Test pioxigraph

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - ase 
   - ipycytoscape
   - networkx
-  - sqlalchemy <2.0.0
-  - rdflib-sqlalchemy
+  - pyoxigraph
+  - oxrdflib
   - pandas
   - owlready2

pyscal_rdf/graph.py

@@ -54,33 +54,29 @@ class RDFGraph:
     def __init__(self, graph_file=None, 
         store="Memory", 
         store_file=None,
-        identifier="default_graph"):
+        identifier="http://default_graph"):
 
         #owlfile = os.path.join(os.path.dirname(__file__), "data/cmso.owl")
         #self.graph.parse(owlfile, format='xml')
         if store == "Memory":
             self.graph = Graph(store="Memory", identifier=identifier)
 
-        elif store=="SQLAlchemy":
-            if store_file is None:
-                raise ValueError("store file is needed if store is not memory")
-            self.graph = Graph(store="SQLAlchemy", identifier=identifier)
-            uri = Literal(f"sqlite:///{store_file}")
-            self.graph.open(uri, create=True)
-
+        elif store=="Oxigraph":
+            self.graph = Graph(store="Oxigraph", identifier=identifier)
+            if store_file is not None:
+                self.graph.open(store_file)
+
         elif inspect.isclass(type(store)):
             try:
                 prpath = store.path
-                dbfile = os.path.join(prpath, 'project.db')
                 #now start sqlalchemy instance
-                self.graph = Graph(store="SQLAlchemy", identifier=identifier)
-                uri = Literal(f"sqlite:///{dbfile}")
-                self.graph.open(uri, create=True)
+                self.graph = Graph(store="Oxigraph", identifier=identifier)
+                self.graph.open(prpath)
             except:
-                raise ValueError("store should be pyiron_project, SQLAlchemy, or Memory")
+                raise ValueError("store should be pyiron_project, Oxigraph, or Memory")
 
         else:
-            raise ValueError("store should be pyiron_project, SQLAlchemy, or Memory")
+            raise ValueError("store should be pyiron_project, Oxigraph, or Memory")
 
         self.graph.bind("cmso", CMSO)
         self.graph.bind("pldo", PLDO)

pyscal_rdf/structure.py

@@ -98,7 +98,7 @@ class StructureGraph(RDFGraph):
     def __init__(self, graph_file=None, 
         store="Memory", 
         store_file=None,
-        identifier="default_graph"):
+        identifier="http://default_graph"):
 
         super().__init__(graph_file=graph_file, store=store, store_file=store_file, identifier=identifier)
         self._element_dict = element_dict