Mercurial > repos > rmarenco > hubarchivecreator

annotate trackHub/tracks_partial.py @ 7:a030b8023882 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 05d9161e2ac41a34a9ab5b1bb9fc012f6512e1ec
author rmarenco
date Tue, 19 Jul 2016 20:33:12 -0400
parents fb5e60d4d18a
children 3233451a3bd6
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1 """
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2 HubAssembly datatype
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3 """
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4 import logging
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6 from galaxy.datatypes.text import Html
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8 log = logging.getLogger( __name__ )
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10 # !!! README !!! The content of this file should be added in tracks.py, but do it carefully!
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11 # Don't erase the existing content
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14 class UCSCTrackHub( Html ):
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15 """
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16 derived class for BioC data structures in Galaxy
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17 """
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19 file_ext = 'trackhub'
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20 composite_type = 'auto_primary_file'
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22 def __init__( self, **kwd ):
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23 Html.__init__( self, **kwd )
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25 def generate_primary_file( self, dataset=None ):
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26 """
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27 This is called only at upload to write the html file
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28 cannot rename the datasets here - they come with the default unfortunately
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29 """
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30 rval = [
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31 '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
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32 This composite dataset is composed of the following files:<p/><ul>' % (
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33 self.file_ext)]
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34 for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
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35 opt_text = ''
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36 if composite_file.optional:
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37 opt_text = ' (optional)'
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38 rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
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39 rval.append('</ul></html>')
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40 return "\n".join(rval)
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41
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42 def set_peek( self, dataset, is_multi_byte=False ):
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43 if not dataset.dataset.purged:
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44 dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
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45 else:
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46 dataset.peek = 'file does not exist'
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47 dataset.blurb = 'file purged from disk'
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48
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49 def display_peek( self, dataset ):
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50 try:
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51 return dataset.peek
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52 except:
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53 return "Track Hub structure: Visualization in UCSC Track Hub"
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54
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55 def sniff( self, filename ):
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56 return False