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1 #!/usr/bin/env python
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2 # ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
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3
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4 # Rewritten by H.E. Cicada Brokaw Dennis from source downloaded from the toolshed.
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5 # Eventually this should be modified to allow downloading of more than just the one library,
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6 # to let the user select what library/location to download, but that would require the
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7 # download tool to generate the list of libraries to download on the fly. Currently
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8 # we are only using the one library.
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9 # Users can create other ones locally and use this tool to add them if they don't want
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10 # to add them by hand.
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11
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12 import argparse
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13 import os
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14 import tarfile
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15 import urllib
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16
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17 from galaxy.util.json import from_json_string, to_json_string
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18
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19 # The following was used by prior program to get input parameters from the json.
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20 # Just leaving here for reference.
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21 #def get_reference_id_name(params):
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22 # genome_id = params['param_dict']['genome_id']
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23 # genome_name = params['param_dict']['genome_name']
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24 # return genome_id, genome_name
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25 #
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26 #def get_url(params):
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27 # trained_url = params['param_dict']['trained_url']
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28 # return trained_url
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29
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30 def download_from_BroadInst(destination):
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31 ctat_resource_lib = 'https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz'
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32 # FIX - Check that the download directory is empty if it exists. Also, can we check if there is enough space on the device as well?
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33 # FIX - Also we want to make sure that destination is absolute fully specified path.
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34 os.mkdir(destination)
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35 full_filepath = os.path.join(destination, 'GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz')
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36
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37 #Download ref: https://dzone.com/articles/how-download-file-python
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38 #f = urllib2.urlopen(ctat_resource_lib)
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39 #data = f.read()
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40 #with open(filepath, 'wb') as code:
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41 # code.write(data)
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42
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43 urllib.urlretrieve(url=ctat_resource_lib, filename=full_filepath)
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44 # Put the following into a try statement, so that if there is a failure something can be printed about it before reraising exception.
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45 tarfile.open(full_filepath, mode='r:*').extractall()
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46 # FIX - There is additional processing that needs to happen for gmap-fusion to work.
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47 # Get the root filename of the extracted file.
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48 # That directory is the actual destination that needs to be set as the ctat_genome_resource_library
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49
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50 def main():
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51 #Parse Command Line
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52 parser = argparse.ArgumentParser()
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53 parser.add_argument('-d', '--download', action="store_true", \
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54 help='Do not use if you already have the CTAT Resource Library that this program downloads.')
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55 parser.add_argument('-g', '--genome_name', default="GRCh38_gencode_v26", \
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56 help='Is used as the selector text of the entry in the data table.')
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57 parser.add_argument('-p', '--destination_path', \
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58 help='Full path of the CTAT Resource Library location or destination.')
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59 parser.add_argument('-o', '--output_filename', \
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60 help='Name of the output file, where the json dictionary will be written.')
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61 args = parser.parse_args()
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62
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63 # All of the input parameters are written by default to the output file prior to
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64 # this program being called.
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65 # But I do not get input values from the json file, but rather from command line.
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66 # Just leaving the following code as a comment, in case it might be useful to someone later.
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67 # params = from_json_string(open(filename).read())
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68 # target_directory = params['output_data'][0]['extra_files_path']
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69 # os.mkdir(target_directory)
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70
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71 if args.download:
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72 ctat_genome_resource_lib_path = download_from_BroadInst(destination=args.destination_path)
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73 else:
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74 # FIX - probably should check if this is a valid path with an actual CTAT Genome Ref Lib there.
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75 ctat_genome_resource_lib_path = args.destination_path
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76
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77 if (args.genome_name is None) or (args.genome_name == ""):
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78 genome_name = "GRCh38_gencode_v26"
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79 else:
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80 genome_name = args.genome_name
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14
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81 # Set the value to the basename of the directory path minus the extension.
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82 # FIX - Need to make sure is unique. This is not good way to do it. Just doing it this way now for testing.
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83 table_entry_value = os.path.basename(ctat_genome_resource_lib_path).split(".")[0]
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84 data_manager_dict = {}
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85 data_manager_dict['data_tables'] = {}
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86 data_manager_dict['data_tables']['ctat_genome_ref_libs'] = []
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87 data_table_entry = dict(value=table_entry_value, name=genome_name, path=ctat_genome_resource_lib_path)
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88 data_manager_dict['data_tables']['ctat_genome_ref_libs'].append(data_table_entry)
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89
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90 # Save info to json file. This is used to transfer data from the DataManager tool, to the data manager,
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91 # which then puts it into the correct .loc file (I think).
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92 open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
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93
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94 if __name__ == "__main__":
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95 main()
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96
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