mint export fails with 'file does not exist' for pages named 'contributing'
and 'license' — these are reserved by Mintlify's GitHub integration layer.
Renamed to contributing-guide.md and project-license.md and updated all
nav entries and cross-links throughout the docs.
Also adds .gitattributes LF rules to prevent CRLF issues from Windows devs.
- Validate docs structure with docs_check.py (Python)
- Validate Mintlify build with mint validate (Node 20 LTS)
- Export static site with mint export, deploy to GitHub Pages
- Deploy job skipped on PRs (validate-only for branches)
- docs.yml: replace mkdocs build/deploy with python docs_check.py;
Mintlify deployment is handled by its own GitHub App
- ci.yml: remove dead paths-ignore refs to deleted mkdocs.yml and
requirements-docs.txt
- OntologyManager: remove red error banner on HTTP 500; always fall back
to empty state silently (error banners reserved for user actions only)
- AlignmentsTab: remove offline-backend warning when both registry and
alignments requests fail; show empty form silently
- ShaclStudio: fix Monarch tokenizer crash — [@] character class prevents
Monaco from misinterpreting @prefix/@base as language-property refs;
wrap beforeMount in try/catch so any Monaco setup failure cannot crash
the React tree
Decision workspace:
- Add AbortController per loadChain() call; abort previous request when a
new decision is selected, preventing stale out-of-order chain responses
- Guard all setState calls with signal.aborted so unmounted component
state updates are skipped; cancel in-flight request on unmount via a
dedicated cleanup effect
SPARQL workspace:
- Guard results table on both result.rows && result.columns to prevent
runtime crash when backend omits columns field
- Use (result.columns ?? []) inside rows.map() to satisfy TypeScript
narrowing inside the closure
- Add .catch() to clipboard.writeText() — silently swallows permission
errors (query remains visible in the editor as fallback)
- Fix CSV export anchor: append to body before click, remove after, to
ensure cross-browser compatibility
Import/Export workspace:
- Fix download anchor: append to document.body before a.click() and
remove afterwards, matching the standard compatible pattern
Lineage workspace:
- Replace 🔗 emoji empty-state icon with lucide-react Link2 for
consistent theming and sizing
Diff & Merge workspace:
- Add "Sample preview" banner above the mock diff table so users know
the displayed fields are illustrative until the backend is connected
OntologyManager:
- Restore non-blocking warning (flash message) when HTTP response is
non-OK and not a 404; network errors (backend down) stay silent
AlignmentsTab:
- When both registry and alignments promises reject, surface a soft
error banner so users know data is missing rather than just empty
Four issues raised in code review:
- Mode.JSON retry now strips response_format from create_kwargs before
calling json_client.chat.completions.create, preventing incompatible
kwargs from being forwarded to a client configured for a different mode.
- Add exc_info=True to the generate_structured fallback warning in the
manual repair loop so the gateway rejection traceback is visible in
production logs, consistent with the other warnings added in this PR.
- Remove the duplicate is_available definition in GroqProvider. Python
silently kept only the second definition; the first (with diagnostic
branching) was dead code and could cause confusion on future edits.
- Validate base_url scheme in OpenAIProvider._init_client. Non-HTTP(S)
schemes (file://, ftp://, javascript:, etc.) are now rejected with a
ValueError at init time, preventing SSRF if base_url originates from
configuration rather than hardcoded values.
Add 3 new tests: SSRF scheme rejection, valid-URL acceptance, and
exc_info presence on the generate_structured fallback warning (20/20 pass).
Update CHANGELOG.md with full description of all fixes under [Unreleased].
Three bugs caused NERExtractor to silently return pattern-based entities
even when method="llm" was configured:
1. exc_info=True missing on method-failure warning in NERExtractor —
the root exception was swallowed, making the gateway error invisible
in logs even with DEBUG enabled.
2. OpenAIProvider.generate_structured always sent response_format=json_object
to the API. Custom/enterprise gateways (Qwen, LLaMA proxies, internal
gateways) often reject this parameter, causing both the instructor path
and the manual repair loop to fail with the same error on every retry.
3. generate_typed manual repair loop had no fallback when generate_structured
itself raised — it retried the same failing call up to max_retries times,
then propagated the error, triggering _extract_fallback (pattern extraction).
Fixes:
- Add exc_info=True to the method-failure warning so the full traceback
appears in logs and users can diagnose the root cause.
- Skip response_format=json_object in OpenAIProvider.generate_structured
when base_url is set (custom endpoint), since standard OpenAI gateways
don't require it and third-party ones reject it.
- In the generate_typed manual repair loop, catch generate_structured
failures and immediately retry via plain generate() + _parse_json,
breaking the retry-the-same-failing-call loop for custom gateways.
Also adds 17 targeted regression tests covering all three bug paths,
including the exact gateway configuration reported in the issue.
- bug_001: top_k_per_entity now uses OR semantics — keep a candidate if
EITHER entity is under quota, preventing high-quality candidates being
silently dropped when a popular counterpart saturates its quota
- bug_002: validate max_results and top_k_per_entity at construction;
negative or non-int values raise ValueError instead of silent empty output
- bug_003: validate min_similarity in [0.0, 1.0] at construction;
out-of-range values raise ValueError
- bug_004: harden ConflictDetector method='relationship' normalization —
always produces List[Dict] before calling detect_relationship_conflicts
- quality_001: update detect_duplicates + incremental_detect docstrings to
reflect configurable sort_by field (not hardcoded 'confidence')
- quality_002: add _normalize_entity_id helper (always str) used in both
_apply_result_limits and _build_duplicate_groups for consistent ID handling
Backward compatible: callers not using new params see no behavior change.
58 tests pass (0 failures)
Fixes#534
- New __init__ params: max_results, top_k_per_entity, min_similarity, sort_by
- _apply_result_limits: drop below min_similarity, sort by sort_by field,
enforce top_k_per_entity per entity, cap at max_results globally
- Wired into detect_duplicates() and incremental_detect()
- 30 new tests in TestResultLimiting; full suite 42/42 passed
Fixes#533
- Removes duplicate `detect_conflicts` definition that was silently overridden,
causing AttributeError for callers passing `method=` or `property_name=` kwargs
- Merges dispatcher logic into the surviving method with `method="all"` default
supporting: "all", "value", "property", "type", "relationship", "temporal",
"logical", "entity"
- Fixes `method="relationship"` incorrectly defaulting `relationships` to the
entities list; now defaults to `[]` with dict normalization
- Removes unreachable dead code block after try/except raise in
`detect_entity_conflicts`
Closes#531
- Replace 5 direct sys.stdout.write() calls in ConsoleProgressDisplay.update()
with self._safe_write() so emoji/block characters are encoded safely on
Windows cp1252 consoles
- Add TestProgressTrackerEncoding regression tests (3 cases) covering
_safe_write, pipeline header, and auto emoji-disable on cp1252
test_retry_logic.py injected sys.modules["openai"] = MagicMock() at module
level so providers.py could be imported without the real openai package.
Those mocks were never restored, leaving openai (and spacy, instructor etc.)
as MagicMock objects for the entire test session. This caused
test_pr482_deepseek_openai tests to receive a MagicMock when importing
openai.OpenAI, making MagicMock(spec=OpenAI) raise InvalidSpecError.
Fix: save original sys.modules entries before injection and restore them
immediately after the semantica imports that needed the mocks complete.
The mock objects remain bound inside the already-imported provider module,
so test_retry_logic tests are unaffected; other test modules now see the
real packages again.
Co-authored-by: Zohaib Hassan <zohaib179949@gmail.com>
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
subprocess.CompletedProcess[str] as a return annotation is not subscriptable
at runtime on Python 3.8, causing test collection to abort before any tests
run. Adding PEP 563 deferred evaluation makes all annotations strings at
import time, restoring 3.8 compatibility without changing behaviour on 3.9+.
Co-authored-by: Zohaib Hassan <zohaib179949@gmail.com>
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
OptionalDependencyBlocker was constructing ModuleNotFoundError with only a
message string, leaving .name as None. _is_missing_dependency checks exc.name
directly (the string-scan fallback was removed when switching to
ModuleNotFoundError), so the ConfigurationError conversion never triggered and
the test asserted the wrong exception type.
Python's import machinery always sets .name to the top-level module name when
it raises ModuleNotFoundError; the blocker now does the same.
Co-authored-by: ZohaibHassan16 <zohaib@hawksight.ai>
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
Bug 1: Replace overbroad `except ImportError` with `except ModuleNotFoundError` in
__getattr__ (__init__.py) and all four optional-backend loaders (methods.py). This
prevents internal import errors inside a backend module from being silently rewritten
into a misleading "package not installed" message. Also simplifies _is_missing_dependency
to rely solely on exc.name now that ModuleNotFoundError always sets it.
Bug 2: Add `except ConfigurationError: raise` before the blanket `except Exception`
handlers in ingest_web, ingest_feed, ingest_repository, and ingest_email. Missing
optional dependencies are expected user-config issues and must not be logged as errors.
Co-authored-by: ZohaibHassan16 <zohaib@hawksight.ai>
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
Backend (semantica/explorer/routes/ontology.py):
- suggest-alignments: add TF-IDF character-ngram embeddings via sklearn
(SimilarityCalculator-compatible cosine scoring) so embedding_similarity
is populated in results; combined score = 0.4*label + 0.6*embedding when
available, falling back to label-only when sklearn is absent
- suggest-alignments: add token-overlap prefilter before SequenceMatcher so
zero-Jaccard pairs are skipped without computing full similarity; add
_MAX_ENTITIES_PER_SIDE=500 per-ontology cap on top of the existing
_MAX_ANALYSIS_NODES global cap
- suggest-alignments: remove dead try/except OntologyEngine.create_alignment
block that always failed silently (no TripletStore configured); replace
with a comment explaining the intentional ephemeral-only storage model
- health: replace O(alignments x entities) any() scans for alignment coverage
with O(1) set membership checks via assessed_ids
- shacl/validate: run rdflib.Graph().parse(format='turtle') syntax check on
the submitted Turtle before returning; invalid syntax now raises 422 instead
of returning a misleading unavailable/success response
Frontend:
- AlignmentsTab: add pairwise alignment matrix section that groups recorded
alignments by (source_ontology, target_ontology) pair; each cell shows
color-coded relation badges per RELATION_COLORS; clicking a badge populates
the create/edit form for quick editing; matrix is shown when at least two
ontologies are loaded
- ShaclStudio: add selectedShapeId state and fullShacl ref; each shape row in
the library is now a clickable button that extracts its Turtle block from
the full SHACL and pre-populates the Monaco editor; a "View all" toggle
restores the full SHACL; selected shape ID is shown in the editor header
- GraphWorkspace: fix viewMode race in external focus effect — call
setSelectedNodeId directly instead of going through focusNode(), which
captured a stale viewMode in its closure; remove focusNode from the
dependency array since it is no longer called
Tests (14 passing, was 11):
- Add test_suggest_alignments_returns_embedding_similarity: asserts
embedding_similarity is non-null when sklearn is available
- Add test_shacl_validate_rejects_invalid_turtle_syntax: asserts 422 on
syntactically invalid Turtle
- Add test_health_alignment_coverage_uses_set_lookup: asserts alignment
dimension score is non-zero after recording an alignment, verifying the
O(1) set lookup path works correctly end-to-end
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
Co-authored-by: ZohaibHassan16 <zohaib@hawksight.ai>
Backend:
- Replace false conforms=True SHACL stub with status=unavailable always;
live validation cannot be wired until OntologyEngine.validate_graph is
connected to a data graph — a stub that returns conforms=True misleads
users editing shapes
- Cap node/edge fetches in health, suggest-alignments, and SHACL generation
at _MAX_ANALYSIS_NODES (5 000) with a logger.warning when the graph
exceeds the limit; unbounded limit=999_999 fetches cause OOM on large graphs
- Set SHACL health dimension score to 0.0 (was 70.0) when status=unavailable;
exclude unavailable dimensions from the total_score average so they neither
inflate nor deflate the result
- Allow alignments to reference external/unloaded URIs (e.g. schema.org)
without raising 404; label falls back to URI fragment or caller-supplied
source_label/target_label fields added to OntologyAlignmentRequest
- Fix _alignment_id to use uuid.NAMESPACE_OID instead of NAMESPACE_URL;
the composite key is not a URL
- Fix _summarize_shapes to normalise \r\n before splitting on .\n so shape
parsing works correctly on Windows line endings
Frontend:
- Wrap handleSave/handleSuggest/handleRemove/handleAcceptSuggestion in
useCallback in AlignmentsTab for consistency with sibling components
- Add ephemeral-storage banner in AlignmentsTab warning that alignments are
session-memory-only and not persisted across restarts
- Fix exportReport in HealthTab to append/remove anchor from document before
clicking and defer URL.revokeObjectURL to avoid Blob URL leak in some browsers
- Derive health dimension grid column count from health.dimensions.length
instead of the hardcoded repeat(5, ...) that breaks if the backend adds
or removes a dimension
- Add minimal Monarch tokenizer for the Monaco turtle language registration
in ShaclStudio so prefix declarations, IRIs, SHACL properties, comments,
and string literals are syntax-highlighted; previously the editor rendered
as plain text despite theme rules being defined
Tests (11 passing, was 5):
- Rename test_shacl_validate_has_stable_contract to
test_shacl_validate_returns_unavailable and assert status == unavailable
- Add test_shacl_validate_rejects_empty_turtle (expects 422)
- Add test_health_returns_404_for_unknown_ontology
- Add test_health_shacl_dimension_is_zero_when_unavailable with total_score check
- Add test_delete_unknown_alignment_returns_404
- Add test_alignment_upsert_is_idempotent (verifies ID stability and created_at
preservation across updates)
- Add test_alignment_accepts_external_uri (verifies no 404 for schema.org URIs)
- Relax test_alignment_suggestions_are_ranked label assertions to substring
checks so the test survives similarity algorithm changes
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
Co-authored-by: ZohaibHassan16 <zohaib@hawksight.ai>
- Fix domain_uri/range_uri always being truthy strings
- Only create rdfs:domain/rdfs:range edges when domain/range are non-empty strings
- Add proper validation with .strip() to handle whitespace-only values
- Apply fix to both 'data' and 'text' mode ontology creation
- Prevents pollution of graph with invalid edges to namespace root
Fixes issue where empty domain/range values like '' or None would still create
edges pointing to namespace root (e.g., 'https://ex/#/') instead of being
properly omitted.
The pattern `<[^>]+>\s+<[^>]+>` in _detect_format() was flagged by CodeQL
(py/polynomial-redos, CWE-1333/730/400) as a polynomial regular expression
on uncontrolled user data.
The `<...>` branch was already unreachable — strings starting with '<' return
'xml' two lines above — but CodeQL does not track that control flow path.
Fix: replace the entire re.match() call with plain startswith / 'in' checks:
- N-Triples with URI subjects are already handled by the XML branch.
- Only blank-node-subject N-Triples (_:word <uri> ...) need detection here,
which is correctly expressed as startswith('_:') and ' <' in stripped.
- Removed the now-unused `import re`.
Closes security advisory #23.
Bug 4 — Upload format misdetected:
- Added xml→'xml' and json→'json-ld' to the extension→format map so
.xml and .json files are no longer misidentified as turtle.
- Changed the fallback from '|| "turtle"' to '?? ""' (empty string for
unknown extensions) so the backend _detect_format() runs instead of
blindly assuming turtle for any unrecognised extension.
- Omit the format key entirely from the load request body when no format
was detected, letting the backend auto-detect from content heuristics.
- Added .n3 to the file picker accept list and dropzone hint text.
Bug 1 — Broken registry filters:
fetchRegistry no longer sends format/kind values (owl/skos/internal/external)
as the status query param; those filters are applied client-side via
filteredEntries which already had the correct logic. Only the text search
param q is delegated to the backend.
Bug 2 — Toggle/refresh URI corruption:
Removed removesuffix('/toggle') and removesuffix('/refresh') from
toggle_ontology and refresh_ontology. Starlette's route regex already
strips the literal suffix from the captured path param; the removesuffix
call was a no-op for normal URIs but corrupted any ontology URI that
legitimately ends with /toggle or /refresh.
Bug 3 — SSRF in URL fetch:
Added _validate_fetch_url() which rejects non-http/https schemes and
resolves the hostname to block private, loopback, link-local, reserved,
and multicast addresses before requests.get() is called. Applied to all
three fetch sites: preview, load, and refresh.
Bug 5 — Inconsistent XML hardening:
_parse_rdf_sync now calls _safe_parse_rdf() from
semantica/explorer/utils/rdf_parser.py instead of g.parse() directly,
applying the existing defusedxml-based XXE protection for RDF/XML inputs.
Bug 6 — Search scans whole graph:
search_entities now calls session.search(q, limit*6) which hits the
GraphSearchIndex instead of fetching up to 999,999 nodes and doing a
linear Python substring scan. Results are post-filtered by _SEARCHABLE_TYPES
and entity_type before being returned up to the requested limit.
- Replace invalid inset-left with inset: 0 0 0 72px on ::before at <=680px
- Add matching mobile inset fix to ::after (was still at 88px)
- Merge duplicate .landing-capability-band CSS rule blocks into one
- Fix non-standard font-weight: 850 -> 800 on .landing-launcher-item-title
- Remove unused eyebrow field from LandingAction type and all data entries
- Extract static 42-dot SVG preview array to module-level PREVIEW_DOTS constant
Co-Authored-By: Zohaib Hassnain <109234410+ZohaibHassan16@users.noreply.github.com>
Co-Authored-By: KaifAhmad1 <kaifahmad087@gmail.com>
- Align _coerce_embedding_vector inner dict-probe key list with
_extract_node_embeddings outer key list (add 'embeddings', reorder to
generic-first) so nested embedding dicts resolve consistently.
- Add TODO comment on _extract_node_embeddings to cache per-session
graph revision and avoid O(N) re-scan on every semantic request.
- Add deprecation docstrings to legacy path-segment routes
(/node/{id}/path and /node/{id}/semantic-neighborhood) documenting
the known slash-in-ID limitation and pointing to the query-param
alternatives.
- Extract _FakeSimilarity to module level so it is shared without
duplication across test classes.
- Rewrite test_legacy_semantic_neighborhood_still_works_for_simple_ids
as a fully isolated TestClient session instead of mutating the
shared module-scoped 'client' fixture, preventing cross-test
state pollution.
- Extract _make_slash_node_session helper to reduce boilerplate in the
slash-safe route tests.
Co-Authored-By: ZohaibHassan16 <109234410+ZohaibHassan16@users.noreply.github.com>
Co-Authored-By: KaifAhmad1 <98801504+KaifAhmad1@users.noreply.github.com>
- Fix dead `if (anchorNodeId)` conditional in buildHeatmapRenderSnapshot
(anchor is always truthy past the early-return guard on line 263)
- Replace O(n) array .includes() with WeakMap-cached Set.has() in
resolveDistanceNodeStyle heatmap path — prevents per-node O(n) scan
during every Sigma reducer pass on large graphs
- Rename GraphDistanceBucketCounts.threeHop → threeHopPlus across
types.ts, graphSceneState.ts, and GraphWorkspace.tsx so the field
name reflects that it accumulates distance ≥ 3, not exactly 3;
update status-strip labels to "3+ hop" accordingly
- Restore hasMetrics guard in PathDistanceIntelPanel to suppress the
empty metric grid <div> when a path result carries no optional metrics
Co-Authored-By: ZohaibHassan16 <zohaib@hawksight.ai>
Co-Authored-By: KaifAhmad1 <mohammadk78600@gmail.com>
- Extract ENTITY_SHAPE_ALIASES and classifyEntityShape into a shared
graphEntityShape.ts utility — resolveEntityShape was duplicated with
divergent signatures in useLoadGraph.ts and graphSceneState.ts; both
now import from one place so aliases can never drift
- graphSceneState.resolveEntityShape falls back to classifyEntityShape
for nodes created programmatically that bypass useLoadGraph
- Fix graphTheme.ts indentation around fullGraphStructure,
fullGraphStructureLayer, and interaction — closing braces were at
wrong indent levels making the nesting visually misleading
- Add comment on fullGraphStructureLayer.mode explaining it is
intentionally "off" as a staged-rollout gate (flip to "auto" to enable
cross-community canvas curve rendering)
Co-authored-by: Mohd Kaif <98801504+KaifAhmad1@users.noreply.github.com>
Co-authored-by: Zohaib Hassnain <109234410+ZohaibHassan16@users.noreply.github.com>
Merge origin/main (Distance Intelligence #502) into feat/explorer-visual-refresh.
Conflict was in the viewModeItems useMemo: the PR's new cluster-based toolbar
structure diverged from main's coreToolbarGroups additions.
Resolution:
- Keep PR's viewModeItems as a clean 3-item segmented control (Full/Grouped/Focused)
- Port Distance Intelligence controls (ego mode, heatmap, structural/semantic overlay)
into a new distanceToolbarItems useMemo that slots into the cluster toolbar as a
"Distance" cluster, visible only when a node is selected
- Wire distanceToolbarItems into toolbarClusters between "local-structure" and
"analysis" clusters
- All other Distance Intelligence additions (state vars, BFS helpers, useEffects,
ego depth slider, GraphInspectorPanel onFocusNode prop) merged cleanly
Co-authored-by: Mohd Kaif <98801504+KaifAhmad1@users.noreply.github.com>
Co-authored-by: Zohaib Hassnain <109234410+ZohaibHassan16@users.noreply.github.com>
Merge blockers (ZohaibHassan16):
- fix: distance-matrix raises HTTP 503 when metric=semantic but no
similarity backend is available, instead of silently returning hop
distances labeled as semantic
- fix: distance-enriched export now requires node_subset (HTTP 422 if
omitted), preventing unbounded all-pairs O(n^2) export over full graph
- fix: DistanceExportRequest default include corrected from ["hops",
"distance_band"] to ["source_id", "target_id", "hop_count",
"distance_band"] so default exports are unambiguous and use the correct
column name
- fix: confidence decay edge weight index now reads graph_dict.get("edges")
or graph_dict.get("relationships") to handle both graph dict shapes,
fixing always-1.0 decay when session returns relationships key
Bot findings (github-code-quality / chatgpt-codex):
- fix: remove unused Iterable import from distance_exporter.py
- fix: remove unused Response import from graph.py
- fix: move logger init before optional KG import; replace empty
except ImportError: pass with logger.debug in distance_exporter.py
- fix: replace two bare except Exception: pass in temporal.distance_history
with logger.warning including source, target, metric, and timestamp context
- fix: remove mixed import style in test_qual003 — use only module import
and reference CausalChainAnalyzer through it
- Fix `import.meta.env.DEV` crash in graphSceneState.ts that broke the
entire test:graph-workspace suite (module load fails in Node.js/tsx)
- Export `resolveGroupedDisplayNodeId` from graphSceneState.ts and
remove the identical copy in GraphWorkspace.tsx
- Add `checkGroupedViewAvailability` helper (Louvain only, no centrality)
so grouped view availability can be checked cheaply on every graph change
- Gate full community graph build (`groupedDisplayCandidate`) on
`viewMode === 'grouped'` to avoid running Louvain + centrality on every
graph version tick when the user is not in grouped view
- Remove dead ternary in `focusNode` where both branches returned `nodeId`
- Add 7 new tests covering resolveGroupedDisplayNodeId,
resolveGroupedDisplayStateSnapshot, and checkGroupedViewAvailability
Co-Authored-By: ZohaibHassan16 <109234410+ZohaibHassan16@users.noreply.github.com>
Co-Authored-By: KaifAhmad1 <mohammadk78600@gmail.com>
Merge conflict resolution:
- Kept fix/graph-motion's conditional layout-stop (only in focused mode)
to preserve live layout motion for derived graphs — the core intent of
this PR.
Must-fix items resolved:
1. plugin.json — removed "hooks": "./hooks/hooks.json" (re-added by this
branch, already removed in PR #489 on main as it is auto-loaded).
Kept "agents": "./agents".
2. Double Louvain per render — added groupedViewAvailable useMemo in
GraphWorkspace (deps: [graphVersion]) that runs community detection
once. Passed result into resolveDisplayGraph and resolveDisplayStateSnapshot
via new groupedViewAvailable option; both functions skip their internal
computeGraphAnalyticsBase call when the value is pre-supplied.
3. graphVersion in displayState deps — removed graphVersion from the
displayState memo dep array. displayState now depends on the stable
boolean groupedViewAvailable, not on every ADD_NODE/ADD_EDGE tick,
so Louvain no longer re-fires on every WebSocket update.
4. hideLabelsOnMove / hideEdgesOnMove flipped to true — intentional:
suppressing labels and edges during pan reduces visual noise and is
part of the flicker-reduction fix described in the PR.
Co-authored-by: ZohaibHassan16 <zohaibhassan1696@gmail.com>
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
1. Prevent active-but-disabled Focused button by only disabling when
viewMode is not already "focused" (viewMode !== "focused" && !canActivateFocusedMode).
2. Generalize inspector fallback copy — stale/invalid node IDs are not
necessarily grouped items, so remove the misleading "Activate Focused
mode" hint.
3. Move pluginRuntimeRef.current read out of render by converting
canActivateFocusedMode from useMemo to useState + useEffect, resolving
two ESLint "cannot access refs during render" errors and the missing
toolbar-memo dependency warning.
Co-authored-by: Sameer6305 <sskadam6305@gmail.com>
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
- Replace deepseek.Client with openai.OpenAI(base_url="https://api.deepseek.com/v1")
in DeepSeekProvider._init_client(); the deepseek PyPI package has no Client class
- Add self.base_url = "https://api.deepseek.com/v1" to DeepSeekProvider.__init__()
(missing from original PR; caused AttributeError on every instantiation)
- Fix verbose_mode NameError in BaseProvider.generate_typed() instructor path
- Update pyproject.toml: llm-deepseek extra now declares openai>=1.0.0
- Update _init_client warning message to reference openai library
- Add 19 tests in tests/semantic_extract/test_pr482_deepseek_openai.py
- Update CHANGELOG.md
Co-authored-by: liling <liling@users.noreply.github.com>
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
- Replace list.sort() on every upsert with bisect.insort() — O(log n) per
insert instead of O(n log n); bulk rebuild still sorts once at the end
- Replace list.remove() in remove() with bisect.bisect_left + pop() — O(log n)
find instead of O(n) scan
- Wrap handle_graph_mutation() index mutations in self._lock — mutation bridge
fires from a background thread and was racing concurrent search/rebuild calls
- Drop source/target upserts in add_edge() — edges don't change node text so
the index documents are identical; removes unnecessary cache invalidation
- Sort tag values in _cache_key() — ["a","b"] and ["b","a"] now share a cache
entry since _passes_filters() uses set intersection (order-independent)
- Restore @app.get("/") root handler missing from this branch vs main
Co-authored-by: ZohaibHassan16 <zohaibhassan16@users.noreply.github.com>
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
- Resolve all merge conflict markers in provenance.py, app.py, .gitignore
- Revert broken session.get_nodes()/get_edges() to session.graph.nodes/edges
- Keep undirected=True ego_graph fix for upstream ancestor traversal
- Add direction field to ProvenanceEdge (upstream/downstream/lateral)
- Group lineage edges in _render_markdown by direction section
- Move ProvenanceNode/ProvenanceEdge/ProvenanceResponse to schemas.py
- Restore complete router import set in app.py (sparql, vocabulary, etc.)
Co-authored-by: Sameer6305 <sameer6305@users.noreply.github.com>
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
- Extend PathResponse with hop_count (len(path)-1) and distance_band
("direct"|"near"|"mid-range"|"distant") as first-class API fields
- Add classify_path_distance() to semantica/utils/helpers.py as the
single source of truth for hop-count thresholds; both the route and
the visualizer import from it, eliminating duplicate threshold logic
- Populate hop_count and distance_band in find_path route via
classify_path_distance(); remove local _classify_distance() copy
- Add highlight_path: list[str] param to KGVisualizer.visualize_network;
path edges rendered as a distance-aware orange trace (opacity and
stroke width scale from direct→distant: 1.0/4px to 0.35/1.5px)
- Fix bidirectional edge lookup: only forward pairs (A→B) along the
path are added to path_edge_set; reverse back-edges in directed
graphs are no longer incorrectly highlighted
- Add logger.warning when highlight_path contains node IDs absent from
the layout position map, surfacing silent no-op mismatches
- Extend frontend PathResponse type in GraphInspectorPanel.tsx and
GraphWorkspaceShell.tsx with hop_count: number and distance_band
literal union to match the updated API contract
- Add 10 new tests: 2 API-level and 8 unit tests covering all four
band boundaries (0, 1, 2, 3, 4, 6, 7, 20 hops); 104 explorer tests
pass, 0 failures introduced
- Update CHANGELOG.md
- PathFinder.bfs_shortest_path() and dijkstra_shortest_path() gain a
directed: bool = True parameter. When False, a temporary undirected
view (graph.to_undirected()) is used for traversal only; the original
directed edges are preserved and returned in the response.
- _make_undirected_view() helper added to PathFinder; falls back safely
for non-NetworkX graph types.
- GET /api/graph/node/{id}/path exposes ?directed=false query param.
- PathResponse gains a directed: bool field echoing the mode used.
- Route now returns 404 on empty path (previously returned 200 with
path: []).
- 21 new tests: 12 unit (TestBidirectionalPathFinding) + 9 API-level
(TestBidirectionalPathRoute). All 120 tests pass.
- CHANGELOG updated under [Unreleased].
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add semantica/kg/knowledge_graph.py with KnowledgeGraph dataclass
(entities, relationships, metadata) plus __len__ and __bool__ helpers
- Export KnowledgeGraph from semantica/kg/__init__.py
- Add KGVisualizer._convert_knowledge_graph() for explicit, non-mutating
conversion from KnowledgeGraph to internal dict format
- Route isinstance(graph, KnowledgeGraph) through _convert_knowledge_graph
inside _normalize_graph so all five visualize_* entry points accept
KnowledgeGraph directly without any manual conversion
- Add TestFormalKnowledgeGraphType (15 tests)
Closes#471
KGVisualizer.visualize_network() (and sibling methods) only accepted a raw
dict. Passing a KnowledgeGraph object — the natural output of
GraphBuilder.build() — silently returned without rendering.
Added _normalize_graph() which duck-types the input: dicts pass through
unchanged; any object exposing .entities / .relationships attributes is
converted to the canonical dict form; anything else raises a clear
ProcessingError naming the offending type.
_normalize_graph() is called as the first statement in visualize_network(),
visualize_communities(), visualize_centrality(), visualize_entity_types(),
and visualize_relationship_matrix().
Also adds 21 tests in tests/visualization/test_kg_visualizer_normalize_graph.py
covering the helper directly, the end-to-end regression for #458, and
a guard that every public method routes through _normalize_graph.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Tools grid:
- Claude Code/Cursor/Codex: 'Native plugin' (plugins/ dirs exist in repo)
- All other tools: 'REST API' (no MCP server impl in codebase — Semantica
has an MCP CLIENT for ingesting from MCP servers, not an MCP server)
- Codex CLI added back (has real plugin bundle at plugins/.codex-plugin/)
Plugin Bundles section:
- Full table of all 17 skills with descriptions matching SKILL.md files
- Full table of all 3 agents (kg-assistant, decision-advisor, explainability)
- Hooks entry referencing plugins/hooks/hooks.json
MCP Client section:
- Correct framing: MCPClient in semantica/ingest/mcp_client.py pulls
data FROM MCP servers into KG (not an MCP server itself)
- Code snippet + supported schemes
REST API Server section:
- Lists all 10 route modules from semantica/explorer/routes/ with paths
- WebSocket /ws endpoint
- Health check
Agno integration section:
- Expanded to table showing all 5 actual files in integrations/agno/
with class names and descriptions matching source code
AI Coding Tools table:
- Corrected connection types and setup notes to match actual code
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add 'AI Coding Tools & IDEs' table under Integrations listing every
tool from the visual grid with connection type and setup note:
Claude Code, Cursor, Windsurf, Claude Desktop, VS Code, GitHub
Copilot, Cline, Roo Code, Continue, Goose, Kilo Code, Aider,
Amazon Q, Zed, Claude SDK, REST API (109 endpoints)
- Add Neo4j to Graph Databases list (was in modules but missing here)
- Add Email and Repository ingestors to Data Sources
- Expand LLM Providers: add Groq, HuggingFace, Ollama entries
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
AI tools grid (removed Gemini CLI, Codex CLI; added VS Code, GitHub
Copilot, Continue, Amazon Q, Zed — all confirmed MCP-supporting tools
with significant user bases in 2026):
Row 1: Claude Code, Cursor, Windsurf, Claude Desktop, VS Code,
GitHub Copilot, Cline, Roo Code
Row 2: Continue, Goose, Kilo Code, Aider, Amazon Q, Zed,
Claude SDK, Any agent REST API
Agentic frameworks grid (added LangGraph and OpenAI Agents SDK, expanded
to 8 entries): Agno, LangChain, LangGraph, LlamaIndex, AutoGen, CrewAI,
OpenAI Agents SDK, Google ADK
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- New '🖥️ Semantica Knowledge Explorer' section placed after Plugins,
with a workspace-tab table (Graph, Timeline, Decisions, Registry,
Entity Resolution, KG Overview, Ontology), a 4-line quick-start
snippet, requirements line, and a pointer to explorer/README.md
- Added explorer/ row to the detailed Modules table with a link
- Added explorer/ bullet to the condensed Modules list
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- GraphWorkspace: set isRunningPredictions=true before link-prediction fetch
and false in finally block; pass isRunningPredictions prop to
LazyGraphInspectorPanel so the inspector button disables and shows a
spinner during the request (was declared but never wired — broke
noUnusedLocals TypeScript build)
- DecisionWorkspace: add AbortController to the /api/decisions useEffect
so the fetch is cancelled on unmount; add per-call AbortController to
handleSelectDecision for /api/decisions/:id/chain; add res.ok guards
before .json() on both fetches; encodeURIComponent on decision_id to
prevent path-injection edge cases
- index.css: add missing @keyframes skeleton-pulse rule (0%/100% opacity
0.45, 50% opacity 0.85) — KGOverviewTab skeletonBarStyle referenced
this animation but it was never defined, leaving skeleton bars static
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Documents all 12 vulnerability fixes (CRITICAL→LOW), 4 post-review bug
fixes, and CodeQL infrastructure changes under [Unreleased] following
the existing Keep a Changelog format.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
fix(agent_memory): implement MemoryItem.to_dict() / from_dict() for safe JSON
persistence — timestamps serialised via isoformat(), embeddings dropped (not
JSON-safe, regenerated on demand); save() and load() now round-trip correctly
without TypeError or AttributeError (Bug #1)
fix(sparql): add asyncio.Semaphore(_SPARQL_MAX_CONCURRENT=4) around graph.query
so timed-out threads cannot exhaust the default ThreadPoolExecutor; add
`truncated: bool` field to SparqlResponse so callers know when the 5 000-row
cap was hit (Bug #2)
fix(export_import): trim _ALLOWED_IMPORT_EXTENSIONS to {.json, .csv} — the only
formats the handler actually parses; removes .graphml/.gexf/.ttl/.rdf that
passed the allowlist check but hit a hard 422 inside the handler (Bug #3)
fix(codeql): remove blanket rule-ID auto-dismiss job; replace with a commented
template for pinning specific alert numbers — prevents future real alerts of
the same rule being silently suppressed (Bug #4)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
semantica/static/ is already in .gitignore but the 19 newly-hashed
build artifacts introduced by the main merge were still tracked.
Runs git rm --cached to complete the untracking so future frontend
builds do not create dirty working-tree diffs.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Bug 1 — non-string IDs crash store():
_resolve_iri() called .startswith() directly on local, causing AttributeError
when upstream graph builders emit integer entity/relationship IDs. Fixed by
coercing local to str() at entry; None/empty returns a safe urn: sentinel.
Bug 2 — prefixed W3C terms mis-resolved under base_uri:
Values like 'owl:Thing' and 'xsd:date' were not recognised as absolute IRIs
and with base_uri set were rewritten to e.g. https://example.com/owl:Thing,
corrupting standard OWL/XSD IRIs in stored triples. Fixed by adding a known-
prefix expansion table (xsd/rdf/rdfs/owl/skos/semantica) that is checked before
base_uri is applied, matching the same prefix map already used in blazegraph_store.
Added 5 regression tests covering both bugs: integer IDs with/without base_uri,
owl:Thing domain/range, xsd:date range, and rdfs:/skos: parent class expansion.
store() was minting urn:entity:, urn:class:, and urn:property: URIs for every
bare local name, even when the ontology carried a namespace.base_uri. This made
instance data and ontology class data irreconcilable in SPARQL joins.
- Extract base_uri from ontology.namespace.base_uri (or ontology.uri as fallback)
- Introduce _resolve_iri(local, kind) closure that appends the local name to
base_uri when present, keeping urn: fallback only when no base URI is known
- Apply _resolve_iri consistently for entity URIs, entity types, relationship
predicates, ontology class URIs, parent class URIs, property URIs, and
property domain/range URIs
- Explicit entity.uri values are never overridden
- Added 9 regression tests in TestTripletStoreOntologyNamespace covering all
IRI expansion paths, urn: fallback, explicit URI passthrough, top-level uri
key fallback, and trailing-slash safety
- Added _resolve_datatype_iri() to expand known prefixes (xsd/rdf/rdfs/owl/skos)
to full IRIs instead of blindly wrapping in <...>, fixing invalid SPARQL like
<xsd:integer>
- Validated language tags against RFC 5646 regex to prevent SPARQL injection
via metadata["lang"] values containing whitespace or punctuation
- Validated datatype IRIs for whitespace/special characters before interpolation
- Extended test suite from 7 to 15 cases covering prefix expansion, injection
rejection, and all accepted input forms
KaifAhmad1