biocypher 0.9.0__tar.gz → 0.9.1__tar.gz

{biocypher-0.9.0 → biocypher-0.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biocypher
-Version: 0.9.0
+Version: 0.9.1
 Summary: A unifying framework for biomedical research knowledge graphs
 Home-page: https://github.com/biocypher/biocypher
 License: MIT

{biocypher-0.9.0 → biocypher-0.9.1}/biocypher/_core.py

@@ -118,6 +118,15 @@ class BioCypher:
         else:
             self._offline = offline
 
+        # Check if pandas/tabular is being used in offline mode
+        if self._offline and self._dbms.lower() in ["pandas", "tabular"]:
+            msg = (
+                f"The '{self._dbms}' DBMS is only available in online mode. "
+                f"If you want to write CSV files, use 'csv' as the DBMS. "
+                f"If you want to use pandas, set 'offline: false' in your configuration."
+            )
+            raise ValueError(msg)
+
         if strict_mode is None:
             self._strict_mode = self.base_config["strict_mode"]
         else:
@@ -225,19 +234,31 @@ class BioCypher:
         The knowledge graph is returned based on the `dbms` parameter in
         the biocypher configuration file.
 
+        TODO: These conditionals are a hack, we need to refactor the in-memory
+        KG to be generic, and simplify access and conversion to output formats.
+
         Returns
         -------
              Any: knowledge graph.
 
         """
+        # If we're using an in-memory KG and it already exists, return it directly
+        if self._in_memory_kg and self._is_online_and_in_memory():
+            return self._in_memory_kg.get_kg()
+
+        # Otherwise, initialize and populate the in-memory KG
         if not self._in_memory_kg:
             self._initialize_in_memory_kg()
         if not self._translator:
             self._get_translator()
-        tnodes = self._translator.translate_entities(self._nodes)
-        tedges = self._translator.translate_entities(self._edges)
-        self._in_memory_kg.add_nodes(tnodes)
-        self._in_memory_kg.add_edges(tedges)
+
+        # These attributes might not exist when using in-memory KG directly
+        if hasattr(self, "_nodes") and hasattr(self, "_edges"):
+            tnodes = self._translator.translate_entities(self._nodes)
+            tedges = self._translator.translate_entities(self._edges)
+            self._in_memory_kg.add_nodes(tnodes)
+            self._in_memory_kg.add_edges(tedges)
+
         return self._in_memory_kg.get_kg()
 
     def _get_deduplicator(self) -> Deduplicator:

{biocypher-0.9.0 → biocypher-0.9.1}/biocypher/_metadata.py

@@ -10,7 +10,7 @@ import pathlib
 
 import toml
 
-_VERSION = "0.9.0"
+_VERSION = "0.9.1"
 
 
 def get_metadata():

{biocypher-0.9.0 → biocypher-0.9.1}/biocypher/output/write/_get_writer.py

@@ -75,7 +75,7 @@ def get_writer(
         instance: an instance of the selected writer class.
 
     """
-    dbms_config = _config(dbms)
+    dbms_config = _config(dbms) or {}
 
     writer = DBMS_TO_CLASS[dbms]
 

{biocypher-0.9.0 → biocypher-0.9.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biocypher"
-version = "0.9.0"
+version = "0.9.1"
 description = "A unifying framework for biomedical research knowledge graphs"
 authors = [
     "Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>",