aiagents4pharma 0.0.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/test_tools_s2_multi.py

@@ -0,0 +1,307 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+import json
+from types import SimpleNamespace
+
+import hydra
+import pytest
+import requests
+from langchain_core.messages import ToolMessage
+from langgraph.types import Command
+
+from aiagents4pharma.talk2scholars.tools.s2.multi_paper_rec import (
+    get_multi_paper_recommendations,
+)
+from aiagents4pharma.talk2scholars.tools.s2.utils import multi_helper
+
+# --- 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": [{"name": "Author X", "authorId": "AX"}],
+                "year": 2019,
+                "citationCount": 12,
+                "url": "http://paperA",
+                "externalIds": {"ArXiv": "arxivA"},
+            },
+            {
+                "paperId": "paperB",
+                "title": "Multi Rec Paper B",
+                "authors": [{"name": "Author Y", "authorId": "AY"}],
+                "year": 2020,
+                "citationCount": 18,
+                "url": "http://paperB",
+                "externalIds": {},
+            },
+            {
+                "paperId": "paperC",
+                "title": "Multi Rec Paper C",
+                "authors": None,  # This paper 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 after 10 attempts."
+        "Please retry the same query.",
+    ):
+        get_multi_paper_recommendations.run(input_data)
+
+
+def test_multi_paper_rec_no_response(monkeypatch):
+    """
+    Test that get_multi_paper_recommendations raises a RuntimeError
+    when no response is obtained. This is simulated by patching 'range'
+    in the module namespace of multi_helper to return an empty iterator,
+    so that the for loop in _fetch_recommendations never iterates and
+    self.response remains None.
+    """
+    # Inject a patched 'range' into the multi_helper module's dictionary.
+    monkeypatch.setitem(multi_helper.__dict__, "range", lambda x: iter([]))
+
+    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 obtain a response from the Semantic Scholar API."
+    ):
+        get_multi_paper_recommendations.run(input_data)

aiagents4pharma/talk2scholars/tests/test_tools_s2_retrieve.py

@@ -0,0 +1,67 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+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
+        # The tool now returns the raw paper ID as the message content
+        content = result.update["messages"][0].content
+        assert content == "123"
+
+    @patch("requests.get")
+    def test_retrieve_semantic_scholar_paper_id_no_results(self, mock_get):
+        """Test retrieving a paper ID when no results are found."""
+        mock_get.return_value.json.return_value = {"data": []}
+        mock_get.return_value.status_code = 200
+        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"}
+            )

aiagents4pharma/talk2scholars/tests/test_tools_s2_search.py

@@ -0,0 +1,286 @@
+"""
+Unit tests for S2 tools functionality.
+"""
+
+from types import SimpleNamespace
+
+import hydra
+import pytest
+import requests
+from langchain_core.messages import ToolMessage
+from langgraph.types import Command
+
+from aiagents4pharma.talk2scholars.tools.s2.search import search_tool
+from aiagents4pharma.talk2scholars.tools.s2.utils import search_helper
+
+# --- Dummy Hydra Config Setup ---
+
+
+class DummyHydraContext:
+    """hydra.initialize context manager that does nothing."""
+
+    def __enter__(self):
+        return None
+
+    def __exit__(self, exc_type, exc_val, traceback):
+        return None
+
+
+# Create a dummy configuration that mimics the expected hydra config
+dummy_config = SimpleNamespace(
+    tools=SimpleNamespace(
+        search=SimpleNamespace(
+            api_endpoint="http://dummy.endpoint",
+            api_fields=["paperId", "title", "authors"],
+        )
+    )
+)
+
+# --- Dummy Response Classes and Functions for requests.get ---
+
+
+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):
+        """access 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_get_success(url, params, timeout):
+    """A dummy requests.get function that returns a successful response."""
+    # Record call parameters for assertions
+    dummy_requests_get_success.called_url = url
+    dummy_requests_get_success.called_params = params
+    dummy_requests_get_success.called_timeout = timeout
+
+    # Simulate a valid API response with three papers;
+    # one paper missing authors should be filtered out.
+    dummy_data = {
+        "data": [
+            {
+                "paperId": "1",
+                "title": "Paper 1",
+                "authors": [{"name": "Author A", "authorId": "A1"}],
+                "year": 2020,
+                "citationCount": 10,
+                "url": "http://paper1",
+                "externalIds": {"ArXiv": "arxiv1"},
+            },
+            {
+                "paperId": "2",
+                "title": "Paper 2",
+                "authors": [{"name": "Author B", "authorId": "B1"}],
+                "year": 2021,
+                "citationCount": 20,
+                "url": "http://paper2",
+                "externalIds": {},
+            },
+            {
+                "paperId": "3",
+                "title": "Paper 3",
+                "authors": None,  # This paper should be filtered out.
+                "year": 2022,
+                "citationCount": 30,
+                "url": "http://paper3",
+                "externalIds": {"ArXiv": "arxiv3"},
+            },
+        ]
+    }
+    return DummyResponse(dummy_data)
+
+
+def dummy_requests_get_no_data(url, params, timeout):
+    """A dummy requests.get function that returns a response without the expected 'data' key."""
+    dummy_requests_get_no_data.called_url = url
+    dummy_requests_get_no_data.called_params = params
+    dummy_requests_get_no_data.called_timeout = timeout
+    # Simulate a response with an unexpected format (missing "data" key)
+    return DummyResponse({"error": "Invalid format"})
+
+
+def dummy_requests_get_no_papers(url, params, timeout):
+    """A dummy requests.get function that returns a response with an empty papers list."""
+    dummy_requests_get_no_papers.called_url = url
+    dummy_requests_get_no_papers.called_params = params
+    dummy_requests_get_no_papers.called_timeout = timeout
+    # Simulate a response with an empty papers list.
+    return DummyResponse({"data": []})
+
+
+def dummy_requests_get_exception(url, params, timeout):
+    """A dummy requests.get function that raises an exception."""
+    dummy_requests_get_exception.called_url = url
+    dummy_requests_get_exception.called_params = params
+    dummy_requests_get_exception.called_timeout = timeout
+    # Simulate a network/connection exception.
+    raise requests.exceptions.RequestException("Connection error")
+
+
+# --- Pytest Fixture to Patch Hydra ---
+@pytest.fixture(autouse=True)
+def patch_hydra(monkeypatch):
+    """hydra patch to mock initialize and compose functions."""
+    # 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_search_tool_success(monkeypatch):
+    """
+    Test that search_tool returns a valid Command object when the API response is successful.
+    Also checks that papers without required fields are filtered out.
+    """
+    monkeypatch.setattr(requests, "get", dummy_requests_get_success)
+
+    tool_call_id = "test_tool_call_id"
+    # Invoke using .run() with a dictionary input.
+    result = search_tool.run(
+        {
+            "query": "machine learning",
+            "tool_call_id": tool_call_id,
+            "limit": 3,
+            "year": "2020",
+        }
+    )
+
+    # Check that a Command is returned with the expected update structure.
+    assert isinstance(result, Command)
+    update = result.update
+    assert "papers" in update
+
+    papers = update["papers"]
+    # Papers with valid 'title' and 'authors' should be included.
+    assert "1" in papers
+    assert "2" in papers
+    # Paper "3" is missing authors and should be filtered out.
+    assert "3" 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 "Number of papers found:" in msg.content
+
+    # Verify that the correct parameters were sent to requests.get.
+    called_params = dummy_requests_get_success.called_params
+    assert called_params["query"] == "machine learning"
+    # The "year" parameter should have been added.
+    assert called_params["year"] == "2020"
+    # The limit is set to min(limit, 100) so it should be 3.
+    assert called_params["limit"] == 3
+    # The fields should be a comma-separated string from the dummy config.
+    assert called_params["fields"] == "paperId,title,authors"
+
+
+def test_search_tool_unexpected_format(monkeypatch):
+    """
+    Test that search_tool raises a RuntimeError when the API response
+    does not include the expected 'data' key.
+    """
+    monkeypatch.setattr(requests, "get", dummy_requests_get_no_data)
+    tool_call_id = "test_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."
+        ),
+    ):
+        search_tool.run(
+            {
+                "query": "test",
+                "tool_call_id": tool_call_id,
+            }
+        )
+
+
+def test_search_tool_no_papers(monkeypatch):
+    """
+    Test that search_tool raises a RuntimeError when the API returns no papers.
+    """
+    monkeypatch.setattr(requests, "get", dummy_requests_get_no_papers)
+    tool_call_id = "test_tool_call_id"
+    with pytest.raises(
+        RuntimeError,
+        match=(
+            "No papers were found for your query. Consider refining your search "
+            "by using more specific keywords or different terms."
+        ),
+    ):
+        search_tool.run(
+            {
+                "query": "test",
+                "tool_call_id": tool_call_id,
+            }
+        )
+
+
+def test_search_tool_requests_exception(monkeypatch):
+    """
+    Test that search_tool raises a RuntimeError when requests.get throws an exception.
+    """
+    monkeypatch.setattr(requests, "get", dummy_requests_get_exception)
+    tool_call_id = "test_tool_call_id"
+    with pytest.raises(
+        RuntimeError,
+        match="Failed to connect to Semantic Scholar API after 10 attempts."
+        "Please retry the same query.",
+    ):
+        search_tool.run(
+            {
+                "query": "test",
+                "tool_call_id": tool_call_id,
+            }
+        )
+
+
+def test_search_tool_no_response(monkeypatch):
+    """
+    Test that search_tool raises a RuntimeError when no response
+    is obtained. This is simulated by patching 'range' in the
+    module namespace of search_helper to return an empty iterator,
+    so that the for-loop in _fetch_papers never iterates and self.response
+    remains None.
+    """
+    # Patch 'range' in the module globals of search_helper.
+    monkeypatch.setitem(search_helper.__dict__, "range", lambda x: iter([]))
+
+    tool_call_id = "test_tool_call_id"
+    with pytest.raises(
+        RuntimeError, match="Failed to obtain a response from the Semantic Scholar API."
+    ):
+        search_tool.run({"query": "test", "tool_call_id": tool_call_id})