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From 184b4a6711c60d90e073828ddcd3a6d328ee6a5e Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Wed, 18 Jan 2023 16:05:57 -0800
Subject: [PATCH 1/5] Fix #817 Check that __open_links exists before trying to
clsoe links
---
src/hdmf/backends/hdf5/h5tools.py | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
index ba8946c60..acf2061ad 100644
--- a/src/hdmf/backends/hdf5/h5tools.py
+++ b/src/hdmf/backends/hdf5/h5tools.py
@@ -746,10 +746,15 @@ def close_linked_files(self):
not, which prevents the linked-to file from being deleted or truncated. Use this method to close all opened,
linked-to files.
"""
- for obj in self.__open_links:
- if obj:
- obj.file.close()
- self.__open_links = []
+ # Make sure
+ try:
+ for obj in self.__open_links:
+ if obj:
+ obj.file.close()
+ except AttributeError: # In case that self.__open_links does not exist on delete
+ pass
+ finally:
+ self.__open_links = []
@docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the GroupBuilder object representing the HDF5 file'},
{'name': 'link_data', 'type': bool,
From c12ea0851f4632c59ecdd626556bee6ddc22b632 Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Wed, 18 Jan 2023 17:32:20 -0800
Subject: [PATCH 2/5] Catch possible missing HDF5IO.__file error
---
src/hdmf/backends/hdf5/h5tools.py | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
index acf2061ad..75044a64a 100644
--- a/src/hdmf/backends/hdf5/h5tools.py
+++ b/src/hdmf/backends/hdf5/h5tools.py
@@ -736,8 +736,15 @@ def close(self, close_links=True):
"""
if close_links:
self.close_linked_files()
- if self.__file is not None:
- self.__file.close()
+ try:
+ if self.__file is not None:
+ self.__file.close()
+ except AttributeError:
+ # Do not do anything in case that self._file does not exist. This
+ # may happen in case that an error occurs before HDF5IO has been fully
+ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises
+ # and error before self.__file has been created
+ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__file")
def close_linked_files(self):
"""Close all opened, linked-to files.
@@ -751,8 +758,12 @@ def close_linked_files(self):
for obj in self.__open_links:
if obj:
obj.file.close()
- except AttributeError: # In case that self.__open_links does not exist on delete
- pass
+ except AttributeError:
+ # Do not do anything in case that self.__open_links does not exist. This
+ # may happen in case that an error occurs before HDF5IO has been fully
+ # setup in __init__, e.g,. if a child class such as NWBHDF5IO raises
+ # and error before self.__open_links has been created.
+ warnings.warn("HDF5IO was not fully initialized before close. Missing self.__open_links.")
finally:
self.__open_links = []
From a43e65d13726936aa2ab49169e265a42c5a1be7f Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Wed, 18 Jan 2023 17:32:55 -0800
Subject: [PATCH 3/5] Add unit test for case where HDF5IO.close is called
before HDF5IO.__init__ is complete
---
tests/unit/test_io_hdf5_h5tools.py | 34 ++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/tests/unit/test_io_hdf5_h5tools.py b/tests/unit/test_io_hdf5_h5tools.py
index 8c03e72f8..0f2f81e31 100644
--- a/tests/unit/test_io_hdf5_h5tools.py
+++ b/tests/unit/test_io_hdf5_h5tools.py
@@ -826,6 +826,40 @@ def test_constructor(self):
self.assertEqual(io.manager, self.manager)
self.assertEqual(io.source, self.path)
+ def test_delete_with_incomplete_construction_missing_file(self):
+ """
+ Here we test what happens when close is called before HDF5IO.__init__ has
+ bee completed. In this case self.__file is missing
+ """
+ class MyHDF5IO(HDF5IO):
+ def __init__(self):
+ raise ValueError("test error")
+ with self.assertWarnsWith(warn_type=UserWarning,
+ exc_msg="HDF5IO was not fully initialized before close. Missing self.__file"):
+ try:
+ with MyHDF5IO() as _:
+ pass
+ except ValueError:
+ pass
+
+ def test_delete_with_incomplete_construction_missing_open_files(self):
+ """
+ Here we test what happens when close is called before HDF5IO.__init__ has
+ bee completed. In this case self.__open_file is missing
+ """
+
+ class MyHDF5IO(HDF5IO):
+ def __init__(self):
+ raise ValueError("test error")
+
+ with self.assertWarnsWith(warn_type=UserWarning,
+ exc_msg="HDF5IO was not fully initialized before close. Missing self.__open_links."):
+ try:
+ with MyHDF5IO() as _:
+ pass
+ except ValueError:
+ pass
+
def test_set_file_mismatch(self):
self.file_obj = File(get_temp_filepath(), 'w')
err_msg = ("You argued %s as this object's path, but supplied a file with filename: %s"
From f79b3a26bdfaee22b8d24bd3094c93be77e5595f Mon Sep 17 00:00:00 2001
From: Oliver Ruebel <oruebel@lbl.gov>
Date: Thu, 19 Jan 2023 13:54:33 -0800
Subject: [PATCH 5/5] Move init of __file and __openlink up to prevent warning
during close
---
src/hdmf/backends/hdf5/h5tools.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/hdmf/backends/hdf5/h5tools.py b/src/hdmf/backends/hdf5/h5tools.py
index 75044a64a..44b9c612c 100644
--- a/src/hdmf/backends/hdf5/h5tools.py
+++ b/src/hdmf/backends/hdf5/h5tools.py
@@ -55,6 +55,9 @@ def __init__(self, **kwargs):
path, manager, mode, comm, file_obj, driver = popargs('path', 'manager', 'mode', 'comm', 'file', 'driver',
kwargs)
+ self.__open_links = [] # keep track of other files opened from links in this file
+ self.__file = None # This will be set below, but set to None first in case an error occurs and we need to close
+
if path is None and file_obj is None:
raise ValueError("You must supply either a path or a file.")
@@ -89,7 +92,6 @@ def __init__(self, **kwargs):
self.__dci_queue = HDF5IODataChunkIteratorQueue() # a queue of DataChunkIterators that need to be exhausted
ObjectMapper.no_convert(Dataset)
self._written_builders = WriteStatusTracker() # track which builders were written (or read) by this IO object
- self.__open_links = [] # keep track of other files opened from links in this file
@property
def comm(self):
|
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