- Convert mcp_server.py to package structure (semantica/mcp_server/)
- Add __init__.py and __main__.py for python -m support
- Add semantica-mcp console script entry point in pyproject.toml
- Fix API method calls (extract -> extract_entities/relations/triplets)
- Remove non-existent _result_cache imports
- Update documentation with both usage methods
Resolves pipx installation issue where semantica.mcp_server was not available.
Provides two ways to run: 'semantica-mcp' command or 'python -m semantica.mcp_server'.
- 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`
* fix(deps): remove gpu extra from [all] to fix Windows installation failure
faiss-gpu has no Windows builds, so semantica[all] failed with
'No matching distribution found for faiss-gpu>=1.7.0' on Windows.
Removed gpu from both [all] lines — semantica[gpu] remains available
as an explicit opt-in for Linux GPU environments.
Closes#532
* docs(changelog): record faiss-gpu Windows installation failure fix (#532)
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>
2026-05-05 13:40:11 +05:30
Mohd KaifandCopilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
* fix(ingest): lazy-load optional ingestion backends
* fix(ingest): address qodo review — use ModuleNotFoundError and guard ConfigurationError
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>
* docs(changelog): record lazy ingest backends fix and qodo review fixes (#535)
Co-authored-by: ZohaibHassan16 <zohaib@hawksight.ai>
Co-authored-by: KaifAhmad1 <mohammadk78600@gmail.com>
* fix(tests): set exc.name on blocker's ModuleNotFoundError to match Python import machinery
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: Zohaib Hassan (@ZohaibHassan16) <zohaib179949@gmail.com>
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
---------
Co-authored-by: KaifAhmad1 <kaifahmad087@gmail.com>
Co-authored-by: Zohaib Hassan (@ZohaibHassan16) <zohaib179949@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.
Mohd Kaif