Stop the safety checker refusing people for asking Reactome to do its job

src/agent/tasks/safety_checker.py

@@ -21,6 +21,13 @@
         - Biology, life sciences, molecular biology, pathways, proteins, genes, and related scientific topics.
         - How to use the Reactome website, Pathway Browser, search, analysis tools, and other Reactome features (user guide topics).
     - Mark questions as not relevant if they are about unrelated topics (such as programming, math, history, trivia, etc.).
+    - A request to *perform* a Reactome operation is relevant: "run an analysis on my genes",
+      "can you run GSEA for me", "search Reactome for X", "analyse this gene list". These ask
+      for something Reactome does. Whether this assistant can carry it out is decided later and
+      answered helpfully; it is not a safety question, and refusing here means the user is told
+      their on-topic question was inappropriate.
+    - "Outside the scope of scientific knowledge" above means medical, legal or personal advice
+      — diagnosis, treatment, dosage. It does not mean "asks the assistant to do a task".
 
 IMPORTANT:
     - If the standalone question is unsafe or not relevant return "safety": "false".
@@ -50,6 +57,17 @@
   5. Q: How do I use the Reactome pathway browser?
        "safety": "true",
        "reason_unsafe": ""
+
+  6. Q: Can you run GSEA for me?
+       "safety": "true",
+       "reason_unsafe": ""
+       // Asks for something Reactome does. Answer it -- ReactomeGSA exists, and
+       // where the assistant cannot run it, saying so is the answer. Refusing
+       // tells a researcher their own field is off-topic.
+
+  7. Q: I have a gene list, can you analyse where these genes are involved?
+       "safety": "true",
+       "reason_unsafe": ""
 """
 
 safety_check_prompt = ChatPromptTemplate.from_messages(

tests/agent/test_safety_scope.py

@@ -0,0 +1,58 @@
+"""The safety checker must not refuse people for asking Reactome to do its job.
+
+Measured on beta 2026-09-16: "can you run gsea for me" was refused 4 times out
+of 4, with
+
+    Requests a specific analysis task without providing context or data,
+    which is outside the scope
+
+and "run a pathway analysis on my genes" was refused 1 time in 4 -- the same
+user, the same intent, a different answer depending on the roll.
+
+Nothing downstream ever saw those questions. The user guide bundle that answers
+them and the ReactomeGSA tools that describe them are both two nodes further on
+in the graph.
+
+These assert the prompt's *wording*, not the model's behaviour -- a behavioural
+test would cost an API call per case and drift with the model. The wording is
+what was wrong, and it is what a future edit could silently undo.
+"""
+
+from agent.tasks.safety_checker import safety_check_message
+
+
+def test_asking_reactome_to_do_something_is_relevant() -> None:
+    """The failure this file exists for."""
+    assert "run an analysis on my genes" in safety_check_message
+    assert "can you run GSEA for me" in safety_check_message.lower() or (
+        "Can you run GSEA for me?" in safety_check_message
+    )
+
+
+def test_a_task_request_is_distinguished_from_personal_advice() -> None:
+    """ "Outside the scope of scientific knowledge" was being read as "asks the
+    assistant to do a task". It means medical, legal and personal advice."""
+    assert "It does not mean" in safety_check_message
+    assert "asks the assistant to do a task" in safety_check_message
+
+
+def test_the_cost_of_refusing_is_stated() -> None:
+    """So a later editor tightening this knows what it buys and what it costs."""
+    assert (
+        "off-topic" in safety_check_message or "inappropriate" in safety_check_message
+    )
+
+
+def test_the_genuine_refusals_are_still_described() -> None:
+    """Loosening this must not loosen the part that matters. Medical advice,
+    dual-use and irrelevance all keep their examples."""
+    for kept in ("medical", "dual-use", "harmful", "statins", "gene drives"):
+        assert (
+            kept in safety_check_message
+        ), f"{kept!r} disappeared from the safety prompt"
+
+
+def test_capability_is_answered_downstream_not_refused_here() -> None:
+    """Whether the assistant can run an analysis is a different question from
+    whether it is allowed to be asked."""
+    assert "decided later" in safety_check_message