Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

annotate data_manager/gtdbtk_database_installer.py @ 2:6ab422fba1a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
author iuc
date Tue, 13 Aug 2024 21:13:43 +0000
parents 629464b96c2e
children c4830a9870fa
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629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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diff changeset
1 #!/usr/bin/env python
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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2
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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3 import argparse
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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4 import gzip
0
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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5 import json
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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6 import os
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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7 import shutil
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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8 import sys
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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9 import tarfile
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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10 from datetime import datetime
0
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
iuc
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11 from urllib.parse import urlparse
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
parents: 0
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12 from urllib.request import Request, urlopen
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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13
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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14 # rather provide the urls based on the release, less error potential for the admins !
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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15 urls = {
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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16 "202": {
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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17 "full": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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18 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/ar122_taxonomy_r202.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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19 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/bac120_taxonomy_r202.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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20 },
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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21 "207": {
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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22 "full": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/gtdbtk_r207_data.tar.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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23 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/ar53_taxonomy_r207.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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24 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/bac120_taxonomy_r207.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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25 },
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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26 "214": {
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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27 "full": "https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/gtdbtk_r214_data.tar.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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28 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release214/214.0/ar53_taxonomy_r214.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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29 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release214/214.0/bac120_taxonomy_r214.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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30 },
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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31 "220": {
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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32 "full": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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33 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/ar53_taxonomy_r220.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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34 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/bac120_taxonomy_r220.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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35 },
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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36 "test": { # using VERSION to check if files are there
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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37 "full": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/VERSION.txt",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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38 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/ar53_taxonomy_r220.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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39 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/bac120_taxonomy_r220.tsv.gz",
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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40 },
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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41 }
0
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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42
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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43
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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44 def url_download(url, target_directory):
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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45 url_parts = urlparse(url)
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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46 tarball = os.path.abspath(
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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47 os.path.join(target_directory, os.path.basename(url_parts.path))
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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48 )
0
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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49 src = None
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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50 dst = None
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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51 try:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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52 req = Request(url)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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53 src = urlopen(req)
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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54 with open(tarball, "wb") as dst:
0
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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55 while True:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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56 chunk = src.read(2**10)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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57 if chunk:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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58 dst.write(chunk)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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59 else:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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60 break
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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61 except Exception as e:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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62 sys.exit(str(e))
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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63 finally:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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64 if src is not None:
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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65 src.close()
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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66 if tarfile.is_tarfile(tarball):
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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67 fh = tarfile.open(tarball, "r:*")
0
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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68 else:
2
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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69 # unzip metadata file
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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70 if ".gz" in tarball:
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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71 with gzip.open(tarball, "rb") as f_in:
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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72 unzipped_file = tarball.strip(".gz")
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
iuc
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73 with open(unzipped_file, "wb") as f_out:
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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74 shutil.copyfileobj(f_in, f_out)
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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75 os.remove(tarball)
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76 folder_of_unzipped_file = os.path.dirname(unzipped_file)
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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77 return folder_of_unzipped_file
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78 else:
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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79 # this is basically only the return for the test not using a tarfile
6ab422fba1a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit ad14947c3e13babe90a6878b45608fe56a16150d
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80 return tarball
0
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81 fh.extractall(target_directory)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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82 fh.close()
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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83 os.remove(tarball)
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84 # The tarball extraction will create a directory named
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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85 # something like release202 in the target_directory, so
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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86 # we need to move the items in that directory to the
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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87 # target directory.
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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88 subdir = next(os.walk(target_directory))[1][0]
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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89 subdir_path = os.path.join(target_directory, subdir)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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90 items = os.listdir(subdir_path)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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91 for item in items:
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92 item_path = os.path.join(subdir_path, item)
629464b96c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 69da0d34ea6e72c0427ec2d3e882c86cbb90833f
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93 shutil.move(item_path, target_directory)
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94 os.rmdir(subdir_path)
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95 return target_directory
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96
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97
2
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98 def download(database_name, release, meta, test, out_file):
0
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99
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100 with open(out_file) as fh:
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101 params = json.load(fh)
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102
2
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103 target_directory = params["output_data"][0]["extra_files_path"]
0
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104 os.makedirs(target_directory)
2
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105
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106 if test:
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107 release = "test"
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108
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109 # download both taxonomy metadata tables
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110 if meta:
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111 url = urls[release]["meta_ar"]
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112 file_path = url_download(url, target_directory)
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113 url = urls[release]["meta_bac"]
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114 file_path = url_download(url, target_directory)
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115 # download the full DB
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116 else:
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117 url = urls[release]["full"]
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118 file_path = url_download(url, target_directory)
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119
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120 time = datetime.utcnow().strftime("%Y-%m-%d")
0
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121
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122 data_manager_json = {"data_tables": {}}
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123 data_manager_entry = {}
2
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124 data_manager_entry["value"] = f"{database_name}_release_{release}_downloaded_{time}"
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125 data_manager_entry["name"] = database_name
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126 data_manager_entry["path"] = file_path
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127 data_manager_entry["version"] = release
0
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128
2
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129 # store in dedicated metadata table
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130 if meta:
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131 data_manager_json["data_tables"][
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132 "gtdbtk_database_metadata_versioned"
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133 ] = data_manager_entry
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134 else:
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135 data_manager_json["data_tables"][
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136 "gtdbtk_database_versioned"
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137 ] = data_manager_entry
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138
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139 with open(out_file, "w") as fh:
0
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140 json.dump(data_manager_json, fh, sort_keys=True)
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141
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142
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143 parser = argparse.ArgumentParser()
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144
2
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145 parser.add_argument(
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146 "--database_name", dest="database_name", help="GTDB-Tk database display name"
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147 )
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148
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149 parser.add_argument("--version", dest="version", help="DB version")
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150
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151 parser.add_argument(
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152 "--release", dest="release", help="Release of the GTDB-Tk database version"
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153 )
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154 parser.add_argument("--out_file", dest="out_file", help="JSON output file")
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155 parser.add_argument(
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156 "--meta",
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157 dest="meta",
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158 action="store_true",
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159 help="Store meta data flag",
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160 )
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161
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162 parser.add_argument(
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163 "--test",
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164 dest="test",
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165 action="store_true",
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166 help="Run test",
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167 )
0
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168
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169 args = parser.parse_args()
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170
2
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171 download(
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172 args.database_name,
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173 args.release,
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174 args.meta,
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175 args.test,
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176 args.out_file,
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177 )