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2 from galaxy.tools.parameters import DataToolParameter
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3
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4 def get_matrix_header( input_dataset ):
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5 """
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6 Not used currently, because the reload of the ckeckboxes did not work.
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7 """
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8 input_handle = open( input_dataset.file_name )
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9 first_header = input_handle.readline()
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10 second_header = input_handle.readline()
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11 return [('%s::%s' % (cname2,cname1), str(int(col_num) + 1), False) for col_num, (cname2, cname1) in enumerate(zip(second_header.split()[1:],first_header.split()[1:])) ]
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12
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13
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14
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15 def _construct_error_map( error_map, rep_dict, rep_parent, child, error_value ):
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16 """
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17 Its no so easy to create a propper error_map for repetitions in Galaxy.
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18 This is a helper function.
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19 """
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20
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21 error_map[ rep_parent ] = [ dict() for t in rep_dict ]
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22 for i in range( len( rep_dict ) ):
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23 error_map[ rep_parent ][i][ child ] = error_value
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24
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25
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26
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27 def validate_input( trans, error_map, param_values, page_param_map ):
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28 """
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29 Validates the user input, before execution.
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30 """
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31 factors = param_values['rep_factorName']
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32 factor_name_list = []
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33 factor_duplication = False
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34 level_duplication = False
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35 overlapping_selection = False
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36
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37 first_condition = True
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38 factor_indieces = list()
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39
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40 for factor in factors:
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41 # factor names should be unique
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42 fn = factor['factorName']
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43 if fn in factor_name_list:
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44 factor_duplication = True
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45 break
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46 factor_name_list.append( fn )
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47
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48 level_name_list = list()
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49 factor_index_list = list()
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50
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51 if first_condition and len( factor['rep_factorLevel'] ) < 2:
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52 # first condition needs to have at least 2 levels
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53 _construct_error_map( error_map, factors, 'rep_factorName', 'rep_factorLevel', [ {'factorLevel': 'The first condition should have at least 2 factor'} for t in factor['rep_factorLevel'] ] )
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54
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55 for level in factor['rep_factorLevel']:
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56 # level names under one factor should be unique
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57 fl = level['factorLevel']
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58 if fl in level_name_list:
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59 level_duplication = True
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60 level_name_list.append( fl )
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61
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62 fi = level['factorIndex']
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63 if fi:
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64 # the checkboxes should not have an overlap
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65 for check in fi:
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66 if check in factor_index_list:
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67 overlapping_selection = True
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68 factor_index_list.append( check )
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69
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70 print set(factor_index_list)
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71 print factor_indieces
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72 if set(factor_index_list) in factor_indieces:
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73 _construct_error_map( error_map, factors, 'rep_factorName', 'rep_factorLevel', [ {'factorLevel': 'It is not allowed to have two identical factors, that means two factors with the same toggeled checked boxes. '} for t in factor['rep_factorLevel'] ] )
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74 else:
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75 factor_indieces.append( set(factor_index_list) )
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76
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77
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78
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79 if level_duplication:
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80 error_map['rep_factorName'] = [ dict() for t in factors ]
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81 for i in range( len( factors ) ):
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82 error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorLevel': 'Factor levels for each factor need to be unique'} for t in factor['rep_factorLevel'] ]
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83 break
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84 if overlapping_selection:
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85 error_map['rep_factorName'] = [ dict() for t in factors ]
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86 for i in range( len( factors ) ):
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87 error_map['rep_factorName'][i]['rep_factorLevel'] = [ {'factorIndex': 'The samples from different factors are not allowed to overlap'} for t in factor['rep_factorLevel'] ]
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88 break
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89
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90 first_condition = False
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91
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92 if factor_duplication:
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93 _construct_error_map( error_map, factors, 'rep_factorName', 'factorName', 'Factor names need to be unique' )
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94 """
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95 error_map['rep_factorName'] = [ dict() for t in factors ]
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96 for i in range( len( factors ) ):
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97 error_map['rep_factorName'][i]['factorName'] = 'Factor names need to be unique'
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98 """
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