Mercurial > repos > rmarenco > hubarchivecreator
view trackHub/tracks_partial.py @ 16:3233451a3bd6 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author | rmarenco |
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date | Sun, 25 Sep 2016 11:25:38 -0400 |
parents | fb5e60d4d18a |
children |
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""" 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)] def create_tree(path, tree): if path[0] in tree: create_tree(path[1:], tree[path[0]]) else: tree[path[0]] = {} if len(path) == 1: return else: create_tree(path[1:], tree[path[0]]) def print_tree(tree, level): if len(tree) == 0: return for vertex in tree: composite_name = vertex bullet_point = '<li><a href="{0}>{0}</a></li>'.format(composite_name) rval.append(bullet_point) # Parent, so need to create a sub <ul> if len(tree[vertex]) > 0: rval.append('<ul>') print_tree(tree[vertex], level+1) rval.append('</ul>') walkable_tree = {} for composite_name_full_path, composite_file in self.get_composite_files(dataset=dataset).iteritems(): paths = composite_name_full_path.split('/') # Prepare the tree from to perform a Depth First Search create_tree(paths, walkable_tree) # Perform a Depth First Search to print all the directory and files properly print_tree(walkable_tree, 0) # 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