Mercurial > repos > rmarenco > hubarchivecreator
annotate trackHub/tracks_partial.py @ 1:fb5e60d4d18a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author | rmarenco |
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date | Wed, 13 Jul 2016 13:36:37 -0400 |
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children | 3233451a3bd6 |
rev | line source |
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fb5e60d4d18a
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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1 """ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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2 HubAssembly datatype |
fb5e60d4d18a
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3 """ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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4 import logging |
fb5e60d4d18a
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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5 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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6 from galaxy.datatypes.text import Html |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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7 |
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8 log = logging.getLogger( __name__ ) |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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9 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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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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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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12 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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13 |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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14 class UCSCTrackHub( Html ): |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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15 """ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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16 derived class for BioC data structures in Galaxy |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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17 """ |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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18 |
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19 file_ext = 'trackhub' |
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20 composite_type = 'auto_primary_file' |
fb5e60d4d18a
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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21 |
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22 def __init__( self, **kwd ): |
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23 Html.__init__( self, **kwd ) |
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24 |
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25 def generate_primary_file( self, dataset=None ): |
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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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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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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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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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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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32 This composite dataset is composed of the following files:<p/><ul>' % ( |
fb5e60d4d18a
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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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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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
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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 |