Added yamlargs.py to SmiServices library

src/library/SmiServices/yamlargs.py

@@ -0,0 +1,121 @@
+""" Convert between command line arguments and yaml file options, e.g.
+yaml_to_args() can insert the values from a yaml file into
+the args you get from argparse.parse_args(), and
+args_into_yaml() can insert the command line arguments into a yaml dict.
+"""
+
+import argparse
+import os
+import pprint
+import sys
+import yaml
+
+
+# NB. this code relies on the fact that argparse stores the options in
+# he parser object like this: parser.__dict__['_option_string_actions'] has
+# '-q': _StoreAction(option_strings=['-q'], dest='QueueName', nargs=None, const=None, default='DefQ', type=None, choices=None, required=False, help='stuff', metavar=None)
+
+
+# ---------------------------------------------------------------------
+def args_into_yaml(yamldict, parser, args):
+    """ This simply updates the yamldict with any options from args
+    which are not the default value, so that args will override yaml.
+    """
+    for arg in parser.__dict__['_option_string_actions']:
+        destname   = parser.__dict__['_option_string_actions'][arg].dest
+        defaultval = parser.__dict__['_option_string_actions'][arg].default
+        argval = vars(args).get(destname, None)
+        if argval != defaultval:
+            yamldict[destname] = argval
+    return
+
+
+def test_args_into_yaml():
+    # Use a hard-coded yaml file, optional
+    yamlfile='/home/arb/src/SMI/SMI_ROOT/configs/smi_dataExtract.yaml'
+    # Define the arguments, some have defaults
+    parser = argparse.ArgumentParser(description='test')
+    parser.add_argument('-y', dest='yamlfile', action="store", help='path to yaml config file', default=yamlfile)
+    parser.add_argument('-i', dest='input', action="store", help='input')
+    parser.add_argument('-q', dest='QueueName', action="store", help='a queue', default='DefQ')
+    parser.add_argument('--opt-unique', dest='unique', action="store_true", help='a boolean option')
+    # Parse the arguments
+    args = parser.parse_args()
+    yamldict = {}
+    args_into_yaml(yamldict, parser, args)
+    assert(yamldict['QueueName'] == 'OverrideQ')
+
+
+# ---------------------------------------------------------------------
+def yaml_to_args(yamldict, parser, args):
+    """ Create argparse.ArgumentParser(),
+    call add_argument() as necessary,
+    call parser.parse_args(), then call
+    yaml.safe_load() and find your dict inside the result,
+    then call yaml_to_args(yamldict, parser, args)
+    which will update the args namespace with the values
+    from the yamldict, but ONLY if the value in args
+    has not been set on the command line as that overrides yaml.
+    e.g. yaml file has
+    MyStuff:
+     myprog:
+       option1: value1
+    yaml_to_args(yaml['MyStuff']['myprog'], parser, args)
+    will set args.option1 = 'value1'
+    """
+    def arg_default(args, argname):
+        for arg in parser.__dict__['_option_string_actions']:
+            if parser.__dict__['_option_string_actions'][arg].dest == argname:
+                return parser.__dict__['_option_string_actions'][arg].default
+
+    for item in yamldict:
+        # See if this item was specified on the command line
+        # by checking if its value is different from default
+        # and ignore the yaml value if so.
+        default_value = arg_default(parser, item)
+        cmdline_value = vars(args).get(item, None)
+        if cmdline_value == default_value:
+            vars(args)[item] = yamldict[item]
+
+
+def test_yaml_to_args(argv = None):
+    # If called from command line then use command line args
+    # otherwise fake some command line args.
+    if argv:
+        sys.argv = argv
+    else:
+        sys.argv.extend(['-q', 'OverrideQ'])
+    # Use a hard-coded yaml file, optional
+    yamlfile='/home/arb/src/SMI/SMI_ROOT/configs/smi_dataExtract.yaml'
+    # Define the arguments, some have defaults
+    parser = argparse.ArgumentParser(description='test')
+    parser.add_argument('-y', dest='yamlfile', action="store", help='path to yaml config file', default=yamlfile)
+    parser.add_argument('-i', dest='input', action="store", help='input')
+    parser.add_argument('-q', dest='QueueName', action="store", help='a queue', default='DefQ')
+    parser.add_argument('--opt-unique', dest='unique', action="store_true", help='a boolean option')
+    # Parse the arguments
+    args = parser.parse_args()
+    # Read the yaml file, or construct one manually
+    try:
+        with open(args.yamlfile) as fd:
+            yamldict = yaml.safe_load(fd)
+    except:
+        yamldict = {}
+        yamldict['DicomAnonymiserOptions'] = { 'AnonFileConsumerOptions': {
+            'QueueName': 'TEST.ExtractFileAnonQueue',
+            'QoSPrefetchCount': 1,
+            'AutoAck': False
+        }}
+    # Run the tests
+    yaml_to_args(yamldict['DicomAnonymiserOptions']['AnonFileConsumerOptions'], parser, args)
+    assert(args.input == None)
+    assert(args.QueueName == 'OverrideQ')
+    assert(args.QoSPrefetchCount == 1)
+    assert(args.AutoAck == False)
+
+
+# ---------------------------------------------------------------------
+if __name__ == '__main__':
+    # You should call this program with -q OverrideQ to pass the test
+    test_args_into_yaml()
+    test_yaml_to_args(sys.argv)