Mercurial > repos > dave > data_manager_selection_background

annotate data_manager/data_manager_selection_background.py @ 1:fa3b4a42d899 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
author dave
date Tue, 24 Aug 2021 15:23:33 +0000
parents 98beedb0e74b
children
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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1 # -*- coding: utf-8 -*-
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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2 import argparse
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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3 import bz2
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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4 import gzip
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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5 import json
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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6 import os
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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7 import shutil
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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8 import sys
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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9 import uuid
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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10 import zipfile
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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11 from urllib.request import urlretrieve
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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12
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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13 # Nice solution to opening compressed files (zip/bz2/gz) transparently
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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14 # https://stackoverflow.com/a/13045892/638445
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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17 class CompressedFile(object):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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18 magic = None
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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19 file_type = None
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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20 mime_type = None
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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21 proper_extension = None
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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23 def __init__(self, f):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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24 # f is an open file or file like object
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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25 self.f = f
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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26 self.accessor = self.open()
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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28 @classmethod
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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29 def is_magic(self, data):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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30 return data.startswith(self.magic)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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31
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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32 def open(self):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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33 return None
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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36 class ZIPFile(CompressedFile):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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37 magic = '\x50\x4b\x03\x04'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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38 file_type = 'zip'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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39 mime_type = 'compressed/zip'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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40
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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41 def open(self):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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42 return zipfile.ZipFile(self.f)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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43
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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44
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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45 class BZ2File(CompressedFile):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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46 magic = '\x42\x5a\x68'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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47 file_type = 'bz2'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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48 mime_type = 'compressed/bz2'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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49
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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50 def open(self):
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51 return bz2.BZ2File(self.f)
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52
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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53
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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54 class GZFile(CompressedFile):
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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55 magic = '\x1f\x8b\x08'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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56 file_type = 'gz'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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57 mime_type = 'compressed/gz'
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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58
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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59 def open(self):
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60 return gzip.GzipFile(self.f)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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61
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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62
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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63 # factory function to create a suitable instance for accessing files
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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64 def get_compressed_file(filename):
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65 with open(filename, 'rb') as f:
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66 start_of_file = f.read(1024)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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67 f.seek(0)
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68 for cls in (ZIPFile, BZ2File, GZFile):
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69 if cls.is_magic(start_of_file):
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70 f.close()
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71 return cls(filename)
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72
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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73 return None
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74
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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75
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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76 def url_download(url):
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77 """Attempt to download gene annotation file from a given url
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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78 :param url: full url to gene annotation file
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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79 :type url: str.
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80 :returns: name of downloaded gene annotation file
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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81 :raises: ContentDecodingError, IOError
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82 """
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83
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dave
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84 # Generate file_name
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dave
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85 file_name = url.split('/')[-1]
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86
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dave
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87 try:
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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88 # download URL (FTP and HTTP work, probably local and data too)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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89 urlretrieve(url, file_name)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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90
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dave
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91 # uncompress file if needed
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dave
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92 cf = get_compressed_file(file_name)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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93 if cf is not None:
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dave
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94 uncompressed_file_name = os.path.splitext(file_name)[0]
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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95 with open(uncompressed_file_name, 'w+') as uncompressed_file:
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dave
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96 shutil.copyfileobj(cf.accessor, uncompressed_file)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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97 os.remove(file_name)
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dave
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98 file_name = uncompressed_file_name
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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99 except IOError as e:
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100 sys.stderr.write('Error occured downloading reference file: %s' % e)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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101 os.remove(file_name)
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dave
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102 return file_name
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103
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104
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dave
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105 def main():
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106 parser = argparse.ArgumentParser(description='Create data manager JSON.')
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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107 parser.add_argument('--output', dest='output', action='store', required=True, help='JSON filename')
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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108 parser.add_argument('--dbkey', dest='dbkey', action='store', default=uuid.uuid4(), help='Data table entry unique ID')
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dave
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109 parser.add_argument('--label', dest='label', action='store', required=True, help='Label to display')
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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110 parser.add_argument('--uri', dest='uri', action='store', help='URI for the sequences')
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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111 parser.add_argument('--dataset', dest='dataset', action='store', help='Path for the sequences')
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112
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dave
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113 args = parser.parse_args()
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114
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115 work_dir = os.getcwd()
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116
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117 if args.uri is not None:
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dave
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118 background_fasta = url_download(args.uri)
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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119 else:
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dave
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120 background_fasta = args.dataset
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121
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dave
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122 table_entry = '%s.fa' % args.dbkey
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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123 shutil.copy(background_fasta, os.path.join(work_dir, table_entry))
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
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124
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dave
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125 # Update Data Manager JSON and write to file
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126 data_manager_entry = {
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127 'data_tables': {
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128 'selection_background': {'value': args.dbkey, 'label': args.label, 'path': table_entry}
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129 }
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130 }
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131
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dave
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132 with open(os.path.join(args.output), 'w+') as fh:
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133 json.dump(data_manager_entry, fh, sort_keys=True)
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134
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135
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dave
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136 if __name__ == '__main__':
98beedb0e74b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit 4854cf92350265cac72ba5bb462e08b8cd239b8b-dirty"
dave
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137 main()