Commit Graph
4 Commits
Author SHA1 Message Date
Nicola Soranzo 8afac1afd5 Use `load_app_properties()` to load Galaxy config file
instead of directly loading it as YAML.
Will make it easier to uniformly deal with changes of format (e.g.
we are deprecating ini now).

Fix traceback:

```
Traceback (most recent call last):
  File "scripts/config_parse.py", line 31, in <module>
    main(args.config_file, args.setting)
  File "scripts/config_parse.py", line 16, in main
    gx_config = GalaxyAppConfiguration(**yaml.safe_load(open(config))["galaxy"])
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/__init__.py", line 125, in safe_load
    return load(stream, SafeLoader)
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/__init__.py", line 81, in load
    return loader.get_single_data()
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/constructor.py", line 49, in get_single_data
    node = self.get_single_node()
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/composer.py", line 39, in get_single_node
    if not self.check_event(StreamEndEvent):
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/parser.py", line 98, in check_event
    self.current_event = self.state()
  File "/home/berntm/.planemo/gx_venv_3/lib/python3.8/site-packages/yaml/parser.py", line 171, in parse_document_start
    raise ParserError(None, None,
yaml.parser.ParserError: expected '<document start>', but found '<scalar>'
  in "/tmp/tmpsffm7of5/galaxy.ini", line 3, column 1
```

when starting Galaxy with a `galaxy.ini` config file (though Galaxy startup
will still fail later).
2022-04-26 09:48:18 +01:00
Dannon Baker 274fcf3bb3 Isort 2022-04-05 13:42:32 -04:00
Dannon Baker 04ed93d81f Make sure config actually exists. Exits silently if nothing found or
no matches.
2022-04-05 09:34:11 -04:00
Dannon Baker cb94125acf Add simple script to load specific options from galaxy config and print either a single value resolved or the loaded config dict 2022-04-04 08:55:11 -04:00