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