Bug fix

Author: maltekuehl

.coverage

@@ -15,6 +15,7 @@ __pycache__/
 /data/
 /node_modules/
 coverage.xml
+.coverage
 
 # docs
 /docs/generated/
@@ -23,3 +24,4 @@ coverage.xml
 # env files
 .env
 *.local
+.vscode

.gitignore

@@ -124,6 +124,13 @@ async def search_protocols(
     filter_params = {}
     if peer_reviewed_only:
         filter_params["filter"] = "peer_reviewed"
+    else:
+        # Default to searching public protocols
+        filter_params["filter"] = "public"
+
+    # Use date ordering instead of relevance (which has a DB error)
+    filter_params["order_field"] = "date"
+    filter_params["order_dir"] = "desc"
 
     response = await client.search_protocols(
         query=query,

src/protocol_mcp/services/protocols_io.py

@@ -1,51 +1,91 @@
 """Mock responses for protocols.io API tests."""
 
 SEARCH_RESPONSE = {
+    "status_code": 0,
     "items": [
         {
             "id": 12345,
             "title": "RNA Extraction from Tissue Samples",
+            "title_html": "RNA Extraction from Tissue Samples",
             "uri": "rna-extraction-from-tissue-samples-abc123",
-            "doi": "10.17504/protocols.io.abc123",
+            "doi": "dx.doi.org/10.17504/protocols.io.abc123",
+            "url": "https://www.protocols.io/view/rna-extraction-from-tissue-samples-abc123",
             "stats": {
                 "number_of_steps": 15,
+                "number_of_views": 1234,
+                "number_of_bookmarks": 5,
+                "number_of_comments": 2,
             },
             "creator": {
                 "name": "Jane Doe",
                 "username": "janedoe",
+                "affiliation": "Test University",
+                "link": None,
+                "image": {
+                    "source": "https://www.protocols.io/img/avatars/001.png",
+                    "placeholder": "https://www.protocols.io/img/avatars/001.png",
+                },
             },
             "version_id": 1,
+            "public": True,
+            "published_on": 1609459200,
+            "created_on": 1609459200,
         },
         {
             "id": 12346,
             "title": "High-Quality RNA Isolation Protocol",
+            "title_html": "High-Quality RNA Isolation Protocol",
             "uri": "high-quality-rna-isolation-xyz789",
-            "doi": "10.17504/protocols.io.xyz789",
+            "doi": "dx.doi.org/10.17504/protocols.io.xyz789",
+            "url": "https://www.protocols.io/view/high-quality-rna-isolation-xyz789",
             "stats": {
                 "number_of_steps": 22,
+                "number_of_views": 567,
+                "number_of_bookmarks": 3,
+                "number_of_comments": 1,
             },
             "creator": {
                 "name": "John Smith",
                 "username": "johnsmith",
+                "affiliation": "Research Institute",
+                "link": None,
+                "image": {
+                    "source": "https://www.protocols.io/img/avatars/002.png",
+                    "placeholder": "https://www.protocols.io/img/avatars/002.png",
+                },
             },
             "version_id": 2,
+            "public": True,
+            "published_on": 1609545600,
+            "created_on": 1609545600,
         },
     ],
     "pagination": {
         "current_page": 1,
         "total_pages": 5,
         "total_results": 47,
         "page_size": 10,
+        "next_page": "https://www.protocols.io/api/v3/protocols?filter=public&key=RNA&page_id=2&page_size=10",
+        "prev_page": None,
+        "first": 0,
+        "last": 47,
+        "changed_on": None,
     },
 }
 
 EMPTY_SEARCH_RESPONSE = {
+    "status_code": 0,
     "items": [],
     "pagination": {
         "current_page": 1,
         "total_pages": 0,
         "total_results": 0,
         "page_size": 10,
+        "next_page": None,
+        "prev_page": None,
+        "first": 0,
+        "last": 0,
+        "changed_on": None,
     },
 }
 

tests/fixtures/protocols_io_responses.py

@@ -19,7 +19,7 @@
 async def test_search_protocols_returns_formatted_results(httpx_mock: HTTPXMock):
     """Test that search returns properly formatted results."""
     httpx_mock.add_response(
-        url="https://www.protocols.io/api/v3/protocols?key=RNA&page_size=10&page_id=1&order_field=relevance",
+        url="https://www.protocols.io/api/v3/protocols?key=RNA&page_size=10&page_id=1&filter=public&order_field=date&order_dir=desc",
         json=SEARCH_RESPONSE,
     )
 
@@ -39,7 +39,7 @@ async def test_search_protocols_returns_formatted_results(httpx_mock: HTTPXMock)
 async def test_search_protocols_handles_empty_results(httpx_mock: HTTPXMock):
     """Test that search handles no results gracefully."""
     httpx_mock.add_response(
-        url="https://www.protocols.io/api/v3/protocols?key=nonexistent_xyz_query&page_size=10&page_id=1&order_field=relevance",
+        url="https://www.protocols.io/api/v3/protocols?key=nonexistent_xyz_query&page_size=10&page_id=1&filter=public&order_field=date&order_dir=desc",
         json=EMPTY_SEARCH_RESPONSE,
     )
 
@@ -53,7 +53,7 @@ async def test_search_protocols_handles_empty_results(httpx_mock: HTTPXMock):
 async def test_search_protocols_with_peer_reviewed_filter(httpx_mock: HTTPXMock):
     """Test that peer_reviewed_only filter is applied."""
     httpx_mock.add_response(
-        url="https://www.protocols.io/api/v3/protocols?key=RNA&page_size=10&page_id=1&order_field=relevance&filter=peer_reviewed",
+        url="https://www.protocols.io/api/v3/protocols?key=RNA&page_size=10&page_id=1&filter=peer_reviewed&order_field=date&order_dir=desc",
         json=SEARCH_RESPONSE,
     )
 
@@ -190,7 +190,7 @@ async def test_search_respects_max_results_bounds(httpx_mock: HTTPXMock):
     """Test that max_results is bounded between 1 and 50."""
     # Test with value > 50 (should be clamped to 50)
     httpx_mock.add_response(
-        url="https://www.protocols.io/api/v3/protocols?key=RNA&page_size=50&page_id=1&order_field=relevance",
+        url="https://www.protocols.io/api/v3/protocols?key=RNA&page_size=50&page_id=1&filter=public&order_field=date&order_dir=desc",
         json=SEARCH_RESPONSE,
     )