Mercurial > repos > iuc > data_manager_mitos

annotate data_manager/data_manager.py @ 1:58bcd38cecb6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
author iuc
date Sun, 22 Nov 2020 18:02:48 +0000
parents c25855a79671
children 5408a9225788
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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
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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:
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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
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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
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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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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
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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
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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
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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
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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
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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
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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
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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]
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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57 tar.extractall(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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58 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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59 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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60
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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61
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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62 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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63 workdir = os.getcwd()
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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64
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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65 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"
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66
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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67 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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68 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
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69 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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70 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
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71 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
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72 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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73
1
58bcd38cecb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
iuc
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74 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"
iuc
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75 params = json.load(fh)
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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76 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"
iuc
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77 os.mkdir(target_directory)
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 # 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"
iuc
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79 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"
iuc
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80 with open(outjson, 'w') as fh:
1
58bcd38cecb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60"
iuc
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81 json.dump(data_manager_json, fh, sort_keys=True)
0
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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82
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
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83
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 if __name__ == '__main__':
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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85 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"
iuc
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86 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"
iuc
parents:
diff changeset
87 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"
iuc
parents:
diff changeset
88 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"
iuc
parents:
diff changeset
89 args = parser.parse_args()
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
90
c25855a79671 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit abf54c57544c5a08701163fb18a15877757d753e"
iuc
parents:
diff changeset
91 main(args.type, args.db, args.out)