PyPI - aiagents4pharma - Versions diffs - 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl - Mend

aiagents4pharma 1.43.0py3-none-any.whl → 1.45.0py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (290) hide show

aiagents4pharma/talk2scholars/tests/{test_pubmed_downloader.py → test_utils_pubmed_downloader.py} RENAMED Viewed

@@ -139,8 +139,7 @@ class TestPubmedDownloaderBasics(unittest.TestCase):
         """<error> node -> return empty string."""
         resp = Mock()
         resp.text = (
-            '<?xml version="1.0"?><OA><error code="idDoesNotExist">'
-            "Invalid PMC ID</error></OA>"
+            '<?xml version="1.0"?><OA><error code="idDoesNotExist">Invalid PMC ID</error></OA>'
         )
         resp.raise_for_status = Mock()
         mock_get.return_value = resp
@@ -299,10 +298,7 @@ class TestPubmedDownloaderEuropePMC(unittest.TestCase):
         resp.status_code = 200
         mock_head.return_value = resp
         result = self.downloader.try_europe_pmc_public("PMC123456")
-        expected = (
-            "https://www.ebi.ac.uk/europepmc/webservices/rest"
-            "?accid=PMC123456&blobtype=pdf"
-        )
+        expected = "https://www.ebi.ac.uk/europepmc/webservices/rest?accid=PMC123456&blobtype=pdf"
         mock_head.assert_called_once_with(expected, timeout=30)
         self.assertEqual(result, expected)
@@ -356,18 +352,14 @@ class TestPubmedDownloaderPMCScrape(unittest.TestCase):
         expected_url = "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123456/"
         expected_headers = {"User-Agent": "Mozilla/5.0 (compatible; test-agent)"}
-        mock_get.assert_called_once_with(
-            expected_url, headers=expected_headers, timeout=30
-        )
-        self.assertEqual(
-            result, "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123456/pdf/test.pdf"
-        )
+        mock_get.assert_called_once_with(expected_url, headers=expected_headers, timeout=30)
+        self.assertEqual(result, "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123456/pdf/test.pdf")
     @patch("requests.get")
     def test_try_pmc_page_scraping_no_pdf(self, mock_get):
         """Test PMC page scraping with no PDF found."""
         resp = Mock()
-        resp.content = "<html><head></head></html>".encode()
+        resp.content = b"<html><head></head></html>"
         resp.raise_for_status = Mock()
         mock_get.return_value = resp
         self.assertEqual(self.downloader.try_pmc_page_scraping_public("PMC123456"), "")
@@ -486,17 +478,13 @@ class TestPubmedDownloaderConstructAndFallbacks(unittest.TestCase):
         """Test fallback chain through multiple sources."""
         with (
             patch.object(self.downloader, "try_oa_api_public", return_value="") as m_oa,
-            patch.object(
-                self.downloader, "try_europe_pmc_public", return_value=""
-            ) as m_eu,
+            patch.object(self.downloader, "try_europe_pmc_public", return_value="") as m_eu,
             patch.object(
                 self.downloader,
                 "try_pmc_page_scraping_public",
                 return_value="http://test.pdf",
             ) as m_scr,
-            patch.object(
-                self.downloader, "try_direct_pmc_url_public", return_value=""
-            ) as m_dir,
+            patch.object(self.downloader, "try_direct_pmc_url_public", return_value="") as m_dir,
         ):
             out = self.downloader.fetch_pdf_url_with_fallbacks_public("PMC123456")
         self.assertEqual(out, "http://test.pdf")
@@ -509,12 +497,8 @@ class TestPubmedDownloaderConstructAndFallbacks(unittest.TestCase):
         """Test fallback chain with direct PMC success."""
         with (
             patch.object(self.downloader, "try_oa_api_public", return_value="") as m_oa,
-            patch.object(
-                self.downloader, "try_europe_pmc_public", return_value=""
-            ) as m_eu,
-            patch.object(
-                self.downloader, "try_pmc_page_scraping_public", return_value=""
-            ) as m_scr,
+            patch.object(self.downloader, "try_europe_pmc_public", return_value="") as m_eu,
+            patch.object(self.downloader, "try_pmc_page_scraping_public", return_value="") as m_scr,
             patch.object(
                 self.downloader,
                 "try_direct_pmc_url_public",
@@ -532,15 +516,9 @@ class TestPubmedDownloaderConstructAndFallbacks(unittest.TestCase):
         """Test fallback chain when all sources fail."""
         with (
             patch.object(self.downloader, "try_oa_api_public", return_value="") as m_oa,
-            patch.object(
-                self.downloader, "try_europe_pmc_public", return_value=""
-            ) as m_eu,
-            patch.object(
-                self.downloader, "try_pmc_page_scraping_public", return_value=""
-            ) as m_scr,
-            patch.object(
-                self.downloader, "try_direct_pmc_url_public", return_value=""
-            ) as m_dir,
+            patch.object(self.downloader, "try_europe_pmc_public", return_value="") as m_eu,
+            patch.object(self.downloader, "try_pmc_page_scraping_public", return_value="") as m_scr,
+            patch.object(self.downloader, "try_direct_pmc_url_public", return_value="") as m_dir,
         ):
             out = self.downloader.fetch_pdf_url_with_fallbacks_public("PMC123456")
         self.assertEqual(out, "")
@@ -587,9 +565,7 @@ class TestPubmedDownloaderIntegration(unittest.TestCase):
         """Test full workflow from PMID to PDF URL."""
         metadata_response = Mock()
         metadata_response.json.return_value = {
-            "records": [
-                {"pmid": "12345678", "pmcid": "PMC123456", "doi": "10.1234/test"}
-            ]
+            "records": [{"pmid": "12345678", "pmcid": "PMC123456", "doi": "10.1234/test"}]
         }
         metadata_response.raise_for_status = Mock()
@@ -631,9 +607,7 @@ class TestPubmedDownloaderIntegration(unittest.TestCase):
         """Test workflow with fallback to alternative sources."""
         metadata_response = Mock()
         metadata_response.json.return_value = {
-            "records": [
-                {"pmid": "12345678", "pmcid": "PMC123456", "doi": "10.1234/test"}
-            ]
+            "records": [{"pmid": "12345678", "pmcid": "PMC123456", "doi": "10.1234/test"}]
         }
         metadata_response.raise_for_status = Mock()
@@ -780,9 +754,7 @@ class TestPubmedDownloaderHelpers(unittest.TestCase):
         """Test that placeholder abstracts return empty snippets."""
         self.assertEqual(self.downloader.get_snippet(""), "")
         self.assertEqual(self.downloader.get_snippet("N/A"), "")
-        self.assertEqual(
-            self.downloader.get_snippet("Abstract available in PubMed"), ""
-        )
+        self.assertEqual(self.downloader.get_snippet("Abstract available in PubMed"), "")
     def test_get_snippet_non_placeholder_delegates_to_base(self):
         """Test that non-placeholder abstracts delegate to base class."""
@@ -793,9 +765,7 @@ class TestPubmedDownloaderHelpers(unittest.TestCase):
     def test_get_paper_identifier_info_without_pmcid_line(self):
         """Test paper identifier info formatting without PMCID."""
-        info = self.downloader.get_paper_identifier_info_public(
-            {"PMID": "999", "PMCID": "N/A"}
-        )
+        info = self.downloader.get_paper_identifier_info_public({"PMID": "999", "PMCID": "N/A"})
         self.assertIn("(PMID: 999)", info)
         self.assertNotIn("PMCID:", info)
@@ -861,14 +831,10 @@ class TestPubmedDownloaderMissingLineCoverage(unittest.TestCase):
             patch.object(self.downloader, "_try_pmc_page_scraping", return_value=""),
             patch.object(self.downloader, "_try_direct_pmc_url", return_value=""),
             patch(
-                "aiagents4pharma.talk2scholars.tools.paper_download.utils."
-                "pubmed_downloader.logger"
+                "aiagents4pharma.talk2scholars.tools.paper_download.utils.pubmed_downloader.logger"
             ) as mock_logger,
         ):
-            result = self.downloader.fetch_pdf_url_with_fallbacks_production(
-                "PMC123456"
-            )
+            result = self.downloader.fetch_pdf_url_with_fallbacks_production("PMC123456")
             self.assertEqual(result, "")
             # Verify the warning log is called
@@ -879,21 +845,15 @@ class TestPubmedDownloaderMissingLineCoverage(unittest.TestCase):
     def test_fetch_pdf_url_with_fallbacks_oa_api_success_early_return(self):
         """Test _fetch_pdf_url_with_fallbacks when OA API succeeds on first try."""
         with (
-            patch.object(
-                self.downloader, "_try_oa_api", return_value="http://oa.pdf"
-            ) as mock_oa,
+            patch.object(self.downloader, "_try_oa_api", return_value="http://oa.pdf") as mock_oa,
             patch.object(self.downloader, "_try_europe_pmc") as mock_eu,
             patch.object(self.downloader, "_try_pmc_page_scraping") as mock_scr,
             patch.object(self.downloader, "_try_direct_pmc_url") as mock_dir,
             patch(
-                "aiagents4pharma.talk2scholars.tools.paper_download.utils."
-                "pubmed_downloader.logger"
+                "aiagents4pharma.talk2scholars.tools.paper_download.utils.pubmed_downloader.logger"
             ) as mock_logger,
         ):
-            result = self.downloader.fetch_pdf_url_with_fallbacks_production(
-                "PMC123456"
-            )
+            result = self.downloader.fetch_pdf_url_with_fallbacks_production("PMC123456")
             self.assertEqual(result, "http://oa.pdf")
             mock_oa.assert_called_once_with("PMC123456")
@@ -901,9 +861,7 @@ class TestPubmedDownloaderMissingLineCoverage(unittest.TestCase):
             mock_scr.assert_not_called()
             mock_dir.assert_not_called()
             # Verify the initial info log is called
-            mock_logger.info.assert_called_with(
-                "Fetching PDF URL for PMCID: %s", "PMC123456"
-            )
+            mock_logger.info.assert_called_with("Fetching PDF URL for PMCID: %s", "PMC123456")
     def test_fetch_pdf_url_with_fallbacks_europe_pmc_success_after_oa_fail(self):
         """Test _fetch_pdf_url_with_fallbacks when Europe PMC succeeds after OA API fails."""
@@ -915,10 +873,7 @@ class TestPubmedDownloaderMissingLineCoverage(unittest.TestCase):
             patch.object(self.downloader, "_try_pmc_page_scraping") as mock_scr,
             patch.object(self.downloader, "_try_direct_pmc_url") as mock_dir,
         ):
-            result = self.downloader.fetch_pdf_url_with_fallbacks_production(
-                "PMC123456"
-            )
+            result = self.downloader.fetch_pdf_url_with_fallbacks_production("PMC123456")
             self.assertEqual(result, "http://eu.pdf")
             mock_oa.assert_called_once_with("PMC123456")
@@ -932,18 +887,13 @@ class TestPubmedDownloaderMissingLineCoverage(unittest.TestCase):
         """Test _fetch_pdf_url_with_fallbacks when PMC scraping succeeds."""
         with (
             patch.object(self.downloader, "_try_oa_api", return_value="") as mock_oa,
-            patch.object(
-                self.downloader, "_try_europe_pmc", return_value=""
-            ) as mock_eu,
+            patch.object(self.downloader, "_try_europe_pmc", return_value="") as mock_eu,
             patch.object(
                 self.downloader, "_try_pmc_page_scraping", return_value="http://scr.pdf"
             ) as mock_scr,
             patch.object(self.downloader, "_try_direct_pmc_url") as mock_dir,
         ):
-            result = self.downloader.fetch_pdf_url_with_fallbacks_production(
-                "PMC123456"
-            )
+            result = self.downloader.fetch_pdf_url_with_fallbacks_production("PMC123456")
             self.assertEqual(result, "http://scr.pdf")
             mock_oa.assert_called_once_with("PMC123456")
@@ -955,20 +905,13 @@ class TestPubmedDownloaderMissingLineCoverage(unittest.TestCase):
         """Test _fetch_pdf_url_with_fallbacks when direct PMC succeeds as last resort."""
         with (
             patch.object(self.downloader, "_try_oa_api", return_value="") as mock_oa,
-            patch.object(
-                self.downloader, "_try_europe_pmc", return_value=""
-            ) as mock_eu,
-            patch.object(
-                self.downloader, "_try_pmc_page_scraping", return_value=""
-            ) as mock_scr,
+            patch.object(self.downloader, "_try_europe_pmc", return_value="") as mock_eu,
+            patch.object(self.downloader, "_try_pmc_page_scraping", return_value="") as mock_scr,
             patch.object(
                 self.downloader, "_try_direct_pmc_url", return_value="http://dir.pdf"
             ) as mock_dir,
         ):
-            result = self.downloader.fetch_pdf_url_with_fallbacks_production(
-                "PMC123456"
-            )
+            result = self.downloader.fetch_pdf_url_with_fallbacks_production("PMC123456")
             self.assertEqual(result, "http://dir.pdf")
             mock_oa.assert_called_once_with("PMC123456")
@@ -1012,8 +955,7 @@ class TestPubmedDownloaderProductionConstructPdfUrl(unittest.TestCase):
         """Test production construct_pdf_url with missing pmcid key."""
         metadata = {"records": [{"doi": "10.1/x"}]}
         with patch(
-            "aiagents4pharma.talk2scholars.tools.paper_download.utils."
-            "pubmed_downloader.logger"
+            "aiagents4pharma.talk2scholars.tools.paper_download.utils.pubmed_downloader.logger"
         ) as mock_logger:
             result = self.downloader.construct_pdf_url(metadata, "12345678")
@@ -1027,8 +969,7 @@ class TestPubmedDownloaderProductionConstructPdfUrl(unittest.TestCase):
         """Test production construct_pdf_url with empty pmcid."""
         metadata = {"records": [{"pmcid": "", "doi": "10.1/x"}]}
         with patch(
-            "aiagents4pharma.talk2scholars.tools.paper_download.utils."
-            "pubmed_downloader.logger"
+            "aiagents4pharma.talk2scholars.tools.paper_download.utils.pubmed_downloader.logger"
         ) as mock_logger:
             result = self.downloader.construct_pdf_url(metadata, "12345678")
@@ -1042,8 +983,7 @@ class TestPubmedDownloaderProductionConstructPdfUrl(unittest.TestCase):
         """Test production construct_pdf_url with N/A pmcid."""
         metadata = {"records": [{"pmcid": "N/A", "doi": "10.1/x"}]}
         with patch(
-            "aiagents4pharma.talk2scholars.tools.paper_download.utils."
-            "pubmed_downloader.logger"
+            "aiagents4pharma.talk2scholars.tools.paper_download.utils.pubmed_downloader.logger"
         ) as mock_logger:
             result = self.downloader.construct_pdf_url(metadata, "12345678")

aiagents4pharma/talk2scholars/tests/{test_read_helper_utils.py → test_utils_read_helper_utils.py} RENAMED Viewed

@@ -27,14 +27,10 @@ dummy_cfg = SimpleNamespace(tools=SimpleNamespace(zotero_read=dummy_zotero_read_
 class TestReadHelperDownloadsFalse(unittest.TestCase):
     """Tests for read_helper download_pdfs=False branches."""
-    @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_pdfs_false_branches(
         self,
         mock_hydra_init,

aiagents4pharma/talk2scholars/tests/{test_s2_utils_ext_ids.py → test_utils_s2_utils_ext_ids.py} RENAMED Viewed

@@ -49,9 +49,7 @@ def patch_hydra(monkeypatch):
             ),
         )
     )
-    monkeypatch.setattr(
-        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
-    )
+    monkeypatch.setattr(hydra, "initialize", lambda version_base, config_path: DummyHydraContext())
     monkeypatch.setattr(hydra, "compose", lambda config_name, overrides: dummy_cfg)
@@ -69,9 +67,7 @@ def test_multi_helper_pmc_and_doi_ids(monkeypatch):
             }
         ]
     }
-    response = SimpleNamespace(
-        status_code=200, json=lambda: data, raise_for_status=lambda: None
-    )
+    response = SimpleNamespace(status_code=200, json=lambda: data, raise_for_status=lambda: None)
     monkeypatch.setattr(requests, "post", lambda *args, **kwargs: response)
     results = rec.process_recommendations()
     ids_list = results["papers"]["p1"]["paper_ids"]
@@ -91,9 +87,7 @@ def test_search_helper_pmc_and_doi_ids(monkeypatch):
             }
         ]
     }
-    response = SimpleNamespace(
-        status_code=200, json=lambda: data, raise_for_status=lambda: None
-    )
+    response = SimpleNamespace(status_code=200, json=lambda: data, raise_for_status=lambda: None)
     monkeypatch.setattr(requests, "get", lambda *args, **kwargs: response)
     results = sd.process_search()
     ids_list = results["papers"]["s1"]["paper_ids"]
@@ -113,9 +107,7 @@ def test_single_helper_pmc_and_doi_ids(monkeypatch):
             }
         ]
     }
-    response = SimpleNamespace(
-        status_code=200, json=lambda: data, raise_for_status=lambda: None
-    )
+    response = SimpleNamespace(status_code=200, json=lambda: data, raise_for_status=lambda: None)
     monkeypatch.setattr(requests, "get", lambda *args, **kwargs: response)
     results = sp.process_recommendations()
     ids_list = results["papers"]["x1"]["paper_ids"]
@@ -395,9 +387,7 @@ def test_single_helper_create_content_snippet(monkeypatch):
 def test_multi_helper_create_content_snippet(monkeypatch):
     """Test that MultiPaperRecData._create_content includes snippets appropriately."""
-    mr = MultiPaperRecData(
-        paper_ids=["a", "b"], limit=2, year="2021", tool_call_id="tid"
-    )
+    mr = MultiPaperRecData(paper_ids=["a", "b"], limit=2, year="2021", tool_call_id="tid")
     mr.filtered_papers = {
         "m1": {"Title": "MTitle1", "Year": "2017", "Abstract": "MOne. MTwo. MThree."},
         "m2": {"Title": "MTitle2", "Year": "2016", "Abstract": ""},

aiagents4pharma/talk2scholars/tests/{test_zotero_human_in_the_loop.py → test_utils_zotero_human_in_the_loop.py} RENAMED Viewed

@@ -3,7 +3,8 @@ Unit tests for Zotero human in the loop in zotero_review.py with structured outp
 """
 import unittest
-from unittest.mock import patch, MagicMock
+from unittest.mock import MagicMock, patch
 from aiagents4pharma.talk2scholars.tools.zotero.zotero_review import zotero_review
@@ -185,22 +186,16 @@ class TestZoteroReviewTool(unittest.TestCase):
         upd = result.update
         self.assertEqual(upd["zotero_write_approval_status"], {"approved": False})
-        self.assertIn(
-            "Human rejected saving papers to Zotero", upd["messages"][0].content
-        )
+        self.assertIn("Human rejected saving papers to Zotero", upd["messages"][0].content)
         mock_fetch.assert_called_once()
         mock_interrupt.assert_called_once()
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.zotero.zotero_review.fetch_papers_for_save"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_review.fetch_papers_for_save")
     @patch("aiagents4pharma.talk2scholars.tools.zotero.zotero_review.interrupt")
     def test_structured_processing_failure(self, mock_interrupt, mock_fetch):
         """Test fallback when structured review processing fails."""
         # Simulate valid fetched papers with multiple entries.
-        papers = {
-            f"p{i}": {"Title": f"Title{i}", "Authors": [f"A{i}"]} for i in range(1, 8)
-        }
+        papers = {f"p{i}": {"Title": f"Title{i}", "Authors": [f"A{i}"]} for i in range(1, 8)}
         mock_fetch.return_value = papers
         mock_interrupt.return_value = "dummy_response"
         # Provide a fake llm_model whose invoke() raises an exception.
@@ -234,9 +229,7 @@ class TestZoteroReviewTool(unittest.TestCase):
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.zotero_review.fetch_papers_for_save",
-        return_value={
-            "p1": {"Title": "Test Paper", "Authors": ["Alice", "Bob", "Charlie"]}
-        },
+        return_value={"p1": {"Title": "Test Paper", "Authors": ["Alice", "Bob", "Charlie"]}},
     )
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.zotero_review.interrupt",

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

@@ -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 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl

aiagents4pharma 1.43.0py3-none-any.whl → 1.45.0py3-none-any.whl