aiagents4pharma 1.27.2__py3-none-any.whl → 1.29.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/test_zotero_write.py

@@ -0,0 +1,626 @@
+"""
+Unit tests for Zotero write tool in zotero_write.py.
+"""
+
+from types import SimpleNamespace
+import unittest
+from unittest.mock import patch, MagicMock
+from langgraph.types import Command
+from aiagents4pharma.talk2scholars.tools.zotero.zotero_write import (
+    zotero_save_tool,
+)
+
+# Dummy Hydra configuration for the Zotero write tool
+dummy_zotero_write_config = SimpleNamespace(
+    user_id="dummy_user_write",
+    library_type="user",
+    api_key="dummy_api_key_write",
+)
+dummy_cfg = SimpleNamespace(
+    tools=SimpleNamespace(zotero_write=dummy_zotero_write_config)
+)
+
+
+class TestZoteroSaveTool(unittest.TestCase):
+    """a test class for the Zotero save tool"""
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_successful_save_direct_state(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test successful saving when the fetched papers are directly provided in the state.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Test Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                },
+                "paper2": {
+                    "Title": "Test Paper 2",
+                    "Abstract": "Abstract 2",
+                    "Date": "2022",
+                    "URL": "http://example2.com",
+                    "Citations": "1",
+                },
+            },
+            "zotero_read": {"paper1": ["/Test Collection"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_1"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+
+        self.assertIsInstance(result, Command)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        content = messages[0].content
+        self.assertIn("Save was successful", content)
+        self.assertIn("Test Collection", content)
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_successful_save_state_key(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test successful saving when the state's last_displayed_papers is a key referencing
+        the actual fetched papers.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": "papers_key",
+            "papers_key": {
+                "paper1": {
+                    "Title": "Test Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {"paper1": ["/Test Collection"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_2"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+        self.assertIsInstance(result, Command)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        content = messages[0].content
+        self.assertIn("Save was successful", content)
+        self.assertIn("Test Collection", content)
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_no_fetched_papers(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that a RuntimeError is raised when there are no fetched papers in the state.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_get_item_collections.return_value = {}
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {},
+            "zotero_read": {"paper1": ["/Test Collection"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        mock_zotero_class.return_value = fake_zot
+
+        tool_call_id = "test_call_3"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        with self.assertRaises(RuntimeError) as context:
+            zotero_save_tool.run(tool_input)
+        self.assertIn("No fetched papers were found to save", str(context.exception))
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_fallback_get_item_collections(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if 'zotero_read' in the state is empty, the fallback
+        using get_item_collections is used.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Test Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {},  # empty mapping triggers fallback
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+
+        # Simulate get_item_collections returning a mapping that includes a match.
+        mock_get_item_collections.return_value = {"paper1": ["/Test Collection"]}
+
+        tool_call_id = "test_call_4"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        self.assertIn("Save was successful", messages[0].content)
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_invalid_collection_path(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that a RuntimeError is raised when the provided collection
+        path does not match any collection.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Test Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {},  # empty mapping; no match available
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_5"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Nonexistent",
+            "state": state,
+        }
+        with self.assertRaises(RuntimeError) as context:
+            zotero_save_tool.run(tool_input)
+        self.assertIn("does not exist in Zotero", str(context.exception))
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_save_failure(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if the Zotero client raises an exception during
+        create_items, a RuntimeError is raised.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Test Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {"paper1": ["/Test Collection"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        fake_zot.create_items.side_effect = Exception("Creation error")
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_6"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        with self.assertRaises(RuntimeError) as context:
+            zotero_save_tool.run(tool_input)
+        self.assertIn("Error saving papers to Zotero", str(context.exception))
+
+    # --- Additional tests to cover missing lines ---
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_get_item_collections_exception(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if get_item_collections raises an exception, the fallback branch
+        raises a RuntimeError.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        # Provide valid fetched papers so we bypass earlier error
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {},  # empty so fallback is triggered
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        mock_zotero_class.return_value = fake_zot
+
+        # Simulate exception in get_item_collections
+        mock_get_item_collections.side_effect = Exception("Mapping error")
+
+        tool_call_id = "test_call_7"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        with self.assertRaises(RuntimeError) as context:
+            zotero_save_tool.run(tool_input)
+        self.assertIn(
+            "Failed to generate collection path mappings", str(context.exception)
+        )
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_zotero_read_string_match(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if an entry in zotero_read is a string that matches the normalized path,
+        it is used as the collection key
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            # zotero_read entry is a string, not a list
+            "zotero_read": {"match_key": "/test collection"},
+            "query": "dummy query",
+        }
+
+        # Return a collection with key "match_key" to simulate a successful match.
+        fake_zot = MagicMock()
+        fake_zot.collections.return_value = [
+            {"key": "match_key", "data": {"name": "Test Collection"}}
+        ]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+        # get_item_collections is not used in this branch.
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_8"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/test collection",
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        # Check for the correct substring in the returned message.
+        self.assertIn(
+            "Papers have been saved to Zotero collection", messages[0].content
+        )
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_direct_match_by_collection_name(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if zotero_read does not yield a match, the tool finds
+        a direct match by collection name
+        in the collections list
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            # Non-matching zotero_read data
+            "zotero_read": {"dummy": ["/other"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        # Collection with name "Test Collection" should match because
+        # f"/Test Collection".lower() equals normalized path.
+        fake_zot.collections.return_value = [
+            {"key": "col1", "data": {"name": "Test Collection"}}
+        ]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_9"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/Test Collection",
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        self.assertIn("Test Collection", messages[0].content)
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_match_by_stripped_name(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if no direct match is found, a match is found by comparing
+        the stripped collection path.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        # Provide state with non-matching zotero_read
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {"dummy": ["/other"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        # Set collection_path without leading slash so that direct matching fails,
+        # but normalized_path.lstrip("/") yields "test", which matches the collection name.
+        fake_zot.collections.return_value = [{"key": "colX", "data": {"name": "test"}}]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_10"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "test",  # no leading slash
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        self.assertIn("test", messages[0].content)
+
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_write.zotero.Zotero")
+    @patch(
+        "aiagents4pharma.talk2scholars.tools.zotero.zotero_write.get_item_collections"
+    )
+    def test_match_by_path_component(
+        self,
+        mock_get_item_collections,
+        mock_zotero_class,
+        mock_hydra_compose,
+        mock_hydra_init,
+    ):
+        """
+        Test that if no full-string match is found, the tool can match
+        by one of the path components.
+        """
+        mock_hydra_compose.return_value = dummy_cfg
+        mock_hydra_init.return_value.__enter__.return_value = None
+
+        state = {
+            "last_displayed_papers": {
+                "paper1": {
+                    "Title": "Paper 1",
+                    "Abstract": "Abstract 1",
+                    "Date": "2021",
+                    "URL": "http://example.com",
+                    "Citations": "0",
+                }
+            },
+            "zotero_read": {"dummy": ["/other"]},
+            "query": "dummy query",
+        }
+
+        fake_zot = MagicMock()
+        # Collection name "bar" should be found via a path component when
+        # collection_path is "/foo/bar"
+        fake_zot.collections.return_value = [{"key": "colBar", "data": {"name": "bar"}}]
+        fake_zot.create_items.return_value = {"success": True}
+        mock_zotero_class.return_value = fake_zot
+        mock_get_item_collections.return_value = {}
+
+        tool_call_id = "test_call_11"
+        tool_input = {
+            "tool_call_id": tool_call_id,
+            "collection_path": "/foo/bar",
+            "state": state,
+        }
+        result = zotero_save_tool.run(tool_input)
+        messages = result.update.get("messages", [])
+        self.assertTrue(len(messages) > 0)
+        self.assertIn("bar", messages[0].content)

aiagents4pharma/talk2scholars/tools/__init__.py

@@ -5,4 +5,5 @@ Import statements
 """
 
 from . import s2
+from . import pdf
 from . import zotero

aiagents4pharma/talk2scholars/tools/pdf/__init__.py

@@ -0,0 +1,5 @@
+'''
+This file is used to import all the modules in the package.
+'''
+
+from . import question_and_answer