From 89d23e9a5cb45bb8878274afac816ff3e0ac30db Mon Sep 17 00:00:00 2001
From: jplfaria <jplfaria@gmail.com>
Date: Tue, 29 Sep 2026 19:50:32 +0000
Subject: [PATCH] fix: allow Empty media (zero compounds) in _load_media and
 _apply_media

Refine _apply_media to distinguish three cases:
- compounds matched: open those exchanges
- compounds present but no match: warning, leave default bounds
- zero compounds (Empty media): close all exchanges

Add regression tests in tests/unit/test_load_media_and_apply_media.py
covering all three cases plus _load_media empty-compound handling.

Fixes ModelSEED/modelseed-api-ops#34
---
 src/modelseed_api/jobs/tasks.py               |  7 +-
 tests/unit/test_load_media_and_apply_media.py | 86 +++++++++++++++++++
 2 files changed, 91 insertions(+), 2 deletions(-)
 create mode 100644 tests/unit/test_load_media_and_apply_media.py

diff --git a/src/modelseed_api/jobs/tasks.py b/src/modelseed_api/jobs/tasks.py
index 8626bed..11f62d5 100644
--- a/src/modelseed_api/jobs/tasks.py
+++ b/src/modelseed_api/jobs/tasks.py
@@ -378,11 +378,14 @@ def _apply_media(cobra_model, ms_media):
         exc_rxn_id = f"EX_{cpd.id}_e0"
         if exc_rxn_id in rxn_ids:
             medium[exc_rxn_id] = cpd.maxFlux or 1000.0
-    cobra_model.medium = medium
     if medium:
+        cobra_model.medium = medium
         logger.info("Applied media: %d exchange reactions open", len(medium))
+    elif ms_media.mediacompounds:
+        logger.warning("Media had no matching exchange reactions — running with default bounds")
     else:
-        logger.info("Applied empty media: all exchange reactions closed")
+        cobra_model.medium = {}
+        logger.info("Applied Empty media: all exchanges closed")
 
 
 def _fix_gapfilling_metadata(ws_data: dict, media_workspace_ref: str | None) -> None:
diff --git a/tests/unit/test_load_media_and_apply_media.py b/tests/unit/test_load_media_and_apply_media.py
new file mode 100644
index 0000000..9809308
--- /dev/null
+++ b/tests/unit/test_load_media_and_apply_media.py
@@ -0,0 +1,86 @@
+"""Unit tests for _load_media and _apply_media.
+
+Regression tests for the bug where _load_media raised ValueError for the
+Empty media (zero compounds), and _apply_media left default exchange bounds
+instead of closing all exchanges for an empty MSMedia.
+"""
+from __future__ import annotations
+
+import json
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from modelseed_api.jobs.tasks import _apply_media, _load_media
+
+
+def _mock_storage(raw_data):
+    """Return a mock storage service that serves raw_data for any path."""
+    ws = MagicMock()
+    ws.get.return_value = [[None, raw_data]]
+    return ws
+
+
+class TestLoadMediaEmpty:
+    def test_empty_json_returns_zero_compound_msmedia(self):
+        raw = json.dumps({"mediacompounds": []})
+        with patch("modelseed_api.jobs.tasks.get_storage_service", return_value=_mock_storage(raw)):
+            ms_media = _load_media("/chenry/public/modelsupport/media/Empty", "tok")
+        assert ms_media is not None
+        assert len(ms_media.mediacompounds) == 0
+
+    def test_empty_dict_returns_zero_compound_msmedia(self):
+        raw = {"mediacompounds": []}
+        with patch("modelseed_api.jobs.tasks.get_storage_service", return_value=_mock_storage(raw)):
+            ms_media = _load_media("/chenry/public/modelsupport/media/Empty", "tok")
+        assert ms_media is not None
+        assert len(ms_media.mediacompounds) == 0
+
+    def test_nonempty_media_still_loads_compounds(self):
+        raw = {"mediacompounds": [{"compound_ref": "~/compounds/cpd00001", "concentration": 0.001, "minFlux": -100, "maxFlux": 100}]}
+        with patch("modelseed_api.jobs.tasks.get_storage_service", return_value=_mock_storage(raw)):
+            ms_media = _load_media("/chenry/public/modelsupport/media/NMS", "tok")
+        assert len(ms_media.mediacompounds) == 1
+
+
+class TestApplyMediaEmpty:
+    def _make_cobra_model(self, exchange_ids):
+        model = MagicMock()
+        reactions = [MagicMock(id=rid) for rid in exchange_ids]
+        model.reactions = reactions
+        model.medium = {"EX_cpd00001_e0": 100.0}
+        return model
+
+    def test_empty_media_closes_all_exchanges(self):
+        from modelseedpy.core.msmedia import MSMedia
+        ms_media = MSMedia("Empty", name="Empty")
+        cobra_model = self._make_cobra_model(["EX_cpd00001_e0", "EX_cpd00002_e0"])
+
+        _apply_media(cobra_model, ms_media)
+
+        cobra_model.__setattr__
+        assert cobra_model.medium == {}
+
+    def test_media_with_matching_compounds_opens_exchanges(self):
+        from modelseedpy.core.msmedia import MSMedia, MediaCompound
+        ms_media = MSMedia("NMS", name="NMS")
+        ms_media.mediacompounds.append(MediaCompound("cpd00001", 100.0, -100.0))
+
+        cobra_model = self._make_cobra_model(["EX_cpd00001_e0", "EX_cpd00002_e0"])
+        _apply_media(cobra_model, ms_media)
+
+        assert cobra_model.medium == {"EX_cpd00001_e0": 100.0}
+
+    def test_media_with_no_matching_reactions_leaves_default_bounds(self):
+        """Compounds present but none match model reactions -- not an Empty case."""
+        from modelseedpy.core.msmedia import MSMedia, MediaCompound
+        ms_media = MSMedia("Weird", name="Weird")
+        ms_media.mediacompounds.append(MediaCompound("cpd99999", 100.0, -100.0))
+
+        original_medium = {"EX_cpd00001_e0": 100.0}
+        cobra_model = self._make_cobra_model(["EX_cpd00001_e0"])
+        cobra_model.medium = original_medium.copy()
+
+        _apply_media(cobra_model, ms_media)
+
+        assert cobra_model.medium == original_medium