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1 """
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2 Ontology datatypes
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3
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4 """
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5 import pkg_resources
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6 pkg_resources.require( "bx-python" )
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7
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8 import logging, os, sys, time, tempfile, shutil
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9 import data
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10 from galaxy import util
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11 from galaxy.datatypes.sniff import *
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12 from galaxy.web import url_for
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13 from cgi import escape
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14 import urllib
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15 from bx.intervals.io import *
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16 from galaxy.datatypes import metadata
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17 from galaxy.datatypes.metadata import MetadataElement
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18 from galaxy.datatypes.tabular import Tabular
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19 import math
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20
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21 log = logging.getLogger(__name__)
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22
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23 class Ontology( data.Text ):
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24 """Any ontology Format"""
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25 file_ext = "ontology"
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26
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27 def init_meta( self, dataset, copy_from=None ):
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28 data.Text.init_meta( self, dataset, copy_from=copy_from )
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29
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30
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31 class Obo( Ontology ):
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32 """OBO Format"""
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33 file_ext = "obo"
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34
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35 def init_meta( self, dataset, copy_from=None ):
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36 data.Text.init_meta( self, dataset, copy_from=copy_from )
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37 def sniff( self, filename ):
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38 """
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39 Determines whether the file is in OBO format
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40 """
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41 headers = get_headers( filename, '\n' )
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42 try:
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43 for hdr in headers:
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44 if hdr and hdr[0].startswith( 'format-version:' ) :
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45 return True
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46 return False
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47 except:
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48 return False
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49
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50 class Owl( Ontology ):
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51 """OWL"""
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52 file_ext = "owl"
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53
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54 def init_meta( self, dataset, copy_from=None ):
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55 data.Text.init_meta( self, dataset, copy_from=copy_from )
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56 def sniff( self, filename ):
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57 """
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58 Determines whether the file is in OWL RDF-XML format
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59 """
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60 headers = get_headers( filename, '\n' )
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61 try:
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62 for hdr in headers:
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63 if hdr and hdr[0].find( '<owl' ) > -1 :
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64 return True
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65 if hdr and hdr[0].find( 'http://www.w3.org/2002/07/owl' ) > -1 :
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66 return True
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67 return False
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68 except:
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69 return False
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70
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71
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72 class OwlRdfXML( Owl ):
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73 """OWL RDF/XML"""
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74
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75 def init_meta( self, dataset, copy_from=None ):
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76 data.Text.init_meta( self, dataset, copy_from=copy_from )
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77 def sniff( self, filename ):
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78 """
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79 Determines whether the file is in OWL RDF-XML format
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80 """
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81 headers = get_headers( filename, '\n' )
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82 try:
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83 for hdr in headers:
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84 if hdr and hdr[0].find( '<owl:Ontology' ) > -1 :
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85 return True
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86 return False
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87 except:
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88 return False
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89
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90
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