changeset 46:33e5c1b7b9af draft

Uploaded

--- a/gdcwebapp.xml	Thu Jun 22 16:34:14 2017 -0400
+++ b/gdcwebapp.xml	Thu Jun 22 22:27:55 2017 -0400
@@ -5,15 +5,7 @@
         <requirement type="package" version="2.7.10">python</requirement>
         <requirement type="package" version="1.0.0">json_collect_data_source</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <command>
-<![CDATA[
-    python '$__tool_directory__/jcds_wrapper.py' '${__app__.config.output_size_limit}' --json_param_file '${output1}' --path '.' --appdata 'tmp'
-]]>
-    </command>
+    <command detect_errors="exit_code">json_collect_data_source.py '${__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" />

--- a/jcds_wrapper.py	Thu Jun 22 16:34:14 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-#!/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__()