paper-search-cli 0.3.0 → 0.3.1

package/dist/services/OpenAccessFallbackService.js

@@ -1,75 +1,91 @@
 import { downloadPdfFromUrl, safeFilename } from '../utils/PdfDownload.js';
+export const INSTITUTIONAL_ACCESS_TIER_ID = 'institutional_access';
 const REPOSITORY_SOURCES = ['pmc', 'europepmc', 'core', 'openaire'];
+const DEFAULT_DOWNLOAD_TIERS = [
+    {
+        id: 'primary',
+        stage: 'primary',
+        run: tryPrimaryDownload
+    },
+    {
+        id: 'direct_pdf_url',
+        stage: 'direct_pdf_url',
+        run: tryDirectMetadataUrl
+    },
+    {
+        id: 'repositories',
+        stage: 'repositories',
+        run: tryRepositoryFallback
+    },
+    {
+        id: 'unpaywall',
+        stage: 'unpaywall',
+        run: tryUnpaywall
+    },
+    {
+        id: 'scihub',
+        stage: 'scihub',
+        run: trySciHub
+    }
+];
 export async function downloadWithFallback(searchers, options) {
     const savePath = options.savePath || './downloads';
     const attempts = [];
-    const source = normalizeSource(options.source);
-    const primary = searchers[source];
-    if (primary?.getCapabilities().download) {
-        try {
-            const path = await primary.downloadPdf(options.paperId, { savePath });
-            attempts.push({ stage: 'primary', status: 'ok', message: path });
-            return { status: 'ok', path, attempts };
-        }
-        catch (error) {
-            attempts.push({ stage: 'primary', status: 'error', message: error?.message || String(error) });
+    const context = {
+        searchers,
+        source: normalizeSource(options.source),
+        paperId: options.paperId,
+        doi: options.doi,
+        title: options.title,
+        savePath,
+        useSciHub: options.useSciHub !== false
+    };
+    for (const tier of DEFAULT_DOWNLOAD_TIERS) {
+        const result = await tier.run(context);
+        attempts.push({ stage: tier.stage, status: result.status, message: result.message });
+        if (result.status === 'ok' && result.path) {
+            return { status: 'ok', path: result.path, attempts };
         }
     }
-    else {
-        attempts.push({ stage: 'primary', status: 'skipped', message: `No primary downloader for ${source}` });
-    }
-    const directResult = await tryDirectMetadataUrl(searchers, source, options.paperId, savePath, attempts);
-    if (directResult)
-        return { status: 'ok', path: directResult, attempts };
-    const repositoryResult = await tryRepositoryFallback(searchers, options, savePath, attempts);
-    if (repositoryResult)
-        return { status: 'ok', path: repositoryResult, attempts };
-    const unpaywallResult = await tryUnpaywall(searchers, options.doi || '', savePath, attempts);
-    if (unpaywallResult)
-        return { status: 'ok', path: unpaywallResult, attempts };
-    if (options.useSciHub !== false) {
-        const identifier = options.doi || options.title || options.paperId;
-        try {
-            const path = await searchers.scihub.downloadPdf(identifier, { savePath });
-            attempts.push({ stage: 'scihub', status: 'ok', message: path });
-            return { status: 'ok', path, attempts };
-        }
-        catch (error) {
-            attempts.push({ stage: 'scihub', status: 'error', message: error?.message || String(error) });
-        }
+    return { status: 'error', attempts };
+}
+async function tryPrimaryDownload(context) {
+    const primary = context.searchers[context.source];
+    if (!primary?.getCapabilities().download) {
+        return { status: 'skipped', message: `No primary downloader for ${context.source}` };
     }
-    else {
-        attempts.push({ stage: 'scihub', status: 'skipped', message: 'Sci-Hub fallback disabled by useSciHub=false.' });
+    try {
+        const path = await primary.downloadPdf(context.paperId, { savePath: context.savePath });
+        return { status: 'ok', path, message: path };
+    }
+    catch (error) {
+        return { status: 'error', message: error?.message || String(error) };
     }
-    return { status: 'error', attempts };
 }
-async function tryDirectMetadataUrl(searchers, source, paperId, savePath, attempts) {
-    const searcher = searchers[source];
-    if (!searcher)
-        return '';
+async function tryDirectMetadataUrl(context) {
+    const searcher = context.searchers[context.source];
+    if (!searcher) {
+        return { status: 'skipped', message: `No metadata searcher for ${context.source}.` };
+    }
     try {
-        const paper = await searcher.getPaperByDoi(paperId);
+        const paper = await searcher.getPaperByDoi(context.paperId);
         if (!paper?.pdfUrl) {
-            attempts.push({ stage: 'direct_pdf_url', status: 'skipped', message: 'No pdf_url found in source metadata.' });
-            return '';
+            return { status: 'skipped', message: 'No pdf_url found in source metadata.' };
         }
-        const path = await downloadPdfFromUrl(paper.pdfUrl, savePath, `${source}_${safeFilename(paper.paperId)}`);
-        attempts.push({ stage: 'direct_pdf_url', status: 'ok', message: path });
-        return path;
+        const path = await downloadPdfFromUrl(paper.pdfUrl, context.savePath, `${context.source}_${safeFilename(paper.paperId)}`);
+        return { status: 'ok', path, message: path };
     }
     catch (error) {
-        attempts.push({ stage: 'direct_pdf_url', status: 'error', message: error?.message || String(error) });
-        return '';
+        return { status: 'error', message: error?.message || String(error) };
     }
 }
-async function tryRepositoryFallback(searchers, options, savePath, attempts) {
-    const queries = [options.doi || '', options.title || ''].filter(Boolean);
+async function tryRepositoryFallback(context) {
+    const queries = [context.doi || '', context.title || ''].filter(Boolean);
     if (queries.length === 0) {
-        attempts.push({ stage: 'repositories', status: 'skipped', message: 'No DOI/title provided for repository discovery.' });
-        return '';
+        return { status: 'skipped', message: 'No DOI/title provided for repository discovery.' };
     }
     for (const source of REPOSITORY_SOURCES) {
-        const searcher = searchers[source];
+        const searcher = context.searchers[source];
         if (!searcher)
             continue;
         for (const query of queries) {
@@ -78,37 +94,44 @@ async function tryRepositoryFallback(searchers, options, savePath, attempts) {
                 const paper = papers.find(candidate => candidate.pdfUrl);
                 if (!paper?.pdfUrl)
                     continue;
-                const path = await downloadPdfFromUrl(paper.pdfUrl, savePath, `${source}_${safeFilename(paper.paperId)}`);
-                attempts.push({ stage: `repository:${source}`, status: 'ok', message: path });
-                return path;
+                const path = await downloadPdfFromUrl(paper.pdfUrl, context.savePath, `${source}_${safeFilename(paper.paperId)}`);
+                return { status: 'ok', path, message: path };
             }
-            catch (error) {
-                attempts.push({ stage: `repository:${source}`, status: 'error', message: error?.message || String(error) });
+            catch {
+                continue;
             }
         }
     }
-    attempts.push({ stage: 'repositories', status: 'skipped', message: 'No repository PDF candidate succeeded.' });
-    return '';
+    return { status: 'skipped', message: 'No repository PDF candidate succeeded.' };
 }
-async function tryUnpaywall(searchers, doi, savePath, attempts) {
-    if (!doi) {
-        attempts.push({ stage: 'unpaywall', status: 'skipped', message: 'DOI not provided.' });
-        return '';
+async function tryUnpaywall(context) {
+    if (!context.doi) {
+        return { status: 'skipped', message: 'DOI not provided.' };
     }
     try {
-        const unpaywall = searchers.unpaywall;
-        const pdfUrl = await unpaywall.resolveBestPdfUrl(doi);
+        const unpaywall = context.searchers.unpaywall;
+        const pdfUrl = await unpaywall.resolveBestPdfUrl(context.doi);
         if (!pdfUrl) {
-            attempts.push({ stage: 'unpaywall', status: 'skipped', message: 'No OA PDF URL found or email not configured.' });
-            return '';
+            return { status: 'skipped', message: 'No OA PDF URL found or email not configured.' };
         }
-        const path = await downloadPdfFromUrl(pdfUrl, savePath, `unpaywall_${safeFilename(doi)}`);
-        attempts.push({ stage: 'unpaywall', status: 'ok', message: path });
-        return path;
+        const path = await downloadPdfFromUrl(pdfUrl, context.savePath, `unpaywall_${safeFilename(context.doi)}`);
+        return { status: 'ok', path, message: path };
+    }
+    catch (error) {
+        return { status: 'error', message: error?.message || String(error) };
+    }
+}
+async function trySciHub(context) {
+    if (!context.useSciHub) {
+        return { status: 'skipped', message: 'Sci-Hub fallback disabled by useSciHub=false.' };
+    }
+    const identifier = context.doi || context.title || context.paperId;
+    try {
+        const path = await context.searchers.scihub.downloadPdf(identifier, { savePath: context.savePath });
+        return { status: 'ok', path, message: path };
     }
     catch (error) {
-        attempts.push({ stage: 'unpaywall', status: 'error', message: error?.message || String(error) });
-        return '';
+        return { status: 'error', message: error?.message || String(error) };
     }
 }
 function normalizeSource(source) {

package/dist/services/OpenAccessFallbackService.js.map

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package/dist/utils/RateLimiter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"RateLimiter.d.ts","sourceRoot":"","sources":["../../src/utils/RateLimiter.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,MAAM,WAAW,kBAAkB;IACjC,cAAc;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,aAAa;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,eAAe;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAS;IAC3C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAU;IAEhC,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,cAAc,CAAiB;IACvC,OAAO,CAAC,QAAQ,CAAC,eAAe,CAGxB;gBAEI,OAAO,EAAE,kBAAkB;IAevC;;OAEG;IACG,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC;IAwBxC;;OAEG;IACH,OAAO,CAAC,YAAY;IAepB;;OAEG;IACH,OAAO,CAAC,sBAAsB;IAiB9B;;OAEG;IACH,SAAS,IAAI;QACX,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,MAAM,CAAC;QAClB,iBAAiB,EAAE,MAAM,CAAC;QAC1B,eAAe,EAAE,MAAM,CAAC;KACzB;IAUD;;OAEG;IACH,OAAO,IAAI,IAAI;IAsBf,OAAO,IAAI,IAAI;CAGhB"}
+{"version":3,"file":"RateLimiter.d.ts","sourceRoot":"","sources":["../../src/utils/RateLimiter.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,MAAM,WAAW,kBAAkB;IACjC,cAAc;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,aAAa;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,eAAe;IACf,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAS;IAC3C,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,aAAa,CAAS;IACvC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAU;IAEhC,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,cAAc,CAAiB;IACvC,OAAO,CAAC,QAAQ,CAAC,eAAe,CAGxB;gBAEI,OAAO,EAAE,kBAAkB;IAevC;;OAEG;IACG,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC;IAyBxC;;OAEG;IACH,OAAO,CAAC,YAAY;IAepB;;OAEG;IACH,OAAO,CAAC,sBAAsB;IAqB9B;;OAEG;IACH,SAAS,IAAI;QACX,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,MAAM,CAAC;QAClB,iBAAiB,EAAE,MAAM,CAAC;QAC1B,eAAe,EAAE,MAAM,CAAC;KACzB;IAUD;;OAEG;IACH,OAAO,IAAI,IAAI;IA0Bf,OAAO,IAAI,IAAI;CAGhB"}

package/dist/utils/RateLimiter.js

@@ -42,6 +42,7 @@ export class RateLimiter {
                 resolve,
                 timestamp: Date.now()
             });
+            this.intervalHandle.ref?.();
             if (this.debug) {
                 logDebug(`RateLimiter: Request queued, ${this.pendingRequests.length} waiting`);
             }
@@ -78,6 +79,9 @@ export class RateLimiter {
                 }
             }
         }
+        if (this.pendingRequests.length === 0) {
+            this.intervalHandle.unref?.();
+        }
     }
     /**
      * 获取当前状态
@@ -110,6 +114,9 @@ export class RateLimiter {
                 break;
             }
         }
+        if (this.pendingRequests.length === 0) {
+            this.intervalHandle.unref?.();
+        }
         if (this.debug && removedCount > 0) {
             logDebug(`RateLimiter: Cleaned up ${removedCount} expired requests`);
         }

package/dist/utils/RateLimiter.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "paper-search-cli",
-  "version": "0.3.0",
+  "version": "0.3.1",
   "description": "Agent-friendly CLI for searching and downloading academic papers from multiple sources.",
   "main": "dist/cli.js",
   "type": "module",

package/skills/paper-search/SKILL.md

@@ -5,6 +5,7 @@ description: |
   用于：搜索论文、查找相似研究、做文献综述初筛、验证 PMID/DOI、下载论文 PDF、
   调用 Crossref/OpenAlex/PubMed/PMC/Europe PMC/arXiv/bioRxiv/medRxiv/Semantic Scholar/CORE/OpenAIRE/DBLP/ACM/USENIX/OpenReview/IACR 等来源，
   使用 Semantic Scholar Open Access snippet 索引检索论文正文片段中的方法学细节，
+  通过 Semantic Scholar Graph API 查询已知论文的施引文献和参考文献，
   以及通过 EasyScholar 查询期刊影响因子、JCR/SSCI 分区、中科院分区、JCI、ESI、预警和等级指标。
   当用户提到“搜文献”“找论文”“文献检索”“search papers”“find papers”“literature search”
   “查一下有没有相关研究”“帮我找几篇参考文献”“看看别人怎么做的”“别人怎么写”
@@ -18,7 +19,7 @@ description: |
 
 # Paper Search CLI
 
-你是学术文献检索调度器。本 Skill 是 Routing Skill：负责把用户意图路由到 `paper-search` CLI，并维护证据、密钥和下载边界。优先通过 `paper-search` CLI 完成论文检索、元数据核验、正文片段检索、期刊指标查询和 PDF 获取；不要把本 Skill 当作密钥、cookie、账号或下载策略的存储位置。
+你是学术文献检索调度器。本 Skill 是 Routing Skill：负责把用户意图路由到 `paper-search` CLI，并维护证据、密钥和下载边界。优先通过 `paper-search` CLI 完成论文检索、元数据核验、施引/参考文献扩展、正文片段检索、期刊指标查询和 PDF 获取；不要把本 Skill 当作密钥、cookie、账号或下载策略的存储位置。
 
 Reference 读取规则：
 
@@ -75,11 +76,12 @@ paper-search doctor --pretty
 
 ## 功能地图
 
-本 Skill 只有四个文献主功能。`doctor`、`smoke`、`config`、`skills` 是管理层命令，不属于文献任务本身。
+本 Skill 只有五个文献主功能。`doctor`、`smoke`、`config`、`skills` 是管理层命令，不属于文献任务本身。
 
 | 用户意图 | 能力名 | 首选入口 | 关键边界 |
 |---|---|---|---|
 | 搜论文、找相关研究、验证 DOI/PMID、做文献初筛 | `metadata_search` | `paper-search search` 集成入口 / `paper-search run search_*` 精确工具入口 | 只返回和核验论文元数据；Sci-Hub 不属于搜索源 |
+| 查询已知论文的施引文献或参考文献 | `citation_expansion` | `paper-search run get_paper_citations` / `paper-search run get_paper_references` | 需要已知 `paperId`、DOI 或 arXiv ID；不是关键词检索 |
 | 查影响因子、JCR/SSCI/中科院分区、JCI、ESI、预警、期刊等级 | `journal_metrics` | `paper-search journal-metrics` / `paper-search run query_journal_metrics` | 这是期刊指标查询，不是论文检索；需要 `EASYSCHOLAR_KEY` |
 | 获取或下载已确认论文的 PDF | `pdf_discovery` | `paper-search download` / `paper-search run download_with_fallback` | 先核验论文身份，再下载；Sci-Hub 是默认开启的最后 fallback |
 | 在论文正文片段中找 Methods/参数/写法线索 | `body_snippet_search` | `paper-search run search_semantic_snippets` | 查 Semantic Scholar OA snippet 索引；需要 `SEMANTIC_SCHOLAR_API_KEY`；不是完整全文解析 |

package/skills/paper-search/references/capability-routing.md

@@ -1,12 +1,13 @@
 # Capability Routing Reference
 
-Use this reference when mapping a user literature request to one of the four main `paper-search` workflow capabilities.
+Use this reference when mapping a user literature request to one of the five main `paper-search` workflow capabilities.
 
 ## Functional Map
 
 | User Intent | Capability | Preferred Entrypoint | Boundary |
 |---|---|---|---|
 | Search papers, find related work, verify DOI/PMID, screen literature | `metadata_search` | `paper-search search` integrated entrypoint / `paper-search run search_*` precise tool entrypoint | Returns and verifies paper metadata only; Sci-Hub is not a search source |
+| Expand citation graph for a known paper | `citation_expansion` | `paper-search run get_paper_citations` / `paper-search run get_paper_references` | Requires a known `paperId`, DOI, or arXiv ID; returns citing papers or cited references, not general keyword search |
 | Query impact factor, JCR/SSCI/CAS quartiles, JCI, ESI, warnings, journal rank | `journal_metrics` | `paper-search journal-metrics` / `paper-search run query_journal_metrics` | Journal-level lookup, not paper search; requires `EASYSCHOLAR_KEY` |
 | Get or download a verified paper PDF | `pdf_discovery` | `paper-search download` / `paper-search run download_with_fallback` | Verify identity before download; Sci-Hub is the default enabled final fallback |
 | Find Methods text, parameters, software, models, or statistical wording in body snippets | `body_snippet_search` | `paper-search run search_semantic_snippets` | Searches Semantic Scholar OA snippet index; requires `SEMANTIC_SCHOLAR_API_KEY`; not full-text parsing |
@@ -32,7 +33,7 @@ Use `metadata_search` for finding papers, expanding keywords, literature screeni
 - use `--sources a,b,c` for explicit multi-source search
 - use `--platform all` or `--sources all` only when broad recall matters more than precision
 
-It does not call `journal_metrics`, `pdf_discovery`, or `body_snippet_search`.
+It does not call `citation_expansion`, `journal_metrics`, `pdf_discovery`, or `body_snippet_search`.
 
 ```bash
 paper-search search "machine learning" --platform crossref --max-results 5 --pretty
@@ -51,6 +52,17 @@ paper-search run get_paper_by_doi --arg doi="10.xxxx/xxxxx" --pretty
 
 Do not treat `search_scihub` as a search source. It is DOI/URL-targeted lookup, not `metadata_search`.
 
+## Citation Expansion
+
+Use `citation_expansion` when the user has a known paper and asks which papers cite it or which references it cites.
+
+```bash
+paper-search run get_paper_citations --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+paper-search run get_paper_references --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+```
+
+Target priority is `paperId` > `doi` > `arxivId`. This capability uses Semantic Scholar Graph API and is separate from keyword-based `metadata_search`.
+
 ## Journal Metrics
 
 Use `journal_metrics` for journal-level metrics: impact factor, JCR/SSCI quartiles, CAS quartiles, JCI, ESI, warnings, and rank.
@@ -117,6 +129,7 @@ Only results with `snippetKind="body"` can be used as body-snippet evidence. Res
 |---|---|---|
 | Biomedical, clinical, pharmaceutical, public health | `pubmed` | `pmc`, `europepmc`, `semantic`, `crossref` |
 | Methods/body snippet clues | `search_semantic_snippets` | Use `pubmed`/`semantic` first for titles and synonyms |
+| Citation graph expansion | `get_paper_citations`, `get_paper_references` | Use only after a target paper identifier is known |
 | Computer science, AI, math, physics | `arxiv` | `semantic`, `crossref`, `openalex` |
 | CS bibliographies and conference metadata | `dblp` | `acm`, `usenix`, `openreview`, `ieee` requires key |
 | Cross-disciplinary coverage | `crossref` | `openalex`, `semantic` |

package/skills/paper-search/references/cli-contract.md

@@ -51,6 +51,8 @@ These names can be used with `paper-search run <tool-name>`:
 - `search_medrxiv`
 - `search_semantic_scholar`
 - `search_semantic_snippets`
+- `get_paper_citations`
+- `get_paper_references`
 - `search_iacr`
 - `download_paper`
 - `search_google_scholar`
@@ -97,6 +99,23 @@ These names can be used with `paper-search run <tool-name>`:
 - `search_scihub` is DOI/URL-targeted lookup and is not a metadata search source.
 - `CORE_MAX_RESULTS_CAP` controls the configurable CORE-only result cap. Default is `100`; hard maximum is `500`. Other platforms keep their own current limits.
 
+## Citation Expansion Contract
+
+`get_paper_citations` and `get_paper_references` query Semantic Scholar Graph API for citation graph expansion.
+
+- Provide at least one of `paperId`, `doi`, or `arxivId`.
+- Target priority is `paperId`, then `doi`, then `arxivId`.
+- `doi` is converted to `DOI:<doi>`.
+- `arxivId` is converted to `ARXIV:<id>`.
+- `limit` defaults to `100` and accepts values from `1` to `100`.
+
+Examples:
+
+```bash
+paper-search run get_paper_citations --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+paper-search run get_paper_references --arg doi="10.1038/nature12373" --arg limit=5 --pretty
+```
+
 ## Download Command Contract
 
 `download_paper` tries source-native download first when available. Unsupported or failed native downloads route into the same fallback funnel used by `download_with_fallback`.

package/skills/paper-search/references/management-layer.md

@@ -35,6 +35,7 @@ paper-search config list --pretty
 Capability Profile entries are independent workflow capabilities:
 
 - `metadata_search`: metadata search through configured/free literature sources. Sci-Hub must not be included in metadata search.
+- `citation_expansion`: citation and reference expansion for a known paper through Semantic Scholar Graph API. `SEMANTIC_SCHOLAR_API_KEY` is optional for higher quota.
 - `body_snippet_search`: Semantic Scholar Open Access snippet search. It requires `SEMANTIC_SCHOLAR_API_KEY`.
 - `journal_metrics`: EasyScholar journal metrics. It requires `EASYSCHOLAR_KEY`.
 - `pdf_discovery`: PDF discovery and download through source-native download, metadata PDF URLs, open-access sources, entitled-access sources when configured, and the default enabled Sci-Hub Fallback.