#!/usr/bin/python
import sys
import os
import json
from pathlib import Path
def _load_json(filepath, post_process=None, ignore_notfound=True):
"""Load json from a file, with optional post processing of contents prior to parsing"""
if os.path.exists(filepath):
try:
with open(filepath, 'r', encoding='utf-8') as json_file:
if post_process:
return json.loads(post_process(json_file.read()))
else:
return json.loads(json_file.read())
except ValueError:
print("JSON decode error from file {} ".format(filepath))
raise
except IOError:
print("Error accessing json file {} ".format(filepath))
raise
else:
if not ignore_notfound:
# should this raise an error?
print("JSON file not found: {}".format(filepath))
raise ValueError
return None
def _recursive_json_overrider( ref_json, flat_input_json ):
"""
Useful function that recursively navigates a pretty arbitrarily structured json config looking
for key-value parameters in the leaves.
"""
special_nodes = [
"Vector_Species_Params", "Malaria_Drug_Params", "TB_Drug_Params", "HIV_Drug_Params", "STI_Network_Params_By_Property", "TBHIV_Drug_Params"
]
if ref_json is None:
print( "Null ref_json (param1) passed into _recursive_json_overrider." )
raise ValueError
for val in ref_json:
#if not leaf, call recursive_json_leaf_reader
if isinstance( ref_json[val], dict ) and val not in special_nodes:
_recursive_json_overrider( ref_json[val], flat_input_json )
# do VSP and MDP as special case. Sigh sigh sigh. Also TBHIV params now, also sigh.
elif val in special_nodes:
# could "genericize" this if we need to... happens to work for now, since both VSP and MDP are 3-levels deep...
if val not in flat_input_json:
flat_input_json[val] = { }
elif val == "STI_Network_Params_By_Property" and not("NONE" in flat_input_json[val].keys()):
continue
for species in ref_json[val]:
if species not in flat_input_json[val]:
if( isinstance( ref_json[val][species], dict ) ):
flat_input_json[val][species] = { }
for param in ref_json[val][species]:
if( isinstance( ref_json[val][species], dict ) ):
if param not in flat_input_json[val][species]:
flat_input_json[val][species][param] = ref_json[val][species][param]
else:
flat_input_json[val][species] = ref_json[val][species]
else:
if val not in flat_input_json:
flat_input_json[val] = ref_json[val]
[docs]def flattenConfig( configjson_path, new_config_name="config.json" ):
"""
Historically called 'flattening' but really a function that takes a parameter override
json config that includes a Default_Config_Path and produces a config.json from the two.
"""
if os.path.exists( configjson_path ) == False:
raise
configjson_flat = {}
#print( "configjson_path = " + configjson_path )
configjson = _load_json(configjson_path)
_recursive_json_overrider( configjson, configjson_flat )
# get defaults from config.json and synthesize output from default and overrides
if "Default_Config_Path" in configjson_flat:
default_config_path = configjson_flat["Default_Config_Path"]
stripped_path = default_config_path.strip()
if stripped_path != default_config_path:
print("Warning: config parameter 'Default_Config_Path' has leading or trailing whitespace in value \"{0}\"."
" Trimming whitespace and continuing.".format(default_config_path))
default_config_path = stripped_path
try:
# This code has always worked by treating the default_configpath as relative the Regression directory.
# No longer doing that, but preserving that capability for back-compat. Going forward, relative to the
# configjson_path.
simdir = Path( configjson_path ).parent
default_config_json = None
if Path( os.path.join( str( simdir ), default_config_path) ).exists():
default_config_json = _load_json(os.path.join( str(simdir), default_config_path))
else:
default_config_json = _load_json(os.path.join( '.', default_config_path))
_recursive_json_overrider( default_config_json, configjson_flat )
except Exception as ex:
print( f"Exception opening default config {default_config_path}: {ex}." )
raise ex
else:
print( "Didn't find 'Default_Config_Path' in '{0}'".format( configjson_path ) )
raise RuntimeError( "Bad Default_Config_Path!!!" )
# still need that parameter top level node
configjson = {}
configjson["parameters"] = configjson_flat
# don't need backslashes in the default config path
# messing with anything else downstream now that it is flattened
if "Default_Config_Path" in configjson["parameters"]:
configjson["parameters"].pop("Default_Config_Path")
# let's write out a flat version in case someone wants
# to use regression examples as configs for debug mode
with open( configjson_path.replace( os.path.basename(configjson_path), new_config_name ), 'w', newline='\r\n') as handle:
handle.write( json.dumps(configjson, sort_keys=True, indent=4) )
return configjson
if __name__ == '__main__':
if len(sys.argv) > 1:
flattenConfig(sys.argv[1])
else:
print ('usage:', sys.argv[0], 'configFile')