Mercurial > repos > iuc > data_manager_pangolin_data

annotate data_manager/pangolin_data_dm.py @ 1:f0214079e0c7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 544fd499de5324afce8f5f9b38ffdaf282f4dfaa
author iuc
date Wed, 25 Sep 2024 15:40:37 +0000
parents 40c380ea283f
children
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40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
1 #!/usr/bin/env python
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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2
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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3 import argparse
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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4 import datetime
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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5 import json
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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6 import operator
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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7 import pathlib
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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8 import shutil
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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9 import subprocess
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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10 import sys
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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11 import tempfile
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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12 from io import StringIO
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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13 from typing import Generator, TextIO
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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14
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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15 import requests
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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16
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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17
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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18 def parse_date(d: str) -> datetime.datetime:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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19 # Parses the publication date from the GitHub API or user input into a datetime object.
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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20 date = None
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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21 try:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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22 date = datetime.datetime.strptime(d, "%Y-%m-%dT%H:%M:%SZ")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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23 except ValueError:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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24 date = datetime.datetime.strptime(d, "%Y-%m-%d")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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25 return date
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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26
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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27
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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28 def get_model_list(package: str) -> Generator[dict, None, None]:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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29 page_num = 0
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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30 while True:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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31 url = f"https://api.github.com/repos/cov-lineages/{package}/releases"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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32 page_num += 1
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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33 response = requests.get(url + f"?page={page_num}")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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34 if response.status_code == 200:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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35 release_list_chunk = json.loads(response.text)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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36 if not release_list_chunk:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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37 # past the last page of results
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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38 return
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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39 for e in release_list_chunk:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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40 if e["prerelease"]:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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41 continue
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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42 yield dict(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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43 tag_name=e["tag_name"],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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44 name=e["name"],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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45 date=parse_date(e["published_at"]),
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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46 tarball_url=e["tarball_url"],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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47 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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48 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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49 response.raise_for_status()
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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50
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51
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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52 def download_and_unpack(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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53 dependency: str, release: str, output_directory: str
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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54 ) -> pathlib.Path:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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55 url = f"git+https://github.com/cov-lineages/{dependency}.git@{release}"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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56 dependency_package_name = dependency.replace("-", "_")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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57 output_path = pathlib.Path(output_directory) / dependency_package_name / release
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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58 with tempfile.TemporaryDirectory() as tmpdir:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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59 pip_command = [
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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60 sys.executable,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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61 "-m",
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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62 "pip",
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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63 "install",
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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64 "--upgrade",
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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65 "--target",
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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66 tmpdir,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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67 url,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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68 ]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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69 # output is saved in tmpdir/dependency, final output needs to be
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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70 # in output_directory/dependency/release
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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71 subprocess.run(pip_command, check=True)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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72 shutil.move(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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73 str(pathlib.Path(tmpdir) / dependency_package_name), str(output_path)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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74 )
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75 return output_path
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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76
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77
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78 def fetch_compatibility_info(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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79 package_name: str,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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80 url: str = "https://raw.githubusercontent.com/cov-lineages/pangolin/master/pangolin/data/data_compatibility.csv",
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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81 ) -> list[dict[str, str]]:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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82 response = requests.get(url)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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83 if response.status_code == 200:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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diff changeset
84 compatibility = read_compatibility_info(StringIO(response.text), package_name)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
85 return compatibility
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
86 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
87 return {}
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
88
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
89
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
90 def read_compatibility_info(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
91 input_file: TextIO, package_name: str
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
92 ) -> list[dict[str, str]]:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
93 compatibility = {}
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
94 for line in input_file:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
95 fields = line.strip().split(",")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
96 if fields[0] != package_name:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
97 continue
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
98 if package_name == "constellations":
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
99 compatibility[fields[1]] = fields[3]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
100 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
101 # for pangolin-data and pangolin-assignment
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
102 compatibility[fields[1]] = fields[2]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
103 return compatibility
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
104
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
105
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
106 def comma_split(args: str) -> list[str]:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
107 return args.split(",")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
108
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
109
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
110 def git_lfs_install():
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
111 """
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
112 'git-lfs install' must be run after installing git-lfs and before cloning a repo
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
113 that uses Git LFS. Code taken from pangolin repo.
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
114 """
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
115 try:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
116 subprocess.run(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
117 ["git-lfs", "install"],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
118 check=True,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
119 stdout=subprocess.PIPE,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
120 stderr=subprocess.PIPE,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
121 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
122 except subprocess.CalledProcessError as e:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
123 stderr = e.stderr.decode("utf-8")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
124 sys.stderr.write(f"Error: {e}:\n{stderr}\n")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
125 sys.exit(-1)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
126
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
127
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
128 if __name__ == "__main__":
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
129
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
130 parser = argparse.ArgumentParser()
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
131 parser.add_argument("--latest", default=False, action="store_true")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
132 parser.add_argument("--version_compatibility_file", type=argparse.FileType())
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
133 parser.add_argument("--versions", type=comma_split)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
134 parser.add_argument("--overwrite", default=False, action="store_true")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
135 parser.add_argument("--known_revisions", type=comma_split)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
136 parser.add_argument("datatable_name")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
137 parser.add_argument("datatable_cache_filename")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
138 parser.add_argument("galaxy_config")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
139 args = parser.parse_args()
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
140
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
141 if args.datatable_name == "pangolin_data":
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
142 package_name = "pangolin-data"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
143 min_version_key = "min_pangolin_version"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
144 elif args.datatable_name == "pangolin_constellations":
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
145 package_name = "constellations"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
146 min_version_key = "min_scorpio_version"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
147 elif args.datatable_name == "pangolin_assignment":
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
148 package_name = "pangolin-assignment"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
149 min_version_key = "min_pangolin_version"
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
150 git_lfs_install()
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
151 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
152 sys.exit(f"Unknown data table {args.datatable_name}")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
153
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
154 with open(args.galaxy_config) as fh:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
155 config = json.load(fh)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
156
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
157 output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
158
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
159 try:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
160 with open(args.datatable_cache_filename) as fh:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
161 data_manager_dict = json.load(fh)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
162 except IOError:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
163 # on the first run this file doesn't exist
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
164 data_manager_dict = {}
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
165
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
166 if "data_tables" in data_manager_dict:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
167 if args.datatable_name not in data_manager_dict["data_tables"]:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
168 # got a data_tables entry, probably from a previous run of this script,
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
169 # but no entry for this specific data table
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
170 data_manager_dict["data_tables"][args.datatable_name] = []
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
171 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
172 # got no entry for data tables, start from scratch
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
173 data_manager_dict = {"data_tables": {args.datatable_name: []}}
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
174
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
175 # known-revisions is populated from the Galaxy `pangolin_data` data table by the wrapper
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
176 if args.known_revisions is not None:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
177 existing_release_tags = set(args.known_revisions)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
178 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
179 existing_release_tags = set()
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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180 if args.latest:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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181 compatibility = fetch_compatibility_info(package_name)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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182 for latest_release in get_model_list(package_name):
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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183 # choose the first release for which we have compatibility info
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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184 version = latest_release["tag_name"].lstrip("v.")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
185 if version in compatibility:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
186 latest_release[min_version_key] = compatibility[version]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
187 break
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
188 if latest_release["tag_name"] in existing_release_tags:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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189 releases = []
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
190 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
191 releases = [latest_release]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
192 else:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
193 compatibility = read_compatibility_info(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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194 args.version_compatibility_file, package_name
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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195 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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196 downloadable_releases = get_model_list(package_name)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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197 releases_wanted = set(args.versions) - set(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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198 [tag.lstrip("v.") for tag in existing_release_tags]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
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diff changeset
199 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
200 releases = []
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
201 for release in downloadable_releases:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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202 version = release["tag_name"].lstrip("v.")
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
203 if version in releases_wanted:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
204 if version in compatibility:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
205 # only add the releases for which we have compatibility info
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
206 release[min_version_key] = compatibility[version]
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
207 releases.append(release)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
208 releases_wanted.remove(version)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
209 if not releases_wanted:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
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diff changeset
210 # we've found all the releases we want
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
211 break
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
212 if releases_wanted:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
213 missing_releases = " ".join(releases_wanted)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
214 sys.exit(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
215 f"Some of the requested releases ({missing_releases}) are not available."
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
216 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
217
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
218 for release in releases:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
219 fname = download_and_unpack(package_name, release["tag_name"], output_directory)
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
220 if fname is not None:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
221 data_manager_dict["data_tables"][args.datatable_name].append(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
222 {
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
223 "value": release["tag_name"],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
224 "description": release["name"],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
225 min_version_key: release[min_version_key],
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
226 "date": release["date"].isoformat(), # ISO 8601 is easily sortable
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
227 "path": str(output_directory / fname),
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
228 }
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
229 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
230 data_manager_dict["data_tables"][args.datatable_name].sort(
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
231 key=operator.itemgetter("value"), reverse=True
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
232 )
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
233 with open(args.datatable_cache_filename, "w") as fh:
40c380ea283f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolin_data commit 902cce06e30ffe8ccba5dc0c3b704eb39fb4c611
iuc
parents:
diff changeset
234 json.dump(data_manager_dict, fh, indent=2, sort_keys=True)