Move CWL functionality to init

example_workflows/arithmetic/cwl.ipynb

@@ -1 +1,97 @@
-{"metadata":{"kernelspec":{"display_name":"Python 3 (ipykernel)","language":"python","name":"python3"},"language_info":{"name":"python","version":"3.12.8","mimetype":"text/x-python","codemirror_mode":{"name":"ipython","version":3},"pygments_lexer":"ipython3","nbconvert_exporter":"python","file_extension":".py"}},"nbformat_minor":5,"nbformat":4,"cells":[{"id":"377fef56-484d-491c-b19e-1be6931e44eb","cell_type":"code","source":"import pickle","metadata":{"trusted":true},"outputs":[],"execution_count":1},{"id":"92e3921b-2bb8-4333-8cfe-4bd27f785d24","cell_type":"code","source":"from python_workflow_definition.cwl.export import load_workflow_json","metadata":{"trusted":true},"outputs":[],"execution_count":2},{"id":"5303c059-8ae4-4557-858e-b4bd64eac711","cell_type":"code","source":"load_workflow_json(file_name=\"workflow.json\")","metadata":{"trusted":true},"outputs":[],"execution_count":3},{"id":"df302bd2-e9b6-4595-979c-67c46414d986","cell_type":"code","source":"! cwltool workflow.cwl workflow.yml","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n  sys.exit(run())\n\u001b[1;30mINFO\u001b[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001b[1;30mINFO\u001b[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001b[1;30mINFO\u001b[0m [workflow ] start\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step get_prod_and_div_0\n\u001b[1;30mINFO\u001b[0m [step get_prod_and_div_0] start\n\u001b[1;30mINFO\u001b[0m [job get_prod_and_div_0] /tmp/hig0p5dd$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/0xeme5n4/stgba321752-0a06-41dd-95c0-f5890f1dfaae/workflow.py \\\n    --function=workflow.get_prod_and_div \\\n    --arg_y=/tmp/0xeme5n4/stg9f21530f-2f98-44e6-80b6-afa2aac5a083/y.pickle \\\n    --arg_x=/tmp/0xeme5n4/stg2e35a78a-a776-48de-b82f-8075d3284a3c/x.pickle\n\u001b[1;30mINFO\u001b[0m [job get_prod_and_div_0] completed success\n\u001b[1;30mINFO\u001b[0m [step get_prod_and_div_0] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] starting step get_sum_1\n\u001b[1;30mINFO\u001b[0m [step get_sum_1] start\n\u001b[1;30mINFO\u001b[0m [job get_sum_1] /tmp/u07nctrs$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/sa53wz5h/stg686b1324-0030-4bfd-bdab-64fc9ee4d491/workflow.py \\\n    --function=workflow.get_sum \\\n    --arg_y=/tmp/sa53wz5h/stg1679a702-ac89-4c84-8cb5-7a57ae9e1834/div.pickle \\\n    --arg_x=/tmp/sa53wz5h/stg6ab588fe-2723-416e-a7b8-648b1a63406e/prod.pickle\n\u001b[1;30mINFO\u001b[0m [job get_sum_1] completed success\n\u001b[1;30mINFO\u001b[0m [step get_sum_1] completed success\n\u001b[1;30mINFO\u001b[0m [workflow ] completed success\n{\n    \"result_file\": {\n        \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n        \"basename\": \"result.pickle\",\n        \"class\": \"File\",\n        \"checksum\": \"sha1$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n        \"size\": 21,\n        \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n    }\n}\u001b[1;30mINFO\u001b[0m Final process status is success\n"}],"execution_count":4},{"id":"2942dbba-ea0a-4d20-be5c-ed9992d09ff8","cell_type":"code","source":"with open(\"result.pickle\", \"rb\") as f:\n    print(pickle.load(f))","metadata":{"trusted":true},"outputs":[{"name":"stdout","output_type":"stream","text":"2.5\n"}],"execution_count":5},{"id":"60e909ee-d0d0-4bd1-81c8-dd5274ae5834","cell_type":"code","source":"","metadata":{"trusted":true},"outputs":[],"execution_count":null}]}
+{
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.12.8",
+   "mimetype": "text/x-python",
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "pygments_lexer": "ipython3",
+   "nbconvert_exporter": "python",
+   "file_extension": ".py"
+  }
+ },
+ "nbformat_minor": 5,
+ "nbformat": 4,
+ "cells": [
+  {
+   "id": "377fef56-484d-491c-b19e-1be6931e44eb",
+   "cell_type": "code",
+   "source": "import pickle",
+   "metadata": {
+    "trusted": true
+   },
+   "outputs": [],
+   "execution_count": 1
+  },
+  {
+   "id": "92e3921b-2bb8-4333-8cfe-4bd27f785d24",
+   "cell_type": "code",
+   "source": "from python_workflow_definition.cwl import load_workflow_json",
+   "metadata": {
+    "trusted": true
+   },
+   "outputs": [],
+   "execution_count": 2
+  },
+  {
+   "id": "5303c059-8ae4-4557-858e-b4bd64eac711",
+   "cell_type": "code",
+   "source": "load_workflow_json(file_name=\"workflow.json\")",
+   "metadata": {
+    "trusted": true
+   },
+   "outputs": [],
+   "execution_count": 3
+  },
+  {
+   "id": "df302bd2-e9b6-4595-979c-67c46414d986",
+   "cell_type": "code",
+   "source": "! cwltool workflow.cwl workflow.yml",
+   "metadata": {
+    "trusted": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": "/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n  sys.exit(run())\n\u001B[1;30mINFO\u001B[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n\u001B[1;30mINFO\u001B[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n\u001B[1;30mINFO\u001B[0m [workflow ] start\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_prod_and_div_0\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] start\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] /tmp/hig0p5dd$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/0xeme5n4/stgba321752-0a06-41dd-95c0-f5890f1dfaae/workflow.py \\\n    --function=workflow.get_prod_and_div \\\n    --arg_y=/tmp/0xeme5n4/stg9f21530f-2f98-44e6-80b6-afa2aac5a083/y.pickle \\\n    --arg_x=/tmp/0xeme5n4/stg2e35a78a-a776-48de-b82f-8075d3284a3c/x.pickle\n\u001B[1;30mINFO\u001B[0m [job get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [step get_prod_and_div_0] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] starting step get_sum_1\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] start\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] /tmp/u07nctrs$ python \\\n    -m \\\n    python_workflow_definition.cwl \\\n    --workflowfile=/tmp/sa53wz5h/stg686b1324-0030-4bfd-bdab-64fc9ee4d491/workflow.py \\\n    --function=workflow.get_sum \\\n    --arg_y=/tmp/sa53wz5h/stg1679a702-ac89-4c84-8cb5-7a57ae9e1834/div.pickle \\\n    --arg_x=/tmp/sa53wz5h/stg6ab588fe-2723-416e-a7b8-648b1a63406e/prod.pickle\n\u001B[1;30mINFO\u001B[0m [job get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [step get_sum_1] completed success\n\u001B[1;30mINFO\u001B[0m [workflow ] completed success\n{\n    \"result_file\": {\n        \"location\": \"file:///home/jovyan/example_workflows/arithmetic/result.pickle\",\n        \"basename\": \"result.pickle\",\n        \"class\": \"File\",\n        \"checksum\": \"sha1$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n        \"size\": 21,\n        \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n    }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n"
+    }
+   ],
+   "execution_count": 4
+  },
+  {
+   "id": "2942dbba-ea0a-4d20-be5c-ed9992d09ff8",
+   "cell_type": "code",
+   "source": "with open(\"result.pickle\", \"rb\") as f:\n    print(pickle.load(f))",
+   "metadata": {
+    "trusted": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": "2.5\n"
+    }
+   ],
+   "execution_count": 5
+  },
+  {
+   "id": "60e909ee-d0d0-4bd1-81c8-dd5274ae5834",
+   "cell_type": "code",
+   "source": "",
+   "metadata": {
+    "trusted": true
+   },
+   "outputs": [],
+   "execution_count": null
+  }
+ ]
+}