scverse · lauraluebbert · Jun 26, 2026 · Jun 24, 2026 · Jun 25, 2026 · Jun 25, 2026
diff --git a/docs/src/en/updates.md b/docs/src/en/updates.md
@@ -8,6 +8,7 @@
 - [`gget pdb`](pdb.md): Added support for the PDBx/mmCIF structure format (fixes [issue 178](https://github.com/scverse/gget/issues/178) and [issue 177](https://github.com/scverse/gget/issues/177)).
   - New `resource="mmcif"` option downloads the structure in PDBx/mmCIF format (`.cif`).
   - The default `resource="pdb"` now automatically falls back to PDBx/mmCIF when the legacy PDB file is unavailable (e.g. for large structures), since the legacy PDB format is being phased out by RCSB. A warning is logged and saved files use the correct extension (`.cif`).
+- [`gget archs4`](archs4.md) (tissue mode): No longer crashes with `KeyError: ['color'] not found in axis` when ARCHS4 intermittently omits the optional `color` column from its CSV response. The column is now dropped only if present. Output also has a deterministic row order (sorted by `median` descending, with `id` as tiebreaker) so equal-median tissues no longer flip order between requests.
 
 
 **Version ≥ 0.30.7** (Jun 21, 2026):  

diff --git a/gget/gget_archs4.py b/gget/gget_archs4.py
@@ -200,11 +200,15 @@ def archs4(
         # Drop NaN rows
         tissue_exp_df = tissue_exp_df.dropna()
 
-        # Drop color columns
-        tissue_exp_df = tissue_exp_df.drop(["color"], axis=1)
-
-        # Sort data frame by median expression
-        tissue_exp_df = tissue_exp_df.sort_values("median", ascending=False)
+        # Drop the "color" column if present (only used for plotting upstream, not by gget).
+        # ARCHS4 intermittently omits this column; use errors="ignore" so a missing
+        # "color" column does not raise a KeyError and crash the request.
+        tissue_exp_df = tissue_exp_df.drop(columns=["color"], errors="ignore")
+
+        # Sort data frame by median expression. Use "id" as a stable tiebreaker so the row
+        # order is deterministic when several tissues share the same median (ARCHS4 returns
+        # tied rows in a varying order between requests otherwise).
+        tissue_exp_df = tissue_exp_df.sort_values(["median", "id"], ascending=[False, True])
         tissue_exp_df = tissue_exp_df.reset_index(drop=True)
 
         if json:

diff --git a/tests/fixtures/test_archs4.json b/tests/fixtures/test_archs4.json
@@ -598,14 +598,6 @@
                 7.62057,
                 8.60009
             ],
-            [
-                "System.Nervous System.CNS.THALAMUS",
-                3.29066,
-                5.995,
-                7.14836,
-                7.83426,
-                8.71165
-            ],
             [
                 "System.Nervous System.CNS.HYPOTHALAMUS",
                 3.44188,
@@ -614,6 +606,14 @@
                 7.99022,
                 8.81727
             ],
+            [
+                "System.Nervous System.CNS.THALAMUS",
+                3.29066,
+                5.995,
+                7.14836,
+                7.83426,
+                8.71165
+            ],
             [
                 "System.Immune System.Lymphoid.BLYMPHOCYTE",
                 5.57377,
@@ -678,14 +678,6 @@
                 7.42671,
                 8.89625
             ],
-            [
-                "System.Immune System.Lymphoid.TLYMPHOCYTE",
-                5.60813,
-                6.60849,
-                6.9754,
-                7.26685,
-                7.85409
-            ],
             [
                 "System.Connective Tissue.Bone marrow.CHONDROCYTE",
                 5.93985,
@@ -694,6 +686,14 @@
                 7.44552,
                 8.78176
             ],
+            [
+                "System.Immune System.Lymphoid.TLYMPHOCYTE",
+                5.60813,
+                6.60849,
+                6.9754,
+                7.26685,
+                7.85409
+            ],
             [
                 "System.Immune System.Myeloid.MACROPHAGE",
                 0.113644,
@@ -702,14 +702,6 @@
                 7.38198,
                 8.46912
             ],
-            [
-                "System.Respiratory System.Lung.LUNG",
-                0.113644,
-                5.88569,
-                6.95675,
-                7.7752,
-                9.18212
-            ],
             [
                 "System.Nervous System.CNS.ASTROCYTE",
                 1.20968,
@@ -718,6 +710,14 @@
                 7.42671,
                 8.33012
             ],
+            [
+                "System.Respiratory System.Lung.LUNG",
+                0.113644,
+                5.88569,
+                6.95675,
+                7.7752,
+                9.18212
+            ],
             [
                 "System.Connective Tissue.Adipose tissue.ADIPOSE",
                 4.26947,
@@ -766,14 +766,6 @@
                 7.98803,
                 9.42561
             ],
-            [
-                "System.Immune System.Myeloid.DENDRITIC CELL",
-                4.2942,
-                6.48802,
-                6.88087,
-                7.39734,
-                8.09957
-            ],
             [
                 "System.Connective Tissue.Adipose tissue.ADIPOCYTE",
                 4.86561,
@@ -782,6 +774,14 @@
                 7.13293,
                 7.71929
             ],
+            [
+                "System.Immune System.Myeloid.DENDRITIC CELL",
+                4.2942,
+                6.48802,
+                6.88087,
+                7.39734,
+                8.09957
+            ],
             [
                 "System.Immune System.Myeloid.MICROGLIA",
                 0.113644,
@@ -798,14 +798,6 @@
                 7.10033,
                 7.57266
             ],
-            [
-                "System.Integumentary System.Skin.FIBROBLAST",
-                0.113644,
-                6.35023,
-                6.8453,
-                7.43403,
-                9.31767
-            ],
             [
                 "System.Digestive System.Esophagus.ESOPHAGUS",
                 0.113644,
@@ -814,6 +806,14 @@
                 8.1174,
                 9.13015
             ],
+            [
+                "System.Integumentary System.Skin.FIBROBLAST",
+                0.113644,
+                6.35023,
+                6.8453,
+                7.43403,
+                9.31767
+            ],
             [
                 "System.Immune System.Myeloid.KUPFFER CELL",
                 6.16327,
@@ -1184,14 +1184,6 @@
                 "q3": 7.62057,
                 "max": 8.60009
             },
-            {
-                "id": "System.Nervous System.CNS.THALAMUS",
-                "min": 3.29066,
-                "q1": 5.995,
-                "median": 7.14836,
-                "q3": 7.83426,
-                "max": 8.71165
-            },
             {
                 "id": "System.Nervous System.CNS.HYPOTHALAMUS",
                 "min": 3.44188,
@@ -1200,6 +1192,14 @@
                 "q3": 7.99022,
                 "max": 8.81727
             },
+            {
+                "id": "System.Nervous System.CNS.THALAMUS",
+                "min": 3.29066,
+                "q1": 5.995,
+                "median": 7.14836,
+                "q3": 7.83426,
+                "max": 8.71165
+            },
             {
                 "id": "System.Immune System.Lymphoid.BLYMPHOCYTE",
                 "min": 5.57377,
@@ -1264,14 +1264,6 @@
                 "q3": 7.42671,
                 "max": 8.89625
             },
-            {
-                "id": "System.Immune System.Lymphoid.TLYMPHOCYTE",
-                "min": 5.60813,
-                "q1": 6.60849,
-                "median": 6.9754,
-                "q3": 7.26685,
-                "max": 7.85409
-            },
             {
                 "id": "System.Connective Tissue.Bone marrow.CHONDROCYTE",
                 "min": 5.93985,
@@ -1280,6 +1272,14 @@
                 "q3": 7.44552,
                 "max": 8.78176
             },
+            {
+                "id": "System.Immune System.Lymphoid.TLYMPHOCYTE",
+                "min": 5.60813,
+                "q1": 6.60849,
+                "median": 6.9754,
+                "q3": 7.26685,
+                "max": 7.85409
+            },
             {
                 "id": "System.Immune System.Myeloid.MACROPHAGE",
                 "min": 0.113644,
@@ -1288,14 +1288,6 @@
                 "q3": 7.38198,
                 "max": 8.46912
             },
-            {
-                "id": "System.Respiratory System.Lung.LUNG",
-                "min": 0.113644,
-                "q1": 5.88569,
-                "median": 6.95675,
-                "q3": 7.7752,
-                "max": 9.18212
-            },
             {
                 "id": "System.Nervous System.CNS.ASTROCYTE",
                 "min": 1.20968,
@@ -1304,6 +1296,14 @@
                 "q3": 7.42671,
                 "max": 8.33012
             },
+            {
+                "id": "System.Respiratory System.Lung.LUNG",
+                "min": 0.113644,
+                "q1": 5.88569,
+                "median": 6.95675,
+                "q3": 7.7752,
+                "max": 9.18212
+            },
             {
                 "id": "System.Connective Tissue.Adipose tissue.ADIPOSE",
                 "min": 4.26947,
@@ -1352,14 +1352,6 @@
                 "q3": 7.98803,
                 "max": 9.42561
             },
-            {
-                "id": "System.Immune System.Myeloid.DENDRITIC CELL",
-                "min": 4.2942,
-                "q1": 6.48802,
-                "median": 6.88087,
-                "q3": 7.39734,
-                "max": 8.09957
-            },
             {
                 "id": "System.Connective Tissue.Adipose tissue.ADIPOCYTE",
                 "min": 4.86561,
@@ -1368,6 +1360,14 @@
                 "q3": 7.13293,
                 "max": 7.71929
             },
+            {
+                "id": "System.Immune System.Myeloid.DENDRITIC CELL",
+                "min": 4.2942,
+                "q1": 6.48802,
+                "median": 6.88087,
+                "q3": 7.39734,
+                "max": 8.09957
+            },
             {
                 "id": "System.Immune System.Myeloid.MICROGLIA",
                 "min": 0.113644,
@@ -1384,14 +1384,6 @@
                 "q3": 7.10033,
                 "max": 7.57266
             },
-            {
-                "id": "System.Integumentary System.Skin.FIBROBLAST",
-                "min": 0.113644,
-                "q1": 6.35023,
-                "median": 6.8453,
-                "q3": 7.43403,
-                "max": 9.31767
-            },
             {
                 "id": "System.Digestive System.Esophagus.ESOPHAGUS",
                 "min": 0.113644,
@@ -1400,6 +1392,14 @@
                 "q3": 8.1174,
                 "max": 9.13015
             },
+            {
+                "id": "System.Integumentary System.Skin.FIBROBLAST",
+                "min": 0.113644,
+                "q1": 6.35023,
+                "median": 6.8453,
+                "q3": 7.43403,
+                "max": 9.31767
+            },
             {
                 "id": "System.Immune System.Myeloid.KUPFFER CELL",
                 "min": 6.16327,
@@ -2614,4 +2614,4 @@
         },
         "expected_result": "ValueError"
     }
-}
+}
diff --git a/tests/test_archs4.py b/tests/test_archs4.py
@@ -1,5 +1,6 @@
 import json
 import unittest
+from unittest.mock import patch
 
 from gget.gget_archs4 import archs4
 
@@ -12,3 +13,25 @@
 
 class TestArchs4(unittest.TestCase, metaclass=from_json(archs4_dict, archs4)):
     pass  # all tests are loaded from json
+
+
+class _FakeResponse:
+    def __init__(self, text):
+        self.ok = True
+        self.content = text.encode("utf-8")
+
+
+class TestArchs4MissingColor(unittest.TestCase):
+    """Network-free regression tests: ARCHS4 intermittently omits the 'color' column from
+    the tissue-expression CSV. gget must not crash with a KeyError when it is absent
+    (the 'color' column is dropped and never used)."""
+
+    _CSV_NO_COLOR = "id,min,q1,median,q3,max\nTissueA,0,1,5,9,10\nTissueB,0,2,8,12,15\n"
+
+    def test_tissue_missing_color_does_not_crash(self):
+        with patch("gget.gget_archs4.requests.post", return_value=_FakeResponse(self._CSV_NO_COLOR)):
+            df = archs4("STAT4", which="tissue", verbose=False)
+        # Returns a valid, sorted data frame without a 'color' column (no KeyError).
+        self.assertEqual(len(df), 2)
+        self.assertNotIn("color", df.columns)
+        self.assertEqual(df.iloc[0]["id"], "TissueB")  # sorted by median descending
diff --git a/tests/test_elm.py b/tests/test_elm.py
@@ -1,4 +1,5 @@
 import json
+import time
 import unittest
 
 from gget.gget_elm import elm
@@ -8,7 +9,14 @@
 with open("./tests/fixtures/test_elm.json") as json_file:
     elm_dict = json.load(json_file)
 
-gget_setup(module="elm")
+for attempt in range(3):
+    try:
+        gget_setup(module="elm")
+        break
+    except RuntimeError as exc:
+        if "ELM database files download failed" not in str(exc) or attempt == 2:
+            raise
+        time.sleep(30)
 
 
 class TestELM(unittest.TestCase):