Mercurial > repos > xuebing > sharplabtool

comparison tools/validation/fix_errors_code.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 # runs after the job (and after the default post-filter)
2
3 import pkg_resources
4 pkg_resources.require( "bx-python" )
5
6 from galaxy import datatypes, jobs, util
7 # needed to reference ParseError types, is this bad?
8 from bx.tabular.io import *
9 from bx.intervals.io import *
10 import sys, tempfile, os
11
12 def validate(incoming):
13 """Validator"""
14 #raise Exception, 'not quite right'
15 pass
16
17 def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
18 """Build a temp file with errors in it"""
19 errors = []
20 for name, data in inp_data.items():
21 validation_errors = data.validation_errors
22 for error in validation_errors:
23 # build dummy class
24 try:
25 temp = eval(error.err_type)()
26 except:
27 temp = object()
28 # stuff attributes
29 temp.__dict__ = util.string_to_object( error.attributes )
30 errors.append(temp)
31 # There *should* only be 1 input, so we assume there is and continue
32 # base64 pickel
33 errors_str = util.object_to_string( errors )
34 # write
35 database_tmp = "./database/tmp" # globaly visible path
36 error_file = tempfile.NamedTemporaryFile(mode="w", dir=database_tmp, suffix=".b64")
37 error_file_name = error_file.name
38 error_file.close()
39 error_file = open(error_file_name, "w")
40 error_file.write(errors_str)
41 error_file.close()
42 param_dict["errorsfile"] = error_file_name
43
44
45 def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
46 # in a perfect world, changes to param_dict would persist
47 # for now, unlink from tool
48 # os.unlink(param_dict["errorsfile"])
49 pass