Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Use cached namespace validation #1149

Merged
merged 3 commits into from
Nov 11, 2022
Merged

Use cached namespace validation #1149

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e1809e3
Update pynwb_utils.py
CodyCBakerPhD Nov 1, 2022
921f67a
Update pynwb_utils.py
CodyCBakerPhD Nov 1, 2022
d7ab706
Update pynwb_utils.py
CodyCBakerPhD Nov 1, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
37 changes: 21 additions & 16 deletions dandi/pynwb_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from fscacher import PersistentCache
import h5py
import hdmf
from packaging.version import Version
import pynwb
from pynwb import NWBHDF5IO
import semantic_version
Expand Down Expand Up @@ -335,23 +336,27 @@ def validate(
path = str(path) # Might come in as pathlib's PATH
errors: List[ValidationResult] = []
try:
with pynwb.NWBHDF5IO(path, "r", load_namespaces=True) as reader:
error_outputs = pynwb.validate(reader)
# TODO: return ValidationResult structs
for error_output in error_outputs:
errors.append(
ValidationResult(
origin=ValidationOrigin(
name="pynwb",
version=pynwb.__version__,
),
severity=Severity.WARNING,
id=f"pywnb.{error_output}",
scope=Scope.FILE,
path=Path(path),
message="Failed to validate.",
)
if Version(pynwb.__version__) >= Version("2.2.0"): # Use cached namespace feature
# argument get_cached_namespaces is True by default
error_outputs, _ = pynwb.validate(paths=[path])
else: # Fallback if an older version
with pynwb.NWBHDF5IO(path=path, mode="r", load_namespaces=True) as reader:
error_outputs = pynwb.validate(io=reader)
# TODO: return ValidationResult structs
for error_output in error_outputs:
errors.append(
ValidationResult(
origin=ValidationOrigin(
name="pynwb",
version=pynwb.__version__,
),
severity=Severity.WARNING,
id=f"pywnb.{error_output}",
scope=Scope.FILE,
path=Path(path),
message="Failed to validate.",
)
)
except Exception as exc:
if devel_debug:
raise
Expand Down