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import subprocess
import re
import sys
from unittest.mock import patch
from io import StringIO
import warnings
from pynwb.testing import TestCase
from pynwb import validate, NWBHDF5IO
# NOTE we use "coverage run -m pynwb.validate" instead of "python -m pynwb.validate"
# so that we can both test pynwb.validate and compute code coverage from that test.
# NOTE we also use "coverage run -p" which will generate a .coverage file with the
# machine name, process id, and a random number appended to the filename to
# simplify collecting and merging coverage data from multiple subprocesses. if "-p"
# is not used, then each "coverage run" will overwrite the .coverage file from a
# previous "coverage run".
# NOTE we run "coverage" as "{sys.executable} -m coverage" to 1. make sure to use
# the same python version, and on Debian systems executable is "python3-coverage", not
# just "coverage".
# NOTE the run_coverage.yml GitHub Action runs "python -m coverage combine" to
# combine the individual coverage reports into one .coverage file.
def run_coverage(extra_args: list[str]):
return subprocess.run(
[sys.executable, "-m", "coverage", "run", "-p", "-m", "pynwb.validate"]
+ extra_args,
capture_output=True
)
class TestValidateCLI(TestCase):
# 1.0.2_nwbfile.nwb has no cached specifications
# 1.0.3_nwbfile.nwb has cached "core" specification
# 1.1.2_nwbfile.nwb has cached "core" and "hdmf-common" specifications
def test_validate_file_no_cache(self):
"""Test that validating a file with no cached spec against the core namespace succeeds."""
result = run_coverage(["tests/back_compat/1.0.2_nwbfile.nwb"])
stderr_regex = re.compile(
r"The file tests/back_compat/1\.0\.2_nwbfile\.nwb has no cached namespace information\. "
r"Falling back to PyNWB namespace information\.\s*"
)
self.assertRegex(result.stderr.decode('utf-8'), stderr_regex)
stdout_regex = re.compile(
r"Validating tests/back_compat/1\.0\.2_nwbfile\.nwb against PyNWB namespace information using namespace "
r"'core'\.\s* - no errors found\.\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_no_cache_bad_ns(self):
"""Test that validating a file with no cached spec against a specified, unknown namespace fails."""
result = run_coverage(["tests/back_compat/1.0.2_nwbfile.nwb", "--ns", "notfound"])
stderr_regex = re.compile(
r"The file tests/back_compat/1\.0\.2_nwbfile\.nwb has no cached namespace information\. "
r"Falling back to PyNWB namespace information\.\s*"
r"The namespace 'notfound' could not be found in PyNWB namespace information as only "
r"\['core'\] is present\.\s*"
)
self.assertRegex(result.stderr.decode('utf-8'), stderr_regex)
self.assertEqual(result.stdout.decode('utf-8'), '')
def test_validate_file_cached(self):
"""Test that validating a file with cached spec against its cached namespace succeeds."""
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb"])
self.assertEqual(result.stderr.decode('utf-8'), '')
stdout_regex = re.compile(
r"Validating tests/back_compat/1\.1\.2_nwbfile\.nwb against cached namespace information using namespace "
r"'core'\.\s* - no errors found\.\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_cached_bad_ns(self):
"""Test that validating a file with cached spec against a specified, unknown namespace fails."""
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--ns", "notfound"])
stderr_regex = re.compile(
r"The namespace 'notfound' could not be found in cached namespace information as only "
r"\['core'\] is present\.\s*"
)
self.assertRegex(result.stderr.decode('utf-8'), stderr_regex)
self.assertEqual(result.stdout.decode('utf-8'), '')
def test_validate_file_cached_extension(self):
"""Test that validating a file with cached spec against the cached namespaces succeeds."""
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb"])
self.assertEqual(result.stderr.decode('utf-8'), '')
stdout_regex = re.compile(
r"Validating tests/back_compat/2\.1\.0_nwbfile_with_extension\.nwb against cached namespace information "
r"using namespace 'ndx-testextension'\.\s* - no errors found\.\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_cached_extension_pass_ns(self):
"""Test that validating a file with cached spec against the extension namespace succeeds."""
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb", "--ns", "ndx-testextension"])
self.assertEqual(result.stderr.decode('utf-8'), '')
stdout_regex = re.compile(
r"Validating tests/back_compat/2\.1\.0_nwbfile_with_extension\.nwb against cached namespace information "
r"using namespace 'ndx-testextension'\.\s* - no errors found\.\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_cached_core(self):
"""Test that validating a file with cached spec against the core namespace succeeds."""
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb", "--ns", "core"])
stdout_regex = re.compile(
r"The namespace 'core' is included by the namespace 'ndx-testextension'. "
r"Please validate against that namespace instead\.\s*"
)
self.assertRegex(result.stderr.decode('utf-8'), stdout_regex)
def test_validate_file_cached_hdmf_common(self):
"""Test that validating a file with cached spec against the hdmf-common namespace fails."""
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--ns", "hdmf-common"])
stderr_regex = re.compile(
r"The namespace 'hdmf-common' is included by the namespace 'core'\. Please validate against that "
r"namespace instead\.\s*",
)
self.assertRegex(result.stderr.decode('utf-8'), stderr_regex)
def test_validate_file_cached_ignore(self):
"""Test that validating a file with cached spec against the core namespace succeeds."""
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--no-cached-namespace"])
self.assertEqual(result.stderr.decode('utf-8'), '')
stdout_regex = re.compile(
r"Validating tests/back_compat/1\.1\.2_nwbfile\.nwb against PyNWB namespace information using namespace "
r"'core'\.\s* - no errors found\.\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_invalid(self):
"""Test that validating an invalid file outputs errors."""
result = run_coverage(["tests/back_compat/1.0.2_str_experimenter.nwb", "--no-cached-namespace"])
stderr_regex = re.compile(
r" - found the following errors:\s*"
r"root/general/experimenter \(general/experimenter\): incorrect shape - expected an array of shape "
r"'\[None\]', got non-array data 'one experimenter'\s*"
)
self.assertRegex(result.stderr.decode('utf-8'), stderr_regex)
stdout_regex = re.compile(
r"Validating tests/back_compat/1\.0\.2_str_experimenter\.nwb against PyNWB namespace information using "
r"namespace 'core'\.\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_list_namespaces_core(self):
"""Test listing namespaces from a file"""
result = run_coverage(["tests/back_compat/1.1.2_nwbfile.nwb", "--list-namespaces"])
self.assertEqual(result.stderr.decode('utf-8'), '')
stdout_regex = re.compile(r"core\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
def test_validate_file_list_namespaces_extension(self):
"""Test listing namespaces from a file with an extension"""
result = run_coverage(["tests/back_compat/2.1.0_nwbfile_with_extension.nwb", "--list-namespaces"])
self.assertEqual(result.stderr.decode('utf-8'), '')
stdout_regex = re.compile(r"ndx-testextension\s*")
self.assertRegex(result.stdout.decode('utf-8'), stdout_regex)
class TestValidateFunction(TestCase):
# 1.0.2_nwbfile.nwb has no cached specifications
# 1.0.3_nwbfile.nwb has cached "core" specification
# 1.1.2_nwbfile.nwb has cached "core" and "hdmf-common" specificaitions
def get_io(self, path):
"""Get an NWBHDF5IO object for the given path, ignoring the warning about ignoring cached namespaces."""
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore",
message=r"Ignoring cached namespace .*",
category=UserWarning,
)
return NWBHDF5IO(str(path), 'r')
def test_validate_io_no_cache(self):
"""Test that validating a file with no cached spec against the core namespace succeeds."""
with self.get_io('tests/back_compat/1.0.2_nwbfile.nwb') as io:
errors = validate(io)
self.assertEqual(errors, [])
def test_validate_io_no_cache_bad_ns(self):
"""Test that validating a file with no cached spec against a specified, unknown namespace fails."""
with self.get_io('tests/back_compat/1.0.2_nwbfile.nwb') as io:
with self.assertRaisesWith(KeyError, "\"'notfound' not a namespace\""):
validate(io, 'notfound')
def test_validate_io_cached(self):
"""Test that validating a file with cached spec against its cached namespace succeeds."""
with self.get_io('tests/back_compat/1.1.2_nwbfile.nwb') as io:
errors = validate(io)
self.assertEqual(errors, [])
def test_validate_io_cached_extension(self):
"""Test that validating a file with cached spec against its cached namespaces succeeds."""
with self.get_io('tests/back_compat/2.1.0_nwbfile_with_extension.nwb') as io:
errors = validate(io)
self.assertEqual(errors, [])
def test_validate_io_cached_extension_pass_ns(self):
"""Test that validating a file with cached extension spec against the extension namespace succeeds."""
with self.get_io('tests/back_compat/2.1.0_nwbfile_with_extension.nwb') as io:
errors = validate(io, 'ndx-testextension')
self.assertEqual(errors, [])
def test_validate_io_cached_core_with_io(self):
"""
For back-compatability, test that validating a file with cached extension spec against the core
namespace succeeds when using the `io` + `namespace` keywords.
"""
with self.get_io(path='tests/back_compat/2.1.0_nwbfile_with_extension.nwb') as io:
results = validate(io=io, namespace="core")
self.assertEqual(results, [])
def test_validate_file_cached_extension(self):
"""
Test that validating a file with cached extension spec against the core
namespace raises an error with the new CLI-mimicing paths keyword.
"""
nwbfile_path = "tests/back_compat/2.1.0_nwbfile_with_extension.nwb"
with patch("sys.stderr", new=StringIO()) as fake_err:
with patch("sys.stdout", new=StringIO()) as fake_out:
results, status = validate(paths=[nwbfile_path], namespace="core", verbose=True)
self.assertEqual(results, [])
self.assertEqual(status, 1)
self.assertEqual(
fake_err.getvalue(),
(
"The namespace 'core' is included by the namespace 'ndx-testextension'. "
"Please validate against that namespace instead.\n"
)
)
self.assertEqual(fake_out.getvalue(), "")
def test_validate_file_cached_core(self):
"""
Test that validating a file with cached core spec with verbose=False.
"""
nwbfile_path = "tests/back_compat/1.1.2_nwbfile.nwb"
with patch("sys.stderr", new=StringIO()) as fake_err:
with patch("sys.stdout", new=StringIO()) as fake_out:
results, status = validate(paths=[nwbfile_path], namespace="core")
self.assertEqual(results, [])
self.assertEqual(status, 0)
self.assertEqual(fake_err.getvalue(), "")
self.assertEqual(fake_out.getvalue(), "")
def test_validate_file_cached_no_cache_bad_ns(self):
"""
Test that validating a file with no cached namespace, a namespace that is not found, and verbose=False.
"""
nwbfile_path = "tests/back_compat/1.0.2_nwbfile.nwb"
with patch("sys.stderr", new=StringIO()) as fake_err:
with patch("sys.stdout", new=StringIO()) as fake_out:
results, status = validate(paths=[nwbfile_path], namespace="notfound")
self.assertEqual(results, [])
self.assertEqual(status, 1)
stderr_regex = (
r"The namespace 'notfound' could not be found in PyNWB namespace information as only "
r"\['core'\] is present.\n"
)
self.assertRegex(fake_err.getvalue(), stderr_regex)
self.assertEqual(fake_out.getvalue(), "")
def test_validate_io_cached_bad_ns(self):
"""Test that validating a file with cached spec against a specified, unknown namespace fails."""
with self.get_io('tests/back_compat/1.1.2_nwbfile.nwb') as io:
with self.assertRaisesWith(KeyError, "\"'notfound' not a namespace\""):
validate(io, 'notfound')
def test_validate_io_cached_hdmf_common(self):
"""Test that validating a file with cached spec against the hdmf-common namespace fails."""
with self.get_io('tests/back_compat/1.1.2_nwbfile.nwb') as io:
# TODO this error should not be different from the error when using the validate script above
msg = "builder must have data type defined with attribute 'data_type'"
with self.assertRaisesWith(ValueError, msg):
validate(io, 'hdmf-common')
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