Mercurial > repos > rmarenco > hubarchivecreator
comparison trackHub/tracks_partial.py @ 1:fb5e60d4d18a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
| author | rmarenco |
|---|---|
| date | Wed, 13 Jul 2016 13:36:37 -0400 |
| parents | |
| children | 3233451a3bd6 |
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| 0:0f3bc17e5ede | 1:fb5e60d4d18a |
|---|---|
| 1 """ | |
| 2 HubAssembly datatype | |
| 3 """ | |
| 4 import logging | |
| 5 | |
| 6 from galaxy.datatypes.text import Html | |
| 7 | |
| 8 log = logging.getLogger( __name__ ) | |
| 9 | |
| 10 # !!! README !!! The content of this file should be added in tracks.py, but do it carefully! | |
| 11 # Don't erase the existing content | |
| 12 | |
| 13 | |
| 14 class UCSCTrackHub( Html ): | |
| 15 """ | |
| 16 derived class for BioC data structures in Galaxy | |
| 17 """ | |
| 18 | |
| 19 file_ext = 'trackhub' | |
| 20 composite_type = 'auto_primary_file' | |
| 21 | |
| 22 def __init__( self, **kwd ): | |
| 23 Html.__init__( self, **kwd ) | |
| 24 | |
| 25 def generate_primary_file( self, dataset=None ): | |
| 26 """ | |
| 27 This is called only at upload to write the html file | |
| 28 cannot rename the datasets here - they come with the default unfortunately | |
| 29 """ | |
| 30 rval = [ | |
| 31 '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\ | |
| 32 This composite dataset is composed of the following files:<p/><ul>' % ( | |
| 33 self.file_ext)] | |
| 34 for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems(): | |
| 35 opt_text = '' | |
| 36 if composite_file.optional: | |
| 37 opt_text = ' (optional)' | |
| 38 rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text)) | |
| 39 rval.append('</ul></html>') | |
| 40 return "\n".join(rval) | |
| 41 | |
| 42 def set_peek( self, dataset, is_multi_byte=False ): | |
| 43 if not dataset.dataset.purged: | |
| 44 dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub" | |
| 45 else: | |
| 46 dataset.peek = 'file does not exist' | |
| 47 dataset.blurb = 'file purged from disk' | |
| 48 | |
| 49 def display_peek( self, dataset ): | |
| 50 try: | |
| 51 return dataset.peek | |
| 52 except: | |
| 53 return "Track Hub structure: Visualization in UCSC Track Hub" | |
| 54 | |
| 55 def sniff( self, filename ): | |
| 56 return False |