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planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
author bgruening
date Sun, 16 Oct 2022 11:52:10 +0000
parents 4f7e6612906b
children
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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1 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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2 Predict next tools in the Galaxy workflows
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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3 using deep learning learning (Transformers)
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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4 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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5 import argparse
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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6 import time
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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8 import extract_workflow_connections
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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9 import prepare_data
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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10 import train_transformer
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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12 if __name__ == "__main__":
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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13 start_time = time.time()
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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15 arg_parser = argparse.ArgumentParser()
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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16 arg_parser.add_argument("-wf", "--workflow_file", required=True, help="workflows tabular file")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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17 arg_parser.add_argument("-tu", "--tool_usage_file", required=True, help="tool usage file")
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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18 # data parameters
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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19 arg_parser.add_argument("-cd", "--cutoff_date", required=True, help="earliest date for taking tool usage")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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20 arg_parser.add_argument("-pl", "--maximum_path_length", required=True, help="maximum length of tool path")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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21 arg_parser.add_argument("-om", "--output_model", required=True, help="trained model path")
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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22 # neural network parameters
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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23 arg_parser.add_argument("-ti", "--n_train_iter", required=True, help="Number of training iterations run to create model")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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24 arg_parser.add_argument("-nhd", "--n_heads", required=True, help="Number of head in transformer's multi-head attention")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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25 arg_parser.add_argument("-ed", "--n_embed_dim", required=True, help="Embedding dimension")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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26 arg_parser.add_argument("-fd", "--n_feed_forward_dim", required=True, help="Feed forward network dimension")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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27 arg_parser.add_argument("-dt", "--dropout", required=True, help="Percentage of neurons to be dropped")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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28 arg_parser.add_argument("-lr", "--learning_rate", required=True, help="Learning rate")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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29 arg_parser.add_argument("-ts", "--te_share", required=True, help="Share of data to be used for testing")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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30 arg_parser.add_argument("-trbs", "--tr_batch_size", required=True, help="Train batch size")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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31 arg_parser.add_argument("-trlg", "--tr_logging_step", required=True, help="Train logging frequency")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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32 arg_parser.add_argument("-telg", "--te_logging_step", required=True, help="Test logging frequency")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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33 arg_parser.add_argument("-tebs", "--te_batch_size", required=True, help="Test batch size")
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34
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35 # get argument values
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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36 args = vars(arg_parser.parse_args())
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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37 tool_usage_path = args["tool_usage_file"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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38 workflows_path = args["workflow_file"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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39 cutoff_date = args["cutoff_date"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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40 maximum_path_length = int(args["maximum_path_length"])
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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42 n_train_iter = int(args["n_train_iter"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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43 te_share = float(args["te_share"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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44 tr_batch_size = int(args["tr_batch_size"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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45 te_batch_size = int(args["te_batch_size"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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47 n_heads = int(args["n_heads"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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48 feed_forward_dim = int(args["n_feed_forward_dim"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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49 embedding_dim = int(args["n_embed_dim"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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50 dropout = float(args["dropout"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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51 learning_rate = float(args["learning_rate"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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52 te_logging_step = int(args["te_logging_step"])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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53 tr_logging_step = int(args["tr_logging_step"])
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54 trained_model_path = args["output_model"]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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56 config = {
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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57 'cutoff_date': cutoff_date,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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58 'maximum_path_length': maximum_path_length,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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59 'n_train_iter': n_train_iter,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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60 'n_heads': n_heads,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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61 'feed_forward_dim': feed_forward_dim,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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62 'embedding_dim': embedding_dim,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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63 'dropout': dropout,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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64 'learning_rate': learning_rate,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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65 'te_share': te_share,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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66 'te_logging_step': te_logging_step,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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67 'tr_logging_step': tr_logging_step,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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68 'tr_batch_size': tr_batch_size,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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69 'te_batch_size': te_batch_size,
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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70 'trained_model_path': trained_model_path
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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71 }
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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72 print("Preprocessing workflows...")
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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73 # Extract and process workflows
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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74 connections = extract_workflow_connections.ExtractWorkflowConnections()
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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75 # Process raw workflow file
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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76 wf_dataframe, usage_df = connections.process_raw_files(workflows_path, tool_usage_path, config)
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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77 workflow_paths, pub_conn = connections.read_tabular_file(wf_dataframe, config)
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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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78 # Process the paths from workflows
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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79 print("Dividing data...")
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e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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80 data = prepare_data.PrepareData(maximum_path_length, te_share)
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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parents: 5
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81 train_data, train_labels, test_data, test_labels, f_dict, r_dict, c_wts, c_tools, tr_tool_freq = data.get_data_labels_matrices(workflow_paths, usage_df, cutoff_date, pub_conn)
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
bgruening
parents: 5
diff changeset
82 print(train_data.shape, train_labels.shape, test_data.shape, test_labels.shape)
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
bgruening
parents: 5
diff changeset
83 train_transformer.create_enc_transformer(train_data, train_labels, test_data, test_labels, f_dict, r_dict, c_wts, c_tools, pub_conn, tr_tool_freq, config)
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
84 end_time = time.time()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
bgruening
parents:
diff changeset
85 print("Program finished in %s seconds" % str(end_time - start_time))