Refactor Format classes so that the base has no implementation

mandible/metadata_mapper/format/format.py

@@ -30,11 +30,30 @@ def __init_subclass__(cls, register: bool = True, **kwargs):
         super().__init_subclass__(**kwargs)
 
     # Begin class definition
+    @abstractmethod
     def get_values(
         self,
         file: IO[bytes],
         keys: Iterable[str],
     ) -> Dict[str, Any]:
+        """Get a list of values from a file"""
+        pass
+
+    @abstractmethod
+    def get_value(self, file: IO[bytes], key: str) -> Any:
+        """Convenience function for getting a single value"""
+        pass
+
+
+@dataclass
+class _SimpleFormat(Format, ABC, register=False):
+    def get_values(
+        self,
+        file: IO[bytes],
+        keys: Iterable[str],
+    ) -> Dict[str, Any]:
+        """Get a list of values from a file"""
+
         with self._parse_data(file) as data:
             return {
                 key: self._eval_key_wrapper(data, key)
@@ -69,7 +88,7 @@ def _eval_key(data, key: str) -> Any:
 # Define placeholders for when extras are not installed
 
 @dataclass
-class _PlaceholderBase(Format, register=False):
+class _PlaceholderBase(_SimpleFormat, register=False):
     """
     Base class for defining placeholder implementations for classes that
     require extra dependencies to be installed
@@ -104,7 +123,7 @@ def __init__(self):
 # Define formats that don't require extra dependencies
 
 @dataclass
-class Json(Format):
+class Json(_SimpleFormat):
     @staticmethod
     @contextlib.contextmanager
     def _parse_data(file: IO[bytes]):
@@ -128,6 +147,8 @@ def __post_init__(self):
         }
 
     def get_values(self, file: IO[bytes], keys: Iterable[str]):
+        """Get a list of values from a file"""
+
         with zipfile.ZipFile(file, "r") as zf:
             file = self._get_file_from_archive(zf)
             return self.format.get_values(file, keys)
@@ -174,15 +195,3 @@ def _matches_filters(self, zipinfo: zipfile.ZipInfo) -> bool:
                 return False
 
         return True
-
-    @staticmethod
-    def _parse_data(file: IO[bytes]):
-        raise NotImplementedError(
-            f"{Zip.__name__}._parse_data should not be called!"
-        )
-
-    @staticmethod
-    def _eval_key(data: dict, key: str):
-        raise NotImplementedError(
-            f"{Zip.__name__}._eval_key should not be called!"
-        )

mandible/metadata_mapper/format/h5.py

@@ -5,11 +5,11 @@
 
 from mandible.h5_parser import normalize
 
-from .format import Format
+from .format import _SimpleFormat
 
 
 @dataclass
-class H5(Format):
+class H5(_SimpleFormat):
     @staticmethod
     def _parse_data(file: IO[bytes]) -> ContextManager[Any]:
         return h5py.File(file, "r")

mandible/metadata_mapper/format/xml.py

@@ -4,11 +4,11 @@
 
 from lxml import etree
 
-from .format import Format
+from .format import _SimpleFormat
 
 
 @dataclass
-class Xml(Format):
+class Xml(_SimpleFormat):
     @staticmethod
     @contextlib.contextmanager
     def _parse_data(file: IO[bytes]) -> Any: