| Previous changeset 43:73d593ff91e4 (2017-06-22) Next changeset 45:b0d8d9cdf942 (2017-06-22) |
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Commit message:
Uploaded 20170622 |
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modified:
gdcwebapp.xml |
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added:
._jcds_wrapper.py jcds_wrapper.py |
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| diff -r 73d593ff91e4 -r bab44ade984c ._jcds_wrapper.py |
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| Binary file ._jcds_wrapper.py has changed |
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| diff -r 73d593ff91e4 -r bab44ade984c gdcwebapp.xml --- a/gdcwebapp.xml Thu Jun 22 14:24:50 2017 -0400 +++ b/gdcwebapp.xml Thu Jun 22 16:34:10 2017 -0400 |
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| @@ -9,7 +9,11 @@ <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> - <command>json_collect_data_source.py '${__app__.config.output_size_limit}' --json_param_file '${output1}' --path '.' --appdata 'tmp'</command> + <command> +<![CDATA[ + python '$__tool_directory__/jcds_wrapper.py' '${__app__.config.output_size_limit}' --json_param_file '${output1}' --path '.' --appdata 'tmp' +]]> + </command> <inputs check_values="False" action="http://bioinf.iasi.cnr.it/gdcwebapp/app.php"> <display>Go to GDCWebApp service $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/async/data_source_gdcwebapp" /> |
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| diff -r 73d593ff91e4 -r bab44ade984c jcds_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jcds_wrapper.py Thu Jun 22 16:34:10 2017 -0400 |
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| @@ -0,0 +1,46 @@ +#!/usr/bin/env python +import json_collect_data_source as jcds +import optparse + +__version__ = "1.0.0" + +def __main__(): + """ Read the JSON return from a data source. Parse each line and request + the data, download to "newfilepath", and write metadata. + + Schema + ------ + + [ {"url":"http://url/to/file.tar.gz", + "name":"My Archive", + "extension":"tar.gz", + "organize":"true", + "metadata":{"db_key":"hg38"}, + "extra_data":[ {"url":"http://url_of_ext_file", + "path":"rel/path/to/ext_file"} + ] + } + ] + + """ + # Parse the command line options + usage = "Usage: jcds_wrapper.py max_size --json_param_file filename [options]" + parser = optparse.OptionParser(usage = usage) + parser.add_option("-j", "--json_param_file", type="string", + action="store", dest="json_param_file", help="json schema return data") + parser.add_option("-p", "--path", type="string", + action="store", dest="path", help="new file path") + # set appdata: temporary directory in which the archives will be decompressed + parser.add_option("-a", "--appdata", type="string", + action="store", dest="appdata", help="appdata folder name") + parser.add_option("-v", "--version", action="store_true", dest="version", + default=False, help="display version and exit") + + (options, args) = parser.parse_args() + if options.version: + print __version__ + else: + jcds.download_from_json_data( options, args ) + + +if __name__ == "__main__": __main__() |