Mercurial > repos > stevecassidy > alveoimport
view alveo_get_item_data.py @ 14:a38315ecf593 draft
planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty
author | stevecassidy |
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date | Wed, 01 Nov 2017 01:18:15 -0400 |
parents | be3fd14899a1 |
children | 5e1b7d922ea3 |
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from __future__ import print_function import argparse import pyalveo import sys import os from fnmatch import fnmatch from util import API_URL, read_item_list def parser(): p = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List") p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key") p.add_argument('--item_list', required=True, action="store", type=str, help="File containing list of item URLs") p.add_argument('--patterns', required=True, action="store", type=str, help="File patterns to download") p.add_argument('--output_path', required=True, action="store", type=str, help="Path to output file") return p.parse_args() # 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': root, '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() 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']['dcterms:identifier'], doc.get_filename()) try: doc.download_content(dir_path=output_path, filename=fname) downloaded.append(doc.get_filename()) except pyalveo.APIError as e: print("ERROR: " + str(e), file=sys.stderr) sys.exit(1) 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) patterns = args.patterns.split(',') download_documents(item_list, patterns, args.output_path) except pyalveo.APIError as e: print("ERROR: " + str(e), file=sys.stderr) sys.exit(1) if __name__ == '__main__': main()