aiagents4pharma 1.28.0__py3-none-any.whl → 1.30.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/test_s2_display.py

@@ -0,0 +1,74 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+# pylint: disable=redefined-outer-name
+import pytest
+from langgraph.types import Command
+from ..tools.s2.display_results import (
+    display_results,
+    NoPapersFoundError as raised_error,
+)
+
+
+@pytest.fixture
+def initial_state():
+    """Provides an empty initial state for tests."""
+    return {"papers": {}, "multi_papers": {}}
+
+
+# Fixed test data for deterministic results
+MOCK_SEARCH_RESPONSE = {
+    "data": [
+        {
+            "paperId": "123",
+            "title": "Machine Learning Basics",
+            "abstract": "An introduction to ML",
+            "year": 2023,
+            "citationCount": 100,
+            "url": "https://example.com/paper1",
+            "authors": [{"name": "Test Author"}],
+        }
+    ]
+}
+
+MOCK_STATE_PAPER = {
+    "123": {
+        "Title": "Machine Learning Basics",
+        "Abstract": "An introduction to ML",
+        "Year": 2023,
+        "Citation Count": 100,
+        "URL": "https://example.com/paper1",
+    }
+}
+
+
+class TestS2Tools:
+    """Unit tests for individual S2 tools"""
+
+    def test_display_results_empty_state(self, initial_state):
+        """Verifies display_results tool behavior when state is empty and raises an exception"""
+        with pytest.raises(
+            raised_error,
+            match="No papers found. A search/rec needs to be performed first.",
+        ):
+            display_results.invoke({"state": initial_state, "tool_call_id": "test123"})
+
+    def test_display_results_shows_papers(self, initial_state):
+        """Verifies display_results tool correctly returns papers from state"""
+        state = initial_state.copy()
+        state["last_displayed_papers"] = "papers"
+        state["papers"] = MOCK_STATE_PAPER
+
+        result = display_results.invoke(
+            input={"state": state, "tool_call_id": "test123"}
+        )
+
+        assert isinstance(result, Command)  # Expect a Command object
+        assert isinstance(result.update, dict)  # Ensure update is a dictionary
+        assert "messages" in result.update
+        assert len(result.update["messages"]) == 1
+        assert (
+            "1 papers found. Papers are attached as an artifact."
+            in result.update["messages"][0].content
+        )

aiagents4pharma/talk2scholars/tests/test_s2_multi.py

@@ -0,0 +1,282 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+import json
+from types import SimpleNamespace
+import pytest
+import requests
+from langgraph.types import Command
+from langchain_core.messages import ToolMessage
+import hydra
+from aiagents4pharma.talk2scholars.tools.s2.multi_paper_rec import (
+    get_multi_paper_recommendations,
+)
+
+# --- Dummy Hydra Config Setup ---
+
+
+class DummyHydraContext:
+    """dummy context manager for mocking Hydra's initialize and compose functions."""
+
+    def __enter__(self):
+        """enter function that returns None."""
+        return None
+
+    def __exit__(self, exc_type, exc_val, traceback):
+        """exit function that does nothing."""
+        return None
+
+
+# Create a dummy configuration that mimics the expected hydra config.
+dummy_config = SimpleNamespace(
+    tools=SimpleNamespace(
+        multi_paper_recommendation=SimpleNamespace(
+            api_endpoint="http://dummy.endpoint/multi",
+            headers={"Content-Type": "application/json"},
+            api_fields=["paperId", "title", "authors"],
+            request_timeout=10,
+        )
+    )
+)
+
+# --- Dummy Response Classes and Functions for requests.post ---
+
+
+class DummyResponse:
+    """A dummy response class for mocking HTTP responses."""
+
+    def __init__(self, json_data, status_code=200):
+        """Initialize a DummyResponse with the given JSON data and status code."""
+        self._json_data = json_data
+        self.status_code = status_code
+
+    def json(self):
+        """Return the JSON data from the response."""
+        return self._json_data
+
+    def raise_for_status(self):
+        """raise an HTTP error for status codes >= 400."""
+        if self.status_code >= 400:
+            raise requests.HTTPError("HTTP Error")
+
+
+def test_dummy_response_no_error():
+    """Test that raise_for_status does not raise an exception for a successful response."""
+    # Create a DummyResponse with a successful status code.
+    response = DummyResponse({"data": "success"}, status_code=200)
+    # Calling raise_for_status should not raise an exception and should return None.
+    assert response.raise_for_status() is None
+
+
+def test_dummy_response_raise_error():
+    """Test that raise_for_status raises an exception for a failing response."""
+    # Create a DummyResponse with a failing status code.
+    response = DummyResponse({"error": "fail"}, status_code=400)
+    # Calling raise_for_status should raise an HTTPError.
+    with pytest.raises(requests.HTTPError):
+        response.raise_for_status()
+
+
+def dummy_requests_post_success(url, headers, params, data, timeout):
+    """dummy_requests_post_success"""
+    # Record call parameters for assertions.
+    dummy_requests_post_success.called_url = url
+    dummy_requests_post_success.called_headers = headers
+    dummy_requests_post_success.called_params = params
+    dummy_requests_post_success.called_data = data
+    dummy_requests_post_success.called_timeout = timeout
+
+    # Simulate a valid API response with three recommended papers;
+    # one paper missing authors should be filtered out.
+    dummy_data = {
+        "recommendedPapers": [
+            {
+                "paperId": "paperA",
+                "title": "Multi Rec Paper A",
+                "authors": ["Author X"],
+                "year": 2019,
+                "citationCount": 12,
+                "url": "http://paperA",
+                "externalIds": {"ArXiv": "arxivA"},
+            },
+            {
+                "paperId": "paperB",
+                "title": "Multi Rec Paper B",
+                "authors": ["Author Y"],
+                "year": 2020,
+                "citationCount": 18,
+                "url": "http://paperB",
+                "externalIds": {},
+            },
+            {
+                "paperId": "paperC",
+                "title": "Multi Rec Paper C",
+                "authors": None,  # This one should be filtered out.
+                "year": 2021,
+                "citationCount": 25,
+                "url": "http://paperC",
+                "externalIds": {"ArXiv": "arxivC"},
+            },
+        ]
+    }
+    return DummyResponse(dummy_data)
+
+
+def dummy_requests_post_unexpected(url, headers, params, data, timeout):
+    """dummy_requests_post_unexpected"""
+    dummy_requests_post_unexpected.called_url = url
+    dummy_requests_post_unexpected.called_headers = headers
+    dummy_requests_post_unexpected.called_params = params
+    dummy_requests_post_unexpected.called_data = data
+    dummy_requests_post_unexpected.called_timeout = timeout
+    # Simulate a response missing the 'recommendedPapers' key.
+    return DummyResponse({"error": "Invalid format"})
+
+
+def dummy_requests_post_no_recs(url, headers, params, data, timeout):
+    """dummy_requests_post_no_recs"""
+    dummy_requests_post_no_recs.called_url = url
+    dummy_requests_post_no_recs.called_headers = headers
+    dummy_requests_post_no_recs.called_params = params
+    dummy_requests_post_no_recs.called_data = data
+    dummy_requests_post_no_recs.called_timeout = timeout
+    # Simulate a response with an empty recommendations list.
+    return DummyResponse({"recommendedPapers": []})
+
+
+def dummy_requests_post_exception(url, headers, params, data, timeout):
+    """dummy_requests_post_exception"""
+    dummy_requests_post_exception.called_url = url
+    dummy_requests_post_exception.called_headers = headers
+    dummy_requests_post_exception.called_params = params
+    dummy_requests_post_exception.called_data = data
+    dummy_requests_post_exception.called_timeout = timeout
+    # Simulate a network exception.
+    raise requests.exceptions.RequestException("Connection error")
+
+
+# --- Pytest Fixture to Patch Hydra ---
+@pytest.fixture(autouse=True)
+def patch_hydra(monkeypatch):
+    """Patch Hydra's initialize and compose functions to return dummy objects."""
+    # Patch hydra.initialize to return our dummy context manager.
+    monkeypatch.setattr(
+        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
+    )
+    # Patch hydra.compose to return our dummy config.
+    monkeypatch.setattr(hydra, "compose", lambda config_name, overrides: dummy_config)
+
+
+# --- Test Cases ---
+
+
+def test_multi_paper_rec_success(monkeypatch):
+    """
+    Test that get_multi_paper_recommendations returns a valid Command object
+    when the API response is successful. Also, ensure that recommendations missing
+    required fields (like authors) are filtered out.
+    """
+    monkeypatch.setattr(requests, "post", dummy_requests_post_success)
+
+    tool_call_id = "test_tool_call_id"
+    input_data = {
+        "paper_ids": ["p1", "p2"],
+        "tool_call_id": tool_call_id,
+        "limit": 2,
+        "year": "2020",
+    }
+    # Call the tool using .run() with a dictionary input.
+    result = get_multi_paper_recommendations.run(input_data)
+
+    # Validate that the result is a Command with the expected update structure.
+    assert isinstance(result, Command)
+    update = result.update
+    assert "multi_papers" in update
+
+    papers = update["multi_papers"]
+    # Papers with valid 'title' and 'authors' should be included.
+    assert "paperA" in papers
+    assert "paperB" in papers
+    # Paper "paperC" is missing authors and should be filtered out.
+    assert "paperC" not in papers
+
+    # Check that a ToolMessage is included in the messages.
+    messages = update.get("messages", [])
+    assert len(messages) == 1
+    msg = messages[0]
+    assert isinstance(msg, ToolMessage)
+    assert "Recommendations based on multiple papers were successful" in msg.content
+
+    # Verify that the correct parameters were sent to requests.post.
+    called_params = dummy_requests_post_success.called_params
+    assert called_params["limit"] == 2  # Should be min(limit, 500)
+    assert called_params["fields"] == "paperId,title,authors"
+    # The year parameter should be present.
+    assert called_params["year"] == "2020"
+
+    # Also check the payload sent in the data.
+    sent_payload = json.loads(dummy_requests_post_success.called_data)
+    assert sent_payload["positivePaperIds"] == ["p1", "p2"]
+    assert sent_payload["negativePaperIds"] == []
+
+
+def test_multi_paper_rec_unexpected_format(monkeypatch):
+    """
+    Test that get_multi_paper_recommendations raises a RuntimeError when the API
+    response does not include the expected 'recommendedPapers' key.
+    """
+    monkeypatch.setattr(requests, "post", dummy_requests_post_unexpected)
+    tool_call_id = "test_tool_call_id"
+    input_data = {
+        "paper_ids": ["p1", "p2"],
+        "tool_call_id": tool_call_id,
+    }
+    with pytest.raises(
+        RuntimeError,
+        match=(
+            "Unexpected response from Semantic Scholar API. The results could not be "
+            "retrieved due to an unexpected format. "
+            "Please modify your search query and try again."
+        ),
+    ):
+        get_multi_paper_recommendations.run(input_data)
+
+
+def test_multi_paper_rec_no_recommendations(monkeypatch):
+    """
+    Test that get_multi_paper_recommendations raises a RuntimeError when the API
+    returns no recommendations.
+    """
+    monkeypatch.setattr(requests, "post", dummy_requests_post_no_recs)
+    tool_call_id = "test_tool_call_id"
+    input_data = {
+        "paper_ids": ["p1", "p2"],
+        "tool_call_id": tool_call_id,
+    }
+    with pytest.raises(
+        RuntimeError,
+        match=(
+            "No recommendations were found for your query. Consider refining your search "
+            "by using more specific keywords or different terms."
+        ),
+    ):
+        get_multi_paper_recommendations.run(input_data)
+
+
+def test_multi_paper_rec_requests_exception(monkeypatch):
+    """
+    Test that get_multi_paper_recommendations raises a RuntimeError when requests.post
+    throws an exception.
+    """
+    monkeypatch.setattr(requests, "post", dummy_requests_post_exception)
+    tool_call_id = "test_tool_call_id"
+    input_data = {
+        "paper_ids": ["p1", "p2"],
+        "tool_call_id": tool_call_id,
+    }
+    with pytest.raises(
+        RuntimeError,
+        match="Failed to connect to Semantic Scholar API. Please retry the same query.",
+    ):
+        get_multi_paper_recommendations.run(input_data)

aiagents4pharma/talk2scholars/tests/test_s2_query.py

@@ -0,0 +1,78 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+# pylint: disable=redefined-outer-name
+from unittest.mock import patch
+from unittest.mock import MagicMock
+import pytest
+from ..tools.s2.query_results import query_results, NoPapersFoundError
+
+
+@pytest.fixture
+def initial_state():
+    """Provides an empty initial state for tests."""
+    return {"papers": {}, "multi_papers": {}}
+
+
+# Fixed test data for deterministic results
+MOCK_SEARCH_RESPONSE = {
+    "data": [
+        {
+            "paperId": "123",
+            "title": "Machine Learning Basics",
+            "abstract": "An introduction to ML",
+            "year": 2023,
+            "citationCount": 100,
+            "url": "https://example.com/paper1",
+            "authors": [{"name": "Test Author"}],
+        }
+    ]
+}
+
+MOCK_STATE_PAPER = {
+    "123": {
+        "Title": "Machine Learning Basics",
+        "Abstract": "An introduction to ML",
+        "Year": 2023,
+        "Citation Count": 100,
+        "URL": "https://example.com/paper1",
+    }
+}
+
+
+class TestS2Tools:
+    """Unit tests for individual S2 tools"""
+
+    def test_query_results_empty_state(self, initial_state):
+        """Tests query_results tool behavior when no papers are found."""
+        with pytest.raises(
+            NoPapersFoundError,
+            match="No papers found. A search needs to be performed first.",
+        ):
+            query_results.invoke(
+                {"question": "List all papers", "state": initial_state}
+            )
+
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.s2.query_results.create_pandas_dataframe_agent"
+    )
+    def test_query_results_with_papers(self, mock_create_agent, initial_state):
+        """Tests querying papers when data is available."""
+        state = initial_state.copy()
+        state["last_displayed_papers"] = "papers"
+        state["papers"] = MOCK_STATE_PAPER
+
+        # Mock the dataframe agent instead of the LLM
+        mock_agent = MagicMock()
+        mock_agent.invoke.return_value = {"output": "Mocked response"}
+
+        mock_create_agent.return_value = (
+            mock_agent  # Mock the function returning the agent
+        )
+
+        # Ensure that the output of query_results is correctly structured
+        result = query_results.invoke({"question": "List all papers", "state": state})
+
+        assert isinstance(result, str)  # Ensure output is a string
+        assert result == "Mocked response"  # Validate the expected response

aiagents4pharma/talk2scholars/tests/test_s2_retrieve.py

@@ -0,0 +1,65 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+# pylint: disable=redefined-outer-name
+from unittest.mock import patch
+import pytest
+from langgraph.types import Command
+from ..tools.s2.retrieve_semantic_scholar_paper_id import (
+    retrieve_semantic_scholar_paper_id,
+)
+
+
+# Fixed test data for deterministic results
+MOCK_SEARCH_RESPONSE = {
+    "data": [
+        {
+            "paperId": "123",
+            "title": "Machine Learning Basics",
+            "abstract": "An introduction to ML",
+            "year": 2023,
+            "citationCount": 100,
+            "url": "https://example.com/paper1",
+            "authors": [{"name": "Test Author"}],
+        }
+    ]
+}
+
+MOCK_STATE_PAPER = {
+    "123": {
+        "Title": "Machine Learning Basics",
+        "Abstract": "An introduction to ML",
+        "Year": 2023,
+        "Citation Count": 100,
+        "URL": "https://example.com/paper1",
+    }
+}
+
+
+class TestS2Tools:
+    """Unit tests for individual S2 tools"""
+
+    @patch("requests.get")
+    def test_retrieve_semantic_scholar_paper_id(self, mock_get):
+        """Tests retrieving a paper ID from Semantic Scholar."""
+        mock_get.return_value.json.return_value = MOCK_SEARCH_RESPONSE
+        mock_get.return_value.status_code = 200
+
+        result = retrieve_semantic_scholar_paper_id.invoke(
+            input={"paper_title": "Machine Learning Basics", "tool_call_id": "test123"}
+        )
+
+        assert isinstance(result, Command)
+        assert "messages" in result.update
+        assert (
+            "Paper ID for 'Machine Learning Basics' is: 123"
+            in result.update["messages"][0].content
+        )
+
+    def test_retrieve_semantic_scholar_paper_id_no_results(self):
+        """Test retrieving a paper ID when no results are found."""
+        with pytest.raises(ValueError, match="No papers found for query: UnknownPaper"):
+            retrieve_semantic_scholar_paper_id.invoke(
+                input={"paper_title": "UnknownPaper", "tool_call_id": "test123"}
+            )