secondArg:
+ type: string
+ inputBinding:
+ position: 2
+
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "*.csv"
\ No newline at end of file
diff --git a/workflows/FixedScript/script.fsx b/workflows/FixedScript/script.fsx
new file mode 100644
index 0000000..581145d
--- /dev/null
+++ b/workflows/FixedScript/script.fsx
@@ -0,0 +1,22 @@
+#r "nuget: FSharp.Data, 5.0.2"
+
+open FSharp.Data
+open System.IO
+
+let args : string array = fsi.CommandLineArgs |> Array.tail
+let first = args.[0]
+let second = args.[1]
+
+let data =
+ CsvFile
+ .Load(first)
+ .Cache()
+
+let r =
+ [
+ yield "Sum_1-2"
+ for row in data.Rows do
+ yield sprintf "%f" ((row.["value_1"].AsFloat()) + (row.["value_2"].AsFloat()))
+ ]
+
+System.IO.File.WriteAllLines(second,r)
\ No newline at end of file
--
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