Merge pull request #39 from TranslatorSRI/pathfinder_models

Pathfinder Testing Models

Author: uhbrar

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "translator_testing_model"
-version = "0.0.0"
+version = "0.4.0"
 description = "This is the project description."
 authors = ["Sierra Moxon <sierra.taylor@gmail.com>", "Richard Bruskiewich <richard.bruskiewich@delphinai.com>"]
 license = "MIT"

src/translator_testing_model/datamodel/pydanticmodel.py

@@ -267,6 +267,12 @@ class TestMetadata(TestEntity):
     tags: Optional[List[str]] = Field(default_factory=list, description="""A human-readable tags for categorical memberships of a TestEntity (preferably a URI or CURIE). Typically used to aggregate instances of TestEntity into formally typed or ad hoc lists.""")
     test_runner_settings: Optional[List[str]] = Field(default_factory=list, description="""Scalar parameters for the TestRunner processing a given TestEntity.""")
 
+class PathfinderPathNode(ConfiguredBaseModel):
+    """
+    Represents an output path node
+    """
+    ids: Optional[List[str]] = Field(None)
+    name: Optional[str] = Field(None)
 
 class TestAsset(TestEntity):
     """
@@ -295,6 +301,34 @@ class TestAsset(TestEntity):
     tags: Optional[List[str]] = Field(default_factory=list, description="""One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection""")
     test_runner_settings: Optional[List[str]] = Field(default_factory=list, description="""Scalar settings for the TestRunner, e.g. \"inferred\"""")
 
+class PathfinderTestAsset(TestEntity):
+    """
+    Represents a Test Asset, which is a single specific instance of TestCase-agnostic semantic parameters representing the specification of a Translator test target with inputs and (expected) outputs.
+    """
+    source_input_id: Optional[str] = Field(None)
+    source_input_name: Optional[str] = Field(None)
+    source_input_category: Optional[str] = Field(None)
+    target_input_id: Optional[str] = Field(None)
+    target_input_name: Optional[str] = Field(None)
+    target_input_category: Optional[str] = Field(None)
+    predicate_id: Optional[str] = Field(None)
+    predicate_name: Optional[str] = Field(None)
+    path_nodes: Optional[List[PathfinderPathNode]] = Field(None)
+    association: Optional[str] = Field(None, description="""Specific Biolink Model association 'category' which applies to the test asset defined knowledge statement""")
+    qualifiers: Optional[List[Qualifier]] = Field(default_factory=list, description="""Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot.""")
+    expected_output: Optional[str] = Field(None)
+    test_issue: Optional[TestIssueEnum] = Field(None)
+    semantic_severity: Optional[SemanticSeverityEnum] = Field(None)
+    in_v1: Optional[bool] = Field(None)
+    well_known: Optional[bool] = Field(None)
+    test_reference: Optional[str] = Field(None, description="""Document URL where original test source particulars are registered (e.g. Github repo)""")
+    test_metadata: Optional[TestMetadata] = Field(None, description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""")
+    id: str = Field(..., description="""A unique identifier for a Test Entity""")
+    name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""")
+    description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""")
+    tags: Optional[List[str]] = Field(default_factory=list, description="""One or more 'tags' slot values (inherited from TestEntity) should generally be defined to specify TestAsset membership in a \"Block List\" collection""")
+    test_runner_settings: Optional[List[str]] = Field(default_factory=list, description="""Scalar settings for the TestRunner, e.g. \"inferred\"""")
+
 
 class AcceptanceTestAsset(TestAsset):
     """
@@ -397,6 +431,24 @@ class TestCase(TestEntity):
     tags: Optional[List[str]] = Field(default_factory=list, description="""One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection.""")
     test_runner_settings: Optional[List[str]] = Field(default_factory=list, description="""Scalar parameters for the TestRunner processing a given TestEntity.""")
 
+class PathfinderTestCase(TestEntity):
+    """
+    Represents a single enumerated instance of Test Case, derived from a  given collection of one or more TestAsset instances (the value of the 'test_assets' slot) which define the 'inputs' and 'outputs' of the TestCase, used to probe a particular test condition.
+    """
+    query_type: Optional[QueryTypeEnum] = Field(None, description="""Type of TestCase query.""")
+    test_assets: List[PathfinderTestAsset] = Field(default_factory=list, description="""One or more 'tags' slot values (inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in 'test_assets' slot (\"Block List\") collection.""")
+    preconditions: Optional[List[str]] = Field(default_factory=list)
+    trapi_template: Optional[TrapiTemplateEnum] = Field(None, description="""A template for a query, which can be used to generate a query for a test case.  note: the current enumerated values for this slot come from the Benchmarks repo config/benchmarks.json \"templates\" collection and refer to the \"name\" field of each template.  Templates themselves are currently stored in the config/[source_name]/templates directory.""")
+    test_case_objective: Optional[TestObjectiveEnum] = Field(None, description="""Testing objective behind specified set of test particulars (e.g. acceptance pass/fail; benchmark; quantitative; standards compliance; graph navigation integrity)""")
+    test_case_source: Optional[TestSourceEnum] = Field(None, description="""Provenance of a specific set of test assets, cases and/or suites.  Or, the person who cares about this,  know about this.  We would like this to be an ORCID eventually, but currently it is just a string.""")
+    qualifiers: Optional[List[Qualifier]] = Field(default_factory=list, description="""Optional qualifiers which constrain to the test asset defined knowledge statement. Note that this field records such qualifier slots and values as tag=value pairs, where the tag is the Biolink Model qualifier slot named and the value is an acceptable (Biolink Model enum?) value of the said qualifier slot.""")
+    components: Optional[List[ComponentEnum]] = Field(default_factory=list, description="""The component that this test case is intended to run against.  Most often this is the ARS for  acceptance tests, but for the Benchmarks repo integration, this can also be individual components of the system like Aragorn, or ARAX.""")
+    test_env: Optional[TestEnvEnum] = Field(None, description="""Deployment environment within which the associated TestSuite is run.""")
+    id: str = Field(..., description="""A unique identifier for a Test Entity""")
+    name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""")
+    description: Optional[str] = Field(None, description="""A human-readable description for a Test Entity""")
+    tags: Optional[List[str]] = Field(default_factory=list, description="""One or more 'tags' slot values (slot inherited from TestEntity) should generally be defined as filters to specify TestAsset membership in a \"Block List\" collection.""")
+    test_runner_settings: Optional[List[str]] = Field(default_factory=list, description="""Scalar parameters for the TestRunner processing a given TestEntity.""")
 
 class AcceptanceTestCase(TestCase):
     """
@@ -467,7 +519,7 @@ class TestSuite(TestEntity):
     """
     test_metadata: Optional[TestMetadata] = Field(None, description="""Test metadata describes the external provenance, cross-references and objectives for a given test.""")
     test_persona: Optional[TestPersonaEnum] = Field(None, description="""A Test persona describes the user or operational context of a given test.""")
-    test_cases: Optional[Dict[str, TestCase]] = Field(default_factory=dict, description="""List of explicitly enumerated Test Cases.""")
+    test_cases: Optional[Dict[str, Union[TestCase, PathfinderTestCase]]] = Field(default_factory=dict, description="""List of explicitly enumerated Test Cases.""")
     test_suite_specification: Optional[TestSuiteSpecification] = Field(None, description="""Declarative specification of a Test Suite of Test Cases whose generation is deferred, (i.e. within a Test Runner) or whose creation is achieved by stream processing of an external data source.""")
     id: str = Field(..., description="""A unique identifier for a Test Entity""")
     name: Optional[str] = Field(None, description="""A human-readable name for a Test Entity""")