Mercurial > repos > iuc > data_manager_mitos

annotate data_manager/data_manager.py @ 2:5408a9225788 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:27:55 +0000
parents 58bcd38cecb6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
1 import argparse
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
2 import json
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
3 import os
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
4 import shutil
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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5 import tarfile
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
6 try:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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7 # For Python 3.0 and later
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
8 from urllib.request import Request, urlopen
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
9 except ImportError:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
10 # Fall back to Python 2 imports
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
11 from urllib2 import Request, urlopen
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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12
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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13 ZENODO = {
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
14 "mitos": "2683856",
1
58bcd38cecb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
iuc
parents: 0
diff changeset
15 "mitos2": "4284483"
0
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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16 }
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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17 NAMES = {
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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18 "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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diff changeset
19 "refseq39": "RefSeq39 (equivalent to MITOS1 data)",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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20 "refseq63m": "RefSeq63 Metazoa",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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21 "refseq63f": "RefSeq63 Fungi",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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22 "refseq63o": "RefSeq63 Opisthokonta",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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23 "refseq89m": "RefSeq89 Metazoa",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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24 "refseq89f": "RefSeq89 Fungi",
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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25 "refseq89o": "RefSeq89 Opisthokonta"
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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26 }
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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27
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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28
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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29 def url_download(tpe, db, workdir):
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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30 """
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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31 download http://ab.inf.uni-tuebingen.de/data/software/megan6/download/FNAME
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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32 to workdir
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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33 and unzip
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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34
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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35 return the name of the resulting dir
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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36 """
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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37 tarfname = os.path.join(workdir, db + ".tar.bz")
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
38 if not os.path.exists(workdir):
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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39 os.makedirs(workdir)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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40 src = None
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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41 dst = None
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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42 try:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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43 req = Request("https://zenodo.org/record/{zenodoid}/files/{db}.tar.bz2?download=1".format(zenodoid=ZENODO[tpe], db=db))
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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44 src = urlopen(req)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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45 with open(tarfname, 'wb') as dst:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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46 while True:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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47 chunk = src.read(2**10)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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48 if chunk:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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49 dst.write(chunk)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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50 else:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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51 break
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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52 finally:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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53 if src:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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54 src.close()
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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55 with tarfile.open(tarfname, "r:bz2") as tar:
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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56 dirname = tar.getnames()[0]
2
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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57
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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58 def is_within_directory(directory, target):
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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59 abs_directory = os.path.abspath(directory)
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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60 abs_target = os.path.abspath(target)
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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61 prefix = os.path.commonprefix([abs_directory, abs_target])
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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62 return prefix == abs_directory
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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63
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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64 def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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65 for member in tar.getmembers():
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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66 member_path = os.path.join(path, member.name)
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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67 if not is_within_directory(path, member_path):
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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68 raise Exception("Attempted Path Traversal in Tar File")
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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69 tar.extractall(path, members, numeric_owner=numeric_owner)
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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70
5408a9225788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 1
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71 safe_extract(tar, workdir)
0
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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72 os.remove(tarfname)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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73 return dirname
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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74
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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75
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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76 def main(tpe, db, outjson):
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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77 workdir = os.getcwd()
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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78
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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79 path = url_download(tpe, db, workdir)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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80
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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81 data_manager_entry = {}
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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82 data_manager_entry['value'] = db
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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83 data_manager_entry['name'] = NAMES[db]
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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84 data_manager_entry['type'] = tpe
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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85 data_manager_entry['path'] = path
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
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86 data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
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87
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58bcd38cecb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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88 with open(outjson) as fh:
58bcd38cecb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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89 params = json.load(fh)
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c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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90 target_directory = params['output_data'][0]['extra_files_path']
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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91 os.mkdir(target_directory)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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92 # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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93 shutil.move(os.path.join(workdir, path), target_directory)
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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94 with open(outjson, 'w') as fh:
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58bcd38cecb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
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95 json.dump(data_manager_json, fh, sort_keys=True)
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c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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96
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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98 if __name__ == '__main__':
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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99 parser = argparse.ArgumentParser(description='Create data manager json.')
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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100 parser.add_argument('--out', action='store', help='JSON filename')
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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101 parser.add_argument('--type', action='store', help='mitos version')
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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102 parser.add_argument('--db', action='store', help='db name')
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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103 args = parser.parse_args()
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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104
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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105 main(args.type, args.db, args.out)