matvenus-cli 0.1.0

package/dist/index.js

@@ -0,0 +1,125 @@
+#!/usr/bin/env node
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const commander_1 = require("commander");
+const commands_1 = require("./commands");
+const program = new commander_1.Command();
+program
+    .name('matwings-venus-cli')
+    .description('Standalone MCP server for VenusFactory protein tools')
+    .version('0.5.0');
+// System command: Search API
+program
+    .command('search-api')
+    .description('Search for API endpoints by keyword')
+    .argument('<keyword>', 'Keyword to search for')
+    .action((keyword) => {
+    const spec = { "info": { "title": "VenusFactory MCP Server", "description": "Standalone MCP server for VenusFactory protein tools", "version": "0.5.0" }, "securitySchemes": [{ "name": "HTTPBearer", "type": "bearer", "envVarName": "BEARER_TOKEN" }], "paths": [{ "path": "/api/tools/predict/functional-residue", "methods": [{ "method": "post", "operationId": "predict_functional_residue", "summary": "Functional Residue", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file" }, "model_name": { "type": "string", "title": "Model Name", "description": "Model name for function prediction, Optional model names: ESM2-650M, Ankh-large, ProtT5-xl-uniref50 ", "default": "ESM2-650M" }, "task": { "type": "string", "title": "Task", "description": "Task: Activity Site, Binding Site, Conserved Site, Motif", "default": "Activity Site" } }, "type": "object", "title": "ResidueFunctionPredictionInput", "description": "Input for functional residue prediction" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "predict-functional-residue" }] }, { "path": "/api/tools/predict/venusx-functional-residue", "methods": [{ "method": "post", "operationId": "venusx_functional_residue_prediction", "summary": "Venusx Functional Residue", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file" }, "task": { "type": "string", "title": "Task", "description": "VenusX task: VenusX-Activity (activity site), VenusX-Binding (binding site), VenusX-Evo (conserved site)", "default": "VenusX-Activity" }, "mode": { "type": "string", "title": "Mode", "description": "Model mode: pro uses Ankh-large (default), light uses ESM2-650M. Model is read from venusx_config.yaml", "default": "pro" } }, "type": "object", "title": "VenusXFunctionalResiduePredictionInput", "description": "Input for VenusX functional site prediction. Uses venusx_config.yaml; default mode=pro." }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusx-functional-residue-prediction" }] }, { "path": "/api/tools/predict/venusg-protein-function", "methods": [{ "method": "post", "operationId": "venusg_protein_function_prediction", "summary": "Venusg Protein Function", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file" }, "task": { "type": "string", "title": "Task", "description": "VenusG task: VenusG-Solubility, VenusG-SubcellularLocalization, VenusG-MembraneProtein, VenusG-Metalionbinding, VenusG-Stability, VenusG-Sortingsignal, VenusG-OptimumTemperature, VenusG-Kcat, VenusG-OptimalPH", "default": "VenusG-Solubility" }, "mode": { "type": "string", "title": "Mode", "description": "Model mode: pro uses ESM2-650M, light uses ProtBert (default). Model is read from venusg_config.yaml", "default": "light" } }, "type": "object", "title": "VenusGProteinFunctionPredictionInput", "description": "Input for VenusG protein-level function prediction. Uses venusg_config.yaml; pro=ESM2-650M, light=ProtBert." }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusg-protein-function-prediction" }] }, { "path": "/api/tools/predict/protein-properties", "methods": [{ "method": "post", "operationId": "predict_protein_properties", "summary": "Protein Properties", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to PDB structure file or FASTA file" }, "task_name": { "type": "string", "title": "Task Name", "description": "Task name: Physical and chemical properties, Relative solvent accessible surface area (PDB only), SASA value (PDB only), Secondary structure (PDB only)", "default": "Physical and chemical properties" } }, "type": "object", "title": "ProteinPropertiesInput", "description": "Input for protein properties generation" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "predict-protein-properties" }] }, { "path": "/api/tools/predict/esmfold", "methods": [{ "method": "post", "operationId": "esmfold_protein_folding", "summary": "Esmfold Folding", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "type": "string", "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "verbose": { "anyOf": [{ "type": "boolean" }, { "type": "null" }], "title": "Verbose", "description": "Whether to print detailed information", "default": true } }, "type": "object", "required": ["sequence"], "title": "ProteinStructurePredictionInput", "description": "Input for protein structure prediction based on ESMFold" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "esmfold-protein-folding" }] }, { "path": "/api/tools/predict/alphafold", "methods": [{ "method": "post", "operationId": "alphafold_protein_folding", "summary": "Alphafold Folding", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "model_version": { "type": "string", "title": "Model Version", "description": "AlphaFold version to use: 'alphafold2' or 'alphafold3'", "default": "alphafold2" }, "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code (for simple single-chain prediction)" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file (.fasta, .fa, or .faa) (for simple single/multi-chain prediction)" }, "sequences": { "anyOf": [{ "items": { "additionalProperties": true, "type": "object" }, "type": "array" }, { "type": "null" }], "title": "Sequences", "description": "List of sequence entities for multi-chain prediction. For AlphaFold2: Only protein chains are supported (DNA/RNA/ligands ignored). For AlphaFold3: Full support for proteins, DNA, RNA, and ligands. Each entity can be: {'protein': {'id': 'A', 'sequence': 'PVLSCGEWQL', 'description': 'Chain A', 'modifications': [{'ptmType': 'HY3', 'ptmPosition': 1}], 'unpairedMsa': '...', 'pairedMsa': '...', 'templates': [...]}} {'dna': {'id': 'C', 'sequence': 'GACCTCT', 'modifications': [{'modificationType': '6OG', 'basePosition': 1}], 'unpairedMsa': '...'}} (AF3 only) {'rna': {'id': 'E', 'sequence': 'AGCU', 'modifications': [{'modificationType': '2MG', 'basePosition': 1}], 'unpairedMsa': '...'}} (AF3 only) {'ligand': {'id': ['F', 'G'], 'ccdCodes': ['ATP']}} or {'ligand': {'id': 'Z', 'smiles': 'CC(=O)OC1C[NH+]2CCC1CC2'}} (AF3 only)" }, "model_seeds": { "anyOf": [{ "items": { "type": "integer" }, "type": "array" }, { "type": "null" }], "title": "Model Seeds", "description": "Random seeds for AlphaFold3 prediction (default: [42])", "default": [42] } }, "type": "object", "title": "AlphaFoldInput", "description": "Input for AlphaFold2/3 protein structure prediction" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "alphafold-protein-folding" }] }, { "path": "/api/tools/predict/diffdock", "methods": [{ "method": "post", "operationId": "diffdock_protein_ligand_docking", "summary": "Diffdock Docking", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "protein_path": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Protein Path", "description": "OSS URL to protein PDB file" }, "protein_sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Protein Sequence", "description": "Protein sequence (will be folded using ESMFold if protein_path not provided)" }, "ligand": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Ligand", "description": "Ligand SMILES string or OSS URL to ligand file (.sdf, .mol2, etc.)" }, "protein_ligand_csv": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Protein Ligand Csv", "description": "OSS URL to CSV file containing multiple protein-ligand pairs with columns: complex_name, protein_path, ligand_description, protein_sequence" }, "num_poses": { "type": "integer", "title": "Num Poses", "description": "Number of poses to generate per complex (default: 10)", "default": 10 } }, "type": "object", "title": "DiffDockInput", "description": "Input for DiffDock protein-ligand docking prediction" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "diffdock-protein-ligand-docking" }] }, { "path": "/api/tools/predict/venusrem-mutation", "methods": [{ "method": "post", "operationId": "venusrem_mutation_prediction", "summary": "Venusrem Mutation", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "task": { "type": "string", "title": "Task", "description": "Prediction task: activity, binding, stability, expression, general (see venusrem_config.yaml)" }, "mode": { "type": "string", "title": "Mode", "description": "Model mode: pro for structure-based multi-model, light for sequence-based multi-model" }, "structure_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Structure File", "description": "OSS URL to structure file (required when mode=pro)" }, "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code (for mode=light)" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file (for mode=light)" }, "config": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Config", "description": "Path to venusrem_config.yaml file (optional)" } }, "type": "object", "required": ["task", "mode"], "title": "VenusREMInput", "description": "Input for VenusREM multi-model mutation prediction (pro/light)" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusrem-mutation-prediction" }] }, { "path": "/api/tools/predict/venusprime-multipoint", "methods": [{ "method": "post", "operationId": "venusprime_multipoint_prediction", "summary": "Venusprime Multipoint", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "mode": { "type": "string", "title": "Mode", "description": "Operation mode: 'train' to train models from experimental data, 'inference' to predict multi-point mutations using trained models", "default": "inference" }, "venus_mode": { "type": "string", "title": "Venus Mode", "description": "Model mode: 'light' for ridge regression (default), 'pro' for sesnet (not implemented yet)", "default": "light" }, "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Wild-type protein sequence (required for train mode if fasta_file not provided)" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file with wild-type sequence (required for train mode if sequence not provided)" }, "experiment_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Experiment File", "description": "OSS URL to CSV file with 'mutant' and 'score' columns for training (required for train mode)" }, "score_col_name": { "type": "string", "title": "Score Col Name", "description": "Name of score column in experiment_file to train" }, "model_path_list": { "anyOf": [{ "items": { "type": "string" }, "type": "array" }, { "type": "null" }], "title": "Model Path List", "description": "List of trained model file paths or OSS URLs (required for inference mode)" }, "site": { "anyOf": [{ "items": { "type": "integer" }, "type": "array" }, { "type": "null" }], "title": "Site", "description": "Mutation site numbers for combination mutations in inference mode (default: [2, 3, 4])", "default": [2, 3, 4] }, "model_num": { "type": "integer", "title": "Model Num", "description": "Number of ensemble models to train (for train mode, default: 5)", "default": 5 }, "batch_size": { "type": "integer", "title": "Batch Size", "description": "Batch size for embedding extraction during training (for train mode, default: 4)", "default": 4 }, "inference_batch_size": { "type": "integer", "title": "Inference Batch Size", "description": "Batch size for embedding extraction during inference (for inference mode, default: 32)", "default": 32 }, "config": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Config", "description": "Path to VenusPrime config YAML file (optional, default: venusprime_config.yaml in script directory)" }, "target_server": { "type": "string", "title": "Target Server", "description": "Target server for job submission: 'slurm' or 'paracloud'", "default": "slurm" } }, "type": "object", "title": "VenusPrimeInput", "description": "Input for VenusPrime multi-point combination mutation prediction (light=ridge regression, pro=reserved)" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusprime-multipoint-prediction" }] }, { "path": "/api/tools/predict/gromacs-md", "methods": [{ "method": "post", "operationId": "gromacs_md", "summary": "Gromacs Md", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "pdb_file": { "type": "string", "title": "Pdb File", "description": "OSS URL to input PDB file" }, "force_field": { "type": "string", "title": "Force Field", "description": "Force field name (default: amber99sb-ildn)", "default": "amber99sb-ildn" }, "water_model": { "type": "string", "title": "Water Model", "description": "Water model (default: tip3p)", "default": "tip3p" }, "temp": { "type": "string", "title": "Temp", "description": "Temperature in K (default: 300)", "default": "300" }, "pressure": { "type": "string", "title": "Pressure", "description": "Pressure in bar (default: 1.0)", "default": "1.0" }, "md_steps": { "type": "string", "title": "Md Steps", "description": "Production MD steps (default: 50000, ~100ns at dt=2fs)", "default": "50000" } }, "type": "object", "required": ["pdb_file"], "title": "GromacsMdInput", "description": "Input for GROMACS MD (build system + production simulation)" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "gromacs-md" }] }, { "path": "/api/tools/predict/gromacs-analysis", "methods": [{ "method": "post", "operationId": "gromacs_analysis", "summary": "Gromacs Analysis", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "tpr_file": { "type": "string", "title": "Tpr File", "description": "OSS URL to .tpr file (from gromacs_md output)" }, "xtc_file": { "type": "string", "title": "Xtc File", "description": "OSS URL to .xtc file (from gromacs_md output)" } }, "type": "object", "required": ["tpr_file", "xtc_file"], "title": "GromacsAnalysisInput", "description": "Input for GROMACS trajectory analysis" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "gromacs-analysis" }] }, { "path": "/api/tools/predict/venusmine-mining", "methods": [{ "method": "post", "operationId": "venusmine_protein_mining", "summary": "Venusmine Mining", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "pdb_file": { "type": "string", "title": "Pdb File", "description": "OSS URL to input PDB file" }, "target_server": { "type": "string", "title": "Target Server", "description": "Target server: 'slurm' for local Slurm cluster, 'paracloud' for remote Paracloud execution (default: 'slurm')", "default": "slurm" } }, "type": "object", "required": ["pdb_file"], "title": "VenusMineInput", "description": "Input for VenusMine protein mining pipeline" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusmine-protein-mining" }] }, { "path": "/api/tools/predict/proteinmpnn-design", "methods": [{ "method": "post", "operationId": "proteinmpnn_sequence_design", "summary": "Proteinmpnn Design", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "pdb_path": { "type": "string", "title": "Pdb Path", "description": "OSS URL to input PDB file" }, "designed_chains": { "anyOf": [{ "items": { "type": "string" }, "type": "array" }, { "type": "null" }], "title": "Designed Chains", "description": "Chain IDs to design (e.g., ['A', 'B']). If None, designs all chains" }, "fixed_chains": { "anyOf": [{ "items": { "type": "string" }, "type": "array" }, { "type": "null" }], "title": "Fixed Chains", "description": "Chain IDs to keep fixed (e.g., ['C', 'D'])" }, "num_sequences": { "type": "integer", "title": "Num Sequences", "description": "Number of sequences to generate (default: 4)", "default": 4 }, "temperatures": { "items": { "type": "number" }, "type": "array", "title": "Temperatures", "description": "Sampling temperatures for sequence generation (default: [0.1])", "default": [0.1] }, "omit_aas": { "type": "string", "title": "Omit Aas", "description": "Amino acids to omit from design (default: 'X')", "default": "X" }, "homomer": { "type": "boolean", "title": "Homomer", "description": "Enable homomer symmetric design for multi-chain proteins (default: False)", "default": false }, "ca_only": { "type": "boolean", "title": "Ca Only", "description": "Use Cα-only mode for backbone representation (default: False)", "default": false } }, "type": "object", "required": ["pdb_path"], "title": "ProteinMPNNInput", "description": "Input for ProteinMPNN sequence design" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "proteinmpnn-sequence-design" }] }, { "path": "/api/tools/predict/rfdiffusion-design", "methods": [{ "method": "post", "operationId": "rfdiffusion_protein_design", "summary": "Rfdiffusion Design", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "input_pdb": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Input Pdb", "description": "OSS URL to input PDB file (optional for unconditional generation)" }, "contig": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Contig", "description": "Contig specification string (e.g., 'A10-20,80' for motif scaffolding)" }, "num_designs": { "type": "integer", "title": "Num Designs", "description": "Number of designs to generate (default: 1)", "default": 1 }, "length": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Length", "description": "Total design length constraint (e.g., '100' or '80-120')" }, "hotspots": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Hotspots", "description": "Hotspot residues specification for binder design (e.g., 'A10,A15,A20')" }, "partial_t": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Partial T", "description": "Noise level for partial diffusion in Angstroms (e.g., 5.0-15.0)" }, "T": { "type": "integer", "title": "T", "description": "Number of diffusion steps (default: 50)", "default": 50 }, "seed_offset": { "type": "integer", "title": "Seed Offset", "description": "Random seed offset (default: 0)", "default": 0 }, "recenter": { "type": "boolean", "title": "Recenter", "description": "Recenter structure (default: True)", "default": true }, "radius": { "type": "number", "title": "Radius", "description": "Radius for neighbor calculation (default: 10.0)", "default": 10 }, "num_recycles": { "type": "integer", "title": "Num Recycles", "description": "Number of recycles (default: 1)", "default": 1 }, "softmax_T": { "type": "number", "title": "Softmax T", "description": "Softmax temperature (default: 1e-5)", "default": 0.00001 }, "write_trb": { "type": "boolean", "title": "Write Trb", "description": "Write .trb files (default: True)", "default": true }, "cautious": { "type": "boolean", "title": "Cautious", "description": "Use cautious mode (default: True)", "default": true }, "align_motif": { "type": "boolean", "title": "Align Motif", "description": "Align motif (default: True)", "default": true }, "final_step": { "type": "integer", "title": "Final Step", "description": "Final diffusion step (default: 1)", "default": 1 }, "guide_scale": { "type": "number", "title": "Guide Scale", "description": "Guidance scale (default: 10.0)", "default": 10 } }, "type": "object", "required": ["input_pdb"], "title": "RFdiffusionInput", "description": "Input for RFdiffusion protein design" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "rfdiffusion-protein-design" }] }, { "path": "/api/tools/results/{tool_call_id}", "methods": [{ "method": "get", "operationId": "get_tool_result", "summary": "Get Tool Result", "description": "获取工具的异步执行结果。\n通过 API Key 鉴权。", "tags": ["tools-results"], "parameters": [{ "name": "tool_call_id", "in": "path", "required": true, "schema": { "type": "string", "title": "Tool Call Id" }, "type": "string" }], "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "id": { "type": "string", "title": "Id", "description": "工具结果ID" }, "session_id": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Session Id", "description": "会话ID" }, "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "工具调用ID" }, "tool_result": { "anyOf": [{}, { "type": "null" }], "title": "Tool Result", "description": "工具执行结果" }, "tool_name": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name", "description": "工具名称" }, "tool_name_desc": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name Desc", "description": "显示工具名称" }, "tool_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Type", "description": "工具类型" }, "tool_args": { "anyOf": [{ "additionalProperties": true, "type": "object" }, { "type": "null" }], "title": "Tool Args", "description": "工具参数" }, "status": { "description": "执行状态：pending(排队中), running(运行中), success(成功), error(错误)", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" }, "started_at": { "type": "string", "format": "date-time", "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "slurm_tasks": { "items": { "properties": { "id": { "type": "string", "title": "Id", "description": "任务ID" }, "slurm_job_id": { "type": "string", "title": "Slurm Job Id", "description": "Slurm作业ID" }, "status": { "type": "string", "title": "Status", "description": "任务状态" }, "task_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Task Type", "description": "任务类型" }, "resource_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Resource Type", "description": "资源类型: GPU/CPU" }, "run_time": { "anyOf": [{ "type": "integer" }, { "type": "null" }], "title": "Run Time", "description": "运行时长（秒）" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "该任务积分消耗" }, "started_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" } }, "type": "object", "required": ["id", "slurm_job_id", "status"], "title": "SlurmTaskInfo", "description": "Slurm任务信息（嵌入ToolResult响应）" }, "type": "array", "title": "Slurm Tasks", "description": "关联的Slurm任务列表" } }, "type": "object", "required": ["id", "tool_call_id", "status", "started_at"], "title": "ToolResultResponse", "description": "工具结果响应模型" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "get-tool-result" }] }, { "path": "/api/tools/results/{tool_call_id}/cancel", "methods": [{ "method": "post", "operationId": "cancel_tool_result", "summary": "Cancel Tool Result", "description": "取消处于 pending 或 running 状态的工具任务。\n如果工具包含 Slurm 任务，会先取消 Slurm 任务再更新状态。\n通过 API Key 鉴权。", "tags": ["tools-results"], "parameters": [{ "name": "tool_call_id", "in": "path", "required": true, "schema": { "type": "string", "title": "Tool Call Id" }, "type": "string" }], "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "id": { "type": "string", "title": "Id", "description": "工具结果ID" }, "session_id": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Session Id", "description": "会话ID" }, "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "工具调用ID" }, "tool_result": { "anyOf": [{}, { "type": "null" }], "title": "Tool Result", "description": "工具执行结果" }, "tool_name": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name", "description": "工具名称" }, "tool_name_desc": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name Desc", "description": "显示工具名称" }, "tool_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Type", "description": "工具类型" }, "tool_args": { "anyOf": [{ "additionalProperties": true, "type": "object" }, { "type": "null" }], "title": "Tool Args", "description": "工具参数" }, "status": { "description": "执行状态：pending(排队中), running(运行中), success(成功), error(错误)", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" }, "started_at": { "type": "string", "format": "date-time", "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "slurm_tasks": { "items": { "properties": { "id": { "type": "string", "title": "Id", "description": "任务ID" }, "slurm_job_id": { "type": "string", "title": "Slurm Job Id", "description": "Slurm作业ID" }, "status": { "type": "string", "title": "Status", "description": "任务状态" }, "task_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Task Type", "description": "任务类型" }, "resource_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Resource Type", "description": "资源类型: GPU/CPU" }, "run_time": { "anyOf": [{ "type": "integer" }, { "type": "null" }], "title": "Run Time", "description": "运行时长（秒）" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "该任务积分消耗" }, "started_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" } }, "type": "object", "required": ["id", "slurm_job_id", "status"], "title": "SlurmTaskInfo", "description": "Slurm任务信息（嵌入ToolResult响应）" }, "type": "array", "title": "Slurm Tasks", "description": "关联的Slurm任务列表" } }, "type": "object", "required": ["id", "tool_call_id", "status", "started_at"], "title": "ToolResultResponse", "description": "工具结果响应模型" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "cancel-tool-result" }] }, { "path": "/api/tools/upload/base64", "methods": [{ "method": "post", "operationId": "upload_file_base64", "summary": "Upload File Base64", "description": "上传 Base64 编码的文件到存储系统。\n用于 Agent 在调用分析工具前上传本地文件并获取 URL。", "tags": ["tools-upload"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "filename": { "type": "string", "title": "Filename", "description": "文件名，例如 'protein.fasta'" }, "content_base64": { "type": "string", "title": "Content Base64", "description": "文件的 Base64 编码内容" } }, "type": "object", "required": ["filename", "content_base64"], "title": "MCPUploadFileRequest" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "upload-file-base-64" }] }] };
+    console.log(`Searching for "${keyword}" in API operations...\n`);
+    let found = false;
+    spec.paths.forEach((p) => {
+        p.methods.forEach((m) => {
+            const searchText = `${m.commandName} ${m.operationId} ${m.summary || ''} ${m.description || ''} ${(m.tags || []).join(' ')}`.toLowerCase();
+            if (searchText.includes(keyword.toLowerCase())) {
+                console.log(`- ${m.commandName.padEnd(30)} [${m.method.toUpperCase()}] ${p.path}`);
+                if (m.summary)
+                    console.log(`  Summary: ${m.summary}`);
+                found = true;
+            }
+        });
+    });
+    if (!found)
+        console.log('No matching operations found.');
+});
+// System command: Show Configuration
+program
+    .command('config')
+    .description('Show current CLI configuration')
+    .action(() => {
+    console.log('Current Configuration:');
+    console.log(`- Base URL: ${baseUrl}`);
+    console.log(`- Base URL Env Var: API_BASE_URL`);
+    const authVars = ["API_BEARER_TOKEN"];
+    if (authVars.length > 0) {
+        console.log('\nAuthentication Environment Variables:');
+        authVars.forEach(v => console.log(`- ${v}`));
+    }
+});
+// System command: Export Tools JSON (for LLM Function Calling)
+program
+    .command('export-tools-json')
+    .description('Export API definitions as JSON for LLM tool calling')
+    .action(() => {
+    const spec = { "info": { "title": "VenusFactory MCP Server", "description": "Standalone MCP server for VenusFactory protein tools", "version": "0.5.0" }, "securitySchemes": [{ "name": "HTTPBearer", "type": "bearer", "envVarName": "BEARER_TOKEN" }], "paths": [{ "path": "/api/tools/predict/functional-residue", "methods": [{ "method": "post", "operationId": "predict_functional_residue", "summary": "Functional Residue", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file" }, "model_name": { "type": "string", "title": "Model Name", "description": "Model name for function prediction, Optional model names: ESM2-650M, Ankh-large, ProtT5-xl-uniref50 ", "default": "ESM2-650M" }, "task": { "type": "string", "title": "Task", "description": "Task: Activity Site, Binding Site, Conserved Site, Motif", "default": "Activity Site" } }, "type": "object", "title": "ResidueFunctionPredictionInput", "description": "Input for functional residue prediction" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "predict-functional-residue" }] }, { "path": "/api/tools/predict/venusx-functional-residue", "methods": [{ "method": "post", "operationId": "venusx_functional_residue_prediction", "summary": "Venusx Functional Residue", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file" }, "task": { "type": "string", "title": "Task", "description": "VenusX task: VenusX-Activity (activity site), VenusX-Binding (binding site), VenusX-Evo (conserved site)", "default": "VenusX-Activity" }, "mode": { "type": "string", "title": "Mode", "description": "Model mode: pro uses Ankh-large (default), light uses ESM2-650M. Model is read from venusx_config.yaml", "default": "pro" } }, "type": "object", "title": "VenusXFunctionalResiduePredictionInput", "description": "Input for VenusX functional site prediction. Uses venusx_config.yaml; default mode=pro." }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusx-functional-residue-prediction" }] }, { "path": "/api/tools/predict/venusg-protein-function", "methods": [{ "method": "post", "operationId": "venusg_protein_function_prediction", "summary": "Venusg Protein Function", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file" }, "task": { "type": "string", "title": "Task", "description": "VenusG task: VenusG-Solubility, VenusG-SubcellularLocalization, VenusG-MembraneProtein, VenusG-Metalionbinding, VenusG-Stability, VenusG-Sortingsignal, VenusG-OptimumTemperature, VenusG-Kcat, VenusG-OptimalPH", "default": "VenusG-Solubility" }, "mode": { "type": "string", "title": "Mode", "description": "Model mode: pro uses ESM2-650M, light uses ProtBert (default). Model is read from venusg_config.yaml", "default": "light" } }, "type": "object", "title": "VenusGProteinFunctionPredictionInput", "description": "Input for VenusG protein-level function prediction. Uses venusg_config.yaml; pro=ESM2-650M, light=ProtBert." }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusg-protein-function-prediction" }] }, { "path": "/api/tools/predict/protein-properties", "methods": [{ "method": "post", "operationId": "predict_protein_properties", "summary": "Protein Properties", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to PDB structure file or FASTA file" }, "task_name": { "type": "string", "title": "Task Name", "description": "Task name: Physical and chemical properties, Relative solvent accessible surface area (PDB only), SASA value (PDB only), Secondary structure (PDB only)", "default": "Physical and chemical properties" } }, "type": "object", "title": "ProteinPropertiesInput", "description": "Input for protein properties generation" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "predict-protein-properties" }] }, { "path": "/api/tools/predict/esmfold", "methods": [{ "method": "post", "operationId": "esmfold_protein_folding", "summary": "Esmfold Folding", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "sequence": { "type": "string", "title": "Sequence", "description": "Protein sequence in single letter amino acid code" }, "verbose": { "anyOf": [{ "type": "boolean" }, { "type": "null" }], "title": "Verbose", "description": "Whether to print detailed information", "default": true } }, "type": "object", "required": ["sequence"], "title": "ProteinStructurePredictionInput", "description": "Input for protein structure prediction based on ESMFold" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "esmfold-protein-folding" }] }, { "path": "/api/tools/predict/alphafold", "methods": [{ "method": "post", "operationId": "alphafold_protein_folding", "summary": "Alphafold Folding", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "model_version": { "type": "string", "title": "Model Version", "description": "AlphaFold version to use: 'alphafold2' or 'alphafold3'", "default": "alphafold2" }, "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code (for simple single-chain prediction)" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file (.fasta, .fa, or .faa) (for simple single/multi-chain prediction)" }, "sequences": { "anyOf": [{ "items": { "additionalProperties": true, "type": "object" }, "type": "array" }, { "type": "null" }], "title": "Sequences", "description": "List of sequence entities for multi-chain prediction. For AlphaFold2: Only protein chains are supported (DNA/RNA/ligands ignored). For AlphaFold3: Full support for proteins, DNA, RNA, and ligands. Each entity can be: {'protein': {'id': 'A', 'sequence': 'PVLSCGEWQL', 'description': 'Chain A', 'modifications': [{'ptmType': 'HY3', 'ptmPosition': 1}], 'unpairedMsa': '...', 'pairedMsa': '...', 'templates': [...]}} {'dna': {'id': 'C', 'sequence': 'GACCTCT', 'modifications': [{'modificationType': '6OG', 'basePosition': 1}], 'unpairedMsa': '...'}} (AF3 only) {'rna': {'id': 'E', 'sequence': 'AGCU', 'modifications': [{'modificationType': '2MG', 'basePosition': 1}], 'unpairedMsa': '...'}} (AF3 only) {'ligand': {'id': ['F', 'G'], 'ccdCodes': ['ATP']}} or {'ligand': {'id': 'Z', 'smiles': 'CC(=O)OC1C[NH+]2CCC1CC2'}} (AF3 only)" }, "model_seeds": { "anyOf": [{ "items": { "type": "integer" }, "type": "array" }, { "type": "null" }], "title": "Model Seeds", "description": "Random seeds for AlphaFold3 prediction (default: [42])", "default": [42] } }, "type": "object", "title": "AlphaFoldInput", "description": "Input for AlphaFold2/3 protein structure prediction" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "alphafold-protein-folding" }] }, { "path": "/api/tools/predict/diffdock", "methods": [{ "method": "post", "operationId": "diffdock_protein_ligand_docking", "summary": "Diffdock Docking", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "protein_path": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Protein Path", "description": "OSS URL to protein PDB file" }, "protein_sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Protein Sequence", "description": "Protein sequence (will be folded using ESMFold if protein_path not provided)" }, "ligand": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Ligand", "description": "Ligand SMILES string or OSS URL to ligand file (.sdf, .mol2, etc.)" }, "protein_ligand_csv": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Protein Ligand Csv", "description": "OSS URL to CSV file containing multiple protein-ligand pairs with columns: complex_name, protein_path, ligand_description, protein_sequence" }, "num_poses": { "type": "integer", "title": "Num Poses", "description": "Number of poses to generate per complex (default: 10)", "default": 10 } }, "type": "object", "title": "DiffDockInput", "description": "Input for DiffDock protein-ligand docking prediction" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "diffdock-protein-ligand-docking" }] }, { "path": "/api/tools/predict/venusrem-mutation", "methods": [{ "method": "post", "operationId": "venusrem_mutation_prediction", "summary": "Venusrem Mutation", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "task": { "type": "string", "title": "Task", "description": "Prediction task: activity, binding, stability, expression, general (see venusrem_config.yaml)" }, "mode": { "type": "string", "title": "Mode", "description": "Model mode: pro for structure-based multi-model, light for sequence-based multi-model" }, "structure_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Structure File", "description": "OSS URL to structure file (required when mode=pro)" }, "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Protein sequence in single letter amino acid code (for mode=light)" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file (for mode=light)" }, "config": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Config", "description": "Path to venusrem_config.yaml file (optional)" } }, "type": "object", "required": ["task", "mode"], "title": "VenusREMInput", "description": "Input for VenusREM multi-model mutation prediction (pro/light)" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusrem-mutation-prediction" }] }, { "path": "/api/tools/predict/venusprime-multipoint", "methods": [{ "method": "post", "operationId": "venusprime_multipoint_prediction", "summary": "Venusprime Multipoint", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "mode": { "type": "string", "title": "Mode", "description": "Operation mode: 'train' to train models from experimental data, 'inference' to predict multi-point mutations using trained models", "default": "inference" }, "venus_mode": { "type": "string", "title": "Venus Mode", "description": "Model mode: 'light' for ridge regression (default), 'pro' for sesnet (not implemented yet)", "default": "light" }, "sequence": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Sequence", "description": "Wild-type protein sequence (required for train mode if fasta_file not provided)" }, "fasta_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Fasta File", "description": "OSS URL to FASTA file with wild-type sequence (required for train mode if sequence not provided)" }, "experiment_file": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Experiment File", "description": "OSS URL to CSV file with 'mutant' and 'score' columns for training (required for train mode)" }, "score_col_name": { "type": "string", "title": "Score Col Name", "description": "Name of score column in experiment_file to train" }, "model_path_list": { "anyOf": [{ "items": { "type": "string" }, "type": "array" }, { "type": "null" }], "title": "Model Path List", "description": "List of trained model file paths or OSS URLs (required for inference mode)" }, "site": { "anyOf": [{ "items": { "type": "integer" }, "type": "array" }, { "type": "null" }], "title": "Site", "description": "Mutation site numbers for combination mutations in inference mode (default: [2, 3, 4])", "default": [2, 3, 4] }, "model_num": { "type": "integer", "title": "Model Num", "description": "Number of ensemble models to train (for train mode, default: 5)", "default": 5 }, "batch_size": { "type": "integer", "title": "Batch Size", "description": "Batch size for embedding extraction during training (for train mode, default: 4)", "default": 4 }, "inference_batch_size": { "type": "integer", "title": "Inference Batch Size", "description": "Batch size for embedding extraction during inference (for inference mode, default: 32)", "default": 32 }, "config": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Config", "description": "Path to VenusPrime config YAML file (optional, default: venusprime_config.yaml in script directory)" }, "target_server": { "type": "string", "title": "Target Server", "description": "Target server for job submission: 'slurm' or 'paracloud'", "default": "slurm" } }, "type": "object", "title": "VenusPrimeInput", "description": "Input for VenusPrime multi-point combination mutation prediction (light=ridge regression, pro=reserved)" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusprime-multipoint-prediction" }] }, { "path": "/api/tools/predict/gromacs-md", "methods": [{ "method": "post", "operationId": "gromacs_md", "summary": "Gromacs Md", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "pdb_file": { "type": "string", "title": "Pdb File", "description": "OSS URL to input PDB file" }, "force_field": { "type": "string", "title": "Force Field", "description": "Force field name (default: amber99sb-ildn)", "default": "amber99sb-ildn" }, "water_model": { "type": "string", "title": "Water Model", "description": "Water model (default: tip3p)", "default": "tip3p" }, "temp": { "type": "string", "title": "Temp", "description": "Temperature in K (default: 300)", "default": "300" }, "pressure": { "type": "string", "title": "Pressure", "description": "Pressure in bar (default: 1.0)", "default": "1.0" }, "md_steps": { "type": "string", "title": "Md Steps", "description": "Production MD steps (default: 50000, ~100ns at dt=2fs)", "default": "50000" } }, "type": "object", "required": ["pdb_file"], "title": "GromacsMdInput", "description": "Input for GROMACS MD (build system + production simulation)" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "gromacs-md" }] }, { "path": "/api/tools/predict/gromacs-analysis", "methods": [{ "method": "post", "operationId": "gromacs_analysis", "summary": "Gromacs Analysis", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "tpr_file": { "type": "string", "title": "Tpr File", "description": "OSS URL to .tpr file (from gromacs_md output)" }, "xtc_file": { "type": "string", "title": "Xtc File", "description": "OSS URL to .xtc file (from gromacs_md output)" } }, "type": "object", "required": ["tpr_file", "xtc_file"], "title": "GromacsAnalysisInput", "description": "Input for GROMACS trajectory analysis" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "gromacs-analysis" }] }, { "path": "/api/tools/predict/venusmine-mining", "methods": [{ "method": "post", "operationId": "venusmine_protein_mining", "summary": "Venusmine Mining", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "pdb_file": { "type": "string", "title": "Pdb File", "description": "OSS URL to input PDB file" }, "target_server": { "type": "string", "title": "Target Server", "description": "Target server: 'slurm' for local Slurm cluster, 'paracloud' for remote Paracloud execution (default: 'slurm')", "default": "slurm" } }, "type": "object", "required": ["pdb_file"], "title": "VenusMineInput", "description": "Input for VenusMine protein mining pipeline" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "venusmine-protein-mining" }] }, { "path": "/api/tools/predict/proteinmpnn-design", "methods": [{ "method": "post", "operationId": "proteinmpnn_sequence_design", "summary": "Proteinmpnn Design", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "pdb_path": { "type": "string", "title": "Pdb Path", "description": "OSS URL to input PDB file" }, "designed_chains": { "anyOf": [{ "items": { "type": "string" }, "type": "array" }, { "type": "null" }], "title": "Designed Chains", "description": "Chain IDs to design (e.g., ['A', 'B']). If None, designs all chains" }, "fixed_chains": { "anyOf": [{ "items": { "type": "string" }, "type": "array" }, { "type": "null" }], "title": "Fixed Chains", "description": "Chain IDs to keep fixed (e.g., ['C', 'D'])" }, "num_sequences": { "type": "integer", "title": "Num Sequences", "description": "Number of sequences to generate (default: 4)", "default": 4 }, "temperatures": { "items": { "type": "number" }, "type": "array", "title": "Temperatures", "description": "Sampling temperatures for sequence generation (default: [0.1])", "default": [0.1] }, "omit_aas": { "type": "string", "title": "Omit Aas", "description": "Amino acids to omit from design (default: 'X')", "default": "X" }, "homomer": { "type": "boolean", "title": "Homomer", "description": "Enable homomer symmetric design for multi-chain proteins (default: False)", "default": false }, "ca_only": { "type": "boolean", "title": "Ca Only", "description": "Use Cα-only mode for backbone representation (default: False)", "default": false } }, "type": "object", "required": ["pdb_path"], "title": "ProteinMPNNInput", "description": "Input for ProteinMPNN sequence design" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "proteinmpnn-sequence-design" }] }, { "path": "/api/tools/predict/rfdiffusion-design", "methods": [{ "method": "post", "operationId": "rfdiffusion_protein_design", "summary": "Rfdiffusion Design", "tags": ["tools-predict"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "input_pdb": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Input Pdb", "description": "OSS URL to input PDB file (optional for unconditional generation)" }, "contig": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Contig", "description": "Contig specification string (e.g., 'A10-20,80' for motif scaffolding)" }, "num_designs": { "type": "integer", "title": "Num Designs", "description": "Number of designs to generate (default: 1)", "default": 1 }, "length": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Length", "description": "Total design length constraint (e.g., '100' or '80-120')" }, "hotspots": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Hotspots", "description": "Hotspot residues specification for binder design (e.g., 'A10,A15,A20')" }, "partial_t": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Partial T", "description": "Noise level for partial diffusion in Angstroms (e.g., 5.0-15.0)" }, "T": { "type": "integer", "title": "T", "description": "Number of diffusion steps (default: 50)", "default": 50 }, "seed_offset": { "type": "integer", "title": "Seed Offset", "description": "Random seed offset (default: 0)", "default": 0 }, "recenter": { "type": "boolean", "title": "Recenter", "description": "Recenter structure (default: True)", "default": true }, "radius": { "type": "number", "title": "Radius", "description": "Radius for neighbor calculation (default: 10.0)", "default": 10 }, "num_recycles": { "type": "integer", "title": "Num Recycles", "description": "Number of recycles (default: 1)", "default": 1 }, "softmax_T": { "type": "number", "title": "Softmax T", "description": "Softmax temperature (default: 1e-5)", "default": 0.00001 }, "write_trb": { "type": "boolean", "title": "Write Trb", "description": "Write .trb files (default: True)", "default": true }, "cautious": { "type": "boolean", "title": "Cautious", "description": "Use cautious mode (default: True)", "default": true }, "align_motif": { "type": "boolean", "title": "Align Motif", "description": "Align motif (default: True)", "default": true }, "final_step": { "type": "integer", "title": "Final Step", "description": "Final diffusion step (default: 1)", "default": 1 }, "guide_scale": { "type": "number", "title": "Guide Scale", "description": "Guidance scale (default: 10.0)", "default": 10 } }, "type": "object", "required": ["input_pdb"], "title": "RFdiffusionInput", "description": "Input for RFdiffusion protein design" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "rfdiffusion-protein-design" }] }, { "path": "/api/tools/results/{tool_call_id}", "methods": [{ "method": "get", "operationId": "get_tool_result", "summary": "Get Tool Result", "description": "获取工具的异步执行结果。\n通过 API Key 鉴权。", "tags": ["tools-results"], "parameters": [{ "name": "tool_call_id", "in": "path", "required": true, "schema": { "type": "string", "title": "Tool Call Id" }, "type": "string" }], "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "id": { "type": "string", "title": "Id", "description": "工具结果ID" }, "session_id": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Session Id", "description": "会话ID" }, "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "工具调用ID" }, "tool_result": { "anyOf": [{}, { "type": "null" }], "title": "Tool Result", "description": "工具执行结果" }, "tool_name": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name", "description": "工具名称" }, "tool_name_desc": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name Desc", "description": "显示工具名称" }, "tool_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Type", "description": "工具类型" }, "tool_args": { "anyOf": [{ "additionalProperties": true, "type": "object" }, { "type": "null" }], "title": "Tool Args", "description": "工具参数" }, "status": { "description": "执行状态：pending(排队中), running(运行中), success(成功), error(错误)", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" }, "started_at": { "type": "string", "format": "date-time", "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "slurm_tasks": { "items": { "properties": { "id": { "type": "string", "title": "Id", "description": "任务ID" }, "slurm_job_id": { "type": "string", "title": "Slurm Job Id", "description": "Slurm作业ID" }, "status": { "type": "string", "title": "Status", "description": "任务状态" }, "task_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Task Type", "description": "任务类型" }, "resource_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Resource Type", "description": "资源类型: GPU/CPU" }, "run_time": { "anyOf": [{ "type": "integer" }, { "type": "null" }], "title": "Run Time", "description": "运行时长（秒）" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "该任务积分消耗" }, "started_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" } }, "type": "object", "required": ["id", "slurm_job_id", "status"], "title": "SlurmTaskInfo", "description": "Slurm任务信息（嵌入ToolResult响应）" }, "type": "array", "title": "Slurm Tasks", "description": "关联的Slurm任务列表" } }, "type": "object", "required": ["id", "tool_call_id", "status", "started_at"], "title": "ToolResultResponse", "description": "工具结果响应模型" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "get-tool-result" }] }, { "path": "/api/tools/results/{tool_call_id}/cancel", "methods": [{ "method": "post", "operationId": "cancel_tool_result", "summary": "Cancel Tool Result", "description": "取消处于 pending 或 running 状态的工具任务。\n如果工具包含 Slurm 任务，会先取消 Slurm 任务再更新状态。\n通过 API Key 鉴权。", "tags": ["tools-results"], "parameters": [{ "name": "tool_call_id", "in": "path", "required": true, "schema": { "type": "string", "title": "Tool Call Id" }, "type": "string" }], "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "id": { "type": "string", "title": "Id", "description": "工具结果ID" }, "session_id": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Session Id", "description": "会话ID" }, "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "工具调用ID" }, "tool_result": { "anyOf": [{}, { "type": "null" }], "title": "Tool Result", "description": "工具执行结果" }, "tool_name": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name", "description": "工具名称" }, "tool_name_desc": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Name Desc", "description": "显示工具名称" }, "tool_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Tool Type", "description": "工具类型" }, "tool_args": { "anyOf": [{ "additionalProperties": true, "type": "object" }, { "type": "null" }], "title": "Tool Args", "description": "工具参数" }, "status": { "description": "执行状态：pending(排队中), running(运行中), success(成功), error(错误)", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" }, "started_at": { "type": "string", "format": "date-time", "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "slurm_tasks": { "items": { "properties": { "id": { "type": "string", "title": "Id", "description": "任务ID" }, "slurm_job_id": { "type": "string", "title": "Slurm Job Id", "description": "Slurm作业ID" }, "status": { "type": "string", "title": "Status", "description": "任务状态" }, "task_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Task Type", "description": "任务类型" }, "resource_type": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Resource Type", "description": "资源类型: GPU/CPU" }, "run_time": { "anyOf": [{ "type": "integer" }, { "type": "null" }], "title": "Run Time", "description": "运行时长（秒）" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "该任务积分消耗" }, "started_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Started At", "description": "开始时间" }, "completed_at": { "anyOf": [{ "type": "string", "format": "date-time" }, { "type": "null" }], "title": "Completed At", "description": "完成时间" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "错误信息" } }, "type": "object", "required": ["id", "slurm_job_id", "status"], "title": "SlurmTaskInfo", "description": "Slurm任务信息（嵌入ToolResult响应）" }, "type": "array", "title": "Slurm Tasks", "description": "关联的Slurm任务列表" } }, "type": "object", "required": ["id", "tool_call_id", "status", "started_at"], "title": "ToolResultResponse", "description": "工具结果响应模型" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "cancel-tool-result" }] }, { "path": "/api/tools/upload/base64", "methods": [{ "method": "post", "operationId": "upload_file_base64", "summary": "Upload File Base64", "description": "上传 Base64 编码的文件到存储系统。\n用于 Agent 在调用分析工具前上传本地文件并获取 URL。", "tags": ["tools-upload"], "parameters": [], "requestBody": { "required": true, "contentType": "application/json", "schema": { "properties": { "filename": { "type": "string", "title": "Filename", "description": "文件名，例如 'protein.fasta'" }, "content_base64": { "type": "string", "title": "Content Base64", "description": "文件的 Base64 编码内容" } }, "type": "object", "required": ["filename", "content_base64"], "title": "MCPUploadFileRequest" }, "isBinary": false }, "responses": [{ "statusCode": "200", "description": "Successful Response", "contentType": "application/json", "schema": { "properties": { "tool_call_id": { "type": "string", "title": "Tool Call Id", "description": "系统生成的调用唯一ID" }, "status": { "description": "调用状态: running, success, error 等", "type": "string", "enum": ["pending", "running", "success", "error"], "title": "ToolResultStatus" }, "result": { "anyOf": [{}, { "type": "null" }], "title": "Result", "description": "如果即时成功，这里是工具的返回结果字典" }, "error_message": { "anyOf": [{ "type": "string" }, { "type": "null" }], "title": "Error Message", "description": "如果有错误，提供错误信息" }, "credits_cost": { "anyOf": [{ "type": "number" }, { "type": "null" }], "title": "Credits Cost", "description": "消费积分" }, "tool_name": { "type": "string", "title": "Tool Name", "description": "执行的工具名" } }, "type": "object", "required": ["tool_call_id", "status", "tool_name"], "title": "ToolInvokeResponse" }, "isBinary": false }, { "statusCode": "422", "description": "Validation Error", "contentType": "application/json", "schema": { "properties": { "detail": { "items": { "properties": { "loc": { "items": { "anyOf": [{ "type": "string" }, { "type": "integer" }] }, "type": "array", "title": "Location" }, "msg": { "type": "string", "title": "Message" }, "type": { "type": "string", "title": "Error Type" } }, "type": "object", "required": ["loc", "msg", "type"], "title": "ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "isBinary": false }], "security": ["HTTPBearer"], "commandName": "upload-file-base-64" }] }] };
+    // Helper to simplify schema for LLM
+    const simplifySchema = (schema) => {
+        if (!schema)
+            return { type: 'string' };
+        if (schema.type === 'object' && schema.properties) {
+            const properties = {};
+            for (const [key, prop] of Object.entries(schema.properties)) {
+                properties[key] = simplifySchema(prop);
+            }
+            return {
+                type: 'object',
+                properties,
+                required: schema.required,
+                description: schema.description
+            };
+        }
+        if (schema.type === 'array' && schema.items) {
+            return {
+                type: 'array',
+                items: simplifySchema(schema.items),
+                description: schema.description
+            };
+        }
+        return {
+            type: schema.type || 'string',
+            description: schema.description,
+            enum: schema.enum
+        };
+    };
+    const tools = spec.paths.flatMap((p) => p.methods.map((m) => {
+        const properties = {};
+        const required = [];
+        // Map parameters
+        m.parameters.forEach((param) => {
+            properties[param.name] = {
+                type: param.type === 'number' ? 'number' : (param.type === 'boolean' ? 'boolean' : 'string'),
+                description: param.description || '',
+            };
+            if (param.required)
+                required.push(param.name);
+        });
+        // Map request body if present
+        if (m.requestBody && m.requestBody.schema) {
+            const bodySchema = simplifySchema(m.requestBody.schema);
+            if (bodySchema.type === 'object' && bodySchema.properties) {
+                // Flatten simple objects or keep as 'body'
+                properties['body'] = bodySchema;
+            }
+            else {
+                properties['body'] = bodySchema;
+            }
+        }
+        return {
+            type: 'function',
+            function: {
+                name: m.operationId,
+                description: m.summary || m.description || `Execute ${m.method.toUpperCase()} on ${p.path}`,
+                parameters: {
+                    type: 'object',
+                    properties,
+                    required: required.length > 0 ? required : undefined,
+                },
+            },
+        };
+    }));
+    console.log(JSON.stringify(tools, null, 2));
+});
+// Create API client with base URL and auth
+const baseUrl = process.env.API_BASE_URL || 'venus.matwings.com';
+// Register all commands
+(0, commands_1.registerCommands)(program, baseUrl);
+program.parse();

package/dist/types.d.ts

@@ -0,0 +1,12 @@
+export interface ApiResponse<T = any> {
+    data: T;
+    status: number;
+    statusText: string;
+    headers: Record<string, string>;
+}
+export interface ApiError {
+    message: string;
+    status: number;
+    statusText: string;
+    data?: any;
+}

package/dist/types.js

@@ -0,0 +1,6 @@
+"use strict";
+// Auto-generated types from OpenAPI specification
+// This file contains type definitions for API responses and requests
+Object.defineProperty(exports, "__esModule", { value: true });
+// Placeholder for generated types from schemas
+// In future versions, this will include types extracted from components.schemas

package/package.json

@@ -0,0 +1,41 @@
+{
+  "name": "matvenus-cli",
+  "version": "0.1.0",
+  "description": "Standalone MCP client for VenusFactory protein tools",
+  "main": "dist/index.js",
+  "bin": {
+    "matvenus-cli": "bin/cli.js"
+  },
+  "author": "matwings",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/matwings/matwings-venus-cli"
+  },
+  "keywords": [
+    "venus",
+    "matwings",
+    "matvenus",
+    "protein",
+    "bio"
+  ],
+  "license": "Apache-2.0",
+  "files": [
+    "dist",
+    "bin",
+    "README.md",
+    "LICENSE",
+    "CHANGELOG.md"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "start": "node dist/index.js",
+    "prepublishOnly": "npm run build"
+  },
+  "dependencies": {
+    "commander": "^12.0.0"
+  },
+  "devDependencies": {
+    "@types/node": "^20.10.0",
+    "typescript": "^5.3.0"
+  }
+}