Mercurial > repos > bgruening > create_tool_recommendation_model

annotate extract_workflow_connections.py @ 6:e94dc7945639 draft default tip

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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 Extract workflow paths from the tabular file containing
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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3 input and output tools
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 random
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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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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7 import utils
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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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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9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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10 class ExtractWorkflowConnections:
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11
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12 def __init__(self):
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13 """ Init method. """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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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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15 def process_raw_files(self, wf_path, tool_popu_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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16 """
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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17 Remove pipe from workflows and popularity tabular files
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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18 """
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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19 print("Removing pipe from tabular datasets...")
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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20 wf_frame = utils.remove_pipe(wf_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 tool_popu_frame = utils.remove_pipe(tool_popu_path)
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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22 return wf_frame, tool_popu_frame
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23
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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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24 def read_tabular_file(self, 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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25 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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26 Read tabular file and extract workflow connections
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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27 """
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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28 print("Reading workflows...")
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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29 workflows = {}
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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30 workflow_paths_dup = ""
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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31 workflow_parents = dict()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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32 workflow_paths = list()
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5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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33 unique_paths = dict()
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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34 standard_connections = dict()
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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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35 for index, row in wf_dataframe.iterrows():
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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36 row = row.tolist()
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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37 row = [str(item).strip() for item in row]
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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38 wf_id = str(row[0])
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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39 if row[1] > config["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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40 in_tool = row[3]
e94dc7945639 planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 24bab7a797f53fe4bcc668b18ee0326625486164
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41 out_tool = row[6]
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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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42 if wf_id not in workflows:
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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43 workflows[wf_id] = list()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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44 if out_tool and in_tool and out_tool != in_tool:
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45 workflows[wf_id].append((out_tool, in_tool))
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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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46 qc = self.__collect_standard_connections(row)
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5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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47 if qc:
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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48 i_t = utils.format_tool_id(in_tool)
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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49 o_t = utils.format_tool_id(out_tool)
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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50 if i_t not in standard_connections:
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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51 standard_connections[i_t] = list()
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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52 if o_t not in standard_connections[i_t]:
5b3c08710e47 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
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53 standard_connections[i_t].append(o_t)
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54 print("Processing workflows...")
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55 wf_ctr = 0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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56 for wf_id in workflows:
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57 wf_ctr += 1
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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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58 workflow_parents[wf_id] = self.__read_workflow(wf_id, workflows[wf_id])
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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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60 for wf_id in workflow_parents:
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61 flow_paths = list()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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62 parents_graph = workflow_parents[wf_id]
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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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63 roots, leaves = self.__get_roots_leaves(parents_graph)
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64 for root in roots:
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65 for leaf in leaves:
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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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66 paths = self.__find_tool_paths_workflow(parents_graph, root, leaf)
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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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67 # reverse the paths as they are computed from leaves to roots leaf
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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68 paths = [tool_path for tool_path in paths]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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69 if len(paths) > 0:
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70 flow_paths.extend(paths)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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71 workflow_paths.extend(flow_paths)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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72 print("Workflows processed: %d" % wf_ctr)
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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74 # remove slashes from the tool ids
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75 wf_paths_no_slash = list()
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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76 for path in workflow_paths:
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77 path_no_slash = [utils.format_tool_id(tool_id) for tool_id in path]
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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78 wf_paths_no_slash.append(path_no_slash)
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80 # collect duplicate paths
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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81 for path in wf_paths_no_slash:
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82 workflow_paths_dup += ",".join(path) + "\n"
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84 # collect unique paths
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85 unique_paths = list(workflow_paths_dup.split("\n"))
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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86 unique_paths = list(filter(None, unique_paths))
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87 random.shuffle(unique_paths)
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88 print("unique_paths: {}".format(len(unique_paths)))
0
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89 no_dup_paths = list(set(unique_paths))
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90 print("no_dup_paths: {}".format(len(no_dup_paths)))
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91 return no_dup_paths, standard_connections
0
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92
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93 def __collect_standard_connections(self, row):
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94 published = row[8].strip()
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95 deleted = row[9].strip()
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96 has_errors = row[10].strip()
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97 if published == "t" and deleted == "f" and has_errors == "f":
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98 return True
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99 return False
0
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100
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101 def __set_compatible_next_tools(self, workflow_paths):
0
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102 """
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103 Find next tools for each tool
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104 """
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105 next_tools = dict()
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106 for path in workflow_paths:
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107 path_split = path.split(",")
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108 for window in range(0, len(path_split) - 1):
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109 current_next_tools = path_split[window: window + 2]
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110 current_tool = current_next_tools[0]
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111 next_tool = current_next_tools[1]
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112 try:
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113 next_tools[current_tool] += "," + next_tool
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114 except Exception:
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115 next_tools[current_tool] = next_tool
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116 for tool in next_tools:
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117 next_tools[tool] = ",".join(list(set(next_tools[tool].split(","))))
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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118 return next_tools
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119
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120 def __read_workflow(self, wf_id, workflow_rows):
0
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121 """
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122 Read all connections for a workflow
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123 """
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124 tool_parents = dict()
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125 for connection in workflow_rows:
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126 in_tool = connection[0]
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127 out_tool = connection[1]
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128 if out_tool not in tool_parents:
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129 tool_parents[out_tool] = list()
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130 if in_tool not in tool_parents[out_tool]:
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131 tool_parents[out_tool].append(in_tool)
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132 return tool_parents
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133
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134 def __get_roots_leaves(self, graph):
0
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135 roots = list()
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136 leaves = list()
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137 all_parents = list()
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138 for item in graph:
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139 all_parents.extend(graph[item])
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140 all_parents = list(set(all_parents))
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141 children = graph.keys()
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142 roots = list(set(all_parents).difference(set(children)))
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143 leaves = list(set(children).difference(set(all_parents)))
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144 return roots, leaves
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145
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146 def __find_tool_paths_workflow(self, graph, start, end, path=[]):
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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147 path = path + [end]
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148 if start == end:
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149 return [path]
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150 path_list = list()
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151 if end in graph:
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152 for node in graph[end]:
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153 if node not in path:
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154 new_tools_paths = self.__find_tool_paths_workflow(graph, start, node, path)
0
9bf25dbe00ad "planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit 7fac577189d01cedd01118a77fc2baaefe7d5cad"
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155 for tool_path in new_tools_paths:
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156 path_list.append(tool_path)
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157 return path_list