matvenus-cli 0.1.0

package/dist/commands/upload_file_base_64.js

@@ -0,0 +1,212 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.register = register;
+const client_1 = require("../client");
+function register(program, baseUrl) {
+    program
+        .command('upload-file-base-64')
+        .description('Upload File Base64')
+        .option('--body <json>', 'Request body as JSON string', (value) => value)
+        .option('--base-url <url>', 'Override base URL')
+        .option('--output <format>', 'Output format: json, table', 'json')
+        .option('--schema', 'Show API schema and exit')
+        .action(async (options) => {
+        if (options.schema) {
+            console.log(JSON.stringify({
+                "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"
+                ]
+            }, null, 2));
+            return;
+        }
+        try {
+            const currentBaseUrl = options.baseUrl || baseUrl;
+            const config = { baseUrl: currentBaseUrl };
+            const path = '/api/tools/upload/base64';
+            const url = path;
+            const body = options.body ? JSON.parse(options.body) : undefined;
+            const response = await (0, client_1.request)(config, {
+                method: 'post',
+                path: url,
+                headers: undefined,
+                body: body,
+                isBinary: false,
+            });
+            const data = response;
+            if (options.output === 'json') {
+                console.log(JSON.stringify(data, null, 2));
+            }
+            else {
+                console.log(data);
+            }
+        }
+        catch (error) {
+            if (error.status) {
+                console.error('API Error:', error.status, error.message);
+                if (error.data) {
+                    console.error(JSON.stringify(error.data, null, 2));
+                }
+            }
+            else {
+                console.error('Error:', error.message);
+            }
+            process.exit(1);
+        }
+    });
+}

package/dist/commands/venusg_protein_function_prediction.d.ts

@@ -0,0 +1,2 @@
+import { Command } from 'commander';
+export declare function register(program: Command, baseUrl: string): void;

package/dist/commands/venusg_protein_function_prediction.js

@@ -0,0 +1,234 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.register = register;
+const client_1 = require("../client");
+function register(program, baseUrl) {
+    program
+        .command('venusg-protein-function-prediction')
+        .description('Venusg Protein Function')
+        .option('--body <json>', 'Request body as JSON string', (value) => value)
+        .option('--base-url <url>', 'Override base URL')
+        .option('--output <format>', 'Output format: json, table', 'json')
+        .option('--schema', 'Show API schema and exit')
+        .action(async (options) => {
+        if (options.schema) {
+            console.log(JSON.stringify({
+                "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"
+                ]
+            }, null, 2));
+            return;
+        }
+        try {
+            const currentBaseUrl = options.baseUrl || baseUrl;
+            const config = { baseUrl: currentBaseUrl };
+            const path = '/api/tools/predict/venusg-protein-function';
+            const url = path;
+            const body = options.body ? JSON.parse(options.body) : undefined;
+            const response = await (0, client_1.request)(config, {
+                method: 'post',
+                path: url,
+                headers: undefined,
+                body: body,
+                isBinary: false,
+            });
+            const data = response;
+            if (options.output === 'json') {
+                console.log(JSON.stringify(data, null, 2));
+            }
+            else {
+                console.log(data);
+            }
+        }
+        catch (error) {
+            if (error.status) {
+                console.error('API Error:', error.status, error.message);
+                if (error.data) {
+                    console.error(JSON.stringify(error.data, null, 2));
+                }
+            }
+            else {
+                console.error('Error:', error.message);
+            }
+            process.exit(1);
+        }
+    });
+}

package/dist/commands/venusmine_protein_mining.d.ts

@@ -0,0 +1,2 @@
+import { Command } from 'commander';
+export declare function register(program: Command, baseUrl: string): void;

package/dist/commands/venusmine_protein_mining.js

@@ -0,0 +1,212 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.register = register;
+const client_1 = require("../client");
+function register(program, baseUrl) {
+    program
+        .command('venusmine-protein-mining')
+        .description('Venusmine Mining')
+        .option('--body <json>', 'Request body as JSON string', (value) => value)
+        .option('--base-url <url>', 'Override base URL')
+        .option('--output <format>', 'Output format: json, table', 'json')
+        .option('--schema', 'Show API schema and exit')
+        .action(async (options) => {
+        if (options.schema) {
+            console.log(JSON.stringify({
+                "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"
+                ]
+            }, null, 2));
+            return;
+        }
+        try {
+            const currentBaseUrl = options.baseUrl || baseUrl;
+            const config = { baseUrl: currentBaseUrl };
+            const path = '/api/tools/predict/venusmine-mining';
+            const url = path;
+            const body = options.body ? JSON.parse(options.body) : undefined;
+            const response = await (0, client_1.request)(config, {
+                method: 'post',
+                path: url,
+                headers: undefined,
+                body: body,
+                isBinary: false,
+            });
+            const data = response;
+            if (options.output === 'json') {
+                console.log(JSON.stringify(data, null, 2));
+            }
+            else {
+                console.log(data);
+            }
+        }
+        catch (error) {
+            if (error.status) {
+                console.error('API Error:', error.status, error.message);
+                if (error.data) {
+                    console.error(JSON.stringify(error.data, null, 2));
+                }
+            }
+            else {
+                console.error('Error:', error.message);
+            }
+            process.exit(1);
+        }
+    });
+}

package/dist/commands/venusprime_multipoint_prediction.d.ts

@@ -0,0 +1,2 @@
+import { Command } from 'commander';
+export declare function register(program: Command, baseUrl: string): void;