Mercurial > repos > stevecassidy > alveoimport
view alveo_item_list_downloader.py @ 4:3a9f20428cff draft
planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
author | stevecassidy |
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date | Wed, 31 Aug 2016 22:07:27 -0400 |
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from __future__ import print_function import json import argparse import pyalveo import sys import os from fnmatch import fnmatch API_URL = 'https://app.alveo.edu.au' # TODO: export constants to a separate module 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_url', required=True, action="store", type=str, help="Item List to download") parser.add_argument('--patterns', required=True, action="store", type=str, help="File patterns to download") parser.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file") return parser.parse_args() def get_item_list(api_key, item_list_url): client = pyalveo.Client(api_key=api_key, api_url=API_URL, use_cache=False) return client.get_item_list(item_list_url) # this file name pattern allows galaxy to discover the dataset designation and type FNPAT = "%(designation)s_%(ext)s" def galaxy_name(itemname, fname): """construct a filename suitable for Galaxy dataset discovery designation - (dataset identifier) is the file basename ext - defines the dataset type and is the file extension """ root, ext = os.path.splitext(fname) ext = ext[1:] # remove initial . fname = FNPAT % {'designation': itemname, 'ext': ext} return fname def download_documents(item_list, patterns, output_path): """ Downloads a list of documents to the directory specificed by output_path. :type documents: list of pyalveo.Document :param documents: Documents 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() filtered_documents = [] for item in items: documents = item.get_documents() for doc in documents: for pattern in patterns: if not pattern == '' and fnmatch(doc.get_filename(), pattern): fname = galaxy_name(item.metadata()['alveo:metadata']['dc:identifier'], doc.get_filename()) try: doc.download_content(dir_path=output_path, filename=fname) downloaded.append(doc.get_filename()) except: # maybe it doesn't exist or we have no access # TODO: report this pass return downloaded def main(): args = parser() try: api_key = open(args.api_key, 'r').read().strip() item_list = get_item_list(api_key, args.item_list_url) patterns = args.patterns.split(',') downloaded = download_documents(item_list, patterns, args.output_path) # write out a list of downloaded files as a result? except pyalveo.APIError as e: print("ERROR: " + str(e), file=sys.stderr) sys.exit(1) if __name__ == '__main__': main()