1010# limitations under the License.
1111
1212import pprint
13+ import re
1314from typing import Dict , Optional , Sequence , Union
1415
16+ from monai .apps .utils import download_url , get_logger
1517from monai .bundle .config_parser import ConfigParser
18+ from monai .config import PathLike
19+ from monai .utils import check_parent_dir , optional_import
1620
21+ validate , _ = optional_import ("jsonschema" , name = "validate" )
22+ ValidationError , _ = optional_import ("jsonschema.exceptions" , name = "ValidationError" )
1723
18- def _update_default_args (args : Optional [Union [str , Dict ]] = None , ** kwargs ) -> Dict :
24+ logger = get_logger (module_name = __name__ )
25+
26+
27+ def _update_args (args : Optional [Union [str , Dict ]] = None , ignore_none : bool = True , ** kwargs ) -> Dict :
1928 """
2029 Update the `args` with the input `kwargs`.
2130 For dict data, recursively update the content based on the keys.
2231
2332 Args:
2433 args: source args to update.
34+ ignore_none: whether to ignore input args with None value, default to `True`.
2535 kwargs: destination args to update.
2636
2737 """
@@ -32,14 +42,26 @@ def _update_default_args(args: Optional[Union[str, Dict]] = None, **kwargs) -> D
3242
3343 # recursively update the default args with new args
3444 for k , v in kwargs .items ():
35- args_ [k ] = _update_default_args (args_ [k ], ** v ) if isinstance (v , dict ) and isinstance (args_ .get (k ), dict ) else v
45+ if ignore_none and v is None :
46+ continue
47+ if isinstance (v , dict ) and isinstance (args_ .get (k ), dict ):
48+ args_ [k ] = _update_args (args_ [k ], ignore_none , ** v )
49+ else :
50+ args_ [k ] = v
3651 return args_
3752
3853
54+ def _log_input_summary (tag : str , args : Dict ):
55+ logger .info (f"\n --- input summary of monai.bundle.scripts.{ tag } )
56+ for name , val in args .items ():
57+ logger .info (f"> { name } { pprint .pformat (val )} )
58+ logger .info ("---\n \n " )
59+
60+
3961def run (
62+ runner_id : Optional [str ] = None ,
4063 meta_file : Optional [Union [str , Sequence [str ]]] = None ,
4164 config_file : Optional [Union [str , Sequence [str ]]] = None ,
42- target_id : Optional [str ] = None ,
4365 args_file : Optional [str ] = None ,
4466 ** override ,
4567):
@@ -51,62 +73,102 @@ def run(
5173 .. code-block:: bash
5274
5375 # Execute this module as a CLI entry:
54- python -m monai.bundle run --meta_file <meta path> --config_file <config path> --target_id trainer
76+ python -m monai.bundle run trainer --meta_file <meta path> --config_file <config path>
5577
5678 # Override config values at runtime by specifying the component id and its new value:
57- python -m monai.bundle run --net#input_chns 1 ...
79+ python -m monai.bundle run trainer --net#input_chns 1 ...
5880
5981 # Override config values with another config file `/path/to/another.json`:
60- python -m monai.bundle run --net %/path/to/another.json ...
82+ python -m monai.bundle run evaluator --net %/path/to/another.json ...
6183
6284 # Override config values with part content of another config file:
63- python -m monai.bundle run --net %/data/other.json#net_arg ...
85+ python -m monai.bundle run trainer --net %/data/other.json#net_arg ...
6486
6587 # Set default args of `run` in a JSON / YAML file, help to record and simplify the command line.
6688 # Other args still can override the default args at runtime:
6789 python -m monai.bundle run --args_file "/workspace/data/args.json" --config_file <config path>
6890
6991 Args:
92+ runner_id: ID name of the runner component or workflow, it must have a `run` method.
7093 meta_file: filepath of the metadata file, if `None`, must be provided in `args_file`.
7194 if it is a list of file paths, the content of them will be merged.
7295 config_file: filepath of the config file, if `None`, must be provided in `args_file`.
7396 if it is a list of file paths, the content of them will be merged.
74- target_id: ID name of the target component or workflow, it must have a `run` method.
7597 args_file: a JSON or YAML file to provide default values for `meta_file`, `config_file`,
76- `target_id ` and override pairs. so that the command line inputs can be simplified.
98+ `runner_id ` and override pairs. so that the command line inputs can be simplified.
7799 override: id-value pairs to override or add the corresponding config content.
78100 e.g. ``--net#input_chns 42``.
79101
80102 """
81- k_v = zip (["meta_file" , "config_file" , "target_id" ], [meta_file , config_file , target_id ])
82- for k , v in k_v :
83- if v is not None :
84- override [k ] = v
85-
86- full_kv = zip (
87- ("meta_file" , "config_file" , "target_id" , "args_file" , "override" ),
88- (meta_file , config_file , target_id , args_file , override ),
89- )
90- print ("\n --- input summary of monai.bundle.scripts.run ---" )
91- for name , val in full_kv :
92- print (f"> { name } { pprint .pformat (val )} )
93- print ("---\n \n " )
94103
95- _args = _update_default_args (args = args_file , ** override )
104+ _args = _update_args (args = args_file , runner_id = runner_id , meta_file = meta_file , config_file = config_file , ** override )
96105 for k in ("meta_file" , "config_file" ):
97106 if k not in _args :
98107 raise ValueError (f"{ k } \n { run .__doc__ } )
108+ _log_input_summary (tag = "run" , args = _args )
99109
100110 parser = ConfigParser ()
101111 parser .read_config (f = _args .pop ("config_file" ))
102112 parser .read_meta (f = _args .pop ("meta_file" ))
103- id = _args .pop ("target_id " , "" )
113+ id = _args .pop ("runner_id " , "" )
104114
105- # the rest key-values in the args are to override config content
115+ # the rest key-values in the _args are to override config content
106116 for k , v in _args .items ():
107117 parser [k ] = v
108118
109119 workflow = parser .get_parsed_content (id = id )
110120 if not hasattr (workflow , "run" ):
111121 raise ValueError (f"The parsed workflow { type (workflow )} \n { run .__doc__ } )
112122 workflow .run ()
123+
124+
125+ def verify_metadata (
126+ meta_file : Optional [Union [str , Sequence [str ]]] = None ,
127+ filepath : Optional [PathLike ] = None ,
128+ create_dir : Optional [bool ] = None ,
129+ hash_val : Optional [str ] = None ,
130+ args_file : Optional [str ] = None ,
131+ ** kwargs ,
132+ ):
133+ """
134+ Verify the provided `metadata` file based on the predefined `schema`.
135+ `metadata` content must contain the `schema` field for the URL of shcema file to download.
136+ The schema standard follows: http://json-schema.org/.
137+
138+ Args:
139+ meta_file: filepath of the metadata file to verify, if `None`, must be provided in `args_file`.
140+ if it is a list of file paths, the content of them will be merged.
141+ filepath: file path to store the downloaded schema.
142+ create_dir: whether to create directories if not existing, default to `True`.
143+ hash_val: if not None, define the hash value to verify the downloaded schema file.
144+ args_file: a JSON or YAML file to provide default values for all the args in this function.
145+ so that the command line inputs can be simplified.
146+ kwargs: other arguments for `jsonschema.validate()`. for more details:
147+ https://python-jsonschema.readthedocs.io/en/stable/validate/#jsonschema.validate.
148+
149+ """
150+
151+ _args = _update_args (
152+ args = args_file , meta_file = meta_file , filepath = filepath , create_dir = create_dir , hash_val = hash_val , ** kwargs
153+ )
154+ _log_input_summary (tag = "verify_metadata" , args = _args )
155+
156+ filepath_ = _args .pop ("filepath" )
157+ create_dir_ = _args .pop ("create_dir" , True )
158+ check_parent_dir (path = filepath_ , create_dir = create_dir_ )
159+
160+ metadata = ConfigParser .load_config_files (files = _args .pop ("meta_file" ))
161+ url = metadata .get ("schema" )
162+ if url is None :
163+ raise ValueError ("must provide the `schema` field in the metadata for the URL of schema file." )
164+ download_url (url = url , filepath = filepath_ , hash_val = _args .pop ("hash_val" , None ), hash_type = "md5" , progress = True )
165+ schema = ConfigParser .load_config_file (filepath = filepath_ )
166+
167+ try :
168+ # the rest key-values in the _args are for `validate` API
169+ validate (instance = metadata , schema = schema , ** _args )
170+ except ValidationError as e :
171+ # as the error message is very long, only extract the key information
172+ logger .info (re .compile (r".*Failed validating" , re .S ).findall (str (e ))[0 ] + f" against schema `{ url } )
173+ return
174+ logger .info ("metadata is verified with no error." )
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