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Drop Python 3.8 support in 5 Pulsar-compatible packages (job_metrics, tool_util, tool_util_models, util, objectstore) and run pyupgrade --py310-plus on their source code. - Bump requires-python from >=3.8 to >=3.10 in all 5 packages - Remove Python 3.8 and 3.9 classifiers - Remove ruff per-file-ignores for UP rules on these paths - Remove backports.zoneinfo conditional dependency - Remove pydyf<0.11 pin from conditional-requirements.txt - Update Makefile pyupgrade target (remove PY38_PYUPGRADE_PATHS) - Update CI workflow to test with Python 3.10 instead of 3.8 Clean up unused deprecated typing imports after pyupgrade Remove now-unused typing imports (Dict, List, Optional, Set, Tuple, Type, Union) that became dead after pyupgrade --py310-plus converted annotations to use built-in types and | syntax. Also run ruff check --fix --select=UP007,UP045 across the entire codebase to convert remaining Optional[X] -> X | None and Union[X, Y] -> X | Y patterns. Enable ruff UP007/UP045 for Python 3.10 union syntax Remove UP007 (Union[X,Y] -> X | Y) and UP045 (Optional[X] -> X | None) from the ruff ignore list and convert all type aliases across the codebase. These rules were deferred while Python 3.9 was supported; requires-python is now >=3.10. A custom script was used because neither ruff --fix nor pyupgrade --py310-plus converts Optional[X]/Union[X,Y] in type alias positions (e.g. X = Union[A, B]) — they only handle annotation positions (e.g. def f(x: Optional[int])). All 167 violations were module-level type aliases. A few edge cases were fixed manually: single-element Union[X,], typing.Union qualified refs, runtime Optional[type] calls, and Annotated[Optional[...]] pydantic fields. Fix UP007 autofix regression with string forward reference type aliases Commit fa6bd955a0 enabled ruff UP007/UP045 and auto-fixed module-level type aliases using Union with string forward references, producing invalid 'str | str' expressions. This was a known ruff bug (charliermarsh/ruff#826) that has since been fixed in later ruff versions, but this codebase was converted before the fix was in place. Revert to Union syntax and restore TYPE_CHECKING imports that ruff's TCH rule cleaned up as a side effect when it thought the forward references were unused.
102 lines
3.2 KiB
Python
102 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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)
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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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