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Enhance retrieval pipelines: 4-stage GraphRAG, DocRAG grounding (#697)
Enhance retrieval pipelines: 4-stage GraphRAG, DocRAG grounding, consistent PROV-O GraphRAG: - Split retrieval into 4 prompt stages: extract-concepts, kg-edge-scoring, kg-edge-reasoning, kg-synthesis (was single-stage) - Add concept extraction (grounding) for per-concept embedding - Filter main query to default graph, ignoring provenance/explainability edges - Add source document edges to knowledge graph DocumentRAG: - Add grounding step with concept extraction, matching GraphRAG's pattern: Question → Grounding → Exploration → Synthesis - Per-concept embedding and chunk retrieval with deduplication Cross-pipeline: - Make PROV-O derivation links consistent: wasGeneratedBy for first entity from Activity, wasDerivedFrom for entity-to-entity chains - Update CLIs (tg-invoke-agent, tg-invoke-graph-rag, tg-invoke-document-rag) for new explainability structure - Fix all affected unit and integration tests
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25 changed files with 1537 additions and 1008 deletions
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@ -15,10 +15,11 @@ from trustgraph.provenance.agent import (
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from trustgraph.provenance.namespaces import (
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RDF_TYPE, RDFS_LABEL,
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PROV_ACTIVITY, PROV_ENTITY, PROV_WAS_DERIVED_FROM, PROV_STARTED_AT_TIME,
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TG_QUERY, TG_THOUGHT, TG_ACTION, TG_ARGUMENTS, TG_OBSERVATION, TG_ANSWER,
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PROV_ACTIVITY, PROV_ENTITY, PROV_WAS_DERIVED_FROM,
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PROV_WAS_GENERATED_BY, PROV_STARTED_AT_TIME,
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TG_QUERY, TG_THOUGHT, TG_ACTION, TG_ARGUMENTS, TG_OBSERVATION,
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TG_QUESTION, TG_ANALYSIS, TG_CONCLUSION, TG_DOCUMENT,
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TG_THOUGHT_DOCUMENT, TG_OBSERVATION_DOCUMENT,
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TG_ANSWER_TYPE, TG_REFLECTION_TYPE, TG_THOUGHT_TYPE, TG_OBSERVATION_TYPE,
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TG_AGENT_QUESTION,
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)
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@ -110,84 +111,107 @@ class TestAgentSessionTriples:
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class TestAgentIterationTriples:
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ITER_URI = "urn:trustgraph:agent:test-session/i1"
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PARENT_URI = "urn:trustgraph:agent:test-session"
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SESSION_URI = "urn:trustgraph:agent:test-session"
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PREV_URI = "urn:trustgraph:agent:test-session/i0"
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def test_iteration_types(self):
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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thought="thinking", action="search", observation="found it",
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="search",
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)
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assert has_type(triples, self.ITER_URI, PROV_ENTITY)
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assert has_type(triples, self.ITER_URI, TG_ANALYSIS)
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def test_iteration_derived_from_parent(self):
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def test_first_iteration_generated_by_question(self):
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"""First iteration uses wasGeneratedBy to link to question activity."""
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="search",
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)
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gen = find_triple(triples, PROV_WAS_GENERATED_BY, self.ITER_URI)
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assert gen is not None
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assert gen.o.iri == self.SESSION_URI
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# Should NOT have wasDerivedFrom
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derived = find_triple(triples, PROV_WAS_DERIVED_FROM, self.ITER_URI)
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assert derived is None
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def test_subsequent_iteration_derived_from_previous(self):
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"""Subsequent iterations use wasDerivedFrom to link to previous iteration."""
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triples = agent_iteration_triples(
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self.ITER_URI, previous_uri=self.PREV_URI,
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action="search",
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)
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derived = find_triple(triples, PROV_WAS_DERIVED_FROM, self.ITER_URI)
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assert derived is not None
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assert derived.o.iri == self.PARENT_URI
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assert derived.o.iri == self.PREV_URI
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# Should NOT have wasGeneratedBy
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gen = find_triple(triples, PROV_WAS_GENERATED_BY, self.ITER_URI)
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assert gen is None
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def test_iteration_label_includes_action(self):
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="graph-rag-query",
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)
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label = find_triple(triples, RDFS_LABEL, self.ITER_URI)
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assert label is not None
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assert "graph-rag-query" in label.o.value
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def test_iteration_thought_inline(self):
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def test_iteration_thought_sub_entity(self):
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"""Thought is a sub-entity with Reflection and Thought types."""
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thought_uri = "urn:trustgraph:agent:test-session/i1/thought"
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thought_doc = "urn:doc:thought-1"
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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thought="I need to search for info",
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="search",
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thought_uri=thought_uri,
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thought_document_id=thought_doc,
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)
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thought = find_triple(triples, TG_THOUGHT, self.ITER_URI)
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assert thought is not None
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assert thought.o.value == "I need to search for info"
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# Iteration links to thought sub-entity
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thought_link = find_triple(triples, TG_THOUGHT, self.ITER_URI)
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assert thought_link is not None
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assert thought_link.o.iri == thought_uri
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# Thought has correct types
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assert has_type(triples, thought_uri, TG_REFLECTION_TYPE)
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assert has_type(triples, thought_uri, TG_THOUGHT_TYPE)
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# Thought was generated by iteration
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gen = find_triple(triples, PROV_WAS_GENERATED_BY, thought_uri)
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assert gen is not None
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assert gen.o.iri == self.ITER_URI
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# Thought has document reference
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doc = find_triple(triples, TG_DOCUMENT, thought_uri)
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assert doc is not None
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assert doc.o.iri == thought_doc
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def test_iteration_thought_document_preferred(self):
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"""When thought_document_id is provided, inline thought is not stored."""
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def test_iteration_observation_sub_entity(self):
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"""Observation is a sub-entity with Reflection and Observation types."""
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obs_uri = "urn:trustgraph:agent:test-session/i1/observation"
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obs_doc = "urn:doc:obs-1"
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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thought="inline thought",
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="search",
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thought_document_id="urn:doc:thought-1",
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observation_uri=obs_uri,
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observation_document_id=obs_doc,
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)
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thought_doc = find_triple(triples, TG_THOUGHT_DOCUMENT, self.ITER_URI)
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assert thought_doc is not None
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assert thought_doc.o.iri == "urn:doc:thought-1"
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thought_inline = find_triple(triples, TG_THOUGHT, self.ITER_URI)
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assert thought_inline is None
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def test_iteration_observation_inline(self):
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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action="search",
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observation="Found 3 results",
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)
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obs = find_triple(triples, TG_OBSERVATION, self.ITER_URI)
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assert obs is not None
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assert obs.o.value == "Found 3 results"
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def test_iteration_observation_document_preferred(self):
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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action="search",
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observation="inline obs",
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observation_document_id="urn:doc:obs-1",
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)
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obs_doc = find_triple(triples, TG_OBSERVATION_DOCUMENT, self.ITER_URI)
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assert obs_doc is not None
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assert obs_doc.o.iri == "urn:doc:obs-1"
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obs_inline = find_triple(triples, TG_OBSERVATION, self.ITER_URI)
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assert obs_inline is None
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# Iteration links to observation sub-entity
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obs_link = find_triple(triples, TG_OBSERVATION, self.ITER_URI)
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assert obs_link is not None
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assert obs_link.o.iri == obs_uri
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# Observation has correct types
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assert has_type(triples, obs_uri, TG_REFLECTION_TYPE)
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assert has_type(triples, obs_uri, TG_OBSERVATION_TYPE)
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# Observation was generated by iteration
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gen = find_triple(triples, PROV_WAS_GENERATED_BY, obs_uri)
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assert gen is not None
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assert gen.o.iri == self.ITER_URI
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# Observation has document reference
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doc = find_triple(triples, TG_DOCUMENT, obs_uri)
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assert doc is not None
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assert doc.o.iri == obs_doc
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def test_iteration_action_recorded(self):
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="graph-rag-query",
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)
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action = find_triple(triples, TG_ACTION, self.ITER_URI)
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@ -197,7 +221,7 @@ class TestAgentIterationTriples:
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def test_iteration_arguments_json_encoded(self):
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args = {"query": "test query", "limit": 10}
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="search",
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arguments=args,
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)
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@ -208,7 +232,7 @@ class TestAgentIterationTriples:
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def test_iteration_default_arguments_empty_dict(self):
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="search",
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)
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arguments = find_triple(triples, TG_ARGUMENTS, self.ITER_URI)
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@ -219,7 +243,7 @@ class TestAgentIterationTriples:
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def test_iteration_no_thought_or_observation(self):
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"""Minimal iteration with just action — no thought or observation triples."""
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triples = agent_iteration_triples(
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self.ITER_URI, self.PARENT_URI,
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self.ITER_URI, question_uri=self.SESSION_URI,
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action="noop",
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)
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thought = find_triple(triples, TG_THOUGHT, self.ITER_URI)
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@ -228,19 +252,19 @@ class TestAgentIterationTriples:
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assert obs is None
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def test_iteration_chaining(self):
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"""Second iteration derives from first iteration, not session."""
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"""First iteration uses wasGeneratedBy, second uses wasDerivedFrom."""
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iter1_uri = "urn:trustgraph:agent:sess/i1"
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iter2_uri = "urn:trustgraph:agent:sess/i2"
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triples1 = agent_iteration_triples(
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iter1_uri, self.PARENT_URI, action="step1",
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iter1_uri, question_uri=self.SESSION_URI, action="step1",
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)
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triples2 = agent_iteration_triples(
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iter2_uri, iter1_uri, action="step2",
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iter2_uri, previous_uri=iter1_uri, action="step2",
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)
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derived1 = find_triple(triples1, PROV_WAS_DERIVED_FROM, iter1_uri)
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assert derived1.o.iri == self.PARENT_URI
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gen1 = find_triple(triples1, PROV_WAS_GENERATED_BY, iter1_uri)
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assert gen1.o.iri == self.SESSION_URI
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derived2 = find_triple(triples2, PROV_WAS_DERIVED_FROM, iter2_uri)
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assert derived2.o.iri == iter1_uri
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@ -253,42 +277,50 @@ class TestAgentIterationTriples:
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class TestAgentFinalTriples:
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FINAL_URI = "urn:trustgraph:agent:test-session/final"
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PARENT_URI = "urn:trustgraph:agent:test-session/i3"
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PREV_URI = "urn:trustgraph:agent:test-session/i3"
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SESSION_URI = "urn:trustgraph:agent:test-session"
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def test_final_types(self):
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triples = agent_final_triples(
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self.FINAL_URI, self.PARENT_URI, answer="42"
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self.FINAL_URI, previous_uri=self.PREV_URI,
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)
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assert has_type(triples, self.FINAL_URI, PROV_ENTITY)
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assert has_type(triples, self.FINAL_URI, TG_CONCLUSION)
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assert has_type(triples, self.FINAL_URI, TG_ANSWER_TYPE)
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def test_final_derived_from_parent(self):
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def test_final_derived_from_previous(self):
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"""Conclusion with iterations uses wasDerivedFrom."""
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triples = agent_final_triples(
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self.FINAL_URI, self.PARENT_URI, answer="42"
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self.FINAL_URI, previous_uri=self.PREV_URI,
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)
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derived = find_triple(triples, PROV_WAS_DERIVED_FROM, self.FINAL_URI)
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assert derived is not None
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assert derived.o.iri == self.PARENT_URI
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assert derived.o.iri == self.PREV_URI
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gen = find_triple(triples, PROV_WAS_GENERATED_BY, self.FINAL_URI)
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assert gen is None
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def test_final_generated_by_question_when_no_iterations(self):
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"""When agent answers immediately, final uses wasGeneratedBy."""
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triples = agent_final_triples(
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self.FINAL_URI, question_uri=self.SESSION_URI,
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)
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gen = find_triple(triples, PROV_WAS_GENERATED_BY, self.FINAL_URI)
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assert gen is not None
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assert gen.o.iri == self.SESSION_URI
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derived = find_triple(triples, PROV_WAS_DERIVED_FROM, self.FINAL_URI)
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assert derived is None
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def test_final_label(self):
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triples = agent_final_triples(
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self.FINAL_URI, self.PARENT_URI, answer="42"
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self.FINAL_URI, previous_uri=self.PREV_URI,
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)
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label = find_triple(triples, RDFS_LABEL, self.FINAL_URI)
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assert label is not None
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assert label.o.value == "Conclusion"
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def test_final_inline_answer(self):
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triples = agent_final_triples(
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self.FINAL_URI, self.PARENT_URI, answer="The answer is 42"
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)
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answer = find_triple(triples, TG_ANSWER, self.FINAL_URI)
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assert answer is not None
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assert answer.o.value == "The answer is 42"
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def test_final_document_reference(self):
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triples = agent_final_triples(
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self.FINAL_URI, self.PARENT_URI,
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self.FINAL_URI, previous_uri=self.PREV_URI,
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document_id="urn:trustgraph:agent:sess/answer",
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)
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doc = find_triple(triples, TG_DOCUMENT, self.FINAL_URI)
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@ -296,29 +328,9 @@ class TestAgentFinalTriples:
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assert doc.o.type == IRI
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assert doc.o.iri == "urn:trustgraph:agent:sess/answer"
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def test_final_document_takes_precedence(self):
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def test_final_no_document(self):
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triples = agent_final_triples(
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self.FINAL_URI, self.PARENT_URI,
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answer="inline",
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document_id="urn:doc:123",
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self.FINAL_URI, previous_uri=self.PREV_URI,
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)
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doc = find_triple(triples, TG_DOCUMENT, self.FINAL_URI)
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assert doc is not None
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answer = find_triple(triples, TG_ANSWER, self.FINAL_URI)
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assert answer is None
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def test_final_no_answer_or_document(self):
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triples = agent_final_triples(self.FINAL_URI, self.PARENT_URI)
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answer = find_triple(triples, TG_ANSWER, self.FINAL_URI)
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doc = find_triple(triples, TG_DOCUMENT, self.FINAL_URI)
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assert answer is None
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assert doc is None
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def test_final_derives_from_session_when_no_iterations(self):
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"""When agent answers immediately, final derives from session."""
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session_uri = "urn:trustgraph:agent:test-session"
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triples = agent_final_triples(
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self.FINAL_URI, session_uri, answer="direct answer"
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)
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derived = find_triple(triples, PROV_WAS_DERIVED_FROM, self.FINAL_URI)
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assert derived.o.iri == session_uri
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