tooluniverse 0.2.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

tooluniverse/data/medlineplus_tools.json

@@ -0,0 +1,141 @@
+[
+  {
+    "name": "MedlinePlus_search_topics_by_keyword",
+    "description": "Search for relevant information in MedlinePlus Web Service by keyword across health topics or other sub-libraries (such as drugs, genetics, etc.).",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "term": {
+          "type": "string",
+          "description": "Search keyword, e.g., \"diabetes\", needs to be URL encoded before passing."
+        },
+        "db": {
+          "type": "string",
+          "enum": ["healthTopics", "healthTopicsSpanish", "drugs", "drugsSpanish", "genetics", "medicalTests", "medicalEncyclopedia"],
+          "description": "Specify the database to search, e.g., healthTopics (English health topics), healthTopicsSpanish (Spanish health topics), drugs (English drugs), etc."
+        },
+        "rettype": {
+          "type": "string",
+          "enum": ["brief", "topic", "all"],
+          "description": "Result return format, options: brief (concise information, default), topic (detailed XML record), all (includes all available information).",
+          "default": "topic"
+        }
+      },
+      "required": ["term", "db"]
+    },
+    "fields": {
+      "endpoint": "https://wsearch.nlm.nih.gov/ws/query?db={db}&term={term}&rettype={rettype}",
+      "input_description": "Input parameters:\n- term: keyword to search (URL encoded);\n- db: database name, e.g., healthTopics, drugs, etc.;\n- rettype: return format, options: brief, topic, all.",
+      "output_description": "Returns MedlinePlus Web Service response XML, will contain title, summary, links, etc. for matching topics, the returned data will be parsed into a Python dictionary for subsequent use."
+    },
+    "type": "MedlinePlusRESTTool"
+  },
+  {
+    "name": "MedlinePlus_connect_lookup_by_code",
+    "description": "Look up corresponding MedlinePlus page information through MedlinePlus Connect Web Service using clinical/drug/test codes (such as ICD-10 CM, RXCUI, LOINC, etc.), supports JSON or XML format return.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "cs": {
+          "type": "string",
+          "description": "Code system OID, e.g., ICD-10 CM=2.16.840.1.113883.6.90, RXCUI=2.16.840.1.113883.6.88, LOINC=2.16.840.1.113883.6.1, etc."
+        },
+        "c": {
+          "type": "string",
+          "description": "Specific code value to query, e.g., \"E11.9\" (ICD-10 CM) or \"637188\" (RXCUI)."
+        },
+        "dn": {
+          "type": "string",
+          "description": "Optional, descriptive name (English) corresponding to the code, for drugs can fill in \"Chantix 0.5 MG Oral Tablet\", can improve matching accuracy.",
+          "default": ""
+        },
+        "language": {
+          "type": "string",
+          "enum": ["en", "es"],
+          "description": "Return information language, \"en\" for English, \"es\" for Spanish, default \"en\".",
+          "default": "en"
+        },
+        "format": {
+          "type": "string",
+          "enum": ["json", "xml"],
+          "description": "Return format, options \"json\" or \"xml\", default \"json\".",
+          "default": "json"
+        }
+      },
+      "required": ["cs", "c"]
+    },
+    "fields": {
+      "endpoint": "https://connect.medlineplus.gov/service?mainSearchCriteria.v.cs={cs}&mainSearchCriteria.v.c={c}&informationRecipient.languageCode.c={language}&knowledgeResponseType={format}&mainSearchCriteria.v.dn={dn}",
+      "input_description": "Input parameters:\n- cs: code system OID;\n- c: specific code value;\n- dn: optional code descriptive name;\n- language: return language (en or es);\n- format: return format (json or xml).",
+      "output_description": "Returns MedlinePlus Connect Web Service response, can include title, links, summary, etc. of MedlinePlus pages matching the code. If format=json, returns JSON format and parses to Python dictionary; if format=xml, returns XML and converts it to dictionary."
+    },
+    "type": "MedlinePlusRESTTool"
+  },
+  {
+    "name": "MedlinePlus_get_genetics_condition_by_name",
+    "description": "Get detailed information from MedlinePlus Genetics corresponding to genetic condition name, supports JSON or XML format return.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "condition": {
+          "type": "string",
+          "description": "URL slug of genetic condition, e.g., \"alzheimer-disease\", must match MedlinePlus page path."
+        },
+        "format": {
+          "type": "string",
+          "enum": ["json", "xml"],
+          "description": "Return format, options \"json\" or \"xml\", default \"json\".",
+          "default": "json"
+        }
+      },
+      "required": ["condition"]
+    },
+    "fields": {
+      "endpoint": "https://medlineplus.gov/download/genetics/condition/{condition}.{format}",
+      "input_description": "Input parameters:\n- condition: genetic condition name (URL slug), e.g., \"alzheimer-disease\";\n- format: return format (json or xml).",
+      "output_description": "Returns JSON or XML data containing detailed information about the genetic condition, data includes consumer version description, symptoms, gene information, treatment options, etc., return value will be parsed into Python dictionary or OrderedDict for subsequent use."
+    },
+    "type": "MedlinePlusRESTTool"
+  },
+  {
+    "name": "MedlinePlus_get_genetics_gene_by_name",
+    "description": "Get detailed information from MedlinePlus Genetics corresponding to gene name, supports JSON or XML format return.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene": {
+          "type": "string",
+          "description": "URL slug of gene name, e.g., \"BRCA1\", must match MedlinePlus page path."
+        },
+        "format": {
+          "type": "string",
+          "enum": ["json", "xml"],
+          "description": "Return format, options \"json\" or \"xml\", default \"json\".",
+          "default": "json"
+        }
+      },
+      "required": ["gene"]
+    },
+    "fields": {
+      "endpoint": "https://medlineplus.gov/download/genetics/gene/{gene}.{format}",
+      "input_description": "Input parameters:\n- gene: gene name (URL slug), e.g., \"BRCA1\";\n- format: return format (json or xml).",
+      "output_description": "Returns JSON or XML data containing detailed gene information, including consumer version description, gene function, related genetic conditions, gene structure, etc., return result will be parsed into Python dictionary or OrderedDict."
+    },
+    "type": "MedlinePlusRESTTool"
+  },
+  {
+    "name": "MedlinePlus_get_genetics_index",
+    "description": "Download index file (XML) of all genetics entries in MedlinePlus, get complete list in one call.",
+    "parameter": {
+      "type": "object",
+      "properties": {},
+      "required": []
+    },
+    "fields": {
+      "endpoint": "https://medlineplus.gov/download/TopicIndex.xml",
+      "input_description": "No input parameters needed, directly call to get complete genetics index.",
+      "output_description": "Returns XML index containing all genetics entries, data will be parsed into Python dictionary or OrderedDict, can be used for offline caching or batch processing."
+    },
+    "type": "MedlinePlusRESTTool"
+  }
+]

tooluniverse/data/monarch_tools.json

@@ -115,4 +115,4 @@
         "type": "Monarch",
         "tool_url": "/search"
     }
-]
+]

tooluniverse/data/openalex_tools.json

@@ -0,0 +1,36 @@
+[
+    {
+        "type": "OpenAlexTool",
+        "name": "openalex_literature_search",
+        "description": "Search for academic literature using OpenAlex API. Retrieves papers with title, abstract, authors, publication year, and organizational affiliations based on search keywords.",
+        "parameter": {
+            "type": "object",
+            "properties": {
+                "search_keywords": {
+                    "type": "string",
+                    "description": "Keywords to search for in paper titles, abstracts, and content. Use relevant scientific terms or phrases."
+                },
+                "max_results": {
+                    "type": "integer",
+                    "description": "Maximum number of papers to retrieve (default: 10, maximum: 200).",
+                    "default": 10,
+                    "minimum": 1,
+                    "maximum": 200
+                },
+                "year_from": {
+                    "type": "integer",
+                    "description": "Start year for publication date filter (e.g., 2020). Optional parameter to limit search to papers published from this year onwards."
+                },
+                "year_to": {
+                    "type": "integer",
+                    "description": "End year for publication date filter (e.g., 2023). Optional parameter to limit search to papers published up to this year."
+                },
+                "open_access": {
+                    "type": "boolean",
+                    "description": "Filter for open access papers only. Set to true for open access papers, false for non-open access, or omit for all papers."
+                }
+            },
+            "required": ["search_keywords"]
+        }
+    }
+]

tooluniverse/data/opentarget_tools.json

@@ -1436,4 +1436,4 @@
         ],
         "type": "OpenTarget"
     }
-]
+]

tooluniverse/data/output_summarization_tools.json

@@ -0,0 +1,101 @@
+[
+  {
+    "type": "AgenticTool",
+    "name": "ToolOutputSummarizer",
+    "description": "AI-powered tool for summarizing long tool outputs, focusing on key information relevant to the original query",
+    "prompt": "You are an expert at summarizing tool outputs. Your task is to analyze the provided tool output and create a concise summary that highlights the most important information relevant to the original query.\n\nTool Output to Summarize:\n{tool_output}\n\nOriginal Query Context:\n{query_context}\n\nTool Name: {tool_name}\nFocus Areas: {focus_areas}\nMaximum Summary Length: {max_length}\n\nPlease provide a well-structured summary that:\n1. Captures the key findings and results\n2. Highlights important data points and metrics\n3. Preserves critical technical details\n4. Maintains the essential structure of the original output\n5. Focuses on information most relevant to the query\n\nReturn the summary in a clear, organized format.",
+    "input_arguments": ["tool_output", "query_context", "tool_name", "focus_areas", "max_length"],
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "tool_output": {
+          "type": "string",
+          "description": "The original tool output to be summarized",
+          "required": true
+        },
+        "query_context": {
+          "type": "string",
+          "description": "Context about the original query that triggered the tool",
+          "required": true
+        },
+        "tool_name": {
+          "type": "string",
+          "description": "Name of the tool that generated the output",
+          "required": true
+        },
+        "focus_areas": {
+          "type": "string",
+          "description": "Specific areas to focus on in the summary",
+          "required": false,
+          "default": "key_findings_and_results"
+        },
+        "max_length": {
+          "type": "integer",
+          "description": "Maximum length of the summary in characters",
+          "required": false,
+          "default": 32000
+        }
+      },
+      "required": ["tool_output", "query_context", "tool_name"]
+    },
+    "configs": {
+      "api_type": "CHATGPT",
+      "model_id": "gpt-4o-1120",
+      "temperature": 0.3,
+      "max_new_tokens": 2048,
+      "return_json": false,
+      "return_metadata": false
+    }
+  },
+  {
+    "type": "ComposeTool",
+    "name": "OutputSummarizationComposer",
+    "description": "Composes output summarization workflow by chunking long outputs, processing each chunk with AI summarization, and merging results",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "tool_output": {
+          "type": "string",
+          "description": "The original tool output to be summarized",
+          "required": true
+        },
+        "query_context": {
+          "type": "string",
+          "description": "Context about the original query",
+          "required": true
+        },
+        "tool_name": {
+          "type": "string",
+          "description": "Name of the tool that generated the output",
+          "required": true
+        },
+        "chunk_size": {
+          "type": "integer",
+          "description": "Size of each chunk for processing",
+          "required": false,
+          "default": 2000
+        },
+        "focus_areas": {
+          "type": "string",
+          "description": "Areas to focus on in summarization",
+          "required": false,
+          "default": "key_findings_and_results"
+        },
+        "max_summary_length": {
+          "type": "integer",
+          "description": "Maximum length of final summary",
+          "required": false,
+          "default": 3000
+        }
+      },
+      "required": ["tool_output", "query_context", "tool_name"]
+    },
+    "auto_load_dependencies": true,
+    "fail_on_missing_tools": false,
+    "required_tools": [
+      "ToolOutputSummarizer"
+    ],
+    "composition_file": "output_summarizer.py",
+    "composition_function": "compose"
+  }
+]