Mercurial > repos > iuc > data_manager_fetch_plasmidfinder

annotate data_manager/plasmidfinder_fetch_database.py @ 0:cc7bbfc5fd16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
author iuc
date Thu, 15 Jun 2023 09:13:55 +0000
parents
children bcd29b6662c2
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cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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1 import argparse
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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2 import json
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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3 import os
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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4 import time
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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5 from pathlib import Path
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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6
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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8 import git
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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9
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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11 class GetPlasmidfinderDataManager:
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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12 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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13 Create the json file with database information for galaxy data manager
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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14 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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15
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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16 def __init__(self,
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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17 plasmidfinder_database="plasmidfinder_database",
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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18 db_name="plasmidfinder_database",
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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19 plasmidfinder_version="latest"):
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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20 self.data_table_name = plasmidfinder_database
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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21 self._db_name = db_name
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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22 self._plasmidfinder_version = plasmidfinder_version
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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23 self._plasmidfinder_date_version = None
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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24 self.data_table_entry = None
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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25 self.plasmidfinder_table_list = None
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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26 self._commit_number = None
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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27
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iuc
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28 def get_data_table_format(self):
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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29 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
iuc
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30 Skeleton of a data_table format
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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31 return: a data table formatted for json output
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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32 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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33 self.data_table_entry = {
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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34 "data_tables": {
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35 self.data_table_name: {}
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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36 }
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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37 }
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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38 return self.data_table_entry
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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39
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40 def get_data_manager(self):
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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41 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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42 Create the empty data table format and add all the information into
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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43 Commit number is added if latest is required instead of version number
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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44 return: The data table with database information
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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45 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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46 self.plasmidfinder_table_list = self.get_data_table_format()
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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47 if self._plasmidfinder_version == "latest":
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48 version_value = self._commit_number
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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49 else:
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50 version_value = self._plasmidfinder_version
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51 plasmidfinder_value = f"plasmidfinder_{self._commit_number}" \
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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52 f"_{self._plasmidfinder_date_version}"
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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53 plasmidfinder_name = f"{version_value}" \
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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54 f"_{self._plasmidfinder_date_version}"
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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55 data_info = dict(value=plasmidfinder_value,
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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56 name=plasmidfinder_name,
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57 date=self._plasmidfinder_date_version,
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58 path=self._db_name)
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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59 self.plasmidfinder_table_list["data_tables"][self.data_table_name] = [data_info]
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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60 return self.plasmidfinder_table_list
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61
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62
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63 class DownloadPlasmidfinderDatabase(GetPlasmidfinderDataManager):
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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64 """
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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65 Download the plasmidfinder database from the bitbucket repository.
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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66 Build the data manager info for galaxy
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67 """
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68
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69 def __init__(self,
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70 output_dir=Path.cwd(),
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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71 plasmidfinder_url="https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master",
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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72 db_name="plasmidfinder_database",
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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73 db_tmp="tmp_database",
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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74 plasmidfinder_version="latest",
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75 json_file_path=None,
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76 date_version=None):
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77
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78 super().__init__()
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79 self.json_file_path = json_file_path
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80 self._output_dir = output_dir
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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81 self._plasmidfinder_url = plasmidfinder_url
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82 self._temporary_folder = db_tmp
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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83 self._db_name = db_name
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84 self._db_name_tar = f'{db_name}.gz'
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85 self._plasmidfinder_version = plasmidfinder_version
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86 self._plasmidfinder_date_version = date_version
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87 self._commit_number = None
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88
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89 def git_clone(self):
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90 git.Repo.clone_from(url=self._plasmidfinder_url, to_path=self._output_dir)
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91 self._plasmidfinder_repository = git.Repo(path=self._output_dir)
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92
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93 def get_commit_number(self):
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94 sha = self._plasmidfinder_repository.head.commit.hexsha
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95 short_sha = self._plasmidfinder_repository.git.rev_parse(sha, short=7)
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96 self._commit_number = short_sha
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97
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98 def get_commit_date(self):
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99 self._plasmidfinder_date_version = time.strftime("%Y_%m_%d", time.gmtime(self._plasmidfinder_repository.head.commit.committed_date))
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100
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101 def download_database(self):
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102 """
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103 Download the plasmidfinder database using git lib
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104 Extract commit and commit date
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105 """
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106 self._output_dir = Path(self._output_dir)
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107 self.git_clone()
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108 if self._plasmidfinder_version != "latest":
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109 self._plasmidfinder_repository.git.checkout(self._plasmidfinder_version)
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110 self.get_commit_number()
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111 self.get_commit_date()
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112
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113 def read_json_input_file(self):
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114 """
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115 Import the json file
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116 """
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117 with open(self.json_file_path) as fh:
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118 params = json.load(fh)
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119 target_dir = params['output_data'][0]['extra_files_path']
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120 os.makedirs(target_dir)
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121 self._output_dir = target_dir
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122
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123 def write_json_infos(self):
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124 """
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125 Write in the imported json file
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126 """
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127 with open(self.json_file_path, 'w') as fh:
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128 json.dump(self.get_data_manager(), fh, sort_keys=True)
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129
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130
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131 def parse_arguments():
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132 """
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133 List of arguments provided by the user
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134 return: parsed arguments
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135 """
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136 # parse options and arguments
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137 arg_parser = argparse.ArgumentParser()
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138 arg_parser.add_argument("data_manager_json",
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139 help="json file from galaxy")
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140 arg_parser.add_argument("-v", "--db_version",
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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141 help="version of the plasmidfinder (latest or 2.1)")
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142 return arg_parser.parse_args()
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143
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144
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145 def main():
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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146 all_args = parse_arguments()
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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147 plasmidfinder_download = DownloadPlasmidfinderDatabase(json_file_path=all_args.data_manager_json, plasmidfinder_version=all_args.db_version)
cc7bbfc5fd16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit f6d40bf94e015c2690e97c4b3533517b812f3bfb
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148 plasmidfinder_download.read_json_input_file()
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149 plasmidfinder_download.download_database()
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150 plasmidfinder_download.write_json_infos()
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151
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152
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153 if __name__ == '__main__':
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154 main()