Mercurial > repos > iuc > data_manager_bakta

annotate data_manager/bakta_build_database.py @ 3:3e73c97f025d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
author iuc
date Fri, 23 Jun 2023 21:37:05 +0000
parents bb463043c93e
children d74850cf4e42
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
parents:
diff changeset
1 import argparse
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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2 import hashlib
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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3 import json
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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4 import os
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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5 import re
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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6 import sys
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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7 import tarfile
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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8 from datetime import datetime
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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9 from pathlib import Path
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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12 import requests
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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15 class GetBaktaDatabaseInfo:
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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16 """
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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17 Extract bakta database information to make a json file for data_manager
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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18 """
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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19
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3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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20 def __init__(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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21 self,
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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22 data_table_name="bakta_database",
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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23 db_name=Path.cwd().joinpath("db"),
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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24 db_version="latest",
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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25 tarball_name="db.tar.gz",
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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26 test_mode=False,
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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27 ):
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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28 self.bakta_table_list = None
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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29 self.db_url = None
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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30 self.db_type = ""
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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31 self.data_table_entry = None
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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32 self.data_table_name = data_table_name
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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33 self.db_name = db_name
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3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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34 self.tar_name = tarball_name
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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35 self.db_version = db_version
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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36 self.DB_VERSIONS_URL = "https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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37 self.DB_TEST_URL = "https://zenodo.org/record/8021032/files/db-versions.json"
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a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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38 self.test_mode = test_mode
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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39
3
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40 def get_database_type(self):
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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41 self.light_db = bool(re.search(pattern="light", string=self.db_version))
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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42 self.db_version = self.db_version.split(sep="_")[0]
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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43 if self.light_db:
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
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44 self.db_type = "light"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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45 self.tar_name = "db-light.tar.gz"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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46 self.md5 = self.fetch_db_versions()["md5-light"]
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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47 else:
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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48 self.md5 = self.fetch_db_versions()["md5"]
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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49
0
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50 def get_data_table_format(self):
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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51 """
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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52 Skeleton of a data_table format
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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53 return: a data table formated for json output
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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54 """
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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55 self.data_table_entry = {"data_tables": {self.data_table_name: {}}}
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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56 return self.data_table_entry
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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57
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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58 def fetch_db_versions(self):
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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59 """
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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60 List bakta database info related to the db_version selected
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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61 """
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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62
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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63 if self.test_mode:
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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64 self.DB_VERSIONS_URL = self.DB_TEST_URL
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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65 try:
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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66 with requests.get(self.DB_VERSIONS_URL) as resp:
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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67 versions = json.loads(resp.content)
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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68 except IOError as e:
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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69 print(e, file=sys.stderr)
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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70 raise e
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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71
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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72 if self.db_version == "latest":
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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73 db_date_list = []
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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74 for db_dic in versions:
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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75 db_date_list.append(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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76 datetime.strptime(db_dic["date"], "%Y-%m-%d").date()
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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77 )
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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78 filtered_version = max(versions, key=lambda x: x["date"])
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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79 else:
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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80 filtered_version = None
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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81 for item in versions:
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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82 if "{0}.{1}".format(item["major"], item["minor"]) == self.db_version:
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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83 filtered_version = item
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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84 break
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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85 if filtered_version is None:
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86 print("No matching version detected in the list")
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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87 else:
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88 self.db_url = f"https://zenodo.org/record/{filtered_version['record']}/files/{self.tar_name}"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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89 return filtered_version
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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90
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91 def get_data_manager(self, bakta_database_info):
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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92 self.bakta_table_list = self.get_data_table_format()
3
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93 bakta_name = (
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94 f"V{bakta_database_info['major']}."
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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95 f"{bakta_database_info['minor']}{self.db_type}_"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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96 f"{bakta_database_info['date']}"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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97 )
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98 tool_version = str(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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99 f"{bakta_database_info['software-min']['major']}."
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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100 f"{bakta_database_info['software-min']['minor']}"
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101 )
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102 data_info = dict(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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103 value=bakta_name,
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104 dbkey=bakta_database_info["record"],
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105 bakta_version=tool_version,
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106 path="db",
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107 )
0
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108 self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
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109 return self.bakta_table_list
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110
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111
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112 class InstallBaktaDatabase(GetBaktaDatabaseInfo):
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113 """
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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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
3
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119 def __init__(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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120 self, db_dir=Path.cwd(), db_name="bakta", db_version="latest", test_mode=False
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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121 ):
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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122 super().__init__()
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123 self.md5 = None
3
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124 self.db_version = db_version
0
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125 self.db_dir = db_dir
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126 self.db_name = db_name
3
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127 self.tarball_path = ""
0
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128 self.test_mode = test_mode
3
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129 self.get_database_type()
0
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130
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131 def download(self):
3
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132 self.db_name = f"{self.db_name}_{self.db_version}{self.db_type}"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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133 bakta_path = Path(self.db_dir).joinpath(self.tar_name)
0
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134 try:
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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135 with bakta_path.open("wb") as fh_out, requests.get(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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136 self.db_url, stream=True) as resp:
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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137 total_length = resp.headers.get("content-length")
0
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138 if total_length is None: # no content length header
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139 for data in resp.iter_content(chunk_size=1024 * 1024):
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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140 fh_out.write(data)
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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141 else:
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142 for data in resp.iter_content(chunk_size=1024 * 1024):
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143 fh_out.write(data)
3
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144 print(f"Download bakta database {self.db_version}")
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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145 self.tarball_path = bakta_path
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146 except IOError:
3
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147 print(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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148 f"ERROR: Could not download file from Zenodo!"
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149 f" url={self.db_url}, to={self.tarball_path}"
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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150 )
0
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151
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152 def untar(self):
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153 db_path = Path(self.db_dir).as_posix()
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154 try:
3
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155 with self.tarball_path.open("rb") as fh_in, tarfile.open(
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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156 fileobj=fh_in, mode="r:gz"
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157 ) as tar_file:
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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158 tar_file.extractall(path=db_path)
3
3e73c97f025d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
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159 print(f"Untar the database in {db_path}")
0
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160 return db_path
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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161 except OSError:
3
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162 sys.exit(f"ERROR: Could not extract {self.tar_name} " f"to {self.db_name}")
0
a19189a128cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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163
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164 def calc_md5_sum(self, buffer_size=1048576):
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165 tarball_path = Path(self.db_dir).joinpath(self.tar_name)
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166 md5 = hashlib.md5()
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167 with tarball_path.open("rb") as fh:
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168 data = fh.read(buffer_size)
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169 while data:
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170 md5.update(data)
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171 data = fh.read(buffer_size)
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172 if md5.hexdigest() == self.md5:
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173 print("\t...md5 control database OK")
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174 else:
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175 print(
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176 f"Error: corrupt database file! "
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177 f"calculated md5 = {md5.hexdigest()}"
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178 f" different from {self.md5} "
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179 )
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180
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181
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182 def parse_arguments():
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183 # parse options and arguments
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184 arg_parser = argparse.ArgumentParser()
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185 arg_parser.add_argument("data_manager_json")
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186 arg_parser.add_argument(
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187 "-d",
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188 "--database_version",
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189 help="Select the database version "
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190 "(major and minor eg. 4.0),"
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191 "default is the latest version",
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192 default="latest",
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193 required=True,
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194 )
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195 arg_parser.add_argument(
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196 "-t",
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197 "--test",
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198 action="store_true",
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199 help="option to test the script with an empty database",
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200 )
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201 return arg_parser.parse_args()
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202
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203
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204 def main():
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205 all_args = parse_arguments()
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206 with open(all_args.data_manager_json) as fh:
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207 params = json.load(fh)
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208 target_dir = params["output_data"][0]["extra_files_path"]
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209 os.makedirs(target_dir)
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210 # init the class to download bakta db
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211 bakta_upload = InstallBaktaDatabase(
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212 test_mode=all_args.test, db_version=all_args.database_version
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213 )
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214 bakta_db = bakta_upload.fetch_db_versions()
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215 # update the path for galaxy
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216 bakta_upload.db_dir = target_dir
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217 # download the database
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218 bakta_upload.download()
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219 # check md5 sum
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220 bakta_upload.calc_md5_sum()
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221 # untar db
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222 bakta_upload.untar()
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223 # make the data_manager metadata
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224 bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db)
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225 with open(all_args.data_manager_json, "w") as fh:
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226 json.dump(bakta_data_manager, fh, sort_keys=True)
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227
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228
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229 if __name__ == "__main__":
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230 main()