Merge pull request #802 from Sameer6305/feat/provenance-shared-storage-wiring

feat(provenance): implement global default storage pattern and fix CLI lineage integration

CHANGELOG.md

@@ -11,6 +11,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- **Global default persistent storage for `ProvenanceManager`, plus a working `provenance` CLI** (#795, #802) by @Sameer6305 and @KaifAhmad1
+  - Every ingestion/processing module (`kg_provenance.py`, `pipeline_provenance.py`, and 20+ other call sites) instantiated its own `ProvenanceManager()` with no `storage_path`, so all of them silently fell back to `InMemoryStorage` and the SQLite audit trail was never actually written. `ProvenanceManager.set_default_storage_path(path)` now sets a class-level default that every no-arg instantiation picks up, and `Semantica.__init__` wires `config.provenance.storage_path` into it automatically during orchestrator init
+  - Added the thread-safe `default_storage_path(path)` context manager (`semantica.provenance.default_storage_path`) for test isolation — it stacks nested overrides and guarantees restoration of the previous default on exit, even on exception, so tests can't leak global state into each other
+  - Fixed `ProvenanceManager.__init__` raising `TypeError` on the CLI's `config=` kwarg, and implemented the four methods the CLI already called but that didn't exist on the class: `lineage()`, `audit_log()`, `export_prov()` (W3C PROV-O turtle/ntriples/jsonld via `rdflib`), and `check()` — unblocking `semantica provenance lineage|audit|export|check` end-to-end
+  - Follow-up review fixes: `track_entity` no longer aliases a caller-supplied `used_entities` list (it copied the reference and later mutated it in place via `.append()`, which could corrupt a list the caller still held); removed dead fallback branches in `orchestrator.py`/`manager.py` left over from not realizing `Config.get()` already resolves dotted paths; added a `--dry-run` option to `provenance audit` to match `provenance export` (previously only the global `--dry-run` flag worked, not a local one); and `provenance check --strict` no longer prints a green "✓" success line immediately before failing — a failing check now renders as a warning before the `ClickException` is raised
+
 - **Markdown round-trip export/import for `AgentMemory`** (#765, #786) by @SaurabhScripts and @Sameer6305
   - `AgentMemory.export(format="markdown")` and `import_data(format="markdown")` add a human-editable, diff-friendly alternative to the existing JSON/dict serialization: one Markdown file per memory item, with `id`, `created_at`, `updated_at`, and `type`/`kind` in required YAML frontmatter and the memory content as the Markdown body
   - Exporting without a `destination` returns a single memory as a Markdown string; exporting a set requires a destination directory and writes one stable, content-hashed filename per memory ID, so re-exporting an unchanged set is byte-for-byte idempotent

semantica/cli.py

@@ -2523,9 +2523,11 @@ def provenance_lineage(cli_ctx: CLIContext, entity_id: str, depth: int, local_js
               default="table", show_default=True)
 @click.option("--output", default=None, type=click.Path())
 @click.option("--json", "local_json", is_flag=True, default=False)
+@click.option("--dry-run", "local_dry", is_flag=True, default=False)
 @click.pass_obj
 def provenance_audit(cli_ctx: CLIContext, since: Optional[str], fmt: str,
-                     output: Optional[str], local_json: bool) -> None:
+                     output: Optional[str], local_json: bool,
+                     local_dry: bool) -> None:
     """Export the audit log.
 
     \b
@@ -2535,6 +2537,9 @@ def provenance_audit(cli_ctx: CLIContext, since: Optional[str], fmt: str,
     cli_ctx = _require_ctx(cli_ctx)
 
     def _action() -> None:
+        if _is_dry(cli_ctx, local_dry):
+            _dry(cli_ctx, "export audit log", since=since, format=fmt, output=output)
+            return
         try:
             from .provenance import ProvenanceManager
             pm = ProvenanceManager(config=cli_ctx.config.to_dict())
@@ -2601,10 +2606,17 @@ def provenance_check(cli_ctx: CLIContext, strict: bool, local_json: bool) -> Non
             result = pm.check(strict=strict)
         except ImportError as exc:
             raise click.ClickException(f"Provenance module not available: {exc}") from exc
+        is_valid = not isinstance(result, dict) or result.get("valid", True)
         if _is_json(cli_ctx, local_json):
             _jecho(result if isinstance(result, dict) else {"valid": bool(result)})
-        else:
+        elif is_valid:
             _ok(cli_ctx, f"Provenance check: {result}")
+        else:
+            _warn(cli_ctx, f"Provenance check: {result}")
+        if strict and not is_valid:
+            raise click.ClickException(
+                f"Provenance integrity check failed: {result.get('errors')} error(s)"
+            )
 
     _run_with_error_handling(_action)
 

semantica/core/config_manager.py

@@ -51,7 +51,6 @@ Author: Semantica Contributors
 License: MIT
 """
 
-import json
 import os
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Union
@@ -67,7 +66,6 @@ from ..utils.helpers import (
     set_nested_value,
 )
 from ..utils.progress_tracker import get_progress_tracker
-from ..utils.validators import validate_config
 
 
 class Config:
@@ -157,6 +155,7 @@ class Config:
         self.security = config_data.get(
             "security", DEFAULT_CONFIG.get("security", {})
         )
+        self.provenance = config_data.get("provenance", {})
         self.custom = config_data.get("custom", {})
 
     def _load_from_env(self, config_dict: Dict[str, Any]) -> None:
@@ -346,6 +345,7 @@ class Config:
             "logging": self.logging,
             "quality": self.quality,
             "security": self.security,
+            "provenance": self.provenance,
             "custom": self.custom,
         }
 

semantica/core/orchestrator.py

@@ -27,11 +27,11 @@ License: MIT
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Union
 
-from ..utils.exceptions import ConfigurationError, ProcessingError
+from ..utils.exceptions import ProcessingError
 from ..utils.logging import get_logger, log_execution_time
 from ..utils.progress_tracker import get_progress_tracker
 from .config_manager import Config, ConfigManager
-from .lifecycle import LifecycleManager, SystemState
+from .lifecycle import LifecycleManager
 from .plugin_registry import PluginRegistry
 
 
@@ -92,7 +92,10 @@ class Semantica:
 
         # Configure global provenance storage path if specified
         try:
-            prov_storage_path = self.config.get("provenance", {}).get("storage_path")
+            # Config.get() already resolves dotted paths against nested dicts
+            # (see get_nested_value), so this single lookup covers both
+            # top-level and config.provenance={"storage_path": ...} shapes.
+            prov_storage_path = self.config.get("provenance.storage_path")
             if prov_storage_path:
                 from ..provenance import ProvenanceManager
                 ProvenanceManager.set_default_storage_path(prov_storage_path)
@@ -640,10 +643,10 @@ class Semantica:
         try:
             # Import key modules to verify they're available
             # These imports don't create instances, just verify module availability
-            from ..ingest import FileIngestor
-            from ..kg import GraphBuilder
-            from ..parse import DocumentParser
-            from ..pipeline import PipelineBuilder
+            from ..ingest import FileIngestor  # noqa: F401
+            from ..kg import GraphBuilder  # noqa: F401
+            from ..parse import DocumentParser  # noqa: F401
+            from ..pipeline import PipelineBuilder  # noqa: F401
 
             self.logger.debug("Framework modules verified and available")
         except (ImportError, OSError) as e:

semantica/provenance/__init__.py

@@ -43,7 +43,7 @@ License: MIT
 
 from .schemas import ProvenanceEntry, SourceReference
 from .storage import ProvenanceStorage, InMemoryStorage, SQLiteStorage
-from .manager import ProvenanceManager
+from .manager import ProvenanceManager, default_storage_path
 from .integrity import compute_checksum, verify_checksum
 
 __all__ = [
@@ -58,6 +58,7 @@ __all__ = [
     
     # Manager
     "ProvenanceManager",
+    "default_storage_path",
     
     # Utilities
     "compute_checksum",

semantica/provenance/manager.py

@@ -24,15 +24,28 @@ Author: Semantica Contributors
 License: MIT
 """
 
-from typing import Optional, List, Dict, Any
+from typing import Optional, List, Dict, Any, Union
 from collections.abc import Mapping
 from datetime import datetime
+from contextlib import contextmanager
+import copy
+import threading
 
-from .schemas import ProvenanceEntry, SourceReference, PropertySource
+from .schemas import ProvenanceEntry, SourceReference
 from .storage import ProvenanceStorage, InMemoryStorage, SQLiteStorage
 from .integrity import compute_checksum
 
 
+@contextmanager
+def default_storage_path(path: Optional[str]):
+    """
+    Context manager for temporarily setting ProvenanceManager._default_storage_path.
+    Guarantees restoration to the previous value on exit (safe for tests).
+    """
+    with ProvenanceManager.default_storage_path(path):
+        yield
+
+
 class ProvenanceManager:
     """
     Unified provenance tracking manager.
@@ -55,17 +68,38 @@ class ProvenanceManager:
     """
     
     _default_storage_path: Optional[str] = None
+    _lock = threading.RLock()
+    _path_stack: List[Optional[str]] = []
 
     @classmethod
-    def set_default_storage_path(cls, path: str) -> None:
+    def set_default_storage_path(cls, path: Optional[str]) -> None:
         """Set a global default storage path for all new instances."""
-        cls._default_storage_path = path
+        with cls._lock:
+            cls._default_storage_path = path
+
+    @classmethod
+    @contextmanager
+    def default_storage_path(cls, path: Optional[str]):
+        """
+        Context manager for temporarily setting the global default storage path.
+        Guarantees restoration to the previous value on exit (safe for tests).
+        """
+        cls._lock.acquire()
+        try:
+            cls._path_stack.append(cls._default_storage_path)
+            cls._default_storage_path = path
+            yield
+        finally:
+            cls._default_storage_path = (
+                cls._path_stack.pop() if cls._path_stack else None
+            )
+            cls._lock.release()
     
     def __init__(
         self,
         storage: Optional[ProvenanceStorage] = None,
         storage_path: Optional[str] = None,
-        config: Optional[Dict[str, Any]] = None,
+        config: Optional[Any] = None,
         **kwargs
     ):
         """
@@ -74,17 +108,27 @@ class ProvenanceManager:
         Args:
             storage: Custom storage backend (optional)
             storage_path: Path to SQLite database (optional, uses in-memory if None)
-            config: Configuration dictionary (optional)
+            config: Configuration dictionary or mapping (optional)
         """
         if storage:
             self.storage = storage
             return
 
         if not storage_path and config:
-            storage_path = config.get("provenance", {}).get("storage_path")
+            if isinstance(config, Mapping):
+                prov_config = config.get("provenance", {})
+                prov_has_path = (
+                    isinstance(prov_config, Mapping)
+                    and "storage_path" in prov_config
+                )
+                if prov_has_path:
+                    storage_path = prov_config.get("storage_path")
+                elif "storage_path" in config:
+                    storage_path = config.get("storage_path")
 
-        if not storage_path and self._default_storage_path:
-            storage_path = self._default_storage_path
+        if not storage_path:
+            with self._lock:
+                storage_path = self._default_storage_path
 
         if storage_path:
             self.storage = SQLiteStorage(storage_path)
@@ -125,12 +169,6 @@ class ProvenanceManager:
         if not isinstance(entity_id, str):
             raise TypeError(f"entity_id must be a string, got {type(entity_id).__name__}")
         
-        if not isinstance(entity_id, str):
-            raise TypeError(f"entity_id must be a string, got {type(entity_id).__name__}")
-        
-        if not isinstance(entity_id, str):
-            raise TypeError(f"entity_id must be a string, got {type(entity_id).__name__}")
-        
         # Check if entity already exists
         existing = self.storage.retrieve(entity_id)
         parent_id = kwargs.get("parent_entity_id")
@@ -166,7 +204,6 @@ class ProvenanceManager:
         if existing:
             # Create a history entry for the previous state
             # Use timestamp or counter for uniqueness
-            import copy
             history_entry = copy.deepcopy(existing)
             history_id = f"{entity_id}:v:{existing.last_updated}"
             
@@ -201,7 +238,8 @@ class ProvenanceManager:
             metadata=metadata or {},
             first_seen=existing.first_seen if existing else datetime.utcnow().isoformat(),
             last_updated=datetime.utcnow().isoformat(),
-            parent_entity_id=parent_id  # Link to history or explicit parent
+            parent_entity_id=parent_id,  # Link to history or explicit parent
+            used_entities=list(kwargs.get("used_entities", [])),
         )
 
         # Make the archived history entry discoverable via trace_lineage()'s
@@ -523,9 +561,11 @@ class ProvenanceManager:
                 if isinstance(meta, dict):
                     aggregated_metadata.update(meta)
         
+        chain_dicts = [entry.to_dict() for entry in lineage_entries]
         return {
             "entity_id": entity_id,
-            "lineage_chain": [entry.to_dict() for entry in lineage_entries],
+            "lineage_chain": chain_dicts,
+            "entries": chain_dicts,
             "source_documents": list(set(
                 e.source_document for e in lineage_entries 
                 if e.source_document
@@ -626,3 +666,170 @@ class ProvenanceManager:
                 if e.source_document
             ))
         }
+
+    # === CLI Integration Methods ===
+
+    def lineage(self, entity_id: str, depth: int = 3) -> Dict[str, Any]:
+        """
+        Get lineage information formatted for CLI display.
+
+        Args:
+            entity_id: ID of the entity to trace lineage for
+            depth: Maximum traversal depth (default: 3)
+
+        Returns:
+            Dict containing entity_id, depth, count, lineage entries, and sources
+        """
+        base_lineage = self.get_lineage(entity_id)
+        entries = base_lineage.get("lineage_chain", [])
+        if len(entries) > depth:
+            entries = entries[:depth]
+        sources = self.get_all_sources(entity_id)
+        return {
+            "entity_id": entity_id,
+            "depth": depth,
+            "chain_length": len(entries),
+            "source_documents": base_lineage.get("source_documents", []),
+            "lineage": entries,
+            "entries": entries,
+            "sources": sources,
+            "metadata": base_lineage.get("metadata", {}),
+        }
+
+    def audit_log(
+        self, since: Optional[str] = None, format: str = "table"
+    ) -> Union[str, List[Dict[str, Any]]]:
+        """
+        Export audit log of provenance entries.
+
+        Args:
+            since: Optional ISO 8601 date string filter
+            format: Output format ('table', 'csv', 'json')
+
+        Returns:
+            Formatted audit log as string or list of dicts
+        """
+        entries = self.storage.retrieve_all()
+        if since:
+            entries = [e for e in entries if getattr(e, "timestamp", "") >= since]
+        entries.sort(key=lambda e: getattr(e, "timestamp", ""))
+
+        if format == "json":
+            return [
+                e.to_dict() if hasattr(e, "to_dict") else getattr(e, "__dict__", {})
+                for e in entries
+            ]
+        elif format == "csv":
+            lines = ["entity_id,entity_type,activity_id,agent_id,timestamp"]
+            for e in entries:
+                ts = getattr(e, "timestamp", "")
+                lines.append(
+                    f"{e.entity_id},{e.entity_type},{e.activity_id},{e.agent_id},{ts}"
+                )
+            return "\n".join(lines)
+        else:
+            lines = [
+                f"{'ENTITY_ID':<20} {'TYPE':<15} {'ACTIVITY':<15} {'TIMESTAMP':<25}"
+            ]
+            lines.append("-" * 75)
+            for e in entries:
+                ts = str(getattr(e, "timestamp", ""))
+                lines.append(
+                    f"{str(e.entity_id):<20} {str(e.entity_type):<15}"
+                    f" {str(e.activity_id):<15} {ts:<25}"
+                )
+            return "\n".join(lines)
+
+    def export_prov(self, format: str = "turtle") -> str:
+        """
+        Export provenance as W3C PROV-O RDF.
+
+        Args:
+            format: RDF format ('turtle', 'ntriples', 'jsonld')
+
+        Returns:
+            Serialized RDF string
+        """
+        from rdflib import Graph, Literal, Namespace, URIRef
+        from rdflib.namespace import RDF, XSD
+
+        PROV = Namespace("http://www.w3.org/ns/prov#")
+        EX = Namespace("http://example.org/ns/")
+
+        g = Graph()
+        g.bind("prov", PROV)
+        g.bind("ex", EX)
+
+        for e in self.storage.retrieve_all():
+            ent_uri = URIRef(EX[str(e.entity_id)])
+            g.add((ent_uri, RDF.type, PROV.Entity))
+
+            if getattr(e, "timestamp", None):
+                g.add(
+                    (
+                        ent_uri,
+                        PROV.generatedAtTime,
+                        Literal(e.timestamp, datatype=XSD.dateTime),
+                    )
+                )
+
+            if getattr(e, "agent_id", None) and e.agent_id != "unknown":
+                ag_uri = URIRef(EX[str(e.agent_id)])
+                g.add((ag_uri, RDF.type, PROV.Agent))
+                g.add((ent_uri, PROV.wasAttributedTo, ag_uri))
+
+            if getattr(e, "activity_id", None) and e.activity_id != "unknown":
+                act_uri = URIRef(EX[str(e.activity_id)])
+                g.add((act_uri, RDF.type, PROV.Activity))
+                g.add((ent_uri, PROV.wasGeneratedBy, act_uri))
+
+            if getattr(e, "parent_entity_id", None):
+                p_uri = URIRef(EX[str(e.parent_entity_id)])
+                g.add((ent_uri, PROV.wasDerivedFrom, p_uri))
+
+            for u_id in getattr(e, "used_entities", []):
+                u_uri = URIRef(EX[str(u_id)])
+                # Emit wasDerivedFrom only when this used entity is not the same
+                # as parent_entity_id — which already carries that triple above.
+                if u_id != getattr(e, "parent_entity_id", None):
+                    g.add((ent_uri, PROV.wasDerivedFrom, u_uri))
+                if getattr(e, "activity_id", None) and e.activity_id != "unknown":
+                    act_uri = URIRef(EX[str(e.activity_id)])
+                    g.add((act_uri, PROV.used, u_uri))
+
+        rdf_format = "json-ld" if format == "jsonld" else format
+        return g.serialize(format=rdf_format)
+
+    def check(self, strict: bool = False) -> Dict[str, Any]:
+        """
+        Validate provenance integrity.
+
+        Args:
+            strict: Whether to perform strict validation
+
+        Returns:
+            Dictionary with validation results
+        """
+        entries = self.storage.retrieve_all()
+        all_ids = {e.entity_id for e in entries}
+
+        missing_refs = []
+        for e in entries:
+            if getattr(e, "parent_entity_id", None):
+                if e.parent_entity_id not in all_ids:
+                    missing_refs.append(f"{e.entity_id} -> {e.parent_entity_id}")
+            for u_id in getattr(e, "used_entities", []):
+                if u_id not in all_ids:
+                    missing_refs.append(f"{e.entity_id} -> {u_id}")
+
+        valid = len(missing_refs) == 0
+        errors = len(missing_refs)
+
+        return {
+            "valid": valid,
+            "total_entries": len(entries),
+            "missing_references": missing_refs,
+            "strict": strict,
+            "errors": errors,
+        }
+

tests/provenance/test_manager.py

@@ -11,7 +11,130 @@ from semantica.provenance import ProvenanceManager, SourceReference
 
 class TestProvenanceManager:
     """Test ProvenanceManager functionality."""
-    
+
+    @pytest.fixture(autouse=True)
+    def reset_default_storage_path(self):
+        original = ProvenanceManager._default_storage_path
+        try:
+            yield
+        finally:
+            ProvenanceManager._default_storage_path = original
+
+    def test_default_storage_path_pattern(self, tmp_path):
+        """Test global default storage pattern, config kwarg, and test-isolation context manager."""
+        from semantica.provenance import default_storage_path, InMemoryStorage, SQLiteStorage
+
+        # 1. Default should fallback to InMemoryStorage when no path/config
+        prov_mgr = ProvenanceManager()
+        assert isinstance(prov_mgr.storage, InMemoryStorage)
+
+        # 2. Config kwarg should extract storage_path gracefully (CLI bug fix)
+        cfg_path = str(tmp_path / "cfg_test.db")
+        cfg = {"provenance": {"storage_path": cfg_path}}
+        prov_mgr = ProvenanceManager(config=cfg)
+        assert isinstance(prov_mgr.storage, SQLiteStorage)
+
+        # 3. Explicit storage_path arg overrides config and default
+        explicit_path = str(tmp_path / "explicit.db")
+        prov_mgr = ProvenanceManager(storage_path=explicit_path, config=cfg)
+        assert isinstance(prov_mgr.storage, SQLiteStorage)
+
+        # 4. default_storage_path context manager should temporarily set default and restore on exit
+        ctx_path = str(tmp_path / "ctx_test.db")
+        with default_storage_path(ctx_path):
+            assert ProvenanceManager._default_storage_path == ctx_path
+            prov_mgr = ProvenanceManager()
+            assert isinstance(prov_mgr.storage, SQLiteStorage)
+
+        # Should be restored after context exit
+        assert ProvenanceManager._default_storage_path is None
+        prov_mgr = ProvenanceManager()
+        assert isinstance(prov_mgr.storage, InMemoryStorage)
+
+        # 5. Guaranteed restoration even on exception
+        exc_path = str(tmp_path / "exception_test.db")
+        try:
+            with ProvenanceManager.default_storage_path(exc_path):
+                assert ProvenanceManager._default_storage_path == exc_path
+                raise RuntimeError("Test exception inside context")
+        except RuntimeError:
+            pass
+        assert ProvenanceManager._default_storage_path is None
+
+        # 6. Nested contexts should restore correctly from stack
+        outer_path = str(tmp_path / "outer.db")
+        inner_path = str(tmp_path / "inner.db")
+        with default_storage_path(outer_path):
+            assert ProvenanceManager._default_storage_path == outer_path
+            with default_storage_path(inner_path):
+                assert ProvenanceManager._default_storage_path == inner_path
+            assert ProvenanceManager._default_storage_path == outer_path
+        assert ProvenanceManager._default_storage_path is None
+
+    def test_default_storage_path_concurrency_safety(self, tmp_path):
+        """Test that default_storage_path context manager is thread-safe under concurrent use."""
+        import threading
+        import time
+        from semantica.provenance import default_storage_path, SQLiteStorage
+
+        errors = []
+
+        def _worker(path, delay):
+            try:
+                with default_storage_path(path):
+                    time.sleep(delay)
+                    prov_mgr = ProvenanceManager()
+                    assert isinstance(prov_mgr.storage, SQLiteStorage)
+                    assert prov_mgr.storage.db_path == path
+            except Exception as e:
+                errors.append(e)
+
+        path_a = str(tmp_path / "thread_a.db")
+        path_b = str(tmp_path / "thread_b.db")
+
+        t1 = threading.Thread(target=_worker, args=(path_a, 0.05))
+        t2 = threading.Thread(target=_worker, args=(path_b, 0.01))
+        t1.start()
+        t2.start()
+        t1.join()
+        t2.join()
+
+        assert not errors, f"Errors in concurrent context worker: {errors}"
+        assert ProvenanceManager._default_storage_path is None
+
+    def test_isolation_part_1_with_context_manager(self, tmp_path):
+        """Part 1: Prove context manager sets default storage path for ProvenanceManager created inside context."""
+        from semantica.provenance import default_storage_path, SQLiteStorage
+        iso_db = str(tmp_path / "iso_part1.db")
+        with default_storage_path(iso_db):
+            prov_mgr = ProvenanceManager()
+            assert isinstance(prov_mgr.storage, SQLiteStorage)
+            assert prov_mgr.storage.db_path == iso_db
+
+    def test_isolation_part_2_no_leakage_after_context(self):
+        """Part 2: Prove that in a SEPARATE test function after context exit, ProvenanceManager falls back to InMemoryStorage without leakage."""
+        from semantica.provenance import InMemoryStorage
+        assert ProvenanceManager._default_storage_path is None
+        prov_mgr = ProvenanceManager()
+        assert isinstance(prov_mgr.storage, InMemoryStorage)
+
+    def test_orchestrator_config_wiring(self, tmp_path):
+        """Test Semantica orchestrator configures ProvenanceManager._default_storage_path."""
+        from semantica.core import Semantica
+        from semantica.provenance import ProvenanceManager, InMemoryStorage, SQLiteStorage
+
+        # 1. No path set in config means InMemoryStorage fallback
+        _ = Semantica()
+        prov_mgr = ProvenanceManager()
+        assert isinstance(prov_mgr.storage, InMemoryStorage)
+
+        # 2. Config with provenance.storage_path sets default storage path
+        test_db = str(tmp_path / "orch_test.db")
+        _ = Semantica(config={"provenance": {"storage_path": test_db}})
+        assert ProvenanceManager._default_storage_path == test_db
+        prov_mgr = ProvenanceManager()
+        assert isinstance(prov_mgr.storage, SQLiteStorage)
+
     def test_initialization(self):
         """Test manager initialization."""
         prov_mgr = ProvenanceManager()
@@ -407,3 +530,71 @@ class TestProvenanceManager:
         assert e2.used_entities[0] in entity_ids, (
             "Archived history entry should be reachable via used_entities in lineage"
         )
+
+    def test_cli_lineage(self):
+        """Test CLI lineage wrapper method on ProvenanceManager."""
+        prov_mgr = ProvenanceManager()
+        prov_mgr.track_entity("e_cli", source="doc_cli")
+        res = prov_mgr.lineage("e_cli", depth=2)
+        assert res["entity_id"] == "e_cli"
+        assert res["depth"] == 2
+        assert isinstance(res["lineage"], list)
+        assert len(res["lineage"]) > 0
+        assert len(res["entries"]) > 0
+        assert res["lineage"][0]["entity_id"] == "e_cli"
+        assert isinstance(res["sources"], list)
+
+    def test_cli_audit_log(self):
+        """Test CLI audit_log wrapper method on ProvenanceManager."""
+        prov_mgr = ProvenanceManager()
+        prov_mgr.track_entity("e_audit", source="doc_audit")
+        res_table = prov_mgr.audit_log(format="table")
+        assert isinstance(res_table, str)
+        assert "ENTITY_ID" in res_table
+        res_csv = prov_mgr.audit_log(format="csv")
+        assert "entity_id,entity_type,activity_id,agent_id,timestamp" in res_csv
+        res_json = prov_mgr.audit_log(format="json")
+        assert isinstance(res_json, list)
+
+    def test_cli_export_prov(self):
+        """Test CLI export_prov method on ProvenanceManager."""
+        prov_mgr = ProvenanceManager()
+        prov_mgr.track_entity("e_parent", source="doc_rdf")
+        prov_mgr.track_entity(
+            "e_child",
+            source="doc_rdf",
+            parent_entity_id="e_parent",
+            used_entities=["e_parent"],
+            activity_id="act_transform",
+        )
+        ttl = prov_mgr.export_prov(format="turtle")
+        assert "prov:Entity" in ttl or "http://www.w3.org/ns/prov#Entity" in ttl
+        assert "wasDerivedFrom" in ttl
+        assert "used" in ttl
+
+    def test_cli_check(self):
+        """Test CLI check integrity method on ProvenanceManager."""
+        prov_mgr = ProvenanceManager()
+        prov_mgr.track_entity("e_valid_parent", source="doc_1")
+        prov_mgr.track_entity(
+            "e_valid_child",
+            source="doc_1",
+            parent_entity_id="e_valid_parent",
+            used_entities=["e_valid_parent"],
+        )
+        check_res = prov_mgr.check(strict=True)
+        assert check_res["valid"] is True
+        assert check_res["total_entries"] >= 2
+        assert check_res["errors"] == 0
+
+        # Confirm non-strict mode still reports valid=False and errors > 0 when references are missing
+        prov_mgr.track_entity(
+            "e_broken_child",
+            source="doc_1",
+            parent_entity_id="non_existent_parent",
+        )
+        check_broken = prov_mgr.check(strict=False)
+        assert check_broken["valid"] is False
+        assert check_broken["errors"] >= 1
+        assert "e_broken_child -> non_existent_parent" in check_broken["missing_references"]
+