Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

annotate data_manager/plasmidfinder_fetch_database.py @ 0:8ad77a9dc91d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
author pimarin
date Tue, 14 Feb 2023 14:25:43 +0000
parents
children 9ef108e34063
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8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
diff changeset
1 import argparse
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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2 import json
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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3 import os
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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4 import tarfile
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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5 from datetime import datetime
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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6 from pathlib import Path
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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7
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pimarin
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8 import requests
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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9
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10
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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11 class GetPlasmidfinderDataManager:
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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12 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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13 Create the json file with database information for galaxy data manager
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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14 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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15
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pimarin
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16 def __init__(self,
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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17 plasmidfinder_database="plasmidfinder_database",
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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18 db_name="plasmidfinder-db",
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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19 plasmidfinder_version="latest"):
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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20 self.data_table_name = plasmidfinder_database
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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21 self._db_name = db_name
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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22 self._plasmidfinder_version = plasmidfinder_version
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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23 self._plasmidfinder_date_version = None
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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24 self.data_table_entry = None
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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25 self.plasmidfinder_table_list = None
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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26 self._commit_number = None
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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27
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pimarin
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28 def get_data_table_format(self):
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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29 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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30 Skeleton of a data_table format
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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31 return: a data table formatted for json output
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pimarin
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32 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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33 self.data_table_entry = {
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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34 "data_tables": {
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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35 self.data_table_name: {}
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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36 }
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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37 }
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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38 return self.data_table_entry
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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39
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pimarin
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40 def get_data_manager(self):
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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41 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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42 Create the empty data table format and add all the information into
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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43 Commit number is added if latest is required instead of version number
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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44 return: The data table with database information
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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45 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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46 self.plasmidfinder_table_list = self.get_data_table_format()
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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47 if self._plasmidfinder_version == "latest":
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pimarin
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48 version_value = self._commit_number
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pimarin
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49 else:
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pimarin
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50 version_value = self._plasmidfinder_version
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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51 plasmidfinder_value = f"plasmidfinder_{self._commit_number}" \
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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52 f"_{self._plasmidfinder_date_version}"
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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53 plasmidfinder_name = f"{version_value}" \
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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54 f"_{self._plasmidfinder_date_version}"
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pimarin
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55 data_info = dict(value=plasmidfinder_value,
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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56 name=plasmidfinder_name,
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pimarin
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57 date=self._plasmidfinder_date_version,
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pimarin
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58 path=self._db_name)
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pimarin
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59 self.plasmidfinder_table_list["data_tables"][self.data_table_name] = [data_info]
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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60 return self.plasmidfinder_table_list
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61
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62
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pimarin
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63 class DownloadPlasmidfinderDatabase(GetPlasmidfinderDataManager):
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64 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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65 Download the plasmidfinder database from the bitbucket repository.
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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66 Build the data manager info for galaxy
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pimarin
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67 """
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68
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pimarin
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69 def __init__(self,
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70 output_dir=Path.cwd(),
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pimarin
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71 plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/get/",
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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72 db_name="plasmidfinder-db",
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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73 db_tmp="tmp_database",
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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74 plasmidfinder_version="latest",
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pimarin
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75 json_file_path=None,
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pimarin
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76 date_version=datetime.now().strftime("%Y-%m-%d")):
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77
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78 super().__init__()
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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79 self.json_file_path = json_file_path
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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80 self._output_dir = output_dir
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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81 self._plasmidfinder_url = plasmidfinder_url
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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82 self._temporary_folder = db_tmp
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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83 self._db_name = db_name
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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84 self._db_name_tar = f'{db_name}.gz'
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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85 self._plasmidfinder_version = plasmidfinder_version
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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86 self._plasmidfinder_date_version = date_version
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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87 self._commit_number = None
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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88
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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89 def extract_db_commit(self, request_header, title_name="content-disposition"):
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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90 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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91 Extract the commit if to add the information as identifier of the download
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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92 @request_header: a request object obtained from requests.get()
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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93 @title_name: the tag to search in the header of the requests object
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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94 return: the value of the commit
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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95 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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96 db_info = request_header.headers[title_name]
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97 commit_number = db_info.split("-")[2].split(".")[0]
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98 return commit_number
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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99
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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100 def untar_files(self, file_path: Path, extracted_path_output: Path):
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101 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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102 untar the download archive
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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103 @file_path: input path of the tar.gz file
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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104 @extracted_path_output: output path of the extract folder
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105 return: the path of the output
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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106 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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107 try:
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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parents:
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108 with file_path.open('rb') as fh_in, \
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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109 tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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110 tar_file.extractall(path=extracted_path_output)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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111 print(f'Untar the database in {extracted_path_output}')
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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112 return extracted_path_output
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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parents:
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113 except OSError:
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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114 os.sys.exit(f'ERROR: Could not extract {file_path}')
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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115
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116 def choose_db_version(self):
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pimarin
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117 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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118 Update the url link depending on the version choosen by user.
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119 This method could be upgraded simply by adding the new versions
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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120 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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121 if self._plasmidfinder_version == "latest":
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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122 self._plasmidfinder_url = f"{self._plasmidfinder_url}master.gz"
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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123 elif self._plasmidfinder_version == "2.1":
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124 self._plasmidfinder_url = f"{self._plasmidfinder_url}1307168.gz"
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125
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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126 def download_database(self):
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127 """
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pimarin
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128 Download the plasmidfinder database using requests lib
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129 Make the directory and temporary directory for download
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130 Untar the download files
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pimarin
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131 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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132 self._output_dir = Path(self._output_dir)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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133 self.choose_db_version()
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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134 try:
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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135 request_info = requests.get(self._plasmidfinder_url)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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136 request_info.raise_for_status()
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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137 self._commit_number = self.extract_db_commit(request_info)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
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138 output_tar_path = self._output_dir.joinpath(self._temporary_folder)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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139 output_tar_path_file = output_tar_path.joinpath(self._db_name_tar)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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140 output_path = self._output_dir.joinpath(self._db_name)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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141 os.makedirs(output_tar_path)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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142 os.makedirs(output_path)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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143 with open(output_tar_path_file, 'wb') as output_dir:
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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144 output_dir.write(request_info.content)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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145 untar_output = self.untar_files(file_path=output_tar_path_file, extracted_path_output=output_tar_path.joinpath(self._db_name))
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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146
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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parents:
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147 self.moove_download_files(older_path=untar_output, new_path=output_path)
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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148 except requests.exceptions.HTTPError as http_error:
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149 print(f"Requests Error: {http_error}")
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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parents:
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150 print(f"Fail to import Plasmidfinder database from {self._plasmidfinder_url}")
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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151
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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parents:
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152 def moove_download_files(self, older_path, new_path, expression_search="*fsa"):
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
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153 """
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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154 Clean downloaded data by mooving fasta files in the final folder
8ad77a9dc91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f3383fdb9a17d1b69d05547cdb96534a5f762bec-dirty
pimarin
parents:
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155 @older_path: previous path where the files are located
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156 @new_path: final path where files will be mooved
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157 @expression_search: keep only file with this expression
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158 """
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159 fasta_files = Path(older_path).rglob(expression_search)
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160 file_list_paths = [file for file in fasta_files if file.is_file()]
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161 [self.keep_filename(pathname=path, output_path=new_path) for path in file_list_paths]
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162
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163 def keep_filename(self, pathname, output_path):
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164 """
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165 Moove files
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166 @pathname: previous path
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167 @output_path: final path
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168 """
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169 Path.replace(pathname, output_path.joinpath(pathname.name))
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170
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171 def read_json_input_file(self):
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172 """
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173 Import the json file
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174 """
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175 with open(self.json_file_path) as fh:
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176 params = json.load(fh)
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177 target_dir = params['output_data'][0]['extra_files_path']
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178 os.makedirs(target_dir)
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179 self._output_dir = target_dir
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180
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181 def write_json_infos(self):
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182 """
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183 Write in the imported json file
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184 """
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185 with open(self.json_file_path, 'w') as fh:
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186 json.dump(self.get_data_manager(), fh, sort_keys=True)
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187
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188
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189 def parse_arguments():
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190 """
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191 List of arguments provided by the user
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192 return: parsed arguments
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193 """
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194 # parse options and arguments
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195 arg_parser = argparse.ArgumentParser()
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196 arg_parser.add_argument("data_manager_json",
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197 help="json file from galaxy")
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198 arg_parser.add_argument("-v", "--db_version",
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199 help="version of the plasmidfinder (latest or 2.1)")
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200 return arg_parser.parse_args()
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201
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202
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203 def main():
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204 all_args = parse_arguments()
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205 plasmidfinder_download = DownloadPlasmidfinderDatabase(json_file_path=all_args.data_manager_json, plasmidfinder_version=all_args.db_version)
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206 plasmidfinder_download.read_json_input_file()
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207 plasmidfinder_download.download_database()
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208 plasmidfinder_download.write_json_infos()
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209
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210
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211 if __name__ == '__main__':
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212 main()