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Merged
axlbonnet merged 4 commits into from
Jun 11, 2025
Merged

fix examples #45

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40325d6
fix download outputs from vip
ethaaalpha May 19, 2025
52037ea
update & fix tutorials
ethaaalpha May 19, 2025
b988566
fix _exists and empty dir condition
ethaaalpha Jun 11, 2025
2391226
correction tests
axlbonnet Jun 11, 2025
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256 changes: 256 additions & 0 deletions examples/tutorials/demo-vipgirder.ipynb
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Open in desktop
Original file line number Diff line number Diff line change
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{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "e4b2f485-cb8b-4e4b-b21c-c381760fc914",
"metadata": {},
"outputs": [],
"source": [
"# for developement\n",
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "markdown",
"id": "096fc6eb",
"metadata": {},
"source": [
"## Use VIP with a Girder server\n",
"Before reading this tutorial we recommand you to see **demo-vipsession** to understand some basis. "
]
},
{
"cell_type": "markdown",
"id": "eec57a9a",
"metadata": {},
"source": [
"### Connection with VIP & Girder"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f2b9532d",
"metadata": {},
"outputs": [],
"source": [
"# Import the class\n",
"from vip_client import VipGirder\n",
"\n",
"VipGirder.init(\n",
" vip_key=\"VIP_API_KEY\",\n",
" girder_key=\"GIRDER_API_KEY\")"
]
},
{
"cell_type": "markdown",
"id": "8d4a4093",
"metadata": {},
"source": [
"### Configuration variables & pipeline info"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f72d24fb-f9f4-45b2-b7bc-0533216932ea",
"metadata": {},
"outputs": [],
"source": [
"# General configuration\n",
"pipeline_id = \"CQUEST/0.6\"\n",
"session_name = \"test_notebook_girder\"\n",
"\n",
"input_settings = {\n",
" \"zipped_folder\": \"/collection/ReproVIPSpectro/data/quest/basis.zip\",\n",
" \"data_file\": \"/collection/ReproVIPSpectro/data/quest/signals\",\n",
" \"parameter_file\": \"/collection/ReproVIPSpectro/data/quest/parameters/quest_param_117T_B.txt\",\n",
"}\n",
"\n",
"# N.B.: Here \"data_file\" leads to a folder, the other arguments lead to single files."
]
},
{
"cell_type": "markdown",
"id": "d06461ab",
"metadata": {},
"source": [
"In `input_settings`, the input files are pointed by Girder paths, usually in format: \"/collection/[collection_name]/[path_to_folder]\". \n",
"- if the path leads to a file, the same file be passed to VIP;\n",
"- If the path leads to a Girder item, all files in this item will be passed to VIP;\n",
"- If the path leads to a Girder folder, all files in this folder will be passed to VIP."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8bc5ad57",
"metadata": {},
"outputs": [],
"source": [
"VipGirder.show_pipeline(pipeline_id)"
]
},
{
"cell_type": "markdown",
"id": "a6df1cdd",
"metadata": {},
"source": [
"### Choose output location"
]
},
{
"cell_type": "markdown",
"id": "25704920",
"metadata": {},
"source": [
"When using girder, you can choose where the outputs will be located. For this tutorial run the cell corresponding to the location that you want!"
]
},
{
"cell_type": "markdown",
"id": "97d7cf93-2ab0-4d07-81b2-654b38480f9a",
"metadata": {},
"source": [
"##### Output on **girder** (default)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "cdaa53b9-eaec-44d7-a342-7b41191fcb4a",
"metadata": {},
"outputs": [],
"source": [
"output_dir=\"/collection/ReproVIPSpectro/test/vip_outputs\"\n",
"\n",
"session = VipGirder(\n",
" session_name=session_name, \n",
" pipeline_id=pipeline_id, \n",
" input_settings=input_settings, \n",
" output_dir=output_dir)"
]
},
{
"cell_type": "markdown",
"id": "1aec7d5d-05e1-4baf-af30-2e9b42e791f1",
"metadata": {},
"source": [
"##### Output on **VIP**"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "25da2f62-e044-4ffd-855f-74881ad5d770",
"metadata": {},
"outputs": [],
"source": [
"session = VipGirder(\n",
" session_name=session_name, \n",
" pipeline_id=pipeline_id, \n",
" input_settings=input_settings, \n",
" output_location=\"vip\")"
]
},
{
"cell_type": "markdown",
"id": "7c726378-93b0-443d-9531-89b42735142d",
"metadata": {},
"source": [
"##### Output on **local computer**"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "bff17ffe-bebc-419d-b68d-ed3b0d2f4cf7",
"metadata": {},
"outputs": [],
"source": [
"session = VipGirder(\n",
" session_name=session_name, \n",
" pipeline_id=pipeline_id, \n",
" input_settings=input_settings, \n",
" output_location=\"local\")"
]
},
{
"cell_type": "markdown",
"id": "2339ec14",
"metadata": {},
"source": [
"### Run & Result"
]
},
{
"cell_type": "markdown",
"id": "4286c3df",
"metadata": {},
"source": [
"Then, you can run the pipeline as usual!"
]
},
{
"cell_type": "markdown",
"id": "ef1ec6d7",
"metadata": {},
"source": [
"##### Workflow running"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d47ee6da-1178-4646-b9f6-a71711dcac01",
"metadata": {},
"outputs": [],
"source": [
"session.launch_pipeline()\n",
"session.monitor_workflows()"
]
},
{
"cell_type": "markdown",
"id": "73066fe4",
"metadata": {},
"source": [
"##### Downloading & Cleaning"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "81f8dc9e-22ab-4603-ae3b-28d83f0a2615",
"metadata": {},
"outputs": [],
"source": [
"session.download_outputs()\n",
"session.finish()"
]
}
],
"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": "3.13.3"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
17 changes: 6 additions & 11 deletions examples/tutorials/demo-vipsession.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@
"metadata": {},
"outputs": [],
"source": [
"my_session.upload_inputs(input_dir);"
"my_session.upload_inputs(input_dir)"
]
},
{
Expand Down Expand Up @@ -169,7 +169,7 @@
"outputs": [],
"source": [
"# Pipeline identifier = App/Version (/!\\ mind the case)\n",
"pipeline_id = \"CQUEST/0.2-egi\""
"pipeline_id = \"CQUEST/0.6\""
]
},
{
Expand Down Expand Up @@ -595,7 +595,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -605,7 +605,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": ".venv",
"language": "python",
"name": "python3"
},
Expand All @@ -619,14 +619,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.8"
"version": "3.11.12"
},
"orig_nbformat": 4,
"vscode": {
"interpreter": {
"hash": "e7370f93d1d0cde622a1f8e1c04877d8463912d04d973331ad4851f04de6915a"
}
}
"orig_nbformat": 4
},
"nbformat": 4,
"nbformat_minor": 2
Expand Down
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