Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.py @ 16:718080c30a76 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit e7c35e529ae95a2c9f2ecd87a3716e6866feabfa
author pimarin
date Fri, 04 Nov 2022 15:46:06 +0000
parents ac4d5e1d1421
children ecb7d3d41366
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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
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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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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7 from datetime import datetime
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8 from pathlib import Path
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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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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10 import requests
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pimarin
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718080c30a76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit e7c35e529ae95a2c9f2ecd87a3716e6866feabfa
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1
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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13 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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14 """
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 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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16 """
0
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17
1
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pimarin
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18 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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19 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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20 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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21 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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22 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
pimarin
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23 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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24 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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25 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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26 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
pimarin
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27 self.db_version = db_version
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pimarin
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28 self.DB_VERSIONS_URL = 'https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json'
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29
1
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30 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
pimarin
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31 """
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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32 Build a data table format for galaxy
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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33 using the bakta database information
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pimarin
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34 @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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35 @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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36 @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
pimarin
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37 to apply a filter on version compatibility
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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38 @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
pimarin
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39 for the database location
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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40 return: a data table formatted for json output
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pimarin
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41 """
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pimarin
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42 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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43 "data_tables": {
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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44 self.data_table_name: {}
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45 }
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46 }
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47 return self.data_table_entry
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48
1
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49 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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50 """
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 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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52 db_version: a string of the version number
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pimarin
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53 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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54 return: info for the select or the latest bakta db version
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 """
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 try:
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57 with requests.get(self.DB_VERSIONS_URL) as resp:
1
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58 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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59 except IOError as e:
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60 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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61 raise e
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62 else:
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63 if db_version == "latest":
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64 db_date_list = []
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65 for db_dic in versions:
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66 db_date_list.append(datetime.strptime(db_dic["date"],
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67 '%Y-%m-%d').date())
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68 filtered_version = next(item for item in versions
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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69 if max(db_date_list))
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70 elif db_version == "test":
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71 filtered_version = {"date": "date_test",
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72 "major": "0",
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73 "minor": "0",
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74 "doi": "10.5281/zenodo.7197299",
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75 "record": "7197299",
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76 "md5": "8b0250c17078742fc12207d4efb0fc1a",
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77 "software-min": {"major": "0",
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78 "minor": "0"}
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79 }
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80 else:
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81 major_version = str(db_version.split(sep=".")[0])
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82 minor_version = str(db_version.split(sep=".")[1])
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83 try:
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84 filtered_version = next(
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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85 item for item in versions
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86 if str(item["major"]) == major_version
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87 and str(item["minor"]) == minor_version)
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88 except StopIteration:
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89 print("No available version detected in the list")
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90 filtered_version = None
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91 if filtered_version is not None:
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92 self.db_url = f"https://zenodo.org/record/" \
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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93 f"{filtered_version['record']}/files/db.tar.gz"
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94 self.db_version = db_version
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95 return filtered_version
0
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96
1
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97 def get_data_manager(self, bakta_database_info, output_path):
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98 self.bakta_table_list = self.get_data_table_format()
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99 bakta_value = f"V{bakta_database_info['major']}." \
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100 f"{bakta_database_info['minor']}_" \
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101 f"{bakta_database_info['date']}"
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102 tool_version = str(f"{bakta_database_info['software-min']['major']}."
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103 f"{bakta_database_info['software-min']['minor']}")
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104 data_info = dict(value=bakta_database_info['record'],
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105 dbkey=bakta_value,
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106 bakta_version=tool_version,
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107 path="db")
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108 self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
1
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109 return self.bakta_table_list
0
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110
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111
1
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112 class InstallBaktaDatabase(GetBaktaDatabaseInfo):
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113 """
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114 Download the bakta database,
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115 check md5 sum,
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116 untar the download db and update for the amrfinderplus database
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117 """
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118
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119 def __init__(self,
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120 db_dir=Path.cwd(),
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121 db_name="bakta",
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122 tarball_name="db.tar.gz"):
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123 super().__init__()
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124 self.md5 = None
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125 self.db_dir = db_dir
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126 self.db_name = db_name
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127 self.tarball_name = tarball_name
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128 self.tarball_path = None
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129
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130 def download(self):
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131 self.db_name = f'{self.db_name}_{self.db_version}'
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132 bakta_path = Path(self.db_dir).joinpath(self.tarball_name)
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133 try:
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134 with bakta_path.open('wb') as fh_out, \
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135 requests.get(self.db_url, stream=True) as resp:
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136 total_length = resp.headers.get('content-length')
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137 if total_length is None: # no content length header
15
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138 for data in resp.iter_content(chunk_size=1024 * 1024):
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139 fh_out.write(data)
1
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140 else:
15
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141 for data in resp.iter_content(chunk_size=1024 * 1024):
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142 fh_out.write(data)
1
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143 print(f'Download bakta database {self.db_version}')
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144 self.tarball_path = bakta_path
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145 except IOError:
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146 print(f'ERROR: Could not download file from Zenodo!'
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147 f' url={self.db_url}, path={self.tarball_name}')
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148
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149 def untar(self):
16
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150 db_path = Path(self.db_dir).as_posix()
1
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151 try:
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152 with self.tarball_path.open('rb') as fh_in, \
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153 tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
16
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154 tar_file.extractall(path=db_path)
1
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155 print(f'Untar the database in {db_path}')
16
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156 return db_path
1
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157 except OSError:
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158 sys.exit(f'ERROR: Could not extract {self.tarball_name} '
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159 f'to {self.db_name}')
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160
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161 def calc_md5_sum(self, buffer_size=1048576):
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162 tarball_path = Path(self.db_dir).joinpath(self.tarball_name)
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163 self.md5 = self.fetch_db_versions(db_version=self.db_version)["md5"]
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164 md5 = hashlib.md5()
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165 with tarball_path.open('rb') as fh:
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166 data = fh.read(buffer_size)
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167 while data:
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168 md5.update(data)
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169 data = fh.read(buffer_size)
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170 if md5.hexdigest() == self.md5:
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171 print('\t...md5 control database OK')
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172 else:
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173 print(f"Error: corrupt database file! "
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174 f"calculated md5 = {md5.hexdigest()}"
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175 f" different from {self.md5} ")
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176
16
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177
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178 """
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179 This is the method to download the amrfinderplus database need by bakta.
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180 Deprecated to use the amrfinderplus data_manager
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181 def update_amrfinderplus_db(self):
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182 amrfinderplus_db_path = f"{self.db_dir}/{self.db_name}/db/amrfinderplus-db"
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183 if self.db_version == "test":
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184 cmd = [
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185 'amrfinder_update',
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186 '--database', str(amrfinderplus_db_path),
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187 '--force_update',
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188 '--help'
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189 ]
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190 else:
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191 cmd = [
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192 'amrfinder_update',
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193 '--database', str(amrfinderplus_db_path),
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194 '--force_update'
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195 ]
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196 proc = sp.run(
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197 cmd,
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198 universal_newlines=True
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199 )
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200 if proc.returncode != 0:
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201 print(f"ERROR: AMRFinderPlus failed! "
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202 f"command: 'amrfinder_update --force_update"
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203 f" --database {amrfinderplus_db_path}'")
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204 else:
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205 print("AMRFinderPlus database download")
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206 """
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207
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208
1
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209 def parse_arguments():
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210 # parse options and arguments
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211 arg_parser = argparse.ArgumentParser()
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212 arg_parser.add_argument("data_manager_json")
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213 arg_parser.add_argument("-d", "--database_version",
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214 help='Select the database version '
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215 '(major and minor eg. 4.0),'
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216 'default is the latest version',
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217 default="latest",
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218 required=True)
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219 arg_parser.add_argument("-t", "--test", action='store_true',
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220 help="option to test the script with an empty database")
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221 return arg_parser.parse_args()
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222
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223
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224 def main():
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225 all_args = parse_arguments()
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226
1
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227 with open(all_args.data_manager_json) as fh:
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228 params = json.load(fh)
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229 target_dir = params['output_data'][0]['extra_files_path']
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230 os.makedirs(target_dir)
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231 # init the class to download bakta db
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232 bakta_upload = InstallBaktaDatabase()
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233 # extract the version
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234 if all_args.test is True:
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235 bakta_db = bakta_upload.fetch_db_versions(
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236 db_version="test")
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237 else:
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238 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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239 db_version=all_args.database_version)
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240 # update the path for galaxy
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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241 bakta_upload.db_dir = target_dir
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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242 # download the 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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243 bakta_upload.download()
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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244 # check md5 sum
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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245 bakta_upload.calc_md5_sum()
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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246 # untar db
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247 bakta_upload.untar()
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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
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248 # make the data_manager metadata
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249 bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db, output_path=target_dir)
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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
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250 with open(all_args.data_manager_json, 'w') as fh:
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c50e8b4f74d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 572bbceeba9a22cdb591d526abda362595f8f0c4
pimarin
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251 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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252
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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253
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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254 if __name__ == '__main__':
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255 main()