tooluniverse 1.0.8__py3-none-any.whl → 1.0.9.1__py3-none-any.whl
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- tooluniverse/__init__.py +8 -0
- tooluniverse/admetai_tool.py +8 -1
- tooluniverse/compose_scripts/output_summarizer.py +87 -33
- tooluniverse/compose_tool.py +2 -2
- tooluniverse/data/adverse_event_tools.json +97 -98
- tooluniverse/data/agentic_tools.json +81 -162
- tooluniverse/data/compose_tools.json +0 -54
- tooluniverse/data/drug_discovery_agents.json +10 -20
- tooluniverse/data/literature_search_tools.json +15 -35
- tooluniverse/data/monarch_tools.json +1 -2
- tooluniverse/data/opentarget_tools.json +8 -16
- tooluniverse/data/output_summarization_tools.json +23 -20
- tooluniverse/data/packages/bioinformatics_core_tools.json +2 -2
- tooluniverse/data/packages/cheminformatics_tools.json +1 -1
- tooluniverse/data/packages/genomics_tools.json +1 -1
- tooluniverse/data/packages/single_cell_tools.json +1 -1
- tooluniverse/data/packages/structural_biology_tools.json +1 -1
- tooluniverse/data/tool_composition_tools.json +2 -4
- tooluniverse/execute_function.py +39 -1
- tooluniverse/logging_config.py +64 -2
- tooluniverse/molecule_2d_tool.py +9 -3
- tooluniverse/molecule_3d_tool.py +9 -3
- tooluniverse/output_hook.py +217 -150
- tooluniverse/smcp.py +8 -1
- tooluniverse/smcp_server.py +92 -201
- tooluniverse/tools/__init__.py +1 -3
- {tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.1.dist-info}/METADATA +3 -2
- {tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.1.dist-info}/RECORD +32 -33
- {tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.1.dist-info}/entry_points.txt +0 -3
- tooluniverse/tools/MultiAgentLiteratureSearch.py +0 -59
- {tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.1.dist-info}/WHEEL +0 -0
- {tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.1.dist-info}/licenses/LICENSE +0 -0
- {tooluniverse-1.0.8.dist-info → tooluniverse-1.0.9.1.dist-info}/top_level.txt +0 -0
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"properties": {
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"text": {
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"type": "string",
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"description": "The biomedical text, abstract, or paper content to be summarized."
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"required": true
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"description": "The biomedical text, abstract, or paper content to be summarized."
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"summary_length": {
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"type": "string",
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"description": "Desired length of summary (e.g., '50', '100', '200 words')."
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"required": true
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"description": "Desired length of summary (e.g., '50', '100', '200 words')."
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"focus_area": {
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"type": "string",
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"description": "What to focus on in the summary (e.g., 'methodology', 'results', 'clinical implications', 'drug interactions')."
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"description": "What to focus on in the summary (e.g., 'methodology', 'results', 'clinical implications', 'drug interactions')."
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"required": [
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"properties": {
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"tool_name": {
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"type": "string",
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"description": "Name of the tool being analyzed"
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"description": "Name of the tool being analyzed"
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"tool_description": {
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"description": "Description of what the tool is supposed to do"
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"description": "Description of what the tool is supposed to do"
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"tool_parameters": {
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"description": "JSON string of tool parameters and their types"
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"description": "JSON string of tool parameters and their types"
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"implementation_code": {
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"description": "The actual implementation code to analyze"
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"description": "The actual implementation code to analyze"
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"test_cases": {
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"description": "JSON string of test cases for the tool"
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"description": "JSON string of test cases for the tool"
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"properties": {
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"research_topic": {
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"description": "The specific medical/research topic for literature review (e.g., 'efficacy of drug X in treating condition Y')."
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"description": "The specific medical/research topic for literature review (e.g., 'efficacy of drug X in treating condition Y')."
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"literature_content": {
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"description": "The literature content, abstracts, full studies, or research papers to review and synthesize."
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"description": "The literature content, abstracts, full studies, or research papers to review and synthesize."
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"description": "Primary focus area for the review (e.g., 'therapeutic efficacy', 'safety profile', 'diagnostic accuracy', 'biomarker validation')."
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"description": "Primary focus area for the review (e.g., 'therapeutic efficacy', 'safety profile', 'diagnostic accuracy', 'biomarker validation')."
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"study_types": {
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"description": "Types of studies to prioritize in the analysis (e.g., 'randomized controlled trials', 'meta-analyses', 'cohort studies', 'case-control studies')."
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"description": "Types of studies to prioritize in the analysis (e.g., 'randomized controlled trials', 'meta-analyses', 'cohort studies', 'case-control studies')."
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"quality_level": {
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"description": "Minimum evidence quality level to include (e.g., 'high quality only', 'moderate and above', 'all available evidence')."
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"description": "Minimum evidence quality level to include (e.g., 'high quality only', 'moderate and above', 'all available evidence')."
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"description": "Scope of the review (e.g., 'comprehensive systematic review', 'rapid review', 'scoping review', 'narrative review')."
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"description": "Scope of the review (e.g., 'comprehensive systematic review', 'rapid review', 'scoping review', 'narrative review')."
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"properties": {
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"context": {
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"description": "Background information, observations, or data description from which to derive hypotheses."
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"description": "Background information, observations, or data description from which to derive hypotheses."
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"domain": {
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"description": "Field of study or research area (e.g., 'neuroscience', 'ecology', 'materials science')."
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"description": "Field of study or research area (e.g., 'neuroscience', 'ecology', 'materials science')."
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"number_of_hypotheses": {
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"description": "Number of hypotheses to generate (e.g., '3', '5')."
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"description": "Number of hypotheses to generate (e.g., '3', '5')."
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"hypothesis_format": {
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"description": "Optional directive on how to structure each hypothesis. Choose from one of the following formats:\n\n1. If–Then Statements: \"If [independent variable condition], then [expected outcome].\"\n2. Null and Alternative (Statistical):\n • H₀ (Null): \"There is no difference/effect/association between X and Y.\"\n • H₁ (Alt): \"There is a difference/effect/association between X and Y.\"\n3. Associative (Correlation-Focused): \"There is a relationship/association between [Variable A] and [Variable B].\"\n4. Directional (Non-If–Then): \"Increasing/decreasing [Variable A] will lead to [directional change] in [Variable B].\"\n5. Comparative (Group Comparison): \"Group A will show higher/lower [dependent measure] compared to Group B under [condition].\"\n6. Mechanistic: \"Because [mechanism or process], [Variable A] will cause [Variable B].\"\n7. Descriptive (Exploratory/Pattern-Oriented): \"Population X exhibits pattern Y in context Z.\"\n\nIf omitted, defaults to concise declarative sentences.",
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"hypothesis": {
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"description": "A clear statement of the research hypothesis to be tested."
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"description": "A clear statement of the research hypothesis to be tested."
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"design_description": {
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"description": "A detailed description of the proposed experimental design, including variables, methods, sample details, and planned analyses."
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"raw_terms": {
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|
"type": "object",
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"description": "The full configuration of the tool to generate test cases for. May include '_optimization_feedback' and '_iteration' fields for feedback-driven test generation."
|
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"required": true
|
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+
"description": "The full configuration of the tool to generate test cases for. May include '_optimization_feedback' and '_iteration' fields for feedback-driven test generation."
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}
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@@ -646,13 +608,11 @@
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"properties": {
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"original_description": {
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"description": "The original description of the tool."
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+
"description": "The original description of the tool."
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"test_results": {
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"type": "string",
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"description": "A JSON string containing a list of test case input/output pairs."
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"required": true
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"description": "A JSON string containing a list of test case input/output pairs."
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}
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"required": [
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@@ -682,13 +642,11 @@
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"properties": {
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"parameter_schema": {
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"type": "string",
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"description": "JSON string of the original parameter schema with properties and descriptions."
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"required": true
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+
"description": "JSON string of the original parameter schema with properties and descriptions."
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},
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"test_results": {
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"type": "string",
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"description": "A JSON string containing test case input/output pairs showing parameter usage."
|
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"required": true
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+
"description": "A JSON string containing test case input/output pairs showing parameter usage."
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}
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"required": [
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@@ -719,18 +677,15 @@
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"properties": {
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"tool_description": {
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"description": "The tool description to evaluate."
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"required": true
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+
"description": "The tool description to evaluate."
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"parameter_descriptions": {
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"description": "JSON string of parameter names and their descriptions."
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"required": true
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+
"description": "JSON string of parameter names and their descriptions."
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},
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"test_results": {
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"type": "string",
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"description": "JSON string containing test case results."
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"required": true
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+
"description": "JSON string containing test case results."
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}
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},
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"required": [
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@@ -764,28 +719,23 @@
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"properties": {
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"tool_description": {
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"description": "Brief description of the desired tool functionality and purpose."
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+
"description": "Brief description of the desired tool functionality and purpose."
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"tool_category": {
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"description": "Target category for the tool (e.g., 'biomedical', 'data_analysis', 'text_processing')."
|
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|
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"required": true
|
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+
"description": "Target category for the tool (e.g., 'biomedical', 'data_analysis', 'text_processing')."
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},
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|
"tool_type": {
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"type": "string",
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|
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"description": "Specific ToolUniverse tool type (e.g., 'AgenticTool', 'RESTTool', 'PythonTool')."
|
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|
-
"required": true
|
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+
"description": "Specific ToolUniverse tool type (e.g., 'AgenticTool', 'RESTTool', 'PythonTool')."
|
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},
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"similar_tools": {
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"type": "string",
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"description": "JSON string containing configurations of similar existing tools for analysis and differentiation."
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|
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"required": true
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+
"description": "JSON string containing configurations of similar existing tools for analysis and differentiation."
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},
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"existing_tools_summary": {
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"type": "string",
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"description": "Summary of existing tools in the ecosystem to avoid duplication and identify gaps."
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"required": true
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+
"description": "Summary of existing tools in the ecosystem to avoid duplication and identify gaps."
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}
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},
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"required": [
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@@ -820,14 +770,12 @@
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"properties": {
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"source_code": {
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"type": "string",
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"description": "The source code to analyze for quality assessment"
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"required": true
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|
+
"description": "The source code to analyze for quality assessment"
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},
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"language": {
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"type": "string",
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"description": "Programming language (python, javascript, etc.)",
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"default": "python"
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|
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"required": false
|
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|
+
"default": "python"
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|
},
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"analysis_depth": {
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|
"type": "string",
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@@ -837,13 +785,11 @@
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|
"security-focused"
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],
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|
"description": "Level of analysis depth to perform",
|
|
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|
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"default": "comprehensive"
|
|
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|
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"required": false
|
|
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+
"default": "comprehensive"
|
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|
},
|
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|
"domain_context": {
|
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|
"type": "string",
|
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|
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"description": "Domain context for specialized analysis (e.g., bioinformatics, web development)"
|
|
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|
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"required": false
|
|
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|
+
"description": "Domain context for specialized analysis (e.g., bioinformatics, web development)"
|
|
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|
}
|
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|
},
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"required": [
|
|
@@ -875,13 +821,11 @@
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"properties": {
|
|
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|
"tool_description": {
|
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|
"type": "string",
|
|
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|
-
"description": "Detailed description of what the tool should accomplish"
|
|
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|
-
"required": true
|
|
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|
+
"description": "Detailed description of what the tool should accomplish"
|
|
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|
},
|
|
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|
"tool_parameters": {
|
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|
"type": "string",
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|
-
"description": "JSON string of parameter schema for the tool"
|
|
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|
-
"required": true
|
|
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|
+
"description": "JSON string of parameter schema for the tool"
|
|
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|
},
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|
"domain": {
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|
"type": "string",
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|
@@ -894,8 +838,7 @@
|
|
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|
"text-processing",
|
|
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|
"general"
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|
],
|
|
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|
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"default": "general"
|
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|
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"required": false
|
|
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|
+
"default": "general"
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|
},
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|
"complexity_level": {
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|
"type": "string",
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|
@@ -905,13 +848,11 @@
|
|
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|
"advanced"
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|
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|
],
|
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|
"description": "Desired complexity level of implementation",
|
|
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|
-
"default": "intermediate"
|
|
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|
-
"required": false
|
|
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|
+
"default": "intermediate"
|
|
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|
},
|
|
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|
"performance_requirements": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "Performance requirements or constraints"
|
|
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|
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"required": false
|
|
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|
+
"description": "Performance requirements or constraints"
|
|
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|
}
|
|
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|
},
|
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|
"required": [
|
|
@@ -943,8 +884,7 @@
|
|
|
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|
"properties": {
|
|
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|
"tool_config": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string of current tool configuration to optimize"
|
|
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|
-
"required": true
|
|
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|
+
"description": "JSON string of current tool configuration to optimize"
|
|
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|
},
|
|
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|
"optimization_focus": {
|
|
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|
"type": "string",
|
|
@@ -956,8 +896,7 @@
|
|
|
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|
"all"
|
|
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|
],
|
|
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|
"description": "Primary optimization focus",
|
|
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|
-
"default": "all"
|
|
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|
-
"required": false
|
|
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|
+
"default": "all"
|
|
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|
},
|
|
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|
"target_audience": {
|
|
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|
"type": "string",
|
|
@@ -968,13 +907,11 @@
|
|
|
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|
"mixed"
|
|
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|
],
|
|
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909
|
"description": "Target user expertise level",
|
|
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|
-
"default": "mixed"
|
|
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|
-
"required": false
|
|
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|
+
"default": "mixed"
|
|
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|
},
|
|
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|
"similar_tools": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string array of similar tools for comparison and benchmarking"
|
|
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|
-
"required": false
|
|
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|
+
"description": "JSON string array of similar tools for comparison and benchmarking"
|
|
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915
|
}
|
|
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|
},
|
|
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|
"required": [
|
|
@@ -1005,8 +942,7 @@
|
|
|
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|
"properties": {
|
|
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|
"tool_config": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string of tool configuration to validate"
|
|
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|
-
"required": true
|
|
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|
+
"description": "JSON string of tool configuration to validate"
|
|
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|
},
|
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|
"domain": {
|
|
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|
"type": "string",
|
|
@@ -1021,19 +957,16 @@
|
|
|
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957
|
"chemistry",
|
|
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|
"physics",
|
|
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|
"general"
|
|
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|
-
]
|
|
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|
-
"required": true
|
|
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|
+
]
|
|
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|
},
|
|
1027
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|
"validation_aspects": {
|
|
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|
"type": "string",
|
|
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964
|
"description": "JSON array string of specific aspects to validate",
|
|
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|
-
"default": "[\"accuracy\", \"methodology\", \"best-practices\"]"
|
|
1031
|
-
"required": false
|
|
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|
+
"default": "[\"accuracy\", \"methodology\", \"best-practices\"]"
|
|
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|
},
|
|
1033
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|
"implementation_code": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "Implementation code to validate (optional)"
|
|
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|
-
"required": false
|
|
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|
+
"description": "Implementation code to validate (optional)"
|
|
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|
}
|
|
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971
|
},
|
|
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|
"required": [
|
|
@@ -1143,13 +1076,11 @@
|
|
|
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|
"properties": {
|
|
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|
"tool_config": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string containing the complete tool configuration including current implementation"
|
|
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|
-
"required": true
|
|
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|
+
"description": "JSON string containing the complete tool configuration including current implementation"
|
|
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|
},
|
|
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1081
|
"quality_evaluation": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string containing quality evaluation results and feedback"
|
|
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|
-
"required": true
|
|
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|
+
"description": "JSON string containing quality evaluation results and feedback"
|
|
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|
}
|
|
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|
},
|
|
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|
"required": [
|
|
@@ -1182,28 +1113,23 @@
|
|
|
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|
"properties": {
|
|
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|
"tool_name": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "The name of the tool"
|
|
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|
-
"required": true
|
|
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|
+
"description": "The name of the tool"
|
|
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|
},
|
|
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|
"tool_description": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "Detailed description of what the tool does"
|
|
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|
-
"required": true
|
|
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|
+
"description": "Detailed description of what the tool does"
|
|
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|
},
|
|
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1122
|
"tool_parameters": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string describing the tool's input parameters and their types"
|
|
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|
-
"required": true
|
|
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|
+
"description": "JSON string describing the tool's input parameters and their types"
|
|
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|
},
|
|
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1126
|
"category": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "The general category or domain the tool belongs to"
|
|
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|
-
"required": true
|
|
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|
+
"description": "The general category or domain the tool belongs to"
|
|
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|
},
|
|
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1130
|
"existing_labels": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON array string of existing labels to consider reusing (optional)"
|
|
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|
-
"required": false
|
|
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|
+
"description": "JSON array string of existing labels to consider reusing (optional)"
|
|
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1133
|
}
|
|
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|
},
|
|
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|
"required": [
|
|
@@ -1234,8 +1160,7 @@
|
|
|
1234
1160
|
"properties": {
|
|
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1161
|
"question": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "The user's question to be answered in a human-like manner."
|
|
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|
-
"required": true
|
|
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|
+
"description": "The user's question to be answered in a human-like manner."
|
|
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1164
|
}
|
|
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1165
|
},
|
|
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|
"required": [
|
|
@@ -1264,13 +1189,11 @@
|
|
|
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|
"properties": {
|
|
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|
"tool_config": {
|
|
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|
"type": "string",
|
|
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|
-
"description": "JSON string of the tool configuration to extract metadata from"
|
|
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|
-
"required": true
|
|
1192
|
+
"description": "JSON string of the tool configuration to extract metadata from"
|
|
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|
},
|
|
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|
"tool_type_mappings": {
|
|
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|
"type": "object",
|
|
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|
-
"description": "A mapping from a simplified toolType to a list of tool_config.type that fall under the toolType (e.g., {'Databases': ['XMLTool']})"
|
|
1273
|
-
"required": false
|
|
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|
+
"description": "A mapping from a simplified toolType to a list of tool_config.type that fall under the toolType (e.g., {'Databases': ['XMLTool']})"
|
|
1274
1197
|
}
|
|
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1198
|
},
|
|
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|
"required": [
|
|
@@ -1303,13 +1226,11 @@
|
|
|
1303
1226
|
"items": {
|
|
1304
1227
|
"type": "string"
|
|
1305
1228
|
},
|
|
1306
|
-
"description": "List of raw metadata strings (e.g., sources, tags) to standardize and group."
|
|
1307
|
-
"required": true
|
|
1229
|
+
"description": "List of raw metadata strings (e.g., sources, tags) to standardize and group."
|
|
1308
1230
|
},
|
|
1309
1231
|
"limit": {
|
|
1310
1232
|
"type": "integer",
|
|
1311
|
-
"description": "If provided, the maximum number of canonical strings to return. The LLM will group terms more aggressively to meet this limit, ensuring all raw strings are mapped."
|
|
1312
|
-
"required": false
|
|
1233
|
+
"description": "If provided, the maximum number of canonical strings to return. The LLM will group terms more aggressively to meet this limit, ensuring all raw strings are mapped."
|
|
1313
1234
|
}
|
|
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},
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"required": [
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@@ -1338,13 +1259,11 @@
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"properties": {
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"tool_a": {
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1340
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"type": "string",
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|
1341
|
-
"description": "JSON string for the primary tool configuration (Tool A)."
|
|
1342
|
-
"required": true
|
|
1262
|
+
"description": "JSON string for the primary tool configuration (Tool A)."
|
|
1343
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},
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1344
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"other_tools": {
|
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"type": "string",
|
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1346
|
-
"description": "JSON string of a list of other tool configurations to compare against Tool A."
|
|
1347
|
-
"required": true
|
|
1266
|
+
"description": "JSON string of a list of other tool configurations to compare against Tool A."
|
|
1348
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|
}
|
|
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|
},
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"required": [
|