mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-09-19 23:44:28 +00:00
77 lines
2.2 KiB
Python
77 lines
2.2 KiB
Python
"""
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Test fixtures primarily for doctests for adapters
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"""
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import re
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import textwrap
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from doctest import ELLIPSIS, NORMALIZE_WHITESPACE
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from typing import Generator
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import yaml
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from sybil import Document, Example, Region, Sybil
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from sybil.parsers.codeblock import PythonCodeBlockParser
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from sybil.parsers.doctest import DocTestParser
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from nwb_linkml import adapters
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# Test adapter generation examples
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ADAPTER_START = re.compile(r"\.\.\s*adapter::")
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ADAPTER_END = re.compile(r"\n\s*\n")
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NWB_KEYS = re.compile(r"(^\s*datasets:\s*\n)|^groups:")
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def _strip_nwb(nwb: str) -> str:
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# strip 'datasets:' keys and decoration left in for readability/context
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nwb = re.sub(NWB_KEYS, "", nwb)
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nwb = re.sub(r"^-", " ", nwb)
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nwb = textwrap.dedent(nwb)
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return nwb
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def test_adapter_block(example: Example) -> None:
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"""
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The linkml generated from a nwb example input should match
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that provided in the docstring.
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See adapters/dataset.py for example usage of .. adapter:: directive
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"""
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cls_name, nwb, linkml_expected = example.parsed
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# get adapter and generate
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adapter_cls = getattr(adapters, cls_name)
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adapter = adapter_cls(cls=nwb)
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res = adapter.build()
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# compare
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generated = yaml.safe_load(res.as_linkml())
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expected = yaml.safe_load(linkml_expected)
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assert generated == expected
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def parse_adapter_blocks(document: Document) -> Generator[Region, None, None]:
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"""
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Parse blocks with adapter directives, yield to test with :func:`.test_adapter_block`
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"""
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for start_match, end_match, source in document.find_region_sources(ADAPTER_START, ADAPTER_END):
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# parse
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sections = re.split(r":\w+?:", source, flags=re.MULTILINE)
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sections = [textwrap.dedent(section).strip() for section in sections]
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sections[1] = _strip_nwb(sections[1])
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yield Region(start_match.start(), end_match.end(), sections, test_adapter_block)
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adapter_parser = Sybil(
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parsers=[parse_adapter_blocks],
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patterns=["adapters/*.py"],
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)
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doctest_parser = Sybil(
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parsers=[DocTestParser(optionflags=ELLIPSIS + NORMALIZE_WHITESPACE), PythonCodeBlockParser()],
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patterns=["*.py"],
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)
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pytest_collect_file = (adapter_parser + doctest_parser).pytest()
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