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1 #!/usr/bin/env python
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2
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3 import gzip
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4 import json
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5 import optparse # using optparse as hydra still python 2.6
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6 import os.path
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7 import shutil
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8
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9 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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10 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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11 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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12 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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13 return data_manager_dict
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14
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15
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16 def get_param(name, params, default=None, check_tab=True):
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17 value = params.get(name)
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18 print name, value
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19 return check_param(name, value, default=default, check_tab=check_tab)
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20
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21
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22 def check_param(name, value, default=None, check_tab=True):
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23 if value in [ None, '', '?' ]:
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24 if default:
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25 print "Using {0} for {1} as no value provided".format( default, name )
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26 value = default
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27 else:
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28 raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
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29 if check_tab and "\t" in value:
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30 raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
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31 return value
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32
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33 def check_extension(extension):
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34 extension = extension.strip()
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35 if extension[0] == ".":
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36 extension = extension[1:]
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37 return extension
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38
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39
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40 def check_path(path, original_extension):
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41 files = os.listdir(path)
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42 check = "." + original_extension
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43 for a_file in files:
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44 if a_file.endswith(check):
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45 return True
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46 raise Exception( 'path {0} does not contain any files ending with {1}'.format( path, check ) )
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47
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48
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49 def main():
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50
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51 #Parse Command Line
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52 parser = optparse.OptionParser()
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53 parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' )
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54 parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' )
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55 (options, args) = parser.parse_args()
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56
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57 data_table_name = check_param("data_table_name", options.data_table_name)
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58 json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
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59
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60 param_dict = json.loads( open( json_output_file ).read() )
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61 params = param_dict.get("param_dict")
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62 print "input params:"
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63 print params
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64
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65 data_table_entry = {}
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66 data_table_entry["original_extension"] = check_extension(get_param("original_extension", params))
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67 data_table_entry["galaxy_extension"] = check_extension(get_param("galaxy_extension", params))
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68 data_table_entry["decompress"] = get_param("decompress", params)
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69 if not (data_table_entry["decompress"] in ["No","Yes"]):
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70 raise Exception( "Only legal values for dcompress are No and Yes." )
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71 data_table_entry["path"] = get_param("path", params)
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72 check_path(data_table_entry["path"], data_table_entry["original_extension"])
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73
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74 basename = os.path.basename(data_table_entry["path"])
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75 filename = os.path.splitext(basename)[0]
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76 data_table_entry["name"] = get_param("name", params, default=filename)
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77 data_table_entry["value"] = get_param("value", params, default=data_table_entry["name"])
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78 data_table_entry["dbkey"] = get_param("dbkey", params, default=data_table_entry["value"])
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79
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80 data_manager_dict = {}
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81 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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82
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83 print "output:"
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84 print data_manager_dict
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85 # save info to json file
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86 with open( json_output_file, 'wb' ) as output_file:
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87 output_file.write( json.dumps( data_manager_dict ) )
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88 output_file.write( "\n" )
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89
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90
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91 if __name__ == "__main__":
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92 main()
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