pass final test

funlib/persistence/graphs/sqlite_graph_database.py

@@ -328,7 +328,7 @@ def read_nodes(
                     for key, val in zip(
                         ["id"] + self.position_attributes + self.node_attrs, values
                     )
-                    if key in read_attrs
+                    if key in read_attrs and val is not None
                 }
                 for values in self.cur.execute(select_statement)
             ]
@@ -337,7 +337,7 @@ def read_nodes(
 
         if isinstance(self.position_attribute, str):
             for data in nodes:
-                data[self.position_attribute] = self.__get_node_pos(data)
+                data[self.position_attribute] = self.__combine_pos(data)
 
         return nodes
 
@@ -605,32 +605,30 @@ def write_nodes(
             raise NotImplementedError(
                 "Fail if exists not implemented for " "file backend"
             )
-        if attributes is not None:
-            raise NotImplementedError("Attributes not implemented for file backend")
         if self.mode == "r":
             raise NotImplementedError("Trying to write to read-only DB")
 
         logger.debug("Writing nodes in %s", roi)
 
+        attrs = attributes if attributes is not None else self.node_attrs
+
         insert_statement = (
             f"INSERT{' OR IGNORE' if not fail_if_exists else ''} INTO {self.nodes_collection_name} "
-            f"(id, {', '.join(self.position_attributes + self.node_attrs)}) VALUES "
-            f"({', '.join(['?'] * (len(self.position_attributes) + len(self.node_attrs) + 1))})"
+            f"(id, {', '.join(self.position_attributes + attrs)}) VALUES "
+            f"({', '.join(['?'] * (len(self.position_attributes) + len(attrs) + 1))})"
         )
 
         to_insert = []
         for node_id, data in nodes.items():
+            data = data.copy()
             pos = self.__get_node_pos(data)
             if roi is not None and not roi.contains(pos):
                 continue
             for i, position_attribute in enumerate(self.position_attributes):
                 data[position_attribute] = pos[i]
             to_insert.append(
                 [node_id]
-                + [
-                    data.get(attr, None)
-                    for attr in self.position_attributes + self.node_attrs
-                ]
+                + [data.get(attr, None) for attr in self.position_attributes + attrs]
             )
 
         if len(to_insert) == 0:
@@ -690,6 +688,11 @@ def __remove_keys(self, dictionary, keys):
 
         return {k: v for k, v in dictionary.items() if k not in keys}
 
+    def __combine_pos(self, n: dict[str, Any]) -> Coordinate:
+        return Coordinate(
+            (n.pop(pos_attr, None) for pos_attr in self.position_attributes)
+        )
+
     def __get_node_pos(self, n: dict[str, Any]) -> Coordinate:
         if isinstance(self.position_attribute, str):
             return Coordinate(n.get(self.position_attribute, (None,) * self.ndim))

tests/test_graph.py

@@ -296,19 +296,21 @@ def test_graph_fail_if_not_exists(provider_factory):
 
 
 def test_graph_write_attributes(provider_factory):
-    graph_provider = provider_factory("w")
+    graph_provider = provider_factory("w", node_attrs=["swip"])
     graph = graph_provider[Roi((0, 0, 0), (10, 10, 10))]
 
     graph.add_node(2, comment="without position")
     graph.add_node(42, position=(1, 1, 1))
     graph.add_node(23, position=(5, 5, 5), swip="swap")
-    graph.add_node(57, position=Coordinate((7, 7, 7)), zap="zip")
+    graph.add_node(57, position=(7, 7, 7), zap="zip")
     graph.add_edge(42, 23)
     graph.add_edge(57, 23)
     graph.add_edge(2, 42)
 
     try:
-        graph_provider.write_nodes(graph.nodes(), attributes=["position", "swip"])
+        graph_provider.write_graph(
+            graph, write_nodes=True, write_edges=False, node_attrs=["swip"]
+        )
     except NotImplementedError:
         pytest.xfail()
     graph_provider.write_edges(
@@ -325,7 +327,6 @@ def test_graph_write_attributes(provider_factory):
             continue
         if "zap" in data:
             del data["zap"]
-        data["position"] = list(data["position"])
         nodes.append((node, data))
 
     compare_nodes = compare_graph.nodes(data=True)