tooluniverse 0.2.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

tooluniverse/medlineplus_tool.py

@@ -0,0 +1,337 @@
+# medlineplus_tool.py
+
+import requests
+import xmltodict
+from typing import Optional, Dict, Any
+import re
+import json
+
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("MedlinePlusRESTTool")
+class MedlinePlusRESTTool(BaseTool):
+    """
+    MedlinePlus REST API tool class.
+    Supports health topic search, code lookup, genetics information retrieval, etc.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.timeout = 10
+        self.endpoint_template = tool_config["fields"]["endpoint"]
+        self.param_schema = tool_config["parameter"]["properties"]
+
+    def _build_url(self, arguments: dict) -> str:
+        """Build complete URL"""
+        url_path = self.endpoint_template
+        placeholders = re.findall(r"\{([^{}]+)\}", url_path)
+
+        for ph in placeholders:
+            if ph not in arguments:
+                return {"error": f"Missing required parameter '{ph}'"}
+            url_path = url_path.replace(f"{{{ph}}}", str(arguments[ph]))
+
+        return url_path
+
+    def _extract_text_content(self, text_item: dict) -> str:
+        """Extract content from text item"""
+        if not isinstance(text_item, dict):
+            return ""
+
+        text = text_item.get("text", {})
+        if not isinstance(text, dict):
+            return ""
+
+        html = text.get("html", "")
+        if isinstance(html, dict) and "html:p" in html:
+            paragraphs = html["html:p"]
+            if isinstance(paragraphs, list):
+                return "\n".join(
+                    [
+                        p.get("#text", "")
+                        for p in paragraphs
+                        if isinstance(p, dict) and "#text" in p
+                    ]
+                )
+        return html.replace("<p>", "").replace("</p>", "\n")
+
+    def _format_response(self, response: Any, tool_name: str) -> Dict[str, Any]:
+        """Format response content"""
+        if not isinstance(response, dict):
+            return {"raw_response": response}
+
+        # Extract text content
+        def get_text_content(data, role):
+            text_list = data.get("text-list", [])
+            if isinstance(text_list, dict):
+                text_list = [text_list]
+            for item in text_list:
+                if isinstance(item, dict) and "text" in item:
+                    text = item["text"]
+                    if text.get("text-role") == role:
+                        return self._extract_text_content(item)
+            return ""
+
+        # Extract list items
+        def get_list_items(
+            data, list_key, item_key, name_key="name", url_key="ghr-page"
+        ):
+            items = []
+            list_data = data.get(list_key, {})
+            if isinstance(list_data, dict):
+                items = list_data.get(item_key, [])
+                if not isinstance(items, list):
+                    items = [items]
+            for item in items:
+                if isinstance(item, dict):
+                    name = item.get(name_key, "")
+                    url = item.get(url_key, "")
+                    items.append(f"{name} ({url})" if url else name)
+            return items
+
+        # Format response based on tool type
+        if tool_name == "MedlinePlus_search_topics_by_keyword":
+            # First print raw response for debugging
+            print("\n🔍 Raw response structure:")
+            print(
+                json.dumps(response, indent=2, ensure_ascii=False)[:2000] + "..."
+                if len(json.dumps(response, indent=2, ensure_ascii=False)) > 2000
+                else json.dumps(response, indent=2, ensure_ascii=False)
+            )
+
+            # Extract topic information from XML structure
+            nlm_result = response.get("nlmSearchResult", {})
+            if not nlm_result:
+                return {"error": "nlmSearchResult node not found"}
+
+            # Get document list
+            document_list = nlm_result.get("list", {}).get("document", [])
+            if not document_list:
+                return {"error": "document list not found"}
+
+            # Ensure document_list is a list
+            if isinstance(document_list, dict):
+                document_list = [document_list]
+
+            formatted_topics = []
+            for doc in document_list:
+                # Get document basic info
+                doc_url = doc.get("@url", "")
+                doc_rank = doc.get("@rank", "")
+
+                # Get content node
+                content = doc.get("content", {})
+                if isinstance(content, dict):
+                    health_topic = content.get("health-topic", {})
+                    if health_topic:
+                        # Extract health topic information
+                        title = health_topic.get("@title", "")
+                        meta_desc = health_topic.get("@meta-desc", "")
+                        topic_url = health_topic.get("@url", doc_url)
+                        language = health_topic.get("@language", "")
+
+                        # Extract aliases
+                        also_called = health_topic.get("also-called", [])
+                        if isinstance(also_called, str):
+                            also_called = [also_called]
+                        elif isinstance(also_called, dict):
+                            also_called = [also_called.get("#text", str(also_called))]
+                        elif not isinstance(also_called, list):
+                            also_called = []
+
+                        # Extract summary
+                        full_summary = health_topic.get("full-summary", "")
+                        if isinstance(full_summary, dict):
+                            full_summary = str(full_summary)
+
+                        # Extract group information
+                        groups = health_topic.get("group", [])
+                        if isinstance(groups, str):
+                            groups = [groups]
+                        elif isinstance(groups, dict):
+                            groups = [groups.get("#text", str(groups))]
+                        elif not isinstance(groups, list):
+                            groups = []
+
+                        formatted_topics.append(
+                            {
+                                "title": title,
+                                "meta_desc": meta_desc,
+                                "url": topic_url,
+                                "language": language,
+                                "rank": doc_rank,
+                                "also_called": also_called,
+                                "summary": (
+                                    full_summary[:500] + "..."
+                                    if len(str(full_summary)) > 500
+                                    else full_summary
+                                ),
+                                "groups": groups,
+                            }
+                        )
+
+            return (
+                {"topics": formatted_topics}
+                if formatted_topics
+                else {"error": "Failed to parse health topic information"}
+            )
+
+        elif tool_name == "MedlinePlus_get_genetics_condition_by_name":
+            return {
+                "name": response.get("name", ""),
+                "description": get_text_content(response, "description"),
+                "genes": get_list_items(
+                    response, "related-gene-list", "related-gene", "gene-symbol"
+                ),
+                "synonyms": [
+                    s.get("synonym", "") for s in response.get("synonym-list", [])
+                ],
+                "ghr_page": response.get("ghr_page", ""),
+            }
+
+        elif tool_name == "MedlinePlus_get_genetics_gene_by_name":
+            gene_summary = response.get("gene-summary", {})
+            return {
+                "name": gene_summary.get("name", ""),
+                "function": get_text_content(gene_summary, "function"),
+                "health_conditions": get_list_items(
+                    gene_summary,
+                    "related-health-condition-list",
+                    "related-health-condition",
+                ),
+                "synonyms": gene_summary.get("synonym-list", {}).get("synonym", []),
+                "ghr_page": gene_summary.get("ghr-page", ""),
+            }
+
+        elif tool_name == "MedlinePlus_connect_lookup_by_code":
+            responses = response.get("knowledgeResponse", [])
+            return (
+                {
+                    "responses": [
+                        {
+                            "title": r.get("title", ""),
+                            "summary": r.get("summary", ""),
+                            "url": r.get("url", ""),
+                        }
+                        for r in responses
+                    ]
+                }
+                if responses
+                else {"error": "No matching code information found"}
+            )
+
+        elif tool_name == "MedlinePlus_get_genetics_index":
+            topics = response.get("genetics_home_reference_topic_list", {}).get(
+                "topic", []
+            )
+            return (
+                {
+                    "topics": [
+                        {"name": t.get("name", ""), "url": t.get("url", "")}
+                        for t in topics
+                    ]
+                }
+                if topics
+                else {"error": "No genetics topics found"}
+            )
+
+        return {"raw_response": response}
+
+    def run(self, arguments: dict):
+        """Execute tool call"""
+        # Validate required parameters
+        for key, prop in self.param_schema.items():
+            if prop.get("required", False) and key not in arguments:
+                return {"error": f"Parameter '{key}' is required."}
+
+        # Build URL
+        url = self._build_url(arguments)
+        if isinstance(url, dict) and "error" in url:
+            return url
+
+        # Print complete URL
+        print(f"\n🔗 Request URL: {url}")
+
+        # Make request
+        try:
+            resp = requests.get(url, timeout=self.timeout)
+            if resp.status_code != 200:
+                return {
+                    "error": f"MedlinePlus returned non-200 status code: {resp.status_code}",
+                    "detail": resp.text,
+                }
+
+            print(f"\n📊 Response status: {resp.status_code}")
+            print(f"📏 Response length: {len(resp.text)} characters")
+            print(f"🔤 First 500 characters of response: {resp.text[:500]}...")
+
+            # Improved parsing logic
+            tool_name = self.tool_config["name"]
+            response_text = resp.text.strip()
+
+            # Decide parsing method based on tool type and content format
+            if url.endswith(".json") or (arguments.get("format") == "json"):
+                # JSON format
+                response = resp.json()
+                print("📋 Parsed as: JSON")
+            elif (
+                url.endswith(".xml")
+                or response_text.startswith("<?xml")
+                or (arguments.get("format") == "xml")
+            ):
+                # XML format
+                response = xmltodict.parse(resp.text)
+                print("📋 Parsed as: XML -> Dictionary")
+            elif tool_name == "MedlinePlus_search_topics_by_keyword":
+                # Search tool defaults to XML
+                response = xmltodict.parse(resp.text)
+                print("📋 Parsed as: XML -> Dictionary (Search tool)")
+            elif tool_name == "MedlinePlus_get_genetics_index":
+                # Genetics index defaults to XML
+                response = xmltodict.parse(resp.text)
+                print("📋 Parsed as: XML -> Dictionary (Genetics index)")
+            else:
+                # Other cases keep original text
+                response = resp.text
+                print("📋 Parsed as: Plain text")
+
+            print(f"🔍 Parsed data type: {type(response)}")
+            if isinstance(response, dict):
+                print(f"🗝️ Top-level dictionary keys: {list(response.keys())}")
+
+            return self._format_response(response, tool_name)
+
+        except requests.RequestException as e:
+            return {"error": f"Failed to request MedlinePlus: {str(e)}"}
+
+    # Tool methods
+    def search_topics_by_keyword(
+        self, term: str, db: str, rettype: str = "brief"
+    ) -> Dict[str, Any]:
+        return self.run({"term": term, "db": db, "rettype": rettype})
+
+    def connect_lookup_by_code(
+        self,
+        cs: str,
+        c: str,
+        dn: Optional[str] = None,
+        language: str = "en",
+        format: str = "json",
+    ) -> Any:
+        args = {"cs": cs, "c": c, "language": language, "format": format}
+        if dn:
+            args["dn"] = dn
+        return self.run(args)
+
+    def get_genetics_condition_by_name(
+        self, condition: str, format: str = "json"
+    ) -> Any:
+        return self.run({"condition": condition, "format": format})
+
+    def get_genetics_gene_by_name(self, gene: str, format: str = "json") -> Any:
+        return self.run({"gene": gene, "format": "json"})
+
+    def get_genetics_index(self) -> Any:
+        return self.run({})

tooluniverse/openalex_tool.py

@@ -0,0 +1,228 @@
+import requests
+import urllib.parse
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+
+@register_tool("OpenAlexTool")
+class OpenAlexTool(BaseTool):
+    """
+    Tool to retrieve literature from OpenAlex based on search keywords.
+    """
+
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.base_url = "https://api.openalex.org/works"
+
+    def run(self, arguments):
+        """Main entry point for the tool."""
+        search_keywords = arguments.get("search_keywords")
+        max_results = arguments.get("max_results", 10)
+        year_from = arguments.get("year_from", None)
+        year_to = arguments.get("year_to", None)
+        open_access = arguments.get("open_access", None)
+
+        return self.search_literature(
+            search_keywords, max_results, year_from, year_to, open_access
+        )
+
+    def search_literature(
+        self,
+        search_keywords,
+        max_results=10,
+        year_from=None,
+        year_to=None,
+        open_access=None,
+    ):
+        """
+        Search for literature using OpenAlex API.
+
+        Parameters:
+            search_keywords (str): Keywords to search for in title, abstract, and content.
+            max_results (int): Maximum number of results to return (default: 10).
+            year_from (int): Start year for publication date filter (optional).
+            year_to (int): End year for publication date filter (optional).
+            open_access (bool): Filter for open access papers only (optional).
+
+        Returns:
+            list: List of dictionaries containing paper information.
+        """
+        # Encode search keywords for URL
+        encoded_keywords = urllib.parse.quote(search_keywords)
+
+        # Build query parameters
+        params = {
+            "search": encoded_keywords,
+            "per-page": min(max_results, 200),  # OpenAlex allows max 200 per page
+            "sort": "cited_by_count:desc",  # Sort by citation count (most cited first)
+            "mailto": "support@openalex.org",  # Polite pool access
+        }
+
+        # Add year filters if provided
+        filters = []
+        if year_from is not None and year_to is not None:
+            filters.append(f"publication_year:{year_from}-{year_to}")
+        elif year_from is not None:
+            filters.append(f"from_publication_date:{year_from}-01-01")
+        elif year_to is not None:
+            filters.append(f"to_publication_date:{year_to}-12-31")
+
+        # Add open access filter if specified
+        if open_access is True:
+            filters.append("is_oa:true")
+        elif open_access is False:
+            filters.append("is_oa:false")
+
+        if filters:
+            params["filter"] = ",".join(filters)
+
+        try:
+            response = requests.get(self.base_url, params=params)
+            response.raise_for_status()
+            data = response.json()
+
+            papers = []
+            for work in data.get("results", []):
+                paper_info = self._extract_paper_info(work)
+                papers.append(paper_info)
+
+            print(
+                f"[OpenAlex] Retrieved {len(papers)} papers for keywords: '{search_keywords}'"
+            )
+            return papers
+
+        except requests.exceptions.RequestException as e:
+            return f"Error retrieving data from OpenAlex: {e}"
+
+    def _extract_paper_info(self, work):
+        """
+        Extract relevant information from a work object returned by OpenAlex API.
+
+        Parameters:
+            work (dict): Work object from OpenAlex API response.
+
+        Returns:
+            dict: Formatted paper information.
+        """
+        # Extract title
+        title = work.get("title", "No title available")
+
+        # Extract abstract (display_name from abstract_inverted_index if available)
+        abstract = None
+        if work.get("abstract_inverted_index"):
+            # Reconstruct abstract from inverted index
+            abstract_dict = work["abstract_inverted_index"]
+            abstract_words = [""] * 500  # Assume max 500 words
+            for word, positions in abstract_dict.items():
+                for pos in positions:
+                    if pos < len(abstract_words):
+                        abstract_words[pos] = word
+            abstract = " ".join([word for word in abstract_words if word]).strip()
+
+        if not abstract:
+            abstract = "Abstract not available"
+
+        # Extract authors
+        authors = []
+        for authorship in work.get("authorships", []):
+            author = authorship.get("author", {})
+            author_name = author.get("display_name", "Unknown Author")
+            authors.append(author_name)
+
+        # Extract publication year
+        publication_year = work.get("publication_year", "Year not available")
+
+        # Extract organizations/affiliations
+        organizations = set()
+        for authorship in work.get("authorships", []):
+            for institution in authorship.get("institutions", []):
+                org_name = institution.get("display_name")
+                if org_name:
+                    organizations.add(org_name)
+
+        # Extract additional useful information
+        venue = (
+            work.get("primary_location", {})
+            .get("source", {})
+            .get("display_name", "Unknown venue")
+        )
+        doi = work.get("doi", "No DOI")
+        citation_count = work.get("cited_by_count", 0)
+        open_access = work.get("open_access", {}).get("is_oa", False)
+        pdf_url = work.get("open_access", {}).get("oa_url")
+
+        return {
+            "title": title,
+            "abstract": abstract,
+            "authors": authors,
+            "year": publication_year,
+            "organizations": list(organizations),
+            "venue": venue,
+            "doi": doi,
+            "citation_count": citation_count,
+            "open_access": open_access,
+            "pdf_url": pdf_url,
+            "openalex_id": work.get("id", ""),
+            "url": work.get("doi") if work.get("doi") else work.get("id", ""),
+        }
+
+    def get_paper_by_doi(self, doi):
+        """
+        Retrieve a specific paper by its DOI.
+
+        Parameters:
+            doi (str): DOI of the paper to retrieve.
+
+        Returns:
+            dict: Paper information or None if not found.
+        """
+        try:
+            # OpenAlex supports DOI lookup directly
+            url = f"https://api.openalex.org/works/https://doi.org/{doi}"
+            params = {"mailto": "support@openalex.org"}
+
+            response = requests.get(url, params=params)
+            response.raise_for_status()
+            work = response.json()
+
+            return self._extract_paper_info(work)
+
+        except requests.exceptions.RequestException as e:
+            print(f"Error retrieving paper by DOI {doi}: {e}")
+            return None
+
+    def get_papers_by_author(self, author_name, max_results=10):
+        """
+        Retrieve papers by a specific author.
+
+        Parameters:
+            author_name (str): Name of the author to search for.
+            max_results (int): Maximum number of results to return.
+
+        Returns:
+            list: List of papers by the author.
+        """
+        try:
+            params = {
+                "filter": f"author.display_name.search:{author_name}",
+                "per-page": min(max_results, 200),
+                "sort": "cited_by_count:desc",
+                "mailto": "support@openalex.org",
+            }
+
+            response = requests.get(self.base_url, params=params)
+            response.raise_for_status()
+            data = response.json()
+
+            papers = []
+            for work in data.get("results", []):
+                paper_info = self._extract_paper_info(work)
+                papers.append(paper_info)
+
+            print(
+                f"[OpenAlex] Retrieved {len(papers)} papers by author: '{author_name}'"
+            )
+            return papers
+
+        except requests.exceptions.RequestException as e:
+            return f"Error retrieving papers by author {author_name}: {e}"