aiagents4pharma 1.30.0__py3-none-any.whl → 1.30.2__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/test_zotero_path.py

@@ -3,10 +3,20 @@ Unit tests for Zotero path utility in zotero_path.py.
 """
 
 import unittest
-from unittest.mock import MagicMock
+from unittest.mock import MagicMock, patch
+import pytest
 from aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path import (
+    fetch_papers_for_save,
+    find_or_create_collection,
+    get_all_collection_paths,
     get_item_collections,
 )
+from aiagents4pharma.talk2scholars.tools.zotero.zotero_read import (
+    zotero_read,
+)
+from aiagents4pharma.talk2scholars.tools.zotero.zotero_write import (
+    zotero_write,
+)
 
 
 class TestGetItemCollections(unittest.TestCase):
@@ -55,3 +65,411 @@ class TestGetItemCollections(unittest.TestCase):
 
         result = get_item_collections(fake_zot)
         self.assertEqual(result, expected_mapping)
+
+
+class TestFindOrCreateCollectionExtra(unittest.TestCase):
+    """Extra tests for the find_or_create_collection function."""
+
+    def setUp(self):
+        """Set up a fake Zotero client with some default collections."""
+        # Set up a fake Zotero client with some default collections.
+        self.fake_zot = MagicMock()
+        self.fake_zot.collections.return_value = [
+            {"key": "parent1", "data": {"name": "Parent", "parentCollection": None}},
+            {"key": "child1", "data": {"name": "Child", "parentCollection": "parent1"}},
+        ]
+
+    def test_empty_path(self):
+        """Test that an empty path returns None."""
+        result = find_or_create_collection(self.fake_zot, "", create_missing=False)
+        self.assertIsNone(result)
+
+    def test_create_collection_with_success_key(self):
+        """
+        Test that when create_missing is True and the response contains a "success" key,
+        the function returns the new collection key.
+        """
+        # Simulate no existing collections (so direct match fails)
+        self.fake_zot.collections.return_value = []
+        # Simulate create_collection returning a dict with a "success" key.
+        self.fake_zot.create_collection.return_value = {
+            "success": {"0": "new_key_success"}
+        }
+        result = find_or_create_collection(
+            self.fake_zot, "/NewCollection", create_missing=True
+        )
+        self.assertEqual(result, "new_key_success")
+        # Verify payload formatting: for a simple (non-nested) path, no parentCollection.
+        args, _ = self.fake_zot.create_collection.call_args
+        payload = args[0]
+        self.assertEqual(payload["name"], "newcollection")
+        self.assertNotIn("parentCollection", payload)
+
+    def test_create_collection_with_successful_key(self):
+        """
+        Test that when create_missing is True and the response contains a "successful" key,
+        the function returns the new collection key.
+        """
+        self.fake_zot.collections.return_value = []
+        self.fake_zot.create_collection.return_value = {
+            "successful": {"0": {"data": {"key": "new_key_successful"}}}
+        }
+        result = find_or_create_collection(
+            self.fake_zot, "/NewCollection", create_missing=True
+        )
+        self.assertEqual(result, "new_key_successful")
+
+    def test_create_collection_exception(self):
+        """
+        Test that if create_collection raises an exception,
+        the function logs the error and returns None.
+        """
+        self.fake_zot.collections.return_value = []
+        self.fake_zot.create_collection.side_effect = Exception("Creation error")
+        result = find_or_create_collection(
+            self.fake_zot, "/NewCollection", create_missing=True
+        )
+        self.assertIsNone(result)
+
+
+class TestZoteroPath:
+    """Tests for the zotero_path utility functions."""
+
+    def test_fetch_papers_for_save_no_papers(self):
+        """Test that fetch_papers_for_save returns None when no papers are available."""
+        # Empty state
+        state = {}
+        assert fetch_papers_for_save(state) is None
+
+        # State with empty last_displayed_papers
+        state = {"last_displayed_papers": ""}
+        assert fetch_papers_for_save(state) is None
+
+        # State with last_displayed_papers pointing to non-existent key
+        state = {"last_displayed_papers": "nonexistent_key"}
+        assert fetch_papers_for_save(state) is None
+
+    def test_fetch_papers_for_save_with_papers(self):
+        """Test that fetch_papers_for_save correctly retrieves papers from state."""
+        # State with direct papers
+        sample_papers = {"paper1": {"Title": "Test Paper"}}
+        state = {"last_displayed_papers": sample_papers}
+        assert fetch_papers_for_save(state) == sample_papers
+
+        # State with papers referenced by key
+        state = {"last_displayed_papers": "zotero_read", "zotero_read": sample_papers}
+        assert fetch_papers_for_save(state) == sample_papers
+
+    @patch("pyzotero.zotero.Zotero")
+    def test_find_or_create_collection_exact_match(self, mock_zotero):
+        """Test that find_or_create_collection correctly finds an exact match."""
+        # Setup mock
+        mock_zot = MagicMock()
+        mock_zotero.return_value = mock_zot
+
+        # Setup collections
+        collections = [
+            {"key": "abc123", "data": {"name": "Curiosity", "parentCollection": None}},
+            {
+                "key": "def456",
+                "data": {"name": "Curiosity1", "parentCollection": "abc123"},
+            },
+            {"key": "ghi789", "data": {"name": "Random", "parentCollection": None}},
+            {"key": "rad123", "data": {"name": "radiation", "parentCollection": None}},
+        ]
+        mock_zot.collections.return_value = collections
+
+        # Test finding "Curiosity"
+        result = find_or_create_collection(mock_zot, "/Curiosity")
+        assert result == "abc123"
+
+        # Test finding with different case
+        result = find_or_create_collection(mock_zot, "/curiosity")
+        assert result == "abc123"
+
+        # Test finding "radiation" - direct match
+        result = find_or_create_collection(mock_zot, "/radiation")
+        assert result == "rad123"
+
+        # Test finding without leading slash
+        result = find_or_create_collection(mock_zot, "radiation")
+        assert result == "rad123"
+
+    @patch("pyzotero.zotero.Zotero")
+    def test_find_or_create_collection_no_match(self, mock_zotero):
+        """Test that find_or_create_collection returns None for non-existent collections."""
+        # Setup mock
+        mock_zot = MagicMock()
+        mock_zotero.return_value = mock_zot
+
+        # Setup collections
+        collections = [
+            {"key": "abc123", "data": {"name": "Curiosity", "parentCollection": None}},
+            {
+                "key": "def456",
+                "data": {"name": "Curiosity1", "parentCollection": "abc123"},
+            },
+        ]
+        mock_zot.collections.return_value = collections
+
+        # Test finding non-existent "Curiosity2"
+        result = find_or_create_collection(mock_zot, "/Curiosity2")
+        assert result is None
+
+        # Test finding non-existent nested path
+        result = find_or_create_collection(mock_zot, "/Curiosity/Curiosity2")
+        assert result is None
+
+    @patch("pyzotero.zotero.Zotero")
+    def test_find_or_create_collection_with_creation(self, mock_zotero):
+        """Test that find_or_create_collection creates collections when requested."""
+        # Setup mock
+        mock_zot = MagicMock()
+        mock_zotero.return_value = mock_zot
+
+        # Setup collections
+        collections = [
+            {"key": "abc123", "data": {"name": "Curiosity", "parentCollection": None}}
+        ]
+        mock_zot.collections.return_value = collections
+
+        # Setup create_collection response
+        mock_zot.create_collection.return_value = {
+            "successful": {"0": {"data": {"key": "new_key"}}}
+        }
+
+        # Test creating "Curiosity2" - note we're expecting lowercase in the call
+        result = find_or_create_collection(mock_zot, "/Curiosity2", create_missing=True)
+        assert result == "new_key"
+        # Use case-insensitive check for the collection name
+        mock_zot.create_collection.assert_called_once()
+        call_args = mock_zot.create_collection.call_args[0][0]
+        assert "name" in call_args
+        assert call_args["name"].lower() == "curiosity2"
+
+        # Test creating nested "Curiosity/Curiosity2"
+        mock_zot.create_collection.reset_mock()
+        result = find_or_create_collection(
+            mock_zot, "/Curiosity/Curiosity2", create_missing=True
+        )
+        assert result == "new_key"
+        # Check that the call includes parentCollection
+        mock_zot.create_collection.assert_called_once()
+        call_args = mock_zot.create_collection.call_args[0][0]
+        assert "name" in call_args
+        assert "parentCollection" in call_args
+        assert call_args["name"].lower() == "curiosity2"
+        assert call_args["parentCollection"] == "abc123"
+
+    @patch("pyzotero.zotero.Zotero")
+    def test_get_all_collection_paths(self, mock_zotero):
+        """Test that get_all_collection_paths returns correct paths."""
+        # Setup mock
+        mock_zot = MagicMock()
+        mock_zotero.return_value = mock_zot
+
+        # Setup collections
+        collections = [
+            {"key": "abc123", "data": {"name": "Curiosity", "parentCollection": None}},
+            {
+                "key": "def456",
+                "data": {"name": "Curiosity1", "parentCollection": "abc123"},
+            },
+            {"key": "ghi789", "data": {"name": "Random", "parentCollection": None}},
+        ]
+        mock_zot.collections.return_value = collections
+
+        # Test getting all paths
+        result = get_all_collection_paths(mock_zot)
+        assert "/Curiosity" in result
+        assert "/Random" in result
+        assert "/Curiosity/Curiosity1" in result
+
+
+class TestZoteroWrite:
+    """Integration tests for zotero_write.py."""
+
+    @pytest.fixture
+    def mock_hydra(self):
+        """Fixture to mock hydra configuration."""
+        with patch("hydra.compose") as mock_compose:
+            cfg = MagicMock()
+            cfg.tools.zotero_write.user_id = "test_user"
+            cfg.tools.zotero_write.library_type = "user"
+            cfg.tools.zotero_write.api_key = "test_key"
+            cfg.tools.zotero_write.zotero = MagicMock()
+            cfg.tools.zotero_write.zotero.max_limit = 50
+            mock_compose.return_value = cfg
+            yield cfg
+
+    @pytest.fixture
+    def mock_zotero(self):
+        """Fixture to mock Zotero client."""
+        with patch("pyzotero.zotero.Zotero") as mock_zot_class:
+            mock_zot = MagicMock()
+            mock_zot_class.return_value = mock_zot
+            yield mock_zot
+
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.fetch_papers_for_save"
+    )
+    def test_zotero_write_no_papers(self, mock_fetch):
+        """When no papers exist (even after approval), the function raises a ValueError."""
+        mock_fetch.return_value = None
+
+        state = {
+            "zotero_write_approval_status": {
+                "approved": True,
+                "collection_path": "/Curiosity",
+            }
+        }
+
+        with pytest.raises(ValueError) as excinfo:
+            zotero_write.run(
+                {
+                    "tool_call_id": "test_id",
+                    "collection_path": "/Curiosity",
+                    "state": state,
+                }
+            )
+        assert "No fetched papers were found to save" in str(excinfo.value)
+
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.fetch_papers_for_save"
+    )
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.find_or_create_collection"
+    )
+    def test_zotero_write_invalid_collection(self, mock_find, mock_fetch, mock_zotero):
+        """Saving to a nonexistent Zotero collection returns an error Command."""
+        sample = {"paper1": {"Title": "Test Paper"}}
+        mock_fetch.return_value = sample
+        mock_find.return_value = None
+        mock_zotero.collections.return_value = [
+            {"key": "k1", "data": {"name": "Curiosity"}},
+            {"key": "k2", "data": {"name": "Random"}},
+        ]
+
+        state = {
+            "zotero_write_approval_status": {
+                "approved": True,
+                "collection_path": "/NonExistent",
+            },
+            "last_displayed_papers": "papers",
+            "papers": sample,
+        }
+
+        result = zotero_write.run(
+            {
+                "tool_call_id": "test_id",
+                "collection_path": "/NonExistent",
+                "state": state,
+            }
+        )
+
+        msg = result.update["messages"][0].content
+        assert "does not exist in Zotero" in msg
+        assert "Curiosity, Random" in msg
+
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.fetch_papers_for_save"
+    )
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.find_or_create_collection"
+    )
+    def test_zotero_write_success(self, mock_find, mock_fetch, mock_hydra, mock_zotero):
+        """A valid approved save returns a success Command with summary."""
+        sample = {"paper1": {"Title": "Test Paper", "Authors": ["Test Author"]}}
+        mock_fetch.return_value = sample
+        mock_find.return_value = "abc123"
+        mock_zotero.collections.return_value = [
+            {"key": "abc123", "data": {"name": "radiation"}}
+        ]
+        mock_zotero.create_items.return_value = {
+            "successful": {"0": {"key": "item123"}}
+        }
+        mock_hydra.tools.zotero_write.zotero.max_limit = 50
+
+        state = {
+            "zotero_write_approval_status": {
+                "approved": True,
+                "collection_path": "/radiation",
+            },
+            "last_displayed_papers": "papers",
+            "papers": sample,
+        }
+
+        result = zotero_write.run(
+            {
+                "tool_call_id": "test_id",
+                "collection_path": "/radiation",
+                "state": state,
+            }
+        )
+
+        msg = result.update["messages"][0].content
+        assert "Save was successful" in msg
+        assert "radiation" in msg
+
+
+class TestZoteroRead:
+    """Integration tests for zotero_read.py."""
+
+    @pytest.fixture
+    def mock_hydra(self):
+        """Fixture to mock hydra configuration."""
+        with patch("hydra.initialize"), patch("hydra.compose") as mock_compose:
+            cfg = MagicMock()
+            cfg.tools.zotero_read.user_id = "test_user"
+            cfg.tools.zotero_read.library_type = "user"
+            cfg.tools.zotero_read.api_key = "test_key"
+            cfg.tools.zotero_read.zotero = MagicMock()
+            cfg.tools.zotero_read.zotero.max_limit = 50
+            cfg.tools.zotero_read.zotero.filter_item_types = [
+                "journalArticle",
+                "conferencePaper",
+            ]
+            mock_compose.return_value = cfg
+            yield cfg
+
+    @pytest.fixture
+    def mock_zotero(self):
+        """Fixture to mock Zotero client."""
+        with patch("pyzotero.zotero.Zotero") as mock_zot_class:
+            mock_zot = MagicMock()
+            mock_zot_class.return_value = mock_zot
+            yield mock_zot
+
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
+    )
+    def test_zotero_read_item_collections_error(
+        self, mock_get_collections, mock_hydra, mock_zotero
+    ):
+        """Test that zotero_read handles errors in get_item_collections."""
+
+        mock_get_collections.side_effect = Exception("Test error")
+
+        mock_zotero.items.return_value = [
+            {
+                "data": {
+                    "key": "paper1",
+                    "title": "Test Paper",
+                    "itemType": "journalArticle",
+                }
+            }
+        ]
+        mock_hydra.tools.zotero_read.zotero.max_limit = 50
+
+        result = zotero_read.run(
+            {
+                "query": "test",
+                "only_articles": True,
+                "tool_call_id": "test_id",
+                "limit": 2,
+            }
+        )
+
+        assert result is not None
+        assert isinstance(result.update, dict)
+        assert "zotero_read" in result.update

aiagents4pharma/talk2scholars/tests/test_zotero_read.py

@@ -7,7 +7,7 @@ import unittest
 from unittest.mock import patch, MagicMock
 from langgraph.types import Command
 from aiagents4pharma.talk2scholars.tools.zotero.zotero_read import (
-    zotero_search_tool,
+    zotero_read,
 )
 
 
@@ -26,7 +26,7 @@ dummy_cfg = SimpleNamespace(tools=SimpleNamespace(zotero_read=dummy_zotero_read_
 
 
 class TestZoteroSearchTool(unittest.TestCase):
-    """test for Zotero search tool"""
+    """Tests for Zotero search tool."""
 
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.zotero_read.get_item_collections"
@@ -41,7 +41,7 @@ class TestZoteroSearchTool(unittest.TestCase):
         mock_zotero_class,
         mock_get_item_collections,
     ):
-        """test valid query"""
+        """Test valid query returns correct Command output."""
         # Setup Hydra mocks
         mock_hydra_compose.return_value = dummy_cfg
         mock_hydra_init.return_value.__enter__.return_value = None
@@ -87,7 +87,7 @@ class TestZoteroSearchTool(unittest.TestCase):
             "tool_call_id": tool_call_id,
             "limit": 2,
         }
-        result = zotero_search_tool.run(tool_input)
+        result = zotero_read.run(tool_input)
 
         # Verify the Command update structure and contents
         self.assertIsInstance(result, Command)
@@ -116,7 +116,7 @@ class TestZoteroSearchTool(unittest.TestCase):
         mock_zotero_class,
         mock_get_item_collections,
     ):
-        """test empty query fetches all items"""
+        """Test empty query fetches all items."""
         mock_hydra_compose.return_value = dummy_cfg
         mock_hydra_init.return_value.__enter__.return_value = None
 
@@ -144,7 +144,7 @@ class TestZoteroSearchTool(unittest.TestCase):
             "tool_call_id": tool_call_id,
             "limit": 2,
         }
-        result = zotero_search_tool.run(tool_input)
+        result = zotero_read.run(tool_input)
 
         update = result.update
         filtered_papers = update["zotero_read"]
@@ -166,7 +166,7 @@ class TestZoteroSearchTool(unittest.TestCase):
         mock_zotero_class,
         mock_get_item_collections,
     ):
-        """test no items returned from Zotero"""
+        """Test no items returned from Zotero."""
         mock_hydra_compose.return_value = dummy_cfg
         mock_hydra_init.return_value.__enter__.return_value = None
 
@@ -183,7 +183,7 @@ class TestZoteroSearchTool(unittest.TestCase):
             "limit": 2,
         }
         with self.assertRaises(RuntimeError) as context:
-            zotero_search_tool.run(tool_input)
+            zotero_read.run(tool_input)
         self.assertIn("No items returned from Zotero", str(context.exception))
 
     @patch(
@@ -199,7 +199,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         mock_zotero_class,
         mock_get_item_collections,
     ):
-        """test no matching papers returned from Zotero"""
+        """
+        Test that when non-research items (e.g. attachments, notes) are returned,
+        they are still included since filtering is disabled.
+        """
         mock_hydra_compose.return_value = dummy_cfg
         mock_hydra_init.return_value.__enter__.return_value = None
 
@@ -240,9 +243,13 @@ class TestZoteroSearchTool(unittest.TestCase):
             "tool_call_id": tool_call_id,
             "limit": 2,
         }
-        with self.assertRaises(RuntimeError) as context:
-            zotero_search_tool.run(tool_input)
-        self.assertIn("No matching papers returned from Zotero", str(context.exception))
+        # Instead of expecting a RuntimeError, we now expect both items to be returned.
+        result = zotero_read.run(tool_input)
+        update = result.update
+        filtered_papers = update["zotero_read"]
+        self.assertIn("paper1", filtered_papers)
+        self.assertIn("paper2", filtered_papers)
+        self.assertEqual(len(filtered_papers), 2)
 
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.zotero_read.get_item_collections"
@@ -257,7 +264,7 @@ class TestZoteroSearchTool(unittest.TestCase):
         mock_zotero_class,
         mock_get_item_collections,
     ):
-        """test items API exception"""
+        """Test items API exception is properly raised."""
         mock_hydra_compose.return_value = dummy_cfg
         mock_hydra_init.return_value.__enter__.return_value = None
         mock_get_item_collections.return_value = {}
@@ -274,7 +281,7 @@ class TestZoteroSearchTool(unittest.TestCase):
             "limit": 2,
         }
         with self.assertRaises(RuntimeError) as context:
-            zotero_search_tool.run(tool_input)
+            zotero_read.run(tool_input)
         self.assertIn("Failed to fetch items from Zotero", str(context.exception))
 
     @patch(
@@ -306,7 +313,7 @@ class TestZoteroSearchTool(unittest.TestCase):
                     "url": "http://example.com",
                     "itemType": "journalArticle",
                 }
-            },  # missing key triggers line 136
+            },  # Missing 'key' field
             {
                 "data": {
                     "key": "paper_valid",
@@ -329,7 +336,7 @@ class TestZoteroSearchTool(unittest.TestCase):
             "tool_call_id": tool_call_id,
             "limit": 2,
         }
-        result = zotero_search_tool.run(tool_input)
+        result = zotero_read.run(tool_input)
 
         update = result.update
         filtered_papers = update["zotero_read"]
@@ -371,7 +378,7 @@ class TestZoteroSearchTool(unittest.TestCase):
             "limit": 2,
         }
         with self.assertRaises(RuntimeError) as context:
-            zotero_search_tool.run(tool_input)
+            zotero_read.run(tool_input)
         self.assertIn("No matching papers returned from Zotero", str(context.exception))
 
     @patch(
@@ -408,5 +415,5 @@ class TestZoteroSearchTool(unittest.TestCase):
             "limit": 2,
         }
         with self.assertRaises(RuntimeError) as context:
-            zotero_search_tool.run(tool_input)
+            zotero_read.run(tool_input)
         self.assertIn("No matching papers returned from Zotero", str(context.exception))