galaxy/test/unit/data/dataset_collections/test_sample_sheet_util.py

from typing import Any

import pytest

from galaxy.exceptions import RequestParameterInvalidException
from galaxy.model.dataset_collections.types.sample_sheet_util import (
    column_definitions_compatible as real_column_definitions_compatible,
    validate_column_definitions as real_validate_column_definitions,
    validate_row as real_validate_row,
)

ALL_ELEMENT_IDENTIFIERS = ["sample1", "sample2", "sample3", "sample4", "sample5"]


def validate_row(row: Any, column_definitions: Any):
    # for testing allow various incompatible data structures to be sent in to assure
    # they fail properly.
    real_validate_row(row, column_definitions, ALL_ELEMENT_IDENTIFIERS)


def validate_column_definitions(column_definitions: Any):
    # for testing allow various incompatible data structures to be sent in to assure
    # they fail properly.
    real_validate_column_definitions(column_definitions)


def column_definitions_compatible(collection_columns: Any, required_columns: Any) -> bool:
    # for testing allow various incompatible data structures to be sent in
    return real_column_definitions_compatible(collection_columns, required_columns)


def test_sample_sheet_validation_skipped_on_empty_definitions():
    validate_row([0, 1], None)  # just ensure no exception is thrown


def test_sample_sheet_validation_number_columns():
    with pytest.raises(RequestParameterInvalidException):
        validate_row([0, 1], [{"type": "int", "name": "replicate number", "default_value": 0, "optional": False}])


def test_sample_sheet_validation_int_type():
    validate_row([1], [{"type": "int", "name": "replicate number", "default_value": 0, "optional": False}])

    with pytest.raises(RequestParameterInvalidException):
        validate_row(["sample1"], [{"type": "int", "name": "replicate number", "default_value": 0, "optional": False}])


def test_sample_sheet_validation_float_type():
    validate_row([1.0], [{"type": "float", "name": "seconds", "optional": False}])

    with pytest.raises(RequestParameterInvalidException):
        validate_row(["sample1"], [{"type": "float", "name": "seconds", "default_value": 0.0, "optional": False}])


def test_sample_sheet_validation_string_type():
    validate_row(["sample1"], [{"type": "string", "name": "condition", "default_value": "none", "optional": False}])

    with pytest.raises(RequestParameterInvalidException):
        validate_row([1], [{"type": "string", "name": "condition", "default_value": "none", "optional": False}])


def test_sample_sheet_validation_boolean_type():
    validate_row([True], [{"type": "boolean", "name": "control?", "optional": False}])

    with pytest.raises(RequestParameterInvalidException):
        validate_row([1], [{"type": "boolean", "name": "control?", "optional": False}])


def test_sample_sheet_element_identifiers_type():
    validate_row(["sample1"], [{"type": "element_identifier", "name": "control_element", "optional": False}])

    with pytest.raises(RequestParameterInvalidException):
        # not an actual element identifier from the rest of the collection
        validate_row(["sample6"], [{"type": "element_identifier", "name": "control_element", "optional": False}])

    with pytest.raises(RequestParameterInvalidException):
        # invalid type
        validate_row([3], [{"type": "element_identifier", "name": "control_element", "optional": False}])


def test_sample_sheet_validation_restrictions():
    validate_row(
        ["control"],
        [
            {
                "type": "string",
                "restrictions": ["treatment", "control"],
                "name": "condition",
                "default_value": "treatment",
                "optional": False,
            }
        ],
    )

    with pytest.raises(RequestParameterInvalidException):
        validate_row(
            ["controlx"],
            [
                {
                    "type": "string",
                    "restrictions": ["treatment", "control"],
                    "name": "condition",
                    "default_value": "treatment",
                    "optional": False,
                }
            ],
        )


def test_sample_sheet_validation_length():
    column_definitions = [
        {
            "type": "string",
            "validators": [{"type": "length", "min": 6}],
            "name": "condition",
            "default_value": "default",
            "optional": False,
        }
    ]
    validate_row(["treatment"], column_definitions)

    with pytest.raises(RequestParameterInvalidException):
        validate_row(["treat"], column_definitions)


def test_sample_sheet_validation_min_max():
    column_definitions = [
        {"type": "int", "validators": [{"type": "in_range", "min": 6}], "name": "replicate number", "optional": False}
    ]
    validate_row([7], column_definitions)

    with pytest.raises(RequestParameterInvalidException):
        validate_row([5], column_definitions)


def test_column_definitions_validators_on_valid_defs():
    column_definitions = [
        {
            "type": "string",
            "restrictions": ["treatment", "control"],
            "name": "condition",
            "default_value": "treatment",
            "optional": False,
        }
    ]
    validate_column_definitions(column_definitions)


def test_column_definitions_validators_invalid_length():
    column_definitions = [
        {
            "type": "string",
            "validators": [{"type": "length", "min": 6}],
            "name": "condition",
            "default_value": "default",
            "optional": False,
        }
    ]
    validate_column_definitions(column_definitions)


def test_column_definitions_do_not_allow_unsafe_validators():
    column_definitions = [
        {
            "type": "string",
            "name": "condition",
            "validators": [
                {"type": "expression", "expression": "False"},
            ],
            "default_value": "default",
            "optional": False,
        }
    ]

    with pytest.raises(RequestParameterInvalidException):
        validate_column_definitions(column_definitions)


def test_column_definitions_do_not_allow_special_characters_in_column_name():
    column_definitions = [
        {
            "type": "string",
            "name": "condition\t",
            "default_value": "default",
            "optional": False,
        }
    ]

    with pytest.raises(RequestParameterInvalidException):
        validate_column_definitions(column_definitions)


# Tests for column_definitions_compatible function


def test_column_definitions_compatible_missing_required_column():
    """Collection without required column is incompatible."""
    required_cols = [{"name": "treatment", "type": "string", "optional": False}]
    collection_cols = [{"name": "replicate", "type": "int", "optional": False}]
    assert column_definitions_compatible(collection_cols, required_cols) is False


def test_column_definitions_compatible_collection_has_no_columns():
    """Collection with no columns can't satisfy requirements."""
    required_cols = [{"name": "treatment", "type": "string", "optional": False}]
    assert column_definitions_compatible(None, required_cols) is False
    assert column_definitions_compatible([], required_cols) is False


def test_column_definitions_compatible_exact_match():
    """Collection with exact same columns is compatible."""
    cols = [
        {"name": "treatment", "type": "string", "optional": False},
        {"name": "replicate", "type": "int", "optional": False},
    ]
    assert column_definitions_compatible(cols, cols) is True


def test_column_definitions_compatible_superset_not_allowed():
    """Collection with extra columns beyond required is incompatible.

    This maybe (probably?) should be allowed - this test is verifying current behavior not
    defining the spec per se.
    """
    required_cols = [{"name": "treatment", "type": "string", "optional": False}]
    collection_cols = [
        {"name": "treatment", "type": "string", "optional": False},
        {"name": "replicate", "type": "int", "optional": False},
        {"name": "batch", "type": "string", "optional": True},
    ]
    assert column_definitions_compatible(collection_cols, required_cols) is False


def test_column_definitions_compatible_type_mismatch():
    """Column with wrong type is incompatible."""
    required_cols = [{"name": "replicate", "type": "int", "optional": False}]
    collection_cols = [{"name": "replicate", "type": "string", "optional": False}]
    assert column_definitions_compatible(collection_cols, required_cols) is False


def test_column_definitions_compatible_multiple_columns():
    """All required columns must be present with correct types."""
    required_cols = [
        {"name": "treatment", "type": "string", "optional": False},
        {"name": "replicate", "type": "int", "optional": False},
    ]
    # Missing replicate
    collection_cols_1 = [{"name": "treatment", "type": "string", "optional": False}]
    assert column_definitions_compatible(collection_cols_1, required_cols) is False

    # Has both with correct types
    collection_cols_2 = [
        {"name": "treatment", "type": "string", "optional": False},
        {"name": "replicate", "type": "int", "optional": False},
    ]
    assert column_definitions_compatible(collection_cols_2, required_cols) is True

    # Has both but replicate has wrong type
    collection_cols_3 = [
        {"name": "treatment", "type": "string", "optional": False},
        {"name": "replicate", "type": "float", "optional": False},
    ]
    assert column_definitions_compatible(collection_cols_3, required_cols) is False


def test_column_definitions_compatible_ignores_validators():
    """Validators/restrictions are not compared - only name and type matter*.

    * Optional probably should matter but I don't think it does currently.
    """
    required_cols = [
        {
            "name": "treatment",
            "type": "string",
            "optional": False,
            "restrictions": ["control", "treated"],
            "validators": [{"type": "length", "min": 5}],
        }
    ]
    # Collection has same column but no restrictions/validators
    collection_cols = [{"name": "treatment", "type": "string", "optional": False}]
    assert column_definitions_compatible(collection_cols, required_cols) is True


def test_column_definitions_compatible_order_must_match():
    """Columns must appear in the same order."""
    required_cols = [
        {"name": "treatment", "type": "string", "optional": False},
        {"name": "replicate", "type": "int", "optional": False},
    ]
    # Same columns but different order
    collection_cols = [
        {"name": "replicate", "type": "int", "optional": False},
        {"name": "treatment", "type": "string", "optional": False},
    ]
    assert column_definitions_compatible(collection_cols, required_cols) is False