Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.config.schema
import logging
from galaxy.exceptions import ConfigurationError
from galaxy.util.yaml_util import ordered_load
log = logging.getLogger(__name__)
OPTION_DEFAULTS = {
"type": "str",
"unknown_option": False,
"default": None,
"desc": None,
}
UNKNOWN_OPTION = {
"type": "str",
"required": False,
"unknown_option": True,
"desc": "Unknown option, may want to remove or report to Galaxy team.",
}
[docs]class Schema:
[docs] def get_app_option(self, name):
try:
raw_option = self.app_schema[name]
except KeyError:
raw_option = UNKNOWN_OPTION
option = OPTION_DEFAULTS.copy()
option.update(raw_option)
return option
[docs]class AppSchema(Schema):
[docs] def __init__(self, schema_path, app_name):
self.raw_schema = self._read_schema(schema_path)
self.description = self.raw_schema.get("desc", None)
app_schema = self.raw_schema["mapping"][app_name]["mapping"]
self._preprocess(app_schema)
super().__init__(app_schema)
def _read_schema(self, path):
with open(path) as f:
return ordered_load(f)
def _preprocess(self, app_schema):
"""Populate schema collections used for app configuration."""
self._defaults = {} # {config option: default value or null}
self._reloadable_options = set() # config options we can reload at runtime
self._paths_to_resolve = {} # {config option: referenced config option}
self._per_host_options = set() # config options that can be set using a per_host config parameter
for key, data in app_schema.items():
self._defaults[key] = data.get("default")
if data.get("reloadable"):
self._reloadable_options.add(key)
if data.get("per_host"):
self._per_host_options.add(key)
if data.get("path_resolves_to"):
self._paths_to_resolve[key] = data.get("path_resolves_to")
@property
def defaults(self):
return self._defaults
@property
def paths_to_resolve(self):
return self._paths_to_resolve
@property
def reloadable_options(self):
return self._reloadable_options
@property
def per_host_options(self):
return self._per_host_options
[docs] def validate_path_resolution_graph(self):
"""This method is for tests only: we SHOULD validate the schema's path resolution graph
as part of automated testing; but we should NOT validate it at runtime.
"""
def check_exists(option, key):
if not option:
message = (
"Invalid schema: property '{}' listed as path resolution target "
"for '{}' does not exist".format(resolves_to, key)
)
raise_error(message)
def check_type_is_str_or_any(option, key):
if option.get("type") not in ("str", "any"):
message = f"Invalid schema: property '{key}' should have type 'str'"
raise_error(message)
def check_is_dag():
visited = set()
for key in self.paths_to_resolve:
visited.clear()
while key:
visited.add(key)
key = self.app_schema[key].get("path_resolves_to")
if key and key in visited:
raise_error("Invalid schema: cycle detected")
def raise_error(message):
log.error(message)
raise ConfigurationError(message)
for key, resolves_to in self.paths_to_resolve.items():
print(key)
parent = self.app_schema.get(resolves_to)
check_exists(parent, key)
check_type_is_str_or_any(parent, key)
check_type_is_str_or_any(self.app_schema[key], key)
check_is_dag() # must be called last: walks entire graph