diff alveo_get_primary_text.py @ 18:5e1b7d922ea3 draft default tip

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit 53cde5cc9b8c1adcccdc3cfa52d8ca82079aeda7

--- a/alveo_get_primary_text.py	Sun Dec 03 18:57:51 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-from __future__ import print_function
-import argparse
-import pyalveo
-import sys
-import os
-
-from util import API_URL, read_item_list
-
-
-def parser():
-    parser = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List")
-    parser.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
-    parser.add_argument('--item_list', required=True, action="store", type=str, help="File containing list of item URLs")
-    parser.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file")
-    return parser.parse_args()
-
-
-# this file name pattern allows galaxy to discover the dataset designation and type
-FNPAT = "%(designation)s_%(ext)s"
-
-
-def galaxy_name(fname, ext):
-    """construct a filename suitable for Galaxy dataset discovery"""
-
-    fname = FNPAT % {'designation': fname, 'ext': ext}
-
-    return fname
-
-
-def download_text(item_list, output_path):
-    """
-    Downloads primary text from a list of items to the directory specified by output_path.
-
-    :type item_list: ItemGroup
-    :param item_list: item list to download
-
-    :type output_path: String
-    :param output_path: directory to download to the documents to
-    """
-    if not os.path.exists(output_path):
-        os.makedirs(output_path)
-
-    downloaded = []
-
-    items = item_list.get_all()
-    for item in items:
-        md = item.metadata()
-        fname = os.path.join(output_path, galaxy_name(md['alveo:metadata']['dcterms:identifier'], 'txt'))
-        content = item.get_primary_text()
-        if content is not None:
-            with open(fname, 'w') as out:
-                out.write(content.decode('utf-8'))
-
-    return downloaded
-
-
-def main():
-    args = parser()
-    try:
-        api_key = open(args.api_key, 'r').read().strip()
-        client = pyalveo.Client(api_url=API_URL, api_key=api_key, use_cache=False)
-        item_list = read_item_list(args.item_list, client)
-        download_text(item_list, args.output_path)
-    except pyalveo.APIError as e:
-        print("ERROR: " + str(e), file=sys.stderr)
-        sys.exit(1)
-
-
-if __name__ == '__main__':
-    main()