Delete items from group (#84)

* Implement delete item for group, dataset and raw

* Matching error messages in tests

* __str__ in Dataset returns __str__ from Dataset.data (memmap object)

Author: lepmik

exdir/core/dataset.py

@@ -262,6 +262,9 @@ def __iter__(self):
         for i in range(self.shape[0]):
             yield self[i]
 
+    def __str__(self):
+        return self.data.__str__()
+
     @property
     def _data(self):
         if self._data_memmap is None:

exdir/core/exdir_object.py

@@ -5,6 +5,7 @@
 from enum import Enum
 import os
 import warnings
+import shutil
 try:
     import pathlib
 except ImportError as e:
@@ -71,6 +72,16 @@ def _create_object_directory(directory, metadata):
             meta_file.write(metadata_string.decode('utf8'))
 
 
+def _remove_object_directory(directory):
+    """
+    Remove object directory and meta file if directory exist.
+    """
+    if not directory.exists():
+        raise IOError("The directory '" + str(directory) + "' does not exist")
+    assert is_inside_exdir(directory)
+    shutil.rmtree(directory)
+
+
 def _default_metadata(typename):
     return {
         EXDIR_METANAME: {

exdir/core/group.py

@@ -457,6 +457,19 @@ def __setitem__(self, name, value):
 
         self[name].value = value
 
+    def __delitem__(self, name):
+        """
+        Delete a child (an object contained in group).
+
+        Parameters
+        ----------
+        name: str
+            name of the existing child
+        """
+        if self.io_mode == self.OpenMode.READ_ONLY:
+            raise IOError("Cannot change data on file in read only 'r' mode")
+        exob._remove_object_directory(self[name].directory)
+
     def keys(self):
         """
         Returns

tests/test_group.py

@@ -27,7 +27,7 @@
 except:
     from collections import KeysView, ValuesView, ItemsView
 
-from exdir.core import Group, File
+from exdir.core import Group, File, Dataset
 from exdir import validation as fv
 from conftest import remove
 
@@ -176,37 +176,87 @@ def test_set_item_intermediate(exdir_tmpfile):
     assert np.array_equal(exdir_tmpfile["group1/group2/group3/dataset"].data, np.array([1, 2, 3]))
 
 
-# TODO uncomment when deletion is implemented
 # Feature: Objects can be unlinked via "del" operator
-# def test_delete(setup_teardown_file):
-#     """Object deletion via "del"."""
-#
-#     f = setup_teardown_file[3]
-#     grp = f.create_group("test")
-#     grp.create_group("foo")
-#
-#     assert "foo" in grp
-#     del grp["foo"]
-#     assert "foo" not in grp
-#
-# def test_nonexisting(setup_teardown_file):
-#     """Deleting non-existent object raises KeyError."""
-#     f = setup_teardown_file[3]
-#     grp = f.create_group("test")
-#
-#     with pytest.raises(KeyError):
-#         del grp["foo"]
-#
-# def test_readonly_delete_exception(setup_teardown_file):
-#     """Deleting object in readonly file raises KeyError."""
-#     f = setup_teardown_file[3]
-#     f.close()
-#
-#     f = File(setup_teardown_folder[1], "r")
-#
-#     with pytest.raises(KeyError):
-#         del f["foo"]
+def test_delete_group(setup_teardown_file):
+    """Object deletion via "del"."""
+
+    f = setup_teardown_file[3]
+    grp = f.create_group("test")
+    grp.create_group("foo")
+
+    assert "foo" in grp
+    del grp["foo"]
+    assert "foo" not in grp
+
+
+def test_delete_group_from_file(setup_teardown_file):
+    """Object deletion via "del"."""
+
+    f = setup_teardown_file[3]
+    grp = f.create_group("test")
+
+    assert "test" in f
+    del f["test"]
+    assert "test" not in f
+
+
+def test_delete_raw(setup_teardown_file):
+    """Object deletion via "del"."""
+
+    f = setup_teardown_file[3]
+    grp = f.create_group("test")
+    grp.create_raw("foo")
 
+    assert "foo" in grp
+    del grp["foo"]
+    assert "foo" not in grp
+
+
+def test_nonexisting(setup_teardown_file):
+    """Deleting non-existent object raises KeyError."""
+    f = setup_teardown_file[3]
+    grp = f.create_group("test")
+    match = "No such object: 'foo' in path *"
+    with pytest.raises(KeyError, match=match):
+        del grp["foo"]
+
+
+def test_readonly_delete_exception(setup_teardown_file):
+    """Deleting object in readonly file raises KeyError."""
+    f = setup_teardown_file[3]
+    f.close()
+
+    f = File(setup_teardown_file[1], "r")
+    match = "Cannot change data on file in read only 'r' mode"
+    with pytest.raises(IOError, match=match):
+        del f["foo"]
+
+
+def test_delete_dataset(setup_teardown_file):
+    """Create new dataset with no conflicts."""
+    f = setup_teardown_file[3]
+    grp = f.create_group("test")
+
+    foo = grp.create_dataset('foo', (10, 3), 'f')
+    assert isinstance(grp['foo'], Dataset)
+    assert foo.shape == (10, 3)
+    bar = grp.require_dataset('bar', data=(3, 10))
+    del foo
+    assert 'foo' in grp
+    del grp['foo']
+    match = "No such object: 'foo' in path *"
+    with pytest.raises(KeyError, match=match):
+        grp['foo']
+    # the "bar" dataset is intact
+    assert isinstance(grp['bar'], Dataset)
+    assert np.all(bar[:] == (3, 10))
+    # even though the dataset is deleted on file, the memmap stays open until
+    # garbage collected
+    del grp['bar']
+    assert bar.shape == (2,)
+    assert np.all(bar[:] == (3, 10))
+    with pytest.raises(KeyError):
+        grp['bar']
 
 # Feature: Objects can be opened via indexing syntax obj[name]
 
@@ -226,6 +276,7 @@ def test_open(setup_teardown_file):
     with pytest.raises(NotImplementedError):
         grp["/test"]
 
+
 def test_open_deep(setup_teardown_file):
     """Simple obj[name] opening."""
     f = setup_teardown_file[3]
@@ -238,12 +289,11 @@ def test_open_deep(setup_teardown_file):
     assert grp3 == grp4
 
 
-
 def test_nonexistent(setup_teardown_file):
     """Opening missing objects raises KeyError."""
     f = setup_teardown_file[3]
-
-    with pytest.raises(KeyError):
+    match = "No such object: 'foo' in path *"
+    with pytest.raises(KeyError, match=match):
         f["foo"]
 
 
@@ -277,12 +327,13 @@ def test_contains_deep(setup_teardown_file):
 # def test_exc(setup_teardown_file):
 #     """'in' on closed group returns False."""
 #     f = setup_teardown_file[3]
-
+#
 #     f.create_group("a")
 #     f.close()
-
+#
 #     assert not "a" in f
 
+
 def test_empty(setup_teardown_file):
     """Empty strings work properly and aren"t contained."""
     f = setup_teardown_file[3]
@@ -314,9 +365,6 @@ def test_trailing_slash(setup_teardown_file):
     assert "a//" in grp
     assert "a////" in grp
 
-
-
-
 # Feature: Standard Python 3 .keys, .values, etc. methods are available
 def test_keys(setup_teardown_file):
     """.keys provides a key view."""