Mercurial > repos > iuc > data_manager_gtdbtk_database_installer

annotate data_manager/gtdbtk_database_installer.py @ 8:6a6175006cb9 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 1019bf0fda897582e2bbdc773aebb3e08e285aae
author iuc
date Mon, 21 Oct 2024 15:49:43 +0000
parents 05f85f5bfc48
children 1a049e50e6b8
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3221e031d107 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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1 #!/usr/bin/env python
3221e031d107 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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3221e031d107 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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3 import argparse
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9dcb593e8a43 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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4 import gzip
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3221e031d107 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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5 import json
3221e031d107 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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6 import os
3221e031d107 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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7 import shutil
3221e031d107 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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8 import sys
3221e031d107 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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9 import tarfile
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05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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10 from datetime import date
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3221e031d107 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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11 from urllib.parse import urlparse
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700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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12 from urllib.request import HTTPError, Request, urlopen
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9dcb593e8a43 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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9dcb593e8a43 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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14 # rather provide the urls based on the release, less error potential for the admins !
9dcb593e8a43 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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15 urls = {
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16 "202": {
9dcb593e8a43 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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17 "full": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/auxillary_files/gtdbtk_r202_data.tar.gz",
3
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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18 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/ar122_metadata_r202.tar.gz",
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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19 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release202/202.0/bac120_metadata_r202.tar.gz",
2
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20 },
9dcb593e8a43 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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21 "207": {
9dcb593e8a43 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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22 "full": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/gtdbtk_r207_data.tar.gz",
3
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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23 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/ar53_metadata_r207.tar.gz",
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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24 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release207/207.0/bac120_metadata_r207.tar.gz",
2
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25 },
9dcb593e8a43 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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26 "214": {
9dcb593e8a43 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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27 "full": "https://data.gtdb.ecogenomic.org/releases/release214/214.0/auxillary_files/gtdbtk_r214_data.tar.gz",
3
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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28 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release214/214.1/ar53_metadata_r214.tsv.gz",
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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29 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release214/214.1/bac120_metadata_r214.tsv.gz",
2
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30 },
9dcb593e8a43 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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31 "220": {
9dcb593e8a43 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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32 "full": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz",
3
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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33 "meta_ar": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/ar53_metadata_r220.tsv.gz",
45d5763ab173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 9f0b54aeff21df342d2593cff59e813b69cc7bad
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34 "meta_bac": "https://data.gtdb.ecogenomic.org/releases/release220/220.0/bac120_metadata_r220.tsv.gz",
2
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35 },
9dcb593e8a43 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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36 }
0
3221e031d107 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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38
4
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39 def is_urlfile(url):
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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40 # Check if online file exists
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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41 try:
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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42 r = urlopen(url) # response
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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43 return r.getcode() < 400
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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44 except HTTPError:
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45 return False
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46
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47
8
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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48 def extract_tar_iteratively(tarball, target_directory):
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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49 """
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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50 Extracts a .tar, .tar.gz, or .tar.bz2 archive iteratively in a memory-efficient manner.
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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51
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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52 This function processes the contents of the archive member-by-member, ensuring only
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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53 one file or directory is loaded into memory at any given time. It handles the creation
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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54 of directories and symbolic links, and streams large files to disk in chunks to avoid
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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55 memory overload.
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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56
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57 Args:
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58 tarball (str): Path to the tar archive (e.g., .tar, .tar.gz, .tar.bz2) to be extracted.
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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59 target_directory (str): The destination directory where the archive content
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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60 will be extracted.
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61
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62 Raises:
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63 OSError: If there is an issue with file or directory creation, or writing to disk.
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64 tarfile.TarError: If there is an issue opening or reading the tar archive.
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65
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66 Example Usage:
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67 extract_tar_iteratively("archive.tar.gz", "/path/to/extract")
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68
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69 Notes:
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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70 - The function supports symbolic and hard links present in the tar archive.
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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71 - It ensures that directories are created before files are extracted.
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72 - Large files are streamed to disk in 1 MB chunks to minimize memory usage.
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73 - This function does not return anything but will populate the target directory with
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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74 the extracted content.
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75 """
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
parents: 7
diff changeset
76
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
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77 with tarfile.open(tarball, "r:*") as fh:
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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78 for member in fh:
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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79 # Full path to where the member should be extracted
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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80 member_path = os.path.join(target_directory, member.name)
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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diff changeset
81
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
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diff changeset
82 if member.isdir():
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
parents: 7
diff changeset
83 # If it's a directory, ensure it exists
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
parents: 7
diff changeset
84 os.makedirs(member_path, exist_ok=True)
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
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85 elif member.isfile():
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
parents: 7
diff changeset
86 # If it's a file, extract it in chunks to avoid memory spikes
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
parents: 7
diff changeset
87 with fh.extractfile(member) as source, open(
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
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88 member_path, "wb"
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
iuc
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89 ) as target:
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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diff changeset
90 shutil.copyfileobj(
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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diff changeset
91 source, target, length=1024 * 1024
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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92 ) # 1 MB chunks
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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93 elif member.issym() or member.islnk():
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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94 # Handle symlinks or hard links if necessary
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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95 target_link = os.path.join(target_directory, member.name)
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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96 if member.issym():
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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97 os.symlink(member.linkname, target_link)
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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98 elif member.islnk():
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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99 os.link(member.linkname, target_link)
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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100
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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101
4
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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102 def url_download(url, target_directory, meta):
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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103
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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104 # download the url
0
3221e031d107 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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105 url_parts = urlparse(url)
2
9dcb593e8a43 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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106 tarball = os.path.abspath(
9dcb593e8a43 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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107 os.path.join(target_directory, os.path.basename(url_parts.path))
9dcb593e8a43 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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108 )
0
3221e031d107 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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109 src = None
3221e031d107 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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110 dst = None
3221e031d107 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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111 try:
3221e031d107 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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112 req = Request(url)
3221e031d107 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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113 src = urlopen(req)
2
9dcb593e8a43 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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114 with open(tarball, "wb") as dst:
0
3221e031d107 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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115 while True:
8
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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116 chunk = src.read(2**16) # Read in 64 KB chunks instead of 1 KB
0
3221e031d107 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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117 if chunk:
3221e031d107 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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118 dst.write(chunk)
3221e031d107 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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119 else:
3221e031d107 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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120 break
3221e031d107 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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121 except Exception as e:
3221e031d107 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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122 sys.exit(str(e))
3221e031d107 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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123 finally:
3221e031d107 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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124 if src is not None:
3221e031d107 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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125 src.close()
4
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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126
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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127 # extract the metadata
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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128 if meta:
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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129 # extract the content of *.tar.gz into the target dir
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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130 if tarfile.is_tarfile(tarball):
8
6a6175006cb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 1019bf0fda897582e2bbdc773aebb3e08e285aae
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131 extract_tar_iteratively(tarball, target_directory)
4
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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132 os.remove(tarball)
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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133 return target_directory # return path to output folder
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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134 # extract the content of *.gz into the target dir
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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135 elif ".gz" in tarball:
2
9dcb593e8a43 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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136 with gzip.open(tarball, "rb") as f_in:
9dcb593e8a43 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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137 unzipped_file = tarball.strip(".gz")
9dcb593e8a43 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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138 with open(unzipped_file, "wb") as f_out:
9dcb593e8a43 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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139 shutil.copyfileobj(f_in, f_out)
4
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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140 os.remove(tarball)
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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141 folder_of_unzipped_file = os.path.dirname(unzipped_file)
2
9dcb593e8a43 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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142 return folder_of_unzipped_file
9dcb593e8a43 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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143 else:
4
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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144 sys.exit(
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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145 "No correct input format for metadata file, must be .tar.gz or .gz"
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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146 )
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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147 else:
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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148 # handle the DB
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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149 # extract the content of the folder in the tar.gz into the target dir
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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150 if tarfile.is_tarfile(tarball):
8
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151 extract_tar_iteratively(tarball, target_directory)
4
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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152 os.remove(tarball)
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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153 else:
700c4fbdd3e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 0bb620025a61de6caa8a93537fec8ea65eda43be
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154 # handle the test case for the DB
2
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155 return tarball
4
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156
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157 # The tarball extraction will create a directory named
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158 # something like release202 in the target_directory, so
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159 # we need to move the items in that directory to the
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160 # target directory.
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161 subdir = next(os.walk(target_directory))[1][0]
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162 subdir_path = os.path.join(target_directory, subdir)
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163 items = os.listdir(subdir_path)
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164 for item in items:
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165 item_path = os.path.join(subdir_path, item)
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166 shutil.move(item_path, target_directory)
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167 os.rmdir(subdir_path)
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168 return target_directory
0
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169
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170
7
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171 def create_data_manager_entry(database_name, release, file_path):
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172 time = date.today().strftime("%Y-%m-%d")
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173 data_manager_entry = {}
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174 data_manager_entry["value"] = (
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175 f"{database_name.replace(' ', '_').lower()}_release_{release}_downloaded_{time}"
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176 )
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177 data_manager_entry["name"] = f"{database_name} - release {release} ({time})"
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178 data_manager_entry["path"] = file_path
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179 data_manager_entry["version"] = release
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180 return data_manager_entry
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181
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182
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183 def download(release, meta, test, out_file):
0
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184
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185 with open(out_file) as fh:
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186 params = json.load(fh)
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187
2
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188 target_directory = params["output_data"][0]["extra_files_path"]
0
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189 os.makedirs(target_directory)
2
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190
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191 if test:
4
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192 # switch the DB to use the test case
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193 urls[release][
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194 "full"
6
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195 ] = "https://zenodo.org/records/13734217/files/release220-test.tar.gz"
4
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196
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197 # make use of the test to check if all urls exists
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198 for _version, items in urls.items():
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199 for url in items.values():
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200 assert is_urlfile(url)
2
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201
7
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202 data_manager_json = {"data_tables": {}}
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203
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204 # download taxonomy metadata tables
2
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205 if meta:
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206 url = urls[release]["meta_ar"]
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207 url_download(url, target_directory, meta)
2
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208 url = urls[release]["meta_bac"]
4
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209 file_path = url_download(url, target_directory, meta)
7
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210
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211 data_manager_json["data_tables"]["gtdbtk_database_metadata_versioned"] = [
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212 create_data_manager_entry("Metadata Tables", release, file_path)
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213 ]
2
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214 # download the full DB
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215 else:
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216 url = urls[release]["full"]
4
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217 file_path = url_download(url, target_directory, meta)
7
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218 data_manager_json["data_tables"]["gtdbtk_database_versioned"] = [
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219 create_data_manager_entry("Full Database", release, file_path)
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220 ]
0
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221
2
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222 # store in dedicated metadata table
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223 with open(out_file, "w") as fh:
0
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224 json.dump(data_manager_json, fh, sort_keys=True)
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225
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226
7
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227 if __name__ == "__main__":
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228 parser = argparse.ArgumentParser()
2
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229
7
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230 parser.add_argument("--version", dest="version", help="DB version")
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231 parser.add_argument(
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232 "--release", dest="release", help="Release of the GTDB-Tk database version"
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233 )
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234 parser.add_argument("--out_file", dest="out_file", help="JSON output file")
05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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235 parser.add_argument(
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236 "--meta",
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237 dest="meta",
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238 action="store_true",
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239 help="Store meta data flag",
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240 )
05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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241 parser.add_argument(
05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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242 "--test",
05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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243 dest="test",
05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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244 action="store_true",
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245 help="Run test",
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246 )
05f85f5bfc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gtdbtk_database_installer commit 671e8c706fa211b6ec1c476d3d1a36d098822fe5
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247 args = parser.parse_args()
2
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248
7
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249 download(
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250 args.release,
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251 args.meta,
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252 args.test,
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253 args.out_file,
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254 )