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KaifAhmad1
db4361ad46
Part A - high-stakes trust blockers: - Invalidation tombstones via ProvenanceManager.invalidate() (archive-then-append, never mutates or deletes) instead of hard delete - Hash-chained integrity: sequence_id/previous_checksum chain every entry to its predecessor; new verify_chain() detects wholesale row deletion that a lone per-row checksum cannot - Typed Agent (AgentRecord: agent_type/is_automated) and Activity (ActivityRecord: start/end timing), wired through all 18 *_provenance.py wrappers - Split parent_entity_id into previous_version_id (correction) vs derived_from_id (cross-source derivation), additive alongside the legacy combined field - Downstream/descendant lineage traversal (get_descendants/trace_descendants, reverse BFS) closing the dead direction="downstream" code path in the Explorer's provenance route - Qualified Association+hadRole and Invalidation in export_prov() - New CLI: provenance invalidate|verify-chain|descendants Part B - general PROV-O spec completeness: - Qualified Generation/Usage/Derivation in export_prov() - wasAssociatedWith, actedOnBehalfOf, wasInformedBy relations - Bitemporal fields (valid_from/valid_until/revision_type/supersedes) plus revision_history()/query_recorded_between(), closing the deprecated kg.ProvenanceTracker's "no direct equivalent yet" migration gaps - prov:Bundle/hadMember membership via bundle_id - Configurable base_uri (--base-uri CLI flag), shared by RDFExporter's NamespaceManager and OWLExporter's default ontology_uri so KG/OWL/PROV exports co-resolve under one namespace instead of three hardcoded ones Bugs fixed along the way: - agent_id was a dead field: no track_* method read it from kwargs - track_entities_batch silently absorbed typed kwargs into the metadata blob - compute_checksum() had to exclude entity_id itself: hashing it made track_entity's versioning-archive relabel permanently orphan any entry already chained from the pre-relabel checksum, a false-positive "broken chain" for a legitimate rename - InMemoryStorage.get_chain_head() ignored the committed head whenever the current transaction had staged entries, corrupting the next chain link - several new ProvenanceEntry fields were wired into the dataclass and export_prov() but not into SQLiteStorage's DDL/INSERT/row-mapping; InMemoryStorage masked the gap. Added a permanent round-trip regression test to catch this class of bug for future field additions Flagged, not fixed (separate pre-existing issues, out of scope for #825): - pipeline/pipeline_provenance.py imports a nonexistent module and wraps a Pipeline dataclass with no run() method - most *_provenance.py wrappers' backing classes are themselves missing or incomplete (context_manager, deduplicator, normalizer, etc.) - kg_provenance.py passes entity_type inside metadata={} instead of as a top-level track_entity() kwarg across most of its call sites
285 lines
9.1 KiB
Python
285 lines
9.1 KiB
Python
"""
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Test W3C PROV-O Compliant Schemas
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Tests for provenance schemas including ProvenanceEntry, SourceReference,
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and PropertySource dataclasses.
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"""
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import pytest
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from datetime import datetime
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from semantica.provenance.schemas import (
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ProvenanceEntry,
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SourceReference,
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PropertySource,
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AgentRecord,
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ActivityRecord,
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Invalidation,
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)
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class TestProvenanceEntry:
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"""Test ProvenanceEntry dataclass."""
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def test_create_basic_entry(self):
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"""Test creating a basic provenance entry."""
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entry = ProvenanceEntry(
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entity_id="entity_1",
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entity_type="entity",
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activity_id="extraction"
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)
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assert entry.entity_id == "entity_1"
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assert entry.entity_type == "entity"
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assert entry.activity_id == "extraction"
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assert entry.agent_id == "semantica"
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assert entry.confidence == 1.0
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def test_entry_with_source_tracking(self):
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"""Test entry with audit-grade source tracking."""
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entry = ProvenanceEntry(
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entity_id="entity_1",
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entity_type="entity",
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activity_id="extraction",
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source_document="DOI:10.1371/journal.pone.0023601",
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source_location="Figure 2",
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source_quote="Total fish biomass increased by 463%",
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confidence=0.92
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)
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assert entry.source_document == "DOI:10.1371/journal.pone.0023601"
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assert entry.source_location == "Figure 2"
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assert entry.source_quote == "Total fish biomass increased by 463%"
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assert entry.confidence == 0.92
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def test_entry_with_lineage(self):
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"""Test entry with parent-child relationships."""
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entry = ProvenanceEntry(
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entity_id="entity_2",
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entity_type="entity",
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activity_id="transformation",
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parent_entity_id="entity_1",
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used_entities=["entity_1", "axiom_1"]
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)
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assert entry.parent_entity_id == "entity_1"
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assert len(entry.used_entities) == 2
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assert "entity_1" in entry.used_entities
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def test_entry_to_dict(self):
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"""Test converting entry to dictionary."""
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entry = ProvenanceEntry(
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entity_id="entity_1",
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entity_type="entity",
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activity_id="extraction"
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)
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data = entry.to_dict()
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assert isinstance(data, dict)
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assert data["entity_id"] == "entity_1"
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assert data["entity_type"] == "entity"
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assert "timestamp" in data
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def test_entry_from_dict(self):
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"""Test creating entry from dictionary."""
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data = {
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"entity_id": "entity_1",
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"entity_type": "entity",
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"activity_id": "extraction",
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"agent_id": "semantica",
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"source_document": "doc_1",
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"confidence": 0.9
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}
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entry = ProvenanceEntry.from_dict(data)
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assert entry.entity_id == "entity_1"
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assert entry.confidence == 0.9
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class TestSourceReference:
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"""Test SourceReference dataclass."""
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def test_create_basic_source(self):
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"""Test creating a basic source reference."""
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source = SourceReference(
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document="DOI:10.1038/s41586-021-03371-z"
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)
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assert source.document == "DOI:10.1038/s41586-021-03371-z"
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assert source.confidence == 1.0
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def test_source_with_location(self):
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"""Test source with page and section."""
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source = SourceReference(
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document="DOI:10.1038/s41586-021-03371-z",
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page=4,
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section="Table S4",
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confidence=0.92
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)
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assert source.page == 4
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assert source.section == "Table S4"
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assert source.confidence == 0.92
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def test_source_to_dict(self):
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"""Test converting source to dictionary."""
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source = SourceReference(
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document="doc_1",
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page=1
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)
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data = source.to_dict()
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assert isinstance(data, dict)
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assert data["document"] == "doc_1"
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assert data["page"] == 1
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class TestPropertySource:
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"""Test PropertySource dataclass."""
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def test_create_property_source(self):
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"""Test creating a property source."""
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source_ref = SourceReference(document="doc_1")
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prop_source = PropertySource(
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property_name="biomass_increase",
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value="463%",
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sources=[source_ref],
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entity_id="cabo_pulmo_mpa"
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)
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assert prop_source.property_name == "biomass_increase"
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assert prop_source.value == "463%"
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assert len(prop_source.sources) == 1
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assert prop_source.entity_id == "cabo_pulmo_mpa"
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def test_property_source_to_dict(self):
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"""Test converting property source to dictionary."""
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source_ref = SourceReference(document="doc_1")
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prop_source = PropertySource(
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property_name="name",
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value="test",
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sources=[source_ref]
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)
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data = prop_source.to_dict()
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assert isinstance(data, dict)
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assert data["property_name"] == "name"
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assert len(data["sources"]) == 1
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class TestProvenanceEntryPart825Fields:
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"""Issue #825, Part A — new additive fields on ProvenanceEntry."""
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def test_defaults(self):
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entry = ProvenanceEntry(entity_id="e1", entity_type="entity", activity_id="act")
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assert entry.agent_type == "software_agent"
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assert entry.is_automated is True
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assert entry.role is None
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assert entry.previous_version_id is None
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assert entry.derived_from_id is None
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assert entry.sequence_id is None
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assert entry.previous_checksum is None
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assert entry.invalidated is False
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assert entry.invalidated_at_time is None
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assert entry.invalidated_by is None
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assert entry.invalidation_reason is None
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# Part B additive fields
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assert entry.activity_started_at_time is None
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assert entry.activity_ended_at_time is None
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assert entry.acted_on_behalf_of is None
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assert entry.informed_by_activities == []
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assert entry.valid_from is None
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assert entry.valid_until is None
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assert entry.revision_type is None
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assert entry.supersedes is None
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assert entry.bundle_id is None
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def test_round_trip_to_dict_from_dict(self):
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entry = ProvenanceEntry(
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entity_id="e1",
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entity_type="entity",
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activity_id="act",
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agent_id="alice",
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agent_type="person",
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is_automated=False,
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role="approver",
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previous_version_id="e1:v:1",
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derived_from_id="source_entity",
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sequence_id=5,
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previous_checksum="abc123",
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invalidated=True,
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invalidated_at_time="2026-01-01T00:00:00",
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invalidated_by="reviewer_jane",
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invalidation_reason="retracted",
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activity_started_at_time="2026-01-01T00:00:00",
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activity_ended_at_time="2026-01-01T00:00:05",
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acted_on_behalf_of="org1",
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informed_by_activities=["ingest_activity"],
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valid_from="2026-01-01",
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valid_until="2026-06-01",
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revision_type="correction",
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supersedes="old_claim",
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bundle_id="ingestion_run_1",
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)
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data = entry.to_dict()
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restored = ProvenanceEntry.from_dict(data)
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assert restored == entry
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class TestActivityRecord:
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"""Issue #825, Part B Tier 1 — minimum-viable typed activity."""
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def test_defaults(self):
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activity = ActivityRecord(id="act1")
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assert activity.activity_type == "process"
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assert activity.started_at_time is None
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assert activity.ended_at_time is None
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def test_round_trip(self):
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activity = ActivityRecord(
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id="bureau_parsing_run_42",
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activity_type="extraction",
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started_at_time="2026-01-01T00:00:00",
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ended_at_time="2026-01-01T00:00:03",
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)
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data = activity.to_dict()
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restored = ActivityRecord.from_dict(data)
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assert restored == activity
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class TestAgentRecord:
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"""Issue #825, Part A item 3 — minimum-viable typed agent."""
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def test_defaults(self):
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agent = AgentRecord(id="bot1")
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assert agent.agent_type == "software_agent"
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assert agent.is_automated is True
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assert agent.name is None
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def test_round_trip(self):
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agent = AgentRecord(id="reviewer_jane", agent_type="person", is_automated=False, name="Jane")
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data = agent.to_dict()
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restored = AgentRecord.from_dict(data)
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assert restored == agent
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class TestInvalidation:
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"""Issue #825, Part A item 1 — tombstone record."""
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def test_round_trip(self):
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inv = Invalidation(
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entity_id="e1",
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invalidated_at_time="2026-01-01T00:00:00",
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invalidated_by="reviewer_jane",
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reason="retracted",
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)
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data = inv.to_dict()
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restored = Invalidation.from_dict(data)
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assert restored == inv
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