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How can I assist you with this file?\r\n\r\nUSER: Please help me debug my code. I can insert triples into the `PersistentGraph`, but when I try to loop through the triples like `self.triples((None, NOne, None))`, nothing is returned.\r\n\r\nASSISTANT: It seems like the issue might be related to how the triples are being inserted and then queried. Given the description of the problem, it's possible that the triples are being inserted into a specific graph context within the `PersistentGraph`, but when querying with `self.triples((None, None, None))`, it's attempting to query the default graph context which might not contain any triples.\r\n\r\nTo address this, we need to ensure that when querying for triples, we're querying across all graph contexts if that's the intended behavior. 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If your application relies on querying specific contexts, ensure that the context is correctly specified when calling the `triples` method.\r\n\r\n* try new version of dependency\r\n\r\n* bump rdflib dep, version","shortMessageHtmlLink":"Trying rdflib-sqlalchemy fork (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2139614895\" data-permission-text=\"Title is private\" data-url=\"https://github.com/BrickSchema/py-brickschema/issues/110\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/BrickSchema/py-brickschema/pull/110/hovercard\" href=\"https://github.com/BrickSchema/py-brickschema/pull/110\">#110</a>)"}},{"before":"65c21ee01ad28180c2a1b6711be6040187ee7903","after":"7b5cf906f3790c2318d4a0f249b7f86d48e8cd4a","ref":"refs/heads/trying-diff-package","pushedAt":"2024-02-21T15:49:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"gtfierro","name":"Gabe 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Since you've performed a hard reset to undo the last commit, I will now provide the changes to revert the `expand` method and the `_expand_helper` method to their state before the commit with hash `b27e5cc`.\r\n\r\nHere are the diffs for those changes:\r\n\r\n```diff\r\n--- brickschema/graph.py\r\n+++ brickschema/graph.py\r\n@@ ... @@\r\n     def expand(\r\n         self, profile, backend=None, simplify=True, ontology_graph=None, iterative=True\r\n     ):\r\n         \"\"\"\r\n         Expands the current graph with the inferred triples under the given entailment regime\r\n         and with the given backend. Possible profiles are:\r\n         - 'rdfs': runs RDFS rules\r\n         - 'owlrl': runs full OWLRL reasoning\r\n         - 'vbis': adds VBIS tags\r\n         - 'shacl': does SHACL-AF reasoning (including tag inference, if the extension is loaded)\r\n@@ ... @@\r\n         elif profile == \"owlrl\":\r\n-            self._inferbackend = OWLRLNaiveInferenceSession()\r\n-            try:\r\n-                if backend is None or backend == \"reasonable\":\r\n-                    self._inferbackend = OWLRLReasonableInferenceSession()\r\n-                    backend = \"reasonable\"\r\n-            except ImportError:\r\n-                warn(\r\n-                    \"Could not load Reasonable reasoner. Needs 'reasonable' option during install.\"\r\n-                )\r\n-                self._inferbackend = OWLRLNaiveInferenceSession()\r\n-\r\n-            try:\r\n-                if backend is None or backend == \"allegrograph\":\r\n-                    self._inferbackend = OWLRLAllegroInferenceSession()\r\n-                    backend = \"allegrograph\"\r\n-            except (ImportError, ConnectionError):\r\n-                warn(\r\n-                    \"Could not load Allegro reasoner. Needs 'allegro' option during install.\"\r\n-                )\r\n-                self._inferbackend = OWLRLNaiveInferenceSession()\r\n+            self._inferbackend = OWLRLReasonableInferenceSession()\r\n         elif profile == \"vbis\":\r\n             self._inferbackend = VBISTagInferenceSession(\r\n                 brick_version=self._brick_version\r\n             )\r\n         else:\r\n             raise Exception(f\"Invalid profile '{profile}'\")\r\n-        self._inferbackend.expand(self)\r\n+        OWLRLNaiveInferenceSession().expand(self)\r\n\r\n         if simplify:\r\n             self.simplify()\r\n         return self\r\n```\r\n\r\nThis diff will revert the changes made to the `expand` method in the `brickschema/graph.py` file, effectively undoing the commit with hash `b27e5cc`.\r\n\r\n* issues with bnodes mean some of these need to use pyshacl\r\n\r\n* bump versions\r\n\r\n* handling skolemization of the data graph\r\n\r\n* remove extra bnodes -- they should all be skolemized\r\n\r\n* fixing topquadrant inferenc to use maxiterations and skolemize to preserve bnode identities\r\n\r\nReverted changes to the `expand` method in `brickschema/graph.py`.\r\n\r\nUSER: I did `git reset --hard HEAD~1` to discard the last edits.\r\n\r\nASSISTANT: Understood. Since you've performed a hard reset to undo the last commit, I will now provide the changes to revert the `expand` method and the `_expand_helper` method to their state before the commit with hash `b27e5cc`.\r\n\r\nHere are the diffs for those changes:\r\n\r\n```diff\r\n--- brickschema/graph.py\r\n+++ brickschema/graph.py\r\n@@ ... @@\r\n     def expand(\r\n         self, profile, backend=None, simplify=True, ontology_graph=None, iterative=True\r\n     ):\r\n         \"\"\"\r\n         Expands the current graph with the inferred triples under the given entailment regime\r\n         and with the given backend. Possible profiles are:\r\n         - 'rdfs': runs RDFS rules\r\n         - 'owlrl': runs full OWLRL reasoning\r\n         - 'vbis': adds VBIS tags\r\n         - 'shacl': does SHACL-AF reasoning (including tag inference, if the extension is loaded)\r\n@@ ... @@\r\n         elif profile == \"owlrl\":\r\n-            self._inferbackend = OWLRLNaiveInferenceSession()\r\n-            try:\r\n-                if backend is None or backend == \"reasonable\":\r\n-                    self._inferbackend = OWLRLReasonableInferenceSession()\r\n-                    backend = \"reasonable\"\r\n-            except ImportError:\r\n-                warn(\r\n-                    \"Could not load Reasonable reasoner. Needs 'reasonable' option during install.\"\r\n-                )\r\n-                self._inferbackend = OWLRLNaiveInferenceSession()\r\n-\r\n-            try:\r\n-                if backend is None or backend == \"allegrograph\":\r\n-                    self._inferbackend = OWLRLAllegroInferenceSession()\r\n-                    backend = \"allegrograph\"\r\n-            except (ImportError, ConnectionError):\r\n-                warn(\r\n-                    \"Could not load Allegro reasoner. Needs 'allegro' option during install.\"\r\n-                )\r\n-                self._inferbackend = OWLRLNaiveInferenceSession()\r\n+            self._inferbackend = OWLRLReasonableInferenceSession()\r\n         elif profile == \"vbis\":\r\n             self._inferbackend = VBISTagInferenceSession(\r\n                 brick_version=self._brick_version\r\n             )\r\n         else:\r\n             raise Exception(f\"Invalid profile '{profile}'\")\r\n-        self._inferbackend.expand(self)\r\n+        OWLRLNaiveInferenceSession().expand(self)\r\n\r\n         if simplify:\r\n             self.simplify()\r\n         return self\r\n```\r\n\r\nThis diff will revert the changes made to the `expand` method in the `brickschema/graph.py` file, effectively undoing the commit with hash `b27e5cc`.\r\n\r\n* issues with bnodes mean some of these need to use pyshacl\r\n\r\n* bump versions\r\n\r\n* handling skolemization of the data graph\r\n\r\n* remove extra bnodes -- they should all be skolemized\r\n\r\n* new skolemize function to deal with spaces in literals\r\n\r\n* Replace `infer` function to run shaclinfer multiple times until skolemized data graph stops changing in size. 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