Integration with rdflib-sqlalchemy, oxrdflib

davidshumway commented 2 years ago

Perhaps this is a Google Colab-only issue?

!pip install rdflib-sqlalchemy
import kglab
from rdflib import plugin, Graph, Literal, URIRef
from rdflib.store import Store
store = plugin.get("SQLAlchemy", Store)(identifier=URIRef("rdflib_test"))
graph = Graph(store)
graph.open(Literal("sqlite://"), create=True)
kg = kglab.KnowledgeGraph(
  name = "...",
  import_graph = graph
)

AttributeError Traceback (most recent call last)
in () ---> 50 import_graph = graph 51 ) 3 frames /content/gdrive/MyDrive/ONR/kglab/kglab/kglab.py in __init__(self, name, base_uri, language, use_gpus, import_graph, namespaces) 111 112 # import relations from another RDF graph, or start from blank --> 113 if import_graph: 114 self._g = import_graph 115 else: /usr/local/lib/python3.7/dist-packages/rdflib/graph.py in __len__(self) 527 return 1 528 --> 529 def __eq__(self, other): 530 return isinstance(other, Graph) and self.identifier == other.identifier 531 /usr/local/lib/python3.7/dist-packages/rdflib_sqlalchemy/store.py in __len__(self, context) 205 (literal, literalContext, 206 ASSERTED_LITERAL_PARTITION), ] --> 207 q = union_select(selects, distinct=True, select_type=COUNT_SELECT) 208 else: 209 selects = [ /usr/local/lib/python3.7/dist-packages/rdflib_sqlalchemy/sql.py in union_select(select_components, distinct, select_type) 54 55 if select_type == COUNT_SELECT: ---> 56 select_clause = table.count(whereClause) 57 elif select_type == CONTEXT_SELECT: 58 select_clause = expression.select([table.c.context], whereClause) AttributeError: 'Alias' object has no attribute 'count'

And oxrdflib:

!pip install oxrdflib
import kglab
import rdflib
kg = kglab.KnowledgeGraph(
  name = "...",
  import_graph = rdflib.Graph(store="OxMemory")
)

ModuleNotFoundError Traceback (most recent call last)
in () ---> 49 import_graph = rdflib.Graph(store="OxMemory") 51 ) 3 frames /content/gdrive/MyDrive/ONR/kglab/kglab/kglab.py in __init__(self, name, base_uri, language, use_gpus, import_graph, namespaces) 114 self._g = import_graph 115 else: --> 116 self._g = rdflib.Graph() 117 118 # initialize the namespaces /usr/local/lib/python3.7/dist-packages/rdflib/graph.py in __init__(self, store, identifier, namespace_manager, base) 325 if self.__namespace_manager is None: 326 self.__namespace_manager = NamespaceManager(self) --> 327 return self.__namespace_manager 328 329 def _set_namespace_manager(self, nm): /usr/local/lib/python3.7/dist-packages/rdflib/plugin.py in get(name, kind) 108 109 --> 110 try: 111 from pkg_resources import iter_entry_points 112 except ImportError: /usr/local/lib/python3.7/dist-packages/rdflib/plugin.py in getClass(self) 69 module = __import__(self.module_path, globals(), locals(), [""]) 70 self._class = getattr(module, self.class_name) ---> 71 return self._class 72 73 ModuleNotFoundError: No module named 'rdflib.plugins.stores.memory'

ceteri commented 2 years ago

Hi @davidshumway, thank you for reporting this. We've begun to work with Oxrdflib and have support in v0.5.3 of kglab:

import kglab
kglab.KnowledgeGraph(store="Oxigraph")

NB: note the change in the name of the store, as of Oxrdflib v0.3.0 on 2022-03-19 https://github.com/oxigraph/oxrdflib/releases/tag/v0.3.0

Pros:

Speed; we've measured cases of SPARQL queries where Oxrdflib runs ~2 orders of magnitude faster than the default RDFlib.Store implementation.

Cons:

Oxrdflib has some troubles with namespaces ... specifically, any prefixes used in a namespace must be explicitly added to each SPARQL query
binding variables do not appear to be working
result rows from a query differ from the default impl when there are OPTIONAL clauses
Oxrdflib uses setup.py to register its RDFlib plugins and it's not clear that this is working properly

We've been able to isolate these issues with a minimum Python code + RDF + SPARQL example, and I'll be opening an issue for Oxrdflib which is linked to this issue.

DerwenAI / kglab

Integration with rdflib-sqlalchemy, oxrdflib #203