From 60115f5a05b2969662ee115f6c78638d86d52203 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 31 Jan 2022 13:09:54 +0100
Subject: [PATCH 01/13] refactor: basic HDF5Driver update

---
 .../second_quantization/hdf5d/hdf5driver.py   | 46 +++++++++++++++++--
 1 file changed, 41 insertions(+), 5 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index 53cf9ef76d..63d890f712 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -12,14 +12,20 @@
 
 """ HDF5 Driver """
 
+import logging
 import os
 import warnings
 
+import h5py
+
+from qiskit_nature.hdf5 import load_from_hdf5
 from qiskit_nature.properties.second_quantization.electronic import ElectronicStructureDriverResult
 
 from ...qmolecule import QMolecule
 from ..electronic_structure_driver import ElectronicStructureDriver
 
+LOGGER = logging.getLogger(__name__)
+
 
 class HDF5Driver(ElectronicStructureDriver):
     """
@@ -62,8 +68,38 @@ def run(self) -> ElectronicStructureDriverResult:
         if not os.path.isfile(hdf5_file):
             raise LookupError(f"HDF5 file not found: {hdf5_file}")
 
-        warnings.filterwarnings("ignore", category=DeprecationWarning)
-        molecule = QMolecule(hdf5_file)
-        warnings.filterwarnings("default", category=DeprecationWarning)
-        molecule.load()
-        return ElectronicStructureDriverResult.from_legacy_driver_result(molecule)
+        legacy_hdf5_file = False
+
+        with h5py.File(hdf5_file, "r") as file:
+            if "origin_driver" in file.keys():
+                legacy_hdf5_file = True
+                LOGGER.warning(
+                    "Your HDF5 file contains the legacy QMolecule object! You should consider "
+                    "converting it to the new property framework."
+                )
+
+        if legacy_hdf5_file:
+            warnings.filterwarnings("ignore", category=DeprecationWarning)
+            molecule = QMolecule(hdf5_file)
+            warnings.filterwarnings("default", category=DeprecationWarning)
+            molecule.load()
+            return ElectronicStructureDriverResult.from_legacy_driver_result(molecule)
+
+        driver_result: ElectronicStructureDriverResult = None
+        for prop in load_from_hdf5(hdf5_file):
+            if not isinstance(prop, ElectronicStructureDriverResult):
+                LOGGER.warning(
+                    "Ignoring the %s object encountered in your HDF5 file. The HDF5Driver must "
+                    "return an ElectronicStructureDriverResult!",
+                    type(prop),
+                )
+                continue
+            if driver_result is None:
+                driver_result = prop
+            else:
+                LOGGER.error(
+                    "The HDF5Driver can only handle a single ElectronicStructureDriverResult within"
+                    " an HDF5 file!"
+                )
+                break
+        return driver_result

From 2e108f6aea0e6586c3fc0506766852275db17467 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 31 Jan 2022 13:22:55 +0100
Subject: [PATCH 02/13] test: test both HDF5 type supports

---
 .../hdf5d/test_driver_hdf5.hdf5               | Bin 15664 -> 48475 bytes
 .../hdf5d/test_driver_hdf5.py                 |  14 +++++
 .../hdf5d/test_driver_hdf5_legacy.hdf5        | Bin 0 -> 15664 bytes
 .../hdf5d/test_driver_hdf5_save.py            |  53 ------------------
 4 files changed, 14 insertions(+), 53 deletions(-)
 create mode 100644 test/drivers/second_quantization/hdf5d/test_driver_hdf5_legacy.hdf5
 delete mode 100644 test/drivers/second_quantization/hdf5d/test_driver_hdf5_save.py

diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.hdf5 b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.hdf5
index 1f6b7af0cd8a6a56c1f6ede2b4f53a555094f86f..30005d318bda96344b57e1811fbef5d539c7ed3e 100644
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zeN*6|{ZKw6OOM&}Igxy^%>Nq|*PTK8{@^X~^U?$MeD$K%&#rc^NxQ0_K1LcuA7J@(
zzf#Iu!Gf!gGhvjUJPZ0W$C+HcT*WYM&d+!Jex8M3LNYDj#{`_dOM^UtH;l`P4DT@|
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diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
index a7cd8f8058..bdf72d07ff 100644
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
+++ b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
@@ -13,6 +13,7 @@
 """ Test Driver HDF5 """
 
 import unittest
+
 from test import QiskitNatureTestCase
 from test.drivers.second_quantization.test_driver import TestDriver
 from qiskit_nature.drivers.second_quantization import HDF5Driver
@@ -31,5 +32,18 @@ def setUp(self):
         self.driver_result = driver.run()
 
 
+class TestDriverHDF5Legacy(QiskitNatureTestCase, TestDriver):
+    """HDF5 Driver legacy file-support tests."""
+
+    def setUp(self):
+        super().setUp()
+        driver = HDF5Driver(
+            hdf5_input=self.get_resource_path(
+                "test_driver_hdf5_legacy.hdf5", "drivers/second_quantization/hdf5d"
+            )
+        )
+        self.driver_result = driver.run()
+
+
 if __name__ == "__main__":
     unittest.main()
diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5_legacy.hdf5 b/test/drivers/second_quantization/hdf5d/test_driver_hdf5_legacy.hdf5
new file mode 100644
index 0000000000000000000000000000000000000000..1f6b7af0cd8a6a56c1f6ede2b4f53a555094f86f
GIT binary patch
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literal 0
HcmV?d00001

diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5_save.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5_save.py
deleted file mode 100644
index 304222ef16..0000000000
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5_save.py
+++ /dev/null
@@ -1,53 +0,0 @@
-# This code is part of Qiskit.
-#
-# (C) Copyright IBM 2020, 2021.
-#
-# This code is licensed under the Apache License, Version 2.0. You may
-# obtain a copy of this license in the LICENSE.txt file in the root directory
-# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
-#
-# Any modifications or derivative works of this code must retain this
-# copyright notice, and modified files need to carry a notice indicating
-# that they have been altered from the originals.
-
-""" Test Driver HDF5 via saved QMolecule on new HDF5 """
-
-import unittest
-import tempfile
-import os
-
-from test import QiskitNatureTestCase
-from test.drivers.second_quantization.test_driver import TestDriver
-from qiskit_nature.drivers.second_quantization import HDF5Driver
-
-
-@unittest.skip("Until the Property framework supports HDF5 storage")
-class TestDriverHDF5Save(QiskitNatureTestCase, TestDriver):
-    """Use HDF5 Driver to test saved HDF5 from QMolecule"""
-
-    def setUp(self):
-        super().setUp()
-        driver = HDF5Driver(
-            hdf5_input=self.get_resource_path(
-                "test_driver_hdf5.hdf5", "drivers/second_quantization/hdf5d"
-            )
-        )
-        temp_qmolecule = driver.run()
-        file, self.save_file = tempfile.mkstemp(suffix=".hdf5")
-        os.close(file)
-        # pylint: disable=no-member
-        temp_qmolecule.save(self.save_file)
-        # Tests are run on self.qmolecule which is from new saved HDF5 file
-        # so save is tested based on getting expected values as per original
-        driver = HDF5Driver(hdf5_input=self.save_file)
-        self.qmolecule = driver.run()
-
-    def tearDown(self):
-        try:
-            os.remove(self.save_file)
-        except OSError:
-            pass
-
-
-if __name__ == "__main__":
-    unittest.main()

From 1dc81110fcfde7b7e119d765cc4cf3ef7e745171 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Thu, 10 Feb 2022 17:50:04 +0100
Subject: [PATCH 03/13] Fix copyright

---
 qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py | 2 +-
 test/drivers/second_quantization/hdf5d/test_driver_hdf5.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index 63d890f712..238c2f0aa1 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2018, 2021.
+# (C) Copyright IBM 2018, 2022.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory
diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
index bdf72d07ff..0875c3b047 100644
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
+++ b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
@@ -1,6 +1,6 @@
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2018, 2021.
+# (C) Copyright IBM 2018, 2022.
 #
 # This code is licensed under the Apache License, Version 2.0. You may
 # obtain a copy of this license in the LICENSE.txt file in the root directory

From f2b17357f4ecf3626f68b252d7e05532b1c15410 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Thu, 10 Feb 2022 17:54:16 +0100
Subject: [PATCH 04/13] test: update new expected HDF5 file

---
 .../hdf5d/test_driver_hdf5.hdf5               | Bin 48475 -> 48547 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.hdf5 b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.hdf5
index 30005d318bda96344b57e1811fbef5d539c7ed3e..132945b7c111480e105a38769a7895168bcebb16 100644
GIT binary patch
delta 363
zcmccpi)rz1rU@F1i#KZ43n>~gKmZ4ncFapJE-A{-g>o4jHg6O%XWb-mM3{x$nKfy0
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zV<s2)G)y*75ZJuJ>j)#nxB{O$3J_L6F3jKq?H!v93QR;HhJYOMqV)<?{ekv95b@0o
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delta 319
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zn73KMtcMlC+F%{R1W~cUI$-h#tJ#x3+bJRo%$m&Ppad6~lq|7%f<p_$n8^h`4U-KN
z1U9emI>HDsuE6Jx0)!Qi3p4mYd&g#j0uxb)As~mmXuSeef1rI2M0|6@Tx9hL3-)kB
z%u!ea6IU=R+WczW2A0WD65^XTZeGqJH-iBJ{5@QPm~=q?M8=cLc06QR(2+H7bM#J_
Tea5?aAU02S-qSRhckeU+YvY>L


From 08de4887b5172d900cc471f0449a106db70fb64d Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 14 Feb 2022 09:04:56 +0100
Subject: [PATCH 05/13] ref: align new HDF5Driver with #554

---
 .../second_quantization/hdf5d/hdf5driver.py   | 32 ++++++-------------
 1 file changed, 10 insertions(+), 22 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index 238c2f0aa1..57dee9b414 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -19,19 +19,23 @@
 import h5py
 
 from qiskit_nature.hdf5 import load_from_hdf5
+from qiskit_nature.properties.second_quantization.second_quantized_property import (
+    GroupedSecondQuantizedProperty,
+)
 from qiskit_nature.properties.second_quantization.electronic import ElectronicStructureDriverResult
 
 from ...qmolecule import QMolecule
-from ..electronic_structure_driver import ElectronicStructureDriver
+from ..base_driver import BaseDriver
 
 LOGGER = logging.getLogger(__name__)
 
 
-class HDF5Driver(ElectronicStructureDriver):
+class HDF5Driver(BaseDriver):
     """
     Qiskit Nature driver for reading an HDF5 file.
 
-    The HDF5 file is one as saved from a :class:`~qiskit_nature.drivers.QMolecule` instance.
+    The HDF5 file is one constructed with :func:`~qiskit_nature.hdf5.save_to_hdf5` or a file
+    containing a legacy :class:`~qiskit_nature.drivers.QMolecule` instance.
     """
 
     def __init__(self, hdf5_input: str = "molecule.hdf5") -> None:
@@ -53,10 +57,10 @@ def work_path(self, new_work_path):
         """Sets work path."""
         self._work_path = new_work_path
 
-    def run(self) -> ElectronicStructureDriverResult:
+    def run(self) -> GroupedSecondQuantizedProperty:
         """
         Returns:
-            ElectronicStructureDriverResult re-constructed from the HDF5 file.
+            GroupedSecondQuantizedProperty re-constructed from the HDF5 file.
 
         Raises:
             LookupError: file not found.
@@ -85,21 +89,5 @@ def run(self) -> ElectronicStructureDriverResult:
             molecule.load()
             return ElectronicStructureDriverResult.from_legacy_driver_result(molecule)
 
-        driver_result: ElectronicStructureDriverResult = None
-        for prop in load_from_hdf5(hdf5_file):
-            if not isinstance(prop, ElectronicStructureDriverResult):
-                LOGGER.warning(
-                    "Ignoring the %s object encountered in your HDF5 file. The HDF5Driver must "
-                    "return an ElectronicStructureDriverResult!",
-                    type(prop),
-                )
-                continue
-            if driver_result is None:
-                driver_result = prop
-            else:
-                LOGGER.error(
-                    "The HDF5Driver can only handle a single ElectronicStructureDriverResult within"
-                    " an HDF5 file!"
-                )
-                break
+        driver_result = load_from_hdf5(hdf5_file)
         return driver_result

From 24009289bf21d1fea37a42f3d8d1b4a1c45d3a62 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 14 Feb 2022 09:43:06 +0100
Subject: [PATCH 06/13] feat: add HDF5Driver.convert utility method

---
 .../second_quantization/hdf5d/hdf5driver.py   | 46 +++++++++++++---
 .../hdf5d/test_driver_hdf5.py                 | 53 +++++++++++++++++++
 2 files changed, 92 insertions(+), 7 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index 57dee9b414..d50c4737c8 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -18,7 +18,7 @@
 
 import h5py
 
-from qiskit_nature.hdf5 import load_from_hdf5
+from qiskit_nature.hdf5 import load_from_hdf5, save_to_hdf5
 from qiskit_nature.properties.second_quantization.second_quantized_property import (
     GroupedSecondQuantizedProperty,
 )
@@ -57,13 +57,11 @@ def work_path(self, new_work_path):
         """Sets work path."""
         self._work_path = new_work_path
 
-    def run(self) -> GroupedSecondQuantizedProperty:
-        """
-        Returns:
-            GroupedSecondQuantizedProperty re-constructed from the HDF5 file.
+    def _get_path(self) -> str:
+        """Returns the absolute path to the HDF5 file.
 
         Raises:
-            LookupError: file not found.
+            LoopupError: file not found.
         """
         hdf5_file = self._hdf5_input
         if self.work_path is not None and not os.path.isabs(hdf5_file):
@@ -72,6 +70,40 @@ def run(self) -> GroupedSecondQuantizedProperty:
         if not os.path.isfile(hdf5_file):
             raise LookupError(f"HDF5 file not found: {hdf5_file}")
 
+        return hdf5_file
+
+    def convert(self, replace: bool = True) -> None:
+        """Converts a legacy QMolecule HDF5 file into the new Property-framework.
+
+        Args:
+            replace: if True, will replace the original HDF5 file. Otherwise `.new` will be used as
+                a suffix.
+
+        Raises:
+            LookupError: file not found.
+        """
+        hdf5_file = self._get_path()
+
+        warnings.filterwarnings("ignore", category=DeprecationWarning)
+        q_mol = QMolecule(hdf5_file)
+        warnings.filterwarnings("default", category=DeprecationWarning)
+        q_mol.load()
+
+        new_hdf5_file = hdf5_file if replace else hdf5_file + ".new"
+
+        driver_result = ElectronicStructureDriverResult.from_legacy_driver_result(q_mol)
+        save_to_hdf5(driver_result, new_hdf5_file, replace=replace)
+
+    def run(self) -> GroupedSecondQuantizedProperty:
+        """
+        Returns:
+            GroupedSecondQuantizedProperty re-constructed from the HDF5 file.
+
+        Raises:
+            LookupError: file not found.
+        """
+        hdf5_file = self._get_path()
+
         legacy_hdf5_file = False
 
         with h5py.File(hdf5_file, "r") as file:
@@ -79,7 +111,7 @@ def run(self) -> GroupedSecondQuantizedProperty:
                 legacy_hdf5_file = True
                 LOGGER.warning(
                     "Your HDF5 file contains the legacy QMolecule object! You should consider "
-                    "converting it to the new property framework."
+                    "converting it to the new property framework. See also HDF5Driver.convert"
                 )
 
         if legacy_hdf5_file:
diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
index 0875c3b047..80ca61caad 100644
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
+++ b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
@@ -12,6 +12,9 @@
 
 """ Test Driver HDF5 """
 
+import os
+import shutil
+import tempfile
 import unittest
 
 from test import QiskitNatureTestCase
@@ -31,6 +34,56 @@ def setUp(self):
         )
         self.driver_result = driver.run()
 
+    def test_convert(self):
+        """Test the legacy-conversion method."""
+        legacy_file_path = self.get_resource_path(
+            "test_driver_hdf5_legacy.hdf5", "drivers/second_quantization/hdf5d"
+        )
+
+        with self.subTest("replace=True"):
+            # pylint: disable=consider-using-with
+            tmp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".hdf5")
+            tmp_file.close()
+            os.unlink(tmp_file.name)
+            shutil.copy(legacy_file_path, tmp_file.name)
+            try:
+                driver = HDF5Driver(tmp_file.name)
+                driver.convert()
+                with self.assertRaises(AssertionError):
+                    # NOTE: we can use assertNoLogs once Python 3.10 is the default
+                    with self.assertLogs(
+                        logger="qiskit_nature.drivers.second_quantization.hdf5d.hdf5driver",
+                        level="WARNING",
+                    ):
+                        driver.run()
+            finally:
+                os.unlink(tmp_file.name)
+
+        with self.subTest("replace=False"):
+            # pylint: disable=consider-using-with
+            tmp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".hdf5")
+            tmp_file.close()
+            os.unlink(tmp_file.name)
+            shutil.copy(legacy_file_path, tmp_file.name)
+            try:
+                driver = HDF5Driver(tmp_file.name)
+                driver.convert(replace=False)
+                with self.assertLogs(
+                    logger="qiskit_nature.drivers.second_quantization.hdf5d.hdf5driver",
+                    level="WARNING",
+                ):
+                    driver.run()
+                with self.assertRaises(AssertionError):
+                    # NOTE: we can use assertNoLogs once Python 3.10 is the default
+                    with self.assertLogs(
+                        logger="qiskit_nature.drivers.second_quantization.hdf5d.hdf5driver",
+                        level="WARNING",
+                    ):
+                        HDF5Driver(tmp_file.name + ".new").run()
+            finally:
+                os.unlink(tmp_file.name)
+                os.unlink(tmp_file.name + ".new")
+
 
 class TestDriverHDF5Legacy(QiskitNatureTestCase, TestDriver):
     """HDF5 Driver legacy file-support tests."""

From 11abf8beb07596c68ac097b7f76779bb1ca59f21 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 14 Feb 2022 09:50:21 +0100
Subject: [PATCH 07/13] Add reno

---
 releasenotes/notes/hdf5-driver-bafbbd8e70ee15a6.yaml | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 releasenotes/notes/hdf5-driver-bafbbd8e70ee15a6.yaml

diff --git a/releasenotes/notes/hdf5-driver-bafbbd8e70ee15a6.yaml b/releasenotes/notes/hdf5-driver-bafbbd8e70ee15a6.yaml
new file mode 100644
index 0000000000..38945bcbc8
--- /dev/null
+++ b/releasenotes/notes/hdf5-driver-bafbbd8e70ee15a6.yaml
@@ -0,0 +1,11 @@
+---
+features:
+  - |
+    The HDF5Driver has been refactored to leverage the new HDF5-integration
+    protocol of Qiskit Nature. The driver still supports loading legacy
+    QMolecule HDF5 files and also provides a conversion utility:
+
+    .. code-block:: python
+
+      driver = HDF5Driver("path_to_qmolecule.hdf5")
+      driver.convert(replace=True)

From da1bec7663f984b15876f00fc0c402355da7ea87 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 14 Feb 2022 10:22:02 +0100
Subject: [PATCH 08/13] Fix linters

---
 .../second_quantization/hdf5d/hdf5driver.py        | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index d50c4737c8..33e8c6b789 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -18,6 +18,7 @@
 
 import h5py
 
+from qiskit_nature import QiskitNatureError
 from qiskit_nature.hdf5 import load_from_hdf5, save_to_hdf5
 from qiskit_nature.properties.second_quantization.second_quantized_property import (
     GroupedSecondQuantizedProperty,
@@ -60,8 +61,11 @@ def work_path(self, new_work_path):
     def _get_path(self) -> str:
         """Returns the absolute path to the HDF5 file.
 
+        Returns:
+            The absolute path to the HDF5 file.
+
         Raises:
-            LoopupError: file not found.
+            LookupError: file not found.
         """
         hdf5_file = self._hdf5_input
         if self.work_path is not None and not os.path.isabs(hdf5_file):
@@ -101,6 +105,7 @@ def run(self) -> GroupedSecondQuantizedProperty:
 
         Raises:
             LookupError: file not found.
+            QiskitNatureError: if the HDF5 file did not contain a GroupedSecondQuantizedProperty.
         """
         hdf5_file = self._get_path()
 
@@ -122,4 +127,11 @@ def run(self) -> GroupedSecondQuantizedProperty:
             return ElectronicStructureDriverResult.from_legacy_driver_result(molecule)
 
         driver_result = load_from_hdf5(hdf5_file)
+
+        if not isinstance(driver_result, GroupedSecondQuantizedProperty):
+            raise QiskitNatureError(
+                f"Expected a GroupedSecondQuantizedProperty but found a {type(driver_result)} "
+                "object instead."
+            )
+
         return driver_result

From 8ba1655175a92136cbda27a587b797e9b201d109 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 21 Feb 2022 14:15:46 +0100
Subject: [PATCH 09/13] refactor: do not replace by default

---
 qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py | 2 +-
 test/drivers/second_quantization/hdf5d/test_driver_hdf5.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index 33e8c6b789..fcbdeaab37 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -76,7 +76,7 @@ def _get_path(self) -> str:
 
         return hdf5_file
 
-    def convert(self, replace: bool = True) -> None:
+    def convert(self, replace: bool = False) -> None:
         """Converts a legacy QMolecule HDF5 file into the new Property-framework.
 
         Args:
diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
index 80ca61caad..203806586a 100644
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
+++ b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
@@ -48,7 +48,7 @@ def test_convert(self):
             shutil.copy(legacy_file_path, tmp_file.name)
             try:
                 driver = HDF5Driver(tmp_file.name)
-                driver.convert()
+                driver.convert(replace=True)
                 with self.assertRaises(AssertionError):
                     # NOTE: we can use assertNoLogs once Python 3.10 is the default
                     with self.assertLogs(

From dd3bee1c1a9634de0726cbfad620c966b1f4ef84 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 21 Feb 2022 14:24:02 +0100
Subject: [PATCH 10/13] refactor: use `_new.hdf5` instead of `.hdf5.new`

---
 .../second_quantization/hdf5d/hdf5driver.py   | 20 ++++++++++---------
 .../hdf5d/test_driver_hdf5.py                 |  8 ++++++--
 2 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index fcbdeaab37..d3a569d28a 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -13,7 +13,7 @@
 """ HDF5 Driver """
 
 import logging
-import os
+import pathlib
 import warnings
 
 import h5py
@@ -58,7 +58,7 @@ def work_path(self, new_work_path):
         """Sets work path."""
         self._work_path = new_work_path
 
-    def _get_path(self) -> str:
+    def _get_path(self) -> pathlib.Path:
         """Returns the absolute path to the HDF5 file.
 
         Returns:
@@ -67,11 +67,11 @@ def _get_path(self) -> str:
         Raises:
             LookupError: file not found.
         """
-        hdf5_file = self._hdf5_input
-        if self.work_path is not None and not os.path.isabs(hdf5_file):
-            hdf5_file = os.path.abspath(os.path.join(self.work_path, hdf5_file))
+        hdf5_file = pathlib.Path(self._hdf5_input)
+        if self.work_path is not None and not hdf5_file.is_absolute():
+            hdf5_file = pathlib.Path(self.work_path) / hdf5_file
 
-        if not os.path.isfile(hdf5_file):
+        if not hdf5_file.is_file():
             raise LookupError(f"HDF5 file not found: {hdf5_file}")
 
         return hdf5_file
@@ -93,10 +93,12 @@ def convert(self, replace: bool = False) -> None:
         warnings.filterwarnings("default", category=DeprecationWarning)
         q_mol.load()
 
-        new_hdf5_file = hdf5_file if replace else hdf5_file + ".new"
+        new_hdf5_file = hdf5_file
+        if not replace:
+            new_hdf5_file = hdf5_file.with_stem(str(hdf5_file.stem) + "_new")
 
         driver_result = ElectronicStructureDriverResult.from_legacy_driver_result(q_mol)
-        save_to_hdf5(driver_result, new_hdf5_file, replace=replace)
+        save_to_hdf5(driver_result, str(new_hdf5_file), replace=replace)
 
     def run(self) -> GroupedSecondQuantizedProperty:
         """
@@ -126,7 +128,7 @@ def run(self) -> GroupedSecondQuantizedProperty:
             molecule.load()
             return ElectronicStructureDriverResult.from_legacy_driver_result(molecule)
 
-        driver_result = load_from_hdf5(hdf5_file)
+        driver_result = load_from_hdf5(str(hdf5_file))
 
         if not isinstance(driver_result, GroupedSecondQuantizedProperty):
             raise QiskitNatureError(
diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
index 203806586a..7497208f58 100644
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
+++ b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
@@ -13,6 +13,7 @@
 """ Test Driver HDF5 """
 
 import os
+import pathlib
 import shutil
 import tempfile
 import unittest
@@ -63,6 +64,9 @@ def test_convert(self):
             # pylint: disable=consider-using-with
             tmp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".hdf5")
             tmp_file.close()
+            new_file_name = pathlib.Path(tmp_file.name).with_stem(
+                str(pathlib.Path(tmp_file.name).stem) + "_new"
+            )
             os.unlink(tmp_file.name)
             shutil.copy(legacy_file_path, tmp_file.name)
             try:
@@ -79,10 +83,10 @@ def test_convert(self):
                         logger="qiskit_nature.drivers.second_quantization.hdf5d.hdf5driver",
                         level="WARNING",
                     ):
-                        HDF5Driver(tmp_file.name + ".new").run()
+                        HDF5Driver(new_file_name).run()
             finally:
                 os.unlink(tmp_file.name)
-                os.unlink(tmp_file.name + ".new")
+                os.unlink(new_file_name)
 
 
 class TestDriverHDF5Legacy(QiskitNatureTestCase, TestDriver):

From 5abfbe4c41e45f240f0f60472e6d6bcb4040eea1 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 21 Feb 2022 14:28:09 +0100
Subject: [PATCH 11/13] refactor: update wording

---
 qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index d3a569d28a..6740e132ac 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -118,7 +118,7 @@ def run(self) -> GroupedSecondQuantizedProperty:
                 legacy_hdf5_file = True
                 LOGGER.warning(
                     "Your HDF5 file contains the legacy QMolecule object! You should consider "
-                    "converting it to the new property framework. See also HDF5Driver.convert"
+                    "converting it to the new property framework, see HDF5Driver.convert"
                 )
 
         if legacy_hdf5_file:

From 5766690be7fdb47313180642060a953d05f8ddc0 Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 21 Feb 2022 15:04:40 +0100
Subject: [PATCH 12/13] fix: Python <3.9 compatibility

---
 qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py | 2 +-
 test/drivers/second_quantization/hdf5d/test_driver_hdf5.py    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index 6740e132ac..cfd47e9559 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -95,7 +95,7 @@ def convert(self, replace: bool = False) -> None:
 
         new_hdf5_file = hdf5_file
         if not replace:
-            new_hdf5_file = hdf5_file.with_stem(str(hdf5_file.stem) + "_new")
+            new_hdf5_file = hdf5_file.with_name(str(hdf5_file.stem) + "_new.hdf5")
 
         driver_result = ElectronicStructureDriverResult.from_legacy_driver_result(q_mol)
         save_to_hdf5(driver_result, str(new_hdf5_file), replace=replace)
diff --git a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
index 7497208f58..2f1a27aec9 100644
--- a/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
+++ b/test/drivers/second_quantization/hdf5d/test_driver_hdf5.py
@@ -64,8 +64,8 @@ def test_convert(self):
             # pylint: disable=consider-using-with
             tmp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".hdf5")
             tmp_file.close()
-            new_file_name = pathlib.Path(tmp_file.name).with_stem(
-                str(pathlib.Path(tmp_file.name).stem) + "_new"
+            new_file_name = pathlib.Path(tmp_file.name).with_name(
+                str(pathlib.Path(tmp_file.name).stem) + "_new.hdf5"
             )
             os.unlink(tmp_file.name)
             shutil.copy(legacy_file_path, tmp_file.name)

From 0df43efc854f09ba15959350b5091207fc821b6f Mon Sep 17 00:00:00 2001
From: Max Rossmannek <oss@zurich.ibm.com>
Date: Mon, 21 Feb 2022 17:07:13 +0100
Subject: [PATCH 13/13] Update docstring

---
 qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
index cfd47e9559..4b8ef77f1d 100644
--- a/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
+++ b/qiskit_nature/drivers/second_quantization/hdf5d/hdf5driver.py
@@ -80,8 +80,8 @@ def convert(self, replace: bool = False) -> None:
         """Converts a legacy QMolecule HDF5 file into the new Property-framework.
 
         Args:
-            replace: if True, will replace the original HDF5 file. Otherwise `.new` will be used as
-                a suffix.
+            replace: if True, will replace the original HDF5 file. Otherwise `_new.hdf5` will be
+                used as a suffix.
 
         Raises:
             LookupError: file not found.