biocypher 0.9.2__py3-none-any.whl → 0.12.3__py3-none-any.whl

biocypher/output/connect/_get_connector.py

@@ -6,7 +6,6 @@ Handles the connecting and writing a Knowledge Graph to a database.
 from biocypher._config import config as _config
 from biocypher._logger import logger
 from biocypher._translate import Translator
-from biocypher.output.connect._neo4j_driver import _Neo4jDriver
 
 logger.debug(f"Loading module {__name__}.")
 
@@ -17,16 +16,32 @@ def get_connector(
     dbms: str,
     translator: Translator,
 ):
-    """
-    Function to return the connector class.
+    """Return the connector class.
 
-    Returns:
+    Returns
+    -------
         class: the connector class
-    """
 
+    Raises
+    ------
+        NotImplementedError: if the DBMS is not supported
+        ImportError: if Neo4j driver is not installed when using Neo4j
+
+    """
     dbms_config = _config(dbms)
 
     if dbms == "neo4j":
+        # Import Neo4j driver only when needed
+        try:
+            from biocypher.output.connect._neo4j_driver import _Neo4jDriver
+        except ImportError as e:
+            msg = (
+                "Neo4j driver is not installed. Install it with: "
+                "pip install biocypher[neo4j] or pip install neo4j>=5.0"
+            )
+            logger.error(msg)
+            raise ImportError(msg) from e
+
         return _Neo4jDriver(
             database_name=dbms_config["database_name"],
             wipe=dbms_config["wipe"],
@@ -36,5 +51,7 @@ def get_connector(
             multi_db=dbms_config["multi_db"],
             translator=translator,
         )
-    else:
-        raise NotImplementedError(f"Online mode is not supported for the DBMS {dbms}.")
+
+    msg = f"Online mode is not supported for the DBMS {dbms}."
+    logger.error(msg)
+    raise NotImplementedError(msg)

biocypher/output/connect/_neo4j_driver.py

@@ -6,12 +6,11 @@ import itertools
 
 from collections.abc import Iterable
 
-import neo4j_utils
-
 from biocypher import _misc
 from biocypher._create import BioCypherEdge, BioCypherNode
 from biocypher._logger import logger
 from biocypher._translate import Translator
+from biocypher.output.connect._neo4j_driver_wrapper import Neo4jDriver
 
 logger.debug(f"Loading module {__name__}.")
 __all__ = ["_Neo4jDriver"]
@@ -20,7 +19,7 @@ __all__ = ["_Neo4jDriver"]
 class _Neo4jDriver:
     """
     Manages a BioCypher connection to a Neo4j database using the
-    ``neo4j_utils.Driver`` class.
+    internal ``Neo4jDriver`` class.
 
     Args:
 
@@ -55,10 +54,12 @@ class _Neo4jDriver:
         wipe: bool = False,
         fetch_size: int = 1000,
         increment_version: bool = True,
+        force_enterprise: bool = False,
+        **kwargs,
     ):
         self.translator = translator
 
-        self._driver = neo4j_utils.Driver(
+        self._driver = Neo4jDriver(
             db_name=database_name,
             db_uri=uri,
             db_user=user,
@@ -67,6 +68,7 @@ class _Neo4jDriver:
             wipe=wipe,
             multi_db=multi_db,
             raise_errors=True,
+            force_enterprise=force_enterprise,
         )
 
         # check for biocypher config in connected graph
@@ -79,6 +81,18 @@ class _Neo4jDriver:
             self._update_meta_graph()
 
     def _update_meta_graph(self):
+        """Update the BioCypher meta graph with version information.
+
+        Requires APOC to be installed. If APOC is not available, this
+        operation is skipped with a warning.
+        """
+        if not self._driver.has_apoc:
+            logger.warning(
+                "APOC plugin is not available. Skipping meta graph update. "
+                "Install APOC to enable version tracking: https://neo4j.com/labs/apoc/"
+            )
+            return
+
         logger.info("Updating Neo4j meta graph.")
 
         # find current version node
@@ -102,8 +116,8 @@ class _Neo4jDriver:
     def init_db(self):
         """
         Used to initialise a property graph database by setting up new
-        constraints. Wipe has been performed by the ``neo4j_utils.Driver``
-        class` already.
+        constraints. Wipe has been performed by the ``Neo4jDriver``
+        class already.
 
         Todo:
             - set up constraint creation interactively depending on the
@@ -137,7 +151,12 @@ class _Neo4jDriver:
                     self._driver.query(s)
 
     def _get_neo4j_version(self):
-        """Get neo4j version."""
+        """Get neo4j version.
+
+        Returns the Neo4j server version. If detection fails, defaults to
+        "5.0.0" to use the newer syntax (which is more likely for new
+        installations).
+        """
         try:
             neo4j_version = self._driver.query(
                 """
@@ -149,8 +168,12 @@ class _Neo4jDriver:
             )[0][0]["version"]
             return neo4j_version
         except Exception as e:
-            logger.warning(f"Error detecting Neo4j version: {e} use default version 4.0.0.")
-            return "4.0.0"
+            logger.warning(
+                f"Error detecting Neo4j version: {e}. "
+                "Defaulting to version 5.0.0 syntax. "
+                "If you're using Neo4j 4.x, this may cause errors."
+            )
+            return "5.0.0"
 
     def add_nodes(self, id_type_tuples: Iterable[tuple]) -> tuple:
         """
@@ -237,6 +260,9 @@ class _Neo4jDriver:
 
         Returns:
             True for success, False otherwise.
+
+        Raises:
+            RuntimeError: If APOC is not available and required for the operation.
         """
 
         try:
@@ -250,6 +276,16 @@ class _Neo4jDriver:
 
             raise ValueError(msg)
 
+        # Check if APOC is available
+        if not self._driver.has_apoc:
+            msg = (
+                "APOC plugin is required for adding nodes. "
+                "Please install APOC in your Neo4j instance. "
+                "See: https://neo4j.com/labs/apoc/"
+            )
+            logger.error(msg)
+            raise RuntimeError(msg)
+
         logger.info(f"Merging {len(entities)} nodes.")
 
         entity_query = (
@@ -336,6 +372,16 @@ class _Neo4jDriver:
         self.add_biocypher_nodes(nodes)
         logger.info(f"Merging {len(rels)} edges.")
 
+        # Check if APOC is available
+        if not self._driver.has_apoc:
+            msg = (
+                "APOC plugin is required for adding edges. "
+                "Please install APOC in your Neo4j instance. "
+                "See: https://neo4j.com/labs/apoc/"
+            )
+            logger.error(msg)
+            raise RuntimeError(msg)
+
         # cypher query
 
         # merging only on the ids of the entities, passing the