aiagents4pharma 1.44.0__py3-none-any.whl → 1.45.1__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/{test_zotero_path.py → test_utils_zotero_path.py}

@@ -4,7 +4,9 @@ Unit tests for Zotero path utility in zotero_path.py.
 
 import unittest
 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,
@@ -92,12 +94,8 @@ class TestFindOrCreateCollectionExtra(unittest.TestCase):
         # 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.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
@@ -114,9 +112,7 @@ class TestFindOrCreateCollectionExtra(unittest.TestCase):
         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
-        )
+        result = find_or_create_collection(self.fake_zot, "/NewCollection", create_missing=True)
         self.assertEqual(result, "new_key_successful")
 
     def test_create_collection_exception(self):
@@ -126,9 +122,7 @@ class TestFindOrCreateCollectionExtra(unittest.TestCase):
         """
         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
-        )
+        result = find_or_create_collection(self.fake_zot, "/NewCollection", create_missing=True)
         self.assertIsNone(result)
 
 
@@ -228,9 +222,7 @@ class TestZoteroPath:
         mock_zotero.return_value = mock_zot
 
         # Setup collections
-        collections = [
-            {"key": "abc123", "data": {"name": "Curiosity", "parentCollection": None}}
-        ]
+        collections = [{"key": "abc123", "data": {"name": "Curiosity", "parentCollection": None}}]
         mock_zot.collections.return_value = collections
 
         # Setup create_collection response
@@ -249,9 +241,7 @@ class TestZoteroPath:
 
         # Test creating nested "Curiosity/Curiosity2"
         mock_zot.create_collection.reset_mock()
-        result = find_or_create_collection(
-            mock_zot, "/Curiosity/Curiosity2", create_missing=True
-        )
+        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()
@@ -314,11 +304,24 @@ class TestZoteroWrite:
             mock_zot_class.return_value = mock_zot
             yield mock_zot
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.fetch_papers_for_save"
-    )
-    def test_zotero_write_no_papers(self, mock_fetch):
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.fetch_papers_for_save")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.zotero.Zotero")
+    def test_zotero_write_no_papers(self, mock_zotero_class, mock_compose, _, mock_fetch):
         """When no papers exist (even after approval), the function raises a ValueError."""
+        # Mock hydra configuration
+        cfg = MagicMock()
+        cfg.user_id = "test_user"
+        cfg.library_type = "user"
+        cfg.api_key = "test_key"
+        mock_compose.return_value = MagicMock()
+        mock_compose.return_value.tools.zotero_write = cfg
+
+        # Mock Zotero client
+        mock_zot = MagicMock()
+        mock_zotero_class.return_value = mock_zot
+
         mock_fetch.return_value = None
 
         state = {
@@ -338,22 +341,37 @@ class TestZoteroWrite:
             )
         assert "No fetched papers were found to save" in str(excinfo.value)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.fetch_papers_for_save"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.fetch_papers_for_save")
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.find_or_create_collection"
     )
-    def test_zotero_write_invalid_collection(self, mock_find, mock_fetch, mock_zotero):
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.compose")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.zotero.Zotero")
+    def test_zotero_write_invalid_collection(
+        self, mock_zotero_class, mock_compose, _, mock_find, mock_fetch
+    ):
         """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 = [
+        # Mock hydra configuration
+        cfg = MagicMock()
+        cfg.user_id = "test_user"
+        cfg.library_type = "user"
+        cfg.api_key = "test_key"
+        mock_compose.return_value = MagicMock()
+        mock_compose.return_value.tools.zotero_write = cfg
+
+        # Mock Zotero client
+        mock_zot = MagicMock()
+        mock_zotero_class.return_value = mock_zot
+        mock_zot.collections.return_value = [
             {"key": "k1", "data": {"name": "Curiosity"}},
             {"key": "k2", "data": {"name": "Random"}},
         ]
 
+        sample = {"paper1": {"Title": "Test Paper"}}
+        mock_fetch.return_value = sample
+        mock_find.return_value = None
+
         state = {
             "zotero_write_approval_status": {
                 "approved": True,
@@ -375,9 +393,7 @@ class TestZoteroWrite:
         assert "does not exist in Zotero" in msg
         assert "Curiosity, Random" in msg
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.fetch_papers_for_save"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.fetch_papers_for_save")
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.find_or_create_collection"
     )
@@ -386,12 +402,8 @@ class TestZoteroWrite:
         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_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 = {
@@ -423,9 +435,7 @@ class TestZoteroRead:
     def mock_hydra(self):
         """Fixture to mock hydra configuration."""
         with (
-            patch(
-                "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.initialize"
-            ),
+            patch("aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.initialize"),
             patch(
                 "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.compose"
             ) as mock_compose,
@@ -453,9 +463,7 @@ class TestZoteroRead:
             mock_zot_class.return_value = mock_zot
             yield mock_zot
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @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
     ):

aiagents4pharma/talk2scholars/tests/{test_zotero_read.py → test_utils_zotero_read.py}

@@ -17,7 +17,6 @@ from aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_pdf_downloader impo
 )
 from aiagents4pharma.talk2scholars.tools.zotero.zotero_read import zotero_read
 
-
 # Dummy Hydra configuration to be used in tests
 dummy_zotero_read_config = SimpleNamespace(
     user_id="dummy_user",
@@ -34,14 +33,10 @@ dummy_cfg = SimpleNamespace(tools=SimpleNamespace(zotero_read=dummy_zotero_read_
 class TestZoteroSearchTool(unittest.TestCase):
     """Tests for Zotero search tool."""
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_valid_query(
         self,
         mock_hydra_init,
@@ -111,14 +106,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         self.assertIn("Query: test", message_content)
         self.assertIn("Number of papers found: 2", message_content)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_empty_query_fetch_all_items(
         self,
         mock_hydra_init,
@@ -159,18 +150,12 @@ class TestZoteroSearchTool(unittest.TestCase):
         update = result.update
         filtered_papers = update["article_data"]
         self.assertIn("paper1", filtered_papers)
-        fake_zot.items.assert_called_with(
-            limit=dummy_cfg.tools.zotero_read.zotero.max_limit
-        )
+        fake_zot.items.assert_called_with(limit=dummy_cfg.tools.zotero_read.zotero.max_limit)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_no_items_returned(
         self,
         mock_hydra_init,
@@ -198,17 +183,11 @@ class TestZoteroSearchTool(unittest.TestCase):
             zotero_read.run(tool_input)
         self.assertIn("No items returned from Zotero", str(context.exception))
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.download_pdfs_in_parallel"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.download_pdfs_in_parallel")
     def test_filtering_no_matching_papers(self, *mocks):
         """Testing filtering when no paper matching"""
         (
@@ -274,14 +253,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         self.assertEqual(filtered_papers["paper1"]["pdf_url"], "/tmp/fake_path.pdf")
         self.assertEqual(filtered_papers["paper1"]["source"], "zotero")
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_items_api_exception(
         self,
         mock_hydra_init,
@@ -309,14 +284,10 @@ class TestZoteroSearchTool(unittest.TestCase):
             zotero_read.run(tool_input)
         self.assertIn("Failed to fetch items from Zotero", str(context.exception))
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_missing_key_in_item(
         self,
         mock_hydra_init,
@@ -370,14 +341,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         self.assertIn("paper_valid", filtered_papers)
         self.assertEqual(len(filtered_papers), 1)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_item_not_dict(
         self,
         mock_hydra_init,
@@ -410,14 +377,10 @@ class TestZoteroSearchTool(unittest.TestCase):
             zotero_read.run(tool_input)
         self.assertIn("No matching papers returned from Zotero", str(context.exception))
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_data_not_dict(
         self,
         mock_hydra_init,
@@ -447,17 +410,11 @@ class TestZoteroSearchTool(unittest.TestCase):
             zotero_read.run(tool_input)
         self.assertIn("No matching papers returned from Zotero", str(context.exception))
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.requests.Session.get"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.requests.Session.get")
     def test_pdf_attachment_success(self, *mocks):
         """Test for pdf attachment success"""
         (
@@ -506,9 +463,7 @@ class TestZoteroSearchTool(unittest.TestCase):
         mock_response = MagicMock()
         mock_response.status_code = 200
         mock_response.iter_content = lambda chunk_size: [b"fake pdf content"]
-        mock_response.headers = {
-            "Content-Disposition": 'attachment; filename="file1.pdf"'
-        }
+        mock_response.headers = {"Content-Disposition": 'attachment; filename="file1.pdf"'}
         mock_response.raise_for_status = lambda: None
         mock_session_get.return_value = mock_response
 
@@ -528,14 +483,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         self.assertEqual(paper["filename"], "file1.pdf")
         self.assertEqual(paper["attachment_key"], "attachment1")
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_pdf_attachment_children_exception(
         self,
         mock_hydra_init,
@@ -590,14 +541,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         self.assertNotIn("filename", filtered_papers["paper1"])
         self.assertNotIn("attachment_key", filtered_papers["paper1"])
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_pdf_attachment_missing_key(
         self,
         mock_hydra_init,
@@ -653,14 +600,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         self.assertNotIn("pdf_url", paper)
         self.assertNotIn("attachment_key", paper)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_pdf_attachment_outer_exception(
         self,
         mock_hydra_init,
@@ -739,14 +682,10 @@ class TestZoteroSearchTool(unittest.TestCase):
         # Should return None on failure
         self.assertIsNone(result)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.zotero_path.get_item_collections")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.zotero.Zotero")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.compose")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.utils.read_helper.hydra.initialize")
     def test_download_pdf_exception_logging(
         self,
         mock_hydra_init,

aiagents4pharma/talk2scholars/tests/{test_zotero_write.py → test_utils_zotero_write.py}

@@ -4,16 +4,12 @@ Unit tests for Zotero write tool in zotero_write.py.
 
 import unittest
 from types import SimpleNamespace
-from unittest.mock import patch, MagicMock
+from unittest.mock import MagicMock, patch
 
 from aiagents4pharma.talk2scholars.tools.zotero.zotero_write import zotero_write
 
-dummy_zotero_write_config = SimpleNamespace(
-    user_id="dummy", library_type="user", api_key="dummy"
-)
-dummy_cfg = SimpleNamespace(
-    tools=SimpleNamespace(zotero_write=dummy_zotero_write_config)
-)
+dummy_zotero_write_config = SimpleNamespace(user_id="dummy", library_type="user", api_key="dummy")
+dummy_cfg = SimpleNamespace(tools=SimpleNamespace(zotero_write=dummy_zotero_write_config))
 
 
 class TestZoteroSaveTool(unittest.TestCase):
@@ -49,9 +45,7 @@ class TestZoteroSaveTool(unittest.TestCase):
             }
         if papers is not None:
             # When papers is provided as dict, use it directly.
-            state["last_displayed_papers"] = (
-                papers if isinstance(papers, dict) else "papers"
-            )
+            state["last_displayed_papers"] = papers if isinstance(papers, dict) else "papers"
             if isinstance(papers, dict):
                 state["papers"] = papers
         return state
@@ -83,9 +77,7 @@ class TestZoteroSaveTool(unittest.TestCase):
     )
     def test_invalid_collection(self, mock_find, mock_fetch):
         """Test when collection path is invalid"""
-        self.fake_zot.collections.return_value = [
-            {"key": "k1", "data": {"name": "Existing"}}
-        ]
+        self.fake_zot.collections.return_value = [{"key": "k1", "data": {"name": "Existing"}}]
         # Provide a valid papers dict so we don't hit the no-papers error.
         state = self.make_state({"p1": {"Title": "X"}}, True)
         result = zotero_write.run(
@@ -143,9 +135,7 @@ class TestZoteroSaveTool(unittest.TestCase):
         self.fake_zot.collections.return_value = [
             {"key": "colKey", "data": {"name": "Test Collection"}}
         ]
-        self.fake_zot.create_items.return_value = {
-            "successful": {"0": {"key": "item1"}}
-        }
+        self.fake_zot.create_items.return_value = {"successful": {"0": {"key": "item1"}}}
         mock_fetch.return_value = {"p1": {"Title": "X"}}
         mock_find.return_value = "colKey"
 

aiagents4pharma/talk2scholars/tools/__init__.py

@@ -4,9 +4,6 @@
 Import statements
 """
 
-from . import s2
-from . import pdf
-from . import zotero
-from . import paper_download
+from . import paper_download, pdf, s2, zotero
 
 __all__ = ["s2", "pdf", "zotero", "paper_download"]

aiagents4pharma/talk2scholars/tools/paper_download/paper_downloader.py

@@ -6,16 +6,17 @@ Supports downloading papers from arXiv, medRxiv, bioRxiv, and PubMed through a s
 
 import logging
 import threading
-from typing import Annotated, Any, List, Literal, Optional
+from typing import Annotated, Any, Literal
 
 import hydra
 from hydra.core.global_hydra import GlobalHydra
-from omegaconf import OmegaConf
 from langchain_core.messages import ToolMessage
 from langchain_core.tools import tool
 from langchain_core.tools.base import InjectedToolCallId
 from langgraph.types import Command
+from omegaconf import OmegaConf
 from pydantic import BaseModel, Field
+
 from .utils.arxiv_downloader import ArxivDownloader
 from .utils.base_paper_downloader import BasePaperDownloader
 from .utils.biorxiv_downloader import BiorxivDownloader
@@ -30,14 +31,14 @@ logger = logging.getLogger(__name__)
 class UnifiedPaperDownloadInput(BaseModel):
     """Input schema for the unified paper download tool."""
 
-    service: Optional[Literal["arxiv", "medrxiv", "biorxiv", "pubmed"]] = Field(
+    service: Literal["arxiv", "medrxiv", "biorxiv", "pubmed"] | None = Field(
         default=None,
         description=(
             "Paper service to download from: 'arxiv', 'medrxiv', 'biorxiv', or 'pubmed'. "
             "If not specified, uses the configured default service."
         ),
     )
-    identifiers: List[str] = Field(
+    identifiers: list[str] = Field(
         description=(
             "List of paper identifiers. Format depends on service:\n"
             "- arxiv: arXiv IDs (e.g., ['1234.5678', '2301.12345'])\n"
@@ -140,12 +141,9 @@ class PaperDownloaderFactory:
                 return PaperDownloaderFactory._cached_config
 
             try:
-
                 # Clear if already initialized
                 if GlobalHydra().is_initialized():
-                    logger.info(
-                        "GlobalHydra already initialized, clearing for config load"
-                    )
+                    logger.info("GlobalHydra already initialized, clearing for config load")
                     GlobalHydra.instance().clear()
 
                 # Load configuration
@@ -156,16 +154,12 @@ class PaperDownloaderFactory:
 
                 # Cache the configuration
                 PaperDownloaderFactory._cached_config = cfg.tools.paper_download
-                logger.info(
-                    "Successfully loaded and cached paper download configuration"
-                )
+                logger.info("Successfully loaded and cached paper download configuration")
 
                 return PaperDownloaderFactory._cached_config
 
             except Exception as e:
-                logger.error(
-                    "Failed to load unified paper download configuration: %s", e
-                )
+                logger.error("Failed to load unified paper download configuration: %s", e)
                 raise RuntimeError(f"Configuration loading failed: {e}") from e
 
     @staticmethod
@@ -181,10 +175,7 @@ class PaperDownloaderFactory:
         Returns:
             Service-specific configuration object
         """
-        if (
-            not hasattr(unified_config, "services")
-            or service not in unified_config.services
-        ):
+        if not hasattr(unified_config, "services") or service not in unified_config.services:
             raise ValueError(f"Service '{service}' not found in configuration")
 
         # Create a simple config object that combines common and service-specific settings
@@ -202,14 +193,10 @@ class PaperDownloaderFactory:
         config_obj = ServiceConfig()
 
         # Handle common config (using helper method to reduce branches)
-        PaperDownloaderFactory._apply_config(
-            config_obj, unified_config.common, "common"
-        )
+        PaperDownloaderFactory._apply_config(config_obj, unified_config.common, "common")
 
         # Handle service-specific config (using helper method to reduce branches)
-        PaperDownloaderFactory._apply_config(
-            config_obj, unified_config.services[service], service
-        )
+        PaperDownloaderFactory._apply_config(config_obj, unified_config.services[service], service)
 
         return config_obj
 
@@ -239,9 +226,7 @@ class PaperDownloaderFactory:
 
         # Method 2: Try direct attribute access
         if hasattr(source_config, "__dict__"):
-            PaperDownloaderFactory._extract_from_dict(
-                config_obj, source_config.__dict__
-            )
+            PaperDownloaderFactory._extract_from_dict(config_obj, source_config.__dict__)
             return
 
         # Method 3: Try items() method
@@ -290,8 +275,8 @@ class PaperDownloaderFactory:
     parse_docstring=True,
 )
 def download_papers(
-    service: Optional[Literal["arxiv", "medrxiv", "biorxiv", "pubmed"]],
-    identifiers: List[str],
+    service: Literal["arxiv", "medrxiv", "biorxiv", "pubmed"] | None,
+    identifiers: list[str],
     tool_call_id: Annotated[str, InjectedToolCallId],
 ) -> Command[Any]:
     """
@@ -334,36 +319,36 @@ def download_papers(
 # Convenience functions for backward compatibility (optional)
 # These functions explicitly specify the service, bypassing the default service config
 def download_arxiv_papers(
-    arxiv_ids: List[str], tool_call_id: Annotated[str, InjectedToolCallId]
+    arxiv_ids: list[str], tool_call_id: Annotated[str, InjectedToolCallId]
 ) -> Command[Any]:
     """Convenience function for downloading arXiv papers (explicitly uses arXiv service)."""
     return _download_papers_impl("arxiv", arxiv_ids, tool_call_id)
 
 
 def download_medrxiv_papers(
-    dois: List[str], tool_call_id: Annotated[str, InjectedToolCallId]
+    dois: list[str], tool_call_id: Annotated[str, InjectedToolCallId]
 ) -> Command[Any]:
     """Convenience function for downloading medRxiv papers (explicitly uses medRxiv service)."""
     return _download_papers_impl("medrxiv", dois, tool_call_id)
 
 
 def download_biorxiv_papers(
-    dois: List[str], tool_call_id: Annotated[str, InjectedToolCallId]
+    dois: list[str], tool_call_id: Annotated[str, InjectedToolCallId]
 ) -> Command[Any]:
     """Convenience function for downloading bioRxiv papers (explicitly uses bioRxiv service)."""
     return _download_papers_impl("biorxiv", dois, tool_call_id)
 
 
 def download_pubmed_papers(
-    pmids: List[str], tool_call_id: Annotated[str, InjectedToolCallId]
+    pmids: list[str], tool_call_id: Annotated[str, InjectedToolCallId]
 ) -> Command[Any]:
     """Convenience function for downloading PubMed papers (explicitly uses PubMed service)."""
     return _download_papers_impl("pubmed", pmids, tool_call_id)
 
 
 def _download_papers_impl(
-    service: Optional[Literal["arxiv", "medrxiv", "biorxiv", "pubmed"]],
-    identifiers: List[str],
+    service: Literal["arxiv", "medrxiv", "biorxiv", "pubmed"] | None,
+    identifiers: list[str],
     tool_call_id: str,
 ) -> Command[Any]:
     """