#!/usr/bin/python
import sys
import json
import os
import warnings
import emod_api.schema_to_class as s2c
[docs]def schema_to_config_subnode( schema_path_in, subnode_list ):
"""
This is the code from regular schema_to_config:
config = json.load(open("default_config.json"), object_hook=s2c.ReadOnlyDict)
os.remove( "default_config.json" )
"""
# 1) initialize the base config
default_config = { "parameters": {} }
default_config[ "parameters" ][ "schema" ] = {}
# 2) Get the whole schema
with open(schema_path_in) as schema_in:
schema = json.loads(schema_in.read())
subnode = schema
for subkey in subnode_list:
subnode = subnode[subkey]
# 3) Get the defaults from a subnode (config)
_set_defaults_for_schema_group(default_config, subnode, schema["idmTypes"])
# 4) Convert to schema-backed 'read-only dict'
config = json.loads(json.dumps(default_config), object_hook=s2c.ReadOnlyDict)
return config
def _set_defaults_for_schema_group( default_config, schema_section, custom_type_schema ):
"""
By making this part of write_default_from_schema its own function, it becomes reusable for the purposes
of Malaria_Drug_params which is a pretty funky part of the schema honestly.
"""
for param in schema_section:
if param == "class":
continue
if 'default' in schema_section[param]:
value = schema_section[param]['default']
default_config[ "parameters" ][ param ] = value
default_config[ "parameters" ][ "schema" ][ param ] = schema_section[ param ]
# Our vectors don't seem to have defaults but we think an empty array is a valid default based on type alone?
elif "type" in schema_section[param] and "Vector" in schema_section[param]["type"]:
default_config[ "parameters" ][ param ] = []
default_config[ "parameters" ][ "schema" ][ param ] = schema_section[ param ]
else:
default_config[ "parameters" ][ param ] = {} # hack for Drug Params.... and for the nested ones.
keys = [x for x in schema_section[ param ].keys()]
# This is all too "special-casey"
if len(keys) == 1:
key = keys[0] # HACK
default_config[ "parameters" ][ "schema" ][ param ] = schema_section[ param ][key]
else:
# e.g., Fractional_Dose_xxx map which has comlex type
# Want to call this but we need the full json so we can access the idmType section
# print( "Don't actually want to do this but just testing the concept." )
default_config[ "parameters" ][ param ] = s2c.get_class_with_defaults( schema_section[ param ][ "type" ], custom_type_schema )
default_config[ "parameters" ][ "schema" ][ param ] = schema_section[ param ]
# Does default_config get passed by reference and modified? :/
[docs]def get_default_config_from_schema(path_to_schema, schema_node=True, as_rod=False, output_filename=None):
"""
This returns a default config object as defined from reading a schema file.
Parameters:
output_filename (str): if not None, the path to write the loaded config to
"""
default_config = {"parameters": {}}
default_config["parameters"]["schema"] = {}
with open(path_to_schema) as raw_json:
schema = json.loads(raw_json.read())
for group in schema["config"]:
_set_defaults_for_schema_group(default_config, schema["config"][group], schema["idmTypes"])
if not schema_node:
print("Removing schema node.")
default_config["parameters"].pop("schema")
if as_rod:
default_config = json.loads(json.dumps(default_config), object_hook=s2c.ReadOnlyDict)
if output_filename is not None:
with open(output_filename, "w") as outfile:
json.dump(default_config, outfile, sort_keys=True, indent=4)
print(f"Wrote '{output_filename}' file.")
return default_config
[docs]def write_default_from_schema(path_to_schema, output_filename='default_config.json', schema_node=True):
"""
DEPRECATED: This function simply calls get_default_config_from_schema with specific arguments.
This function writes out a default config file as defined from reading a schema file.
It's as good as the schema it's given. Note that this is designed to work with a schema from
a disease-specific build, otherwise it may contain a lot of params from other disease types.
"""
warnings.warn("Calls to write_default_from_schema() should be updated to use get_default_config_from_schema()",
DeprecationWarning)
get_default_config_from_schema(path_to_schema=path_to_schema, output_filename=output_filename,
schema_node=schema_node)
return output_filename
[docs]def load_default_config_as_rod( config ):
"""
Parameters:
config (string/path): path to default or base config.json
Returns:
config (as ReadOnlyDict) with schema ready for schema-verified param sets.
"""
if not os.path.exists( config ):
print( f"{config} not found." )
return None
config_rod = None
with open( config ) as conf:
config_rod = json.load( conf, object_hook=s2c.ReadOnlyDict )
return config_rod
[docs]def get_config_from_default_and_params(config_path=None, set_fn=None, config=None, verbose=False):
"""
Use this function to create a valid config.json file from a schema-derived
base config, a callback that sets your parameters of interest
Parameters:
config_path (string/path): Path to valid config.json
config: read-only dict configuration object. Pass this XOR the config_path.
set_fn (function): Callback that sets params with implicit schema enforcement.
Returns:
config: read-only dict
"""
if not ((config_path is None) ^ (config is None)):
raise Exception('Must specify either a default config_path or config, not neither or both.')
if verbose:
print(f"DEBUG: get_config_from_default_and_params invoked with "
f"config_path: {config_path}, config: {config is not None}, {set_fn}.")
# load default config from file if a path was given
if config_path is not None:
config = load_default_config_as_rod(config_path)
if verbose:
print("DEBUG: Calling set_fn.")
# now that we have a config (either given or loaded from file), call the (possibly given) callback on it
if set_fn is not None:
config = set_fn(config)
return config
[docs]def write_config_from_default_and_params( config_path, set_fn, config_out_path ):
"""
Use this function to create a valid config.json file from a schema-derived
base config, a callback that sets your parameters of interest, and an output path.
Parameters:
config_path (string/path): Path to valid config.json
set_fn (function): Callback that sets params with implicit schema enforcement.
config_out_path: (string/path) Path to write new config.json
Returns:
Nothing
"""
print( f"DEBUG: write_config_from_default_and_params invoked with {config_path}, {set_fn}, and {config_out_path}." )
config = get_config_from_default_and_params(config_path=config_path, set_fn=set_fn)
print( "DEBUG: Calling finalize." )
config.parameters.finalize()
print( "DEBUG: Writing output file." )
with open( config_out_path, "w" ) as outfile:
json.dump( config, outfile, sort_keys=True, indent=4 )
def _write_config_using_schema():
"""
This is really a demo function
"""
config_rod = load_default_config_as_rod( "default_config.json" )
# set some parameters...
config_rod.parameters.Enable_Demographics_Builtin = 1
config_rod.parameters.x_Base_Population = 10
config_rod.parameters.Enable_Birth = 1
# purge all params that aren't depends-on-enabled, implicit
# purge schema
config_rod.parameters.finalize()
with open( "my_config.json", "w" ) as outfile:
json.dump( config_rod, outfile, sort_keys=True, indent=4 )
print( "Wrote 'my_config.json'file." )
return config_rod
def _do_main():
if len( sys.argv ) == 1:
print( "Usage: emod_api.default_from_schema <schema.json>" )
else:
write_default_from_schema( sys.argv[1] )
if __name__=="__main__":
_do_main()
