Added tool version directories for validation and visualization tools directories.

tools/validation/fix_errors_code.py

@@ -1,49 +0,0 @@
-# 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