Signature introspection and the resulting call were sharing one
try/except, so a genuine bug inside a backend's get_causal_chain
(raising an unrelated TypeError) was misread as a signature mismatch,
causing an identical retry call before the real error surfaced.
Split introspection from the call so a successfully-introspected call
happens exactly once; the trial-and-error cascade now only runs when
inspect.signature itself fails. Also adds the CHANGELOG entry for
#781/#817, which was missing.
- Add safe input validation and bounds clamping on max_depth (1..100) to prevent DoS/memory exhaustion
- Use inspect.signature for accurate keyword dispatch with precise TypeError fallback
- Prevent masking of genuine internal TypeError exceptions inside graph backends
- Add security and input hardening regression tests
- Support legacy (depth kwarg) and positional-only get_causal_chain backend signatures in fallback path
- Add regression tests for signature compatibility
- Return explicit error dictionary when graph lacks get_causal_chain instead of silent empty list
- Forward direction and max_depth in fallback graph.get_causal_chain call
- Add regression tests for error signaling and parameter forwarding
* feat(triplet_store): add Altair Anzo triplet store backend
Adds AnzoStore as a fourth peer to BlazegraphStore/RDF4JStore/JenaStore,
speaking plain SPARQL 1.1 over HTTP (no new dependency needed). The one
structural difference from the existing backends is that Anzo addresses
data by a dataset/graphmart URI rather than a short namespace/repository
name, so the endpoint path percent-encodes it. Reuses the shared
sparql_escaping.py helpers and wires "anzo" into TripletStore's backend
dispatch and config env vars.
Closes#813
* fix(triplet_store): correct AnzoStore SPARQL syntax and validate IRIs
Addresses review findings from Qodo and Codex on PR #814:
- get_triplets(): constraints are now expressed via FILTER(...) instead of
bare equality expressions appended inside the WHERE group graph pattern
(e.g. "?s ?p ?o ?s = <...>"), which is not valid SPARQL and was rejected
by standards-compliant endpoints.
- bulk_load(): named-graph inserts now nest the GRAPH block inside the
INSERT DATA braces (INSERT DATA { GRAPH <g> { ... } }) per the SPARQL 1.1
Update grammar, instead of "INSERT DATA GRAPH <g> { ... }".
- bulk_load()/_build_insert_data()/delete_triplet()/get_triplets() now
validate subject/predicate/graph URIs via sparql_escaping.validate_uri
before interpolating them into SPARQL Update/Query strings, closing an
injection path where a value containing ">" or "}" could break out of
the intended <...> token.
- Corrected the store_type docstring/usage example: Anzo's linked-data-set
store type is "lds", not "dataset".
Extended tests/triplet_store/test_anzo_store.py with coverage for the
corrected query shapes and the new validation/injection-rejection paths
(38 tests total, up from 32). Full tests/triplet_store/ suite: 299/299
passing.
* test(triplet_store): expand AnzoStore regression coverage
---------
Co-authored-by: Sameer6305 <sskadam6305@gmail.com>
* refactor(provenance): centralize duplicated store-and-swallow logic into _save_entry() (closes#784)
- Added ProvenanceManager._save_entry(entry) as the single shared
checksum-compute + storage.store() + graceful-failure-swallow
pipeline, previously duplicated identically across track_entity,
track_relationship, track_chunk, and track_property_source.
- track_entities_batch/track_chunks_batch already delegate to
track_entity/track_chunk in a loop, so they inherit the fix for
free — left untouched, confirmed no direct duplication there.
- Byte-for-byte preserves today's swallow-and-continue behavior and
comment text; this is an architecture-only refactor. The silent-
failure behavior itself is unchanged and out of scope here — a fix
to it now only needs to happen in one place instead of four.
- Added 4 new regression tests (previously 0 of the 4 single-item
methods had failure-path coverage) proving storage.store() raising
is still caught and each method still returns its ProvenanceEntry.
Tests: tests/provenance/ 228 passed (+4 new), tests/explorer/test_provenance_manager_wiring.py 8 passed. 236/236, 0 failed.
* fix(provenance): drop out-of-transaction store attempt in track_entity fallback
The _save_entry refactor changed track_entity's pre-build exception
fallback (entry is None branch) to call _save_entry(), which makes a
real self.storage.store(entry) call. The original code only computed
a checksum here and never attempted storage again, since this branch
fires when something already failed before the entry was built inside
the atomic transaction. Storing outside that transaction bypasses the
BEGIN IMMEDIATE serialization #807 added, risking the same race it
fixed. Restored checksum-only behavior and added a regression test
asserting storage.store is not called on this path.
Also removed an untested hasattr(_store_with_conn) defensive branch
added during the refactor that wasn't in the original code, and added
a changelog entry.
---------
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
Two review findings on #807/#812:
- retrieve() and trace_lineage() were routed through transaction()'s
BEGIN IMMEDIATE, so plain reads took SQLite's writer lock and
serialized behind every other read/write, defeating the WAL
concurrency this PR was meant to add. They now use a dedicated
_read_connection() (configured, no explicit BEGIN).
- track_entity()/track_chunk() swallowed all internal storage
exceptions unconditionally, so a single item's failure inside
track_entities_batch()/track_chunks_batch()'s shared transaction
never reached the batch loop's per-item except, inflating
tracked_count for entries that were never persisted. Both now
re-raise when called with a shared _conn (batch context) while
still degrading gracefully on standalone calls.
Added regression tests for both, corrected the CHANGELOG entry and
docs that described the prior (overly broad) behavior.
- Reuse lineage['integrity_verified'] in _build_provenance in O(1) time when available, eliminating redundant SHA-256 verification loops across lineage chains.
- Improve compute_checksum dictionary handling in semantica/provenance/integrity.py so None values fall back cleanly to ProvenanceEntry defaults.
- Move json and verify_checksum imports to module top-level in semantica/provenance/manager.py to avoid function-local import overhead during get_lineage calls.
- Extend ProvenanceNode in semantica/explorer/schemas.py with audit evidence fields: source_document, source_location, source_quote, confidence, and checksum.
- Update _transform_audit_lineage in semantica/explorer/routes/provenance.py to populate these evidence fields for each lineage node from ProvenanceEntry records, while keeping default None values for orphan nodes.
- Include source_document, confidence, and checksum in markdown report rendering (_render_markdown) so exported markdown reports surface attribution and integrity evidence.
- Add unit test test_provenance_audit_evidence_fields_preserved in test_provenance_manager_wiring.py verifying that evidence fields are present across /api/provenance JSON responses and exported JSON/markdown reports.
- Update verify_checksum and compute_checksum in semantica/provenance/integrity.py to support both ProvenanceEntry objects and serialized dictionary entries.
- Add integrity_verified flag computed via verify_checksum to the dictionary returned by ProvenanceManager.get_lineage().
- Update _build_provenance in semantica/explorer/routes/provenance.py to verify every returned lineage entry before labeling the result as source=audit. If verification fails due to missing checksums or corrupted records, log a warning and fall back cleanly to graph traversal.
- Add unit test test_provenance_manager_wiring_checksum_failure_falls_back in test_provenance_manager_wiring.py verifying that tampered lineage entries trigger fallback to source=graph_traversal.
- Fix _transform_audit_lineage to classify all non-downstream ancestor derivation edges as 'upstream' instead of 'lateral', correcting multi-hop lineage direction in JSON and markdown reports.
- Add GraphSession.set_provenance_storage_path() to explicitly reject conflicting preconfigured storage paths or path mutations after provenance_manager initialization.
- Update create_app() to call active_session.set_provenance_storage_path(prov_path), preventing silent retention of conflicting paths or un-redirectable cached managers.
- Remove unused logging import in app.py.
- Add comprehensive unit tests in test_provenance_manager_wiring.py for upstream edge classification, markdown report grouping, conflicting path rejection, and manager initialization lockouts.
- Explorer's /api/provenance now queries the audit-grade ProvenanceManager
(SQLite-backed, checksummed) first, falling back to the naive 2-hop
graph traversal when no audit records exist for a node.
- Fixed a process-global mutable-state risk in the initial approach:
provenance storage path is threaded per-session via GraphSession,
not via ProvenanceManager's global set_default_storage_path classmethod.
- Added source: 'audit' | 'graph_traversal' to the response so callers
can distinguish which path served the data.
- Documented a known limitation: ProvenanceManager currently only
traces upstream/ancestor lineage, not descendants — the naive
fallback remains the only source for downstream relationships until
ProvenanceManager gains a reverse lookup (tracked separately).
- Warns (rather than silently no-ops) if a provided session's
provenance_manager was already constructed before create_app()
applied a provenance_storage_path.
- Never lets a provenance-manager failure crash the route; degrades
to the naive path with a logged warning instead.
Tests: 5 new tests in test_provenance_manager_wiring.py covering the
audit path, empty-record fallback, storage-failure degradation, app
startup wiring, and cross-session storage isolation. Full
tests/explorer/ + tests/provenance/ suite passing, order-invariant.
- README: get_table_lineage() takes table_name first, then catalog/schema
keyword args — the example had them in the wrong order, which would have
queried lineage for the wrong fully-qualified table when copy-pasted.
- modules.md: the ingest example used DatabricksIngestor without importing
it, causing a NameError if copy-pasted as-is.
- guides/ingest.md: corrected the claim that Databricks/Snowflake ingestors
return "the same shape as DBIngestor" — DBIngestor.execute_query() returns
a raw List[Dict] with no wrapper, unlike DatabricksData/SnowflakeData.
Makes enterprise lakehouse/warehouse ingestion (Databricks Unity Catalog +
Delta Lake, Snowflake) a first-class, prominently documented capability
across the README and guides, and adds matching runnable examples to
docs/guides/ingest.md. Also fixes several pre-existing inaccuracies caught
while auditing the ingest module docs against the actual source:
WebIngestor has no ingest_urls() (only singular ingest_url()), XMLIngestor's
XSD option is schema_path (not validate_xsd) and belongs on ingest() not the
constructor, and the "Available ingestors" list was missing DatabricksIngestor
while listing several classes not actually exported from semantica.ingest.
Extracts the row-cap-and-truncate loop (duplicated between the
CONSTRUCT/DESCRIBE and SELECT branches) into a shared _cap_rows()
helper, and adds a test for the previously-uncovered CONSTRUCT/DESCRIBE
truncation path. Addresses review nits on PR #805.
- Revert create_ontology silently falling back to a near-empty ontology on
generation failure; restores the HTTPException(500) behavior from #770/#787
that this PR had accidentally undone (and re-enables TestOntologyCreateFailures)
- Fold sh:Warning/sh:Info severity pySHACL results into the /shacl/validate
response's violations array instead of silently dropping them, so a
non-conforming report is never returned with an empty violations list
- Share a single nodes/edges fetch between _generated_shacl_for_uri and
_data_graph_turtle_for_uri via new _fetch_analysis_graph(), so /health
no longer re-queries and re-truncation-checks the same ontology twice
* fix(security): restrict Neptune cookbook SG, add VPC flow logs, harden IaC scan suppressions
Addresses open GHAS code scanning alerts:
- Neptune cookbook stack (neptune-setup.yaml) no longer opens the Bolt/OpenCypher
port to 0.0.0.0/0; a required ClientCidr parameter must be supplied instead.
Updated 21_Amazon_Neptune_Store.ipynb deploy instructions to match.
- Added VPC Flow Logs (CloudWatch Logs + IAM role) to the same stack.
- Documented why an account-wide IAM password policy resource does not belong
in a disposable per-learner CFN stack, with a justified ts:skip.
- Added inline `checkov:skip` / `ts:skip` comments to the knowledge-explorer
Helm templates (deployment/service/configmap) as a second suppression path
for the CKV_K8S_21/AC_K8S_0086/AC_K8S_0080 false positives, since the prior
annotation-only suppression was not being honored by the scanner.
* docs(changelog): document the Neptune and Helm chart security scan fixes
* fix(security): correct flow-log IAM scope and ClientCidr regex from review
- FlowLogRole granted logs:CreateLogStream/PutLogEvents on the bare log
group ARN, but those actions apply to log streams, not the group itself;
scoped them to "${FlowLogGroup.Arn}:log-stream:*" instead and moved the
Describe* actions (which don't support group/stream-level resource
restriction) to Resource: "*", matching AWS's documented flow-log IAM
policy shape. Without this, flow log delivery could silently fail.
- ClientCidr's AllowedPattern only checked digit count (1-3 digits per
octet), so malformed values like 999.999.999.999/32 passed parameter
validation and would only fail later when CloudFormation tried to
create the security group rule. Tightened the regex to enforce valid
IPv4 octet ranges (0-255) and prefix lengths (0-32).
* fix(security): harden IAM policy in neptune-setup and standardize Helm chart scan suppressions
- neptune-setup.yaml: split FlowLogRole policy into account-level statement (CreateLogGroup, DescribeLogGroups, DescribeLogStreams with Resource: '*') and log-group-scoped statement (CreateLogStream, PutLogEvents with !GetAtt FlowLogGroup.Arn) per AWS VPC Flow Logs least-privilege documentation.
- deployment.yaml: remove unreliable file-header skip comments (# checkov:skip / # ts:skip) and replace with resource-level metadata.annotations (checkov.io/skip and runterrascan.io/skip). Update seccomp rule ID from CKV_K8S_28 to checkov's actual seccomp rule CKV_K8S_31 on both Deployment and pod-template metadata.
- configmap.yaml / service.yaml: remove stale # ts:skip=AC_K8S_0086 file-header comments and add runterrascan.io/skip resource-level metadata annotations for consistency across all chart templates.
- .checkov.yaml: update documentation to explain resource-level metadata.annotations and reference CKV_K8S_31.
---------
Co-authored-by: Sameer6305 <sskadam6305@gmail.com>
mikemikimike