Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.py @ 25:9adbf01a8929 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit ed22b0f3b7b651e240154a08c9313585def1cfe5
author pimarin
date Mon, 13 Feb 2023 11:36:50 +0000
parents 9d4bc7853eca
children 0408796bce2a
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faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
pimarin
parents: 0
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1 import argparse
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9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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2 import hashlib
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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3 import json
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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4 import os
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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5 import sys
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
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6 import tarfile
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pimarin
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7 from datetime import datetime
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8 from pathlib import Path
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9
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1
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pimarin
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11 import requests
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pimarin
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pimarin
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faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
pimarin
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14 class GetBaktaDatabaseInfo:
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
pimarin
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15 """
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pimarin
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16 Extract bakta database information to make a json file for data_manager
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
pimarin
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17 """
0
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pimarin
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19 def __init__(self,
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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20 data_table_name="bakta_database",
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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21 db_name=Path.cwd().joinpath("db"),
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22 db_version="latest",
c90380f8bbbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 8eb28a93e6f2688bb2f3f85aea0389e1b1148816-dirty
pimarin
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23 test_mode=False):
1
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pimarin
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24 self.bakta_table_list = None
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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25 self.db_url = None
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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26 self.data_table_entry = None
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pimarin
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27 self.data_table_name = data_table_name
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
pimarin
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28 self.db_name = db_name
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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29 self.db_version = db_version
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30 self.DB_VERSIONS_URL = 'https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json'
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31 self.DB_TEST_URL = 'https://zenodo.org/record/7360542/files/db-versions.json'
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32 self.test_mode = test_mode
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33
1
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34 def get_data_table_format(self):
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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35 """
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pimarin
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36 Skeleton of a data_table format
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37 return: a data table formated for json output
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38 """
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39 self.data_table_entry = {
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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40 "data_tables": {
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41 self.data_table_name: {}
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42 }
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43 }
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44 return self.data_table_entry
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45
1
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46 def fetch_db_versions(self, db_version="latest"):
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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47 """
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48 List bakta database info related to the db_version selected
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49 """
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pimarin
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50 if self.test_mode is True:
c90380f8bbbc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 8eb28a93e6f2688bb2f3f85aea0389e1b1148816-dirty
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51 self.DB_VERSIONS_URL = self.DB_TEST_URL
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52 try:
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53 with requests.get(self.DB_VERSIONS_URL) as resp:
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54 versions = json.loads(resp.content)
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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55 except IOError as e:
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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56 print(e, file=sys.stderr)
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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57 raise e
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58 else:
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59 if db_version == "latest":
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60 db_date_list = []
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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61 for db_dic in versions:
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62 db_date_list.append(datetime.strptime(db_dic["date"],
faae5d8ce0cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 4c11a77fb4c0bb74c0c4ae381c85971e01ed973e-dirty
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63 '%Y-%m-%d').date())
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64 filtered_version = max(versions, key=lambda x: x['date'])
1
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65 else:
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66 filtered_version = None
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67 for item in versions:
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68 if '{0}.{1}'.format(item["major"], item["minor"]) == db_version:
04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
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69 filtered_version = item
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70 break
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71 if filtered_version is None:
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72 print("No matching version detected in the list")
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73 if filtered_version is not None:
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74 self.db_url = f"https://zenodo.org/record/" \
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75 f"{filtered_version['record']}/files/db.tar.gz"
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76 self.db_version = db_version
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77 return filtered_version
0
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78
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79 def get_data_manager(self, bakta_database_info):
1
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80 self.bakta_table_list = self.get_data_table_format()
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81 bakta_value = f"V{bakta_database_info['major']}." \
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82 f"{bakta_database_info['minor']}_" \
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83 f"{bakta_database_info['date']}"
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84 tool_version = str(f"{bakta_database_info['software-min']['major']}."
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85 f"{bakta_database_info['software-min']['minor']}")
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86 data_info = dict(value=bakta_database_info['record'],
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87 dbkey=bakta_value,
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88 bakta_version=tool_version,
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89 path="db")
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90 self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
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91 return self.bakta_table_list
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92
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93
1
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94 class InstallBaktaDatabase(GetBaktaDatabaseInfo):
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95 """
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96 Download the bakta database,
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97 check md5 sum,
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98 untar the download db and update for the amrfinderplus database
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99 """
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100
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101 def __init__(self,
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102 db_dir=Path.cwd(),
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103 db_name="bakta",
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104 tarball_name="db.tar.gz",
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105 test_mode=False):
1
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106 super().__init__()
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107 self.md5 = None
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108 self.db_dir = db_dir
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109 self.db_name = db_name
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110 self.tarball_name = tarball_name
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111 self.tarball_path = None
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112 self.test_mode = test_mode
1
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113
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114 def download(self):
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115 self.db_name = f'{self.db_name}_{self.db_version}'
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116 bakta_path = Path(self.db_dir).joinpath(self.tarball_name)
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117 try:
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118 with bakta_path.open('wb') as fh_out, \
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119 requests.get(self.db_url, stream=True) as resp:
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120 total_length = resp.headers.get('content-length')
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121 if total_length is None: # no content length header
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122 for data in resp.iter_content(chunk_size=1024 * 1024):
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123 fh_out.write(data)
1
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124 else:
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125 for data in resp.iter_content(chunk_size=1024 * 1024):
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126 fh_out.write(data)
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127 print(f'Download bakta database {self.db_version}')
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128 self.tarball_path = bakta_path
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129 except IOError:
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130 print(f'ERROR: Could not download file from Zenodo!'
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131 f' url={self.db_url}, path={self.tarball_name}')
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132
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133 def untar(self):
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134 db_path = Path(self.db_dir).as_posix()
1
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135 try:
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136 with self.tarball_path.open('rb') as fh_in, \
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137 tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
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138 tar_file.extractall(path=db_path)
1
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139 print(f'Untar the database in {db_path}')
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140 return db_path
1
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141 except OSError:
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142 sys.exit(f'ERROR: Could not extract {self.tarball_name} '
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143 f'to {self.db_name}')
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144
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145 def calc_md5_sum(self, buffer_size=1048576):
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146 tarball_path = Path(self.db_dir).joinpath(self.tarball_name)
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147 self.md5 = self.fetch_db_versions(db_version=self.db_version)["md5"]
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148 md5 = hashlib.md5()
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149 with tarball_path.open('rb') as fh:
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150 data = fh.read(buffer_size)
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151 while data:
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152 md5.update(data)
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153 data = fh.read(buffer_size)
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154 if md5.hexdigest() == self.md5:
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155 print('\t...md5 control database OK')
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156 else:
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157 print(f"Error: corrupt database file! "
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158 f"calculated md5 = {md5.hexdigest()}"
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159 f" different from {self.md5} ")
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160
16
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161
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162 """
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163 This is the method to download the amrfinderplus database need by bakta.
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164 Deprecated to use the amrfinderplus data_manager
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165 def update_amrfinderplus_db(self):
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166 amrfinderplus_db_path = f"{self.db_dir}/{self.db_name}/db/amrfinderplus-db"
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167 if self.db_version == "test":
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168 cmd = [
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169 'amrfinder_update',
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170 '--database', str(amrfinderplus_db_path),
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171 '--force_update',
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172 '--help'
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173 ]
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174 else:
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175 cmd = [
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176 'amrfinder_update',
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177 '--database', str(amrfinderplus_db_path),
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178 '--force_update'
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179 ]
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180 proc = sp.run(
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181 cmd,
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182 universal_newlines=True
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183 )
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184 if proc.returncode != 0:
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185 print(f"ERROR: AMRFinderPlus failed! "
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186 f"command: 'amrfinder_update --force_update"
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187 f" --database {amrfinderplus_db_path}'")
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188 else:
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189 print("AMRFinderPlus database download")
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190 """
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191
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192
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193 def parse_arguments():
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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 arg_parser.add_argument("-d", "--database_version",
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198 help='Select the database version '
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199 '(major and minor eg. 4.0),'
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200 'default is the latest version',
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201 default="latest",
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202 required=True)
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203 arg_parser.add_argument("-t", "--test", action='store_true',
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204 help="option to test the script with an empty database")
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205 return arg_parser.parse_args()
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206
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207
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208 def main():
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209 all_args = parse_arguments()
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210 with open(all_args.data_manager_json) as fh:
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211 params = json.load(fh)
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212 target_dir = params['output_data'][0]['extra_files_path']
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213 os.makedirs(target_dir)
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214 # init the class to download bakta db
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215 bakta_upload = InstallBaktaDatabase(test_mode=all_args.test)
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216 bakta_db = bakta_upload.fetch_db_versions(db_version=all_args.database_version)
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217 # update the path for galaxy
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218 bakta_upload.db_dir = target_dir
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219 # download the database
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220 bakta_upload.download()
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221 # check md5 sum
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222 bakta_upload.calc_md5_sum()
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223 # untar db
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224 bakta_upload.untar()
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225 # make the data_manager metadata
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226 bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db)
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227 with open(all_args.data_manager_json, 'w') as fh:
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228 json.dump(bakta_data_manager, fh, sort_keys=True)
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229
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230
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231 if __name__ == '__main__':
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232 main()