fixup! Push down HCA specifics to a Bundle subclass (#4940)

scripts/can_bundle.py

@@ -38,7 +38,7 @@
 from azul.plugins import (
     RepositoryPlugin,
 )
-from azul.plugins.anvil import (
+from azul.plugins.metadata.anvil.bundle import (
     AnvilBundle,
 )
 from azul.types import (

src/azul/indexer/__init__.py

@@ -431,11 +431,12 @@ def _reject_joiner(self, value: AnyJSON):
                 msg = f'{config.manifest_column_joiner!r} is disallowed in metadata'
                 raise RequirementError(msg, self.fqid)
 
+    @abstractmethod
     def reject_joiner(self):
         """
         Raise a requirement error if the given string is found in the bundle
         """
-        self._reject_joiner(self.to_json())
+        raise NotImplementedError
 
     @classmethod
     @abstractmethod

src/azul/plugins/metadata/anvil/__init__.py

@@ -12,7 +12,7 @@
     MetadataPlugin,
     Sorting,
 )
-from azul.plugins.anvil import (
+from azul.plugins.metadata.anvil.bundle import (
     AnvilBundle,
 )
 from azul.plugins.metadata.anvil.indexer.transform import (
@@ -67,7 +67,11 @@ def transformer_types(self) -> Iterable[Type[BaseTransformer]]:
             FileTransformer,
         )
 
-    def transformers(self, bundle: AnvilBundle, *, delete: bool) -> Iterable[BaseTransformer]:
+    def transformers(self,
+                     bundle: AnvilBundle,
+                     *,
+                     delete: bool
+                     ) -> Iterable[BaseTransformer]:
         return [
             transformer_cls(bundle=bundle, deleted=delete)
             for transformer_cls in self.transformer_types()

src/azul/plugins/anvil.py → src/azul/plugins/metadata/anvil/bundle.py

@@ -83,6 +83,9 @@ class AnvilBundle(Bundle[BUNDLE_FQID], ABC):
     entities: dict[EntityReference, MutableJSON] = attr.ib(factory=dict)
     links: set[Link[EntityReference]] = attr.ib(factory=set)
 
+    def reject_joiner(self):
+        pass
+
     def to_json(self) -> MutableJSON:
         return {
             'entities': {

src/azul/plugins/metadata/anvil/indexer/transform.py

@@ -53,7 +53,7 @@
 from azul.indexer.transform import (
     Transformer,
 )
-from azul.plugins.anvil import (
+from azul.plugins.metadata.anvil.bundle import (
     AnvilBundle,
     Link,
 )

src/azul/plugins/metadata/hca/__init__.py

@@ -17,7 +17,7 @@
     MetadataPlugin,
     Sorting,
 )
-from azul.plugins.hca import (
+from azul.plugins.metadata.hca.bundle import (
     HCABundle,
 )
 from azul.plugins.metadata.hca.indexer.aggregate import (
@@ -64,7 +64,11 @@ def transformer_types(self) -> Iterable[Type[BaseTransformer]]:
             BundleTransformer
         )
 
-    def transformers(self, bundle: HCABundle, *, delete: bool) -> Iterable[BaseTransformer]:
+    def transformers(self,
+                     bundle: HCABundle,
+                     *,
+                     delete: bool
+                     ) -> Iterable[BaseTransformer]:
         api_bundle = api.Bundle(uuid=bundle.uuid,
                                 version=bundle.version,
                                 manifest=bundle.manifest,

src/azul/plugins/hca.py → src/azul/plugins/metadata/hca/bundle.py

@@ -38,6 +38,10 @@ class HCABundle(Bundle[BUNDLE_FQID], ABC):
     """
     metadata_files: MutableJSON
 
+    def reject_joiner(self):
+        self._reject_joiner(self.manifest)
+        self._reject_joiner(self.metadata_files)
+
     def to_json(self) -> MutableJSON:
         return {
             'manifest': self.manifest,

src/azul/plugins/metadata/hca/indexer/transform.py

@@ -86,7 +86,7 @@
 from azul.openapi import (
     schema,
 )
-from azul.plugins.hca import (
+from azul.plugins.metadata.hca.bundle import (
     HCABundle,
 )
 from azul.plugins.metadata.hca.indexer.aggregate import (

src/azul/plugins/repository/canned/__init__.py

@@ -47,7 +47,7 @@
     RepositoryFileDownload,
     RepositoryPlugin,
 )
-from azul.plugins.hca import (
+from azul.plugins.metadata.hca.bundle import (
     HCABundle,
 )
 from azul.time import (
@@ -81,7 +81,7 @@ class CannedBundle(HCABundle[CannedBundleFQID]):
 
     @classmethod
     def canning_qualifier(cls) -> str:
-        return 'gh'
+        return 'gh.hca'
 
     def drs_path(self, manifest_entry: JSON) -> Optional[str]:
         return 'dss'

src/azul/plugins/repository/dss/__init__.py

@@ -47,7 +47,7 @@
     RepositoryFileDownload,
     RepositoryPlugin,
 )
-from azul.plugins.hca import (
+from azul.plugins.metadata.hca.bundle import (
     HCABundle,
 )
 from azul.time import (
@@ -86,7 +86,7 @@ class DSSBundle(HCABundle[DSSBundleFQID]):
 
     @classmethod
     def canning_qualifier(cls) -> str:
-        return 'dss'
+        return 'dss.hca'
 
     def drs_path(self, manifest_entry: JSON) -> str:
         file_uuid = manifest_entry['uuid']

src/azul/plugins/repository/tdr_anvil/__init__.py

@@ -37,7 +37,7 @@
     EntityReference,
     EntityType,
 )
-from azul.plugins.anvil import (
+from azul.plugins.metadata.anvil.bundle import (
     AnvilBundle,
     Key,
     KeyReference,
@@ -115,6 +115,10 @@ class TDRAnvilBundle(AnvilBundle[AnvilBundleFQID], TDRBundle):
     def extension(cls) -> str:
         return 'tdr.anvil'
 
+    @classmethod
+    def canning_qualifier(cls) -> str:
+        return super().canning_qualifier() + '.anvil'
+
     def add_entity(self,
                    entity: EntityReference,
                    version: str,

src/azul/plugins/repository/tdr_hca/__init__.py

@@ -50,7 +50,7 @@
     EntityReference,
     EntityType,
 )
-from azul.plugins.hca import (
+from azul.plugins.metadata.hca.bundle import (
     HCABundle,
 )
 from azul.plugins.repository.tdr import (
@@ -177,6 +177,10 @@ def extract_field(field: attr.Attribute) -> tuple[str, Any]:
 
 class TDRHCABundle(HCABundle[TDRBundleFQID], TDRBundle):
 
+    @classmethod
+    def canning_qualifier(cls) -> str:
+        return super().canning_qualifier() + '.hca'
+
     def add_entity(self,
                    *,
                    entity_key: str,

test/integration_test.py

@@ -130,7 +130,7 @@
     MetadataPlugin,
     RepositoryPlugin,
 )
-from azul.plugins.anvil import (
+from azul.plugins.metadata.anvil.bundle import (
     Link,
 )
 from azul.plugins.repository.tdr import (