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annotate wine_quality.py @ 3:f542f29a920c draft default tip

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit 293e7a2e4cc40479ce83dca0168d17b314f9b607
author siwaa
date Mon, 09 Dec 2024 11:26:35 +0000
parents 143b15001522
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143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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1 #!/usr/bin/env python
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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2 # coding: utf-8
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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3
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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4 ######### ######### ######### ######### ######### ######### #########
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5 #
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6 # File created from fidlemore/model_wine_lightning/wine_quality_predict.py
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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7 #
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8 # Modifications :
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9 #
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10 # - restore sanitized text for -data value
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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11 #
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12 # - quality.txt file containing only quality value (extracted from report)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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13 #
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14 ######### ######### ######### ######### ######### ######### #########
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15
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16 ###############################################################################
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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17 # Module : model_wine_lightning
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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18 #
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19 # This code has been extracted from 01-DNN-Wine-Regression-lightning.ipynb
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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20 # (fidle-tp/fidle-master-3.0.11/Wine.Lightning) then modified.
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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21 # Only last part kept :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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22 # - Restore saved model from checkpoint
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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23 # - Evaluate the model not kept
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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24 # - Make some predictions 1 prediction
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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25 #
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26 # Inputs :
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27 #
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28 # Data of wine for which quality is going to be predicted is given
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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29 # by -data_json_filepath or by -data (only one of both).
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30 #
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31 # -data_json_filepath : data file path (.json) containing data.
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32 # -data : data (string format)
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33 #
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34 # Example of wine data : { "fixed acidity": 11.2,
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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35 # "volatile acidity": 0.28,
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36 # "citric acid": 0.56,
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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37 # "residual sugar": 1.9,
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38 # "chlorides": 0.075,
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39 # "free sulfur dioxide": 17,
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40 # "total sulfur dioxide": 60,
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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41 # "density": 0.998,
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42 # "pH": 3.16,
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43 # "sulphates": 0.58,
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44 # "alcohol": 9.8 }
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45 #
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46 # -model_ckpt_filepath : checkpoint model file path (.ckpt) to be loaded.
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47 #
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48 # -norm_config_json_filepath : normalization configuration file (.json)
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49 # containing information (norm_config) that has been returned by the model
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50 # wine_quality_train_eval running.
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51 #
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52 # Outputs :
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53 #
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54 # Output files under "OUTPUTS" folder (must exist !!!)
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55 #
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56 # - Quality prediction value (float)
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57 #
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58 # - Report file (report_json_filepath) (.json) containing:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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59 # - Quality prediction value
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60 # - Wine data
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61 # - error message, more message, warning message
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62 #
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63 # - Log files into Wine.Lightning/run/LWINE1/logs/reg_logs
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64 #
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65 # - Screen display containing running information
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66 #
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67 ###############################################################################
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68
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69 # <img width="800px" src="../fidle/img/header.svg"></img>
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70 #
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71 # # <!-- TITLE --> [LWINE1] - Wine quality prediction with a Dense Network (DNN)
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72 # <!-- DESC --> Another example of regression, with a wine quality prediction, using PyTorch Lightning
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73 # <!-- AUTHOR : Achille Mbogol Touye (EFFILIA-MIAI/SIMaP) -->
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74 #
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75 # ## Objectives :
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76 # - Predict the **quality of wines**, based on their analysis
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77 # - Understanding the principle and the architecture of a regression with a dense neural network with backup and restore of the trained model.
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78 #
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79 # The **[Wine Quality datasets](https://archive.ics.uci.edu/ml/datasets/wine+Quality)** are made up of analyses of a large number of wines, with an associated quality (between 0 and 10)
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80 # This dataset is provide by :
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81 # Paulo Cortez, University of Minho, Guimarães, Portugal, http://www3.dsi.uminho.pt/pcortez
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82 # A. Cerdeira, F. Almeida, T. Matos and J. Reis, Viticulture Commission of the Vinho Verde Region(CVRVV), Porto, Portugal, @2009
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83 # This dataset can be retreive at [University of California Irvine (UCI)](https://archive-beta.ics.uci.edu/ml/datasets/wine+quality)
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84 #
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85 #
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86 # Due to privacy and logistic issues, only physicochemical and sensory variables are available
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87 # There is no data about grape types, wine brand, wine selling price, etc.
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88 #
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89 # - fixed acidity
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90 # - volatile acidity
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91 # - citric acid
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92 # - residual sugar
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93 # - chlorides
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94 # - free sulfur dioxide
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95 # - total sulfur dioxide
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96 # - density
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97 # - pH
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98 # - sulphates
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99 # - alcohol
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100 # - quality (score between 0 and 10)
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101 #
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102 # ## What we're going to do :
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103 #
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104 # - (Retrieve data)
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105 # - (Preparing the data)
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106 # - (Build a model)
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107 # - Train and save the model
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108 # - Restore saved model
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109 # - Evaluate the model
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110 # - Make some predictions
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111 #
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112 HEAD = "[wine_quality/wine_quality]"
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113
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114 # ## Step 1 - Import and init
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115 print("\n"+HEAD,"# ## Step 1 - Import and init\n")
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116
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117 # Import some packages
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118 import os
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119 import pandas as pd
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120 import torch
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121 import torchvision.transforms as T
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122 from model_wine_lightning.modules.data_load import NormalizeFeatures
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123 from model_wine_lightning.modules.data_load import ToTensorFeatures
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124 from model_wine_lightning.modules.model import LitRegression
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125 import fidle
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126 import json
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127 import argparse
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128 from pprint import pprint
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129
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130 OUTPUTS_PATH = "OUTPUTS" # must exit !!!
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131
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132 error_msg, warn_msg, more_msg = "", "", "" # default
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133
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134 report_json_filepath = os.path.join(OUTPUTS_PATH, "report.json")
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135 quality_txt_filepath = os.path.join(OUTPUTS_PATH, "quality.txt")
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136 report = dict() # init
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137 pred = 99.99 # default
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138
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139 data_json_filepath, data = None, None
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140 model_ckpt_filepath = None
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141 norm_config_json_filepath, norm_config = None, None
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142
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143 try:
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144 def is_not_given(argument):
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145 return ((argument is None) or (argument == 'None'))
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146 def is_given(argument):
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147 return ((argument is not None) and (argument != 'None'))
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148
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149 if not os.path.exists(OUTPUTS_PATH): # cas isfile non traite
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150 os.mkdir(OUTPUTS_PATH)
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151 message = "Outputs folder '"+OUTPUTS_PATH+" does not exist => created."
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152 warn_msg += message + " "
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153 print(HEAD, "Warning :", message)
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154
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155 if not os.path.isdir(OUTPUTS_PATH):
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156 message = "Outputs folder '" + OUTPUTS_PATH + "' must exist."
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157 error_msg += message + " "
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158 raise Exception(message)
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159
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160 # ## INPUTS
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parents:
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161 print("\n"+HEAD, "# ## INPUTS\n")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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162
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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163 desc_text = "Predict Quality of a Wine"
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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164 parser = argparse.ArgumentParser(prog='wine_quality_predict',
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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165 description=desc_text)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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166
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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167 help_required_keys = "\"fixed acidity\";\"volatile acidity\";\"citric acid\";\"residual sugar\";\"chlorides\";\"free sulfur dioxide\";\"total sulfur dioxide\";\"density\";\"pH\";\"sulphates\";\"alcohol\""
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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168 help_text = "data file path (.json), required keys:"+help_required_keys
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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169 parser.add_argument("-data_json_filepath", type=str, help=help_text)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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170 help_text = "data in string format, required keys:"+help_required_keys
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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171 parser.add_argument("-data", type=str, help=help_text)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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172
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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173 help_text = "checkpoint model file path (.ckpt)"
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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174 parser.add_argument("-model_ckpt_filepath", type=str, help=help_text)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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175
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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176 help_text = "normalization configuration file path (.json), "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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177 help_text += "information returned by wine_quality_train_eval runnig."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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178 parser.add_argument("-norm_config_json_filepath", type=str, help=help_text)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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179
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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180 args = parser.parse_args()
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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181 # 1 and only 1 among -data_json_filepath and -data
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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182 if is_given(args.data_json_filepath) and is_given(args.data):
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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183 message = "Both -data_json_filepath and -data given "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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184 message += "(1 and only 1 of -data_json_filepath and -data expected) "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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185 message += "=> STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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186 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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187 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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188 if is_not_given(args.data_json_filepath) and is_not_given(args.data):
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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189 message = "NO data_json_filepath and NO -data given. "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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190 message += "(1 and only 1 of -data_json_filepath and -data expected) "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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191 message += "=> STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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192 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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193 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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194
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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195 path = args.data_json_filepath
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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196 if is_given(path) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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197 if os.path.isfile(path) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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198 data_json_filepath = path
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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199 print(HEAD, "data_json_filepath used :", data_json_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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200 try :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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201 inputfile = open(data_json_filepath, 'r')
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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202 data = json.load(inputfile)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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203 except:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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204 message = "Failed to get json data from "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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205 message += "'" + data_json_filepath+ "'" + " file."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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206 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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207 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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208 else :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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209 message = path+ "data_json_filepath file not found => STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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210 error_msg += message + ""
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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211 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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212
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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213 if is_given(args.data) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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214 data_text = args.data
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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215 try :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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216
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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217 # restore sanitized text
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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218 MAPPING = {'>': '__gt__', '<': '__lt__', "'": '__sq__', '"': '__dq__', '[': '__ob__', ']': '__cb__', '{': '__oc__', '}': '__cc__', '@': '__at__', '\n': '__cn__', '\r': '__cr__', '\t': '__tc__', '#': '__pd__'}
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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219 for key, value in MAPPING.items():
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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220 data_text = data_text.replace(value, key)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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221 data = json.loads(data_text) # get data
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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222
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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223 except:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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224 message = "Failed to get json data from string '"+data_text+"'"
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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225 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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226 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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227
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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228 path = args.model_ckpt_filepath
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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229 if is_given(path) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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230 if os.path.isfile(path) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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231 model_ckpt_filepath = path
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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232 print(HEAD, "model_ckpt_filepath used :", model_ckpt_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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233 else :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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234 message = path+ "model_ckpt_filepath file not found => STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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235 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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236 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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237 else:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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238 message = "NO model_ckpt_filepath given => STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
239 error_msg += message + ""
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
240 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
241
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
siwaa
parents:
diff changeset
242 path = args.norm_config_json_filepath
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
243 if is_given(path) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
244 if os.path.isfile(path) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
245 norm_config_json_filepath = path
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
246 print(HEAD, "norm_config_json_filepath used :",
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
247 norm_config_json_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
siwaa
parents:
diff changeset
248 try :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
249 inputfile = open(norm_config_json_filepath, 'r')
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
250 norm_config = json.load(inputfile)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
siwaa
parents:
diff changeset
251 except:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
252 message = "Failed to get json norm_config from "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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253 message += "'" + norm_config_json_filepath+ "'" + "file."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
254 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
255 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
256 else :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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257 message = path+ "norm_config_json_filepath file not found => STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
258 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
259 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
260 else:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
261 message = "NO norm_config_json_filepath given => STOP."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
262 error_msg += message + ""
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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263 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
264
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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265 print(HEAD, "INPUTS:")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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266 print("- data:", data)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
267 print("- model checkpoint:", model_ckpt_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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268 print("- norm_config:", norm_config)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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269
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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270 # Init Fidle environment
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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271 print("\n"+HEAD, "# Init Fidle environment\n")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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272 run_id, run_dir, datasets_dir = fidle.init('LWINE1_predict')
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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273
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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274 # Verbosity during training :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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275 # - 0 = silent
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
276 # - 1 = progress bar
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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277 # - 2 = one line per epoch
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
278 fit_verbosity = 1
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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279
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
280 # Override parameters (batch mode) - Just forget this cell
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
281 fidle.override('fit_verbosity')
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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282
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
283 # ## Step 7 - Restore model :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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284 print("\n"+HEAD, "# ## Step 7 - Restore model :\n")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
285
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
286 # ### 7.1 - Reload model
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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287 print("\n"+HEAD, "# ### 7.1 - Reload model\n")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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diff changeset
288 loaded_model = LitRegression.load_from_checkpoint(model_ckpt_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
289 print(HEAD, "Model loaded from checkpoint: ", model_ckpt_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
290 print("Loaded:", loaded_model)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
291
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
292 ## ### 7.2 - Evaluate model : Not kept
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
293
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
294 # ### 7.3 - Make a prediction
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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295 print("\n"+HEAD, "# ### 7.3 - Make a prediction\n")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
296
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
297 mean_json = norm_config['mean_json']
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
298 std_json = norm_config['std_json']
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
299 min_json = norm_config['min_json']
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
300 max_json = norm_config['max_json']
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
301 print(HEAD, "Use Normalization mean: ", mean_json)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
302 print(HEAD, "Use Normalization std: ", std_json)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
303 print(HEAD, "Use Normalization min: ", min_json)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
304 print(HEAD, "Use Normalization max: ", max_json)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
305 NF = NormalizeFeatures(mean_json, std_json, min_json, max_json)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
306 if not NF.is_in_domain(data):
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
307 message = "data values out of domain => no prediction."
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
308 error_msg += message + " "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
309 raise Exception(message)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
310 features = NF.get_features(data)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
311 transform = T.Compose([NF, ToTensorFeatures()])
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
312 sample = transform(features)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
313
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
314 # Sets the model in evaluation mode
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
315 loaded_model.eval()
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
316
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
317 # Perform inference using the loaded model
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
318 y_pred = loaded_model(sample)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
diff changeset
319 pred = y_pred[0][0].item()
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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parents:
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320 print(HEAD, ":")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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321 print("Quality prediction :", f'{pred:.2f}', " , for wine data:")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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322 pprint(data)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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323
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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324 # ## OUTPUTS
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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325 print("\n"+HEAD, "# ## OUTPUTS\n")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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326
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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327 # Report (json) :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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328 # - quality prediction value
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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329 # - wine data
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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330 # - error message, more message, warning message
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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331 report["quality"] = pred
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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332 report["data"] = data
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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333 report["model_ckpt_filepath"] = model_ckpt_filepath
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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334 report["norm_config"] = norm_config
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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335
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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336 fidle.end()
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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337
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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338 except Exception as e :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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339 error_msg += type(e).__name__ + str(e.args) + ". "
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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340
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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341 if error_msg != "": report["error"] = error_msg
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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342 if more_msg != "": report["more"] = more_msg
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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343 if warn_msg != "": report["warning"] = warn_msg
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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344
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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345 print("OUTPUT:", "Quality prediction :", pred)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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346
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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347 print("OUTPUT:", "Report: ")
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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348 pprint(report)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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349
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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350 ## Save Report as .json file
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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351 #try:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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352 # with open(report_json_filepath, "w") as outfile:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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353 # json.dump(report, outfile)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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354 # print("OUTPUT:", "Report file (containing report) :", report_json_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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355 #except :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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356 # pass
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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357
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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358 # Save quality alone into .txt file
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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359 try:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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360 with open(quality_txt_filepath, "w") as outfile:
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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361 outfile.write(str(pred))
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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362 print("OUTPUT:", "Quality file (containing quality value) :",
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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363 quality_txt_filepath)
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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364 except :
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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365 pass
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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366
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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367 # ---
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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368 # <img width="80px" src="../fidle/img/logo-paysage.svg"></img>
143b15001522 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit e7c4e447552083db7eaecbdf139a7c359fe9becc
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369