Mercurial > repos > iuc > data_manager_selection_background

annotate data_manager/data_manager_selection_background.py @ 0:bb5794942b5e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
author iuc
date Fri, 20 Aug 2021 21:03:25 +0000
parents
children 0bd1cd5eac51
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0
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
diff changeset
1 # -*- coding: utf-8 -*-
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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2 import argparse
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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3 import bz2
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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4 import gzip
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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5 import json
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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6 import os
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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7 import shutil
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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8 import sys
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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9 import uuid
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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10 import zipfile
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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11
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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12 from six.moves.urllib.request import urlretrieve
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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13
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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14 # Nice solution to opening compressed files (zip/bz2/gz) transparently
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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15 # https://stackoverflow.com/a/13045892/638445
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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17
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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18 class CompressedFile(object):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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19 magic = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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20 file_type = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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21 mime_type = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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22 proper_extension = None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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23
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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24 def __init__(self, f):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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25 # f is an open file or file like object
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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26 self.f = f
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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27 self.accessor = self.open()
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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28
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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29 @classmethod
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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30 def is_magic(self, data):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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31 return data.startswith(self.magic)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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32
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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33 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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34 return None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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35
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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36
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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37 class ZIPFile(CompressedFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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38 magic = '\x50\x4b\x03\x04'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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39 file_type = 'zip'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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40 mime_type = 'compressed/zip'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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41
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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42 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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43 return zipfile.ZipFile(self.f)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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44
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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45
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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46 class BZ2File(CompressedFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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47 magic = '\x42\x5a\x68'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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48 file_type = 'bz2'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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49 mime_type = 'compressed/bz2'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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50
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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51 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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52 return bz2.BZ2File(self.f)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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53
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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54
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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55 class GZFile(CompressedFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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56 magic = '\x1f\x8b\x08'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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57 file_type = 'gz'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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58 mime_type = 'compressed/gz'
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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59
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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60 def open(self):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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61 return gzip.GzipFile(self.f)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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62
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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63
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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64 # factory function to create a suitable instance for accessing files
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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65 def get_compressed_file(filename):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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66 with open(filename, 'rb') as f:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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67 start_of_file = f.read(1024)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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68 f.seek(0)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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69 for cls in (ZIPFile, BZ2File, GZFile):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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70 if cls.is_magic(start_of_file):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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71 f.close()
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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72 return cls(filename)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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73
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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74 return None
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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75
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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76
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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77 def url_download(url):
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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78 """Attempt to download gene annotation file from a given url
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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79 :param url: full url to gene annotation file
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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80 :type url: str.
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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81 :returns: name of downloaded gene annotation file
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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82 :raises: ContentDecodingError, IOError
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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83 """
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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84
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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85 # Generate file_name
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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86 file_name = url.split('/')[-1]
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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87
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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88 try:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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89 # download URL (FTP and HTTP work, probably local and data too)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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90 urlretrieve(url, file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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91
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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92 # uncompress file if needed
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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93 cf = get_compressed_file(file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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94 if cf is not None:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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95 uncompressed_file_name = os.path.splitext(file_name)[0]
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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96 with open(uncompressed_file_name, 'w+') as uncompressed_file:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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97 shutil.copyfileobj(cf.accessor, uncompressed_file)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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98 os.remove(file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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99 file_name = uncompressed_file_name
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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100 except IOError as e:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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101 sys.stderr.write('Error occured downloading reference file: %s' % e)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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102 os.remove(file_name)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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103 return file_name
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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104
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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105
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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106 def main():
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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107 parser = argparse.ArgumentParser(description='Create data manager JSON.')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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108 parser.add_argument('--output', dest='output', action='store', required=True, help='JSON filename')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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109 parser.add_argument('--dbkey', dest='dbkey', action='store', default=uuid.uuid4(), help='Data table entry unique ID')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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110 parser.add_argument('--label', dest='label', action='store', required=True, help='Label to display')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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111 parser.add_argument('--uri', dest='uri', action='store', help='URI for the sequences')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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112 parser.add_argument('--dataset', dest='dataset', action='store', help='Path for the sequences')
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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113
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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114 args = parser.parse_args()
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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115
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iuc
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116 work_dir = os.getcwd()
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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117
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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118 if args.uri is not None:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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119 background_fasta = url_download(args.uri)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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120 else:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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121 background_fasta = args.dataset
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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122
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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123 table_entry = '%s.fa' % args.dbkey
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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124 shutil.copy(background_fasta, os.path.join(work_dir, table_entry))
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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125
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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126 # Update Data Manager JSON and write to file
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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127 data_manager_entry = {
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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128 'data_tables': {
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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129 'bealign_selection': {'value': args.dbkey, 'label': args.label, 'path': table_entry}
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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130 }
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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131 }
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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132
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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133 with open(os.path.join(args.output), 'w+') as fh:
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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134 json.dump(data_manager_entry, fh, sort_keys=True)
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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135
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
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136
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
parents:
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137 if __name__ == '__main__':
bb5794942b5e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c"
iuc
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138 main()