nwb-linkml/nwb_linkml/conftest.py

77 lines
2.2 KiB
Python

"""
Test fixtures primarily for doctests for adapters
"""
import re
import textwrap
from doctest import ELLIPSIS, NORMALIZE_WHITESPACE
from typing import Generator
import yaml
from sybil import Document, Example, Region, Sybil
from sybil.parsers.codeblock import PythonCodeBlockParser
from sybil.parsers.doctest import DocTestParser
from nwb_linkml import adapters
# Test adapter generation examples
ADAPTER_START = re.compile(r"\.\.\s*adapter::")
ADAPTER_END = re.compile(r"\n\s*\n")
NWB_KEYS = re.compile(r"(^\s*datasets:\s*\n)|^groups:")
def _strip_nwb(nwb: str) -> str:
# strip 'datasets:' keys and decoration left in for readability/context
nwb = re.sub(NWB_KEYS, "", nwb)
nwb = re.sub(r"^-", " ", nwb)
nwb = textwrap.dedent(nwb)
return nwb
def test_adapter_block(example: Example) -> None:
"""
The linkml generated from a nwb example input should match
that provided in the docstring.
See adapters/dataset.py for example usage of .. adapter:: directive
"""
cls_name, nwb, linkml_expected = example.parsed
# get adapter and generate
adapter_cls = getattr(adapters, cls_name)
adapter = adapter_cls(cls=nwb)
res = adapter.build()
# compare
generated = yaml.safe_load(res.as_linkml())
expected = yaml.safe_load(linkml_expected)
assert generated == expected
def parse_adapter_blocks(document: Document) -> Generator[Region, None, None]:
"""
Parse blocks with adapter directives, yield to test with :func:`.test_adapter_block`
"""
for start_match, end_match, source in document.find_region_sources(ADAPTER_START, ADAPTER_END):
# parse
sections = re.split(r":\w+?:", source, flags=re.MULTILINE)
sections = [textwrap.dedent(section).strip() for section in sections]
sections[1] = _strip_nwb(sections[1])
yield Region(start_match.start(), end_match.end(), sections, test_adapter_block)
adapter_parser = Sybil(
parsers=[parse_adapter_blocks],
patterns=["adapters/*.py"],
)
doctest_parser = Sybil(
parsers=[DocTestParser(optionflags=ELLIPSIS + NORMALIZE_WHITESPACE), PythonCodeBlockParser()],
patterns=["providers/git.py"],
)
pytest_collect_file = (adapter_parser + doctest_parser).pytest()