/tools/validation/fix_errors_code.py
https://bitbucket.org/h_morita_dbcls/galaxy-central · Python · 49 lines · 44 code · 3 blank · 2 comment · 1 complexity · 34f8daf9fa6f36712e3e3453a490dcef MD5 · raw file
- # runs after the job (and after the default post-filter)
- import pkg_resources
- pkg_resources.require( "bx-python" )
- from galaxy import datatypes, jobs, util
- # needed to reference ParseError types, is this bad?
- from bx.tabular.io import *
- from bx.intervals.io import *
- import sys, tempfile, os
- def validate(incoming):
- """Validator"""
- #raise Exception, 'not quite right'
- pass
- def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
- """Build a temp file with errors in it"""
- errors = []
- for name, data in inp_data.items():
- validation_errors = data.validation_errors
- for error in validation_errors:
- # build dummy class
- try:
- temp = eval(error.err_type)()
- except:
- temp = object()
- # stuff attributes
- temp.__dict__ = util.string_to_object( error.attributes )
- errors.append(temp)
- # There *should* only be 1 input, so we assume there is and continue
- # base64 pickel
- errors_str = util.object_to_string( errors )
- # write
- database_tmp = "./database/tmp" # globaly visible path
- error_file = tempfile.NamedTemporaryFile(mode="w", dir=database_tmp, suffix=".b64")
- error_file_name = error_file.name
- error_file.close()
- error_file = open(error_file_name, "w")
- error_file.write(errors_str)
- error_file.close()
- param_dict["errorsfile"] = error_file_name
-
-
- def exec_after_process( app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
- # in a perfect world, changes to param_dict would persist
- # for now, unlink from tool
- # os.unlink(param_dict["errorsfile"])
- pass