/tools/new_operations/operation_filter.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 99 lines · 68 code · 14 blank · 17 comment · 22 complexity · a6dfa24a9ebcbeed24614fda1ec831ff MD5 · raw file

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