Parameterize plugins with bundle class

DataBiosphere · Apr 15, 2023 · debe0a8 · debe0a8
1 parent b6e9b0e
commit debe0a8
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Showing 8 changed files with 16 additions and 12 deletions.
diff --git a/src/azul/plugins/__init__.py b/src/azul/plugins/__init__.py
@@ -136,8 +136,10 @@ class ManifestFormat(Enum):
 
 T = TypeVar('T', bound='Plugin')
 
+BUNDLE = TypeVar('BUNDLE', bound=Bundle)
 
-class Plugin(ABC):
+
+class Plugin(ABC, Generic[BUNDLE]):
     """
     A base class for Azul plugins. Concrete plugins shouldn't inherit this
     class directly but one of the subclasses of this class. This class just
@@ -207,7 +209,7 @@ def _load(cls, plugin_type_name: str, plugin_package_name: str) -> Type[T]:
         return plugin_cls
 
 
-class MetadataPlugin(Plugin):
+class MetadataPlugin(Plugin[BUNDLE]):
 
     @classmethod
     def type_name(cls) -> str:
@@ -226,7 +228,7 @@ def transformer_types(self) -> Iterable[Type[Transformer]]:
 
     @abstractmethod
     def transformers(self,
-                     bundle: Bundle,
+                     bundle: BUNDLE,
                      *,
                      delete: bool
                      ) -> Iterable[Transformer]:
@@ -418,7 +420,7 @@ def filter_stage(self) -> 'Type[FilterStage]':
         raise NotImplementedError
 
 
-class RepositoryPlugin(Generic[SOURCE_SPEC, SOURCE_REF, BUNDLE_FQID], Plugin):
+class RepositoryPlugin(Plugin[BUNDLE], Generic[BUNDLE, SOURCE_SPEC, SOURCE_REF, BUNDLE_FQID]):
 
     @classmethod
     def type_name(cls) -> str:

diff --git a/src/azul/plugins/metadata/anvil/__init__.py b/src/azul/plugins/metadata/anvil/__init__.py
@@ -45,7 +45,7 @@
 )
 
 
-class Plugin(MetadataPlugin, AnvilPlugin):
+class Plugin(MetadataPlugin[Bundle], AnvilPlugin):
 
     @property
     def exposed_indices(self) -> Mapping[str, Sorting]:

diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py
@@ -56,7 +56,7 @@
 )
 
 
-class Plugin(MetadataPlugin, HCAPlugin):
+class Plugin(MetadataPlugin[Bundle], HCAPlugin):
 
     def transformer_types(self) -> Iterable[Type[BaseTransformer]]:
         return (

diff --git a/src/azul/plugins/repository/canned/__init__.py b/src/azul/plugins/repository/canned/__init__.py
@@ -85,7 +85,7 @@ def drs_path(self, manifest_entry: JSON) -> Optional[str]:
 
 
 @dataclass(frozen=True)
-class Plugin(HCAPlugin, RepositoryPlugin[SimpleSourceSpec, CannedSourceRef, CannedBundleFQID]):
+class Plugin(HCAPlugin, RepositoryPlugin[CannedBundle, SimpleSourceSpec, CannedSourceRef, CannedBundleFQID]):
     _sources: Set[SimpleSourceSpec]
 
     @classmethod

diff --git a/src/azul/plugins/repository/dss/__init__.py b/src/azul/plugins/repository/dss/__init__.py
@@ -91,7 +91,7 @@ def drs_path(self, manifest_entry: JSON) -> str:
         return str(furl(path=(file_uuid,), args={'version': file_version}))
 
 
-class Plugin(HCAPlugin, RepositoryPlugin[SimpleSourceSpec, DSSSourceRef, DSSBundleFQID]):
+class Plugin(HCAPlugin, RepositoryPlugin[DSSBundle, SimpleSourceSpec, DSSSourceRef, DSSBundleFQID]):
 
     @classmethod
     def create(cls, catalog: CatalogName) -> RepositoryPlugin:

diff --git a/src/azul/plugins/repository/tdr.py b/src/azul/plugins/repository/tdr.py
@@ -1,4 +1,5 @@
 from abc import (
+    ABC,
     abstractmethod,
 )
 from collections.abc import (
@@ -44,6 +45,7 @@
     SourcedBundleFQID,
 )
 from azul.plugins import (
+    BUNDLE,
     RepositoryFileDownload,
     RepositoryPlugin,
 )
@@ -70,7 +72,7 @@ class TDRBundleFQID(SourcedBundleFQID[TDRSourceRef]):
     pass
 
 
-class TDRBundle(Bundle[TDRBundleFQID]):
+class TDRBundle(Bundle[TDRBundleFQID], ABC):
 
     def drs_path(self, manifest_entry: JSON) -> Optional[str]:
         return manifest_entry.get('drs_path')
@@ -87,7 +89,7 @@ def _parse_drs_path(self, drs_uri: str) -> str:
 
 
 @attr.s(kw_only=True, auto_attribs=True, frozen=True)
-class TDRPlugin(RepositoryPlugin[SOURCE_SPEC, SOURCE_REF, BUNDLE_FQID]):
+class TDRPlugin(RepositoryPlugin[BUNDLE, SOURCE_SPEC, SOURCE_REF, BUNDLE_FQID]):
     _sources: Set[TDRSourceSpec]
 
     @classmethod

diff --git a/src/azul/plugins/repository/tdr_anvil/__init__.py b/src/azul/plugins/repository/tdr_anvil/__init__.py
@@ -199,7 +199,7 @@ def _parse_drs_uri(self, file_ref: Optional[str]) -> Optional[str]:
             return self._parse_drs_path(file_ref)
 
 
-class Plugin(AnvilPlugin, TDRPlugin[TDRSourceSpec, TDRSourceRef, AnvilBundleFQID]):
+class Plugin(AnvilPlugin, TDRPlugin[TDRAnvilBundle, TDRSourceSpec, TDRSourceRef, AnvilBundleFQID]):
 
     @cached_property
     def _version(self):

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -284,7 +284,7 @@ def _parse_drs_uri(self,
             return None
 
 
-class Plugin(HCAPlugin, TDRPlugin[TDRSourceSpec, TDRSourceRef, TDRBundleFQID]):
+class Plugin(HCAPlugin, TDRPlugin[TDRHCABundle, TDRSourceSpec, TDRSourceRef, TDRBundleFQID]):
 
     def list_partitions(self,
                         source: TDRSourceRef