Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.py @ 14:bcac3aa1f494 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit b082e89a0090f9c4b2a257bb06b7c6f141b42650-dirty
author pimarin
date Wed, 02 Nov 2022 16:14:09 +0000
parents c50e8b4f74d7
children ac4d5e1d1421
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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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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
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5 import subprocess as sp
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 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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7 import tarfile
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8 from datetime import datetime
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9 from pathlib import Path
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1
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pimarin
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11 import requests
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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12 from alive_progress import alive_bar
0
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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1
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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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18
1
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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
pimarin
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21 db_name=Path.cwd().joinpath("db"),
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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22 db_version="latest"):
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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23 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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24 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
pimarin
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25 self.data_table_entry = 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_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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27 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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28 self.db_version = db_version
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29 self.DB_VERSIONS_URL = 'https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json'
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30
1
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31 def get_data_table_format(self):
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32 """
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33 Build a data table format for galaxy
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34 using the bakta database information
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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35 @str database_value: string of the database 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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36 @str database_date: string of the database date of build (YY-M-D)
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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37 @str database_bakta_version: string of the version of bakta tool
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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38 to apply a filter on version compatibility
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39 @str database_path: string of the database path
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 for the database location
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41 return: a data table formatted for json output
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42 """
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43 self.data_table_entry = {
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44 "data_tables": {
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45 self.data_table_name: {}
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46 }
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47 }
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48 return self.data_table_entry
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49
1
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50 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
pimarin
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51 """
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pimarin
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52 Use method from bakta tool to extract database info
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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53 db_version: a string of the version number
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54 in the galaxy wrapper list or just 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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55 return: info for the select or the latest bakta db version
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56 """
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57 try:
11
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58 with requests.get(self.DB_VERSIONS_URL) as resp:
1
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59 versions = json.loads(resp.content)
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60 except IOError as e:
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61 print(e, file=sys.stderr)
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62 raise e
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63 else:
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64 if db_version == "latest":
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65 db_date_list = []
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66 for db_dic in versions:
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67 db_date_list.append(datetime.strptime(db_dic["date"],
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68 '%Y-%m-%d').date())
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69 max(db_date_list)
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70 filtered_version = next(item for item in versions
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71 if max(db_date_list))
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72 elif db_version == "test":
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73 filtered_version = {"date": "date_test",
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74 "major": "0",
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75 "minor": "0",
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76 "doi": "10.5281/zenodo.7197299",
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77 "record": "7197299",
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78 "md5": "8b0250c17078742fc12207d4efb0fc1a",
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79 "software-min": {"major": "0",
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80 "minor": "0"}
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81 }
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82 else:
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83 major_version = str(db_version.split(sep=".")[0])
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84 minor_version = str(db_version.split(sep=".")[1])
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85 try:
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86 filtered_version = next(
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87 item for item in versions
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88 if str(item["major"]) == major_version
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89 and str(item["minor"]) == minor_version)
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90 except StopIteration:
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91 print("No available version detected in the list")
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92 filtered_version = None
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93 if filtered_version is not None:
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94 self.db_url = f"https://zenodo.org/record/" \
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95 f"{filtered_version['record']}/files/db.tar.gz"
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96 self.db_version = db_version
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97 return filtered_version
0
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98
1
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99 def get_data_manager(self, bakta_database_info, output_path):
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100 self.bakta_table_list = self.get_data_table_format()
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101 bakta_value = f"bakta_{bakta_database_info['major']}." \
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102 f"{bakta_database_info['minor']}"
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103 data_info = dict(value=bakta_value,
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104 dbkey=bakta_database_info['date'],
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105 database_record=bakta_database_info['record'],
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106 bakta_version=str(
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107 f"{bakta_database_info['software-min']['major']}."
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108 f"{bakta_database_info['software-min']['minor']}"
11
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109 ),
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110 path=output_path)
1
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111 self.bakta_table_list["data_tables"][self.data_table_name] = data_info
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112 return self.bakta_table_list
0
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113
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114
1
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115 class InstallBaktaDatabase(GetBaktaDatabaseInfo):
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116 """
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117 Download the bakta database,
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118 check md5 sum,
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119 untar the download db and update for the amrfinderplus database
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120 """
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121
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122 def __init__(self,
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123 db_dir=Path.cwd(),
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124 db_name="bakta",
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125 tarball_name="db.tar.gz"):
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126 super().__init__()
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127 self.md5 = None
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128 self.db_dir = db_dir
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129 self.db_name = db_name
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130 self.tarball_name = tarball_name
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131 self.tarball_path = None
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132
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133 def download(self):
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134 self.db_name = f'{self.db_name}_{self.db_version}'
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135 bakta_path = Path(self.db_dir).joinpath(self.tarball_name)
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136 try:
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137 with bakta_path.open('wb') as fh_out, \
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138 requests.get(self.db_url, stream=True) as resp:
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139 total_length = resp.headers.get('content-length')
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140 if total_length is None: # no content length header
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141 with alive_bar() as bar:
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142 for data in resp.iter_content(chunk_size=1024 * 1024):
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143 fh_out.write(data)
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144 bar()
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145 else:
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146 total_length = int(int(total_length) / 1024)
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147 with alive_bar(total=total_length) as bar:
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148 for data in resp.iter_content(chunk_size=1024 * 1024):
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149 fh_out.write(data)
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150 bar(incr=len(data) / 1024)
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151 print(f'Download bakta database {self.db_version}')
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152 self.tarball_path = bakta_path
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153 except IOError:
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154 print(f'ERROR: Could not download file from Zenodo!'
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155 f' url={self.db_url}, path={self.tarball_name}')
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156
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157 def untar(self):
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158 db_path = Path(self.db_dir).joinpath(self.db_name)
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159 try:
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160 with self.tarball_path.open('rb') as fh_in, \
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161 tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
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162 tar_file.extractall(path=str(db_path))
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163 print(f'Untar the database in {db_path}')
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164 return db_path.as_posix()
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165 except OSError:
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166 sys.exit(f'ERROR: Could not extract {self.tarball_name} '
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167 f'to {self.db_name}')
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168
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169 def calc_md5_sum(self, buffer_size=1048576):
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170 tarball_path = Path(self.db_dir).joinpath(self.tarball_name)
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171 self.md5 = self.fetch_db_versions(db_version=self.db_version)["md5"]
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172 md5 = hashlib.md5()
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173 with tarball_path.open('rb') as fh:
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174 data = fh.read(buffer_size)
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175 while data:
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176 md5.update(data)
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177 data = fh.read(buffer_size)
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178 if md5.hexdigest() == self.md5:
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179 print('\t...md5 control database OK')
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180 else:
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181 print(f"Error: corrupt database file! "
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182 f"calculated md5 = {md5.hexdigest()}"
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183 f" different from {self.md5} ")
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184
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185 def update_amrfinderplus_db(self):
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186 amrfinderplus_db_path = f"{self.db_dir}/{self.db_name}/db/amrfinderplus-db"
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187 if self.db_version == "test":
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188 cmd = [
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189 'amrfinder_update',
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190 '--database', str(amrfinderplus_db_path),
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191 '--force_update',
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192 '--help'
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193 ]
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194 else:
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195 cmd = [
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196 'amrfinder_update',
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197 '--database', str(amrfinderplus_db_path),
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198 '--force_update'
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199 ]
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200 proc = sp.run(
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201 cmd,
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202 universal_newlines=True
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203 )
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204 if proc.returncode != 0:
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205 print(f"ERROR: AMRFinderPlus failed! "
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206 f"command: 'amrfinder_update --force_update"
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207 f" --database {amrfinderplus_db_path}'")
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208 else:
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209 print("AMRFinderPlus database download")
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210
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211
1
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212 def parse_arguments():
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213 # parse options and arguments
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214 arg_parser = argparse.ArgumentParser()
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215 arg_parser.add_argument("data_manager_json")
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216 arg_parser.add_argument("-d", "--database_version",
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217 help='Select the database version '
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218 '(major and minor eg. 4.0),'
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219 'default is the latest version',
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220 default="latest",
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221 required=True)
11
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222 arg_parser.add_argument("-t", "--test", action='store_true',
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223 help="option to test the script with an empty database")
1
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224 return arg_parser.parse_args()
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225
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226
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227 def main():
1
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228 all_args = parse_arguments()
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229
1
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230 with open(all_args.data_manager_json) as fh:
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231 data_manager_input = json.load(fh)
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232
1
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233 target_dir = data_manager_input['output_data'][0]['extra_files_path']
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234 os.makedirs(target_dir)
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235
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236 # init the class to download bakta db
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237 bakta_upload = InstallBaktaDatabase()
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238 # extract the version
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239 if all_args.test is True:
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240 bakta_db = bakta_upload.fetch_db_versions(
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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241 db_version="test")
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242 else:
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243 bakta_db = bakta_upload.fetch_db_versions(
c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
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244 db_version=all_args.database_version)
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245 # update the path for galaxy
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246 bakta_upload.db_dir = target_dir
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247 # download the database
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248 bakta_upload.download()
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249 # check md5 sum
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250 bakta_upload.calc_md5_sum()
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251 # untar db
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252 bakta_extracted_path = bakta_upload.untar()
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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253 # update for amrfinderplus
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254 bakta_upload.update_amrfinderplus_db()
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255 # make the data_manager metadata
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256 bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=bakta_extracted_path)
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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257 with open(all_args.data_manager_json, 'w') as fh:
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258 json.dump(bakta_data_manager, fh, sort_keys=True)
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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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259
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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260
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261 if __name__ == '__main__':
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262 main()