Mercurial > repos > pimarin > data_manager_bakta

annotate data_manager/bakta_build_database.py @ 18:04bee0f935a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
author pimarin
date Wed, 09 Nov 2022 15:49:56 +0000
parents ecb7d3d41366
children c90380f8bbbc
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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
diff changeset
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"
pimarin
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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"
pimarin
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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"
pimarin
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5 import sys
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04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
pimarin
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6 # import subprocess
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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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7 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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8 from datetime import datetime
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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"
pimarin
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9 from pathlib import Path
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pimarin
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10 # implement pip as a subprocess:
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04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
pimarin
parents: 17
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11 # subprocess.check_call([sys.executable, '-m', 'pip', 'install', 'requests'])
17
ecb7d3d41366 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit e7c35e529ae95a2c9f2ecd87a3716e6866feabfa-dirty
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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 import requests
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pimarin
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1
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pimarin
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16 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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17 """
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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18 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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19 """
0
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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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21 def __init__(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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22 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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23 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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24 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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25 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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26 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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27 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
pimarin
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28 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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29 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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30 self.db_version = db_version
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pimarin
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31 self.DB_VERSIONS_URL = 'https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json'
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32
1
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33 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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34 """
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pimarin
parents: 17
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35 Skeleton of a data_table format
04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
pimarin
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36 return: a data table formated for json output
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37 """
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pimarin
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38 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
pimarin
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39 "data_tables": {
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 self.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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41 }
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42 }
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 return self.data_table_entry
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44
1
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pimarin
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45 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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46 """
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pimarin
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47 List bakta database info depending of the db_version selected
1
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48 """
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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49 try:
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pimarin
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50 with requests.get(self.DB_VERSIONS_URL) as resp:
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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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51 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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52 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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53 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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54 raise 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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55 else:
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 if 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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57 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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58 for db_dic 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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59 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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60 '%Y-%m-%d').date())
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pimarin
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61 filtered_version = max(versions, key=lambda x: x['date'])
1
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62 elif db_version == "test":
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63 filtered_version = {"date": "date_test",
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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64 "major": "0",
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65 "minor": "0",
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66 "doi": "10.5281/zenodo.7197299",
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67 "record": "7197299",
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68 "md5": "8b0250c17078742fc12207d4efb0fc1a",
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69 "software-min": {"major": "0",
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70 "minor": "0"}
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71 }
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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72 else:
18
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pimarin
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73 filtered_version = None
04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
pimarin
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74 for item in versions:
04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
pimarin
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75 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
pimarin
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76 filtered_version = item
04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
pimarin
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77 break
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78 if filtered_version is None:
04bee0f935a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 476cb50265f7dcb492fa2d0f03f595b1363faf7a
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79 print("No matching version detected in the list")
1
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80 if filtered_version is not None:
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81 self.db_url = f"https://zenodo.org/record/" \
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82 f"{filtered_version['record']}/files/db.tar.gz"
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83 self.db_version = db_version
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84 return filtered_version
0
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85
1
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86 def get_data_manager(self, bakta_database_info, output_path):
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87 self.bakta_table_list = self.get_data_table_format()
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88 bakta_value = f"V{bakta_database_info['major']}." \
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89 f"{bakta_database_info['minor']}_" \
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90 f"{bakta_database_info['date']}"
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91 tool_version = str(f"{bakta_database_info['software-min']['major']}."
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92 f"{bakta_database_info['software-min']['minor']}")
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93 data_info = dict(value=bakta_database_info['record'],
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94 dbkey=bakta_value,
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95 bakta_version=tool_version,
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96 path="db")
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97 self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
1
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98 return self.bakta_table_list
0
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99
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100
1
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101 class InstallBaktaDatabase(GetBaktaDatabaseInfo):
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102 """
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103 Download the bakta database,
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104 check md5 sum,
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105 untar the download db and update for the amrfinderplus database
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106 """
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107
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108 def __init__(self,
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109 db_dir=Path.cwd(),
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110 db_name="bakta",
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111 tarball_name="db.tar.gz"):
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112 super().__init__()
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113 self.md5 = None
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114 self.db_dir = db_dir
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115 self.db_name = db_name
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116 self.tarball_name = tarball_name
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117 self.tarball_path = None
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118
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119 def download(self):
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120 self.db_name = f'{self.db_name}_{self.db_version}'
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121 bakta_path = Path(self.db_dir).joinpath(self.tarball_name)
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122 try:
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123 with bakta_path.open('wb') as fh_out, \
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124 requests.get(self.db_url, stream=True) as resp:
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125 total_length = resp.headers.get('content-length')
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126 if total_length is None: # no content length header
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127 for data in resp.iter_content(chunk_size=1024 * 1024):
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128 fh_out.write(data)
1
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129 else:
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130 for data in resp.iter_content(chunk_size=1024 * 1024):
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131 fh_out.write(data)
1
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132 print(f'Download bakta database {self.db_version}')
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133 self.tarball_path = bakta_path
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134 except IOError:
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135 print(f'ERROR: Could not download file from Zenodo!'
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136 f' url={self.db_url}, path={self.tarball_name}')
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137
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138 def untar(self):
16
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139 db_path = Path(self.db_dir).as_posix()
1
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140 try:
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141 with self.tarball_path.open('rb') as fh_in, \
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142 tarfile.open(fileobj=fh_in, mode='r:gz') as tar_file:
16
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143 tar_file.extractall(path=db_path)
1
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144 print(f'Untar the database in {db_path}')
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145 return db_path
1
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146 except OSError:
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147 sys.exit(f'ERROR: Could not extract {self.tarball_name} '
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148 f'to {self.db_name}')
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149
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150 def calc_md5_sum(self, buffer_size=1048576):
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151 tarball_path = Path(self.db_dir).joinpath(self.tarball_name)
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152 self.md5 = self.fetch_db_versions(db_version=self.db_version)["md5"]
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153 md5 = hashlib.md5()
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154 with tarball_path.open('rb') as fh:
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155 data = fh.read(buffer_size)
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156 while data:
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157 md5.update(data)
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158 data = fh.read(buffer_size)
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159 if md5.hexdigest() == self.md5:
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160 print('\t...md5 control database OK')
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161 else:
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162 print(f"Error: corrupt database file! "
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163 f"calculated md5 = {md5.hexdigest()}"
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164 f" different from {self.md5} ")
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165
16
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166
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167 """
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168 This is the method to download the amrfinderplus database need by bakta.
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169 Deprecated to use the amrfinderplus data_manager
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170 def update_amrfinderplus_db(self):
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171 amrfinderplus_db_path = f"{self.db_dir}/{self.db_name}/db/amrfinderplus-db"
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172 if self.db_version == "test":
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173 cmd = [
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174 'amrfinder_update',
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175 '--database', str(amrfinderplus_db_path),
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176 '--force_update',
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177 '--help'
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178 ]
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179 else:
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180 cmd = [
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181 'amrfinder_update',
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182 '--database', str(amrfinderplus_db_path),
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183 '--force_update'
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184 ]
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185 proc = sp.run(
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186 cmd,
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187 universal_newlines=True
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188 )
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189 if proc.returncode != 0:
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190 print(f"ERROR: AMRFinderPlus failed! "
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191 f"command: 'amrfinder_update --force_update"
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192 f" --database {amrfinderplus_db_path}'")
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193 else:
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194 print("AMRFinderPlus database download")
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195 """
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196
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197
1
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198 def parse_arguments():
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199 # parse options and arguments
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200 arg_parser = argparse.ArgumentParser()
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201 arg_parser.add_argument("data_manager_json")
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202 arg_parser.add_argument("-d", "--database_version",
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203 help='Select the database version '
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204 '(major and minor eg. 4.0),'
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205 'default is the latest version',
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206 default="latest",
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207 required=True)
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208 arg_parser.add_argument("-t", "--test", action='store_true',
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209 help="option to test the script with an empty database")
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210 return arg_parser.parse_args()
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211
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212
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213 def main():
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214 all_args = parse_arguments()
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215
1
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216 with open(all_args.data_manager_json) as fh:
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217 params = json.load(fh)
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218 target_dir = params['output_data'][0]['extra_files_path']
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219 os.makedirs(target_dir)
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220 # init the class to download bakta db
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221 bakta_upload = InstallBaktaDatabase()
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222 # extract the version
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223 if all_args.test is True:
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224 bakta_db = bakta_upload.fetch_db_versions(
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225 db_version="test")
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226 else:
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227 bakta_db = bakta_upload.fetch_db_versions(
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228 db_version=all_args.database_version)
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229 # update the path for galaxy
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230 bakta_upload.db_dir = target_dir
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231 # download the database
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232 bakta_upload.download()
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233 # check md5 sum
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234 bakta_upload.calc_md5_sum()
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235 # untar db
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236 bakta_upload.untar()
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237 # make the data_manager metadata
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238 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
pimarin
parents: 0
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239 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
parents: 10
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240 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"
pimarin
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241
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
parents:
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242
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
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243 if __name__ == '__main__':
9d08486abf8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit 5f320f165a7f454193df36cc2ec77a87d50ec80f-dirty"
pimarin
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244 main()