Mercurial > repos > yating-l > hubarchivecreator

annotate trackHub/tracks_partial.py @ 18:f23321937d46 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
author yating-l
date Thu, 29 Dec 2016 10:34:28 -0500
parents 3e0c61b52a06
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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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5
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6 from galaxy.datatypes.text import Html
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7
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8 log = logging.getLogger( __name__ )
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9
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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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12
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13
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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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18
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19 file_ext = 'trackhub'
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20 composite_type = 'auto_primary_file'
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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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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
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35 def create_tree(path, tree):
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36 if path[0] in tree:
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37 create_tree(path[1:], tree[path[0]])
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38 else:
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39 tree[path[0]] = {}
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40 if len(path) == 1:
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41 return
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42 else:
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43 create_tree(path[1:], tree[path[0]])
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44
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45 def print_tree(tree, level):
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46 if len(tree) == 0:
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47 return
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48
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49 for vertex in tree:
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50 composite_name = vertex
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51 bullet_point = '<li><a href="{0}>{0}</a></li>'.format(composite_name)
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52 rval.append(bullet_point)
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53 # Parent, so need to create a sub <ul>
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54 if len(tree[vertex]) > 0:
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55 rval.append('<ul>')
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56 print_tree(tree[vertex], level+1)
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57 rval.append('</ul>')
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58
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59 walkable_tree = {}
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60
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61 for composite_name_full_path, composite_file in self.get_composite_files(dataset=dataset).iteritems():
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62 paths = composite_name_full_path.split('/')
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63 # Prepare the tree from to perform a Depth First Search
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64 create_tree(paths, walkable_tree)
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65
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66 # Perform a Depth First Search to print all the directory and files properly
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67 print_tree(walkable_tree, 0)
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68
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69 # rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
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70 rval.append('</ul></html>')
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71 return "\n".join(rval)
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72
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73 def set_peek( self, dataset, is_multi_byte=False ):
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74 if not dataset.dataset.purged:
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75 dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
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76 else:
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77 dataset.peek = 'file does not exist'
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78 dataset.blurb = 'file purged from disk'
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79
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80 def display_peek( self, dataset ):
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81 try:
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82 return dataset.peek
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83 except:
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84 return "Track Hub structure: Visualization in UCSC Track Hub"
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85
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86 def sniff( self, filename ):
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87 return False