hotfix pymongo collection issue

matthiasprobst · Dec 14, 2024 · 660310b · 660310b
1 parent d028a1f
commit 660310b
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Showing 5 changed files with 60 additions and 58 deletions.
diff --git a/docs/userguide/database/mongoDB.ipynb b/docs/userguide/database/mongoDB.ipynb
diff --git a/h5rdmtoolbox/database/mongo.py b/h5rdmtoolbox/database/mongo.py
@@ -6,7 +6,8 @@
 
 import h5py
 import numpy as np
-import pymongo
+from pymongo.collection import Collection
+from pymongo.errors import InvalidDocument
 
 from .interface import ExtHDF5DBInterface
 from .. import protected_attributes
@@ -182,7 +183,7 @@ def _generate_dataset_document(
 
 def _insert_dataset(
         dataset: h5py.Dataset,
-        collection: pymongo.collection.Collection,
+        collection: Collection,
         axis=None,
         update: bool = True,
         ignore_attrs: List[str] = None,
@@ -213,7 +214,7 @@ def _insert_dataset(
 
 def _insert_group(
         group: h5py.Group,
-        collection: pymongo.collection.Collection,
+        collection: Collection,
         recursive: bool = False,
         update: bool = True,
         include_dataset: bool = True,
@@ -236,8 +237,8 @@ def _insert_group(
         tree["filename"] = filename
         try:
             collection.insert_one(make_dict_mongo_compatible(tree))
-        except pymongo.errors.InvalidDocument as e:
-            raise pymongo.errors.InvalidDocument(
+        except InvalidDocument as e:
+            raise InvalidDocument(
                 f'Could not insert dict: \n{make_dict_mongo_compatible(tree)}\nOriginal error: {e}') from e
         return collection
 
@@ -308,7 +309,7 @@ class MongoDB(ExtHDF5DBInterface):
     (see module `lazy`).
     """
 
-    def __init__(self, collection: pymongo.collection.Collection):
+    def __init__(self, collection: Collection):
         self.collection = collection
 
     def insert_dataset(self, dataset: h5py.Dataset, **kwargs):

diff --git a/requirements.txt b/requirements.txt
@@ -13,7 +13,7 @@ python-forge==18.6.0
 requests>=2.32.3
 rdflib>=7.0.0
 # database:
-pymongo>=4.2.0,<4.9.0
+pymongo>=4.2.0,<=4.10.1
 # csv
 pandas>=1.4.3
 # snt

diff --git a/setup.cfg b/setup.cfg
@@ -43,7 +43,7 @@ install_requires =
 
 [options.extras_require]
 database=
-    pymongo>=4.2.0,<4.9.0
+    pymongo>=4.2.0,<=4.10.1
 layout_validation=
     tabulate>=0.8.10,<=0.9.0
 csv =

diff --git a/tests/database/test_mongo.py b/tests/database/test_mongo.py
@@ -8,6 +8,7 @@
 import mongomock
 import numpy as np
 import pymongo
+from pymongo.errors import ServerSelectionTimeoutError
 from skimage.feature import graycomatrix, graycoprops
 from sklearn.datasets import load_digits  # ! pip install scikit-learn
 
@@ -25,7 +26,7 @@
     def get_client():
         print('Using real mongoDB server over mongomock')
         return pymongo.MongoClient()
-except pymongo.errors.ServerSelectionTimeoutError as err:
+except ServerSelectionTimeoutError as err:
 
     def get_client():
         print('Using mongomock')