Mercurial > repos > rmarenco > hubarchivecreator

"""
HubAssembly datatype
"""
import logging

from galaxy.datatypes.text import Html

log = logging.getLogger( __name__ )

# !!! README !!! The content of this file should be added in tracks.py, but do it carefully!
# Don't erase the existing content


class UCSCTrackHub( Html ):
    """
    derived class for BioC data structures in Galaxy
    """

    file_ext = 'trackhub'
    composite_type = 'auto_primary_file'

    def __init__( self, **kwd ):
        Html.__init__( self, **kwd )

    def generate_primary_file( self, dataset=None ):
        """
        This is called only at upload to write the html file
        cannot rename the datasets here - they come with the default unfortunately
        """
        rval = [
            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
            This composite dataset is composed of the following files:<p/><ul>' % (
                self.file_ext)]
        for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
            rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
        rval.append('</ul></html>')
        return "\n".join(rval)

    def set_peek( self, dataset, is_multi_byte=False ):
        if not dataset.dataset.purged:
            dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
        else:
            dataset.peek = 'file does not exist'
            dataset.blurb = 'file purged from disk'

    def display_peek( self, dataset ):
        try:
            return dataset.peek
        except:
            return "Track Hub structure: Visualization in UCSC Track Hub"

    def sniff( self, filename ):
        return False
author	rmarenco
date	Wed, 20 Jul 2016 12:29:08 -0400
parents	fb5e60d4d18a
children	3233451a3bd6