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1 # runs after the job (and after the default post-filter)
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2 import os
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3 from galaxy import eggs
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4 from galaxy import jobs
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5 from galaxy.tools.parameters import DataToolParameter
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6
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7 from galaxy.jobs.handler import JOB_ERROR
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8
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9 # Older py compatibility
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10 try:
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11 set()
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12 except:
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13 from sets import Set as set
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14
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15 #def exec_before_process(app, inp_data, out_data, param_dict, tool=None):
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16 # """Sets the name of the data"""
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17 # dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] )
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18 # if len(dbkeys) != 1:
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19 # raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>'
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20
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21 def validate_input( trans, error_map, param_values, page_param_map ):
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22 dbkeys = set()
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23 data_param_names = set()
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24 data_params = 0
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25 for name, param in page_param_map.iteritems():
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26 if isinstance( param, DataToolParameter ):
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27 # for each dataset parameter
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28 if param_values.get(name, None) != None:
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29 dbkeys.add( param_values[name].dbkey )
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30 data_params += 1
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31 # check meta data
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32 try:
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33 param = param_values[name]
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34 if isinstance( param.datatype, trans.app.datatypes_registry.get_datatype_by_extension( 'gff' ).__class__ ):
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35 # TODO: currently cannot validate GFF inputs b/c they are not derived from interval.
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36 pass
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37 else: # Validate interval datatype.
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38 startCol = int( param.metadata.startCol )
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39 endCol = int( param.metadata.endCol )
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40 chromCol = int( param.metadata.chromCol )
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41 if param.metadata.strandCol is not None:
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42 strandCol = int ( param.metadata.strandCol )
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43 else:
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44 strandCol = 0
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45 except:
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46 error_msg = "The attributes of this dataset are not properly set. " + \
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47 "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
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48 error_map[name] = error_msg
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49 data_param_names.add( name )
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50 if len( dbkeys ) > 1:
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51 for name in data_param_names:
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52 error_map[name] = "All datasets must belong to same genomic build, " \
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53 "this dataset is linked to build '%s'" % param_values[name].dbkey
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54 if data_params != len(data_param_names):
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55 for name in data_param_names:
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56 error_map[name] = "A dataset of the appropriate type is required"
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57
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58 # Commented out by INS, 5/30/2007. What is the PURPOSE of this?
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59 def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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60 """Verify the output data after each run"""
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61 items = out_data.items()
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62
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63 for name, data in items:
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64 try:
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65 if stderr and len( stderr ) > 0:
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66 raise Exception( stderr )
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67
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68 except Exception, exc:
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69 data.blurb = JOB_ERROR
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70 data.state = JOB_ERROR
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71
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72 ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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73 ## pass
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74
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75
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76 def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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77 exec_after_process(
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78 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
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79
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80 # strip strand column if clusters were merged
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81 items = out_data.items()
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82 for name, data in items:
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83 if param_dict['returntype'] == True:
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84 data.metadata.chromCol = 1
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85 data.metadata.startCol = 2
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86 data.metadata.endCol = 3
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87 # merge always clobbers strand
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88 data.metadata.strandCol = None
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89
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90
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91 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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92 exec_after_process(
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93 app, inp_data, out_data, param_dict, tool=tool, stdout=stdout, stderr=stderr)
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94
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95 # strip strand column if clusters were merged
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96 if param_dict["returntype"] == '1':
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97 items = out_data.items()
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98 for name, data in items:
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99 data.metadata.strandCol = None
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