Source code for galaxy.datatypes.tracks

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

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

    from galaxy.model import DatasetInstance

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]class UCSCTrackHub(Html): """ Datatype for UCSC TrackHub """ file_ext = "trackhub" composite_type = "auto_primary_file"
[docs] def generate_primary_file(self, dataset: GeneratePrimaryFileDataset) -> str: """ 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(f'<li><a href="{composite_name}">{composite_name}</a>{opt_text}') rval.append("</ul></html>") return "\n".join(rval)
[docs] def set_peek(self, dataset: "DatasetInstance", **kwd) -> None: 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: "DatasetInstance") -> str: try: return dataset.peek except Exception: return "Track Hub structure: Visualization in UCSC Track Hub"
[docs] def sniff(self, filename: str) -> bool: return False