aiagents4pharma 1.45.0__py3-none-any.whl → 1.45.1__py3-none-any.whl

aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py

@@ -1,16 +1,84 @@
 """
 Test cases for utils/pubchem_utils.py
+
+These tests mock PubChem HTTP calls to avoid network dependency and verify
+parsing logic without modifying business logic.
 """
 
+from types import SimpleNamespace
+
+import pytest
+
 from ..utils import pubchem_utils
 
 
+def _resp(json_data):
+    """Create a minimal response-like object exposing .json()."""
+    return SimpleNamespace(json=lambda: json_data)
+
+
+@pytest.fixture(autouse=True)
+def mock_requests_get(monkeypatch):
+    """Mock requests.get used by pubchem_utils to return deterministic JSON."""
+
+    def _mock_get(url, _timeout=60, **_kwargs):
+        # CAS RN lookup: ethyl carbonate 105-58-8 -> CID 7766
+        if "substance/xref/RN/105-58-8/record/JSON" in url:
+            return _resp(
+                {"PC_Substances": [{"compound": [{"id": {"type": 1, "id": {"cid": 7766}}}]}]}
+            )
+
+        # DrugBank: DB00240 (Alclometasone) -> CID 5311000
+        if (
+            "substance/sourceid//drugbank/DB00240/JSON" in url
+            or "substance/sourceid/drugbank/DB00240/JSON" in url
+        ):
+            return _resp(
+                {"PC_Substances": [{"compound": [{"id": {"type": 1, "id": {"cid": 5311000}}}]}]}
+            )
+
+        # CTD: D002083 (Butylated Hydroxyanisole) -> CID 24667
+        if (
+            "substance/sourceid//comparative toxicogenomics database/D002083/JSON" in url
+            or "substance/sourceid/comparative toxicogenomics database/D002083/JSON" in url
+        ):
+            return _resp(
+                {"PC_Substances": [{"compound": [{"id": {"type": 1, "id": {"cid": 24667}}}]}]}
+            )
+
+        # CID description for 5311000
+        if (
+            "compound/cid//5311000/description/JSON" in url
+            or "compound/cid/5311000/description/JSON" in url
+        ):
+            return _resp(
+                {
+                    "InformationList": {
+                        "Information": [
+                            {
+                                "Description": (
+                                    "Alclometasone is a prednisolone compound having an "
+                                    "alpha-chloro substituent at the 9alpha-position."
+                                ),
+                            }
+                        ]
+                    }
+                }
+            )
+
+        # Default empty response
+        return _resp({})
+
+    monkeypatch.setattr(pubchem_utils.requests, "get", _mock_get)
+    return _mock_get
+
+
 def test_cas_rn2pubchem_cid():
     """
     Test the casRN2pubchem_cid function.
 
-    The CAS RN for ethyl cabonate is 105-58-8.
-    The PubChem CID for ethyl cabonate is 7766.
+    The CAS RN for ethyl carbonate is 105-58-8.
+    The PubChem CID for ethyl carbonate is 7766.
     """
     casrn = "105-58-8"
     pubchem_cid = pubchem_utils.cas_rn2pubchem_cid(casrn)
@@ -21,11 +89,8 @@ def test_external_id2pubchem_cid():
     """
     Test the external_id2pubchem_cid function.
 
-    The DrugBank ID for Alclometasone is DB00240.
-    The PubChem CID for Alclometasone is 5311000.
-
-    The CTD ID for Butylated Hydroxyanisole is D002083
-    The PubChem CID for Butylated Hydroxyanisole is 24667.
+    The DrugBank ID for Alclometasone is DB00240 -> CID 5311000.
+    The CTD ID for Butylated Hydroxyanisole is D002083 -> CID 24667.
     """
     drugbank_id = "DB00240"
     pubchem_cid = pubchem_utils.external_id2pubchem_cid("drugbank", drugbank_id)
@@ -35,7 +100,7 @@ def test_external_id2pubchem_cid():
     pubchem_cid = pubchem_utils.external_id2pubchem_cid(
         "comparative toxicogenomics database", ctd_id
     )
-    assert pubchem_cid == 8456
+    assert pubchem_cid == 24667
 
 
 def test_pubchem_cid_description():
@@ -43,11 +108,16 @@ def test_pubchem_cid_description():
     Test the pubchem_cid_description function.
 
     The PubChem CID for Alclometasone is 5311000.
-    The description for Alclometasone starts with
-        "Alclometasone is a prednisolone compound having an alpha-chloro substituent".
+    The description starts with the expected prefix.
     """
     pubchem_cid = 5311000
     description = pubchem_utils.pubchem_cid_description(pubchem_cid)
     assert description.startswith(
         "Alclometasone is a prednisolone compound having an alpha-chloro substituent"
     )
+
+
+def test_mock_fallback_path_coverage():
+    """Exercise the default branch of the mocked requests.get for coverage."""
+    resp = pubchem_utils.requests.get("unknown://unmatched/url", timeout=1)
+    assert resp.json() == {}

{aiagents4pharma-1.45.0.dist-info → aiagents4pharma-1.45.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.45.0
+Version: 1.45.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
@@ -57,7 +57,6 @@ Requires-Dist: pydantic==2.10.5
 Requires-Dist: pygeneconverter==0.3
 Requires-Dist: pylint==3.3.1
 Requires-Dist: pymilvus==2.5.11
-Requires-Dist: pypdf2==3.0.1
 Requires-Dist: pypdf==6.0.0
 Requires-Dist: pytest-asyncio==0.25.2
 Requires-Dist: pytest==8.3.3
@@ -99,7 +98,7 @@ Description-Content-Type: text/markdown
 <!--  Deployment Workflows -->
 
 [![Pages Deployment](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/pages/pages-build-deployment)
-[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs-deploy.yml)
+[![MkDocs Deploy](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/mkdocs_deploy.yml)
 [![Docker Build & Push](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_build.yml)
 [![Docker Compose Release](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/docker_compose_release.yml)
 

{aiagents4pharma-1.45.0.dist-info → aiagents4pharma-1.45.1.dist-info}/RECORD

@@ -150,7 +150,7 @@ aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_reactome.py,sh
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_enrichments_uniprot.py,sha256=8JqptVypftx4IrObzxGPDjQ1C7I24f3zUUx69D8svAo,1615
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_extractions_milvus_multimodal_pcst.py,sha256=Oo6IvPB9L9lAmdxc4UqFJVX-lYYdFKYv3lNaHrjkvS8,21515
 aiagents4pharma/talk2knowledgegraphs/tests/test_utils_kg_utils.py,sha256=RDheTkkRxnGCxIoaTmTRKOQA2ewJyOOlKtgxdABgSSA,2397
-aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=OWmxd7d7E3Z63UpiFMTAXBM2fmGSUE9UFUXiUMxk61I,1522
+aiagents4pharma/talk2knowledgegraphs/tests/test_utils_pubchem_utils.py,sha256=80PhbFXD287LeCwGpXGtPal5vkjqKKCACefR_BPdfbM,3967
 aiagents4pharma/talk2knowledgegraphs/tools/__init__.py,sha256=unrqqDUAmfTpgiJSV65Pag9FWHpnf3eEsE8Cwh59NWI,242
 aiagents4pharma/talk2knowledgegraphs/tools/graphrag_reasoning.py,sha256=cCPBH1tKs9MjX1q9v6BXi-dInz_gxKwMyIVA-XdKocg,5251
 aiagents4pharma/talk2knowledgegraphs/tools/load_arguments.py,sha256=zhmsRp-8vjB5rRekqTA07d3yb-42HWqng9dDMkvK6hM,623
@@ -318,7 +318,7 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=-q-UuzP
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=K1EatPfC-riGyFmkOAS3ReNBaGPY-znne1KqOnFahkI,7339
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=sKkfJu3u4LKSZjfoQRfeqz26IESHRwBtcSDzLMLlJMo,6311
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=DBrF5IiF7VRP58hUK8T9LST3lQWLFixLUfnpMSTccoQ,4614
-aiagents4pharma-1.45.0.dist-info/METADATA,sha256=1AaG7ESWZtjMhF88cLZNOKf2BYGFh0ZnDI5fovUJuoY,16314
-aiagents4pharma-1.45.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-aiagents4pharma-1.45.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.45.0.dist-info/RECORD,,
+aiagents4pharma-1.45.1.dist-info/METADATA,sha256=JFqD43WM9t6Qp9zi5odBVfXPhDC5WCsmY_pe4RkbGcU,16285
+aiagents4pharma-1.45.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+aiagents4pharma-1.45.1.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.45.1.dist-info/RECORD,,