Unverified Commit bb87560d authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Move definition of ``DatasetCollectionDescriptionT`` before its use 

Fix the following error on py37-test_galaxy_packages_for_pulsar tests:

```
FAILED tests/tool_util/test_input_models.py::test_input_collection_type - pydantic.errors.PydanticUserError: `ParsedTool` is not fully defined; you should define `DatasetCollectionDescriptionT`, then call `ParsedTool.model_rebuild()`.
```

Also:
- Removed unused types:
  - `IncomingNotRequiredDatasetCollectionDescriptionT`
  - `IncomingNotRequiredDatasetCollectionDescription`
  - `IncomingToolOutputBaseModel`
parent e3279f14

lib/galaxy/tool_util_models/tool_outputs.py

+29 −34
Original line number Diff line number Diff line
@@ -26,8 +26,6 @@ AnyT = TypeVar("AnyT") 
NotRequired = Annotated[Optional[AnyT], Field(None)]

IncomingNotRequiredBoolT = TypeVar("IncomingNotRequiredBoolT")

IncomingNotRequiredStringT = TypeVar("IncomingNotRequiredStringT")

IncomingNotRequiredDatasetCollectionDescriptionT = TypeVar("IncomingNotRequiredDatasetCollectionDescriptionT")

IncomingNotRequiredDatasetCollectionDescription = NotRequired[List["DatasetCollectionDescriptionT"]]



# Use IncomingNotRequired when concrete key: Optional[str] = None would be incorrect
@@ -40,7 +38,33 @@ class GenericToolOutputBaseModel(BaseModel, Generic[IncomingNotRequiredBoolT, In 
    hidden: IncomingNotRequiredBoolT





IncomingToolOutputBaseModel = GenericToolOutputBaseModel[NotRequired[bool], NotRequired[str]]

DiscoverViaT = Literal["tool_provided_metadata", "pattern"]

SortKeyT = Literal["filename", "name", "designation", "dbkey"]

SortCompT = Literal["lexical", "numeric"]





class DatasetCollectionDescription(BaseModel):

    discover_via: DiscoverViaT

    format: Optional[str]

    visible: bool

    assign_primary_output: bool

    directory: Optional[str]

    recurse: bool

    match_relative_path: bool





class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):

    discover_via: Literal["tool_provided_metadata"]





class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):

    discover_via: Literal["pattern"]

    sort_key: SortKeyT

    sort_comp: SortCompT

    pattern: str





DatasetCollectionDescriptionT = Union[FilePatternDatasetCollectionDescription, ToolProvidedMetadataDatasetCollection]





class GenericToolOutputDataset(
@@ -51,7 +75,7 @@ class GenericToolOutputDataset( 
    format: Annotated[IncomingNotRequiredStringT, Field(description="The short name for the output datatype.")]

    format_source: Optional[str] = None

    metadata_source: Optional[str] = None

    discover_datasets: Optional[List["DatasetCollectionDescriptionT"]] = None

    discover_datasets: Optional[List[DatasetCollectionDescriptionT]] = None

    from_work_dir: Optional[

        Annotated[

            str,
@@ -79,7 +103,7 @@ class ToolOutputCollectionStructure(BaseModel): 
    collection_type_source: Optional[str] = None

    collection_type_from_rules: Optional[str] = None

    structured_like: Optional[str] = None

    discover_datasets: Optional[List["DatasetCollectionDescriptionT"]] = None

    discover_datasets: Optional[List[DatasetCollectionDescriptionT]] = None





class GenericToolOutputCollection(
@@ -116,35 +140,6 @@ class ToolOutputBoolean(ToolOutputSimple): 
    type: Literal["boolean"]





DiscoverViaT = Literal["tool_provided_metadata", "pattern"]

SortKeyT = Literal["filename", "name", "designation", "dbkey"]

SortCompT = Literal["lexical", "numeric"]





class DatasetCollectionDescription(BaseModel):

    discover_via: DiscoverViaT

    format: Optional[str]

    visible: bool

    assign_primary_output: bool

    directory: Optional[str]

    recurse: bool

    match_relative_path: bool





class ToolProvidedMetadataDatasetCollection(DatasetCollectionDescription):

    discover_via: Literal["tool_provided_metadata"]





class FilePatternDatasetCollectionDescription(DatasetCollectionDescription):

    discover_via: Literal["pattern"]

    sort_key: SortKeyT

    sort_comp: SortCompT

    pattern: str





DatasetCollectionDescriptionT = Union[FilePatternDatasetCollectionDescription, ToolProvidedMetadataDatasetCollection]





IncomingToolOutputT = Union[

    IncomingToolOutputDataset,

    IncomingToolOutputCollection,