Mercurial > repos > goeckslab > ludwig_predict
annotate ludwig_experiment.py @ 2:afc8ed4a1838 draft default tip
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit 008bc5a8ee2c80f70fc224a23b5d2cd0c8ef1810
author | goeckslab |
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date | Fri, 14 Mar 2025 16:50:00 +0000 |
parents | b0627acfa4f4 |
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rev | line source |
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0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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changeset
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1 import json |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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2 import logging |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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changeset
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3 import os |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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4 import pickle |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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5 import sys |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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6 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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7 from ludwig.experiment import cli |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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changeset
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8 from ludwig.globals import ( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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9 DESCRIPTION_FILE_NAME, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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10 PREDICTIONS_PARQUET_FILE_NAME, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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11 TEST_STATISTICS_FILE_NAME, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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12 TRAIN_SET_METADATA_FILE_NAME |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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13 ) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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14 from ludwig.utils.data_utils import get_split_path |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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15 from ludwig.visualize import get_visualizations_registry |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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16 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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17 from model_unpickler import SafeUnpickler |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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18 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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19 import pandas as pd |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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20 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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21 from utils import ( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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changeset
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22 encode_image_to_base64, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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changeset
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23 get_html_closing, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
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24 get_html_template |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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25 ) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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26 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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27 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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28 logging.basicConfig(level=logging.DEBUG) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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29 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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30 LOG = logging.getLogger(__name__) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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31 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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32 setattr(pickle, 'Unpickler', SafeUnpickler) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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33 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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34 # visualization |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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35 output_directory = None |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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36 for ix, arg in enumerate(sys.argv): |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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37 if arg == "--output_directory": |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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38 output_directory = sys.argv[ix+1] |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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39 break |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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40 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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41 viz_output_directory = os.path.join(output_directory, "visualizations") |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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changeset
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42 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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43 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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44 def get_output_feature_name(experiment_dir, output_feature=0): |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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45 """Helper function to extract specified output feature name. |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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46 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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47 :param experiment_dir: Path to the experiment directory |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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48 :param output_feature: position of the output feature the description.json |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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49 :return output_feature_name: name of the first output feature name |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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50 from the experiment |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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51 """ |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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52 if os.path.exists(os.path.join(experiment_dir, DESCRIPTION_FILE_NAME)): |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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53 description_file = os.path.join(experiment_dir, DESCRIPTION_FILE_NAME) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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54 with open(description_file, "rb") as f: |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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55 content = json.load(f) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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56 output_feature_name = \ |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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57 content["config"]["output_features"][output_feature]["name"] |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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58 dataset_path = content["dataset"] |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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59 return output_feature_name, dataset_path |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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60 return None, None |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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61 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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62 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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63 def check_file(file_path): |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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64 """Check if the file exists; return None if it doesn't.""" |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
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65 return file_path if os.path.exists(file_path) else None |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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66 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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67 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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68 def make_visualizations(ludwig_output_directory_name): |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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69 ludwig_output_directory = os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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70 output_directory, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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71 ludwig_output_directory_name, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
diff
changeset
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72 ) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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73 visualizations = [ |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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74 "confidence_thresholding", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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75 "confidence_thresholding_data_vs_acc", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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76 "confidence_thresholding_data_vs_acc_subset", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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77 "confidence_thresholding_data_vs_acc_subset_per_class", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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78 "confidence_thresholding_2thresholds_2d", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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79 "confidence_thresholding_2thresholds_3d", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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80 "binary_threshold_vs_metric", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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81 "roc_curves", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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82 "roc_curves_from_test_statistics", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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83 "calibration_1_vs_all", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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84 "calibration_multiclass", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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85 "confusion_matrix", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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86 "frequency_vs_f1", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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87 "learning_curves", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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|
88 ] |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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|
89 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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|
90 # Check existence of required files |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
goeckslab
parents:
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|
91 training_statistics = check_file(os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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|
92 ludwig_output_directory, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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93 "training_statistics.json", |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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|
94 )) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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parents:
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|
95 test_statistics = check_file(os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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96 ludwig_output_directory, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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97 TEST_STATISTICS_FILE_NAME, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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|
98 )) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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99 ground_truth_metadata = check_file(os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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100 ludwig_output_directory, |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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101 "model", |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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102 TRAIN_SET_METADATA_FILE_NAME, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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103 )) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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104 probabilities = check_file(os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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105 ludwig_output_directory, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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106 PREDICTIONS_PARQUET_FILE_NAME, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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107 )) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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108 |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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109 output_feature, dataset_path = get_output_feature_name( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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110 ludwig_output_directory) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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111 ground_truth = None |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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112 split_file = None |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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113 if dataset_path: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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114 ground_truth = check_file(dataset_path) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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115 split_file = check_file(get_split_path(dataset_path)) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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116 |
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117 if (not output_feature) and (test_statistics): |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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118 test_stat = os.path.join(test_statistics) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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119 with open(test_stat, "rb") as f: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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120 content = json.load(f) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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121 output_feature = next(iter(content.keys())) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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122 |
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123 for viz in visualizations: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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124 viz_func = get_visualizations_registry()[viz] |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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125 try: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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126 viz_func( |
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127 training_statistics=[training_statistics] |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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128 if training_statistics else [], |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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129 test_statistics=[test_statistics] if test_statistics else [], |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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|
130 probabilities=[probabilities] if probabilities else [], |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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131 top_n_classes=[0], |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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132 output_feature_name=output_feature if output_feature else "", |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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133 ground_truth_split=2, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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134 top_k=3, |
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135 ground_truth_metadata=ground_truth_metadata, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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136 ground_truth=ground_truth, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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137 split_file=split_file, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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138 output_directory=viz_output_directory, |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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139 normalize=False, |
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140 file_format="png", |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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141 ) |
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142 except Exception as e: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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143 LOG.info(f"Visualization: {viz}") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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144 LOG.info(f"Error: {e}") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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145 |
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146 |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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147 def convert_parquet_to_csv(ludwig_output_directory_name): |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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148 """Convert the predictions Parquet file to CSV.""" |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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149 ludwig_output_directory = os.path.join( |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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150 output_directory, ludwig_output_directory_name) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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151 parquet_path = os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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152 ludwig_output_directory, "predictions.parquet") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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153 csv_path = os.path.join( |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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154 ludwig_output_directory, "predictions_parquet.csv") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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155 |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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156 try: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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157 df = pd.read_parquet(parquet_path) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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158 df.to_csv(csv_path, index=False) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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159 LOG.info(f"Converted Parquet to CSV: {csv_path}") |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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160 except Exception as e: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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161 LOG.error(f"Error converting Parquet to CSV: {e}") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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162 |
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163 |
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164 def generate_html_report(title, ludwig_output_directory_name): |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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165 # ludwig_output_directory = os.path.join( |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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166 # output_directory, ludwig_output_directory_name) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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167 |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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168 # test_statistics_html = "" |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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169 # # Read test statistics JSON and convert to HTML table |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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170 # try: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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171 # test_statistics_path = os.path.join( |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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172 # ludwig_output_directory, TEST_STATISTICS_FILE_NAME) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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173 # with open(test_statistics_path, "r") as f: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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174 # test_statistics = json.load(f) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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175 # test_statistics_html = "<h2>Test Statistics</h2>" |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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176 # test_statistics_html += json_to_html_table( |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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177 # test_statistics) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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178 # except Exception as e: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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179 # LOG.info(f"Error reading test statistics: {e}") |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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180 |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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181 # Convert visualizations to HTML |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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182 plots_html = "" |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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183 if len(os.listdir(viz_output_directory)) > 0: |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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184 plots_html = "<h2>Visualizations</h2>" |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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185 for plot_file in sorted(os.listdir(viz_output_directory)): |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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186 plot_path = os.path.join(viz_output_directory, plot_file) |
0a7b83ddda17
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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187 if os.path.isfile(plot_path) and plot_file.endswith((".png", ".jpg")): |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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188 encoded_image = encode_image_to_base64(plot_path) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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189 plots_html += ( |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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190 f'<div class="plot">' |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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191 f'<h3>{os.path.splitext(plot_file)[0]}</h3>' |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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192 '<img src="data:image/png;base64,' |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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193 f'{encoded_image}" alt="{plot_file}">' |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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194 f'</div>' |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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195 ) |
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196 |
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197 # Generate the full HTML content |
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198 html_content = f""" |
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199 {get_html_template()} |
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200 <h1>{title}</h1> |
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201 {plots_html} |
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202 {get_html_closing()} |
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203 """ |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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204 |
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205 # Save the HTML report |
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206 title: str |
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207 report_name = title.lower().replace(" ", "_") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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208 report_path = os.path.join(output_directory, f"{report_name}_report.html") |
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209 with open(report_path, "w") as report_file: |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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210 report_file.write(html_content) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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211 |
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212 LOG.info(f"HTML report generated at: {report_path}") |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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213 |
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214 |
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215 if __name__ == "__main__": |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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216 |
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217 cli(sys.argv[1:]) |
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218 |
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219 ludwig_output_directory_name = "experiment_run" |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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220 |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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221 make_visualizations(ludwig_output_directory_name) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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222 convert_parquet_to_csv(ludwig_output_directory_name) |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
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223 generate_html_report("Ludwig Experiment", ludwig_output_directory_name) |