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recalcitrantsupplantnicholascarashleysommer
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Add initial implementation of RDF Patch parser. (#2863)
* Add initial implementation of RDF Patch parser. * Add example, run Black & Ruff * Ruff again * Add docstring for Patch Operations + add class to All declaration to fix sphinx build. * Black again * Add parsing of <_:identifier> style bnodes; switch to line by line parsing. * Remove unused mypy comment. * Add mypy exclusions (comments); the code will not enter these methods if self.line is None in the first place. * Remove mypy comment. * Add ignore to 181. * Add RDF Patch to Parser documentation. * Correct Patch Parser Name. Remove unnecssary return statements. * Remove unneccessary deskolemize from examples. * Attempt to fix failing test. --------- Co-authored-by: Nicholas Car <[email protected]> Co-authored-by: Ashley Sommer <[email protected]>
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‎docs/plugin_parsers.rst

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@@ -24,6 +24,7 @@ json-ld :class:`~rdflib.plugins.parsers.jsonld.JsonLDParser`
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hext :class:`~rdflib.plugins.parsers.hext.HextuplesParser`
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n3 :class:`~rdflib.plugins.parsers.notation3.N3Parser`
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nquads :class:`~rdflib.plugins.parsers.nquads.NQuadsParser`
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patch :class:`~rdflib.plugins.parsers.patch.RDFPatchParser`
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nt :class:`~rdflib.plugins.parsers.ntriples.NTParser`
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trix :class:`~rdflib.plugins.parsers.trix.TriXParser`
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turtle :class:`~rdflib.plugins.parsers.notation3.TurtleParser`

‎examples/parse_patch.py

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from rdflib import Dataset
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def main():
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# RDF patch data
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add_patch = """
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TX .
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A _:bn1 <http://example.org/predicate1> "object1" .
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A _:bn1 <http://example.org/predicate2> "object2" .
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TC .
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"""
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delete_patch = """
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TX .
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D _:bn1 <http://example.org/predicate1> "object1" .
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TC .
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"""
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ds = Dataset()
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# Apply add patch
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ds.parse(data=add_patch, format="patch")
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print("After add patch:")
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for triple in ds:
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print(triple)
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# Apply delete patch
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ds.parse(data=delete_patch, format="patch")
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print("After delete patch:")
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for triple in ds:
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print(triple)
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if __name__ == "__main__":
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main()

‎rdflib/plugin.py

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@@ -488,6 +488,14 @@ def plugins(
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"HextuplesParser",
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)
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# Register RDF Patch Parsers
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register(
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"patch",
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Parser,
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"rdflib.plugins.parsers.patch",
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"RDFPatchParser",
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)
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# Register SPARQL Processors
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register(
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"sparql",

‎rdflib/plugins/parsers/patch.py

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from __future__ import annotations
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from codecs import getreader
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from enum import Enum
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from typing import TYPE_CHECKING, Any, MutableMapping, Optional, Union
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from rdflib.exceptions import ParserError as ParseError
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from rdflib.graph import Dataset
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from rdflib.parser import InputSource
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from rdflib.plugins.parsers.nquads import NQuadsParser
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# Build up from the NTriples parser:
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from rdflib.plugins.parsers.ntriples import r_nodeid, r_tail, r_uriref, r_wspace
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from rdflib.term import BNode, URIRef
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if TYPE_CHECKING:
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import typing_extensions as te
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__all__ = ["RDFPatchParser", "Operation"]
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_BNodeContextType = MutableMapping[str, BNode]
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class Operation(Enum):
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"""
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Enum of RDF Patch operations.
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Operations:
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- `AddTripleOrQuad` (A): Adds a triple or quad.
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- `DeleteTripleOrQuad` (D): Deletes a triple or quad.
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- `AddPrefix` (PA): Adds a prefix.
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- `DeletePrefix` (PD): Deletes a prefix.
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- `TransactionStart` (TX): Starts a transaction.
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- `TransactionCommit` (TC): Commits a transaction.
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- `TransactionAbort` (TA): Aborts a transaction.
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- `Header` (H): Specifies a header.
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"""
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AddTripleOrQuad = "A"
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DeleteTripleOrQuad = "D"
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AddPrefix = "PA"
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DeletePrefix = "PD"
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TransactionStart = "TX"
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TransactionCommit = "TC"
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TransactionAbort = "TA"
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Header = "H"
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class RDFPatchParser(NQuadsParser):
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def parse( # type: ignore[override]
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self,
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inputsource: InputSource,
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sink: Dataset,
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bnode_context: Optional[_BNodeContextType] = None,
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skolemize: bool = False,
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**kwargs: Any,
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) -> Dataset:
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"""
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Parse inputsource as an RDF Patch file.
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:type inputsource: `rdflib.parser.InputSource`
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:param inputsource: the source of RDF Patch formatted data
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:type sink: `rdflib.graph.Dataset`
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:param sink: where to send parsed data
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:type bnode_context: `dict`, optional
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:param bnode_context: a dict mapping blank node identifiers to `~rdflib.term.BNode` instances.
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See `.W3CNTriplesParser.parse`
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"""
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assert sink.store.context_aware, (
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"RDFPatchParser must be given" " a context aware store."
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)
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# type error: Incompatible types in assignment (expression has type "ConjunctiveGraph", base class "W3CNTriplesParser" defined the type as "Union[DummySink, NTGraphSink]")
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self.sink: Dataset = Dataset(store=sink.store)
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self.skolemize = skolemize
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source = inputsource.getCharacterStream()
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if not source:
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source = inputsource.getByteStream()
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source = getreader("utf-8")(source)
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if not hasattr(source, "read"):
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raise ParseError("Item to parse must be a file-like object.")
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self.file = source
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self.buffer = ""
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while True:
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self.line = __line = self.readline()
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if self.line is None:
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break
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try:
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self.parsepatch(bnode_context)
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except ParseError as msg:
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raise ParseError("Invalid line (%s):\n%r" % (msg, __line))
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return self.sink
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def parsepatch(self, bnode_context: Optional[_BNodeContextType] = None) -> None:
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self.eat(r_wspace)
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# From spec: "No comments should be included (comments start # and run to end
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# of line)."
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if (not self.line) or self.line.startswith("#"):
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return # The line is empty or a comment
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# if header, transaction, skip
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operation = self.operation()
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self.eat(r_wspace)
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if operation in [Operation.AddTripleOrQuad, Operation.DeleteTripleOrQuad]:
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self.add_or_remove_triple_or_quad(operation, bnode_context)
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elif operation == Operation.AddPrefix:
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self.add_prefix()
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elif operation == Operation.DeletePrefix:
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self.delete_prefix()
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def add_or_remove_triple_or_quad(
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self, operation, bnode_context: Optional[_BNodeContextType] = None
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) -> None:
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self.eat(r_wspace)
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if (not self.line) or self.line.startswith("#"):
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return # The line is empty or a comment
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subject = self.labeled_bnode() or self.subject(bnode_context)
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self.eat(r_wspace)
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predicate = self.predicate()
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self.eat(r_wspace)
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obj = self.labeled_bnode() or self.object(bnode_context)
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self.eat(r_wspace)
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context = self.labeled_bnode() or self.uriref() or self.nodeid(bnode_context)
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self.eat(r_tail)
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if self.line:
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raise ParseError("Trailing garbage")
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# Must have a context aware store - add on a normal Graph
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# discards anything where the ctx != graph.identifier
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if operation == Operation.AddTripleOrQuad:
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if context:
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self.sink.get_context(context).add((subject, predicate, obj))
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else:
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self.sink.default_context.add((subject, predicate, obj))
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elif operation == Operation.DeleteTripleOrQuad:
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if context:
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self.sink.get_context(context).remove((subject, predicate, obj))
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else:
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self.sink.default_context.remove((subject, predicate, obj))
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def add_prefix(self):
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# Extract prefix and URI from the line
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prefix, ns, _ = self.line.replace('"', "").replace("'", "").split(" ") # type: ignore[union-attr]
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ns_stripped = ns.strip("<>")
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self.sink.bind(prefix, ns_stripped)
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def delete_prefix(self):
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prefix, _, _ = self.line.replace('"', "").replace("'", "").split(" ") # type: ignore[union-attr]
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self.sink.namespace_manager.bind(prefix, None, replace=True)
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def operation(self) -> Operation:
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for op in Operation:
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if self.line.startswith(op.value): # type: ignore[union-attr]
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self.eat_op(op.value)
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return op
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raise ValueError(
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f'Invalid or no Operation found in line: "{self.line}". Valid Operations '
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f"codes are {', '.join([op.value for op in Operation])}"
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)
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def eat_op(self, op: str) -> None:
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self.line = self.line.lstrip(op) # type: ignore[union-attr]
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def nodeid(
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self, bnode_context: Optional[_BNodeContextType] = None
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) -> Union[te.Literal[False], BNode, URIRef]:
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if self.peek("_"):
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return BNode(self.eat(r_nodeid).group(1))
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return False
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def labeled_bnode(self):
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if self.peek("<_"):
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plain_uri = self.eat(r_uriref).group(1)
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bnode_id = r_nodeid.match(plain_uri).group(1) # type: ignore[union-attr]
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return BNode(bnode_id)
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return False

‎test/data/patch/add_and_delete_bnode_triples.rdp

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TX .
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A _:bn1 <http://example.org/predicate1> "object1" <http://example.org/graph1> .
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A _:bn1 <http://example.org/predicate2> "object2" <http://example.org/graph1> .
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A _:bn1 <http://example.org/predicate3> "object3" <http://example.org/graph1> .
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D _:bn1 <http://example.org/predicate2> "object2" <http://example.org/graph1> .
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TC .

‎test/data/patch/add_and_delete_labeled_bnode_quads.rdp

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TX .
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A <_:bn1> <http://example.org/predicate1> "object1" <http://example.org/graph1> .
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A <_:bn1> <http://example.org/predicate2> "object2" <http://example.org/graph1> .
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A <_:bn1> <http://example.org/predicate3> "object3" <http://example.org/graph1> .
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D <_:bn1> <http://example.org/predicate2> "object2" <http://example.org/graph1> .
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TC .

‎test/data/patch/add_and_delete_prefix.rdp

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TX .
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PA present <http://some-other-ns#> .
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PA removed <http://ns-for-prefix-to-remove#> .
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PD removed <http://ns-for-prefix-to-remove#> .
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A <http://ns-for-prefix-to-remove#test-subj> <http://ns-for-prefix-to-remove#test-pred> "object1" .
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TC .

‎test/data/patch/add_and_delete_triples.rdp

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TX .
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A <http://example.org/subject1> <http://example.org/predicate1> "object1" .
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A <http://example.org/subject1> <http://example.org/predicate2> "object2" <http://example.org/graph1> .
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D <http://example.org/subject1> <http://example.org/predicate1> "object1" .
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D <http://example.org/subject1> <http://example.org/predicate2> "object2" <http://example.org/graph1> .
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TC .

‎test/data/patch/add_bnode_graph.rdp

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TX .
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A _:bn1 <http://example.org/predicate1> "object1" _:bn1 .
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TC .

‎test/data/patch/add_bnode_quad.rdp

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TX .
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A _:bn1 <http://example.org/predicate1> "object1" <https://graph-1> .
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TC .

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