aiagents4pharma 1.29.0__py3-none-any.whl → 1.30.1__py3-none-any.whl

aiagents4pharma/talk2scholars/tools/s2/query_results.py

@@ -44,7 +44,7 @@ def query_results(question: str, state: Annotated[dict, InjectedState]) -> str:
         raise NoPapersFoundError(
             "No papers found. A search needs to be performed first."
         )
-    context_key = state.get("last_displayed_papers","pdf_data")
+    context_key = state.get("last_displayed_papers", "pdf_data")
     dic_papers = state.get(context_key)
     df_papers = pd.DataFrame.from_dict(dic_papers, orient="index")
     df_agent = create_pandas_dataframe_agent(

aiagents4pharma/talk2scholars/tools/s2/search.py

@@ -14,6 +14,7 @@ from langchain_core.tools.base import InjectedToolCallId
 from langgraph.types import Command
 from pydantic import BaseModel, Field
 
+# pylint: disable=R0914,R0912,R0915
 # Configure logging
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -27,7 +28,7 @@ class SearchInput(BaseModel):
         "Be specific and include relevant academic terms."
     )
     limit: int = Field(
-        default=5, description="Maximum number of results to return", ge=1, le=100
+        default=10, description="Maximum number of results to return", ge=1, le=100
     )
     year: Optional[str] = Field(
         default=None,
@@ -75,14 +76,26 @@ def search_tool(
         params["year"] = year
 
     # Wrap API call in try/except to catch connectivity issues
-    try:
-        response = requests.get(endpoint, params=params, timeout=10)
-        response.raise_for_status()  # Raises HTTPError for bad responses
-    except requests.exceptions.RequestException as e:
-        logger.error("Failed to connect to Semantic Scholar API: %s", e)
-        raise RuntimeError(
-            "Failed to connect to Semantic Scholar API. Please retry the same query."
-        ) from e
+    response = None
+    for attempt in range(10):
+        try:
+            response = requests.get(endpoint, params=params, timeout=10)
+            response.raise_for_status()  # Raises HTTPError for bad responses
+            break  # Exit loop if request is successful
+        except requests.exceptions.RequestException as e:
+            logger.error(
+                "Attempt %d: Failed to connect to Semantic Scholar API: %s",
+                attempt + 1,
+                e,
+            )
+            if attempt == 9:  # Last attempt
+                raise RuntimeError(
+                    "Failed to connect to Semantic Scholar API after 10 attempts."
+                    "Please retry the same query."
+                ) from e
+
+    if response is None:
+        raise RuntimeError("Failed to obtain a response from the Semantic Scholar API.")
 
     data = response.json()
 
@@ -108,11 +121,22 @@ def search_tool(
     # Create a dictionary to store the papers
     filtered_papers = {
         paper["paperId"]: {
-            "paper_id": paper["paperId"],
+            "semantic_scholar_paper_id": paper["paperId"],
             "Title": paper.get("title", "N/A"),
             "Abstract": paper.get("abstract", "N/A"),
             "Year": paper.get("year", "N/A"),
+            "Publication Date": paper.get("publicationDate", "N/A"),
+            "Venue": paper.get("venue", "N/A"),
+            # "Publication Venue": (paper.get("publicationVenue") or {}).get("name", "N/A"),
+            # "Venue Type": (paper.get("publicationVenue") or {}).get("name", "N/A"),
+            "Journal Name": (paper.get("journal") or {}).get("name", "N/A"),
+            # "Journal Volume": paper.get("journal", {}).get("volume", "N/A"),
+            # "Journal Pages": paper.get("journal", {}).get("pages", "N/A"),
             "Citation Count": paper.get("citationCount", "N/A"),
+            "Authors": [
+                f"{author.get('name', 'N/A')} (ID: {author.get('authorId', 'N/A')})"
+                for author in paper.get("authors", [])
+            ],
             "URL": paper.get("url", "N/A"),
             "arxiv_id": paper.get("externalIds", {}).get("ArXiv", "N/A"),
         }
@@ -126,11 +150,15 @@ def search_tool(
     top_papers = list(filtered_papers.values())[:3]
     top_papers_info = "\n".join(
         [
-            f"{i+1}. {paper['Title']} ({paper['Year']})"
+            f"{i+1}. {paper['Title']} ({paper['Year']}; "
+            f"semantic_scholar_paper_id: {paper['semantic_scholar_paper_id']}; "
+            f"arXiv ID: {paper['arxiv_id']})"
             for i, paper in enumerate(top_papers)
         ]
     )
 
+    logger.info("-----------Filtered %d papers", len(filtered_papers))
+
     content = (
         "Search was successful. Papers are attached as an artifact. "
         "Here is a summary of the search results:\n"
@@ -138,7 +166,7 @@ def search_tool(
     content += f"Number of papers found: {len(filtered_papers)}\n"
     content += f"Query: {query}\n"
     content += f"Year: {year}\n" if year else ""
-    content += "Top papers:\n" + top_papers_info
+    content += "Top 3 papers:\n" + top_papers_info
 
     return Command(
         update={

aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py

@@ -14,6 +14,7 @@ from langchain_core.tools.base import InjectedToolCallId
 from langgraph.types import Command
 from pydantic import BaseModel, Field
 
+# pylint: disable=R0914,R0912,R0915
 # Configure logging
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -44,7 +45,7 @@ class SinglePaperRecInput(BaseModel):
 def get_single_paper_recommendations(
     paper_id: str,
     tool_call_id: Annotated[str, InjectedToolCallId],
-    limit: int = 5,
+    limit: int = 10,
     year: Optional[str] = None,
 ) -> Command[Any]:
     """
@@ -85,16 +86,28 @@ def get_single_paper_recommendations(
         params["year"] = year
 
     # Wrap API call in try/except to catch connectivity issues and check response format
-    try:
-        response = requests.get(endpoint, params=params, timeout=cfg.request_timeout)
-        response.raise_for_status()  # Raises HTTPError for bad responses
-    except requests.exceptions.RequestException as e:
-        logger.error(
-            "Failed to connect to Semantic Scholar API for recommendations: %s", e
-        )
-        raise RuntimeError(
-            "Failed to connect to Semantic Scholar API. Please retry the same query."
-        ) from e
+    response = None
+    for attempt in range(10):
+        try:
+            response = requests.get(
+                endpoint, params=params, timeout=cfg.request_timeout
+            )
+            response.raise_for_status()  # Raises HTTPError for bad responses
+            break  # Exit loop if request is successful
+        except requests.exceptions.RequestException as e:
+            logger.error(
+                "Attempt %d: Failed to connect to Semantic Scholar API for recommendations: %s",
+                attempt + 1,
+                e,
+            )
+            if attempt == 9:  # Last attempt
+                raise RuntimeError(
+                    "Failed to connect to Semantic Scholar API after 10 attempts."
+                    "Please retry the same query."
+                ) from e
+
+    if response is None:
+        raise RuntimeError("Failed to obtain a response from the Semantic Scholar API.")
 
     logger.info(
         "API Response Status for recommendations of paper %s: %s",
@@ -125,11 +138,22 @@ def get_single_paper_recommendations(
     # Extract paper ID and title from recommendations
     filtered_papers = {
         paper["paperId"]: {
-            "paper_id": paper["paperId"],
+            "semantic_scholar_paper_id": paper["paperId"],
             "Title": paper.get("title", "N/A"),
             "Abstract": paper.get("abstract", "N/A"),
             "Year": paper.get("year", "N/A"),
+            "Publication Date": paper.get("publicationDate", "N/A"),
+            "Venue": paper.get("venue", "N/A"),
+            # "Publication Venue": (paper.get("publicationVenue") or {}).get("name", "N/A"),
+            # "Venue Type": (paper.get("publicationVenue") or {}).get("name", "N/A"),
+            "Journal Name": (paper.get("journal") or {}).get("name", "N/A"),
+            # "Journal Volume": paper.get("journal", {}).get("volume", "N/A"),
+            # "Journal Pages": paper.get("journal", {}).get("pages", "N/A"),
             "Citation Count": paper.get("citationCount", "N/A"),
+            "Authors": [
+                f"{author.get('name', 'N/A')} (ID: {author.get('authorId', 'N/A')})"
+                for author in paper.get("authors", [])
+            ],
             "URL": paper.get("url", "N/A"),
             "arxiv_id": paper.get("externalIds", {}).get("ArXiv", "N/A"),
         }
@@ -141,7 +165,10 @@ def get_single_paper_recommendations(
     top_papers = list(filtered_papers.values())[:3]
     top_papers_info = "\n".join(
         [
-            f"{i+1}. {paper['Title']} ({paper['Year']})"
+            # f"{i+1}. {paper['Title']} ({paper['Year']})"
+            f"{i+1}. {paper['Title']} ({paper['Year']}; "
+            f"semantic_scholar_paper_id: {paper['semantic_scholar_paper_id']}; "
+            f"arXiv ID: {paper['arxiv_id']})"
             for i, paper in enumerate(top_papers)
         ]
     )
@@ -153,10 +180,9 @@ def get_single_paper_recommendations(
         "Papers are attached as an artifact. "
         "Here is a summary of the recommendations:\n"
     )
-    content += f"Number of papers found: {len(filtered_papers)}\n"
+    content += f"Number of recommended papers found: {len(filtered_papers)}\n"
     content += f"Query Paper ID: {paper_id}\n"
-    content += f"Year: {year}\n" if year else ""
-    content += "Top papers:\n" + top_papers_info
+    content += "Here are a few of these papers:\n" + top_papers_info
 
     return Command(
         update={

aiagents4pharma/talk2scholars/tools/zotero/zotero_read.py

@@ -104,9 +104,10 @@ def zotero_search_tool(
 
     # Define filter criteria
     filter_item_types = cfg.zotero.filter_item_types if only_articles else []
-    filter_excluded_types = (
-        cfg.zotero.filter_excluded_types
-    )  # Exclude non-research items
+    logger.debug("Filtering item types: %s", filter_item_types)
+    # filter_excluded_types = (
+    #     cfg.zotero.filter_excluded_types
+    # )  # Exclude non-research items
 
     # Filter and format papers
     filtered_papers = {}
@@ -119,19 +120,19 @@ def zotero_search_tool(
         if not isinstance(data, dict):
             continue
 
-        item_type = data.get("itemType")
+        item_type = data.get("itemType", "N/A")
         logger.debug("Item type: %s", item_type)
 
         # Exclude attachments, notes, and other unwanted types
-        if (
-            not item_type
-            or not isinstance(item_type, str)
-            or item_type in filter_excluded_types  # Skip attachments & notes
-            or (
-                only_articles and item_type not in filter_item_types
-            )  # Skip non-research types
-        ):
-            continue
+        # if (
+        #     not item_type
+        #     or not isinstance(item_type, str)
+        #     or item_type in filter_excluded_types  # Skip attachments & notes
+        #     or (
+        #         only_articles and item_type not in filter_item_types
+        #     )  # Skip non-research types
+        # ):
+        #     continue
 
         key = data.get("key")
         if not key:
@@ -140,13 +141,29 @@ def zotero_search_tool(
         # Use the imported utility function's mapping to get collection paths
         collection_paths = item_to_collections.get(key, ["/Unknown"])
 
+        # Extract metadata safely
         filtered_papers[key] = {
             "Title": data.get("title", "N/A"),
             "Abstract": data.get("abstractNote", "N/A"),
-            "Date": data.get("date", "N/A"),
+            "Publication Date": data.get(
+                "date", "N/A"
+            ),  # Correct field for publication date
             "URL": data.get("url", "N/A"),
             "Type": item_type if isinstance(item_type, str) else "N/A",
-            "Collections": collection_paths,  # Now displays full paths
+            "Collections": collection_paths,  # Displays full collection paths
+            "Citation Count": data.get("citationCount", "N/A"),  # Shows citations
+            "Venue": data.get("venue", "N/A"),  # Displays venue
+            "Publication Venue": data.get(
+                "publicationTitle", "N/A"
+            ),  # Matches with Zotero Write
+            "Journal Name": data.get("journalAbbreviation", "N/A"),  # Journal Name
+            # "Journal Volume": data.get("volume", "N/A"),  # Journal Volume
+            # "Journal Pages": data.get("pages", "N/A"),  # Journal Pages
+            "Authors": [
+                f"{creator.get('firstName', '')} {creator.get('lastName', '')}".strip()
+                for creator in data.get("creators", [])  # Prevents NoneType error
+                if isinstance(creator, dict) and creator.get("creatorType") == "author"
+            ],
         }
 
     if not filtered_papers:
@@ -170,7 +187,7 @@ def zotero_search_tool(
     content += " And here is a summary of the retrieval results:\n"
     content += f"Number of papers found: {len(filtered_papers)}\n"
     content += f"Query: {query}\n"
-    content += "Top papers:\n" + top_papers_info
+    content += "Here are a few of these papers:\n" + top_papers_info
 
     return Command(
         update={

aiagents4pharma/talk2scholars/tools/zotero/zotero_write.py

@@ -185,21 +185,53 @@ def zotero_save_tool(
     # Format papers for Zotero and assign to the specified collection
     zotero_items = []
     for paper_id, paper in fetched_papers.items():
-        title = paper.get("Title", paper.get("title", "N/A"))
-        abstract = paper.get("Abstract", paper.get("abstractNote", "N/A"))
-        date = paper.get("Date", paper.get("date", "N/A"))
-        url = paper.get("URL", paper.get("url", paper.get("URL", "N/A")))
-        citations = paper.get("Citations", "N/A")
+        title = paper.get("Title", "N/A")
+        abstract = paper.get("Abstract", "N/A")
+        publication_date = paper.get("Publication Date", "N/A")  # Use Publication Date
+        url = paper.get("URL", "N/A")
+        citations = paper.get("Citation Count", "N/A")
+        venue = paper.get("Venue", "N/A")
+        publication_venue = paper.get("Publication Venue", "N/A")
+        journal_name = paper.get("Journal Name", "N/A")
+        journal_volume = paper.get("Journal Volume", "N/A")
+        journal_pages = paper.get("Journal Pages", "N/A")
+
+        # Convert Authors list to Zotero format
+        authors = [
+            (
+                {
+                    "creatorType": "author",
+                    "firstName": name.split(" ")[0],
+                    "lastName": " ".join(name.split(" ")[1:]),
+                }
+                if " " in name
+                else {"creatorType": "author", "lastName": name}
+            )
+            for name in [
+                author.split(" (ID: ")[0] for author in paper.get("Authors", [])
+            ]
+        ]
 
         zotero_items.append(
             {
                 "itemType": "journalArticle",
                 "title": title,
                 "abstractNote": abstract,
-                "date": date,
+                "date": publication_date,  # Now saving full publication date
                 "url": url,
                 "extra": f"Paper ID: {paper_id}\nCitations: {citations}",
                 "collections": [matched_collection_key],
+                "publicationTitle": (
+                    publication_venue if publication_venue != "N/A" else venue
+                ),  # Use publication venue if available
+                "journalAbbreviation": journal_name,  # Save Journal Name
+                "volume": (
+                    journal_volume if journal_volume != "N/A" else None
+                ),  # Save Journal Volume
+                "pages": (
+                    journal_pages if journal_pages != "N/A" else None
+                ),  # Save Journal Pages
+                "creators": authors,  # Save authors list properly
             }
         )
 
@@ -232,7 +264,7 @@ def zotero_save_tool(
             for i, paper in enumerate(top_papers)
         ]
     )
-    content += "Here are the top articles:\n" + top_papers_info
+    content += "Here are a few of these articles:\n" + top_papers_info
 
     return Command(
         update={

{aiagents4pharma-1.29.0.dist-info → aiagents4pharma-1.30.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.29.0
+Version: 1.30.1
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
@@ -23,7 +23,7 @@ Requires-Dist: langchain-experimental==0.3.3
 Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
 Requires-Dist: langchain-openai==0.2.5
 Requires-Dist: langchain_ollama==0.2.3
-Requires-Dist: langgraph_supervisor==0.0.4
+Requires-Dist: langgraph_supervisor==0.0.9
 Requires-Dist: matplotlib==3.9.2
 Requires-Dist: openai==1.59.4
 Requires-Dist: ollama==0.4.7

{aiagents4pharma-1.29.0.dist-info → aiagents4pharma-1.30.1.dist-info}/RECORD

@@ -135,75 +135,84 @@ aiagents4pharma/talk2knowledgegraphs/utils/enrichments/pubchem_strings.py,sha256
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/__init__.py,sha256=7gwwtfzKhB8GuOBD47XRi0NprwEXkOzwNl5eeu-hDTI,86
 aiagents4pharma/talk2knowledgegraphs/utils/extractions/pcst.py,sha256=m5p0yoJb7I19ua5yeQfXPf7c4r6S1XPwttsrM7Qoy94,9336
 aiagents4pharma/talk2scholars/__init__.py,sha256=gphERyVKZHvOnMQsml7TIHlaIshHJ75R1J3FKExkfuY,120
-aiagents4pharma/talk2scholars/agents/__init__.py,sha256=ZwFiHOlDGJk1601J5xEZDy0btPzqiOk2UCocKxohde8,168
-aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=TABzGSOg7I0_fJ0qybBVqZDdrU8YCjyG_m-kasO4WgE,2854
-aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=c9-_z5qp5Zkgh6piEIlgI4uo4OMXD3janZNmfYwnFCg,3729
+aiagents4pharma/talk2scholars/agents/__init__.py,sha256=inLJpRDlT80RNSi3OFNi2lpbbTisQgzNkMYTvnhFjVY,203
+aiagents4pharma/talk2scholars/agents/main_agent.py,sha256=KdKbnc-5zxktLUkzEZHC3bvn8_iKa8Kk4So90i48cdE,3275
+aiagents4pharma/talk2scholars/agents/paper_download_agent.py,sha256=wrK9CPy5evH56fyOZ2BlkBfY5aEj6tefc4jSDPVzYvs,3041
+aiagents4pharma/talk2scholars/agents/pdf_agent.py,sha256=xt_bgCTVJ6jOCkhc_rHh8pngq4uS8kuNOevuP3eC-sA,3702
 aiagents4pharma/talk2scholars/agents/s2_agent.py,sha256=ua1bjKE2HBKZuLnDn8me5fuV1lSvdZbwAlo3Yp27TT4,4659
 aiagents4pharma/talk2scholars/agents/zotero_agent.py,sha256=5jfIJiLsRdlCJjkF7BQMkP5PsEY_Gr7SfztWKozbUGo,4223
 aiagents4pharma/talk2scholars/configs/__init__.py,sha256=tf2gz8n7M4ko6xLdX_C925ELVIxoP6SgkPcbeh59ad4,151
-aiagents4pharma/talk2scholars/configs/config.yaml,sha256=dQIMg3jLGYAudkc1Zz85qqvFf-HdVXPfewUfAfPNNzU,501
+aiagents4pharma/talk2scholars/configs/config.yaml,sha256=-8X0_gTmjEuXAeIrnppw3Npy8HICelHZOvTKEScI-rs,596
 aiagents4pharma/talk2scholars/configs/agents/__init__.py,sha256=yyh7PB2oY_JulnpSQCWS4wwCH_uzIdt47O2Ay48x_oU,75
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/__init__.py,sha256=64GEWAoKOd_YHLi27eSOcOC5eSLK0IG_FNra3ZBt02Y,146
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=rZfZ_dJArjlznHzusjxCnOjhptLTyejFiB0euV5R13c,662
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/main_agent/default.yaml,sha256=GZRqZoUy8eAWXyd9GJDh-A4mYSJOhnkid6TaIJTGBeU,1192
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/paper_download_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/pdf_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=sn6vX6r-P0CR7UWS63ZqCmMKKn4As8pZoITRWx8sdoo,1151
+aiagents4pharma/talk2scholars/configs/agents/talk2scholars/s2_agent/default.yaml,sha256=UIYkr060IpoLHMXVPxGAjrkCJSjX7H0DzcFSasyW6sE,1185
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/agents/talk2scholars/zotero_agent/default.yaml,sha256=lWBreotqsu1jlHi1uZ9vY60zi-MiiG2VuHxo5IoAvkE,1112
 aiagents4pharma/talk2scholars/configs/app/__init__.py,sha256=JoSZV6N669kGMv5zLDszwf0ZjcRHx9TJfIqGhIIdPXE,70
 aiagents4pharma/talk2scholars/configs/app/frontend/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=wsELBdRLv6UqZ9QZfwpS7K4xfMj5s-a99-aXqIs6WEI,868
+aiagents4pharma/talk2scholars/configs/app/frontend/default.yaml,sha256=A6nYjrgzEyRv5JYsGN7oqNX4-tufMBZ6mg-A7bMX6V4,906
 aiagents4pharma/talk2scholars/configs/tools/__init__.py,sha256=GwpgnRrfjyZDVsangewSVTG3H3GBYM6s_YaQd9-zI10,238
+aiagents4pharma/talk2scholars/configs/tools/download_arxiv_paper/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
-aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=QV7HrG7NdjBEjTMszh27MbGBYMbf_78V3sCGftdTtvo,442
+aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml,sha256=comNgL9hRpH--IWuEsrN6hV5WdrJmh-ZsRh7hbryVhg,631
 aiagents4pharma/talk2scholars/configs/tools/question_and_answer/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py,sha256=fqQQ-GlRcbzru2KmEk3oMma0R6_SzGM8dOXzYeU4oVA,46
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