|
0
|
1 # runs after the job (and after the default post-filter)
|
|
|
2 import os
|
|
|
3 from galaxy.tools.parameters import DataToolParameter
|
|
|
4
|
|
|
5 from galaxy.jobs.handler import JOB_ERROR
|
|
|
6
|
|
|
7 # Older py compatibility
|
|
|
8 try:
|
|
|
9 set()
|
|
|
10 except:
|
|
|
11 from sets import Set as set
|
|
|
12
|
|
|
13 #def exec_before_process(app, inp_data, out_data, param_dict, tool=None):
|
|
|
14 # """Sets the name of the data"""
|
|
|
15 # dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] )
|
|
|
16 # if len(dbkeys) != 1:
|
|
|
17 # raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>'
|
|
|
18
|
|
|
19 def validate_input( trans, error_map, param_values, page_param_map ):
|
|
|
20 dbkeys = set()
|
|
|
21 data_param_names = set()
|
|
|
22 data_params = 0
|
|
|
23 for name, param in page_param_map.iteritems():
|
|
|
24 if isinstance( param, DataToolParameter ):
|
|
|
25 # for each dataset parameter
|
|
|
26 if param_values.get(name, None) != None:
|
|
|
27 dbkeys.add( param_values[name].dbkey )
|
|
|
28 data_params += 1
|
|
|
29 # check meta data
|
|
|
30 try:
|
|
|
31 param = param_values[name]
|
|
|
32 if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ):
|
|
|
33 # TODO: currently cannot validate GFF inputs b/c they are not derived from interval.
|
|
|
34 pass
|
|
|
35 else: # Validate interval datatype.
|
|
|
36 startCol = int( param.metadata.startCol )
|
|
|
37 endCol = int( param.metadata.endCol )
|
|
|
38 chromCol = int( param.metadata.chromCol )
|
|
|
39 if param.metadata.strandCol is not None:
|
|
|
40 strandCol = int ( param.metadata.strandCol )
|
|
|
41 else:
|
|
|
42 strandCol = 0
|
|
|
43 except:
|
|
|
44 error_msg = "The attributes of this dataset are not properly set. " + \
|
|
|
45 "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
|
|
|
46 error_map[name] = error_msg
|
|
|
47 data_param_names.add( name )
|
|
|
48 if len( dbkeys ) > 1:
|
|
|
49 for name in data_param_names:
|
|
|
50 error_map[name] = "All datasets must belong to same genomic build, " \
|
|
|
51 "this dataset is linked to build '%s'" % param_values[name].dbkey
|
|
|
52 if data_params != len(data_param_names):
|
|
|
53 for name in data_param_names:
|
|
|
54 error_map[name] = "A dataset of the appropriate type is required"
|
|
|
55
|
|
|
56 # Commented out by INS, 5/30/2007. What is the PURPOSE of this?
|
|
|
57 def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
|
|
|
58 """Verify the output data after each run"""
|
|
|
59 items = out_data.items()
|
|
|
60
|
|
|
61 for name, data in items:
|
|
|
62 try:
|
|
|
63 if stderr and len( stderr ) > 0:
|
|
|
64 raise Exception( stderr )
|
|
|
65
|
|
|
66 except Exception, exc:
|
|
|
67 data.blurb = JOB_ERROR
|
|
|
68 data.state = JOB_ERROR
|
|
|
69
|
|
|
70 ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
|
|
|
71 ## pass
|
|
|
72
|
|
|
73
|
|
|
74 def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
|
|
|
75 exec_after_process(
|
|
|
76 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
|
|
|
77
|
|
|
78 # strip strand column if clusters were merged
|
|
|
79 items = out_data.items()
|
|
|
80 for name, data in items:
|
|
|
81 if param_dict['returntype'] == True:
|
|
|
82 data.metadata.chromCol = 1
|
|
|
83 data.metadata.startCol = 2
|
|
|
84 data.metadata.endCol = 3
|
|
|
85 # merge always clobbers strand
|
|
|
86 data.metadata.strandCol = None
|
|
|
87
|
|
|
88
|
|
|
89 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
|
|
|
90 exec_after_process(
|
|
|
91 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
|
|
|
92
|
|
|
93 # strip strand column if clusters were merged
|
|
|
94 if param_dict["returntype"] == '1':
|
|
|
95 items = out_data.items()
|
|
|
96 for name, data in items:
|
|
|
97 data.metadata.strandCol = None
|
