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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().__init__(**kwargs)
[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="{}">{}</a>{}'.format(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