Mercurial > repos > pimarin > amrfinderplus_data_manager

annotate data_manager/amrfinderplus_data_manager.py @ 0:4974dd6207d6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
author pimarin
date Mon, 14 Nov 2022 14:53:21 +0000
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4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
parents:
diff changeset
1 import argparse
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
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2 import json
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
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3 import os
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
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4 import re
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
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5 import subprocess as sp
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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6
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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7 from datetime import datetime
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
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8 from pathlib import Path
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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9
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10
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pimarin
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11 class GetDataManager:
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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12
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13 def __init__(self):
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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14 self.data_table_name = "amrfinderplus_database"
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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15 self._db_name = "amrfinderplus-db"
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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16 self._db_path = Path().absolute()
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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17 self._today = datetime.now().strftime("%Y-%m-%d_%H:%M")
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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18
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19 def get_data_table_format(self):
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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20 """
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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21 Skeleton of a data_table format
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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22 return: a data table formatted for json output
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
pimarin
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23 """
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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24 self.data_table_entry = {
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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25 "data_tables": {
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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26 self.data_table_name: {}
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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27 }
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28 }
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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29 return self.data_table_entry
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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30
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31 def get_data_manager(self, amrfinderplus_version):
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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32 self.amrfinderplus_table_list = self.get_data_table_format()
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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33
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34 data_info = dict(value=self._today,
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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35 name=amrfinderplus_version,
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36 path=self._db_name)
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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37 self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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38 return self.amrfinderplus_table_list
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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39
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40 def update_amrfinderplus_db(self):
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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41 amrfinderplus_db_path = Path(self._db_path).joinpath(self._db_name)
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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42 cmd = [
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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43 'amrfinder_update',
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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44 '--database', str(amrfinderplus_db_path),
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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45 '--force_update'
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46 ]
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47 print(cmd)
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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48 proc = sp.run(
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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49 cmd,
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50 stdout=sp.PIPE,
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51 stderr=sp.PIPE,
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52 universal_newlines=True
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53 )
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54 if (proc.returncode != 0):
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55 print(
4974dd6207d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit 25a0413337c540dc9f26bc7ee097d493f0d148ca-dirty
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56 f"ERROR: AMRFinderPlus failed! command: 'amrfinder_update --force_update --database {amrfinderplus_db_path}', error code: {proc.returncode}")
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57 else:
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58 return amrfinderplus_db_path
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59
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60 def get_amrfinderplus_version(self, amrfinderplus_path):
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61 version_file = Path(f'{amrfinderplus_path}/latest/version.txt')
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62 with open(version_file, "r") as version:
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63 version_value = version.read()
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64 version_value = re.sub("\n", "", version_value)
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65 return version_value
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66
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67 def parse_arguments(self):
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68 # parse options and arguments
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69 arg_parser = argparse.ArgumentParser()
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70 arg_parser.add_argument("data_manager_json")
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71 arg_parser.add_argument("-t", "--test", action='store_true',
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72 help="option to test the script with an lighted database")
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73 return arg_parser.parse_args()
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74
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75 def read_json_input_file(self, json_file_path):
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76 with open(json_file_path) as fh:
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77 params = json.load(fh)
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78 target_dir = params['output_data'][0]['extra_files_path']
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79 os.makedirs(target_dir)
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80 return Path(target_dir)
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81
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82 def write_json_infos(self, json_file_path, data_manager_infos):
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83 with open(json_file_path, 'w') as fh:
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84 json.dump(data_manager_infos, fh, sort_keys=True)
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85
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86
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87 def main():
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88 # init the class
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89 amrfinderplus_download = GetDataManager()
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90 # import the arguments
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91 all_args = amrfinderplus_download.parse_arguments()
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92 # read the json input from galaxy to define the db path
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93 path_to_download = amrfinderplus_download.read_json_input_file(json_file_path=all_args.data_manager_json)
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94 # change the path to th json information
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95 amrfinderplus_download._db_path = path_to_download
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96 # download the last amrfinderplus database
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97 amrfinder_output = amrfinderplus_download.update_amrfinderplus_db()
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98 # extract the version number of the database
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99 amrfinder_version = amrfinderplus_download.get_amrfinderplus_version(amrfinder_output)
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100 # make a dic with database information
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101 amrfinderplus_json_output = amrfinderplus_download.get_data_manager(amrfinder_version)
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102 amrfinderplus_download.write_json_infos(json_file_path=all_args.data_manager_json,
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103 data_manager_infos=amrfinderplus_json_output)
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104
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105
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106 if __name__ == '__main__':
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107 main()