Repository: Project-MONAI/MONAI

I have access to a python code repository in the directory /testbed . You can explore and modify files using the available tools. Consider the following issue description:

<issue_description>
make 'meta_file' optional for `monai.bundle run`
**Is your feature request related to a problem? Please describe.**
make it possible to instantiate components via CLI without providing a metadata file.
</issue_description>

Can you help me implement the necessary changes to the repository so that the requirements specified in the <issue_description> are met?
I've already taken care of all changes to any of the test files described in the <issue_description>. This means you DON'T have to modify the testing logic or any of the tests in any way!
Also the development Python environment is already set up for you (i.e., all dependencies already installed), so you don't need to install other packages.
Your task is to make the minimal changes to non-test files in the /testbed directory to ensure the <issue_description> is satisfied.

Follow these phases to resolve the issue:

Phase 1. READING: read the problem and reword it in clearer terms
   1.1 If there are code or config snippets. Express in words any best practices or conventions in them.
   1.2 Hightlight message errors, method names, variables, file names, stack traces, and technical details.
   1.3 Explain the problem in clear terms.
   1.4 Enumerate the steps to reproduce the problem.
   1.5 Hightlight any best practices to take into account when testing and fixing the issue

Phase 2. RUNNING: install and run the tests on the repository
   2.1 Activate the environment by running  
       ./opt/miniconda3/etc/profile.d/conda.sh ; conda activate testbed
   2.2 Follow the readme
   2.3 Install the environment and anything needed
   2.4 Iterate and figure out how to run the tests

Phase 3. EXPLORATION: find the files that are related to the problem and possible solutions
   3.1 Use `grep` to search for relevant methods, classes, keywords and error messages.
   3.2 Identify all files related to the problem statement.
   3.3 Propose the methods and files to fix the issue and explain why.
   3.4 From the possible file locations, select the most likely location to fix the issue.

Phase 4. TEST CREATION: before implementing any fix, create a script to reproduce and verify the issue.
   4.1 Look at existing test files in the repository to understand the test format/structure.
   4.2 Create a minimal reproduction script that reproduces the located issue.
   4.3 Run the reproduction script to confirm you are reproducing the issue.
   4.4 Adjust the reproduction script as necessary.

Phase 5. FIX ANALYSIS: state clearly the problem and how to fix it
   5.1 State clearly what the problem is.
   5.2 State clearly where the problem is located.
   5.3 State clearly how the test reproduces the issue.
   5.4 State clearly the best practices to take into account in the fix.
   5.5 State clearly how to fix the problem.

Phase 6. FIX IMPLEMENTATION: Edit the source code to implement your chosen solution.
   6.1 Make minimal, focused changes to fix the issue.

Phase 7. VERIFICATION: Test your implementation thoroughly.
   7.1 Run your reproduction script to verify the fix works.
   7.2 Add edge cases to your test script to ensure comprehensive coverage.
   7.3 Run existing tests related to the modified code to ensure you haven't broken anything.

8. FINAL REVIEW: Carefully re-read the problem description and compare your changes with the base commit 8e1aacf5ee7f4e62e9f0f25a9e1a3c37a09439ca.
   8.1 Ensure you've fully addressed all requirements.
   8.2 Run any tests in the repository related to:
     8.2.1 The issue you are fixing
     8.2.2 The files you modified
     8.2.3 The functions you changed
   8.3 If any tests fail, revise your implementation until all tests pass

Be thorough in your exploration, testing, and reasoning. It's fine if your thinking process is lengthy - quality and completeness are more important than brevity.

Gold patch:
diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -133,9 +133,8 @@ def run(
         python -m monai.bundle run --args_file "/workspace/data/args.json" --config_file <config path>
 
     Args:
-        runner_id: ID name of the runner component or workflow, it must have a `run` method.
-        meta_file: filepath of the metadata file, if `None`, must be provided in `args_file`.
-            if it is a list of file paths, the content of them will be merged.
+        runner_id: ID name of the runner component or workflow, it must have a `run` method. Defaults to ``""``.
+        meta_file: filepath of the metadata file, if it is a list of file paths, the content of them will be merged.
         config_file: filepath of the config file, if `None`, must be provided in `args_file`.
             if it is a list of file paths, the content of them will be merged.
         args_file: a JSON or YAML file to provide default values for `runner_id`, `meta_file`,
@@ -146,14 +145,14 @@ def run(
     """
 
     _args = _update_args(args=args_file, runner_id=runner_id, meta_file=meta_file, config_file=config_file, **override)
-    for k in ("meta_file", "config_file"):
-        if k not in _args:
-            raise ValueError(f"{k} is required for 'monai.bundle run'.\n{run.__doc__}")
+    if "config_file" not in _args:
+        raise ValueError(f"`config_file` is required for 'monai.bundle run'.\n{run.__doc__}")
     _log_input_summary(tag="run", args=_args)
 
     parser = ConfigParser()
     parser.read_config(f=_args.pop("config_file"))
-    parser.read_meta(f=_args.pop("meta_file"))
+    if "meta_file" in _args:
+        parser.read_meta(f=_args.pop("meta_file"))
     id = _args.pop("runner_id", "")
 
     # the rest key-values in the _args are to override config content
@@ -162,8 +161,8 @@ def run(
 
     workflow = parser.get_parsed_content(id=id)
     if not hasattr(workflow, "run"):
-        raise ValueError(f"The parsed workflow {type(workflow)} does not have a `run` method.\n{run.__doc__}")
-    workflow.run()
+        raise ValueError(f"The parsed workflow {type(workflow)} (id={id}) does not have a `run` method.\n{run.__doc__}")
+    return workflow.run()
 
 
 def verify_metadata(
@@ -171,6 +170,7 @@ def verify_metadata(
     filepath: Optional[PathLike] = None,
     create_dir: Optional[bool] = None,
     hash_val: Optional[str] = None,
+    hash_type: Optional[str] = None,
     args_file: Optional[str] = None,
     **kwargs,
 ):
@@ -185,6 +185,7 @@ def verify_metadata(
         filepath: file path to store the downloaded schema.
         create_dir: whether to create directories if not existing, default to `True`.
         hash_val: if not None, define the hash value to verify the downloaded schema file.
+        hash_type: if not None, define the hash type to verify the downloaded schema file. Defaults to "md5".
         args_file: a JSON or YAML file to provide default values for all the args in this function.
             so that the command line inputs can be simplified.
         kwargs: other arguments for `jsonschema.validate()`. for more details:
@@ -193,7 +194,13 @@ def verify_metadata(
     """
 
     _args = _update_args(
-        args=args_file, meta_file=meta_file, filepath=filepath, create_dir=create_dir, hash_val=hash_val, **kwargs
+        args=args_file,
+        meta_file=meta_file,
+        filepath=filepath,
+        create_dir=create_dir,
+        hash_val=hash_val,
+        hash_type=hash_type,
+        **kwargs,
     )
     _log_input_summary(tag="verify_metadata", args=_args)
 
@@ -205,7 +212,13 @@ def verify_metadata(
     url = metadata.get("schema")
     if url is None:
         raise ValueError("must provide the `schema` field in the metadata for the URL of schema file.")
-    download_url(url=url, filepath=filepath_, hash_val=_args.pop("hash_val", None), hash_type="md5", progress=True)
+    download_url(
+        url=url,
+        filepath=filepath_,
+        hash_val=_args.pop("hash_val", None),
+        hash_type=_args.pop("hash_type", "md5"),
+        progress=True,
+    )
     schema = ConfigParser.load_config_file(filepath=filepath_)
 
     try:


Test patch:
diff --git a/tests/test_bundle_verify_metadata.py b/tests/test_bundle_verify_metadata.py
--- a/tests/test_bundle_verify_metadata.py
+++ b/tests/test_bundle_verify_metadata.py
@@ -20,16 +20,24 @@
 from parameterized import parameterized
 
 from monai.bundle import ConfigParser
-from tests.utils import skip_if_windows
+from tests.utils import download_url_or_skip_test, skip_if_windows, testing_data_config
 
-TEST_CASE_1 = [
-    os.path.join(os.path.dirname(__file__), "testing_data", "metadata.json"),
-    os.path.join(os.path.dirname(__file__), "testing_data", "schema.json"),
-]
+SCHEMA_FILE = os.path.join(os.path.dirname(__file__), "testing_data", "schema.json")
+
+TEST_CASE_1 = [os.path.join(os.path.dirname(__file__), "testing_data", "metadata.json"), SCHEMA_FILE]
 
 
 @skip_if_windows
 class TestVerifyMetaData(unittest.TestCase):
+    def setUp(self):
+        self.config = testing_data_config("configs", "test_meta_file")
+        download_url_or_skip_test(
+            url=self.config["url"],
+            filepath=SCHEMA_FILE,
+            hash_val=self.config.get("hash_val"),
+            hash_type=self.config.get("hash_type", "sha256"),
+        )
+
     @parameterized.expand([TEST_CASE_1])
     def test_verify(self, meta_file, schema_file):
         logging.basicConfig(stream=sys.stdout, level=logging.INFO)
@@ -38,10 +46,8 @@ def test_verify(self, meta_file, schema_file):
             def_args_file = os.path.join(tempdir, "def_args.json")
             ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
 
-            hash_val = "e3a7e23d1113a1f3e6c69f09b6f9ce2c"
-
             cmd = [sys.executable, "-m", "monai.bundle", "verify_metadata", "--meta_file", meta_file]
-            cmd += ["--filepath", schema_file, "--hash_val", hash_val, "--args_file", def_args_file]
+            cmd += ["--filepath", schema_file, "--hash_val", self.config["hash_val"], "--args_file", def_args_file]
             ret = subprocess.check_call(cmd)
             self.assertEqual(ret, 0)
 
@@ -50,15 +56,9 @@ def test_verify_error(self):
         with tempfile.TemporaryDirectory() as tempdir:
             filepath = os.path.join(tempdir, "schema.json")
             metafile = os.path.join(tempdir, "metadata.json")
+            meta_dict = {"schema": self.config["url"], "wrong_meta": "wrong content"}
             with open(metafile, "w") as f:
-                json.dump(
-                    {
-                        "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/"
-                        "download/0.8.1/meta_schema_202203171008.json",
-                        "wrong_meta": "wrong content",
-                    },
-                    f,
-                )
+                json.dump(meta_dict, f)
 
             cmd = [sys.executable, "-m", "monai.bundle", "verify_metadata", metafile, "--filepath", filepath]
             ret = subprocess.check_call(cmd)
diff --git a/tests/test_integration_bundle_run.py b/tests/test_integration_bundle_run.py
--- a/tests/test_integration_bundle_run.py
+++ b/tests/test_integration_bundle_run.py
@@ -11,6 +11,7 @@
 
 import json
 import os
+import shutil
 import subprocess
 import sys
 import tempfile
@@ -28,57 +29,80 @@
 TEST_CASE_2 = [os.path.join(os.path.dirname(__file__), "testing_data", "inference.yaml"), (128, 128, 128)]
 
 
+class _Runnable42:
+    def __init__(self, val=1):
+        self.val = val
+
+    def run(self):
+        assert self.val == 42  # defined in `TestBundleRun.test_tiny``
+        return self.val
+
+
 class TestBundleRun(unittest.TestCase):
+    def setUp(self):
+        self.data_dir = tempfile.mkdtemp()
+
+    def tearDown(self):
+        shutil.rmtree(self.data_dir)
+
+    def test_tiny(self):
+        config_file = os.path.join(self.data_dir, "tiny_config.json")
+        with open(config_file, "w") as f:
+            json.dump({"": {"_target_": "tests.test_integration_bundle_run._Runnable42", "val": 42}}, f)
+        cmd = [sys.executable, "-m", "monai.bundle", "run", "--config_file", config_file]
+        ret = subprocess.check_call(cmd)
+        self.assertEqual(ret, 0)
+
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
     def test_shape(self, config_file, expected_shape):
         test_image = np.random.rand(*expected_shape)
-        with tempfile.TemporaryDirectory() as tempdir:
-            filename = os.path.join(tempdir, "image.nii")
-            nib.save(nib.Nifti1Image(test_image, np.eye(4)), filename)
-
-            # generate default args in a JSON file
-            def_args = {"config_file": "will be replaced by `config_file` arg"}
-            def_args_file = os.path.join(tempdir, "def_args.json")
-            ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
-
-            meta = {"datalist": [{"image": filename}], "output_dir": tempdir, "window": (96, 96, 96)}
-            # test YAML file
-            meta_file = os.path.join(tempdir, "meta.yaml")
-            ConfigParser.export_config_file(config=meta, filepath=meta_file, fmt="yaml")
-
-            # test override with file, up case postfix
-            overridefile1 = os.path.join(tempdir, "override1.JSON")
-            with open(overridefile1, "w") as f:
-                # test override with part of the overriding file
-                json.dump({"move_net": "$@network_def.to(@device)"}, f)
-            os.makedirs(os.path.join(tempdir, "jsons"), exist_ok=True)
-            overridefile2 = os.path.join(tempdir, "jsons/override2.JSON")
-            with open(overridefile2, "w") as f:
-                # test override with the whole overriding file
-                json.dump("Dataset", f)
-
-            saver = LoadImage(image_only=True)
-
-            if sys.platform == "win32":
-                override = "--network $@network_def.to(@device) --dataset#_target_ Dataset"
-            else:
-                override = f"--network %{overridefile1}#move_net --dataset#_target_ %{overridefile2}"
-            # test with `monai.bundle` as CLI entry directly
-            cmd = f"-m monai.bundle run evaluator --postprocessing#transforms#2#output_postfix seg {override}"
-            la = [f"{sys.executable}"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
-            test_env = os.environ.copy()
-            print(f"CUDA_VISIBLE_DEVICES in {__file__}", test_env.get("CUDA_VISIBLE_DEVICES"))
-            ret = subprocess.check_call(la + ["--args_file", def_args_file], env=test_env)
-            self.assertEqual(ret, 0)
-            self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_seg.nii.gz")).shape, expected_shape)
-
-            # here test the script with `google fire` tool as CLI
-            cmd = "-m fire monai.bundle.scripts run --runner_id evaluator"
-            cmd += f" --evaluator#amp False {override}"
-            la = [f"{sys.executable}"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
-            ret = subprocess.check_call(la, env=test_env)
-            self.assertEqual(ret, 0)
-            self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_trans.nii.gz")).shape, expected_shape)
+        tempdir = self.data_dir
+        filename = os.path.join(tempdir, "image.nii")
+        nib.save(nib.Nifti1Image(test_image, np.eye(4)), filename)
+
+        # generate default args in a JSON file
+        def_args = {"config_file": "will be replaced by `config_file` arg"}
+        def_args_file = os.path.join(tempdir, "def_args.json")
+        ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
+
+        meta = {"datalist": [{"image": filename}], "output_dir": tempdir, "window": (96, 96, 96)}
+        # test YAML file
+        meta_file = os.path.join(tempdir, "meta.yaml")
+        ConfigParser.export_config_file(config=meta, filepath=meta_file, fmt="yaml")
+
+        # test override with file, up case postfix
+        overridefile1 = os.path.join(tempdir, "override1.JSON")
+        with open(overridefile1, "w") as f:
+            # test override with part of the overriding file
+            json.dump({"move_net": "$@network_def.to(@device)"}, f)
+        os.makedirs(os.path.join(tempdir, "jsons"), exist_ok=True)
+        overridefile2 = os.path.join(tempdir, "jsons/override2.JSON")
+        with open(overridefile2, "w") as f:
+            # test override with the whole overriding file
+            json.dump("Dataset", f)
+
+        saver = LoadImage(image_only=True)
+
+        if sys.platform == "win32":
+            override = "--network $@network_def.to(@device) --dataset#_target_ Dataset"
+        else:
+            override = f"--network %{overridefile1}#move_net --dataset#_target_ %{overridefile2}"
+        # test with `monai.bundle` as CLI entry directly
+        cmd = f"-m monai.bundle run evaluator --postprocessing#transforms#2#output_postfix seg {override}"
+        la = [f"{sys.executable}"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
+        test_env = os.environ.copy()
+        print(f"CUDA_VISIBLE_DEVICES in {__file__}", test_env.get("CUDA_VISIBLE_DEVICES"))
+        ret = subprocess.check_call(la + ["--args_file", def_args_file], env=test_env)
+        self.assertEqual(ret, 0)
+        self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_seg.nii.gz")).shape, expected_shape)
+
+        # here test the script with `google fire` tool as CLI
+        cmd = "-m fire monai.bundle.scripts run --runner_id evaluator"
+        cmd += f" --evaluator#amp False {override}"
+        la = [f"{sys.executable}"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
+        ret = subprocess.check_call(la, env=test_env)
+        self.assertEqual(ret, 0)
+        self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_trans.nii.gz")).shape, expected_shape)
 
 
 if __name__ == "__main__":
diff --git a/tests/testing_data/data_config.json b/tests/testing_data/data_config.json
--- a/tests/testing_data/data_config.json
+++ b/tests/testing_data/data_config.json
@@ -67,5 +67,12 @@
             "hash_type": "sha256",
             "hash_val": "a260b3a40f82dfe37c58d26a612bcf7bef0d27c6fed096226b0e4e9fb364168e"
         }
+    },
+    "configs": {
+        "test_meta_file": {
+            "url": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_202203171008.json",
+            "hash_type": "md5",
+            "hash_val": "e3a7e23d1113a1f3e6c69f09b6f9ce2c"
+        }
     }
 }