Bring the recorded Genomic Intelligence fixtures to contract revision 16

tests/sequence_scoring_tests/test_genomic_intelligence.py

@@ -80,7 +80,7 @@
     "data": {
         "task": "promoter",
         "model": "g0-promoter-2000bp",
-        "input": {"sequence_name": "demo", "sequence_length": 400},
+        "input": {"sequence_name": "demo"},
         "summary": {"total_windows": 1, "promoter_windows": 0, "threshold_used": 0.5},
         "regions": [],
         "window_details": [
@@ -103,7 +103,7 @@
     "data": {
         "task": "splice",
         "model": "g0-splice-bigbird",
-        "input": {"sequence_name": "demo", "sequence_length": 1200},
+        "input": {"sequence_name": "demo"},
         "summary": {"total_sites": 1, "donor_sites": 1, "acceptor_sites": 0, "total_windows": 1},
         "sites": [
             {
@@ -126,7 +126,7 @@
     "data": {
         "task": "enhancer",
         "model": "g0-deepstarr",
-        "input": {"sequence_name": "demo", "sequence_length": 1200},
+        "input": {"sequence_name": "demo"},
         "summary": {"total_windows": 1, "dev_score_max": -0.91, "hk_score_max": -0.09},
         "windows": [
             {
@@ -148,7 +148,7 @@
     "data": {
         "task": "chromatin",
         "model": "g0-deepsea",
-        "input": {"sequence_name": "demo", "sequence_length": 1200},
+        "input": {"sequence_name": "demo"},
         "summary": {
             "total_windows": 1,
             "total_annotations": 383,
@@ -164,7 +164,7 @@
     "data": {
         "task": "annotation",
         "model": "g0-annotation",
-        "input": {"sequence_name": "demo", "sequence_length": 25000},
+        "input": {"sequence_name": "demo"},
         "summary": {"total_transcripts": 1, "forward_strand": 1, "reverse_strand": 0},
         "transcripts": [
             {
@@ -186,7 +186,7 @@
     "data": {
         "task": "expression",
         "model": "g0-expression",
-        "input": {"sequence_name": "demo", "sequence_length": 9198},
+        "input": {"sequence_name": "demo", "description": "K562 RNA-seq", "tss_index": 4599},
         "summary": {},
         "prediction": {
             "expression": 0.95,
@@ -203,7 +203,7 @@
         "task": "find_genes_and_predict_expression",
         "annotation_model": "g0-annotation",
         "expression_model": "g0-expression",
-        "input": {"sequence_name": "HBB", "sequence_length": 25000},
+        "input": {"sequence_name": "HBB", "description": "HBB locus"},
         "summary": {"genes_found": 2, "genes_predicted": 1, "genes_skipped": 1},
         "annotation": {},
         "expression_predictions": [
@@ -304,14 +304,65 @@ def test_parse_expression_reads_applied_window_from_meta() -> None:
     assert result.scored_window == [0, 9198]
 
 
+def test_recorded_input_echoes_carry_no_derived_key() -> None:
+    """No recorded ``data.input`` carries a key the service stopped echoing.
+
+    Contract revision 16 (2026-09-06) made every ``data.input`` a closed object:
+    ``additionalProperties: false``, every field required. The published shapes
+    are ``{sequence_name}`` for promoter / splice / enhancer / chromatin /
+    annotation, ``{sequence_name, description, tss_index}`` for expression, and
+    ``{sequence_name, description}`` for the composite workflow.
+
+    These fixtures are recorded bodies, so nothing upstream keeps them honest --
+    a stale one simply describes a service that no longer exists, and the client
+    it exercises goes on passing. This test is that check. It deliberately does
+    not cover the adversarial payload below, which keeps the removed keys on
+    purpose.
+    """
+    derived = {"sequence_length", "submitted_sequence_length", "scored_window"}
+    recorded = {
+        "promoter": _PROMOTER_PAYLOAD,
+        "splice": _SPLICE_PAYLOAD,
+        "enhancer": _ENHANCER_PAYLOAD,
+        "chromatin": _CHROMATIN_PAYLOAD,
+        "annotation": _ANNOTATION_PAYLOAD,
+        "expression": _EXPRESSION_PAYLOAD,
+        "workflow": _WORKFLOW_PAYLOAD,
+    }
+    for task, payload in recorded.items():
+        echo = payload["data"]["input"]
+        assert derived.isdisjoint(echo), f"{task} echo still carries {derived & set(echo)}"
+
+
+def test_the_recorded_expression_echo_matches_the_published_shape() -> None:
+    """Expression echoes exactly its three inputs, and the composite its two."""
+    assert set(_EXPRESSION_PAYLOAD["data"]["input"]) == {
+        "sequence_name",
+        "description",
+        "tss_index",
+    }
+    assert set(_WORKFLOW_PAYLOAD["data"]["input"]) == {"sequence_name", "description"}
+
+
 def test_parse_expression_takes_the_submitted_length_from_meta_not_the_echo() -> None:
     """``sequence_length`` is the submission, read from ``meta``.
 
-    ``data.input`` carries a ``sequence_length`` of its own holding the 9,198 bp
-    scored window, so the two disagree for any locus longer than one window.
-    Only ``meta.sequence_length`` is in the published schema; the echo is an
-    untyped object no contract pin covers. This payload makes them disagree so
-    that reading the echo fails here rather than in a user's report.
+    ``data.input`` used to carry a ``sequence_length`` of its own holding the
+    9,198 bp scored window, so the two disagreed for any locus longer than one
+    window. The service dropped that key from the echo at contract revision 13
+    (2026-09-03), then dropped ``submitted_sequence_length`` and
+    ``scored_window`` at revision 16 (2026-09-06), which also made every
+    ``data.input`` a typed, closed object -- ``additionalProperties: false``,
+    every field required, and covered by the consumer pins for the first time.
+    Only ``meta`` carries the derived numbers: ``meta.sequence_length`` for the
+    submission and ``meta.task_specific_counts.scored_window`` for the window.
+
+    A recorded body is not the live document, so being closed upstream does not
+    stop an older payload -- or a replayed cassette -- still carrying the
+    removed keys. That is what this test is for: the payload below keeps all
+    three and makes them disagree with ``meta``, so reading the echo fails here
+    rather than in a user's report. Do not "fix" this fixture by making it match
+    the current contract; its whole value is that it does not.
     """
     payload = {
         "data": {
@@ -600,7 +651,7 @@ def _install_session(
     return session
 
 
-_GOOD_DATA = {"model": "g0-promoter-2000bp", "input": {"sequence_length": 400}, "summary": {"total_windows": 1}}
+_GOOD_DATA = {"model": "g0-promoter-2000bp", "input": {"sequence_name": "demo"}, "summary": {"total_windows": 1}}
 
 _BAD_SUMMARY_PAYLOAD: dict[str, Any] = {"data": {**_GOOD_DATA, "summary": "all good"}, "meta": _META}
 
@@ -1087,9 +1138,15 @@ def test_gi_expression_benchmark() -> None:
     result = output.results[0]
     # This locus is longer than one window, so it is the only place the two
     # quantities can be told apart: sequence_length must be what was submitted
-    # (meta), and the window must stay 9,198 wide. data.input carries a
-    # sequence_length of its own holding the window -- reading that one is the
-    # mistake these two assertions exist to catch.
+    # (meta), and the window must stay 9,198 wide. data.input used to carry a
+    # sequence_length of its own holding the window, and reading that one
+    # instead of meta is the mistake these two assertions exist to catch. The
+    # service dropped that key at contract revision 13 on 2026-09-03, and at
+    # revision 16 on 2026-09-06 dropped scored_window and
+    # submitted_sequence_length too, closing data.input against extra keys. So
+    # today a reader of the echo gets None rather than the window -- still
+    # wrong, and still caught here. This is a live call, so it also fails if
+    # the service ever reopens the echo and a reader drifts back to it.
     assert result.sequence_length == len(locus)
     assert result.scored_window is not None
     assert result.scored_window[1] - result.scored_window[0] == EXPRESSION_WINDOW_BP