biocypher 0.9.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

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/_metadata.py

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

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.dist-info → biocypher-0.9.1.dist-info}/METADATA

@@ -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.dist-info → biocypher-0.9.1.dist-info}/RECORD

@@ -5,13 +5,13 @@ biocypher/_config/test_config.yaml,sha256=Np8jeS5_EP6HHOvMKb7B_Tkyqd5YaYlYz_DVsX
 biocypher/_config/test_schema_config.yaml,sha256=D1600WgEj3iTXrumVU9LIivJHJO36iaxfkOgyam9zVU,3129
 biocypher/_config/test_schema_config_disconnected.yaml,sha256=Qm8FLxEn2spHcyj_5F859KjcDvKSxNhxDvi4b4LLkvQ,68
 biocypher/_config/test_schema_config_extended.yaml,sha256=wn3A76142hhjnImhMF6RODbCFESTJ2TtPvcFdIFsAT0,3309
-biocypher/_core.py,sha256=CGbGHX3-JuJsQJsmLFsFNylPiPiJx83aXq05ocPSeUA,26354
+biocypher/_core.py,sha256=S8frW62bc0V9M6gwU5l_D2ESa-7xwbOTffRuPqbIbT0,27382
 biocypher/_create.py,sha256=QsvXrwEQ8k0uNXvCG06UKejvw-QsJwzSaumrBjx9n1k,9884
 biocypher/_deduplicate.py,sha256=rtglcaLRaVzNjLtaPwTGP8VvCM4PHYQ5CZ-cm32CrKQ,4840
 biocypher/_get.py,sha256=2kjiBFu_onGUhgOpV7IMfGX67jyY1rpHg_GWncEUdrc,13278
 biocypher/_logger.py,sha256=y9dh3SPJOCWXnkFSYSK7aj_-pB7zlAkNCf43Dp1lt74,2941
 biocypher/_mapping.py,sha256=ntspG2C_NaQODhWTBFk0CDvolkOCjtqlQ9E-NkJAuTg,9030
-biocypher/_metadata.py,sha256=RArwucSNiwB9Ced95zgocZgRvQwX_u9brIi0CYGCAdQ,1415
+biocypher/_metadata.py,sha256=Eop3cijNQBsHWeOO8zbBmN_2ICJutZziDPvWppV474M,1415
 biocypher/_misc.py,sha256=N8aDg8j3EEcKf9ZRqzSNruUEUK4RixCy1vQ1V4maGxk,6079
 biocypher/_ontology.py,sha256=lipZxU3aj6zrTbBrJZmCW6IRCuz-KQG3AfbYCVq6aFE,33133
 biocypher/_translate.py,sha256=9E19eLRL0VnxxDuiNhZ5vu54XyKXnfLuBhCgNcL9yAE,17000
@@ -26,7 +26,7 @@ biocypher/output/in_memory/_networkx.py,sha256=cSOSAreP7S3oeGT6noZ1kAIvSnkVnU3NU
 biocypher/output/in_memory/_pandas.py,sha256=Ot2jbK5t_YLHqw0BUv9Z_qWNy9r6IX1LYEyejOSJzos,3288
 biocypher/output/write/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/write/_batch_writer.py,sha256=_Dao7z4KN0Uhr86oOOWYEDrIUikR7T0v1SJC2Btd8Y4,38745
-biocypher/output/write/_get_writer.py,sha256=xaZXoid0UP2uG_Z0XBJFpPXjmBRoKaBRNQG61iA7Rk8,4379
+biocypher/output/write/_get_writer.py,sha256=JozRWCMhvh65aQAlcGiiD5x3Nl1HSW8mK1Zf2nTSOzI,4385
 biocypher/output/write/_writer.py,sha256=y0dWI-RyQdrBLr9Fs91Y9KcCMjnlCaKJT0eWsIS2hG4,7158
 biocypher/output/write/graph/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biocypher/output/write/graph/_arangodb.py,sha256=xue3hm_DVB5pMR5qqfGXlXll3RpILA0tXos2J-as1-E,7906
@@ -38,7 +38,7 @@ biocypher/output/write/relational/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeR
 biocypher/output/write/relational/_csv.py,sha256=m0BSQXts88Qu5AEvoIgnwRz54ia38g4VN3PaA3LCYM8,2807
 biocypher/output/write/relational/_postgresql.py,sha256=RckQJBiuwvDmHAyXxS8zCavYqDecHHWW_piofurokfQ,11965
 biocypher/output/write/relational/_sqlite.py,sha256=BuGWOeeNA83lbUvjpkzqcR9_baWLsbfmLXBKe4O1EPE,2105
-biocypher-0.9.0.dist-info/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
-biocypher-0.9.0.dist-info/METADATA,sha256=uhjbUoT1ZgKl0Rwk_vTiZOv5nOi7KUBQztsbVQehHJI,10643
-biocypher-0.9.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biocypher-0.9.0.dist-info/RECORD,,
+biocypher-0.9.1.dist-info/LICENSE,sha256=oejgxuxyjSnyPw3YPloz6-dCBB_nYizJ4jDQnr-xZUU,1082
+biocypher-0.9.1.dist-info/METADATA,sha256=Qjy-T-iNXAn0wye7-NbLivn7ZPz80ZrOu8utum7_4vk,10643
+biocypher-0.9.1.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+biocypher-0.9.1.dist-info/RECORD,,