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comparison homerDatatypes.py @ 2:7268cbc535e5 draft

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findpeaks and maketagdirectory
author kevyin
date Fri, 23 Nov 2012 00:30:27 -0500
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1:59d58008c40d 2:7268cbc535e5
1 """
2 homer composite datatypes
3 Use at your peril
4 Kevin Ying
5 for the homer wrapper
6
7 Nov 2012
8 """
9
10 import logging, os, sys, time, tempfile, shutil, string, glob
11 import data
12 from galaxy import util
13 from cgi import escape
14 import urllib, binascii
15 from galaxy.web import url_for
16 from galaxy.datatypes import metadata
17 from galaxy.datatypes.metadata import MetadataElement
18 from galaxy.datatypes.data import Text
19 from galaxy.datatypes.tabular import Tabular
20 from galaxy.datatypes.images import Html
21 from galaxy.datatypes.interval import Interval
22 from galaxy.util.hash_util import *
23
24 gal_Log = logging.getLogger(__name__)
25 verbose = False
26
27 class HomerTagDirectory(Html):
28 """
29 base class to use for homer tag directory datatypes
30 composite datatype elements
31 stored in extra files path
32 """
33
34 #MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='HomerTagDirectory',
35 #readonly=True, set_in_upload=False)
36
37 composite_type = 'auto_primary_file'
38 #allow_datatype_change = False
39 file_ext = 'homerTagDirectory'
40
41 def __init__(self, **kwd):
42 Html.__init__(self, **kwd)
43 self.add_composite_file('tagInfo.txt', description="tagInfo")
44 self.add_composite_file('tagAutocorrelation.txt', description="tagAutocorrelation")
45 self.add_composite_file('tagCountDistribution.txt', description="tagCountDistribution")
46 self.add_composite_file('tagLengthDistribution.txt', description="tagLengthDistribution")
47
48 def generate_primary_file(self, dataset=None):
49 rval = ['<html><head><title>Homer Tag Directory Galaxy Composite Dataset </title></head><p/>']
50 rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
51 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
52 fn = composite_name
53 opt_text = ''
54 if composite_file.optional:
55 opt_text = ' (optional)'
56 if composite_file.get('description'):
57 rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
58 else:
59 rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
60 rval.append( '</ul></div></html>' )
61 return "\n".join( rval )
62
63
64 def regenerate_primary_file(self,dataset):
65 """
66 cannot do this until we are setting metadata
67 """
68 #bn = dataset.metadata.base_name
69 efp = dataset.extra_files_path
70 flist = os.listdir(efp)
71 rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)]
72 for i,fname in enumerate(flist):
73 sfname = os.path.split(fname)[-1]
74 f,e = os.path.splitext(fname)
75 rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
76 rval.append( '</ul></body></html>' )
77 f = file(dataset.file_name,'w')
78 f.write("\n".join( rval ))
79 f.write('\n')
80 f.close()
81
82 def get_mime(self):
83 """Returns the mime type of the datatype"""
84 return 'text/html'
85
86 def set_meta( self, dataset, **kwd ):
87
88 """
89 for homer maketagdirectory eg
90
91 """
92 Html.set_meta( self, dataset, **kwd )
93 if kwd.get('overwrite') == False:
94 if verbose:
95 gal_Log.debug('@@@ HomerTagDirectory set_meta called with overwrite = False')
96 return True
97 try:
98 efp = dataset.extra_files_path
99 except:
100 if verbose:
101 gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
102 return False
103 try:
104 flist = os.listdir(efp)
105 except:
106 if verbose: gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
107 return False
108 if len(flist) == 0:
109 if verbose:
110 gal_Log.debug('@@@ HomerTagDirectory set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
111 return False
112 self.regenerate_primary_file(dataset)
113 if not dataset.info:
114 dataset.info = 'Galaxy HomerTagDirectory datatype object'
115 if not dataset.blurb:
116 dataset.blurb = 'Composite file - Homer Galaxy toolkit'
117 return True
118