Gate gene DE methods in pairwise; centralise DE-method vocabulary

src/mcp_tools/pipelines/anova.py

@@ -4,7 +4,11 @@
 
 from md_python.models.dataset_builders import MinimalDataset
 from md_python.models.dataset_builders._methods import (
+    _APEGLM_SEED_RANGE,
     _DE_METHODS_PER_ENTITY,
+    _DESEQ2_ALPHA_RANGE,
+    _DESEQ2_LFC_SHRINKAGE,
+    _EDGER_NORM_METHODS,
     _ENTITY_TYPES,
     _de_method_key,
 )
@@ -196,26 +200,28 @@ def run_anova(
             f"Allowed: {sorted(allowed_de)}"
         )
     if de_method == "edgeR":
-        if edger_norm_method not in {"TMM", "RLE", "upperquartile", "none"}:
+        if edger_norm_method not in _EDGER_NORM_METHODS:
             raise ValueError(
-                "edger_norm_method must be one of: TMM, RLE, upperquartile, none "
-                f"(got '{edger_norm_method}')"
+                "edger_norm_method must be one of: "
+                f"{sorted(_EDGER_NORM_METHODS)} (got '{edger_norm_method}')"
             )
     if de_method == "DESeq2":
-        if deseq2_lfc_shrinkage not in {"none", "apeglm", "ashr", "normal"}:
+        if deseq2_lfc_shrinkage not in _DESEQ2_LFC_SHRINKAGE:
             raise ValueError(
-                "deseq2_lfc_shrinkage must be one of: none, apeglm, ashr, normal "
-                f"(got '{deseq2_lfc_shrinkage}')"
+                "deseq2_lfc_shrinkage must be one of: "
+                f"{sorted(_DESEQ2_LFC_SHRINKAGE)} (got '{deseq2_lfc_shrinkage}')"
             )
-        if not 0.0 <= deseq2_alpha <= 1.0:
+        _alpha_lo, _alpha_hi = _DESEQ2_ALPHA_RANGE
+        if not _alpha_lo <= deseq2_alpha <= _alpha_hi:
             raise ValueError(
-                "deseq2_alpha must be between 0 and 1 "
+                f"deseq2_alpha must be between {_alpha_lo} and {_alpha_hi} "
                 f"(got {deseq2_alpha})"
             )
         if deseq2_lfc_shrinkage == "apeglm":
-            if not 0 <= apeglm_seed <= 2147483647:
+            _seed_lo, _seed_hi = _APEGLM_SEED_RANGE
+            if not _seed_lo <= apeglm_seed <= _seed_hi:
                 raise ValueError(
-                    "apeglm_seed must be between 0 and 2147483647 "
+                    f"apeglm_seed must be between {_seed_lo} and {_seed_hi} "
                     f"(got {apeglm_seed})"
                 )
 

src/mcp_tools/pipelines/pairwise.py

@@ -5,6 +5,13 @@
 from typing import Any, Dict, List, Optional
 
 from md_python.models.dataset_builders import PairwiseComparisonDataset
+from md_python.models.dataset_builders._methods import (
+    _APEGLM_SEED_RANGE,
+    _DE_METHODS_PER_ENTITY,
+    _DESEQ2_ALPHA_RANGE,
+    _DESEQ2_LFC_SHRINKAGE,
+    _EDGER_NORM_METHODS,
+)
 from md_python.models.metadata import SampleMetadata
 
 from .. import mcp
@@ -227,6 +234,49 @@ def run_pairwise_comparison(
             "matches what the server actually does. Re-confirm with the user.\n\n"
         )
 
+    # DE method gating. Only entity_type='gene' accepts edgeR / DESeq2;
+    # protein/peptide/metabolite/ptm are limma-only. Validate here so an invalid
+    # combo fails fast with a clear message instead of being rejected downstream
+    # by the server. (run_pairwise_comparison_bulk routes through this function,
+    # so it inherits the gate.) Allowed values come from _methods.py; this block
+    # is intentionally kept separate from anova.py's so the two can diverge.
+    allowed_de = _DE_METHODS_PER_ENTITY.get(entity_type)
+    if allowed_de is None:
+        raise ValueError(
+            f"unknown entity_type '{entity_type}'. "
+            f"Allowed: {sorted(_DE_METHODS_PER_ENTITY)}"
+        )
+    if de_method not in allowed_de:
+        raise ValueError(
+            f"de_method '{de_method}' not allowed for entity_type='{entity_type}'. "
+            f"Allowed: {sorted(allowed_de)}"
+        )
+    if de_method == "edgeR":
+        if edger_norm_method not in _EDGER_NORM_METHODS:
+            raise ValueError(
+                "edger_norm_method must be one of: "
+                f"{sorted(_EDGER_NORM_METHODS)} (got '{edger_norm_method}')"
+            )
+    if de_method == "DESeq2":
+        if deseq2_lfc_shrinkage not in _DESEQ2_LFC_SHRINKAGE:
+            raise ValueError(
+                "deseq2_lfc_shrinkage must be one of: "
+                f"{sorted(_DESEQ2_LFC_SHRINKAGE)} (got '{deseq2_lfc_shrinkage}')"
+            )
+        _alpha_lo, _alpha_hi = _DESEQ2_ALPHA_RANGE
+        if not _alpha_lo <= deseq2_alpha <= _alpha_hi:
+            raise ValueError(
+                f"deseq2_alpha must be between {_alpha_lo} and {_alpha_hi} "
+                f"(got {deseq2_alpha})"
+            )
+        if deseq2_lfc_shrinkage == "apeglm":
+            _seed_lo, _seed_hi = _APEGLM_SEED_RANGE
+            if not _seed_lo <= apeglm_seed <= _seed_hi:
+                raise ValueError(
+                    f"apeglm_seed must be between {_seed_lo} and {_seed_hi} "
+                    f"(got {apeglm_seed})"
+                )
+
     dataset_id = PairwiseComparisonDataset(
         input_dataset_ids=input_dataset_ids,
         dataset_name=dataset_name,

src/md_python/models/dataset_builders/_methods.py

@@ -133,6 +133,25 @@ def _batch_correction_technique_key(entity_type: str) -> str:
     "ptm": frozenset({"limma"}),
 }
 
+# Companion-parameter vocabularies for the gene DE engines — the allowed values
+# edgeR / DESeq2 accept. Mirror of MDFlexiComparisons process_r.py on
+# 2026-05-27: the ``edger_norm_method`` / ``deseq2_lfc_shrinkage`` Literals and
+# the ``deseq2_alpha`` / ``apeglm_seed`` numberrange ge/le bounds.
+#
+# These are the SINGLE source for the allowed values, so a sync check only has
+# to compare this file against process_r.py. The per-tool gating in
+# ``pairwise.py`` and ``anova.py`` reads these constants but keeps its own
+# validation block — the two tools can validate differently or be updated in
+# different orders without coupling.
+_EDGER_NORM_METHODS: frozenset[str] = frozenset(
+    {"TMM", "RLE", "upperquartile", "none"}
+)
+_DESEQ2_LFC_SHRINKAGE: frozenset[str] = frozenset(
+    {"none", "apeglm", "ashr", "normal"}
+)
+_DESEQ2_ALPHA_RANGE: tuple[float, float] = (0.0, 1.0)  # (ge, le)
+_APEGLM_SEED_RANGE: tuple[int, int] = (0, 2147483647)  # (ge, le)
+
 
 def _de_method_key(entity_type: str) -> str:
     """Wire-format key for the per-entity de_method field.