diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml index 544498d..ccf786d 100644 --- a/.github/workflows/codeql.yml +++ b/.github/workflows/codeql.yml @@ -35,7 +35,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 # Initializes the CodeQL tools for scanning. - name: Initialize CodeQL diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml index 721e0c6..0a4816f 100644 --- a/.github/workflows/python-ci.yml +++ b/.github/workflows/python-ci.yml @@ -20,13 +20,13 @@ jobs: if: "!contains(github.event.head_commit.message, 'skipci')" runs-on: ubuntu-latest env: - USING_COVERAGE: '3.9' + USING_COVERAGE: '3.11' strategy: matrix: - python: ['3.8', '3.9'] + python: ['3.8', '3.9', '3.10', '3.11'] steps: - name: Checkout Repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Setup Python uses: actions/setup-python@v5 @@ -60,7 +60,7 @@ jobs: contents: read steps: - name: Checkout 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b/tests/test_manifest_strands.py index ac0fd3d..3ee6f54 100644 --- a/tests/test_manifest_strands.py +++ b/tests/test_manifest_strands.py @@ -308,3 +308,8 @@ def test_error_raised_if_multiple_datasets_have_same_name(self): with self.assertRaises(KeyError): twine.validate_input_manifest(source=input_manifest) + + def test_missing_optional_manifest_does_not_raise_error(self): + """Test that not providing an optional strand doesn't result in a validation error.""" + twine = Twine(source={"output_manifest": {"datasets": {}, "optional": True}}) + twine.validate(output_manifest=None) diff --git a/tests/test_schema_strands.py b/tests/test_schema_strands.py index d60dece..44c8d40 100644 --- a/tests/test_schema_strands.py +++ b/tests/test_schema_strands.py @@ -111,6 +111,11 @@ def test_valid_with_extra_values(self): Twine(source=VALID_SCHEMA_TWINE).validate_configuration_values(source=configuration_valid_with_extra_field) + def test_missing_optional_values_do_not_raise_error(self): + """Test that not providing an optional strand doesn't result in a validation error.""" + twine = Twine(source={"configuration_values_schema": {"optional": True}}) + twine.validate(configuration_values=None) + if __name__ == "__main__": unittest.main() diff --git a/tests/test_twine.py b/tests/test_twine.py index f59cddf..ad5fbf2 100644 --- a/tests/test_twine.py +++ b/tests/test_twine.py @@ -124,3 +124,37 @@ def test_available_strands_properties(self): ) self.assertEqual(twine.available_manifest_strands, {"output_manifest"}) + + def test_required_strands_property(self): + """Test that the required strands property is correct.""" + twines = [ + { + "configuration_values_schema": {}, + "input_values_schema": {}, + "output_values_schema": {}, + "output_manifest": {"datasets": {}}, + }, + { + "configuration_values_schema": {"optional": True}, + "input_values_schema": {}, + "output_values_schema": {}, + "output_manifest": {"datasets": {}, "optional": True}, + }, + { + "configuration_values_schema": {"optional": False}, + "input_values_schema": {}, + "output_values_schema": {}, + "output_manifest": {"datasets": {}, "optional": False}, + }, + ] + + expected_required_strands = [ + {"configuration_values", "input_values", "output_values", "output_manifest"}, + {"input_values", "output_values"}, + {"configuration_values", "input_values", "output_values", "output_manifest"}, + ] + + for twine, expected in zip(twines, expected_required_strands): + with self.subTest(twine=twine): + twine = Twine(source=twine) + self.assertEqual(twine.required_strands, expected) diff --git a/twined/schema/twine_schema.json b/twined/schema/twine_schema.json index 0974502..aaab048 100644 --- a/twined/schema/twine_schema.json +++ b/twined/schema/twine_schema.json @@ -37,6 +37,10 @@ "manifest": { "type": "object", "properties": { + "optional": { + "type": "boolean", + "description": "This should be `true` if the manifest is optional." + }, "datasets": { "type": "object", "description": "A list of entries, each describing a dataset that should be attached to / made available to the digital twin", @@ -92,10 +96,20 @@ ] } }, - "configuration_manifest": {"$ref": "#/$defs/manifest"}, + "configuration_manifest": { + "$ref": "#/$defs/manifest" + }, "configuration_values_schema": { "type": "object", - "required": ["properties"] + "properties": { + "properties": { + "type": "object" + }, + "optional": { + "type": "boolean", + "description": "This should be `true` if the configuration values are optional." + } + } }, "credentials": { "type": "array", @@ -118,13 +132,35 @@ "additionalProperties": false } }, - "input_manifest": {"$ref": "#/$defs/manifest"}, + "input_manifest": { + "$ref": "#/$defs/manifest" + }, "input_values_schema": { - "type": "object" + "type": "object", + "properties": { + "properties": { + "type": "object" + }, + "optional": { + "type": "boolean", + "description": "This should be `true` if the input values are optional." + } + } + }, + "output_manifest": { + "$ref": "#/$defs/manifest" }, - "output_manifest": {"$ref": "#/$defs/manifest"}, "output_values_schema": { - "type": "object" + "type": "object", + "properties": { + "properties": { + "type": "object" + }, + "optional": { + "type": "boolean", + "description": "This should be `true` if the output values are optional." + } + } } } } diff --git a/twined/twine.py b/twined/twine.py index 0b44188..ce8725e 100644 --- a/twined/twine.py +++ b/twined/twine.py @@ -55,10 +55,16 @@ class Twine: """ def __init__(self, **kwargs): + self._available_strands = set() + self._required_strands = set() + for name, strand in self._load_twine(**kwargs).items(): setattr(self, name, strand) + self._available_strands.add(trim_suffix(name, "_schema")) + + if isinstance(strand, dict) and not strand.get("optional", False): + self._required_strands.add(trim_suffix(name, "_schema")) - self._available_strands = set(trim_suffix(name, "_schema") for name in vars(self)) self._available_manifest_strands = self._available_strands & set(MANIFEST_STRANDS) def _load_twine(self, source=None): @@ -216,7 +222,7 @@ def _validate_all_expected_datasets_are_present_in_manifest(self, manifest_kind, def available_strands(self): """Get the names of strands that are found in this twine. - :return set: + :return set(str): """ return self._available_strands @@ -224,10 +230,18 @@ def available_strands(self): def available_manifest_strands(self): """Get the names of the manifest strands that are found in this twine. - :return set: + :return set(str): """ return self._available_manifest_strands + @property + def required_strands(self): + """Get the names of strands that are required in this twine. + + :return set(str): + """ + return self._required_strands + def validate_children(self, source, **kwargs): """Validate that the children values, passed as either a file or a json string, are correct.""" # TODO cache this loaded data keyed on a hashed version of kwargs @@ -339,7 +353,7 @@ def _get_cls(name, cls): """Getter that will return cls[name] if cls is a dict or cls otherwise""" return cls.get(name, None) if isinstance(cls, dict) else cls - def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs): + def validate(self, allow_extra=False, cls=None, **kwargs): """Validate strands from sources provided as keyword arguments Usage: @@ -350,12 +364,10 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs): credentials=credentials, children=children, cls=CLASS_MAP, - allow_missing=False, allow_extra=False, ) ``` - :param bool allow_missing: If strand is present in the twine, but the source is equal to None, allow validation to continue. :param bool allow_extra: If strand is present in the sources, but not in the twine, allow validation to continue (only strands in the twine will be validated and converted, others will be returned as-is) :param any cls: optional dict of classes keyed on strand name (alternatively, one single class which will be applied to strands) which will be instantiated with the validated source data. :return dict: dict of validated and initialised sources @@ -363,6 +375,7 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs): # pop any strand name:data pairs out of kwargs and into their own dict source_kwargs = tuple(name for name in kwargs.keys() if name in ALL_STRANDS) sources = dict((name, kwargs.pop(name)) for name in source_kwargs) + for strand_name, strand_data in sources.items(): if not allow_extra: if (strand_data is not None) and (strand_name not in self.available_strands): @@ -370,11 +383,10 @@ def validate(self, allow_missing=False, allow_extra=False, cls=None, **kwargs): f"Source data is provided for '{strand_name}' but no such strand is defined in the twine" ) - if not allow_missing: - if (strand_name in self.available_strands) and (strand_data is None): - raise exceptions.TwineValueException( - f"The '{strand_name}' strand is defined in the twine, but no data is provided in sources" - ) + if (strand_name in self.required_strands) and (strand_data is None): + raise exceptions.TwineValueException( + f"The '{strand_name}' strand is defined in the twine, but no data is provided in sources" + ) if strand_data is not None: # TODO Consider reintroducing a skip based on whether cls is already instantiated. For now, leave it the