From 9ed717773534b26d37e9eb9ea6869272a8d92700 Mon Sep 17 00:00:00 2001
From: Daniel Loos <dloos@bgc-jena.mpg.de>
Date: Wed, 4 Dec 2024 15:38:08 +0100
Subject: [PATCH] Add ogc-app-cwl

---
 ogc-app-cwl/Dockerfile  |  4 +++
 ogc-app-cwl/example.cwl | 74 +++++++++++++++++++++++++++++++++++++++++
 ogc-app-cwl/run.jl      |  1 +
 ogc-app-cwl/run.sh      |  5 +++
 4 files changed, 84 insertions(+)
 create mode 100644 ogc-app-cwl/Dockerfile
 create mode 100644 ogc-app-cwl/example.cwl
 create mode 100755 ogc-app-cwl/run.jl
 create mode 100755 ogc-app-cwl/run.sh

diff --git a/ogc-app-cwl/Dockerfile b/ogc-app-cwl/Dockerfile
new file mode 100644
index 0000000..7eb4e55
--- /dev/null
+++ b/ogc-app-cwl/Dockerfile
@@ -0,0 +1,4 @@
+FROM julia:1.10
+WORKDIR /work
+ADD run.jl ./
+ENTRYPOINT ["/work/run.jl"]
diff --git a/ogc-app-cwl/example.cwl b/ogc-app-cwl/example.cwl
new file mode 100644
index 0000000..d260085
--- /dev/null
+++ b/ogc-app-cwl/example.cwl
@@ -0,0 +1,74 @@
+#!/usr/bin/env cwl-runner
+
+$graph:
+- class: Workflow
+  label: add numbers
+  doc: Example workflow adding two numbers in Julia
+
+  inputs:
+    a:
+      label: a
+      doc: The first summand
+      type: double
+    b:
+      label: b
+      doc: The second summand
+      type: double
+
+  outputs:
+    c:
+      doc: the sum of the two numbers
+      type: double
+      outputSource: add/c
+
+  steps:
+    add:
+      in:
+        a: a
+        b: b
+      run: '#cmd-add'
+      out:
+      - c
+  id: add-numbers
+- class: CommandLineTool
+
+  requirements:
+    DockerRequirement:
+      dockerPull: danlooo/cwl-example:latest
+    InlineJavascriptRequirement: {}
+
+  inputs:
+    a:
+      type: double
+      inputBinding:
+        position: 1
+    b:
+      type: double
+      inputBinding:
+        position: 2
+
+  outputs:
+    c:
+      type: double
+      outputBinding:
+        glob: stdout.txt
+        outputEval: $(parseFloat(self[0].contents))
+        loadContents: true
+  stdout: stdout.txt
+  id: cmd-add
+$namespaces:
+  edam: http://edamontology.org/
+  s: https://schema.org/
+$schemas:
+- https://schema.org/version/latest/schemaorg-current-https.rdf
+- http://edamontology.org/EDAM_1.18.owl
+cwlVersion: v1.2
+s:author:
+- class: s:Person
+  s:email: fairsendd@bgc-jena.mpg.de
+  s:identifier: https://orcid.org/0000-0002-4024-4443
+  s:name: Daniel Loos
+s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
+s:codeRepository: https://github.com/EarthyScience/FAIRSenDD/
+s:dateCreated: '2024-10-28'
+s:license: https://spdx.org/licenses/Apache-2.0
diff --git a/ogc-app-cwl/run.jl b/ogc-app-cwl/run.jl
new file mode 100755
index 0000000..717042f
--- /dev/null
+++ b/ogc-app-cwl/run.jl
@@ -0,0 +1 @@
+#! /usr/bin/env julia
\ No newline at end of file
diff --git a/ogc-app-cwl/run.sh b/ogc-app-cwl/run.sh
new file mode 100755
index 0000000..27d19f5
--- /dev/null
+++ b/ogc-app-cwl/run.sh
@@ -0,0 +1,5 @@
+#! /usr/bin/env sh
+
+docker build . -t danlooo/cwl-example
+docker push danlooo/cwl-example
+cwltool example.cwl#add-numbers -a 1.2 -b 3.4
\ No newline at end of file