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langchain[minor], community[minor]: Implement Ontotext GraphDB QA Chain (#16019)
- **Description:** Implement Ontotext GraphDB QA Chain - **Issue:** N/A - **Dependencies:** N/A - **Twitter handle:** @OntotextGraphDB
This commit is contained in:
Neli Hateva
GitHub
@@ -0,0 +1,213 @@
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from __future__ import annotations
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import os
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from typing import (
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TYPE_CHECKING,
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List,
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Optional,
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Union,
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)
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if TYPE_CHECKING:
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import rdflib
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class OntotextGraphDBGraph:
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"""Ontotext GraphDB https://graphdb.ontotext.com/ wrapper for graph operations.
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*Security note*: Make sure that the database connection uses credentials
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that are narrowly-scoped to only include necessary permissions.
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Failure to do so may result in data corruption or loss, since the calling
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code may attempt commands that would result in deletion, mutation
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of data if appropriately prompted or reading sensitive data if such
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data is present in the database.
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The best way to guard against such negative outcomes is to (as appropriate)
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limit the permissions granted to the credentials used with this tool.
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See https://python.langchain.com/docs/security for more information.
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"""
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def __init__(
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self,
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query_endpoint: str,
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query_ontology: Optional[str] = None,
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local_file: Optional[str] = None,
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local_file_format: Optional[str] = None,
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) -> None:
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"""
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Set up the GraphDB wrapper
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:param query_endpoint: SPARQL endpoint for queries, read access
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If GraphDB is secured,
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set the environment variables 'GRAPHDB_USERNAME' and 'GRAPHDB_PASSWORD'.
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:param query_ontology: a `CONSTRUCT` query that is executed
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on the SPARQL endpoint and returns the KG schema statements
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Example:
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'CONSTRUCT {?s ?p ?o} FROM <https://example.com/ontology/> WHERE {?s ?p ?o}'
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Currently, DESCRIBE queries like
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'PREFIX onto: <https://example.com/ontology/>
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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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DESCRIBE ?term WHERE {
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?term rdfs:isDefinedBy onto:
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}'
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are not supported, because DESCRIBE returns
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the Symmetric Concise Bounded Description (SCBD),
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i.e. also the incoming class links.
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In case of large graphs with a million of instances, this is not efficient.
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Check https://github.com/eclipse-rdf4j/rdf4j/issues/4857
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:param local_file: a local RDF ontology file.
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Supported RDF formats:
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Turtle, RDF/XML, JSON-LD, N-Triples, Notation-3, Trig, Trix, N-Quads.
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If the rdf format can't be determined from the file extension,
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pass explicitly the rdf format in `local_file_format` param.
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:param local_file_format: Used if the rdf format can't be determined
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from the local file extension.
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One of "json-ld", "xml", "n3", "turtle", "nt", "trig", "nquads", "trix"
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Either `query_ontology` or `local_file` should be passed.
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"""
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if query_ontology and local_file:
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raise ValueError("Both file and query provided. Only one is allowed.")
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if not query_ontology and not local_file:
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raise ValueError("Neither file nor query provided. One is required.")
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try:
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import rdflib
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from rdflib.plugins.stores import sparqlstore
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except ImportError:
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raise ValueError(
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"Could not import rdflib python package. "
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"Please install it with `pip install rdflib`."
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)
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auth = self._get_auth()
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store = sparqlstore.SPARQLStore(auth=auth)
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store.open(query_endpoint)
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self.graph = rdflib.Graph(store, identifier=None, bind_namespaces="none")
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self._check_connectivity()
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if local_file:
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ontology_schema_graph = self._load_ontology_schema_from_file(
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local_file, local_file_format
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)
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else:
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self._validate_user_query(query_ontology)
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ontology_schema_graph = self._load_ontology_schema_with_query(
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query_ontology
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)
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self.schema = ontology_schema_graph.serialize(format="turtle")
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@staticmethod
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def _get_auth() -> Union[tuple, None]:
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"""
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Returns the basic authentication configuration
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"""
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username = os.environ.get("GRAPHDB_USERNAME", None)
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password = os.environ.get("GRAPHDB_PASSWORD", None)
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if username:
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if not password:
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raise ValueError(
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"Environment variable 'GRAPHDB_USERNAME' is set, "
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"but 'GRAPHDB_PASSWORD' is not set."
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)
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else:
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return username, password
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return None
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def _check_connectivity(self) -> None:
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"""
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Executes a simple `ASK` query to check connectivity
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"""
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try:
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self.graph.query("ASK { ?s ?p ?o }")
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except ValueError:
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raise ValueError(
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"Could not query the provided endpoint. "
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"Please, check, if the value of the provided "
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"query_endpoint points to the right repository. "
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"If GraphDB is secured, please, "
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"make sure that the environment variables "
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"'GRAPHDB_USERNAME' and 'GRAPHDB_PASSWORD' are set."
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)
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@staticmethod
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def _load_ontology_schema_from_file(local_file: str, local_file_format: str = None):
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"""
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Parse the ontology schema statements from the provided file
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"""
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import rdflib
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if not os.path.exists(local_file):
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raise FileNotFoundError(f"File {local_file} does not exist.")
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if not os.access(local_file, os.R_OK):
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raise PermissionError(f"Read permission for {local_file} is restricted")
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graph = rdflib.ConjunctiveGraph()
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try:
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graph.parse(local_file, format=local_file_format)
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except Exception as e:
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raise ValueError(f"Invalid file format for {local_file} : ", e)
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return graph
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@staticmethod
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def _validate_user_query(query_ontology: str) -> None:
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"""
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Validate the query is a valid SPARQL CONSTRUCT query
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"""
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from pyparsing import ParseException
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from rdflib.plugins.sparql import prepareQuery
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if not isinstance(query_ontology, str):
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raise TypeError("Ontology query must be provided as string.")
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try:
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parsed_query = prepareQuery(query_ontology)
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except ParseException as e:
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raise ValueError("Ontology query is not a valid SPARQL query.", e)
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if parsed_query.algebra.name != "ConstructQuery":
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raise ValueError(
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"Invalid query type. Only CONSTRUCT queries are supported."
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)
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def _load_ontology_schema_with_query(self, query: str):
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"""
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Execute the query for collecting the ontology schema statements
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"""
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from rdflib.exceptions import ParserError
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try:
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results = self.graph.query(query)
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except ParserError as e:
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raise ValueError(f"Generated SPARQL statement is invalid\n{e}")
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return results.graph
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@property
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def get_schema(self) -> str:
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"""
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Returns the schema of the graph database in turtle format
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"""
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return self.schema
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def query(
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self,
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query: str,
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) -> List[rdflib.query.ResultRow]:
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"""
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Query the graph.
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"""
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from rdflib.exceptions import ParserError
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from rdflib.query import ResultRow
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try:
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res = self.graph.query(query)
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except ParserError as e:
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raise ValueError(f"Generated SPARQL statement is invalid\n{e}")
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return [r for r in res if isinstance(r, ResultRow)]
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