Mercurial > repos > rmarenco > hubarchivecreator

annotate trackHub/tracks_partial.py @ 29:7e8a8b732db3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Wed, 16 May 2018 18:04:20 -0400
parents 3233451a3bd6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
1 """
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
2 HubAssembly datatype
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
3 """
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
4 import logging
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
5
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
6 from galaxy.datatypes.text import Html
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
7
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
8 log = logging.getLogger( __name__ )
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
9
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
10 # !!! README !!! The content of this file should be added in tracks.py, but do it carefully!
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
11 # Don't erase the existing content
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
12
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
13
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
14 class UCSCTrackHub( Html ):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
15 """
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
16 derived class for BioC data structures in Galaxy
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
17 """
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
18
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
19 file_ext = 'trackhub'
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
20 composite_type = 'auto_primary_file'
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
21
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
22 def __init__( self, **kwd ):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
23 Html.__init__( self, **kwd )
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
24
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
25 def generate_primary_file( self, dataset=None ):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
26 """
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
27 This is called only at upload to write the html file
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
28 cannot rename the datasets here - they come with the default unfortunately
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
29 """
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
30 rval = [
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
31 '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
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
rmarenco
parents:
diff changeset
33 self.file_ext)]
16
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
34
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
35 def create_tree(path, tree):
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
36 if path[0] in tree:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
37 create_tree(path[1:], tree[path[0]])
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
38 else:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
39 tree[path[0]] = {}
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
40 if len(path) == 1:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
41 return
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
42 else:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
43 create_tree(path[1:], tree[path[0]])
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
44
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
45 def print_tree(tree, level):
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
46 if len(tree) == 0:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
47 return
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
48
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
49 for vertex in tree:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
50 composite_name = vertex
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
51 bullet_point = '<li><a href="{0}>{0}</a></li>'.format(composite_name)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
52 rval.append(bullet_point)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
53 # Parent, so need to create a sub <ul>
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
54 if len(tree[vertex]) > 0:
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
55 rval.append('<ul>')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
56 print_tree(tree[vertex], level+1)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
57 rval.append('</ul>')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
58
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
59 walkable_tree = {}
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
60
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
61 for composite_name_full_path, composite_file in self.get_composite_files(dataset=dataset).iteritems():
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
62 paths = composite_name_full_path.split('/')
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
63 # Prepare the tree from to perform a Depth First Search
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
64 create_tree(paths, walkable_tree)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
65
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
66 # Perform a Depth First Search to print all the directory and files properly
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
67 print_tree(walkable_tree, 0)
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
68
3233451a3bd6 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
rmarenco
parents: 1
diff changeset
69 # rval.append('<li><a href="%s">%s</a>%s' % (composite_name, composite_name, opt_text))
1
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
70 rval.append('</ul></html>')
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
71 return "\n".join(rval)
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
72
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
73 def set_peek( self, dataset, is_multi_byte=False ):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
74 if not dataset.dataset.purged:
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
75 dataset.peek = "Track Hub structure: Visualization in UCSC Track Hub"
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
76 else:
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
77 dataset.peek = 'file does not exist'
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
78 dataset.blurb = 'file purged from disk'
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
79
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
80 def display_peek( self, dataset ):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
81 try:
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
82 return dataset.peek
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
83 except:
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
84 return "Track Hub structure: Visualization in UCSC Track Hub"
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
85
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
86 def sniff( self, filename ):
fb5e60d4d18a planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
rmarenco
parents:
diff changeset
87 return False