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annotate compressed.py @ 1:70d78b7ce093 draft default tip

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planemo upload commit a978c98767df89e56b192fc450370559a00e47b9-dirty
author tiagoantao
date Sun, 13 Mar 2016 13:23:44 -0400
parents b0ed47130f0d
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1
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2 """
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3 Compressed classes
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4 """
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5
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6 import mimetypes, logging, os, os.path, sys, time, tempfile, shutil, string, glob, re, zipfile, tarfile
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7
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8 from galaxy.datatypes.data import Data
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9 from galaxy.datatypes.sniff import *
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10 from cgi import escape
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11 from inspect import isclass
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12 from galaxy import util
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13 from galaxy.datatypes.metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions
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14 from galaxy.util import inflector
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15 from galaxy.util.checkers import *
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16 from galaxy.util.bunch import Bunch
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17 from galaxy.util.odict import odict
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18 from galaxy.util.sanitize_html import sanitize_html
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19 from galaxy.datatypes import data
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20
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21
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22 log = logging.getLogger(__name__)
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23
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24 class Zip( Data ):
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25 file_ext = "zip"
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26
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27 def set_peek( self, dataset, is_multi_byte=False ):
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28 """Set the peek and blurb text"""
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29 if not dataset.dataset.purged:
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30 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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31 else:
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32 dataset.peek = 'file does not exist'
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33 dataset.blurb = 'file purged from disk'
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34
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35 def sniff( self, filename ):
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36 if (check_zip( filename )):
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37 return True
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38 return False
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39
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40
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41 class Tgz( Data ):
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42 file_ext = "tar.gz"
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43
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44 def set_peek( self, dataset, is_multi_byte=False ):
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45 """Set the peek and blurb text"""
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46 if not dataset.dataset.purged:
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47 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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48 else:
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49 dataset.peek = 'file does not exist'
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50 dataset.blurb = 'file purged from disk'
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51
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52 def sniff( self, filename ):
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53 is_gzipped, is_valid = check_gzip( filename )
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54 is_tar = tarfile.is_tarfile( filename )
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55 return (is_gzipped and is_valid and is_tar)
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56
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57
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58 class Tbz2( Data ):
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59 file_ext = "tar.bz2"
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60
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61 def set_peek( self, dataset, is_multi_byte=False ):
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62 """Set the peek and blurb text"""
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63 if not dataset.dataset.purged:
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64 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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65 else:
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66 dataset.peek = 'file does not exist'
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67 dataset.blurb = 'file purged from disk'
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68
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69 def sniff( self, filename ):
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70 is_bzipped, is_valid = check_bz2( filename )
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71 is_tar = tarfile.is_tarfile( filename )
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72 return (is_bzipped and is_valid and is_tar)
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73
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74
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75 class Fastqgz( Data ):
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76 file_ext = "fastq.gz"
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77
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78 def set_peek( self, dataset, is_multi_byte=False ):
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79 """Set the peek and blurb text"""
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80 if not dataset.dataset.purged:
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81 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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82 else:
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83 dataset.peek = 'file does not exist'
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84 dataset.blurb = 'file purged from disk'
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85
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86 def sniff( self, filename ):
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87 is_gzipped, is_valid = check_gzip( filename )
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88 is_tar = tarfile.is_tarfile( filename )
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89 return (is_gzipped and is_valid and not is_tar)
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90
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91 class Fastqbz2( Data ):
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92 file_ext = "fastq.bz2"
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93
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94 def set_peek( self, dataset, is_multi_byte=False ):
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95 """Set the peek and blurb text"""
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96 if not dataset.dataset.purged:
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97 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
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98 else:
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99 dataset.peek = 'file does not exist'
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100 dataset.blurb = 'file purged from disk'
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101
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102 def sniff( self, filename ):
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103 is_bzipped, is_valid = check_bz2( filename )
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104 is_tar = tarfile.is_tarfile( filename )
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105 return (is_bzipped and is_valid and not is_tar)