Release v1.7.3

Author: Robbie1977

RELEASE_NOTES_v1.7.3.md

@@ -0,0 +1,5 @@
+## What's Changed
+
+- Rewrite `resolve_entity` and `resolve_combination` HA API requests that receive FlyBase IDs to use the preferred VFB term name before querying Chado.
+- Return `NOT_FOUND` instead of passing raw IDs to Chado when no preferred name/label can be derived from VFB term info.
+- Add focused HA API validation tests covering query normalization, ID rewriting, and the no-fallback path.

setup.py

@@ -3,7 +3,7 @@
 
 here = path.abspath(path.dirname(__file__))
 
-__version__ = "1.7.2"
+__version__ = "1.7.3"
 
 # Get the long description from the README file
 with open(path.join(here, 'README.md')) as f:

src/test/test_ha_api_validation.py

@@ -0,0 +1,92 @@
+"""Unit tests for HA API resolver query normalization and rewriting."""
+
+import pytest
+
+import vfbquery.ha_api as ha_api
+
+
+def test_parse_resolver_query_trims_whitespace():
+    query = ha_api._parse_resolver_query("  P{VT054895-GAL4.DBD}  ")
+
+    assert query == "P{VT054895-GAL4.DBD}"
+
+
+def test_rewrite_resolve_entity_query_uses_name_for_feature_ids(monkeypatch):
+    class DummyVfb:
+        def get_term_info(self, query, preview=False):
+            assert query == "FBgn0000490"
+            assert preview is False
+            return {"Name": "dpp"}
+
+    monkeypatch.setattr(ha_api, "_vfb", DummyVfb(), raising=False)
+
+    query = ha_api._rewrite_resolve_entity_query("fbGN0000490")
+
+    assert query == "dpp"
+
+
+def test_rewrite_resolve_combination_query_uses_name_for_fbco_ids(monkeypatch):
+    class DummyVfb:
+        def get_term_info(self, query, preview=False):
+            assert query == "FBco0000052"
+            assert preview is False
+            return {"Name": "GMR37H08-ZpGAL4DBD in attP2"}
+
+    monkeypatch.setattr(ha_api, "_vfb", DummyVfb(), raising=False)
+
+    query = ha_api._rewrite_resolve_combination_query("fbco0000052")
+
+    assert query == "GMR37H08-ZpGAL4DBD in attP2"
+
+
+def test_rewrite_resolve_entity_query_returns_none_when_no_term_info_name(monkeypatch):
+    class DummyVfb:
+        def get_term_info(self, query, preview=False):
+            assert query == "FBst0007144"
+            assert preview is False
+            return None
+
+    monkeypatch.setattr(ha_api, "_vfb", DummyVfb(), raising=False)
+
+    query = ha_api._rewrite_resolve_entity_query("fbst0007144")
+
+    assert query is None
+
+
+def test_run_resolve_entity_returns_not_found_when_id_cannot_be_rewritten(monkeypatch):
+    class DummyVfb:
+        def get_term_info(self, query, preview=False):
+            assert query == "FBst0007144"
+            assert preview is False
+            return None
+
+        def resolve_entity(self, query):
+            raise AssertionError("Chado resolver should not receive raw IDs")
+
+    monkeypatch.setattr(ha_api, "_vfb", DummyVfb(), raising=False)
+
+    result = ha_api._run_resolve_entity("fbst0007144")
+
+    assert result == {"match_type": "NOT_FOUND", "results": []}
+
+
+def test_run_resolve_combination_returns_not_found_when_id_cannot_be_rewritten(monkeypatch):
+    class DummyVfb:
+        def get_term_info(self, query, preview=False):
+            assert query == "FBco0000052"
+            assert preview is False
+            return None
+
+        def resolve_combination(self, query):
+            raise AssertionError("Chado resolver should not receive raw IDs")
+
+    monkeypatch.setattr(ha_api, "_vfb", DummyVfb(), raising=False)
+
+    result = ha_api._run_resolve_combination("fbco0000052")
+
+    assert result == {"match_type": "NOT_FOUND", "results": []}
+
+
+def test_parse_resolver_query_requires_query():
+    with pytest.raises(ValueError, match="Missing required parameter: query"):
+        ha_api._parse_resolver_query("   ")

src/vfbquery/__init__.py

@@ -98,4 +98,4 @@ def clear_solr_cache(query_type: str, term_id: str) -> bool:
     __solr_caching_available__ = False
 
 # Version information
-__version__ = "1.7.2"
+__version__ = "1.7.3"

src/vfbquery/flybase_combo_pubs.py

@@ -7,7 +7,12 @@
 
 
 def resolve_combination(name_or_id):
-    """Resolve a combination name, synonym, or FBco ID.
+    """Resolve a combination name or synonym.
+
+    This Python helper still accepts FBco IDs for backwards compatibility.
+    The HA API ``/resolve_combination`` endpoint prefers unresolved query text
+    and, if an FBco ID slips through, rewrites it to the combination name via
+    VFB term_info before resolving.
 
     Resolution order:
       1. If FBco ID: direct lookup by feature.uniquename

src/vfbquery/flybase_stocks.py

@@ -18,7 +18,12 @@ def _run_query(conn, sql, params):
 
 
 def resolve_entity(name_or_id):
-    """Resolve a user-provided name, symbol, or FlyBase ID to a canonical FlyBase feature.
+    """Resolve a user-provided name or symbol to a canonical FlyBase feature.
+
+    This Python helper still accepts FlyBase IDs for backwards compatibility.
+    The HA API ``/resolve_entity`` endpoint prefers unresolved query text and,
+    if an ID slips through, rewrites it to the feature name via VFB term_info
+    before resolving.
 
     Resolution order for names (not IDs):
       1. Exact match on feature.name

src/vfbquery/ha_api.py

@@ -15,6 +15,12 @@
 Endpoints (mirrors v3-cached.virtualflybrain.org):
     GET /get_term_info?id=<short_form>
     GET /run_query?id=<short_form>&query_type=<QueryType>
+    GET /resolve_entity?query=<name_or_symbol>         # IDs rewritten to names
+    GET /find_stocks?id=<resolved_flybase_feature_id>
+    GET /resolve_combination?query=<name_or_synonym>   # IDs rewritten to names
+    GET /find_combo_publications?id=<resolved_fbco_id>
+    GET /list_connectome_datasets
+    GET /query_connectivity?upstream_type=<name>&downstream_type=<name>
     GET /health
     GET /status          — queue depth, cache stats & worker utilisation
 
@@ -28,6 +34,7 @@
 import json
 import logging
 import os
+import re
 import sys
 import asyncio
 import time
@@ -53,6 +60,8 @@
 # or --workers CLI flag.
 DEFAULT_WORKERS = 10
 DEFAULT_MAX_QUEUE_DEPTH = 200
+_FLYBASE_FEATURE_ID_RE = re.compile(r"^FB(?:gn|al|ti|st|co)\d+$", re.IGNORECASE)
+_FBCO_ID_RE = re.compile(r"^FBco\d+$", re.IGNORECASE)
 
 
 # ---------------------------------------------------------------------------
@@ -317,7 +326,10 @@ def _run_query(short_form, func_name):
 
 def _run_resolve_entity(name_or_id):
     """Execute resolve_entity in a worker process."""
-    return _vfb.resolve_entity(name_or_id)
+    query = _rewrite_resolve_entity_query(name_or_id)
+    if query is None:
+        return {"match_type": "NOT_FOUND", "results": []}
+    return _vfb.resolve_entity(query)
 
 
 def _run_find_stocks(feature_id, collection_filter):
@@ -327,7 +339,10 @@ def _run_find_stocks(feature_id, collection_filter):
 
 def _run_resolve_combination(name_or_id):
     """Execute resolve_combination in a worker process."""
-    return _vfb.resolve_combination(name_or_id)
+    query = _rewrite_resolve_combination_query(name_or_id)
+    if query is None:
+        return {"match_type": "NOT_FOUND", "results": []}
+    return _vfb.resolve_combination(query)
 
 
 def _run_find_combo_publications(fbco_id):
@@ -368,6 +383,72 @@ def _convert_numpy_types(obj):
         return obj
 
 
+def _parse_resolver_query(query):
+    """Normalise a resolver query parameter."""
+    normalized = (query or "").strip()
+    if not normalized:
+        raise ValueError("Missing required parameter: query")
+    return normalized
+
+
+def _canonicalize_flybase_feature_id(feature_id):
+    """Return canonical FlyBase casing for a supported feature ID."""
+    match = re.match(r"^FB(gn|al|ti|st|co)(\d+)$", feature_id or "", re.IGNORECASE)
+    if not match:
+        return feature_id
+    return f"FB{match.group(1).lower()}{match.group(2)}"
+
+
+def _canonicalize_fbco_id(fbco_id):
+    """Return canonical FlyBase casing for an FBco ID."""
+    match = re.match(r"^FBco(\d+)$", fbco_id or "", re.IGNORECASE)
+    if not match:
+        return fbco_id
+    return f"FBco{match.group(1)}"
+
+
+def _preferred_term_info_query(term_info):
+    """Pick a stable name/label from VFB term_info."""
+    if not isinstance(term_info, dict):
+        return None
+
+    candidate = (term_info.get("Name") or "").strip()
+    if candidate:
+        return candidate
+
+    meta = term_info.get("Meta")
+    if isinstance(meta, dict):
+        for key in ("Symbol", "Name"):
+            candidate = (meta.get(key) or "").strip()
+            if candidate:
+                match = re.match(r"^\[(.+)\]\([^)]+\)$", candidate)
+                return match.group(1) if match else candidate
+
+    return None
+
+
+def _rewrite_resolve_entity_query(name_or_id):
+    """Rewrite a FlyBase feature ID to a preferred VFB term name."""
+    query = _parse_resolver_query(name_or_id)
+    if not _FLYBASE_FEATURE_ID_RE.match(query):
+        return query
+
+    canonical_id = _canonicalize_flybase_feature_id(query)
+    term_info = _vfb.get_term_info(canonical_id, preview=False)
+    return _preferred_term_info_query(term_info)
+
+
+def _rewrite_resolve_combination_query(name_or_id):
+    """Rewrite an FBco ID to a preferred VFB term name."""
+    query = _parse_resolver_query(name_or_id)
+    if not _FBCO_ID_RE.match(query):
+        return query
+
+    canonical_id = _canonicalize_fbco_id(query)
+    term_info = _vfb.get_term_info(canonical_id, preview=False)
+    return _preferred_term_info_query(term_info)
+
+
 # ---------------------------------------------------------------------------
 # HTTP handlers
 # ---------------------------------------------------------------------------
@@ -667,10 +748,12 @@ async def _dispatch_to_pool(request, cache_key, worker_fn, *args):
 
 
 async def handle_resolve_entity(request):
-    """GET /resolve_entity?query=<name_or_id>"""
-    query = request.query.get("query")
-    if not query:
-        return web.json_response({"error": "Missing required parameter: query"}, status=400)
+    """GET /resolve_entity?query=<name_or_symbol>"""
+    try:
+        query = _parse_resolver_query(request.query.get("query"))
+    except ValueError as exc:
+        return web.json_response({"error": str(exc)}, status=400)
+
     return await _dispatch_to_pool(
         request, f"resolve_entity:{query}", _run_resolve_entity, query
     )
@@ -689,10 +772,12 @@ async def handle_find_stocks(request):
 
 
 async def handle_resolve_combination(request):
-    """GET /resolve_combination?query=<name_or_id>"""
-    query = request.query.get("query")
-    if not query:
-        return web.json_response({"error": "Missing required parameter: query"}, status=400)
+    """GET /resolve_combination?query=<name_or_synonym>"""
+    try:
+        query = _parse_resolver_query(request.query.get("query"))
+    except ValueError as exc:
+        return web.json_response({"error": str(exc)}, status=400)
+
     return await _dispatch_to_pool(
         request, f"resolve_combination:{query}", _run_resolve_combination, query
     )