comparison ontology.py @ 0:b4db4eaf8fff draft default tip

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0:b4db4eaf8fff

"""
Ontology datatypes

"""
import pkg_resources
pkg_resources.require( "bx-python" )

import logging, os, sys, time, tempfile, shutil
import data
from galaxy import util
from galaxy.datatypes.sniff import *
from galaxy.web import url_for
from cgi import escape
import urllib
from bx.intervals.io import *
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.tabular import Tabular
import math

log = logging.getLogger(__name__)

class Ontology( data.Text ):
    """Any ontology Format"""
    file_ext = "ontology"

    def init_meta( self, dataset, copy_from=None ):
        data.Text.init_meta( self, dataset, copy_from=copy_from )


class Obo( Ontology ):
    """OBO Format"""
    file_ext = "obo"

    def init_meta( self, dataset, copy_from=None ):
        data.Text.init_meta( self, dataset, copy_from=copy_from )
    def sniff( self, filename ):
        """
        Determines whether the file is in OBO format
        """
        headers = get_headers( filename, '\n' )
        try:
            for hdr in headers:
                if hdr and hdr[0].startswith( 'format-version:' ) :
                    return True
            return False
        except:
            return False

class Owl( Ontology ):
    """OWL"""
    file_ext = "owl"

    def init_meta( self, dataset, copy_from=None ):
        data.Text.init_meta( self, dataset, copy_from=copy_from )
    def sniff( self, filename ):
        """
        Determines whether the file is in OWL RDF-XML format
        """
        headers = get_headers( filename, '\n' )
        try:
            for hdr in headers:
                if hdr and hdr[0].find( '<owl' ) > -1 :
                    return True
                if hdr and hdr[0].find( 'http://www.w3.org/2002/07/owl' ) > -1 :
                    return True
            return False
        except:
            return False


class OwlRdfXML( Owl ):
    """OWL RDF/XML"""

    def init_meta( self, dataset, copy_from=None ):
        data.Text.init_meta( self, dataset, copy_from=copy_from )
    def sniff( self, filename ):
        """
        Determines whether the file is in OWL RDF-XML format
        """
        headers = get_headers( filename, '\n' )
        try:
            for hdr in headers:
                if hdr and hdr[0].find( '<owl:Ontology' ) > -1 :
                    return True
            return False
        except:
            return False