This script will list and retrieve files from JGI using the curl API. It will return a list of all files available for download for a given query organism.
positional arguments: organism_abbreviation organism name formatted per JGI's abbreviation. For example, 'Nematostella vectensis' is abbreviated by JGI as 'Nemve1'. The appropriate abbreviation may be found by searching for the organism on JGI; the name used in the URL of the 'Info' page for that organism is the correct abbreviation. The full URL may also be used for this argument (default: None) optional arguments: -h, --help show this help message and exit -x [XML], --xml [XML] specify a local xml file for the query instead of retrieving a new copy from JGI (default: None) -c, --configure initiate configuration dialog to overwrite existing user/password configuration (default: False) -s, --syntax_help -f, --filter_files filter organism results by config categories instead of reporting all files listed by JGI for the query (work in progress) (default: False) -u, --usage print verbose usage information and exit (default: False) -n RETRY_N, --retry_n RETRY_N number of times to retry downloading files with errors (0 to skip such files) (default: 4) -l logfile, --load_failed logfile retry downloading from URLs listed in log file (default: None) -r REGEX, --regex REGEX Regex pattern to use to auto-select and download files (no interactive prompt) (default: None) -a, --all Auto-select and download all files for query (no interactive prompt) (default: False)
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