Mercurial > repos > iuc > data_manager_bakta

annotate data_manager/bakta_build_database.py @ 5:ba7b35caf55c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
author iuc
date Thu, 20 Jun 2024 19:13:47 +0000
parents b71b550553b2
children
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a84adf8c8a4a 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
a84adf8c8a4a 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
a84adf8c8a4a 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
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c0bd27c2bc9b 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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4 import re
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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5 import sys
a84adf8c8a4a 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 tarfile
a84adf8c8a4a 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 from datetime import datetime
a84adf8c8a4a 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 pathlib import Path
a84adf8c8a4a 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
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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11 import requests
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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12
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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14 class GetBaktaDatabaseInfo:
a84adf8c8a4a 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 """
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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16 Extract bakta database information to make a json file for data_manager
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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17 """
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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18
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c0bd27c2bc9b 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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19 def __init__(
c0bd27c2bc9b 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 self,
c0bd27c2bc9b 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 data_table_name="bakta_database",
c0bd27c2bc9b 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 db_version="latest",
c0bd27c2bc9b 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 tarball_name="db.tar.gz",
c0bd27c2bc9b 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 test_mode=False,
c0bd27c2bc9b 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 ):
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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26 self.bakta_table_list = None
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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27 self.db_url = None
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b71b550553b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e
iuc
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28 self.db_name = "bakta-db"
3
c0bd27c2bc9b 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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29 self.db_type = ""
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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30 self.data_table_entry = None
a84adf8c8a4a 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_name = data_table_name
3
c0bd27c2bc9b 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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32 self.tar_name = tarball_name
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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33 self.db_version = db_version
3
c0bd27c2bc9b 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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34 self.DB_VERSIONS_URL = "https://raw.githubusercontent.com/oschwengers/bakta/master/db-versions.json"
5
ba7b35caf55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
iuc
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35 self.DB_TEST_URL = "https://zenodo.org/record/11381156/files/db-versions.json"
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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36 self.test_mode = test_mode
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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37
3
c0bd27c2bc9b 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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38 def get_database_type(self):
c0bd27c2bc9b 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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39 self.light_db = bool(re.search(pattern="light", string=self.db_version))
c0bd27c2bc9b 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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40 self.db_version = self.db_version.split(sep="_")[0]
c0bd27c2bc9b 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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41 if self.light_db:
c0bd27c2bc9b 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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42 self.db_type = "light"
c0bd27c2bc9b 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 self.tar_name = "db-light.tar.gz"
c0bd27c2bc9b 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.md5 = self.fetch_db_versions()["md5-light"]
c0bd27c2bc9b 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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45 else:
c0bd27c2bc9b 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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46 self.md5 = self.fetch_db_versions()["md5"]
c0bd27c2bc9b 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
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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48 def get_data_table_format(self):
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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49 """
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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50 Skeleton of a data_table format
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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51 return: a data table formated for json output
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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52 """
3
c0bd27c2bc9b 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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53 self.data_table_entry = {"data_tables": {self.data_table_name: {}}}
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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54 return self.data_table_entry
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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55
3
c0bd27c2bc9b 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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56 def fetch_db_versions(self):
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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57 """
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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58 List bakta database info related to the db_version selected
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
iuc
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59 """
3
c0bd27c2bc9b 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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60
c0bd27c2bc9b 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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61 if self.test_mode:
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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62 self.DB_VERSIONS_URL = self.DB_TEST_URL
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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63 try:
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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64 with requests.get(self.DB_VERSIONS_URL) as resp:
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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65 versions = json.loads(resp.content)
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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66 except IOError as e:
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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67 print(e, file=sys.stderr)
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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68 raise e
3
c0bd27c2bc9b 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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69
c0bd27c2bc9b 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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70 if self.db_version == "latest":
c0bd27c2bc9b 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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71 db_date_list = []
c0bd27c2bc9b 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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72 for db_dic in versions:
c0bd27c2bc9b 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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73 db_date_list.append(
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
parents: 1
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74 datetime.strptime(db_dic["date"], "%Y-%m-%d").date()
c0bd27c2bc9b 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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75 )
c0bd27c2bc9b 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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76 filtered_version = max(versions, key=lambda x: x["date"])
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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77 else:
3
c0bd27c2bc9b 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 = None
c0bd27c2bc9b 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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79 for item in versions:
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
parents: 1
diff changeset
80 if "{0}.{1}".format(item["major"], item["minor"]) == self.db_version:
c0bd27c2bc9b 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 filtered_version = item
c0bd27c2bc9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 487cb35fe55883ac6eeb8dda58b56c9ca2ec0a85
iuc
parents: 1
diff changeset
82 break
c0bd27c2bc9b 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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83 if filtered_version is None:
c0bd27c2bc9b 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 print("No matching version detected in the list")
c0bd27c2bc9b 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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diff changeset
85 else:
c0bd27c2bc9b 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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86 self.db_url = f"https://zenodo.org/record/{filtered_version['record']}/files/{self.tar_name}"
c0bd27c2bc9b 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 return filtered_version
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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88
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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89 def get_data_manager(self, bakta_database_info):
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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90 self.bakta_table_list = self.get_data_table_format()
3
c0bd27c2bc9b 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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91 bakta_name = (
c0bd27c2bc9b 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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92 f"V{bakta_database_info['major']}."
c0bd27c2bc9b 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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93 f"{bakta_database_info['minor']}{self.db_type}_"
c0bd27c2bc9b 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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94 f"{bakta_database_info['date']}"
c0bd27c2bc9b 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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95 )
c0bd27c2bc9b 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 tool_version = str(
c0bd27c2bc9b 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 f"{bakta_database_info['software-min']['major']}."
c0bd27c2bc9b 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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98 f"{bakta_database_info['software-min']['minor']}"
c0bd27c2bc9b 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 )
c0bd27c2bc9b 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 data_info = dict(
c0bd27c2bc9b 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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101 value=bakta_name,
c0bd27c2bc9b 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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102 dbkey=bakta_database_info["record"],
c0bd27c2bc9b 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 bakta_version=tool_version,
4
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104 path=self.db_name,
3
c0bd27c2bc9b 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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105 )
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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106 self.bakta_table_list["data_tables"][self.data_table_name] = [data_info]
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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107 return self.bakta_table_list
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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108
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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109
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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110 class InstallBaktaDatabase(GetBaktaDatabaseInfo):
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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111 """
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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112 Download the bakta database,
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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113 check md5 sum,
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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114 untar the download db and update for the amrfinderplus database
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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115 """
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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116
3
c0bd27c2bc9b 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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117 def __init__(
4
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118 self,
b71b550553b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e
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119 db_dir=Path.cwd(),
b71b550553b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e
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120 db_name="bakta-db",
b71b550553b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e
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121 db_version="latest",
b71b550553b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e
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122 test_mode=False
3
c0bd27c2bc9b 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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123 ):
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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124 super().__init__()
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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125 self.md5 = None
3
c0bd27c2bc9b 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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126 self.db_version = db_version
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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127 self.db_dir = db_dir
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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128 self.db_name = db_name
3
c0bd27c2bc9b 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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129 self.tarball_path = ""
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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130 self.test_mode = test_mode
3
c0bd27c2bc9b 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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131 self.get_database_type()
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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132
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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133 def download(self):
3
c0bd27c2bc9b 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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134 bakta_path = Path(self.db_dir).joinpath(self.tar_name)
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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135 try:
3
c0bd27c2bc9b 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 with bakta_path.open("wb") as fh_out, requests.get(
c0bd27c2bc9b 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 self.db_url, stream=True) as resp:
5
ba7b35caf55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
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diff changeset
138 # total_length = resp.headers.get("content-length")
ba7b35caf55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
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139 for data in resp.iter_content(chunk_size=1024 * 1024):
ba7b35caf55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
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140 fh_out.write(data)
3
c0bd27c2bc9b 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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141 print(f"Download bakta database {self.db_version}")
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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142 self.tarball_path = bakta_path
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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143 except IOError:
3
c0bd27c2bc9b 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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144 print(
c0bd27c2bc9b 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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145 f"ERROR: Could not download file from Zenodo!"
c0bd27c2bc9b 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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146 f" url={self.db_url}, to={self.tarball_path}"
c0bd27c2bc9b 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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147 )
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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148
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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149 def untar(self):
4
b71b550553b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit 404dc5eae30884c5814e463921eb3678bbd6878e
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150 db_path = Path(self.db_dir).joinpath(self.db_name)
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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151 try:
3
c0bd27c2bc9b 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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152 with self.tarball_path.open("rb") as fh_in, tarfile.open(
c0bd27c2bc9b 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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153 fileobj=fh_in, mode="r:gz"
c0bd27c2bc9b 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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154 ) as tar_file:
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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155 tar_file.extractall(path=db_path)
3
c0bd27c2bc9b 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 print(f"Untar the database in {db_path}")
0
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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157 except OSError:
4
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158 sys.exit(f"ERROR: Could not extract {self.tar_name} " f"to {db_path}")
5
ba7b35caf55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
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diff changeset
159 if not self.test_mode:
ba7b35caf55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bakta_database commit e0ce56ac52cff0e8f85e546440d28ca46853b11d
iuc
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160 self.move_files(db_path=db_path)
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161 self.db_dir = db_path.resolve()
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162
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163 def delete_folder(self, path):
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164 for sub in path.iterdir():
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165 if sub.is_dir() and sub.name != "latest":
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166 self.delete_folder(sub)
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167 else:
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168 sub.unlink()
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169 path.rmdir()
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170
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171 def move_files(self, db_path):
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172 if db_path.joinpath("db-light").is_dir():
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173 input_dir = db_path.joinpath("db-light")
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174 elif db_path.joinpath("db").is_dir():
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175 input_dir = db_path.joinpath("db")
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176 output_dir = db_path
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177 for file in input_dir.iterdir():
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178 if file.is_file(): # to avoid moving amrfinder-plus folder
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179 output = output_dir.joinpath(file.name)
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180 file.rename(output)
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181 self.delete_folder(input_dir)
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182
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183 def calc_md5_sum(self, buffer_size=1048576):
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184 tarball_path = Path(self.db_dir).joinpath(self.tar_name)
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185 md5 = hashlib.md5()
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186 with tarball_path.open("rb") as fh:
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187 data = fh.read(buffer_size)
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188 while data:
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189 md5.update(data)
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190 data = fh.read(buffer_size)
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191 if md5.hexdigest() == self.md5:
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192 print("\t...md5 control database OK")
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193 else:
3
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194 print(
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195 f"Error: corrupt database file! "
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196 f"calculated md5 = {md5.hexdigest()}"
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197 f" different from {self.md5} "
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198 )
0
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199
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200
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201 def parse_arguments():
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202 # parse options and arguments
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203 arg_parser = argparse.ArgumentParser()
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204 arg_parser.add_argument("data_manager_json")
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205 arg_parser.add_argument(
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206 "-d",
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207 "--database_version",
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208 help="Select the database version "
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209 "(major and minor eg. 4.0),"
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210 "default is the latest version",
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211 default="latest",
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212 required=True,
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213 )
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214 arg_parser.add_argument(
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215 "-t",
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216 "--test",
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217 action="store_true",
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218 help="option to test the script with an empty database",
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219 )
0
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220 return arg_parser.parse_args()
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221
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222
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223 def main():
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224 all_args = parse_arguments()
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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225 with open(all_args.data_manager_json) as fh:
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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226 params = json.load(fh)
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227 target_dir = Path(params["output_data"][0]["extra_files_path"])
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228 target_dir.mkdir(parents=True, exist_ok=True)
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229 # init the class to download bakta db
3
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230 bakta_upload = InstallBaktaDatabase(
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231 test_mode=all_args.test, db_version=all_args.database_version
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232 )
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233 bakta_db = bakta_upload.fetch_db_versions()
0
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234 # update the path for galaxy
5
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235 bakta_upload.db_dir = target_dir.absolute()
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236 # download the database
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237 bakta_upload.download()
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238 # check md5 sum
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239 bakta_upload.calc_md5_sum()
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240 # untar db
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241 bakta_upload.untar()
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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242 # make the data_manager metadata
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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243 bakta_data_manager = bakta_upload.get_data_manager(bakta_database_info=bakta_db)
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c0bd27c2bc9b 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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244 with open(all_args.data_manager_json, "w") as fh:
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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245 json.dump(bakta_data_manager, fh, sort_keys=True)
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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246
a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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247
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c0bd27c2bc9b 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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248 if __name__ == "__main__":
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a84adf8c8a4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bakta commit fba6deae1d3707e0c14202433d0495e157745afd
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249 main()