Merge branch 'main' into stable

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [0.9.0](https://github.com/brsynth/neo4jsbml/tree/0.9.0) (2023-01-27)
+
+[Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.8.3...0.9.0)
+
+**Merged pull requests:**
+
+- chore\(deps\): bump actions/upload-artifact from 2 to 3 [\#4](https://github.com/brsynth/neo4jsbml/pull/4) ([dependabot[bot]](https://github.com/apps/dependabot))
+
 ## [0.8.3](https://github.com/brsynth/neo4jsbml/tree/0.8.3) (2023-01-16)
 
 [Full Changelog](https://github.com/brsynth/neo4jsbml/compare/0.8.0...0.8.3)

README.md

@@ -44,7 +44,6 @@ python -m neo4jsbml \
     --input-user-str "neo4j" \
     --input-password-file <file> \
     --input-database-str <str> \
-    --input-batch-int <int> \
     # Config file
     --input-config-file <file> \
 

src/neo4jsbml/__main__.py

@@ -44,12 +44,6 @@ def main():
         default="neo4j",
         help="The name of the database",
     )
-    parser_dbb.add_argument(
-        "--input-batch-int",
-        default=connect.Connect.BATCH,
-        type=int,
-        help="The number of items to include in a batch",
-    )
     parser_dbb_config = parser.add_argument_group(
         "Database connection - Configuration file"
     )
@@ -111,7 +105,6 @@ def main():
             user=args.input_user_str,
             database=args.input_database_str,
             password_path=args.input_password_file,
-            batch=args.input_batch_int,
         )
     if con.is_connected() is False:
         logging.error("Unable to connect to the database")

src/neo4jsbml/_version.py

@@ -1,2 +1,2 @@
 __app_name__ = "neo4jsbml"
-__version__ = "0.9.0"
+__version__ = "0.9.1"

src/neo4jsbml/connect.py

@@ -26,8 +26,6 @@ class Connect(metaclass=singleton.Singleton):
         the password to connect to the database
     password_path: Optional[str]
         the password provided by a file
-    batch: Optional[int] (default: 5000)
-        number of transactions before a commit for Neo4j
     stats: Dict[str, int]
         statistics dictionnary updated by create_nodes(), create_relationships
         Keys: nodes, relationships
@@ -53,7 +51,6 @@ def from_config(cls, path: str) -> "Connect"
         create a Connect from an .ini file
     """
 
-    BATCH = 5000
     PROTOCOLS = ["neo4j", "bolt"]
 
     def __init__(
@@ -65,7 +62,6 @@ def __init__(
         port: int = 7687,
         password: Optional[str] = None,
         password_path: Optional[str] = None,
-        batch: Optional[int] = None,
     ) -> None:
         self.protocol = protocol
         self.url = url
@@ -83,9 +79,6 @@ def __init__(
             )
         else:
             self.driver = neo4j.GraphDatabase.driver(self.uri)
-        self.batch = Connect.BATCH
-        if batch:
-            self.batch = int(batch)
         self.stats: Dict[str, int] = {}
 
     def is_connected(self) -> bool:
@@ -213,9 +206,5 @@ def from_config(cls, path: str) -> "Connect":
                 data["database"] = section.get("name")
             if section.get("password"):
                 data["password"] = section.get("password")
-        if config.has_section("parameters"):
-            section = config["parameters"]
-            if section.get("batch"):
-                data["batch"] = section.get("batch")
 
         return Connect(**data)

src/neo4jsbml/sbml.py

@@ -165,7 +165,7 @@ def find_by_label(
 
                 try:
                     cur_id = eval("from_obj.%s()" % (methods[0],))
-                except:
+                except Exception:
                     continue
                 if cur_id == to_id:
                     dbb_rel = srelationship.SRelationship(
@@ -213,7 +213,7 @@ def find_by_relationships(
 
             try:
                 to_id = eval("from_obj.%s()" % (methods[0],))
-            except:
+            except Exception:
                 continue
             if self.validate_id(value=to_id):
                 dbb_rel = srelationship.SRelationship(
@@ -246,7 +246,7 @@ def find_by_relationships(
 
             try:
                 from_id = eval("to_obj.%s()" % (methods[0],))
-            except:
+            except Exception:
                 continue
             if self.validate_id(value=from_id):
                 dbb_rel = srelationship.SRelationship(
@@ -500,8 +500,8 @@ def format_relationships(
                 % (from_label, to_label, arrow_rel.label)
             )
         if self.tag is not None:
-            for srel in res:
-                srel.add_property(label="tag", value=self.tag)
+            for srelation in res:
+                srelation.add_property(label="tag", value=self.tag)
         return res
 
     def validate_id(self, value: Any) -> bool:

template/config.ini

@@ -7,6 +7,3 @@ port = 7687
 user = neo4j
 password = abc
 name = neo4j
-
-[parameters]
-batch = 5000

tests/dataset/config.ini

@@ -7,6 +7,3 @@ port = 7687
 user = neo4j
 password = abc
 name = neo4j
-
-[parameters]
-batch = 5000

tests/test_connect.py

@@ -65,4 +65,3 @@ def test_from_config(self, neo4j_config):
         assert con_b.user == "neo4j"
         assert con_b.database == "neo4j"
         assert con_b.password == "test"
-        assert con_b.batch == 5000