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Merge pull request #340 from oicr-gsi/release-1.4.0
Release 1.4.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -8,49 +8,83 @@ | |
| sys.path.pop(0) # do not import from script directory | ||
|
|
||
| import argparse | ||
| import logging | ||
| from tempfile import TemporaryDirectory | ||
| import djerba.util.mini.constants as constants | ||
| from djerba.util.mini.main import main, arg_processor, MiniDjerbaScriptError | ||
| from djerba.util.mini.mdc import MDCFormatError | ||
| from djerba.version import get_djerba_version | ||
|
|
||
| def get_parser(): | ||
| """Construct the parser for command-line arguments""" | ||
| parser = argparse.ArgumentParser( | ||
| description='Mini-Djerba: A tool for updating bioinformatics clinical reports', | ||
| epilog='Run any subcommand with -h/--help for additional information' | ||
| epilog='For details, run any subcommand with -h/--help, or visit https://djerba.readthedocs.io/en/latest/mini_djerba.html' | ||
| ) | ||
| parser.add_argument('-d', '--debug', action='store_true', help='More verbose logging') | ||
| parser.add_argument('-v', '--verbose', action='store_true', help='Verbose logging') | ||
| parser.add_argument('-q', '--quiet', action='store_true', help='Logging for error messages only') | ||
| parser.add_argument('-l', '--log-path', help='Output file for log messages; defaults to STDERR') | ||
| parser.add_argument('--version', action='store_true', help='Print the version number and exit') | ||
| subparsers = parser.add_subparsers(title='subcommands', help='sub-command help', dest='subparser_name') | ||
| ready_parser = subparsers.add_parser(constants.READY, help='Ready an MDC (mini-Djerba config) file') | ||
| ready_parser.add_argument('-j', '--json', metavar='PATH', help='Existing report JSON. Optional, if not given will generate a blank config file.') | ||
| ready_parser.add_argument('-o', '--out', metavar='PATH', default='config.mdc', help='Output path. Optional, defaults to config.mdc in the current directory.') | ||
| update_parser = subparsers.add_parser(constants.UPDATE, help='Update an existing JSON report file; render HTML and optional PDF') | ||
| setup_parser = subparsers.add_parser(constants.SETUP, help='Set up an MDC (mini-Djerba config) file') | ||
| setup_parser.add_argument('-j', '--json', metavar='PATH', help='Existing report JSON. Optional, if not given will generate a blank config file.') | ||
| setup_parser.add_argument('-o', '--out', metavar='PATH', default='config.mdc', help='Output path. Optional, defaults to config.mdc in the current directory.') | ||
| render_parser = subparsers.add_parser(constants.RENDER, help='Render a JSON report file to HTML and optional PDF, with no changes') | ||
| render_parser.add_argument('-j', '--json', metavar='PATH', required=True, help='Path to the Djerba report JSON file to be updated') | ||
| render_parser.add_argument('-o', '--out-dir', metavar='DIR', default='.', help='Directory for output files. Optional, defaults to the current directory.') | ||
| render_parser.add_argument('-w', '--work-dir', metavar='PATH', help='Path to workspace directory; optional, defaults to a temporary directory') | ||
| render_parser.add_argument('--no-pdf', action='store_true', help='Do not generate PDF output from HTML') | ||
| update_parser = subparsers.add_parser(constants.UPDATE, help='Render a JSON file to HTML and optional PDF, with updates from an MDC file') | ||
| update_parser.add_argument('-c', '--config', metavar='PATH', required=True, help='Path to an MDC (mini-Djerba config) file') | ||
| update_parser.add_argument('-f', '--force', action='store_true', help='Force update of mismatched plugin versions') | ||
| update_parser.add_argument('-j', '--json', metavar='PATH', required=True, help='Path to the Djerba report JSON file to be updated') | ||
| update_parser.add_argument('-o', '--out-dir', metavar='DIR', default='.', help='Directory for output files. Optional, defaults to the current directory.') | ||
| update_parser.add_argument('-p', '--pdf', action='store_true', help='Generate PDF output from HTML') | ||
| update_parser.add_argument('-u', '--write-json', action='store_true', help='Write updated JSON to the output directory') | ||
| update_parser.add_argument('-w', '--work-dir', metavar='PATH', help='Path to workspace directory; optional, defaults to a temporary directory') | ||
| update_parser.add_argument('--no-pdf', action='store_true', help='Do not generate PDF output from HTML') | ||
| return parser | ||
|
|
||
| if __name__ == '__main__': | ||
| parser = get_parser() | ||
| if len(sys.argv) == 1: | ||
| parser.print_help(sys.stderr) | ||
| sys.exit(1) | ||
| # suppress the error stacktrace unless verbose logging is in effect | ||
| error_message = None | ||
| args = parser.parse_args() | ||
| ap = arg_processor(args) | ||
| if args.version: | ||
| print("Djerba core version {0}".format(get_djerba_version())) | ||
| sys.exit(0) | ||
| if not (args.verbose or args.debug or args.quiet): | ||
| args.silent = True | ||
| else: | ||
| args.silent = False | ||
| try: | ||
| with TemporaryDirectory(prefix='mini_djerba_') as tmp_dir: | ||
| main(tmp_dir, ap.get_log_level(), ap.get_log_path()).run(args) | ||
| if hasattr(args, 'no_pdf'): | ||
| args.pdf = not args.no_pdf | ||
| ap = arg_processor(args) | ||
| if hasattr(args, 'work_dir') and args.work_dir != None: | ||
| main(args.work_dir, ap.get_log_level(), ap.get_log_path()).run(args) | ||
| else: | ||
| with TemporaryDirectory(prefix='mini_djerba_') as tmp_dir: | ||
| main(tmp_dir, ap.get_log_level(), ap.get_log_path()).run(args) | ||
| except MDCFormatError as err: | ||
| msg = "Configuration error: Please check the -c/--config file and try again." | ||
| print(msg, file=sys.stderr) | ||
| raise | ||
| error_message = "Error reading the -c/--config file: {0}".format(err) | ||
| if not args.silent: | ||
| raise | ||
| except OSError as err: | ||
| error_message = "Filesystem error: {0}".format(err) | ||
| if not args.silent: | ||
| raise | ||
| except Exception as err: | ||
| msg = "Unexpected Mini-Djerba error! Contact the developers." | ||
| raise MiniDjerbaScriptError(msg) from err | ||
| error_message = "Unexpected Mini-Djerba error! Run with --verbose or --debug for details.\n"+\ | ||
| "If errors persist:\n"+\ | ||
| "- Email [email protected]\n"+\ | ||
| "- Please DO NOT include personal health information (PHI)" | ||
| if not args.silent: | ||
| raise MiniDjerbaScriptError(error_message) from err | ||
| if error_message: | ||
| # only called if logging is "silent" | ||
| print(error_message, file=sys.stderr) | ||
| sys.exit(1) | ||
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