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Merge pull request #45 from ethaaalpha/fix-examples
fix examples
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‎examples/tutorials/demo-vipgirder.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "e4b2f485-cb8b-4e4b-b21c-c381760fc914",
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"metadata": {},
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"outputs": [],
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"source": [
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"# for developement\n",
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"%load_ext autoreload\n",
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"%autoreload 2"
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]
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},
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{
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"cell_type": "markdown",
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"id": "096fc6eb",
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"metadata": {},
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"source": [
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"## Use VIP with a Girder server\n",
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"Before reading this tutorial we recommand you to see **demo-vipsession** to understand some basis. "
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]
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},
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{
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"cell_type": "markdown",
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"id": "eec57a9a",
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"metadata": {},
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"source": [
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"### Connection with VIP & Girder"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "f2b9532d",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Import the class\n",
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"from vip_client import VipGirder\n",
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"\n",
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"VipGirder.init(\n",
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" vip_key=\"VIP_API_KEY\",\n",
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" girder_key=\"GIRDER_API_KEY\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "8d4a4093",
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"metadata": {},
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"source": [
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"### Configuration variables & pipeline info"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "f72d24fb-f9f4-45b2-b7bc-0533216932ea",
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"metadata": {},
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"outputs": [],
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"source": [
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"# General configuration\n",
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"pipeline_id = \"CQUEST/0.6\"\n",
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"session_name = \"test_notebook_girder\"\n",
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"\n",
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"input_settings = {\n",
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" \"zipped_folder\": \"/collection/ReproVIPSpectro/data/quest/basis.zip\",\n",
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" \"data_file\": \"/collection/ReproVIPSpectro/data/quest/signals\",\n",
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" \"parameter_file\": \"/collection/ReproVIPSpectro/data/quest/parameters/quest_param_117T_B.txt\",\n",
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"}\n",
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"\n",
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"# N.B.: Here \"data_file\" leads to a folder, the other arguments lead to single files."
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]
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},
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{
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"cell_type": "markdown",
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"id": "d06461ab",
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"metadata": {},
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"source": [
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"In `input_settings`, the input files are pointed by Girder paths, usually in format: \"/collection/[collection_name]/[path_to_folder]\". \n",
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"- if the path leads to a file, the same file be passed to VIP;\n",
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"- If the path leads to a Girder item, all files in this item will be passed to VIP;\n",
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"- If the path leads to a Girder folder, all files in this folder will be passed to VIP."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "8bc5ad57",
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"metadata": {},
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"outputs": [],
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"source": [
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"VipGirder.show_pipeline(pipeline_id)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "a6df1cdd",
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"metadata": {},
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"source": [
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"### Choose output location"
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]
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},
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{
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"cell_type": "markdown",
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"id": "25704920",
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"metadata": {},
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"source": [
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"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!"
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]
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},
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{
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"cell_type": "markdown",
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"id": "97d7cf93-2ab0-4d07-81b2-654b38480f9a",
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"metadata": {},
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"source": [
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"##### Output on **girder** (default)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "cdaa53b9-eaec-44d7-a342-7b41191fcb4a",
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"metadata": {},
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"outputs": [],
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"source": [
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"output_dir=\"/collection/ReproVIPSpectro/test/vip_outputs\"\n",
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"\n",
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"session = VipGirder(\n",
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" session_name=session_name, \n",
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" pipeline_id=pipeline_id, \n",
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" input_settings=input_settings, \n",
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" output_dir=output_dir)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "1aec7d5d-05e1-4baf-af30-2e9b42e791f1",
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"metadata": {},
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"source": [
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"##### Output on **VIP**"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "25da2f62-e044-4ffd-855f-74881ad5d770",
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"metadata": {},
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"outputs": [],
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"source": [
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"session = VipGirder(\n",
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" session_name=session_name, \n",
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" pipeline_id=pipeline_id, \n",
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" input_settings=input_settings, \n",
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" output_location=\"vip\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "7c726378-93b0-443d-9531-89b42735142d",
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"metadata": {},
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"source": [
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"##### Output on **local computer**"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "bff17ffe-bebc-419d-b68d-ed3b0d2f4cf7",
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"metadata": {},
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"outputs": [],
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"source": [
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"session = VipGirder(\n",
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" session_name=session_name, \n",
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" pipeline_id=pipeline_id, \n",
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" input_settings=input_settings, \n",
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" output_location=\"local\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "2339ec14",
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"metadata": {},
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"source": [
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"### Run & Result"
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]
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},
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{
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"cell_type": "markdown",
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"id": "4286c3df",
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"metadata": {},
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"source": [
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"Then, you can run the pipeline as usual!"
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]
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},
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{
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"cell_type": "markdown",
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"id": "ef1ec6d7",
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"metadata": {},
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"source": [
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"##### Workflow running"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d47ee6da-1178-4646-b9f6-a71711dcac01",
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"metadata": {},
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"outputs": [],
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"source": [
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"session.launch_pipeline()\n",
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"session.monitor_workflows()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "73066fe4",
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"metadata": {},
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"source": [
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"##### Downloading & Cleaning"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "81f8dc9e-22ab-4603-ae3b-28d83f0a2615",
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"metadata": {},
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"outputs": [],
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"source": [
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"session.download_outputs()\n",
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"session.finish()"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.13.3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎examples/tutorials/demo-vipsession.ipynb‎

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"metadata": {},
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"outputs": [],
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"source": [
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"my_session.upload_inputs(input_dir);"
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"my_session.upload_inputs(input_dir)"
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]
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},
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{
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"outputs": [],
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"source": [
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"# Pipeline identifier = App/Version (/!\\ mind the case)\n",
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"pipeline_id = \"CQUEST/0.2-egi\""
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"pipeline_id = \"CQUEST/0.6\""
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]
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},
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"cell_type": "code",
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"execution_count": null,
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"outputs": [],
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": ".venv",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.8"
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"version": "3.11.12"
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},
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"orig_nbformat": 4,
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"vscode": {
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"interpreter": {
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"hash": "e7370f93d1d0cde622a1f8e1c04877d8463912d04d973331ad4851f04de6915a"
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}
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}
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"orig_nbformat": 4
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},
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"nbformat": 4,
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"nbformat_minor": 2

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