Unverified Commit 5fcc4585 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19715 from jmchilton/assertion_linter_fixes 

[24.2] Assertion linter fixes
parents bcb5d55b e6aee8b4

lib/galaxy/tool_util/verify/assertion_models.py

+1466 −12

File changed.

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lib/galaxy/tool_util/verify/codegen.py

+55 −4
Original line number Diff line number Diff line
@@ -95,7 +95,7 @@ def check_regex(v: typing.Any): 
def check_non_negative_if_set(v: typing.Any):

    if v is not None:

        try:

            assert v >= 0

            assert float(v) >= 0

        except TypeError:

            raise AssertionError(f"Invalid type found {v}")

    return v
@@ -137,6 +137,31 @@ class base_{{assertion.name}}_model(AssertionModel): 
{% endif %}





class base_{{assertion.name}}_model_relaxed(AssertionModel):

    '''base model for {{assertion.name}} describing attributes.'''

{% for parameter in assertion.parameters %}

{% if not parameter.is_deprecated %}

    {{ parameter.name }}: {{ parameter.lax_type_str }} = Field(

        {{ parameter.field_default_str }},

        description={{ assertion.name }}_{{ parameter.name }}_description,

    )

{% endif %}

{% endfor %}

{% if assertion.children in ["required", "allowed"] %}

    children: typing.Optional["assertion_list"] = None

    asserts: typing.Optional["assertion_list"] = None



{% if assertion.children == "required" %}

    @model_validator(mode='before')

    @classmethod

    def validate_children(self, data: typing.Any):

        if isinstance(data, dict) and 'children' not in data and 'asserts' not in data:

            raise ValueError("At least one of 'children' or 'asserts' must be specified for this assertion type.")

        return data

{% endif %}

{% endif %}





class {{assertion.name}}_model(base_{{assertion.name}}_model):

    r\"\"\"{{ assertion.docstring }}\"\"\"

    that: Literal["{{assertion.name}}"] = "{{assertion.name}}"
@@ -144,6 +169,10 @@ class {{assertion.name}}_model(base_{{assertion.name}}_model): 
class {{assertion.name}}_model_nested(AssertionModel):

    r\"\"\"Nested version of this assertion model.\"\"\"

    {{assertion.name}}: base_{{assertion.name}}_model



class {{assertion.name}}_model_relaxed(base_{{assertion.name}}_model_relaxed):

    r\"\"\"{{ assertion.docstring }}\"\"\"

    that: Literal["{{assertion.name}}"] = "{{assertion.name}}"

{% endfor %}



any_assertion_model_flat = Annotated[typing.Union[
@@ -158,8 +187,17 @@ any_assertion_model_nested = typing.Union[ 
{% endfor %}

]



any_assertion_model_flat_relaxed = Annotated[typing.Union[

{% for assertion in assertions %}

    {{assertion.name}}_model_relaxed,

{% endfor %}

], Field(discriminator="that")]



assertion_list = RootModel[typing.List[typing.Union[any_assertion_model_flat, any_assertion_model_nested]]]



# used to model what the XML conversion should look like - not meant to be consumed outside of

# of Galaxy internals / linting.

relaxed_assertion_list = RootModel[typing.List[any_assertion_model_flat_relaxed]]



class assertion_dict(AssertionModel):

{% for assertion in assertions %}
@@ -310,7 +348,20 @@ class AssertionParameter: 


    @property

    def type_str(self) -> str:

        raw_type_str = as_type_str(self.type)

        raw_type_str = as_type_str(self.type, strict=True)

        validators = self.validators[:]

        if self.xml_type_str == "Bytes":

            validators.append("check_bytes")

            validators.append("check_non_negative_if_int")

        if len(validators) > 0:

            validation_str = ",".join([f"BeforeValidator({v})" for v in validators])

            return f"Annotated[{raw_type_str}, {validation_str}]"



        return raw_type_str



    @property

    def lax_type_str(self) -> str:

        raw_type_str = as_type_str(self.type, strict=False)

        validators = self.validators[:]

        if self.xml_type_str == "Bytes":

            validators.append("check_bytes")
@@ -395,11 +446,11 @@ def as_xml_type(target_type) -> str: 
    return "xs:string"





def as_type_str(target_type):

def as_type_str(target_type, strict=True):

    if get_origin(target_type) is Annotated:

        args = get_args(target_type)

        if len(args) > 1:

            if args[1].json_type:

            if args[1].json_type and strict:

                return args[1].json_type



        return as_type_str(args[0])

lib/galaxy/tool_util/verify/parse.py

+21 −0
Original line number Diff line number Diff line
@@ -29,6 +29,8 @@ from galaxy.tool_util.parser.util import ( 
    boolean_true_and_false_values,

    parse_tool_version_with_defaults,

)

from galaxy.tool_util.parser.xml import __parse_assert_list_from_elem

from galaxy.tool_util.verify.assertion_models import relaxed_assertion_list

from galaxy.tool_util.verify.interactor import (

    InvalidToolTestDict,

    ToolTestDescription,
@@ -587,3 +589,22 @@ def split_if_str(value): 
    if split:

        value = value.split(",")

    return value





# convert the sort internal structure used by the tool library {tag: string, attributes: dict, children: []}

# into the YAML structure consumed by the test framework {that: string, **atributes}

def tag_structure_to_that_structure(raw_assert):

    as_json = {"that": raw_assert["tag"], **raw_assert.get("attributes", {})}

    children = raw_assert.get("children")

    if children:

        as_json["children"] = list(map(tag_structure_to_that_structure, children))

    return as_json





def assertion_xml_els_to_models(asserts_raw) -> relaxed_assertion_list:

    asserts_raw = __parse_assert_list_from_elem(asserts_raw)



    to_yaml_assertions = []

    for raw_assert in asserts_raw or []:

        to_yaml_assertions.append(tag_structure_to_that_structure(raw_assert))

    return relaxed_assertion_list.model_validate(to_yaml_assertions)

test/unit/tool_util/test_assertion_models.py

+11 −2
Original line number Diff line number Diff line 
import sys

from string import Template



import lxml.etree as ET

import pytest

from pydantic import ValidationError



from galaxy.tool_util.verify.assertion_models import assertion_list

from galaxy.tool_util.verify.codegen import galaxy_xsd_path

from galaxy.tool_util.verify.parse import assertion_xml_els_to_models

from galaxy.util.commands import shell

from galaxy.util.unittest_utils import skip_unless_executable
@@ -92,6 +94,8 @@ valid_xml_assertions = [ 
    """<has_n_columns n="30" />""",

    """<has_n_columns n="30" delta="4" />""",

    """<has_n_columns n="30" delta="4" sep=" " comment="###" />""",

    """<has_image_width min="500" />""",

    """<has_image_height min="500" />""",

]



invalid_assertions = [
@@ -207,11 +211,11 @@ if sys.version_info < (3, 8): # noqa: UP036 
    pytest.skip(reason="Pydantic assertion models require python3.8 or higher", allow_module_level=True)





def test_valid_models_validate():

def test_valid_json_models_validate():

    assertion_list.model_validate(valid_assertions)





def test_invalid_models_do_not_validate():

def test_invalid_json_models_do_not_validate():

    for invalid_assertion in invalid_assertions:

        with pytest.raises(ValidationError):

            assertion_list.model_validate([invalid_assertion])
@@ -235,3 +239,8 @@ def test_invalid_xsd(tmp_path): 
        tool_path.write_text(tool_xml)

        ret = shell(["xmllint", "--nowarning", "--noout", "--schema", galaxy_xsd_path, str(tool_path)])

        assert ret != 0, f"{assertion_xml} validated when error expected"





def test_valid_xml_models_validate_after_json_transform():

    for assertion_xml in valid_xml_assertions:

        assertion_xml_els_to_models([ET.fromstring(assertion_xml)])