test(reactome): cover remaining lines for codecov (#114)

Add a network-free TestReactomeOffline class that mocks http_json to
cover _strip_html passthrough, the pathways/search/entity parsing,
verbose logging, 404 and non-404 error branches, the entity name
fallback/summation, and resource/query validation. gget_reactome.py now
98% (only the import-time PackageNotFoundError version fallback, lines
16-17, remains, which is un-coverable in an installed environment).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: 2 people

tests/test_reactome.py

@@ -1,6 +1,8 @@
 import json
 import unittest
+from unittest.mock import patch
 
+import gget.gget_reactome as gget_reactome
 import pandas as pd
 from gget.gget_reactome import reactome
 
@@ -61,5 +63,113 @@ def test_reactome_pathways_no_results_network(self):
         self.assertEqual(list(df.columns), ["stable_id", "name", "species", "schema_class", "in_disease"])
 
 
+class TestReactomeOffline(unittest.TestCase):
+    """Network-free tests of the Reactome parsing/branch logic (issue #114).
+
+    All HTTP access goes through gget_reactome.http_json, which is mocked here.
+    """
+
+    def test_strip_html_passthrough(self):
+        # Non-string values pass through unchanged.
+        self.assertIsNone(gget_reactome._strip_html(None))
+        self.assertEqual(gget_reactome._strip_html(123), 123)
+        self.assertEqual(gget_reactome._strip_html("<span>TP53</span>"), "TP53")
+
+    @patch.object(gget_reactome, "http_json")
+    def test_pathways_parsing_verbose(self, mock_http):
+        mock_http.return_value = [
+            {
+                "stId": "R-HSA-1",
+                "displayName": "Pathway A",
+                "speciesName": "Homo sapiens",
+                "schemaClass": "Pathway",
+                "isInDisease": False,
+            }
+        ]
+        df = reactome("P04637", resource="pathways", species="Homo sapiens", verbose=True)
+        self.assertEqual(df.iloc[0]["stable_id"], "R-HSA-1")
+        self.assertEqual(df.iloc[0]["species"], "Homo sapiens")
+
+    @patch.object(gget_reactome, "http_json")
+    def test_pathways_404_returns_empty(self, mock_http):
+        mock_http.side_effect = RuntimeError("Reactome returned HTTP 404")
+        df = reactome("NOTREAL", resource="pathways", verbose=False)
+        self.assertEqual(len(df), 0)
+
+    @patch.object(gget_reactome, "http_json")
+    def test_pathways_other_error_raises(self, mock_http):
+        mock_http.side_effect = RuntimeError("Reactome returned HTTP 500")
+        with self.assertRaises(RuntimeError):
+            reactome("P04637", resource="pathways", verbose=False)
+
+    @patch.object(gget_reactome, "http_json")
+    def test_search_parsing_species_types_verbose(self, mock_http):
+        mock_http.return_value = {
+            "results": [
+                {
+                    "entries": [
+                        {
+                            "stId": "R-HSA-9",
+                            "name": "<span class='highlighting'>TP53</span>",
+                            "exactType": "Protein",
+                            "species": ["Homo sapiens"],
+                            "id": 12345,
+                        }
+                    ]
+                }
+            ]
+        }
+        df = reactome("TP53", resource="search", species="9606", types="Protein", verbose=True)
+        self.assertEqual(df.iloc[0]["stable_id"], "R-HSA-9")
+        self.assertEqual(df.iloc[0]["name"], "TP53")  # HTML stripped
+        self.assertEqual(df.iloc[0]["species"], "Homo sapiens")  # list flattened
+
+    @patch.object(gget_reactome, "http_json")
+    def test_search_404_returns_empty(self, mock_http):
+        mock_http.side_effect = RuntimeError("Reactome returned HTTP 404")
+        df = reactome("zzzz", resource="search", verbose=False)
+        self.assertEqual(len(df), 0)
+
+    @patch.object(gget_reactome, "http_json")
+    def test_search_other_error_raises(self, mock_http):
+        mock_http.side_effect = RuntimeError("Reactome returned HTTP 503")
+        with self.assertRaises(RuntimeError):
+            reactome("TP53", resource="search", verbose=False)
+
+    @patch.object(gget_reactome, "http_json")
+    def test_entity_name_fallback_and_summation(self, mock_http):
+        # displayName missing -> fall back to first of name list; summation HTML stripped.
+        mock_http.return_value = {
+            "stId": "R-HSA-6804754",
+            "displayName": None,
+            "name": ["Regulation of TP53 Activity"],
+            "schemaClass": "Pathway",
+            "speciesName": "Homo sapiens",
+            "isInDisease": False,
+            "summation": [{"text": "<p>Some <b>summary</b>.</p>"}],
+        }
+        result = reactome("R-HSA-6804754", resource="entity", json=True, verbose=True)
+        self.assertEqual(result[0]["name"], "Regulation of TP53 Activity")
+        self.assertEqual(result[0]["summation"], "Some summary.")
+
+    @patch.object(gget_reactome, "http_json")
+    def test_entity_404_raises_valueerror(self, mock_http):
+        mock_http.side_effect = RuntimeError("Reactome returned HTTP 404")
+        with self.assertRaises(ValueError):
+            reactome("R-HSA-0", resource="entity", verbose=False)
+
+    @patch.object(gget_reactome, "http_json")
+    def test_entity_other_error_raises(self, mock_http):
+        mock_http.side_effect = RuntimeError("Reactome returned HTTP 500")
+        with self.assertRaises(RuntimeError):
+            reactome("R-HSA-6804754", resource="entity", verbose=False)
+
+    def test_invalid_resource_and_empty_query(self):
+        with self.assertRaises(ValueError):
+            reactome("TP53", resource="banana", verbose=False)
+        with self.assertRaises(ValueError):
+            reactome("   ", resource="pathways", verbose=False)
+
+
 if __name__ == "__main__":
     unittest.main()