fix(tests): stub geo2r metadata in autoscan no-matrix test

biolearn/data_library.py

@@ -1029,7 +1029,15 @@ def _check_keys_exist(self, data, keys: list[str]):
 
     def _create_metadata(self, metadata_query_url):
         response = requests.get(metadata_query_url)
-        json_data = response.json()
+        response.raise_for_status()
+        try:
+            json_data = response.json()
+        except ValueError as e:
+            # NCBI serves an HTML CAPTCHA page when it blocks automated requests
+            raise ValueError(
+                f"GEO metadata query did not return JSON: {metadata_query_url}. "
+                "NCBI may be blocking automated requests."
+            ) from e
         smaples = [item for item in json_data["GeoMetaData"]]
         return self._convert_to_metadata_df(self.metadata_keys, smaples)
 

biolearn/test/test_autoscan_geo_matrix_parser.py

@@ -1,6 +1,12 @@
+import pandas as pd
 import pytest
+from unittest.mock import Mock, patch
 
-from biolearn.data_library import DataLibrary, NoMatrixDataError
+from biolearn.data_library import (
+    AutoScanGeoMatrixParser,
+    DataLibrary,
+    NoMatrixDataError,
+)
 from biolearn.util import get_data_file
 
 
@@ -28,5 +34,29 @@ def test_series_has_no_matrix_data_error():
         library_file=get_data_file("geo_autoscan_library.yaml")
     )
 
-    with pytest.raises(NoMatrixDataError):
-        library.get("GSE121633").load()
+    # geo2r now answers scripted requests with a CAPTCHA page, so stub the
+    # metadata call and exercise only the matrix check under test
+    stub_metadata = pd.DataFrame({"id": ["GSE121633"]})
+    with patch.object(
+        AutoScanGeoMatrixParser, "_create_metadata", return_value=stub_metadata
+    ):
+        with pytest.raises(NoMatrixDataError):
+            library.get("GSE121633").load()
+
+
+def test_metadata_query_non_json_response_error():
+    parser = AutoScanGeoMatrixParser(
+        {
+            "matrix_file": "unused",
+            "metadata_keys_parse": {},
+            "metadata_query": "unused",
+        }
+    )
+    html_response = Mock()
+    html_response.json.side_effect = ValueError("Expecting value")
+
+    with patch(
+        "biolearn.data_library.requests.get", return_value=html_response
+    ):
+        with pytest.raises(ValueError, match="did not return JSON"):
+            parser._create_metadata("https://example.org/geo2r")