helixlife-expert-cli 0.5.2 → 0.5.3
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/README.md +3 -5
- package/cli/bin/helixlife-expert.js +1 -1
- package/cli/dist/modules/proposal/commands/basic-params.d.ts +5 -0
- package/cli/dist/modules/proposal/commands/basic-params.d.ts.map +1 -0
- package/cli/dist/modules/proposal/commands/basic-params.js +9 -0
- package/cli/dist/modules/proposal/commands/basic-params.js.map +1 -0
- package/cli/dist/modules/proposal/commands/basic-run.d.ts +7 -0
- package/cli/dist/modules/proposal/commands/basic-run.d.ts.map +1 -0
- package/cli/dist/modules/proposal/commands/basic-run.js +11 -0
- package/cli/dist/modules/proposal/commands/basic-run.js.map +1 -0
- package/cli/dist/modules/proposal/constants.d.ts +3 -3
- package/cli/dist/modules/proposal/constants.d.ts.map +1 -1
- package/cli/dist/modules/proposal/constants.js +8 -3
- package/cli/dist/modules/proposal/constants.js.map +1 -1
- package/cli/dist/modules/proposal/index.d.ts.map +1 -1
- package/cli/dist/modules/proposal/index.js +32 -4
- package/cli/dist/modules/proposal/index.js.map +1 -1
- package/cli/dist/modules/shared/result-wrapper.d.ts +1 -1
- package/cli/dist/modules/shared/result-wrapper.d.ts.map +1 -1
- package/cli/dist/modules/shared/workflow-app/command.js +1 -1
- package/cli/dist/modules/shared/workflow-app/command.js.map +1 -1
- package/cli/dist/modules/shared/workflow-app/index.js +1 -1
- package/cli/dist/modules/shared/workflow-app/index.js.map +1 -1
- package/package.json +1 -1
package/README.md
CHANGED
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@@ -62,7 +62,7 @@ npm publish
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> **发布约定**：本仓库 npm 包**不含** Skill。每次发给用户一个专家目录；替换 Agent 侧 Skill 即可，**不必**为此升 CLI 版本。
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安装 / 升级 / 错误码的正文只维护在 `cli/skills/_fragments/common.md
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安装 / 升级 / 错误码的正文只维护在 `cli/skills/_fragments/common.md`，由 `npm run sync:skills` 写入各专家的 `references/common.md`。**不要**把 `_fragments` 或整个 `cli/skills/` 发给用户。
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### 交付某一个专家
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@@ -128,7 +128,7 @@ helixlife-expert-cli/
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| SCI 写作 | `helixlife-expert sci outline create` | 已实现（拟定主题/确认提纲/生成全文三步流程） |
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| 数据分析 | `helixlife-expert analysis tool exec` | 已实现（本 CLI 直接调用菜单、生信统一入口与上传接口） |
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| 文献调研 | `helixlife-expert literature workflow run` | 已实现（信息调研/结构化拆解/文献阅读/研究假设四工作流） |
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| 课题方案 | `helixlife-expert proposal clinical run` |
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| 课题方案 | `helixlife-expert proposal clinical run` | 已实现（基础研究、临床研究五工作流、生信方案） |
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Meta 分析专家迁移自 `helixlife-service-cli` 的 `workbench meta`，命令树为 `meta workflow|topic|picos|criteria|retrieve|screening|extraction|analysis|writing`。进入任何 Meta 业务命令前必须先通过 `helixlife-expert site-configs --format=json` 探测（细则见 `cli/skills/helixlife-expert-meta/references/meta.md`）。
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数据分析专家由本 CLI 直接执行：`helixlife-expert analysis tool search|menus|inspect|cloud|specific-search|prepare|exec` 与 `helixlife-expert analysis history list|view|download|rename|delete|save`。菜单与菜单详情走 `agent_api` 的 `/api/v1/agent/client/tool/menus`，生信统一入口走 `/api/v1/agent/client/bio-api`；文件上传仍取 `/api/v1/agent/upload/config` 后直传 OSS。凭证与其他专家相同，读 `~/.config/helixlife/`。Skill 细则见 `cli/skills/helixlife-expert-analysis/references/`（路由索引 + 393 项冻结目录 + 执行手册）。
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课题方案专家先做基础 / 临床 / 生信三方向识别（证据不唯一时由 Skill
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临床研究与生信方案由本 CLI 直接调用工作流接口，与文献调研共用 `shared/workflow-app` 调用层，同为「`params` 取动态表单 → `run` 填参执行」两步式。临床命令树为 `proposal clinical list|params|run`，五个 source（`diagnostic-study` 诊断、`prognosis-study` 预后、`treatment-trial` 疗效试验、`treatment-cohort` 疗效队列、`etiology-study` 病因）的研究目的字段已被后端锁成单一选项，因而 source 即等价于研究目的，疗效方向需再按研究设计二选一；生信为单一工作流 `bioinfo-planner`，命令树 `proposal bioinfo params|run`，不设 `--source`；该方向在 Skill 侧多一步套路定位，冻结目录 `bioinfo-pattern-catalog-v1.json`（67 条，含一句话概述与数据层面），由 `references/bioinfo-patterns.md` 做召回索引与可行性核对，CLI 本身不解析该目录。临床表单声明 `output_text` 与 `output_reference` 两路输出，实测后端通常只回 `output_text`（参考文献并在正文末章），渲染层对缺失的已声明输出直接跳过。该专家不走 `site-configs` 门禁（细则见 `cli/skills/helixlife-expert-proposal/references/proposal.md`）。
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课题方案专家先做基础 / 临床 / 生信三方向识别（证据不唯一时由 Skill 弹选择器兜底）。三个方向都由本 CLI 直接调用工作流接口，与文献调研共用 `shared/workflow-app` 调用层，同为「`params` 取动态表单 → `run` 填参执行」两步式。基础研究为单一工作流 `experimental-design`，命令树 `proposal basic params|run`，不设 `--source`。临床命令树为 `proposal clinical list|params|run`，五个 source（`diagnostic-study` 诊断、`prognosis-study` 预后、`treatment-trial` 疗效试验、`treatment-cohort` 疗效队列、`etiology-study` 病因）的研究目的字段已被后端锁成单一选项，因而 source 即等价于研究目的，疗效方向需再按研究设计二选一；生信为单一工作流 `bioinfo-planner`，命令树 `proposal bioinfo params|run`，不设 `--source`；该方向在 Skill 侧多一步套路定位，冻结目录 `bioinfo-pattern-catalog-v1.json`（67 条，含一句话概述与数据层面），由 `references/bioinfo-patterns.md` 做召回索引与可行性核对，CLI 本身不解析该目录。临床表单声明 `output_text` 与 `output_reference` 两路输出，实测后端通常只回 `output_text`（参考文献并在正文末章），渲染层对缺失的已声明输出直接跳过。该专家不走 `site-configs` 门禁（细则见 `cli/skills/helixlife-expert-proposal/references/proposal.md`）。
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Meta / 基金（国自然）模块额外引入运行时依赖：`@resvg/resvg-js`（SVG→PNG）、`docx`（Word 导出）、`pdf-lib`（PDF 导出）。
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{"version":3,"file":"basic-params.d.ts","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/basic-params.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAI3D,wBAAsB,sBAAsB,CAAC,OAAO,EAAE;IACpD,MAAM,EAAE,YAAY,CAAC;CACtB,GAAG,OAAO,CAAC,IAAI,CAAC,CAKhB"}
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import { runWorkflowParams } from "../../shared/workflow-app/index.js";
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import { PROPOSAL_BASIC_WORKFLOW } from "../constants.js";
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export async function runBasicWorkflowParams(options) {
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await runWorkflowParams({
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workflow: PROPOSAL_BASIC_WORKFLOW,
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format: options.format,
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});
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}
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//# sourceMappingURL=basic-params.js.map
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{"version":3,"file":"basic-params.js","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/basic-params.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iBAAiB,EAAE,MAAM,oCAAoC,CAAC;AACvE,OAAO,EAAE,uBAAuB,EAAE,MAAM,iBAAiB,CAAC;AAE1D,MAAM,CAAC,KAAK,UAAU,sBAAsB,CAAC,OAE5C;IACC,MAAM,iBAAiB,CAAC;QACtB,QAAQ,EAAE,uBAAuB;QACjC,MAAM,EAAE,OAAO,CAAC,MAAM;KACvB,CAAC,CAAC;AACL,CAAC"}
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{"version":3,"file":"basic-run.d.ts","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/basic-run.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAI3D,wBAAsB,gBAAgB,CAAC,OAAO,EAAE;IAC9C,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,YAAY,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC,IAAI,CAAC,CAOhB"}
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import { runWorkflowRun } from "../../shared/workflow-app/index.js";
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import { PROPOSAL_BASIC_WORKFLOW } from "../constants.js";
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export async function runBasicWorkflow(options) {
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await runWorkflowRun({
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workflow: PROPOSAL_BASIC_WORKFLOW,
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inputsFile: options.inputsFile,
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format: options.format,
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fresh: options.fresh,
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});
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}
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//# sourceMappingURL=basic-run.js.map
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{"version":3,"file":"basic-run.js","sourceRoot":"","sources":["../../../../src/modules/proposal/commands/basic-run.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,oCAAoC,CAAC;AACpE,OAAO,EAAE,uBAAuB,EAAE,MAAM,iBAAiB,CAAC;AAE1D,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,OAItC;IACC,MAAM,cAAc,CAAC;QACnB,QAAQ,EAAE,uBAAuB;QACjC,UAAU,EAAE,OAAO,CAAC,UAAU;QAC9B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,KAAK,EAAE,OAAO,CAAC,KAAK;KACrB,CAAC,CAAC;AACL,CAAC"}
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import type { WorkflowDefinition } from "../shared/workflow-app/index.js";
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export declare const PROPOSAL_EXPERT_ID = "proposal";
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export declare const PROPOSAL_EXPERT_TITLE = "\u8BFE\u9898\u65B9\u6848\u4E13\u5BB6";
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/**
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/** 三大方向均走工作流接口：基础研究、临床研究、生信方案 */
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export declare const PROPOSAL_DIRECTIONS: readonly [{
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readonly status: "available";
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}];
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/**
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export declare const
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/** 基础研究只有一个工作流，source 固定，不对用户暴露选择 */
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export declare const PROPOSAL_BASIC_WORKFLOW: WorkflowDefinition;
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export type ClinicalWorkflowSource = "diagnostic-study" | "prognosis-study" | "treatment-trial" | "etiology-study" | "treatment-cohort";
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export interface ClinicalWorkflow extends WorkflowDefinition {
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{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../../../src/modules/proposal/constants.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAC;AAE1E,eAAO,MAAM,kBAAkB,aAAa,CAAC;AAC7C,eAAO,MAAM,qBAAqB,yCAAW,CAAC;AAE9C,
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{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../../../src/modules/proposal/constants.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAC;AAE1E,eAAO,MAAM,kBAAkB,aAAa,CAAC;AAC7C,eAAO,MAAM,qBAAqB,yCAAW,CAAC;AAE9C,iCAAiC;AACjC,eAAO,MAAM,mBAAmB;;;;;;;;;;;;EAItB,CAAC;AAEX,qCAAqC;AACrC,eAAO,MAAM,uBAAuB,EAAE,kBAKrC,CAAC;AAEF,MAAM,MAAM,sBAAsB,GAC9B,kBAAkB,GAClB,iBAAiB,GACjB,iBAAiB,GACjB,gBAAgB,GAChB,kBAAkB,CAAC;AAEvB,MAAM,WAAW,gBAAiB,SAAQ,kBAAkB;IAC1D,MAAM,EAAE,sBAAsB,CAAC;IAC/B,+CAA+C;IAC/C,SAAS,EAAE,IAAI,GAAG,IAAI,GAAG,IAAI,GAAG,IAAI,CAAC;IACrC,kCAAkC;IAClC,MAAM,EAAE,MAAM,CAAC;CAChB;AAID,eAAO,MAAM,2BAA2B,EAAE,SAAS,gBAAgB,EAyClE,CAAC;AAEF,eAAO,MAAM,yBAAyB,0BAErC,CAAC;AAEF,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,gBAAgB,GAAG,SAAS,CAG9E;AAED,wBAAgB,qBAAqB,CAAC,GAAG,EAAE,MAAM,GAAG,gBAAgB,CASnE;AAED,qCAAqC;AACrC,eAAO,MAAM,yBAAyB,EAAE,kBAKvC,CAAC"}
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export const PROPOSAL_EXPERT_ID = "proposal";
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export const PROPOSAL_EXPERT_TITLE = "课题方案专家";
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{ id: "basic", title: "基础研究", status: "available" },
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{ id: "clinical", title: "临床研究", status: "available" },
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export const PROPOSAL_BASIC_WORKFLOW = {
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source: "experimental-design",
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name: "基础研究方案设计",
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title: "基础研究",
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purpose: "围绕细胞、动物与分子机制等实验设定，产出基础研究课题方案",
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};
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{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../../src/modules/proposal/constants.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAC;AAGzE,MAAM,CAAC,MAAM,kBAAkB,GAAG,UAAU,CAAC;AAC7C,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC;AAE9C,
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{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../../src/modules/proposal/constants.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAC;AAGzE,MAAM,CAAC,MAAM,kBAAkB,GAAG,UAAU,CAAC;AAC7C,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC;AAE9C,iCAAiC;AACjC,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC,EAAE,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE;IACnD,EAAE,EAAE,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE;IACtD,EAAE,EAAE,EAAE,SAAS,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE;CAC7C,CAAC;AAEX,qCAAqC;AACrC,MAAM,CAAC,MAAM,uBAAuB,GAAuB;IACzD,MAAM,EAAE,qBAAqB;IAC7B,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,MAAM;IACb,OAAO,EAAE,8BAA8B;CACxC,CAAC;AAiBF,8BAA8B;AAC9B,8DAA8D;AAC9D,MAAM,CAAC,MAAM,2BAA2B,GAAgC;IACtE;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,MAAM;QACZ,KAAK,EAAE,MAAM;QACb,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,uBAAuB;QAC/B,OAAO,EAAE,kCAAkC;KAC5C;IACD;QACE,MAAM,EAAE,iBAAiB;QACzB,IAAI,EAAE,MAAM;QACZ,KAAK,EAAE,MAAM;QACb,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,aAAa;QACrB,OAAO,EAAE,8BAA8B;KACxC;IACD;QACE,MAAM,EAAE,iBAAiB;QACzB,IAAI,EAAE,QAAQ;QACd,KAAK,EAAE,QAAQ;QACf,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,MAAM;QACd,OAAO,EAAE,kBAAkB;KAC5B;IACD;QACE,MAAM,EAAE,gBAAgB;QACxB,IAAI,EAAE,MAAM;QACZ,KAAK,EAAE,MAAM;QACb,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,MAAM;QACd,OAAO,EAAE,8BAA8B;KACxC;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,MAAM;QACZ,KAAK,EAAE,QAAQ;QACf,SAAS,EAAE,IAAI;QACf,MAAM,EAAE,MAAM;QACd,OAAO,EAAE,2BAA2B;KACrC;CACF,CAAC;AAEF,MAAM,CAAC,MAAM,yBAAyB,GAAG,2BAA2B,CAAC,GAAG,CACtE,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CACtB,CAAC;AAEF,MAAM,UAAU,oBAAoB,CAAC,GAAW;IAC9C,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACvC,OAAO,2BAA2B,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,KAAK,KAAK,CAAC,CAAC;AAC3E,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,GAAW;IAC/C,MAAM,QAAQ,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAC;IAC3C,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,QAAQ,CAAC;IAClB,CAAC;IACD,MAAM,IAAI,cAAc,CACtB,kBAAkB,CAAC,gBAAgB,EACnC,UAAU,GAAG,QAAQ,yBAAyB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAC7D,CAAC;AACJ,CAAC;AAED,qCAAqC;AACrC,MAAM,CAAC,MAAM,yBAAyB,GAAuB;IAC3D,MAAM,EAAE,iBAAiB;IACzB,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,QAAQ;IACf,OAAO,EAAE,2BAA2B;CACrC,CAAC"}
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/modules/proposal/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;
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1
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/modules/proposal/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAwBzC,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAyI/D"}
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@@ -1,15 +1,16 @@
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1
1
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import { emitJson, parseOutputFormat } from "../../core/index.js";
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import { PROPOSAL_BIOINFO_WORKFLOW, PROPOSAL_CLINICAL_SOURCES, PROPOSAL_CLINICAL_WORKFLOWS, PROPOSAL_DIRECTIONS, PROPOSAL_EXPERT_ID, PROPOSAL_EXPERT_TITLE, } from "./constants.js";
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2
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import { PROPOSAL_BASIC_WORKFLOW, PROPOSAL_BIOINFO_WORKFLOW, PROPOSAL_CLINICAL_SOURCES, PROPOSAL_CLINICAL_WORKFLOWS, PROPOSAL_DIRECTIONS, PROPOSAL_EXPERT_ID, PROPOSAL_EXPERT_TITLE, } from "./constants.js";
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3
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import { runListClinicalWorkflows } from "./commands/clinical-list.js";
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4
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import { runClinicalWorkflowParams } from "./commands/clinical-params.js";
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5
|
import { runClinicalWorkflow } from "./commands/clinical-run.js";
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6
|
+
import { runBasicWorkflowParams } from "./commands/basic-params.js";
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7
|
+
import { runBasicWorkflow } from "./commands/basic-run.js";
|
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6
8
|
import { runBioinfoWorkflowParams } from "./commands/bioinfo-params.js";
|
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7
9
|
import { runBioinfoWorkflow } from "./commands/bioinfo-run.js";
|
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8
10
|
import { WORKFLOW_RUN_FRESH_HINT as FRESH_HINT } from "../shared/workflow-app/index.js";
|
|
9
11
|
const CLINICAL_SOURCE_HINT = `工作流：${PROPOSAL_CLINICAL_SOURCES.join(" | ")}`;
|
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10
12
|
// 注册课题方案专家命名空间。
|
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11
|
-
//
|
|
12
|
-
// 临床研究与生信方案走「查表单 → 填参执行」两步式工作流命令。
|
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13
|
+
// 基础研究、临床研究与生信方案均走「查表单 → 填参执行」两步式工作流命令。
|
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13
14
|
export function registerProposalCommands(program) {
|
|
14
15
|
const proposal = program
|
|
15
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|
.command(PROPOSAL_EXPERT_ID)
|
|
@@ -26,6 +27,10 @@ export function registerProposalCommands(program) {
|
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26
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|
title: PROPOSAL_EXPERT_TITLE,
|
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27
28
|
implemented: true,
|
|
28
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|
directions: PROPOSAL_DIRECTIONS,
|
|
30
|
+
basicWorkflow: {
|
|
31
|
+
source: PROPOSAL_BASIC_WORKFLOW.source,
|
|
32
|
+
title: PROPOSAL_BASIC_WORKFLOW.title,
|
|
33
|
+
},
|
|
29
34
|
clinicalWorkflows: PROPOSAL_CLINICAL_WORKFLOWS.map((item) => ({
|
|
30
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|
source: item.source,
|
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31
36
|
title: item.title,
|
|
@@ -36,7 +41,30 @@ export function registerProposalCommands(program) {
|
|
|
36
41
|
source: PROPOSAL_BIOINFO_WORKFLOW.source,
|
|
37
42
|
title: PROPOSAL_BIOINFO_WORKFLOW.title,
|
|
38
43
|
},
|
|
39
|
-
note: "
|
|
44
|
+
note: "基础研究、临床研究与生信方案均由本 CLI 直接调用工作流接口",
|
|
45
|
+
});
|
|
46
|
+
});
|
|
47
|
+
const basic = proposal
|
|
48
|
+
.command("basic")
|
|
49
|
+
.description("基础研究方案：单一工作流，无需指定 source");
|
|
50
|
+
basic
|
|
51
|
+
.command("params")
|
|
52
|
+
.description("查询基础研究方案的动态表单字段与输出定义")
|
|
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|
+
.option("--format <format>", "输出格式：markdown | json", "markdown")
|
|
54
|
+
.action(async (opts) => {
|
|
55
|
+
await runBasicWorkflowParams({ format: parseOutputFormat(opts.format) });
|
|
56
|
+
});
|
|
57
|
+
basic
|
|
58
|
+
.command("run")
|
|
59
|
+
.description("按填好的参数生成基础研究方案")
|
|
60
|
+
.requiredOption("--inputs-file <path>", "JSON 文件 {字段名: 值}")
|
|
61
|
+
.option("--format <format>", "输出格式：markdown | json", "markdown")
|
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62
|
+
.option("--fresh", FRESH_HINT)
|
|
63
|
+
.action(async (opts) => {
|
|
64
|
+
await runBasicWorkflow({
|
|
65
|
+
inputsFile: opts.inputsFile,
|
|
66
|
+
format: parseOutputFormat(opts.format),
|
|
67
|
+
fresh: opts.fresh,
|
|
40
68
|
});
|
|
41
69
|
});
|
|
42
70
|
const clinical = proposal
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/modules/proposal/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,QAAQ,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AAClE,OAAO,EACL,yBAAyB,EACzB,yBAAyB,EACzB,2BAA2B,EAC3B,mBAAmB,EACnB,kBAAkB,EAClB,qBAAqB,GACtB,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AACvE,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAC;AAC1E,OAAO,EAAE,mBAAmB,EAAE,MAAM,4BAA4B,CAAC;AACjE,OAAO,EAAE,wBAAwB,EAAE,MAAM,8BAA8B,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAE,uBAAuB,IAAI,UAAU,EAAE,MAAM,iCAAiC,CAAC;AAExF,MAAM,oBAAoB,GAAG,OAAO,yBAAyB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;AAE5E,gBAAgB;AAChB,
|
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1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/modules/proposal/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,QAAQ,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAC;AAClE,OAAO,EACL,uBAAuB,EACvB,yBAAyB,EACzB,yBAAyB,EACzB,2BAA2B,EAC3B,mBAAmB,EACnB,kBAAkB,EAClB,qBAAqB,GACtB,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AACvE,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAC;AAC1E,OAAO,EAAE,mBAAmB,EAAE,MAAM,4BAA4B,CAAC;AACjE,OAAO,EAAE,sBAAsB,EAAE,MAAM,4BAA4B,CAAC;AACpE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,wBAAwB,EAAE,MAAM,8BAA8B,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAE,uBAAuB,IAAI,UAAU,EAAE,MAAM,iCAAiC,CAAC;AAExF,MAAM,oBAAoB,GAAG,OAAO,yBAAyB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;AAE5E,gBAAgB;AAChB,wCAAwC;AACxC,MAAM,UAAU,wBAAwB,CAAC,OAAgB;IACvD,MAAM,QAAQ,GAAG,OAAO;SACrB,OAAO,CAAC,kBAAkB,CAAC;SAC3B,WAAW,CAAC,qBAAqB,CAAC,CAAC;IAEtC,QAAQ;SACL,OAAO,CAAC,MAAM,CAAC;SACf,WAAW,CAAC,sBAAsB,CAAC;QACpC,6CAA6C;SAC5C,MAAM,CAAC,mBAAmB,EAAE,kCAAkC,EAAE,MAAM,CAAC;SACvE,MAAM,CAAC,GAAG,EAAE;QACX,QAAQ,CAAC;YACP,EAAE,EAAE,IAAI;YACR,MAAM,EAAE,kBAAkB;YAC1B,KAAK,EAAE,qBAAqB;YAC5B,WAAW,EAAE,IAAI;YACjB,UAAU,EAAE,mBAAmB;YAC/B,aAAa,EAAE;gBACb,MAAM,EAAE,uBAAuB,CAAC,MAAM;gBACtC,KAAK,EAAE,uBAAuB,CAAC,KAAK;aACrC;YACD,iBAAiB,EAAE,2BAA2B,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;gBAC5D,MAAM,EAAE,IAAI,CAAC,MAAM;gBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;gBACjB,SAAS,EAAE,IAAI,CAAC,SAAS;gBACzB,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAC;YACH,eAAe,EAAE;gBACf,MAAM,EAAE,yBAAyB,CAAC,MAAM;gBACxC,KAAK,EAAE,yBAAyB,CAAC,KAAK;aACvC;YACD,IAAI,EAAE,iCAAiC;SACxC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IAEL,MAAM,KAAK,GAAG,QAAQ;SACnB,OAAO,CAAC,OAAO,CAAC;SAChB,WAAW,CAAC,0BAA0B,CAAC,CAAC;IAE3C,KAAK;SACF,OAAO,CAAC,QAAQ,CAAC;SACjB,WAAW,CAAC,sBAAsB,CAAC;SACnC,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,KAAK,EAAE,IAAwB,EAAE,EAAE;QACzC,MAAM,sBAAsB,CAAC,EAAE,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IAC3E,CAAC,CAAC,CAAC;IAEL,KAAK;SACF,OAAO,CAAC,KAAK,CAAC;SACd,WAAW,CAAC,gBAAgB,CAAC;SAC7B,cAAc,CAAC,sBAAsB,EAAE,kBAAkB,CAAC;SAC1D,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC;SAC7B,MAAM,CACL,KAAK,EAAE,IAA6D,EAAE,EAAE;QACtE,MAAM,gBAAgB,CAAC;YACrB,UAAU,EAAE,IAAI,CAAC,UAAU;YAC3B,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC;YACtC,KAAK,EAAE,IAAI,CAAC,KAAK;SAClB,CAAC,CAAC;IACL,CAAC,CACF,CAAC;IAEJ,MAAM,QAAQ,GAAG,QAAQ;SACtB,OAAO,CAAC,UAAU,CAAC;SACnB,WAAW,CAAC,yBAAyB,CAAC,CAAC;IAE1C,QAAQ;SACL,OAAO,CAAC,MAAM,CAAC;SACf,WAAW,CAAC,iBAAiB,CAAC;SAC9B,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,CAAC,IAAwB,EAAE,EAAE;QACnC,wBAAwB,CAAC,EAAE,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IACvE,CAAC,CAAC,CAAC;IAEL,QAAQ;SACL,OAAO,CAAC,QAAQ,CAAC;SACjB,WAAW,CAAC,uBAAuB,CAAC;SACpC,cAAc,CAAC,mBAAmB,EAAE,oBAAoB,CAAC;SACzD,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,KAAK,EAAE,IAAwC,EAAE,EAAE;QACzD,MAAM,yBAAyB,CAAC;YAC9B,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC;SACvC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IAEL,QAAQ;SACL,OAAO,CAAC,KAAK,CAAC;SACd,WAAW,CAAC,gBAAgB,CAAC;SAC7B,cAAc,CAAC,mBAAmB,EAAE,oBAAoB,CAAC;SACzD,cAAc,CAAC,sBAAsB,EAAE,kBAAkB,CAAC;SAC1D,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC;SAC7B,MAAM,CACL,KAAK,EAAE,IAKN,EAAE,EAAE;QACH,MAAM,mBAAmB,CAAC;YACxB,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;YAC3B,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC;YACtC,KAAK,EAAE,IAAI,CAAC,KAAK;SAClB,CAAC,CAAC;IACL,CAAC,CACF,CAAC;IAEJ,MAAM,OAAO,GAAG,QAAQ;SACrB,OAAO,CAAC,SAAS,CAAC;SAClB,WAAW,CAAC,0BAA0B,CAAC,CAAC;IAE3C,OAAO;SACJ,OAAO,CAAC,QAAQ,CAAC;SACjB,WAAW,CAAC,oBAAoB,CAAC;SACjC,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,KAAK,EAAE,IAAwB,EAAE,EAAE;QACzC,MAAM,wBAAwB,CAAC,EAAE,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IAC7E,CAAC,CAAC,CAAC;IAEL,OAAO;SACJ,OAAO,CAAC,KAAK,CAAC;SACd,WAAW,CAAC,gBAAgB,CAAC;SAC7B,cAAc,CAAC,sBAAsB,EAAE,kBAAkB,CAAC;SAC1D,MAAM,CAAC,mBAAmB,EAAE,sBAAsB,EAAE,UAAU,CAAC;SAC/D,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC;SAC7B,MAAM,CACL,KAAK,EAAE,IAA6D,EAAE,EAAE;QACtE,MAAM,kBAAkB,CAAC;YACvB,UAAU,EAAE,IAAI,CAAC,UAAU;YAC3B,MAAM,EAAE,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC;YACtC,KAAK,EAAE,IAAI,CAAC,KAAK;SAClB,CAAC,CAAC;IACL,CAAC,CACF,CAAC;AACN,CAAC"}
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@@ -46,7 +46,7 @@ export interface WorkbenchResultHandoff {
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46
46
|
missingInfoEmpty?: boolean;
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47
|
/** 基金 Step3：提纲已确认，可进全文 */
|
|
48
48
|
readyForArticle?: boolean;
|
|
49
|
-
/**
|
|
49
|
+
/** 工作流执行记录 ID，供结果串联 */
|
|
50
50
|
runRecordId?: string;
|
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51
51
|
}
|
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52
|
export interface WorkbenchResult<T> {
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@@ -1 +1 @@
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-
{"version":3,"file":"result-wrapper.d.ts","sourceRoot":"","sources":["../../../src/modules/shared/result-wrapper.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;GAmBG;AAIH,8BAA8B;AAC9B,eAAO,MAAM,gBAAgB,iHAUnB,CAAC;AAEX,MAAM,MAAM,cAAc,GAAG,CAAC,OAAO,gBAAgB,CAAC,CAAC,MAAM,CAAC,CAAC;AAE/D,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,yCAAyC;IACzC,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,sBAAsB;IACrC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,0BAA0B;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,gDAAgD;IAChD,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,0CAA0C;IAC1C,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,4EAA4E;IAC5E,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,mDAAmD;IACnD,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,wDAAwD;IACxD,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,0BAA0B;IAC1B,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,
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1
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+
{"version":3,"file":"result-wrapper.d.ts","sourceRoot":"","sources":["../../../src/modules/shared/result-wrapper.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;GAmBG;AAIH,8BAA8B;AAC9B,eAAO,MAAM,gBAAgB,iHAUnB,CAAC;AAEX,MAAM,MAAM,cAAc,GAAG,CAAC,OAAO,gBAAgB,CAAC,CAAC,MAAM,CAAC,CAAC;AAE/D,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,yCAAyC;IACzC,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,sBAAsB;IACrC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,0BAA0B;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,gDAAgD;IAChD,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,0CAA0C;IAC1C,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,4EAA4E;IAC5E,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,mDAAmD;IACnD,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,wDAAwD;IACxD,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,0BAA0B;IAC1B,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,uBAAuB;IACvB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,eAAe,CAAC,CAAC;IAChC,KAAK,EAAE,mBAAmB,CAAC;IAC3B,QAAQ,CAAC,EAAE,sBAAsB,CAAC;IAClC,IAAI,EAAE,IAAI,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC;CAC/B;AA4BD;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,CAAC,SAAS,MAAM,EAClD,MAAM,EAAE,CAAC,EACT,IAAI,EAAE;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,CAAC,EAAE,MAAM,CAAA;CAAE,EACxC,OAAO,CAAC,EAAE,sBAAsB,GAC/B,eAAe,CAAC,CAAC,CAAC,CA2BpB;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,CAAC,SAAS,MAAM,EACtD,MAAM,EAAE,CAAC,GACR,IAAI,CAAC,CAAC,EAAE,cAAc,CAAC,CAEzB"}
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@@ -1,5 +1,5 @@
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1
1
|
// 工作流 params / run 两个命令体的共享实现。
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2
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-
//
|
|
2
|
+
// 文献调研、课题方案（基础研究 / 临床研究 / 生信方案）等专家只需提供各自的工作流定义。
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|
3
3
|
import { createHash } from "node:crypto";
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4
4
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import { existsSync, mkdirSync, readFileSync, statSync, writeFileSync } from "node:fs";
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|
5
5
|
import { basename, join, resolve } from "node:path";
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@@ -1 +1 @@
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|
1
|
-
{"version":3,"file":"command.js","sourceRoot":"","sources":["../../../../src/modules/shared/workflow-app/command.ts"],"names":[],"mappings":"AAAA,+BAA+B;AAC/B,
|
|
1
|
+
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@@ -1,4 +1,4 @@
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1
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-
// AI
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1
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+
// AI 应用工作流共用调用层：文献调研、基础研究、临床研究、生信方案共用
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2
2
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export { buildWorkflowAppHeaders, WORKFLOW_APP_EXECUTE_PATH, WORKFLOW_APP_DETAIL_PATH, WORKFLOW_APP_USER_IDENTITY, WORKFLOW_APP_RESPONSE_MODE, } from "./constants.js";
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3
3
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export { fetchWorkflowConfig, fetchWorkflowAppName } from "./api.js";
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4
4
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export { applyDefaults, buildQuery, componentLabel, prepareQuery, validateAnyOf, validateMaxLength, validateRequired, validateSelectValues, } from "./form.js";
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/modules/shared/workflow-app/index.ts"],"names":[],"mappings":"AAAA,
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1
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+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/modules/shared/workflow-app/index.ts"],"names":[],"mappings":"AAAA,sCAAsC;AACtC,OAAO,EACL,uBAAuB,EACvB,yBAAyB,EACzB,wBAAwB,EACxB,0BAA0B,EAC1B,0BAA0B,GAC3B,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAE,mBAAmB,EAAE,oBAAoB,EAAE,MAAM,UAAU,CAAC;AACrE,OAAO,EACL,aAAa,EACb,UAAU,EACV,cAAc,EACd,YAAY,EACZ,aAAa,EACb,iBAAiB,EACjB,gBAAgB,EAChB,oBAAoB,GACrB,MAAM,WAAW,CAAC;AACnB,OAAO,EAAE,eAAe,EAAE,uBAAuB,EAAE,MAAM,UAAU,CAAC;AACpE,OAAO,EACL,eAAe,EACf,iBAAiB,EACjB,cAAc,EACd,uBAAuB,GACxB,MAAM,cAAc,CAAC"}
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