Dev

src/schnetpack/data/atoms.py

@@ -374,13 +374,14 @@ def _get_properties(
         return properties
 
     # Metadata
-
     @property
     def metadata(self):
-        return self.conn.metadata
+        with connect(self.datapath, use_lock_file=False) as conn:
+            return conn.metadata
 
     def _set_metadata(self, val: Dict[str, Any]):
-        self.conn.metadata = val
+        with connect(self.datapath, use_lock_file=False) as conn:
+            conn.metadata = val
 
     def update_metadata(self, **kwargs):
         assert all(
@@ -477,7 +478,7 @@ def add_system(
                 `available_properties` of the dataset.
 
         """
-        self._add_system(self.conn, atoms, atoms_metadata, **properties)
+        self._add_system(atoms, atoms_metadata, **properties)
 
     def add_systems(
         self,
@@ -511,15 +512,13 @@ def add_systems(
             atoms_list, property_list, atoms_metadata_list
         ):
             self._add_system(
-                self.conn,
                 atoms,
                 atoms_metadata,
                 **prop,
             )
 
     def _add_system(
         self,
-        conn,
         atoms: Optional[Atoms] = None,
         atoms_metadata: Optional[Dict[str, Any]] = None,
         **properties,
@@ -543,28 +542,30 @@ def _add_system(
         if atoms_metadata is None:
             atoms_metadata = {}
 
-        # add available properties to database
-        valid_props = set().union(
-            conn.metadata["_property_unit_dict"].keys(),
-            [structure.Z, structure.R, structure.cell, structure.pbc],
-        )
-        for pname in properties:
-            if pname not in valid_props:
-                logger.warning(
-                    f"Property `{pname}` is not a defined property for this dataset and "
-                    + f"will be ignored. If it should be included, it has to be "
-                    + f"provided together with its unit when calling "
-                    + f"AseAtomsData.create()."
-                )
-
-        data = {}
-        for pname in conn.metadata["_property_unit_dict"].keys():
-            if pname in properties:
-                data[pname] = properties[pname]
-            else:
-                raise AtomsDataError("Required property missing:" + pname)
+        with connect(self.datapath, use_lock_file=False) as conn:
+            prop_keys = conn.metadata["_property_unit_dict"].keys()
 
-        conn.write(atoms, data=data, key_value_pairs=atoms_metadata)
+            valid_props = set().union(
+                prop_keys,
+                [structure.Z, structure.R, structure.cell, structure.pbc],
+            )
+            for pname in properties:
+                if pname not in valid_props:
+                    logger.warning(
+                        f"Property `{pname}` is not a defined property for this dataset and "
+                        + f"will be ignored. If it should be included, it has to be "
+                        + f"provided together with its unit when calling "
+                        + f"AseAtomsData.create()."
+                    )
+
+            data = {}
+            for pname in prop_keys:
+                if pname in properties:
+                    data[pname] = properties[pname]
+                else:
+                    raise AtomsDataError("Required property missing:" + pname)
+
+            conn.write(atoms, data=data, key_value_pairs=atoms_metadata)
 
 
 def create_dataset(

src/schnetpack/datasets/qm9.py

@@ -31,9 +31,18 @@ class QM9(AtomsDataModule):
     References:
 
         .. [#qm9_1] https://ndownloader.figshare.com/files/3195404
-
     """
 
+    base_urls = [
+        "https://ndownloader.figshare.com/files/",
+        "https://springernature.figshare.com/ndownloader/files/",
+    ]
+    file_ids = {
+        "data": "3195389",
+        "atomrefs": "3195395",
+        "uncharacterized": "3195404",
+    }
+
     # properties
     A = "rotational_constant_A"
     B = "rotational_constant_B"
@@ -127,6 +136,18 @@ def __init__(
 
         self.remove_uncharacterized = remove_uncharacterized
 
+    def _download_file(self, file_id: str, destination: str):
+        for base_url in self.base_urls:
+            url = f"{base_url}{file_id}"
+            try:
+                request.urlretrieve(url, destination)
+                return
+            except Exception:
+                logging.warning(f"Could not download from {url}, trying next source...")
+        raise AtomsDataModuleError(
+            f"Could not download file with id {file_id} from any source."
+        )
+
     def prepare_data(self):
         if not os.path.exists(self.datapath):
             property_unit_dict = {
@@ -179,9 +200,8 @@ def prepare_data(self):
 
     def _download_uncharacterized(self, tmpdir):
         logging.info("Downloading list of uncharacterized molecules...")
-        at_url = "https://ndownloader.figshare.com/files/3195404"
         tmp_path = os.path.join(tmpdir, "uncharacterized.txt")
-        request.urlretrieve(at_url, tmp_path)
+        self._download_file(self.file_ids["uncharacterized"], tmp_path)
         logging.info("Done.")
 
         uncharacterized = []
@@ -193,9 +213,8 @@ def _download_uncharacterized(self, tmpdir):
 
     def _download_atomrefs(self, tmpdir):
         logging.info("Downloading GDB-9 atom references...")
-        at_url = "https://ndownloader.figshare.com/files/3195395"
         tmp_path = os.path.join(tmpdir, "atomrefs.txt")
-        request.urlretrieve(at_url, tmp_path)
+        self._download_file(self.file_ids["atomrefs"], tmp_path)
         logging.info("Done.")
 
         props = [QM9.zpve, QM9.U0, QM9.U, QM9.H, QM9.G, QM9.Cv]
@@ -214,9 +233,7 @@ def _download_data(
         logging.info("Downloading GDB-9 data...")
         tar_path = os.path.join(tmpdir, "gdb9.tar.gz")
         raw_path = os.path.join(tmpdir, "gdb9_xyz")
-        url = "https://ndownloader.figshare.com/files/3195389"
-
-        request.urlretrieve(url, tar_path)
+        self._download_file(self.file_ids["data"], tar_path)
         logging.info("Done.")
 
         logging.info("Extracting files...")