initial sketch

setup.py

@@ -33,7 +33,7 @@
     include_package_data=True,  # Includes files described in MANIFEST.in in the installation
     install_requires=install_requires,
     # zarr<2.18.0 because of https://github.com/NeurodataWithoutBorders/nwbinspector/pull/460
-    extras_require=dict(dandi=["dandi>=0.39.2", "zarr<2.18.0"], zarr=["hdmf_zarr>=0.3.0", "zarr<2.18.0"]),
+    extras_require=dict(dandi=["dandi>=0.39.2", "zarr<2.18.0", "remfile"], zarr=["hdmf_zarr>=0.3.0", "zarr<2.18.0"]),
     entry_points={"console_scripts": ["nwbinspector=nwbinspector._inspection_cli:_inspect_all_cli"]},
     license="BSD-3-Clause",
     classifiers=[

src/nwbinspector/__init__.py

@@ -2,13 +2,13 @@
 from ._registration import available_checks, register_check
 from ._types import Importance, Severity, InspectorMessage
 from ._configuration import load_config, validate_config, configure_checks
-from ._inspection import (
+from ._nwb_inspection import (
     inspect_all,
     inspect_nwbfile,
     inspect_nwbfile_object,
     run_checks,
 )
-from ._inspection import inspect_nwb  # TODO: remove after 7/1/2023
+from ._nwb_inspection import inspect_nwb  # TODO: remove after 7/1/2023
 from ._formatting import (
     format_messages,
     print_to_console,
@@ -18,6 +18,7 @@
     InspectorOutputJSONEncoder,
 )
 from ._organization import organize_messages
+from ._dandi_inspection import inspect_dandiset, inspect_dandi_file_path
 from .checks import *  # These need to be imported to trigger registration with 'available_checks', but are not exposed
 
 default_check_registry = {check.__name__: check for check in available_checks}
@@ -32,6 +33,8 @@
     "load_config",
     "configure_checks",
     "InspectorOutputJSONEncoder",
+    "inspect_dandiset",
+    "inspect_dandi_file_path",
     "inspect_all",
     "inspect_nwbfile",
     "inspect_nwbfile_object",

src/nwbinspector/_dandi_inspection.py

@@ -0,0 +1,171 @@
+import pathlib
+from typing import Union, Iterable, Literal
+
+import h5py
+import pynwb
+
+from ._types import InspectorMessage, Importance
+from ._nwb_inspection import inspect_nwbfile_object
+
+
+def inspect_dandiset(
+    *,
+    dandiset_id: str,
+    dandiset_version: Union[str, Literal["draft"], None] = None,
+    checks: Optional[list] = None,
+    ignore: Optional[List[str]] = None,
+    select: Optional[List[str]] = None,
+    importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
+    client: Union["dandi.dandiapi.DandiAPIClient", None] = None,
+) -> Iterable[InspectorMessage]:
+    """
+    Inspect a Dandiset for common issues.
+
+    Parameters
+    ----------
+    dandiset_id : six-digit string, "draft", or None
+        The six-digit ID of the Dandiset.
+    dandiset_version : string
+        The specific published version of the Dandiset to inspect.
+        If None, the latest version is used.
+        If there are no published versions, then 'draft' is used instead.
+    checks : list, optional
+        list of checks to run
+    ignore: list, optional
+        Names of functions to skip.
+    select: list, optional
+        Names of functions to pick out of available checks.
+    importance_threshold : string or Importance, optional
+        Ignores tests with an assigned importance below this threshold.
+        Importance has three levels:
+
+            CRITICAL
+                - potentially incorrect data
+            BEST_PRACTICE_VIOLATION
+                - very suboptimal data representation
+            BEST_PRACTICE_SUGGESTION
+                - improvable data representation
+
+        The default is the lowest level, BEST_PRACTICE_SUGGESTION.
+    client: dandi.dandiapi.DandiAPIClient
+        The client object can be passed to avoid re-instantiation over an iteration.
+    """
+    if client is None:
+        import dandi.dandiapi
+
+        client = dandi.dandiapi.DandiAPIClient()
+
+    dandiset = client.get_dandiset(dandiset_id=dandiset_id, version_id=dandiset_version)
+
+    if not any(
+        asset_type.get("identifier", "") != "RRID:SCR_015242"  # Identifier for NWB standard
+        for asset_type in dandiset.get_raw_metadata().get("assetsSummary", {}).get("dataStandard", [])
+    ):
+        yield iter([])
+
+    for asset in dandiset.get_assets():
+        if ".nwb" not in pathlib.Path(asset.path).suffixes:
+            continue
+
+        dandi_s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)
+        yield _insect_dandi_s3_nwb(
+            dandi_s3_url=dandi_s3_url,
+            dandiset_id=dandiset_id,
+            dandiset_version=dandiset_version,
+            checks=checks,
+            ignore=ignore,
+            select=select,
+            importance_threshold=importance_threshold,
+            client=client,
+        )
+
+    pass
+
+
+def inspect_dandi_file_path(
+    *,
+    dandi_file_path: str,
+    dandiset_id: str,
+    dandiset_version: Union[str, Literal["draft"], None] = None,
+    checks: Optional[list] = None,
+    ignore: Optional[List[str]] = None,
+    select: Optional[List[str]] = None,
+    importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
+    client: Union["dandi.dandiapi.DandiAPIClient", None] = None,
+) -> Iterable[InspectorMessage]:
+    """
+    Inspect a Dandifile for common issues.
+
+    Parameters
+    ----------
+    dandi_file_path : string
+        The path to the Dandifile as seen on the archive; e.g., 'sub-123_ses-456+ecephys.nwb'.
+    dandiset_id : six-digit string, "draft", or None
+        The six-digit ID of the Dandiset.
+    dandiset_version : string
+        The specific published version of the Dandiset to inspect.
+        If None, the latest version is used.
+        If there are no published versions, then 'draft' is used instead.
+    checks : list, optional
+        list of checks to run
+    ignore: list, optional
+        Names of functions to skip.
+    select: list, optional
+        Names of functions to pick out of available checks.
+    importance_threshold : string or Importance, optional
+        Ignores tests with an assigned importance below this threshold.
+        Importance has three levels:
+
+            CRITICAL
+                - potentially incorrect data
+            BEST_PRACTICE_VIOLATION
+                - very suboptimal data representation
+            BEST_PRACTICE_SUGGESTION
+                - improvable data representation
+
+        The default is the lowest level, BEST_PRACTICE_SUGGESTION.
+    client: dandi.dandiapi.DandiAPIClient
+        The client object can be passed to avoid re-instantiation over an iteration.
+    """
+    if client is None:
+        import dandi.dandiapi
+
+        client = dandi.dandiapi.DandiAPIClient()
+
+    dandiset = client.get_dandiset(dandiset_id=dandiset_id, version_id=dandiset_version)
+    asset = dandiset.get_asset_by_path(path=dandi_file_path)
+    dandi_s3_url = asset.get_content_url(follow_redirects=1, strip_query=True)
+
+    yield _insect_dandi_s3_nwb(
+        dandi_s3_url=dandi_s3_url,
+        checks=checks,
+        ignore=ignore,
+        select=select,
+        importance_threshold=importance_threshold,
+        client=client,
+    )
+
+
+def _insect_dandi_s3_nwb(
+    *,
+    dandi_s3_url: str,
+    checks: Union[list, None] = None,
+    ignore: Union[List[str], None] = None,
+    select: Union[List[str], None] = None,
+    importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
+) -> Iterable[InspectorMessage]:
+    import remfile
+
+    byte_stream = remfile.File(url=dandi_s3_url)
+    file = h5py.File(name=byte_stream)
+    io = pynwb.NWBHDF5IO(file=file)
+    nwbfile = io.read()
+
+    yield inspect_nwbfile_object(
+        nwbfile_object=nwbfile,
+        checks=checks,
+        config="dandi",
+        ignore=ignore,
+        select=select,
+        importance_threshold=importance_threshold,
+    )

src/nwbinspector/_inspection.py → src/nwbinspector/_nwb_inspection.py

@@ -372,7 +372,7 @@ def inspect_nwbfile_object(
     ignore: Optional[List[str]] = None,
     select: Optional[List[str]] = None,
     importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
-) -> List[InspectorMessage]:
+) -> Iterable[InspectorMessage]:
     """
     Inspect an in-memory NWBFile object and return suggestions for improvements according to best practices.
 

src/nwbinspector/nwbinspector/__init__.py

@@ -16,7 +16,7 @@
     load_config,
     configure_checks,
 )
-from .._inspection import (
+from .._nwb_inspection import (
     inspect_all,
     inspect_nwb,  # TODO: remove
     inspect_nwbfile,