matvenus-cli 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +22 -0
- package/LICENSE +201 -0
- package/README.md +408 -0
- package/bin/cli.js +3 -0
- package/dist/client.d.ts +13 -0
- package/dist/client.js +62 -0
- package/dist/commands/alphafold_protein_folding.d.ts +2 -0
- package/dist/commands/alphafold_protein_folding.js +262 -0
- package/dist/commands/cancel_tool_result.d.ts +2 -0
- package/dist/commands/cancel_tool_result.js +388 -0
- package/dist/commands/diffdock_protein_ligand_docking.d.ts +2 -0
- package/dist/commands/diffdock_protein_ligand_docking.js +252 -0
- package/dist/commands/esmfold_protein_folding.d.ts +2 -0
- package/dist/commands/esmfold_protein_folding.js +219 -0
- package/dist/commands/get_tool_result.d.ts +2 -0
- package/dist/commands/get_tool_result.js +388 -0
- package/dist/commands/gromacs_analysis.d.ts +2 -0
- package/dist/commands/gromacs_analysis.js +212 -0
- package/dist/commands/gromacs_md.d.ts +2 -0
- package/dist/commands/gromacs_md.js +236 -0
- package/dist/commands/index.d.ts +2 -0
- package/dist/commands/index.js +39 -0
- package/dist/commands/predict_functional_residue.d.ts +2 -0
- package/dist/commands/predict_functional_residue.js +234 -0
- package/dist/commands/predict_protein_properties.d.ts +2 -0
- package/dist/commands/predict_protein_properties.js +228 -0
- package/dist/commands/proteinmpnn_sequence_design.d.ts +2 -0
- package/dist/commands/proteinmpnn_sequence_design.js +271 -0
- package/dist/commands/rfdiffusion_protein_design.d.ts +2 -0
- package/dist/commands/rfdiffusion_protein_design.js +333 -0
- package/dist/commands/upload_file_base_64.d.ts +2 -0
- package/dist/commands/upload_file_base_64.js +212 -0
- package/dist/commands/venusg_protein_function_prediction.d.ts +2 -0
- package/dist/commands/venusg_protein_function_prediction.js +234 -0
- package/dist/commands/venusmine_protein_mining.d.ts +2 -0
- package/dist/commands/venusmine_protein_mining.js +212 -0
- package/dist/commands/venusprime_multipoint_prediction.d.ts +2 -0
- package/dist/commands/venusprime_multipoint_prediction.js +322 -0
- package/dist/commands/venusrem_mutation_prediction.d.ts +2 -0
- package/dist/commands/venusrem_mutation_prediction.js +260 -0
- package/dist/commands/venusx_functional_residue_prediction.d.ts +2 -0
- package/dist/commands/venusx_functional_residue_prediction.js +234 -0
- package/dist/index.d.ts +2 -0
- package/dist/index.js +125 -0
- package/dist/types.d.ts +12 -0
- package/dist/types.js +6 -0
- package/package.json +41 -0
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.register = register;
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const client_1 = require("../client");
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function register(program, baseUrl) {
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program
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.command('venusprime-multipoint-prediction')
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.description('Venusprime Multipoint')
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.option('--body <json>', 'Request body as JSON string', (value) => value)
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.option('--base-url <url>', 'Override base URL')
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.option('--output <format>', 'Output format: json, table', 'json')
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.option('--schema', 'Show API schema and exit')
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.action(async (options) => {
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if (options.schema) {
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console.log(JSON.stringify({
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"method": "post",
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"operationId": "venusprime_multipoint_prediction",
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"summary": "Venusprime Multipoint",
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"tags": [
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"tools-predict"
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],
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"parameters": [],
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"requestBody": {
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"required": true,
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"contentType": "application/json",
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"schema": {
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"properties": {
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"mode": {
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"type": "string",
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"title": "Mode",
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"description": "Operation mode: 'train' to train models from experimental data, 'inference' to predict multi-point mutations using trained models",
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"default": "inference"
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},
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"venus_mode": {
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"type": "string",
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"title": "Venus Mode",
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"description": "Model mode: 'light' for ridge regression (default), 'pro' for sesnet (not implemented yet)",
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"default": "light"
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},
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"sequence": {
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"anyOf": [
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"type": "string"
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{
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"type": "null"
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}
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],
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"title": "Sequence",
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"description": "Wild-type protein sequence (required for train mode if fasta_file not provided)"
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},
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"fasta_file": {
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"type": "null"
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}
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],
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"title": "Fasta File",
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"description": "OSS URL to FASTA file with wild-type sequence (required for train mode if sequence not provided)"
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},
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"experiment_file": {
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"type": "null"
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}
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],
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"title": "Experiment File",
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"description": "OSS URL to CSV file with 'mutant' and 'score' columns for training (required for train mode)"
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},
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"score_col_name": {
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"type": "string",
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"title": "Score Col Name",
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"description": "Name of score column in experiment_file to train"
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},
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"model_path_list": {
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},
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"type": "array"
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},
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{
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"type": "null"
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}
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],
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"title": "Model Path List",
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"description": "List of trained model file paths or OSS URLs (required for inference mode)"
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},
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"site": {
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"anyOf": [
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"items": {
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"type": "integer"
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},
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"type": "array"
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"type": "null"
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}
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],
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"title": "Site",
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"description": "Mutation site numbers for combination mutations in inference mode (default: [2, 3, 4])",
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"default": [
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2,
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3,
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4
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]
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},
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"model_num": {
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"type": "integer",
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"title": "Model Num",
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"description": "Number of ensemble models to train (for train mode, default: 5)",
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"default": 5
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},
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"batch_size": {
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"type": "integer",
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"title": "Batch Size",
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"description": "Batch size for embedding extraction during training (for train mode, default: 4)",
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"default": 4
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},
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"inference_batch_size": {
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"type": "integer",
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"title": "Inference Batch Size",
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"description": "Batch size for embedding extraction during inference (for inference mode, default: 32)",
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"default": 32
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},
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"config": {
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"anyOf": [
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"type": "string"
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},
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"type": "null"
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}
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],
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"title": "Config",
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"description": "Path to VenusPrime config YAML file (optional, default: venusprime_config.yaml in script directory)"
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},
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"target_server": {
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"type": "string",
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"title": "Target Server",
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"description": "Target server for job submission: 'slurm' or 'paracloud'",
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"default": "slurm"
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}
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},
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"type": "object",
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"title": "VenusPrimeInput",
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"description": "Input for VenusPrime multi-point combination mutation prediction (light=ridge regression, pro=reserved)"
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},
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"isBinary": false
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},
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"responses": [
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{
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"statusCode": "200",
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"description": "Successful Response",
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"contentType": "application/json",
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"schema": {
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"properties": {
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"tool_call_id": {
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"type": "string",
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"title": "Tool Call Id",
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"description": "系统生成的调用唯一ID"
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},
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"status": {
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"description": "调用状态: running, success, error 等",
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"type": "string",
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"enum": [
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"pending",
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"running",
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"success",
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"error"
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],
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"title": "ToolResultStatus"
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},
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"result": {
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"anyOf": [
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{},
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"type": "null"
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}
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],
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"title": "Result",
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"description": "如果即时成功，这里是工具的返回结果字典"
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},
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"error_message": {
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"anyOf": [
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"type": "string"
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},
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{
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"type": "null"
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}
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],
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"title": "Error Message",
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"description": "如果有错误，提供错误信息"
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},
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"credits_cost": {
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"anyOf": [
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{
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"type": "number"
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},
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"type": "null"
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}
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],
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"title": "Credits Cost",
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"description": "消费积分"
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},
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"tool_name": {
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"type": "string",
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"title": "Tool Name",
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"description": "执行的工具名"
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}
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},
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"type": "object",
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"required": [
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"tool_call_id",
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"status",
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"tool_name"
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],
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"title": "ToolInvokeResponse"
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},
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"isBinary": false
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},
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{
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"statusCode": "422",
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"description": "Validation Error",
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"contentType": "application/json",
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"schema": {
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"properties": {
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"detail": {
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"items": {
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"properties": {
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"loc": {
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"items": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "integer"
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}
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]
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},
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"type": "array",
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"title": "Location"
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},
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"msg": {
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"type": "string",
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"title": "Message"
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},
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"type": {
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"type": "string",
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"title": "Error Type"
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}
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},
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"type": "object",
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"required": [
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"loc",
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"msg",
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"type"
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],
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"title": "ValidationError"
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},
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"type": "array",
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"title": "Detail"
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}
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},
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"type": "object",
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"title": "HTTPValidationError"
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},
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"isBinary": false
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}
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],
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"security": [
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"HTTPBearer"
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]
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}, null, 2));
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return;
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}
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try {
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const currentBaseUrl = options.baseUrl || baseUrl;
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const config = { baseUrl: currentBaseUrl };
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const path = '/api/tools/predict/venusprime-multipoint';
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const url = path;
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const body = options.body ? JSON.parse(options.body) : undefined;
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const response = await (0, client_1.request)(config, {
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method: 'post',
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path: url,
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headers: undefined,
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body: body,
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isBinary: false,
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});
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const data = response;
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if (options.output === 'json') {
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console.log(JSON.stringify(data, null, 2));
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}
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else {
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console.log(data);
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}
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}
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catch (error) {
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if (error.status) {
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console.error('API Error:', error.status, error.message);
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if (error.data) {
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console.error(JSON.stringify(error.data, null, 2));
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}
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.register = register;
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const client_1 = require("../client");
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function register(program, baseUrl) {
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program
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.command('venusrem-mutation-prediction')
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.description('Venusrem Mutation')
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.option('--body <json>', 'Request body as JSON string', (value) => value)
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.option('--base-url <url>', 'Override base URL')
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.option('--output <format>', 'Output format: json, table', 'json')
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.option('--schema', 'Show API schema and exit')
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.action(async (options) => {
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if (options.schema) {
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console.log(JSON.stringify({
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"method": "post",
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"operationId": "venusrem_mutation_prediction",
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"summary": "Venusrem Mutation",
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"tags": [
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"tools-predict"
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],
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"parameters": [],
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"requestBody": {
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"required": true,
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"contentType": "application/json",
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"schema": {
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"properties": {
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"task": {
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"type": "string",
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"title": "Task",
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"description": "Prediction task: activity, binding, stability, expression, general (see venusrem_config.yaml)"
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},
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"mode": {
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"type": "string",
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"title": "Mode",
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"description": "Model mode: pro for structure-based multi-model, light for sequence-based multi-model"
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},
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"structure_file": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "null"
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}
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],
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"title": "Structure File",
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"description": "OSS URL to structure file (required when mode=pro)"
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},
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"sequence": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "null"
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}
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],
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"title": "Sequence",
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"description": "Protein sequence in single letter amino acid code (for mode=light)"
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},
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"fasta_file": {
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"anyOf": [
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{
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"type": "string"
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{
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"type": "null"
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}
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],
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"title": "Fasta File",
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"description": "OSS URL to FASTA file (for mode=light)"
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},
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"config": {
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"anyOf": [
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{
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"type": "string"
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{
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"type": "null"
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}
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],
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"title": "Config",
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"description": "Path to venusrem_config.yaml file (optional)"
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}
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},
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"type": "object",
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"required": [
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"task",
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"mode"
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],
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"title": "VenusREMInput",
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"description": "Input for VenusREM multi-model mutation prediction (pro/light)"
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},
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"isBinary": false
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},
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"responses": [
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{
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"statusCode": "200",
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"description": "Successful Response",
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"contentType": "application/json",
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"schema": {
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"properties": {
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"tool_call_id": {
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"type": "string",
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"title": "Tool Call Id",
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"description": "系统生成的调用唯一ID"
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},
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"status": {
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"description": "调用状态: running, success, error 等",
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"type": "string",
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"enum": [
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"pending",
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"running",
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"success",
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"error"
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],
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"title": "ToolResultStatus"
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},
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"result": {
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{},
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{
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"type": "null"
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}
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],
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"title": "Result",
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"description": "如果即时成功，这里是工具的返回结果字典"
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},
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"error_message": {
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},
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{
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"type": "null"
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}
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],
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"title": "Error Message",
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"description": "如果有错误，提供错误信息"
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},
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"credits_cost": {
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"anyOf": [
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{
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"type": "number"
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},
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{
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"type": "null"
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}
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],
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"title": "Credits Cost",
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"description": "消费积分"
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},
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"tool_name": {
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"type": "string",
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"title": "Tool Name",
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"description": "执行的工具名"
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}
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},
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"type": "object",
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"required": [
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"tool_call_id",
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"status",
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"tool_name"
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],
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"title": "ToolInvokeResponse"
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},
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"isBinary": false
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},
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{
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"statusCode": "422",
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"description": "Validation Error",
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"contentType": "application/json",
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"schema": {
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"properties": {
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"detail": {
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"items": {
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"properties": {
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"loc": {
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"items": {
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"anyOf": [
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{
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"type": "string"
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},
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{
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"type": "integer"
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}
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]
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},
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"type": "array",
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"title": "Location"
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},
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"msg": {
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"type": "string",
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"title": "Message"
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},
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"type": {
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"type": "string",
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"title": "Error Type"
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}
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},
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"type": "object",
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"required": [
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"loc",
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"msg",
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"type"
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],
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"title": "ValidationError"
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},
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"type": "array",
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"title": "Detail"
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}
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},
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"type": "object",
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"title": "HTTPValidationError"
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},
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"isBinary": false
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}
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],
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"security": [
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"HTTPBearer"
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]
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223
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}, null, 2));
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return;
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225
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+
}
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226
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try {
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227
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const currentBaseUrl = options.baseUrl || baseUrl;
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228
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const config = { baseUrl: currentBaseUrl };
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229
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+
const path = '/api/tools/predict/venusrem-mutation';
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230
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+
const url = path;
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231
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+
const body = options.body ? JSON.parse(options.body) : undefined;
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232
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const response = await (0, client_1.request)(config, {
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method: 'post',
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path: url,
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headers: undefined,
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body: body,
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isBinary: false,
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});
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const data = response;
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240
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if (options.output === 'json') {
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console.log(JSON.stringify(data, null, 2));
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}
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else {
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console.log(data);
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}
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}
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247
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+
catch (error) {
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248
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if (error.status) {
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249
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console.error('API Error:', error.status, error.message);
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250
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if (error.data) {
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console.error(JSON.stringify(error.data, null, 2));
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252
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}
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253
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}
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254
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else {
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255
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console.error('Error:', error.message);
|
|
256
|
+
}
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257
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process.exit(1);
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258
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}
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259
|
+
});
|
|
260
|
+
}
|