Mercurial > repos > pimarin > data_manager_amrfinderplus

annotate data_manager/data_manager_amrfinderplus.py @ 0:8e1bbef44e19 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
author pimarin
date Thu, 10 Nov 2022 15:10:15 +0000
parents
children 254479b50f86
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8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
parents:
diff changeset
1 import argparse
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
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2 import json
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
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3 import os
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
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4 import re
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
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5 from datetime import datetime
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
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6 from pathlib import Path
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
pimarin
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7 import subprocess as sp
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
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8
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9
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pimarin
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10 class GetDataManager:
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11
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12 def __init__(self):
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13 self.data_table_name = "amrfinderplus_database"
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14 self._db_name = "amrfinderplus-db"
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15 self._db_path = Path().absolute()
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16 self._today = datetime.now().strftime("%Y-%m-%d_%H:%M")
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17
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18 def get_data_table_format(self):
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19 """
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20 Skeleton of a data_table format
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21 return: a data table formatted for json output
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22 """
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pimarin
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23 self.data_table_entry = {
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24 "data_tables": {
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25 self.data_table_name: {}
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26 }
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27 }
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28 return self.data_table_entry
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29
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30 def get_data_manager(self, amrfinderplus_version):
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31 self.amrfinderplus_table_list = self.get_data_table_format()
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32
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33 data_info = dict(value=self._today,
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34 name=amrfinderplus_version,
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35 path=self._db_name)
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36 self.amrfinderplus_table_list["data_tables"][self.data_table_name] = [data_info]
8e1bbef44e19 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_amrfinderplus commit a7bd2bf9c3e46c3524ee640bb60c8062b3257217-dirty
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37 return self.amrfinderplus_table_list
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38
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39 def update_amrfinderplus_db(self, path):
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pimarin
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40 amrfinderplus_db_path = path.joinpath(self._db_name)
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41 cmd = [
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42 'amrfinder_update',
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43 '--database', str(amrfinderplus_db_path),
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44 '--force_update'
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45 ]
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46 print('cmd=%s', cmd)
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47 proc = sp.run(
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48 cmd,
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49 stdout=sp.PIPE,
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50 stderr=sp.PIPE,
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51 universal_newlines=True
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52 )
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53 if(proc.returncode != 0):
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54 print(f"ERROR: AMRFinderPlus failed! command: 'amrfinder_update --force_update --database {amrfinderplus_db_path}', error code: {proc.returncode}")
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55 else:
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56 return amrfinderplus_db_path
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57
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58 def get_amrfinderplus_version(self, amrfinderplus_path):
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59 version_file = Path(f'{amrfinderplus_path}/latest/version.txt')
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60 with open(version_file, "r") as version:
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61 version_value = version.read()
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62 version_value = re.sub("\n", "", version_value)
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63 return version_value
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64
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65 def parse_arguments(self):
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66 # parse options and arguments
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67 arg_parser = argparse.ArgumentParser()
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68 arg_parser.add_argument("data_manager_json")
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69 arg_parser.add_argument("-t", "--test", action='store_true',
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70 help="option to test the script with an lighted database")
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71 return arg_parser.parse_args()
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72
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73 def read_json_input_file(self, json_file_path):
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74 with open(json_file_path) as fh:
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75 params = json.load(fh)
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76 target_dir = params['output_data'][0]['extra_files_path']
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77 os.makedirs(target_dir)
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78 return target_dir
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79
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80 def write_json_infos(self, json_file_path, data_manager_infos):
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81 with open(json_file_path, 'w') as fh:
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82 json.dump(data_manager_infos, fh, sort_keys=True)
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83
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84
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85 def main():
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86 # init the class
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87 amrfinderplus_download = GetDataManager()
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88 # import the arguments
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89 all_args = amrfinderplus_download.parse_arguments()
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90 # read the json input from galaxy to define the db path
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91 path_to_download = amrfinderplus_download.read_json_input_file(json_file_path=all_args.data_manager_json)
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92 # change the path to th json information
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93 amrfinderplus_download._db_path = path_to_download
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94 # download the last amrfinderplus database
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95 amrfinder_output = amrfinderplus_download.update_amrfinderplus_db(amrfinderplus_download._db_path)
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96 # extract the version number of the database
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97 amrfinder_version = amrfinderplus_download.get_amrfinderplus_version(amrfinder_output)
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98 # make a dic with database information
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99 amrfinderplus_json_output = amrfinderplus_download.get_data_manager(amrfinder_version)
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100 amrfinderplus_download.write_json_infos(json_file_path=all_args.data_manager_json,
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101 data_manager_infos=amrfinderplus_json_output)
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102
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103
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104 if __name__ == '__main__':
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105 main()