Mercurial > repos > jaredgk > ppp_vcf_to_ima

comparison parse_functions.py @ 0:1ad9c146ebb4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jaredgk
date Fri, 19 Oct 2018 14:36:02 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1ad9c146ebb4
1 try:
2 import ConfigParser
3 except ImportError:
4 import configparser as ConfigParser
5 import argparse
6 import sys
7
8 is_python3 = (sys.version_info[0] == 3)
9
10
11
12 def parseOption(val):
13 """Given a value read from a config file, returns appropriately formatted
14 python variable.
15
16 -If `val` == 'None', returns None variable
17 -If `val` == 'True', returns True
18 -If `val` == 'False', returns False
19 -If `val` is a float, returns float-casted val
20 -If `val` is an int and not a float, returns an int-casted val
21 -If none of these criteria are met, returns the input value
22
23 Parameters
24 ----------
25 val : str
26 String from dict created by config parser
27
28 Output
29 ------
30 val : multi
31 Parsed config value for use with argparse
32
33
34 """
35 if val == 'None':
36 return None
37 if val == 'True':
38 return True
39 if val == 'False':
40 return False
41 try:
42 a = int(val)
43 b = float(val)
44 if a == b:
45 return int(val)
46 return float(val)
47 except:
48 pass
49 return val
50
51 def getConfigFilename(arglist, flag='--conf'):
52 """Reads argument list to determine if there is a config file provided.
53
54 Used to work with argparse. If `flag` is present in the input array,
55 the next argument is assumed to be the filename for the config file.
56
57 Parameters
58 ----------
59 arglist : list
60 List of all arguments to input function, from either sys.argv or a
61 custom list
62 flag : str (optional) ('--conf')
63 Command-line flag to look for in arglist to signify next element
64 is filename for config options
65
66 Returns
67 -------
68 config_filename : str (None)
69 Name of config file if 'flag' is present in arglist, otherwise
70 defaults to None
71 is_first : bool
72 Will be true if `flag` is first element of arglist. Used for method
73 to allow required args to be passed from config file.
74
75 """
76 config_filename = None
77 is_first = False
78 if flag in arglist:
79 idx = arglist.index(flag)
80 config_filename = arglist[idx+1]
81 if idx == 0:
82 is_first = True
83 return config_filename,is_first
84 return None,is_first
85
86
87 def defaultsDictForFunction(func_name, config_name):
88 """Creates a dict with default values for a given function.
89
90 Given an input config file and a function name, this function will
91 read in all values from the given section of the config file, then
92 remove the variables that are used in the config file to define
93 parameters for multiple functions.
94
95 Parameters
96 ----------
97 func_name : str
98 Name of function section of config file. (May not necessarily
99 be name of function in code)
100 config_name : str
101 Name of config file
102
103 Returns
104 -------
105 d_func : dict
106 Dictionary with all attributes for the given function. Values written
107 as 'None' in config file will not be added, so normal defaults
108 can be used.
109
110
111 """
112 if is_python3:
113 config = ConfigParser.ConfigParser()
114 else:
115 config = ConfigParser.SafeConfigParser()
116 config.read(config_name)
117 d_vars = dict(config.items("DEFAULT"))
118 d_hold = dict(config.items(func_name))
119 d_func = {}
120 for k in d_hold.keys():
121 if k not in d_vars:
122 val = parseOption(d_hold[k])
123 if val is not None:
124 d_func[k] = val
125 return d_func
126
127 def makeRequiredList(argdict, reqlist):
128 """Grabs required args from argument dict created by configparser.
129
130 Generates a list of required parameters that will be passed in lieu of
131 a regular arglist or sys.argv. Must be ordered in the same way they will
132 be input to argparse.
133
134 Parameters
135 ----------
136 argdict : dict
137 Dictionary of arguments returned from defaultsDictForFunction.
138 reqlist : list
139 List of required arguments, in order that they should be passed to
140 argparse.
141
142 Returns
143 -------
144 req_arglist : list
145 List of required argument values for given function, in order for
146 passing to argparse
147
148 Exceptions
149 ----------
150 Argument value in argdict for required arg is None
151
152
153
154 """
155 req_arglist = []
156 for arg in reqlist:
157 argval = argdict[arg]
158 if argval is None:
159 raise Exception("Value for required argument %s cannot be None"
160 % argval)
161 req_arglist.append(argdict[arg])
162 return req_arglist
163
164
165 def checkRequired(required_args, defaults):
166 for req in required_args:
167 if req in defaults and req[defaults] is not None:
168 raise Exception(('Required argument %s has value present '
169 ' in config file (%s) and command line' %
170 (req, defaults[req])))
171
172
173 def getArgsWithConfig(parser, sys_args, required_args, func_name):
174 config_name, req_included = getConfigFilename(sys_args)
175 if config_name is not None:
176 defaults = defaultsDictForFunction(func_name, config_name)
177 if not req_included:
178 checkRequired(required_args, defaults)
179 parser.set_defaults(**defaults)
180 if not req_included:
181 return parser.parse_args(sys_args)
182 else:
183 req_args = makeRequiredList(defaults, required_args)
184 return parser.parse_args(req_args)