How to use the refgenconf.DownloadJsonError function in refgenconf

To help you get started, we’ve selected a few refgenconf examples, based on popular ways it is used in public projects.

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github databio / refgenie / refgenie / refgenie.py View on Github external
num_servers = 0
            # Keep all servers so that child updates maintain server list
            server_list = rgc[CFG_SERVERS_KEY]
            bad_servers = []
            for server_url in rgc[CFG_SERVERS_KEY]:
                num_servers += 1
                try:
                    rgc[CFG_SERVERS_KEY] = server_url
                    pfx, genomes, assets, recipes = _exec_list(rgc, args.command == LIST_REMOTE_CMD, args.genome)
                    if assets is None and genomes is None:
                        continue
                    _LOGGER.info("{} genomes: {}".format(pfx, genomes))
                    if args.command != LIST_REMOTE_CMD:  # Not implemented yet
                        _LOGGER.info("{} recipes: {}".format(pfx, recipes))
                    _LOGGER.info("{} assets:\n{}\n".format(pfx, assets))
                except (DownloadJsonError, ConnectionError):
                    bad_servers.append(server_url)
                    continue
            if num_servers >= len(server_list) and bad_servers:
                _LOGGER.error("Could not list assets from the following server(s): {}".format(bad_servers))
            # Restore original server list, even when we couldn't find assets on a server
            rgc[CFG_SERVERS_KEY] = server_list
        else:  # Only check local assets once
            _LOGGER.info("Server subscriptions: {}".format(", ".join(rgc[CFG_SERVERS_KEY])))
            pfx, genomes, assets, recipes = _exec_list(rgc, args.command == LIST_REMOTE_CMD, args.genome)
            _LOGGER.info("{} genomes: {}".format(pfx, genomes))
            if args.command != LIST_REMOTE_CMD:  # Not implemented yet
                _LOGGER.info("{} recipes: {}".format(pfx, recipes))
            _LOGGER.info("{} assets:\n{}".format(pfx, assets))

    elif args.command == GETSEQ_CMD:
        rgc = RefGenConf(filepath=gencfg, writable=False)

refgenconf

A standardized configuration object for reference genome assemblies

BSD-2-Clause
Latest version published 3 years ago

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