update cached namespace retrieval in validation tests (#1961)

* filter out warnings when getting namespaces in test.py * make get_cached_namespaces function public * replace get_namespaces function * update code block in docstring * update CHANGELOG.md --------- Co-authored-by: Ryan Ly <[email protected]>
NeurodataWithoutBorders · Sep 9, 2024 · 6196568 · 6196568
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 ### Enhancements and minor changes
 - Added support for numpy 2.0. @mavaylon1 [#1956](https://github.com/NeurodataWithoutBorders/pynwb/pull/1956)
+- Make `get_cached_namespaces_to_validate` a public function @stephprince [#1961](https://github.com/NeurodataWithoutBorders/pynwb/pull/1961)
 
 ### Documentation and tutorial enhancements
 - Added pre-release pull request instructions to release process documentation @stephprince [#1928](https://github.com/NeurodataWithoutBorders/pynwb/pull/1928)

diff --git a/src/pynwb/validate.py b/src/pynwb/validate.py
@@ -29,7 +29,7 @@ def _validate_helper(io: HDMFIO, namespace: str = CORE_NAMESPACE) -> list:
     return validator.validate(builder)
 
 
-def _get_cached_namespaces_to_validate(
+def get_cached_namespaces_to_validate(
     path: str, driver: Optional[str] = None, aws_region: Optional[str] = None,
 ) -> Tuple[List[str], BuildManager, Dict[str, str]]:
     """
@@ -39,14 +39,18 @@ def _get_cached_namespaces_to_validate(
     -------
     The following example illustrates how we can use this function to validate against namespaces
     cached in a file. This is useful, e.g., when a file was created using an extension
-    >>> from pynwb import validate
-    >>> from pynwb.validate import _get_cached_namespaces_to_validate
-    >>> path = "my_nwb_file.nwb"
-    >>> validate_namespaces, manager, cached_namespaces = _get_cached_namespaces_to_validate(path)
-    >>> with NWBHDF5IO(path, "r", manager=manager) as reader:
-    >>>     errors = []
-    >>>     for ns in validate_namespaces:
-    >>>         errors += validate(io=reader, namespace=ns)
+
+    .. code-block:: python
+
+        from pynwb import validate
+        from pynwb.validate import get_cached_namespaces_to_validate
+        path = "my_nwb_file.nwb"
+        validate_namespaces, manager, cached_namespaces = get_cached_namespaces_to_validate(path)
+        with NWBHDF5IO(path, "r", manager=manager) as reader:
+            errors = []
+            for ns in validate_namespaces:
+                errors += validate(io=reader, namespace=ns)
+
     :param path: Path for the NWB file
     :return: Tuple with:
       - List of strings with the most specific namespace(s) to use for validation.
@@ -149,7 +153,7 @@ def validate(**kwargs):
         io_kwargs = dict(path=path, mode="r", driver=driver)
 
         if use_cached_namespaces:
-            cached_namespaces, manager, namespace_dependencies = _get_cached_namespaces_to_validate(
+            cached_namespaces, manager, namespace_dependencies = get_cached_namespaces_to_validate(
                 path=path, driver=driver
             )
             io_kwargs.update(manager=manager)
@@ -231,7 +235,7 @@ def validate_cli():
 
     if args.list_namespaces:
         for path in args.paths:
-            cached_namespaces, _, _ = _get_cached_namespaces_to_validate(path=path)
+            cached_namespaces, _, _ = get_cached_namespaces_to_validate(path=path)
             print("\n".join(cached_namespaces))
     else:
         validation_errors, validation_status = validate(

diff --git a/test.py b/test.py
@@ -153,6 +153,7 @@ def validate_nwbs():
     examples_nwbs = glob.glob('*.nwb')
 
     import pynwb
+    from pynwb.validate import get_cached_namespaces_to_validate
 
     for nwb in examples_nwbs:
         try:
@@ -171,17 +172,7 @@ def validate_nwbs():
                         for err in errors:
                             print("Error: %s" % err)
 
-                def get_namespaces(nwbfile):
-                    comp = run(["python", "-m", "pynwb.validate",
-                               "--list-namespaces", nwbfile],
-                               stdout=PIPE, stderr=STDOUT, universal_newlines=True, timeout=30)
-
-                    if comp.returncode != 0:
-                        return []
-
-                    return comp.stdout.split()
-
-                namespaces = get_namespaces(nwb)
+                namespaces, _, _ = get_cached_namespaces_to_validate(nwb)
 
                 if len(namespaces) == 0:
                     FAILURES += 1

diff --git a/tests/integration/ros3/test_ros3.py b/tests/integration/ros3/test_ros3.py
@@ -1,6 +1,6 @@
 from pynwb import NWBHDF5IO
 from pynwb import validate
-from pynwb.validate import _get_cached_namespaces_to_validate
+from pynwb.validate import get_cached_namespaces_to_validate
 from pynwb.testing import TestCase
 import urllib.request
 import h5py
@@ -85,7 +85,7 @@ def test_dandi_get_cached_namespaces(self):
                 )
             }
         }
-        found_namespaces, _, found_namespace_dependencies = _get_cached_namespaces_to_validate(
+        found_namespaces, _, found_namespace_dependencies = get_cached_namespaces_to_validate(
             path=self.s3_test_path, driver="ros3"
         )