helixlife-expert-cli 0.5.6 → 0.5.7
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 +5 -5
- package/cli/dist/core/env-config.d.ts.map +1 -1
- package/cli/dist/core/env-config.js +3 -2
- package/cli/dist/core/env-config.js.map +1 -1
- package/cli/dist/core/token/index.d.ts +2 -2
- package/cli/dist/core/token/index.d.ts.map +1 -1
- package/cli/dist/core/token/index.js +23 -8
- package/cli/dist/core/token/index.js.map +1 -1
- package/cli/dist/modules/analysis/index.js +1 -1
- package/cli/dist/modules/analysis/index.js.map +1 -1
- package/package.json +1 -1
package/README.md
CHANGED
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@@ -8,16 +8,16 @@
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```bash
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npm install -g helixlife-expert-cli
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# 请求凭证由外部环境写入 ~/.
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# 请求凭证由外部环境写入 ~/.open-science-pro/platform-auth.json
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helixlife-expert upgrade # 检查并按需升级到 npm 最新版
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```
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接口基址与请求凭证：
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- 配置：`~/.config/helixlife/config.json`
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- Token：`~/.
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- Token：`~/.open-science-pro/platform-auth.json`（JSON 字段 `token`）
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Token 相对用户主目录的路径在 Windows 与 macOS 上一致：`.open-science-pro/platform-auth.json`（Windows 为 `%USERPROFILE%\.open-science-pro\platform-auth.json`，macOS 为 `$HOME/.open-science-pro/platform-auth.json`）。
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## 环境地址
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@@ -138,7 +138,7 @@ SCI 写作专家迁移自 `helixlife-service-cli` 的 `workbench sci`，命令
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文献调研专家提供四个工作流（`WF01` 信息调研、`WF02` 结构化拆解、`WF03` 文献阅读、`WF04` 研究假设），命令树为 `literature workflow list|params|run`。四者均为「`params` 取动态表单 → `run` 填参执行」两步式，表单字段由后端实时返回，CLI 不做本地映射。主线为 WF01 → WF02 → WF04，工作流间数据由 Agent 串联，CLI 不隐式串。该专家不走 `site-configs` 门禁（细则见 `cli/skills/helixlife-expert-literature/references/literature.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 `~/.
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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 `~/.open-science-pro/platform-auth.json`。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 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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{"version":3,"file":"env-config.d.ts","sourceRoot":"","sources":["../../src/core/env-config.ts"],"names":[],"mappings":"
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{"version":3,"file":"env-config.d.ts","sourceRoot":"","sources":["../../src/core/env-config.ts"],"names":[],"mappings":"AAeA,eAAO,MAAM,eAAe,cAAc,CAAC;AAG3C,eAAO,MAAM,sBAAsB,gBAAgB,CAAC;AAGpD,eAAO,MAAM,eAAe,+BAAgC,CAAC;AAC7D,MAAM,MAAM,YAAY,GAAG,CAAC,OAAO,eAAe,CAAC,CAAC,MAAM,CAAC,CAAC;AAG5D,MAAM,WAAW,WAAW;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAGD,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI,YAAY,CAKzE;AAGD,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAExD;AAGD,wBAAgB,kBAAkB,IAAI,MAAM,CAE3C;AAID,wBAAgB,eAAe,IAAI,WAAW,GAAG,SAAS,CAuBzD;AAGD,wBAAgB,eAAe,CAAC,MAAM,EAAE,WAAW,GAAG,IAAI,CAIzD;AAGD,wBAAgB,sBAAsB,CACpC,GAAG,EAAE,YAAY,EACjB,KAAK,EAAE,MAAM,GACZ,WAAW,CAQb;AAGD,wBAAgB,gBAAgB,IAAI,IAAI,CAUvC"}
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//
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// 本地配置文件读写：~/.config/helixlife/config.json。
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// 请求凭证不在此目录，见 token 模块的 ~/.open-science-pro/platform-auth.json。
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// 仅在用户显式调用 `helixlife-expert config set` 时落盘，避免隐式副作用。
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// 存储完整接口基址覆盖（api / agent_api），缺省字段回退代码内生产默认值。
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import { existsSync, mkdirSync, readFileSync, writeFileSync, unlinkSync, } from "node:fs";
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import { homedir } from "node:os";
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import { dirname, join } from "node:path";
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//
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// 本地配置文件固定目录：~/.config/helixlife/
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export const CONFIG_DIR_NAME = "helixlife";
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// 本地配置文件名（后续所有运行时可覆盖变量均写入此文件）
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export const LOCAL_CONFIG_FILE_NAME = "config.json";
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{"version":3,"file":"env-config.js","sourceRoot":"","sources":["../../src/core/env-config.ts"],"names":[],"mappings":"AAAA,
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{"version":3,"file":"env-config.js","sourceRoot":"","sources":["../../src/core/env-config.ts"],"names":[],"mappings":"AAAA,4CAA4C;AAC5C,gEAAgE;AAChE,sDAAsD;AACtD,8CAA8C;AAC9C,OAAO,EACL,UAAU,EACV,SAAS,EACT,YAAY,EACZ,aAAa,EACb,UAAU,GACX,MAAM,SAAS,CAAC;AACjB,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAE1C,kCAAkC;AAClC,MAAM,CAAC,MAAM,eAAe,GAAG,WAAW,CAAC;AAE3C,8BAA8B;AAC9B,MAAM,CAAC,MAAM,sBAAsB,GAAG,aAAa,CAAC;AAEpD,2CAA2C;AAC3C,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,KAAK,EAAE,WAAW,CAAU,CAAC;AAS7D,iBAAiB;AACjB,MAAM,UAAU,mBAAmB,CAAC,KAAc;IAChD,OAAO,CACL,OAAO,KAAK,KAAK,QAAQ;QACxB,eAAqC,CAAC,QAAQ,CAAC,KAAK,CAAC,CACvD,CAAC;AACJ,CAAC;AAED,sBAAsB;AACtB,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,KAAK,CAAC,IAAI,EAAE,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;AAC1C,CAAC;AAED,gDAAgD;AAChD,MAAM,UAAU,kBAAkB;IAChC,OAAO,IAAI,CAAC,OAAO,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,sBAAsB,CAAC,CAAC;AAC7E,CAAC;AAED,0BAA0B;AAC1B,wCAAwC;AACxC,MAAM,UAAU,eAAe;IAC7B,MAAM,QAAQ,GAAG,kBAAkB,EAAE,CAAC;IACtC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,YAAY,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,IAAI,EAAE,CAAC;QAClD,IAAI,CAAC,GAAG;YAAE,OAAO,SAAS,CAAC;QAC3B,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAA4B,CAAC;QAC1D,MAAM,MAAM,GAAgB,EAAE,CAAC;QAE/B,IAAI,OAAO,MAAM,CAAC,GAAG,KAAK,QAAQ,IAAI,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;YACxD,MAAM,CAAC,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAC9C,CAAC;QACD,IAAI,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ,IAAI,MAAM,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,CAAC;YACpE,MAAM,CAAC,SAAS,GAAG,kBAAkB,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;QAC1D,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,SAAS,CAAC;IACnB,CAAC;AACH,CAAC;AAED,iCAAiC;AACjC,MAAM,UAAU,eAAe,CAAC,MAAmB;IACjD,MAAM,QAAQ,GAAG,kBAAkB,EAAE,CAAC;IACtC,SAAS,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAClD,aAAa,CAAC,QAAQ,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC;AACnE,CAAC;AAED,8BAA8B;AAC9B,MAAM,UAAU,sBAAsB,CACpC,GAAiB,EACjB,KAAa;IAEb,MAAM,OAAO,GAAG,eAAe,EAAE,IAAI,EAAE,CAAC;IACxC,MAAM,IAAI,GAAgB;QACxB,GAAG,OAAO;QACV,CAAC,GAAG,CAAC,EAAE,kBAAkB,CAAC,KAAK,CAAC;KACjC,CAAC;IACF,eAAe,CAAC,IAAI,CAAC,CAAC;IACtB,OAAO,IAAI,CAAC;AACd,CAAC;AAED,mCAAmC;AACnC,MAAM,UAAU,gBAAgB;IAC9B,MAAM,QAAQ,GAAG,kBAAkB,EAAE,CAAC;IACtC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO;IACT,CAAC;IACD,IAAI,CAAC;QACH,UAAU,CAAC,QAAQ,CAAC,CAAC;IACvB,CAAC;IAAC,MAAM,CAAC;QACP,OAAO;IACT,CAAC;AACH,CAAC"}
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export declare const TOKEN_DIR_NAME = "
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export declare const TOKEN_FILE_NAME = "
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export declare const TOKEN_DIR_NAME = ".open-science-pro";
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export declare const TOKEN_FILE_NAME = "platform-auth.json";
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export declare function getTokenFilePath(): string;
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export declare function loadTokenFromFile(): string | undefined;
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//# sourceMappingURL=index.d.ts.map
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/core/token/index.ts"],"names":[],"mappings":"
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/core/token/index.ts"],"names":[],"mappings":"AAOA,eAAO,MAAM,cAAc,sBAAsB,CAAC;AAGlD,eAAO,MAAM,eAAe,uBAAuB,CAAC;AAIpD,wBAAgB,gBAAgB,IAAI,MAAM,CAEzC;AAGD,wBAAgB,iBAAiB,IAAI,MAAM,GAAG,SAAS,CAwBtD"}
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// 凭证固定落盘目录：用户主目录下的 .open-science-pro
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// Windows: C:\Users\<用户名>\.open-science-pro
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// macOS: /Users/<用户名>/.open-science-pro
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export const TOKEN_DIR_NAME = ".open-science-pro";
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// 凭证固定文件名。内容为 JSON：{ "token": "<凭证>" }
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export const TOKEN_FILE_NAME = "platform-auth.json";
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}
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export function loadTokenFromFile() {
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}
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}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/core/token/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAEjC,
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/core/token/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAEjC,qCAAqC;AACrC,4CAA4C;AAC5C,0CAA0C;AAC1C,MAAM,CAAC,MAAM,cAAc,GAAG,mBAAmB,CAAC;AAElD,uCAAuC;AACvC,MAAM,CAAC,MAAM,eAAe,GAAG,oBAAoB,CAAC;AAEpD,sBAAsB;AACtB,uEAAuE;AACvE,MAAM,UAAU,gBAAgB;IAC9B,OAAO,IAAI,CAAC,OAAO,EAAE,EAAE,cAAc,EAAE,eAAe,CAAC,CAAC;AAC1D,CAAC;AAED,uDAAuD;AACvD,MAAM,UAAU,iBAAiB;IAC/B,MAAM,QAAQ,GAAG,gBAAgB,EAAE,CAAC;IACpC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC1B,OAAO,SAAS,CAAC;IACnB,CAAC;IAED,IAAI,CAAC;QACH,MAAM,OAAO,GAAG,YAAY,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,IAAI,EAAE,CAAC;QACtD,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,OAAO,SAAS,CAAC;QACnB,CAAC;QACD,MAAM,MAAM,GAAY,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;QAC5C,IAAI,CAAC,MAAM,IAAI,OAAO,MAAM,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;YACnE,OAAO,SAAS,CAAC;QACnB,CAAC;QACD,MAAM,KAAK,GAAI,MAA8B,CAAC,KAAK,CAAC;QACpD,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;YAC9B,OAAO,SAAS,CAAC;QACnB,CAAC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC;QAC7B,OAAO,OAAO,IAAI,SAAS,CAAC;IAC9B,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,SAAS,CAAC;IACnB,CAAC;AACH,CAAC"}
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note: "分析/绘图由本 CLI 直接调用菜单、生信统一入口与上传接口，凭证为 ~/.
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note: "分析/绘图由本 CLI 直接调用菜单、生信统一入口与上传接口，凭证为 ~/.open-science-pro/platform-auth.json",
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48
48
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});
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49
49
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});
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50
50
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const tool = analysis.command("tool").description("检索、检视并执行数据分析工具");
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@@ -1 +1 @@
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1
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-
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1
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+
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|