Merge read_directly into read_h5ad (#25)

* Merge read_directly into read_h5ad

* update read unit test

* File property

---------

Co-authored-by: Roman Mukhin <[email protected]>

cap_anndata/cap_anndata.py

@@ -28,6 +28,10 @@ def __init__(self, file: h5py.File, path_to_content: str = "/") -> None:
         self._path_to_content = path_to_content
         self._X: X_NOTATION = None
 
+    @property
+    def file(self) -> h5py.File:
+        return self._file
+
     @property
     def X(self) -> X_NOTATION:
         if self._X is None:
@@ -394,3 +398,11 @@ def __repr__(self) -> str:
 
     def __str__(self) -> str:
         return self.create_repr()
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, *args):
+        if self._file is not None:
+            self._file.close()
+        logger.debug("CapAnnData closed!")

cap_anndata/reader.py

@@ -1,14 +1,13 @@
 import logging
-import contextlib
 import h5py
+import warnings
 
 from cap_anndata import CapAnnData
 
 
 logger = logging.getLogger(__name__)
 
 
-@contextlib.contextmanager
 def read_h5ad(file_path: str, edit: bool = False):
     """
     This is the main read method for CapAnnData.
@@ -21,24 +20,30 @@ def read_h5ad(file_path: str, edit: bool = False):
         file = h5py.File(file_path, mode)
         cap_adata = CapAnnData(file)
         logger.debug(f"Successfully read anndata file path {file_path}")
-        yield cap_adata
+        return cap_adata
 
     except Exception as error:
         logger.error(f"Error during read anndata file at path: {file_path}, error = {error}!")
         raise error
 
-    finally:
-        file.close()
-        logger.debug("AnnData closed!")
 
+def deprecated(message):
+  def deprecated_decorator(func):
+      def deprecated_func(*args, **kwargs):
+          warnings.warn("{} is a deprecated function. {}".format(func.__name__, message),
+                        category=DeprecationWarning,
+                        stacklevel=2)
+          warnings.simplefilter('default', DeprecationWarning)
+          return func(*args, **kwargs)
+      return deprecated_func
+  return deprecated_decorator
 
+
+# TODO: remove deprecated function
+@deprecated("It will be removed in the next version of package. Please replace it with `read_h5ad`.")
 def read_directly(file_path: str, edit: bool = False) -> CapAnnData:
     """
     Must be used only in specific cases.
     User is responsible to close the h5py file when the work with CapAnnData instance done.
     """
-    mode = "r+" if edit else "r"
-    logger.debug(f"Read file {file_path} mode={mode} directly...")
-    file = h5py.File(file_path, mode)
-    cap_adata = CapAnnData(file)
-    return cap_adata
+    return read_h5ad(file_path, edit)

test/test_reader.py

@@ -3,20 +3,57 @@
 
 from cap_anndata.reader import read_h5ad, read_directly
 from test.context import get_base_anndata
+import pytest
 
 
-def test_read_anndata_file():
+def prepare_h5ad_file(name):
     adata = get_base_anndata()
     temp_folder = tempfile.mkdtemp()
-    file_path = os.path.join(temp_folder, "test_read_anndata_file.h5ad")
+    file_path = os.path.join(temp_folder, name)
     adata.write_h5ad(file_path)
-    del adata
+    return file_path
 
-    with read_h5ad(file_path=file_path) as cap_adata:
+
+@pytest.mark.parametrize("edit", [True, False])
+def test_read_in_context(edit):
+    file_path = prepare_h5ad_file("test_read_in_context.h5ad")
+
+    with read_h5ad(file_path=file_path, edit=edit) as cap_adata:
         assert cap_adata is not None, "CapAnnData file must be valid!"
+        cap_adata.read_obs()
+        cap_adata.read_uns()
+        if edit:
+            cap_adata.overwrite()
+
+    os.remove(file_path)
+
+
+@pytest.mark.parametrize("edit", [True, False])
+def test_read_as_function(edit):
+    file_path = prepare_h5ad_file("test_read_as_function.h5ad")
+
+    cap_adata = read_h5ad(file_path=file_path, edit=edit)
+    assert cap_adata is not None, "CapAnnData file must be valid!"
+    cap_adata.read_obs()
+    cap_adata.read_uns()
+    if edit:
+        cap_adata.overwrite()
+
+    cap_adata.file.close()
+    os.remove(file_path)
+
+
+@pytest.mark.parametrize("edit", [True, False])
+def test_read_directly(edit):
+    # TODO: remove deprecated function and unit test
+    file_path = prepare_h5ad_file("test_read_directly.h5ad")
 
-    cap_adata = read_directly(file_path=file_path)
+    cap_adata = read_directly(file_path=file_path, edit=edit)
     assert cap_adata is not None, "CapAnnData file must be valid!"
-    cap_adata._file.close()
+    cap_adata.read_obs()
+    cap_adata.read_uns()
+    if edit:
+        cap_adata.overwrite()
 
+    cap_adata.file.close()
     os.remove(file_path)