annotate jcds_wrapper.py @ 44:bab44ade984c draft

Uploaded 20170622
author fabio
date Thu, 22 Jun 2017 16:34:10 -0400
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1 #!/usr/bin/env python
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2 import json_collect_data_source as jcds
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3 import optparse
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4
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5 __version__ = "1.0.0"
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6
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7 def __main__():
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8 """ Read the JSON return from a data source. Parse each line and request
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9 the data, download to "newfilepath", and write metadata.
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10
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11 Schema
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12 ------
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13
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14 [ {"url":"http://url/to/file.tar.gz",
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15 "name":"My Archive",
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16 "extension":"tar.gz",
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17 "organize":"true",
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18 "metadata":{"db_key":"hg38"},
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19 "extra_data":[ {"url":"http://url_of_ext_file",
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20 "path":"rel/path/to/ext_file"}
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21 ]
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22 }
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23 ]
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24
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25 """
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26 # Parse the command line options
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27 usage = "Usage: jcds_wrapper.py max_size --json_param_file filename [options]"
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28 parser = optparse.OptionParser(usage = usage)
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29 parser.add_option("-j", "--json_param_file", type="string",
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30 action="store", dest="json_param_file", help="json schema return data")
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31 parser.add_option("-p", "--path", type="string",
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32 action="store", dest="path", help="new file path")
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33 # set appdata: temporary directory in which the archives will be decompressed
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34 parser.add_option("-a", "--appdata", type="string",
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35 action="store", dest="appdata", help="appdata folder name")
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36 parser.add_option("-v", "--version", action="store_true", dest="version",
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37 default=False, help="display version and exit")
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38
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39 (options, args) = parser.parse_args()
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40 if options.version:
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41 print __version__
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42 else:
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43 jcds.download_from_json_data( options, args )
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46 if __name__ == "__main__": __main__()