test

.github/actions/action.yml

@@ -47,11 +47,15 @@ runs:
         username: ${{ github.repository_owner }}
         password: ${{ github.token }}
 
-    # - name: Generate OGC application package process CWL
-    #   run: python3 ${{ github.action_path }}/generate_app_pack.py ${{ inputs.algorithm-config-path }} ${{ env.REPO_NAME }}:${{ env.BRANCH }}
-    #   shell: bash
-    #   env:
-    #     GITHUB_ACTION_PATH: ${{ github.action_path }}
+    - name: Generate OGC application package process CWL
+      run: python3 ${{ github.action_path }}/generate_app_pack.py nasa/algorithm_config.yml process.cwl ${{ github.action_path }}/templates/process.cwl
+      shell: bash
+      env:
+        GITHUB_ACTION_PATH: ${{ github.action_path }}
+
+    - name: List
+      run: ls -la
+      shell: bash
 
     # - name: Extract metadata (tags, labels) for Docker
     #   id: meta

.github/actions/generate_app_pack.py

@@ -0,0 +1,54 @@
+import yaml
+import json
+import argparse
+
+def yaml_to_cwl(yaml_file, cwl_file, template_file):
+    with open(yaml_file, 'r') as f:
+        config = yaml.safe_load(f)
+
+    with open(template_file, 'r') as f:
+        workflow = yaml.safe_load(f)
+
+    workflow["$graph"][0]["label"] = config["algorithm_name"]
+    workflow["$graph"][0]["doc"] = config["algorithm_description"]
+    workflow["$graph"][0]["id"] = config["algorithm_name"]
+    workflow["$graph"][1]["requirements"]["DockerRequirement"]["dockerPull"] = config["algorithm_name"]
+    workflow["$graph"][1]["baseCommand"] = "/app/" + config["algorithm_name"] + "/" + config["run_command"]
+
+    workflow_inputs = workflow["$graph"][0]["inputs"]
+    process_inputs = workflow["$graph"][1]["inputs"]
+    step_inputs = workflow["$graph"][0]["steps"]["process"]["in"]
+
+    for param in config.get("inputs", {}).get("positional", []):
+        input_name = param["name"]
+        input_type = "Directory" if param.get("type", True) else "string"
+
+        workflow_inputs[input_name] = {
+            "doc": param["description"],
+            "label": param["description"],
+            "type": input_type
+        }
+
+        process_inputs[input_name] = {
+            "type": input_type,
+            "inputBinding": {
+                "position": len(process_inputs) + 1,
+                "prefix": f"--{input_name}"
+            }
+        }
+
+        step_inputs[input_name] = input_name
+
+    with open(cwl_file, 'w') as f:
+        yaml.dump(workflow, f, default_flow_style=False, sort_keys=False)
+
+    print(f"CWL workflow saved to {cwl_file}")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Convert YAML config to CWL workflow.")
+    parser.add_argument("yaml_file", help="Path to the input algorithm YAML configuration file.")
+    parser.add_argument("cwl_file", help="Path to the output CWL workflow file.")
+    parser.add_argument("template_file", help="Path to the CWL template file.")
+
+    args = parser.parse_args()
+    yaml_to_cwl(args.yaml_file, args.cwl_file, args.template_file)

.github/actions/templates/process.cwl

@@ -0,0 +1,42 @@
+cwlVersion: v1.2
+$graph:
+  - class: Workflow
+    label: ""
+    doc: ""
+    id: ""
+    inputs: {}
+    outputs:
+      out:
+        type: Directory
+        outputSource: process/outputs_result
+    steps:
+      process:
+        run: "#process"
+        in: {}
+        out:
+          - outputs_result
+
+  - class: CommandLineTool
+    id: process
+    requirements:
+      DockerRequirement:
+        dockerPull: ""
+      NetworkAccess:
+        networkAccess: true
+      EnvVarRequirement:
+        envDef:
+          PATH: "/opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+    baseCommand: ""
+    arguments: []
+    inputs: {}
+    outputs:
+      outputs_result:
+        outputBinding:
+          glob: ./output*
+        type: Directory
+
+$namespaces:
+  s: https://schema.org/
+s:softwareVersion: 1.0.0
+schemas:
+- http://schema.org/version/9.0/schemaorg-current-http.rdf