#!/usr/bin/env python """ A command line helper for common operations performed by Galaxy maintainers. Encodes and decodes IDs, returns Dataset IDs if provided an HDA or LDDA id, returns the disk path of a dataset. """ import argparse import os import sys sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, "lib")) import galaxy.config from galaxy.model.mapping import init_models_from_config from galaxy.security import idencoding from galaxy.util.script import ( app_properties_from_args, populate_config_args, ) parser = argparse.ArgumentParser() populate_config_args(parser) parser.add_argument("-e", "--encode-id", dest="encode_id", help="Encode an ID") parser.add_argument("-d", "--decode-id", dest="decode_id", help="Decode an ID") parser.add_argument("--hda", dest="hda_id", help="Display HistoryDatasetAssociation info") parser.add_argument("--ldda", dest="ldda_id", help="Display LibraryDatasetDatasetAssociation info") args = parser.parse_args() app_properties = app_properties_from_args(args) config = galaxy.config.Configuration(**app_properties) helper = idencoding.IdEncodingHelper(id_secret=app_properties.get("id_secret")) model = init_models_from_config(config) if args.encode_id: print(f'Encoded "{args.encode_id}": {helper.encode_id(args.encode_id)}') if args.decode_id: print(f'Decoded "{args.decode_id}": {helper.decode_id(args.decode_id)}') if args.hda_id: try: hda_id = int(args.hda_id) except Exception: hda_id = int(helper.decode_id(args.hda_id)) hda = model.session.get(model.HistoryDatasetAssociation, hda_id) print(f'HDA "{hda.id}" is Dataset "{hda.dataset.id}" at: {hda.get_file_name()}') if args.ldda_id: try: ldda_id = int(args.ldda_id) except Exception: ldda_id = int(helper.decode_id(args.ldda_id)) ldda = model.session.get(model.LibraryDatasetDatasetAssociation, ldda_id) print(f'LDDA "{ldda.id}" is Dataset "{ldda.dataset.id}" at: {ldda.get_file_name()}')