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mvdbeek
175ad89d20
Tag each `UserToolSource` / `Citation` validator with a stable `PydanticCustomError` code (`dynamic_tool.blank_string`, `dynamic_tool.blank_container`, `dynamic_tool.undeclared_input_ref`, `dynamic_tool.output_unclaimed`, `dynamic_tool.citation_*`) so external validators can match codes instead of substring-matching Pydantic's English phrasing. Move the test corpus into `user_tool_source_validation_cases.yml`, mirroring the `parameter_specification.yml` pattern, so downstream validators (the TS port in galaxy-tool-util-ts, MCP clients, IDE plugins) can replay the same conformance cases. The Python test now loads the YAML and parametrizes over it; cases assert by stable error code plus optional location and message-substring.
104 lines
3.2 KiB
Python
104 lines
3.2 KiB
Python
"""Direct tests for the semantic validators on ``UserToolSource``.
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The corpus of cases lives in ``user_tool_source_validation_cases.yml`` so it
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can be replayed by external validators (the TS port in
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``galaxy-tool-util-ts``, MCP clients, IDE plugins). Each case overrides
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``VALID_TOOL`` with its ``doc`` and either validates cleanly (``valid: true``)
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or raises a ``ValidationError`` whose distilled output matches the listed
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``expected_errors`` by stable error ``code``.
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Container *shape* is enforced by the lint framework, not pydantic — see
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``test_container_shape_lint.py``.
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"""
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from copy import deepcopy
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from pathlib import Path
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from typing import (
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Any,
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Dict,
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List,
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)
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import pytest
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import yaml
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from pydantic import ValidationError
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from galaxy.tool_util_models import (
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format_validation_errors,
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UserToolSource,
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)
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from galaxy.util.resources import resource_string
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VALID_TOOL: Dict[str, Any] = {
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"class": "GalaxyUserTool",
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"id": "my-cool-tool",
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"name": "My Cool Tool",
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"version": "0.1.0",
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"description": "A cool tool.",
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"container": "quay.io/biocontainers/python:3.13",
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"shell_command": "head -n '$(inputs.n_lines)' '$(inputs.data_input.path)' > out.txt",
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"inputs": [
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{"type": "integer", "name": "n_lines"},
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{"type": "data", "name": "data_input"},
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],
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"outputs": [
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{"type": "data", "name": "out", "from_work_dir": "out.txt"},
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],
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"citations": [
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{"type": "doi", "content": "10.1234/abc.def"},
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],
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}
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def _load_cases() -> List[Dict[str, Any]]:
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try:
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yaml_str = resource_string(__name__, "user_tool_source_validation_cases.yml")
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except AttributeError:
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# Fallback for invocations that bypass importlib.resources; resolve
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# relative to this file rather than cwd.
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yaml_str = (Path(__file__).parent / "user_tool_source_validation_cases.yml").read_text()
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return yaml.safe_load(yaml_str)["cases"]
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CASES = _load_cases()
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def _doc_for(case: Dict[str, Any]) -> Dict[str, Any]:
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base = deepcopy(VALID_TOOL)
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base.update(case.get("doc") or {})
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return base
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def _flatten_loc(loc: Any) -> str:
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if isinstance(loc, (list, tuple)):
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return ".".join(str(p) for p in loc if p != "__root__")
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return str(loc)
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@pytest.mark.parametrize("case", CASES, ids=lambda c: c["name"])
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def test_user_tool_source_corpus(case: Dict[str, Any]) -> None:
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doc = _doc_for(case)
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if case.get("valid"):
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UserToolSource.model_validate(doc)
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return
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with pytest.raises(ValidationError) as info:
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UserToolSource.model_validate(doc)
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if "expected_format" in case:
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assert format_validation_errors(info.value) == case["expected_format"]
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raised = [{"loc": _flatten_loc(err["loc"]), "code": err["type"], "msg": err["msg"]} for err in info.value.errors()]
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for expected in case.get("expected_errors") or []:
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match = next(
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(
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e
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for e in raised
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if e["code"] == expected["code"]
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and ("loc" not in expected or e["loc"] == expected["loc"])
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and ("msg_contains" not in expected or expected["msg_contains"] in e["msg"])
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),
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None,
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)
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assert match is not None, f"no error matched {expected!r}; raised={raised!r}"
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