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cwl.load_workflow_json -> cwl.pwd_to_cwl #103

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136 changes: 94 additions & 42 deletions example_workflows/arithmetic/cwl.ipynb
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Original file line number Diff line number Diff line change
@@ -1,97 +1,149 @@
{
"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",
"execution_count": 1,
"id": "377fef56-484d-491c-b19e-1be6931e44eb",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 1
"source": [
"import pickle"
]
},
{
"id": "92e3921b-2bb8-4333-8cfe-4bd27f785d24",
"cell_type": "code",
"source": "from python_workflow_definition.cwl import load_workflow_json",
"execution_count": null,
"id": "92e3921b-2bb8-4333-8cfe-4bd27f785d24",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 2
"source": [
"from python_workflow_definition.cwl import pwd_to_cwl"
]
},
{
"id": "5303c059-8ae4-4557-858e-b4bd64eac711",
"cell_type": "code",
"source": "load_workflow_json(file_name=\"workflow.json\")",
"execution_count": null,
"id": "5303c059-8ae4-4557-858e-b4bd64eac711",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": 3
"source": [
"pwd_to_cwl(file_name=\"workflow.json\")"
]
},
{
"id": "df302bd2-e9b6-4595-979c-67c46414d986",
"cell_type": "code",
"source": "! cwltool workflow.cwl workflow.yml",
"execution_count": 4,
"id": "df302bd2-e9b6-4595-979c-67c46414d986",
"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$3dfd802cefb317cc7138af1e3a299f565c74ddec\",\n \"size\": 21,\n \"path\": \"/home/jovyan/example_workflows/arithmetic/result.pickle\"\n }\n}\u001B[1;30mINFO\u001B[0m Final process status is success\n"
"text": [
"/srv/conda/envs/notebook/bin/cwltool:11: DeprecationWarning: Nesting argument groups is deprecated.\n",
" sys.exit(run())\n",
"\u001b[1;30mINFO\u001b[0m /srv/conda/envs/notebook/bin/cwltool 3.1.20250110105449\n",
"\u001b[1;30mINFO\u001b[0m Resolved 'workflow.cwl' to 'file:///home/jovyan/example_workflows/arithmetic/workflow.cwl'\n",
"\u001b[1;30mINFO\u001b[0m [workflow ] start\n",
"\u001b[1;30mINFO\u001b[0m [workflow ] starting step get_prod_and_div_0\n",
"\u001b[1;30mINFO\u001b[0m [step get_prod_and_div_0] start\n",
"\u001b[1;30mINFO\u001b[0m [job get_prod_and_div_0] /tmp/hig0p5dd$ 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
"source": [
"! cwltool workflow.cwl workflow.yml"
]
},
{
"id": "2942dbba-ea0a-4d20-be5c-ed9992d09ff8",
"cell_type": "code",
"source": "with open(\"result.pickle\", \"rb\") as f:\n print(pickle.load(f))",
"execution_count": 5,
"id": "2942dbba-ea0a-4d20-be5c-ed9992d09ff8",
"metadata": {
"trusted": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": "2.5\n"
"text": [
"2.5\n"
]
}
],
"execution_count": 5
"source": [
"with open(\"result.pickle\", \"rb\") as f:\n",
" print(pickle.load(f))"
]
},
{
"id": "60e909ee-d0d0-4bd1-81c8-dd5274ae5834",
"cell_type": "code",
"source": "",
"execution_count": null,
"id": "60e909ee-d0d0-4bd1-81c8-dd5274ae5834",
"metadata": {
"trusted": true
},
"outputs": [],
"execution_count": null
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.8"
}
]
},
"nbformat": 4,
"nbformat_minor": 5
}
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