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Source code for galaxy.datatypes.tracks

Datatype classes for tracks/track views within galaxy.
import logging

from galaxy.datatypes.text import Html
from . import binary

log = logging.getLogger(__name__)

# GeneTrack is no longer supported but leaving the datatype since
# files of this type may still exist
[docs]class GeneTrack(binary.Binary): edam_data = "data_3002" edam_format = "format_2919" file_ext = "genetrack"
[docs] def __init__(self, **kwargs): super(GeneTrack, self).__init__(**kwargs)
# self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' ) # def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): #Force target_frame to be 'galaxy_main' # return binary.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) # def genetrack_link( self, hda, type, app, base_url ): # ret_val = [] # if hda.dataset.has_data(): # Get the disk file name and data id # file_name = hda.dataset.get_file_name() # data_id = quote_plus( str( hda.id ) ) # galaxy_url = quote_plus( "%s%s" % ( base_url, url_for( controller = 'tool_runner', tool_id='predict2genetrack' ) ) ) # Make it secure # hashkey = quote_plus( hmac_new( app.config.tool_secret, file_name ) ) # encoded = quote_plus( binascii.hexlify( file_name ) ) # for name, url in util.get_genetrack_sites(): # if name.lower() in app.config.genetrack_display_sites: # send both parameters filename and hashkey # link = "%s?filename=%s&hashkey=%s&input=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, galaxy_url ) # ret_val.append( ( name, link ) ) # return ret_val
[docs]class UCSCTrackHub(Html): """ Datatype for UCSC TrackHub """ file_ext = 'trackhub' composite_type = 'auto_primary_file'
[docs] def __init__(self, **kwd): Html.__init__(self, **kwd)
[docs] 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).items(): 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)
[docs] 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'
[docs] def display_peek(self, dataset): try: return dataset.peek except Exception: return "Track Hub structure: Visualization in UCSC Track Hub"
[docs] def sniff(self, filename): return False