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