Implement dump and raise error for dumps

Author: rly

src/linkml_arrays/dumpers/hdf5_dumper.py

@@ -39,14 +39,16 @@ def _iterate_element(
 class Hdf5Dumper(Dumper):
     """Dumper class for LinkML models to HDF5 files."""
 
-    # TODO is this the right method to overwrite? it does not dump a string
-    def dumps(
+    def dump(
         self,
         element: Union[YAMLRoot, BaseModel],
+        to_file: str,
         schemaview: SchemaView,
-        output_file_path: Union[str, Path],
         **kwargs,
     ):
         """Dump the element to an HDF5 file."""
-        with h5py.File(output_file_path, "w") as f:
+        with h5py.File(to_file, "w") as f:
             _iterate_element(element, schemaview, f)
+
+    def dumps(self, element: Union[YAMLRoot, BaseModel], **kwargs):
+        raise NotImplementedError("This method is not sensible for this dumper.")

src/linkml_arrays/dumpers/xarray_dumpers.py

@@ -97,32 +97,36 @@ def _iterate_element(
 class XarrayNetCDFDumper(Dumper):
     """Dumper class for LinkML models to HDF5 files."""
 
-    # TODO is this the right method to overwrite? it does not dump a string
-    def dumps(
+    def dump(
         self,
         element: Union[YAMLRoot, BaseModel],
+        to_file: str,
         schemaview: SchemaView,
-        output_file_path: Union[str, Path],
         **kwargs,
     ):
         """Dump the element to an HDF5 file."""
         datatree = DataTree()
         datatree = _iterate_element(element, schemaview, datatree)
-        datatree.to_netcdf(output_file_path, engine='h5netcdf')
+        datatree.to_netcdf(to_file, engine='h5netcdf')
+
+    def dumps(self, element: Union[YAMLRoot, BaseModel], **kwargs):
+        raise NotImplementedError("This method is not sensible for this dumper.")
 
 
 class XarrayZarrDumper(Dumper):
     """Dumper class for LinkML models to HDF5 files."""
 
-    # TODO is this the right method to overwrite? it does not dump a string
-    def dumps(
+    def dump(
         self,
         element: Union[YAMLRoot, BaseModel],
+        to_file: str,
         schemaview: SchemaView,
-        output_file_path: Union[str, Path],
         **kwargs,
     ):
         """Dump the element to an HDF5 file."""
         datatree = DataTree()
         datatree = _iterate_element(element, schemaview, datatree)
-        datatree.to_zarr(output_file_path)
+        datatree.to_zarr(to_file)
+
+    def dumps(self, element: Union[YAMLRoot, BaseModel], **kwargs):
+        raise NotImplementedError("This method is not sensible for this dumper.")

src/linkml_arrays/dumpers/zarr_directory_store_dumper.py

@@ -39,15 +39,17 @@ def _iterate_element(
 class ZarrDirectoryStoreDumper(Dumper):
     """Dumper class for LinkML models to Zarr directory stores."""
 
-    # TODO is this the right method to overwrite? it does not dump a string
-    def dumps(
+    def dump(
         self,
         element: Union[YAMLRoot, BaseModel],
+        to_file: str,
         schemaview: SchemaView,
-        output_file_path: Union[str, Path],
         **kwargs,
     ):
         """Dump the element to a Zarr directory store."""
-        store = zarr.DirectoryStore(output_file_path)
+        store = zarr.DirectoryStore(to_file)
         root = zarr.group(store=store, overwrite=True)
         _iterate_element(element, schemaview, root)
+
+    def dumps(self, element: Union[YAMLRoot, BaseModel], **kwargs):
+        raise NotImplementedError("This method is not sensible for this dumper.")

tests/test_dumpers/test_dumpers.py

@@ -155,7 +155,7 @@ def test_xarray_zarr_dumper(tmp_path):
     container = _create_container()
     schemaview = SchemaView(GROUND_TRUTH_DIR / "temperature_schema.yaml")
     output_file_path = tmp_path / "my_container_xarray.zarr"
-    XarrayZarrDumper().dumps(container, schemaview=schemaview, output_file_path=output_file_path)
+    XarrayZarrDumper().dump(container, to_file=output_file_path, schemaview=schemaview)
 
     assert os.path.exists(output_file_path)
     root = zarr.group(store=output_file_path)
@@ -188,7 +188,7 @@ def test_xarray_netcdf_dumper(tmp_path):
     container = _create_container()
     schemaview = SchemaView(GROUND_TRUTH_DIR / "temperature_schema.yaml")
     output_file_path = tmp_path / "my_container.nc"
-    XarrayNetCDFDumper().dumps(container, schemaview=schemaview, output_file_path=output_file_path)
+    XarrayNetCDFDumper().dump(container, to_file=output_file_path, schemaview=schemaview)
 
     assert os.path.exists(output_file_path)
     datatree = open_datatree(output_file_path, engine='h5netcdf')
@@ -219,7 +219,7 @@ def test_hdf5_dumper(tmp_path):
 
     schemaview = SchemaView(GROUND_TRUTH_DIR / "temperature_schema.yaml")
     output_file_path = tmp_path / "my_container.h5"
-    Hdf5Dumper().dumps(container, schemaview=schemaview, output_file_path=output_file_path)
+    Hdf5Dumper().dump(container, to_file=output_file_path, schemaview=schemaview)
 
     assert os.path.exists(output_file_path)
     with h5py.File(output_file_path, "r") as f:
@@ -249,9 +249,7 @@ def test_zarr_directory_store_dumper(tmp_path):
 
     schemaview = SchemaView(GROUND_TRUTH_DIR / "temperature_schema.yaml")
     output_file_path = tmp_path / "my_container.zarr"
-    ZarrDirectoryStoreDumper().dumps(
-        container, schemaview=schemaview, output_file_path=output_file_path
-    )
+    ZarrDirectoryStoreDumper().dump(container, to_file=output_file_path, schemaview=schemaview)
 
     assert os.path.exists(output_file_path)