Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation

annotate data_manager/data_manager.py @ 48:e4b92f2ca217 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:36:02 +0000
parents 3a02b8ab423a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
47
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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diff changeset
1 # -*- coding: utf-8 -*-
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9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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2 import argparse
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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3 import bz2
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9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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4 import datetime
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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5 import gzip
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9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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6 import json
9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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7 import os
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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8 import shutil
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9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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9 import sys
9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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10 import uuid
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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11 import zipfile
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9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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12
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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14 # Nice solution to opening compressed files (zip/bz2/gz) transparently
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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15 # https://stackoverflow.com/a/13045892/638445
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
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17 class CompressedFile(object):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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18 magic = None
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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19 file_type = None
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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20 mime_type = None
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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21 proper_extension = None
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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23 def __init__(self, f):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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24 # f is an open file or file like object
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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25 self.f = f
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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26 self.accessor = self.open()
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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28 @classmethod
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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29 def is_magic(self, data):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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30 return data.startswith(self.magic)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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32 def open(self):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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33 return None
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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36 class ZIPFile(CompressedFile):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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37 magic = '\x50\x4b\x03\x04'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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38 file_type = 'zip'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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39 mime_type = 'compressed/zip'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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41 def open(self):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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42 return zipfile.ZipFile(self.f)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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45 class BZ2File(CompressedFile):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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46 magic = '\x42\x5a\x68'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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47 file_type = 'bz2'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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48 mime_type = 'compressed/bz2'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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50 def open(self):
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51 return bz2.BZ2File(self.f)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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54 class GZFile(CompressedFile):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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55 magic = '\x1f\x8b\x08'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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56 file_type = 'gz'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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57 mime_type = 'compressed/gz'
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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59 def open(self):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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60 return gzip.GzipFile(self.f)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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63 # factory function to create a suitable instance for accessing files
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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64 def get_compressed_file(filename):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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65 with open(filename, 'rb') as f:
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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66 start_of_file = f.read(1024)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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67 f.seek(0)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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68 for cls in (ZIPFile, BZ2File, GZFile):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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69 if cls.is_magic(start_of_file):
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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70 f.close()
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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71 return cls(filename)
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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72
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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73 return None
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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74
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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75
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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76 try:
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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77 # For Python 3.0 and later
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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78 from urllib.request import urlretrieve
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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79 except ImportError:
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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80 # Fall back to Python 2's urllib2
3a02b8ab423a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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81 from urllib import urlretrieve
46
9346d2955707 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_gene_annotation/ commit 8652f36a3a3838dca989426961561e81432acf4f
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82
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83
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84 def url_download(url):
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85 """Attempt to download gene annotation file from a given url
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86 :param url: full url to gene annotation file
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87 :type url: str.
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88 :returns: name of downloaded gene annotation file
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89 :raises: ContentDecodingError, IOError
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90 """
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91
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92 # Generate file_name
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93 file_name = url.split('/')[-1]
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94
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95 try:
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96 # download URL (FTP and HTTP work, probably local and data too)
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97 urlretrieve(url, file_name)
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98
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99 # uncompress file if needed
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100 cf = get_compressed_file(file_name)
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101 if cf is not None:
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102 uncompressed_file_name = os.path.splitext(file_name)[0]
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103 with open(uncompressed_file_name, 'w+') as uncompressed_file:
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104 shutil.copyfileobj(cf.accessor, uncompressed_file)
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105 os.remove(file_name)
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106 file_name = uncompressed_file_name
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107 except IOError as e:
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108 sys.stderr.write('Error occured downloading reference file: %s' % e)
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109 os.remove(file_name)
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110 return file_name
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111
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112
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113 def main():
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114 parser = argparse.ArgumentParser(description='Create data manager JSON.')
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115 parser.add_argument('--out', dest='output', action='store', help='JSON filename')
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116 parser.add_argument('--name', dest='name', action='store', default=uuid.uuid4(), help='Data table entry unique ID')
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117 parser.add_argument('--url', dest='url', action='store', help='Url to download gtf file from')
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118
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119 args = parser.parse_args()
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120
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121 work_dir = os.getcwd()
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122
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123 # Attempt to download gene annotation file from given url
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124 gene_annotation_file_name = url_download(args.url)
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125
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126 # Update Data Manager JSON and write to file
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127 data_manager_entry = {
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128 'data_tables': {
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129 'gff_gene_annotations': {
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130 'value': str(datetime.datetime.now()),
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131 'dbkey': str(args.name),
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132 'name': gene_annotation_file_name,
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133 'path': os.path.join(work_dir, gene_annotation_file_name)
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134 }
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135 }
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136 }
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137
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138 with open(os.path.join(args.output), 'w+') as fh:
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139 json.dump(data_manager_entry, fh, sort_keys=True)
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140
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141
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142 if __name__ == '__main__':
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143 main()