3482 3829 Add ConfigParser to recursively parse config content

docs/source/api.rst

@@ -7,6 +7,7 @@ API Reference
    :maxdepth: 1
 
    apps
+   bundle
    transforms
    losses
    networks

docs/source/apps.rst

@@ -19,8 +19,8 @@ Applications
     :members:
 
 
-Clara MMARs
------------
+`Clara MMARs`
+-------------
 .. autofunction:: download_mmar
 
 .. autofunction:: load_from_mmar
@@ -29,25 +29,6 @@ Clara MMARs
     :annotation:
 
 
-Model Manifest
---------------
-
-.. autoclass:: ComponentLocator
-    :members:
-
-.. autoclass:: ConfigComponent
-    :members:
-
-.. autoclass:: ConfigExpression
-    :members:
-
-.. autoclass:: ConfigItem
-    :members:
-
-.. autoclass:: ReferenceResolver
-    :members:
-
-
 `Utilities`
 -----------
 

docs/source/bundle.rst

@@ -0,0 +1,34 @@
+:github_url: https://github.com/Project-MONAI/MONAI
+
+.. _bundle:
+
+Model Bundle
+============
+.. currentmodule:: monai.bundle
+
+`Config Item`
+-------------
+.. autoclass:: Instantiable
+    :members:
+
+.. autoclass:: ComponentLocator
+    :members:
+
+.. autoclass:: ConfigComponent
+    :members:
+
+.. autoclass:: ConfigExpression
+    :members:
+
+.. autoclass:: ConfigItem
+    :members:
+
+`Reference Resolver`
+--------------------
+.. autoclass:: ReferenceResolver
+    :members:
+
+`Config Parser`
+---------------
+.. autoclass:: ConfigParser
+    :members:

docs/source/conf.py

@@ -40,6 +40,7 @@
     "engines",
     "data",
     "apps",
+    "bundle",
     "config",
     "handlers",
     "losses",

monai/README.md

@@ -2,6 +2,8 @@
 
 * **apps**: high level medical domain specific deep learning applications.
 
+* **bundle**: components to build the portable self-descriptive model bundle.
+
 * **config**: for system configuration and diagnostic output.
 
 * **csrc**: for C++/CUDA extensions.

monai/__init__.py

@@ -49,6 +49,7 @@
 
 __all__ = [
     "apps",
+    "bundle",
     "config",
     "data",
     "engines",

monai/apps/__init__.py

@@ -10,6 +10,5 @@
 # limitations under the License.
 
 from .datasets import CrossValidation, DecathlonDataset, MedNISTDataset
-from .manifest import ComponentLocator, ConfigComponent, ConfigExpression, ConfigItem, ReferenceResolver
 from .mmars import MODEL_DESC, RemoteMMARKeys, download_mmar, get_model_spec, load_from_mmar
 from .utils import SUPPORTED_HASH_TYPES, check_hash, download_and_extract, download_url, extractall, get_logger, logger

monai/apps/manifest/__init__.py → monai/bundle/__init__.py

@@ -9,5 +9,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from .config_item import ComponentLocator, ConfigComponent, ConfigExpression, ConfigItem
+from .config_item import ComponentLocator, ConfigComponent, ConfigExpression, ConfigItem, Instantiable
+from .config_parser import ConfigParser
 from .reference_resolver import ReferenceResolver

monai/apps/manifest/config_item.py → monai/bundle/config_item.py

@@ -10,6 +10,7 @@
 # limitations under the License.
 
 import inspect
+import os
 import sys
 import warnings
 from abc import ABC, abstractmethod
@@ -128,7 +129,7 @@ def __init__(self, config: Any, id: str = "") -> None:
         self.config = config
         self.id = id
 
-    def get_id(self) -> Optional[str]:
+    def get_id(self) -> str:
         """
         Get the ID name of current config item, useful to identify config items during parsing.
 
@@ -153,6 +154,9 @@ def get_config(self):
         """
         return self.config
 
+    def __repr__(self) -> str:
+        return str(self.config)
+
 
 class ConfigComponent(ConfigItem, Instantiable):
     """
@@ -187,7 +191,7 @@ class ConfigComponent(ConfigItem, Instantiable):
         locator: a ``ComponentLocator`` to convert a module name string into the actual python module.
             if `None`, a ``ComponentLocator(excludes=excludes)`` will be used.
         excludes: if ``locator`` is None, create a new ``ComponentLocator`` with ``excludes``.
-            See also: :py:class:`monai.apps.manifest.ComponentLocator`.
+            See also: :py:class:`monai.bundle.ComponentLocator`.
 
     """
 
@@ -291,7 +295,7 @@ class ConfigExpression(ConfigItem):
     .. code-block:: python
 
         import monai
-        from monai.apps.manifest import ConfigExpression
+        from monai.bundle import ConfigExpression
 
         config = "$monai.__version__"
         expression = ConfigExpression(config, id="test", globals={"monai": monai})
@@ -304,6 +308,9 @@ class ConfigExpression(ConfigItem):
 
     """
 
+    prefix = "$"
+    run_eval = False if os.environ.get("MONAI_EVAL_EXPR", "1") == "0" else True
+
     def __init__(self, config: Any, id: str = "", globals: Optional[Dict] = None) -> None:
         super().__init__(config=config, id=id)
         self.globals = globals
@@ -320,10 +327,12 @@ def evaluate(self, locals: Optional[Dict] = None):
         value = self.get_config()
         if not ConfigExpression.is_expression(value):
             return None
-        return eval(value[1:], self.globals, locals)
+        if not self.run_eval:
+            return f"{value[len(self.prefix) :]}"
+        return eval(value[len(self.prefix) :], self.globals, locals)
 
-    @staticmethod
-    def is_expression(config: Union[Dict, List, str]) -> bool:
+    @classmethod
+    def is_expression(cls, config: Union[Dict, List, str]) -> bool:
         """
         Check whether the config is an executable expression string.
         Currently, a string starts with ``"$"`` character is interpreted as an expression.
@@ -332,4 +341,4 @@ def is_expression(config: Union[Dict, List, str]) -> bool:
             config: input config content to check.
 
         """
-        return isinstance(config, str) and config.startswith("$")
+        return isinstance(config, str) and config.startswith(cls.prefix)