Fbtp stocks

src/test/test_flybase_combo_pubs.py

@@ -2,6 +2,17 @@
 import pytest
 
 from vfbquery.flybase_combo_pubs import resolve_combination, find_combo_publications
+from vfbquery.vfb_queries import get_flybase_combo_pubs
+
+
+def assert_single_selection_id(result):
+    """A result table must declare exactly one `selection_id` identity column,
+    hidden at order -1, so the website doesn't consume a visible data column as
+    the row identity (regression: FBrf column went missing on the site)."""
+    headers = result["headers"]
+    sel = [c for c, m in headers.items() if m.get("type") == "selection_id"]
+    assert len(sel) == 1, f"expected exactly one selection_id column, got {sel}"
+    assert headers[sel[0]]["order"] == -1, "selection_id column must be hidden (order -1)"
 
 KNOWN_COMBO_ID = "FBco0000052"
 KNOWN_COMBO_SYNONYM = "MB002B"
@@ -89,3 +100,20 @@ def test_nonexistent_combo(self):
     def test_invalid_id_prefix(self):
         with pytest.raises(ValueError, match="Expected FBco"):
             find_combo_publications("FBgn0000490")
+
+
+class TestComboPubsTableSchema:
+    @pytest.mark.integration
+    def test_single_selection_id_column(self):
+        result = get_flybase_combo_pubs(KNOWN_COMBO_ID, return_dataframe=False, limit=3)
+        assert_single_selection_id(result)
+
+    @pytest.mark.integration
+    def test_fbrf_is_a_visible_column(self):
+        # fbrf must be a normal displayed column, not the (hidden) identity.
+        result = get_flybase_combo_pubs(KNOWN_COMBO_ID, return_dataframe=False, limit=3)
+        fbrf = result["headers"]["fbrf"]
+        assert fbrf["type"] == "text"
+        assert fbrf["order"] >= 0
+        if result["rows"]:
+            assert result["rows"][0]["id"] == result["rows"][0]["fbrf"]

src/test/test_flybase_stocks.py

@@ -2,6 +2,18 @@
 import pytest
 
 from vfbquery.flybase_stocks import resolve_entity, find_stocks
+from vfbquery.vfb_queries import get_flybase_stocks
+
+
+def assert_single_selection_id(result):
+    """A result table must declare exactly one `selection_id` identity column,
+    hidden at order -1. Without it the website consumes the first visible data
+    column as the row identity and drops it from the table (regression: the
+    Stock ID / FBrf columns went missing on the site)."""
+    headers = result["headers"]
+    sel = [c for c, m in headers.items() if m.get("type") == "selection_id"]
+    assert len(sel) == 1, f"expected exactly one selection_id column, got {sel}"
+    assert headers[sel[0]]["order"] == -1, "selection_id column must be hidden (order -1)"
 
 # Known stable test entities
 KNOWN_GENE_SYMBOL = "dpp"
@@ -154,6 +166,47 @@ def test_stock_includes_collection(self):
         assert any("Bloomington" in str(s.get("collection", "")) for s in stocks)
 
 
+class TestFindStocksConstruct:
+    # FBtp0000352 = P{GawB} — a widely-used construct carried by many insertions.
+    KNOWN_CONSTRUCT_ID = "FBtp0000352"
+
+    @pytest.mark.integration
+    def test_known_construct_returns_stocks(self):
+        # A construct is not held in stocks directly; stocks are propagated from
+        # the FBti insertions producedby it.
+        stocks = find_stocks(self.KNOWN_CONSTRUCT_ID)
+        assert len(stocks) > 0
+        assert all("stock_id" in s for s in stocks)
+
+    @pytest.mark.integration
+    def test_construct_stocks_have_fbst(self):
+        stocks = find_stocks(self.KNOWN_CONSTRUCT_ID)
+        assert any(s["stock_id"].startswith("FBst") for s in stocks)
+
+    @pytest.mark.integration
+    def test_construct_collection_filter(self):
+        all_stocks = find_stocks(self.KNOWN_CONSTRUCT_ID)
+        filtered = find_stocks(self.KNOWN_CONSTRUCT_ID, collection_filter="Bloomington")
+        assert 0 < len(filtered) <= len(all_stocks)
+        for s in filtered:
+            if s.get("collection"):
+                assert "Bloomington" in s["collection"]
+
+    @pytest.mark.integration
+    def test_construct_stocks_via_allele_path(self):
+        # FBtp0000162 = P{CaSpeR-3}: has stocks ONLY through alleles made from it
+        # (zero via the producedby-insertion route). Regression guard for the
+        # multi-path UNION — a single insertion-only query returns 0 here.
+        stocks = find_stocks("FBtp0000162")
+        assert len(stocks) > 0
+        assert all(s["stock_id"].startswith("FBst") for s in stocks)
+
+    @pytest.mark.integration
+    def test_nonexistent_construct(self):
+        stocks = find_stocks("FBtp9999999999")
+        assert stocks == []
+
+
 class TestFindStocksCombination:
     @pytest.mark.integration
     def test_known_combination(self):
@@ -172,6 +225,25 @@ def test_nonexistent_combination(self):
         assert stocks == []
 
 
+class TestFindStocksTableSchema:
+    CONSTRUCT_WITH_STOCKS = "FBtp0000352"  # P{GawB}
+
+    @pytest.mark.integration
+    def test_single_selection_id_column(self):
+        result = get_flybase_stocks(self.CONSTRUCT_WITH_STOCKS, return_dataframe=False, limit=3)
+        assert_single_selection_id(result)
+
+    @pytest.mark.integration
+    def test_stock_id_is_a_visible_column(self):
+        # stock_id must be a normal displayed column, not the (hidden) identity.
+        result = get_flybase_stocks(self.CONSTRUCT_WITH_STOCKS, return_dataframe=False, limit=3)
+        stock_id = result["headers"]["stock_id"]
+        assert stock_id["type"] == "text"
+        assert stock_id["order"] >= 0
+        # and the hidden identity carries the same FBst value
+        assert result["rows"][0]["id"] == result["rows"][0]["stock_id"]
+
+
 class TestFindStocksEdgeCases:
     @pytest.mark.integration
     def test_nonexistent_gene_id(self):

src/vfbquery/flybase_stocks.py

@@ -1,4 +1,4 @@
-"""Find FlyBase stocks for genes, alleles, insertions, or split system combinations."""
+"""Find FlyBase stocks for genes, alleles, insertions, transgenic constructs, or split system combinations."""
 import re
 
 import pandas as pd
@@ -30,7 +30,7 @@ def resolve_entity(name_or_id):
       2. Synonym match via feature_synonym (case-insensitive ILIKE)
       3. Broad match via feature.name ILIKE '%query%'
 
-    :param name_or_id: Gene name, allele symbol, or FlyBase ID (FBgn/FBal/FBti/FBst/FBco)
+    :param name_or_id: Gene name, allele symbol, or FlyBase ID (FBgn/FBal/FBti/FBtp/FBst/FBco)
     :return: dict with 'match_type' and 'results' list
     """
     conn = get_connection(statement_timeout_ms=30000)
@@ -308,6 +308,63 @@ def _resolve_entity_impl(conn, name_or_id):
   AND s.is_obsolete = false
 """
 
+_CONSTRUCT_STOCKS_SQL = """
+WITH all_stocks AS (
+  -- A construct (FBtp) is not itself held in stocks; it reaches them three ways.
+  -- Path 1 alone misses ~1,400 construct/stock pairs and leaves 127 constructs
+  -- (e.g. FBtp0000162 P{CaSpeR-3}) with zero stocks despite carrying some.
+
+  -- Path 1: construct <- producedby - FBti insertion -> genotype -> stock
+  SELECT DISTINCT s.uniquename AS stock_id, s.name AS stock_number,
+         g.uniquename AS genotype, sc.uniquename AS collection
+  FROM feature tp
+  JOIN feature_relationship fr2 ON tp.feature_id = fr2.object_id
+  JOIN cvterm c2 ON fr2.type_id = c2.cvterm_id AND c2.name = 'producedby'
+  JOIN feature ti ON fr2.subject_id = ti.feature_id AND ti.is_obsolete = false
+  JOIN feature_genotype fg ON ti.feature_id = fg.feature_id
+  JOIN genotype g ON fg.genotype_id = g.genotype_id
+  JOIN stock_genotype sg ON g.genotype_id = sg.genotype_id
+  JOIN stock s ON sg.stock_id = s.stock_id AND s.is_obsolete = false
+  LEFT JOIN stockcollection_stock scs ON s.stock_id = scs.stock_id
+  LEFT JOIN stockcollection sc ON scs.stockcollection_id = sc.stockcollection_id
+  WHERE tp.uniquename = %(feature_id)s AND tp.is_obsolete = false
+
+  UNION
+
+  -- Path 2: construct -> genotype -> stock (construct sits directly in the genotype)
+  SELECT DISTINCT s.uniquename, s.name, g.uniquename, sc.uniquename
+  FROM feature tp
+  JOIN feature_genotype fg ON tp.feature_id = fg.feature_id
+  JOIN genotype g ON fg.genotype_id = g.genotype_id
+  JOIN stock_genotype sg ON g.genotype_id = sg.genotype_id
+  JOIN stock s ON sg.stock_id = s.stock_id AND s.is_obsolete = false
+  LEFT JOIN stockcollection_stock scs ON s.stock_id = scs.stock_id
+  LEFT JOIN stockcollection sc ON scs.stockcollection_id = sc.stockcollection_id
+  WHERE tp.uniquename = %(feature_id)s AND tp.is_obsolete = false
+
+  UNION
+
+  -- Path 3: construct <- (associated_with|derived_tp_assoc_alleles) - allele
+  --         -> genotype -> stock (allele made from this construct, held directly)
+  SELECT DISTINCT s.uniquename, s.name, g.uniquename, sc.uniquename
+  FROM feature tp
+  JOIN feature_relationship fr1 ON tp.feature_id = fr1.object_id
+  JOIN cvterm cr ON fr1.type_id = cr.cvterm_id
+    AND cr.name IN ('associated_with', 'derived_tp_assoc_alleles')
+  JOIN feature al ON fr1.subject_id = al.feature_id AND al.is_obsolete = false
+  JOIN cvterm cal ON al.type_id = cal.cvterm_id AND cal.name = 'allele'
+  JOIN feature_genotype fg ON al.feature_id = fg.feature_id
+  JOIN genotype g ON fg.genotype_id = g.genotype_id
+  JOIN stock_genotype sg ON g.genotype_id = sg.genotype_id
+  JOIN stock s ON sg.stock_id = s.stock_id AND s.is_obsolete = false
+  LEFT JOIN stockcollection_stock scs ON s.stock_id = scs.stock_id
+  LEFT JOIN stockcollection sc ON scs.stockcollection_id = sc.stockcollection_id
+  WHERE tp.uniquename = %(feature_id)s AND tp.is_obsolete = false
+)
+SELECT stock_id, stock_number, genotype, collection
+FROM all_stocks
+"""
+
 _STOCK_DETAILS_SQL = """
 SELECT
     s.uniquename AS stock_id,
@@ -374,6 +431,21 @@ def _find_stocks_insertion(conn, feature_id, collection_filter=None):
     return _run_query(conn, sql, params)
 
 
+def _find_stocks_construct(conn, construct_id, collection_filter=None):
+    """Find stocks for a transgenic construct (FBtp) via three UNION paths.
+
+    A construct is not itself held in stocks; it reaches them through
+    (1) the FBti insertions producedby it, (2) direct genotype membership, and
+    (3) alleles made from it (associated_with / derived_tp_assoc_alleles) that
+    are held directly. Path 1 alone leaves 127 constructs with zero stocks.
+    """
+    sql = _CONSTRUCT_STOCKS_SQL
+    params = {"feature_id": construct_id}
+    sql = _add_collection_filter(sql, params, collection_filter, use_where=True)
+    sql += "ORDER BY collection, stock_number;"
+    return _run_query(conn, sql, params)
+
+
 def _find_stocks_combination(conn, combo_id, collection_filter=None):
     """Find stocks for a split system combination via its component alleles."""
     components = _run_query(conn, _COMBO_COMPONENTS_SQL, {"combo_id": combo_id})
@@ -411,14 +483,16 @@ def find_stocks(feature_id, collection_filter=None):
       - FBgn: gene (4-path UNION, 120s timeout)
       - FBal: allele (3-path UNION, 60s timeout)
       - FBti: insertion (direct, 60s timeout)
+      - FBtp: transgenic construct (via its insertions, 120s timeout)
       - FBco: combination (component alleles, 60s timeout)
       - FBst: stock details (direct lookup, 60s timeout)
 
-    :param feature_id: FlyBase ID (FBgn/FBal/FBti/FBco/FBst)
+    :param feature_id: FlyBase ID (FBgn/FBal/FBti/FBtp/FBco/FBst)
     :param collection_filter: Optional stock collection name filter (e.g. "Bloomington")
     :return: list of stock dicts
     """
-    timeout = 120000 if feature_id.startswith("FBgn") else 60000
+    # FBgn (gene) and FBtp (construct) fan out to many insertions, so allow longer.
+    timeout = 120000 if feature_id.startswith(("FBgn", "FBtp")) else 60000
     conn = get_connection(statement_timeout_ms=timeout)
 
     try:
@@ -428,14 +502,16 @@ def find_stocks(feature_id, collection_filter=None):
             df = _find_stocks_allele(conn, feature_id, collection_filter)
         elif feature_id.startswith("FBti"):
             df = _find_stocks_insertion(conn, feature_id, collection_filter)
+        elif feature_id.startswith("FBtp"):
+            df = _find_stocks_construct(conn, feature_id, collection_filter)
         elif feature_id.startswith("FBco"):
             df = _find_stocks_combination(conn, feature_id, collection_filter)
         elif feature_id.startswith("FBst"):
             df = _find_stock_details(conn, feature_id)
         else:
             raise ValueError(
                 f"Unrecognised ID prefix: {feature_id}. "
-                "Expected FBgn, FBal, FBti, FBst, or FBco."
+                "Expected FBgn, FBal, FBti, FBtp, FBst, or FBco."
             )
 
         if df.empty:

src/vfbquery/vfb_queries.py

@@ -1383,7 +1383,11 @@ def term_info_parse_object(results, short_form):
                 },
             })
 
-        # FlyBase stock finder — for Feature terms (FBgn/FBal/FBti/FBtp/FBco/FBst)
+        # FlyBase stock finder. Prefix-gated (not by a single SuperType): genes
+        # and combinations aren't `Feature` nodes but still have stocks. Every
+        # prefix here has a matching router branch in flybase_stocks.find_stocks
+        # — FBtp (construct) resolves via its insertions, direct genotype
+        # membership, and the alleles made from it.
         sf = vfbTerm.term.core.short_form
         if sf.startswith(("FBgn", "FBal", "FBti", "FBtp", "FBco", "FBst")):
             q = FindStocks_to_schema(termInfo["Name"], {"short_form": sf})
@@ -4770,6 +4774,11 @@ def get_flybase_stocks(short_form: str, return_dataframe=True, limit: int = -1):
     rows = []
     for s in stocks:
         rows.append({
+            # Hidden identity column (the FBst the row is about). Without a
+            # `selection_id`-typed column the website consumes the first data
+            # column as the row identity and hides it — which dropped Stock ID
+            # from the table. See the `id` header below.
+            'id': s.get('stock_id', ''),
             'stock_id': s.get('stock_id', ''),
             'stock_number': s.get('stock_number', ''),
             'genotype': s.get('genotype', ''),
@@ -4784,6 +4793,7 @@ def get_flybase_stocks(short_form: str, return_dataframe=True, limit: int = -1):
         return pd.DataFrame(rows)
 
     headers = {
+        'id': {'title': 'ID', 'type': 'selection_id', 'order': -1},
         'stock_id': {'title': 'Stock ID', 'type': 'text', 'order': 0},
         'stock_number': {'title': 'Stock Number', 'type': 'text', 'order': 1},
         'genotype': {'title': 'Genotype', 'type': 'text', 'order': 2},
@@ -4813,6 +4823,10 @@ def get_flybase_combo_pubs(short_form: str, return_dataframe=True, limit: int =
     rows = []
     for p in pubs:
         rows.append({
+            # Hidden identity column (the FBrf the row is about). Mirrors the
+            # stocks fix: without a `selection_id` column the website consumes
+            # the first data column (FBrf) as the row identity and hides it.
+            'id': p.get('fbrf', ''),
             'fbrf': p.get('fbrf', ''),
             'title': p.get('title', ''),
             'year': p.get('year', ''),
@@ -4831,6 +4845,7 @@ def get_flybase_combo_pubs(short_form: str, return_dataframe=True, limit: int =
         return pd.DataFrame(rows)
 
     headers = {
+        'id': {'title': 'ID', 'type': 'selection_id', 'order': -1},
         'fbrf': {'title': 'FBrf', 'type': 'text', 'order': 0},
         'title': {'title': 'Title', 'type': 'text', 'order': 1},
         'year': {'title': 'Year', 'type': 'text', 'order': 2},