mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
Nicola Soranzo
8afac1afd5
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).
32 lines
1.1 KiB
Python
32 lines
1.1 KiB
Python
import argparse
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import os
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import pprint
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import sys
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
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from galaxy.config import GalaxyAppConfiguration
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from galaxy.util.properties import load_app_properties
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def main(config, setting):
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# Use explicit config, then env, then guess.
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config = config or os.environ.get("GALAXY_CONFIG_FILE", "config/galaxy.yml")
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if config and os.path.exists(config):
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app_properties = load_app_properties(config_file=config)
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gx_config = GalaxyAppConfiguration(**app_properties)
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if setting:
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print(gx_config.get(setting))
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else:
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pprint.pprint(gx_config.config_dict)
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if __name__ == "__main__":
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arg_parser = argparse.ArgumentParser(description="Fetch values from Galaxy config, or print all set values.")
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# add optional 'setting' argument
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arg_parser.add_argument("-s", "--setting", default=None, help="setting")
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arg_parser.add_argument(
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"-c", "--config-file", default=None, help="Galaxy config file (defaults to config/galaxy.ini)"
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)
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args = arg_parser.parse_args()
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main(args.config_file, args.setting)
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